ChemWiki - User contributions [en]

Mod:Hunt Research Group

2020-08-17T00:12:49Z

Phunt: /* HPC Resources */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===Report and Paper Writing===
#procedures [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/report_procedures link]
#advice [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/report_writing link]
#report components [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/report_components link]
#files to provide when writing a paper [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/paper link]

===Group Admin===
#Which files to store on the database and database template [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/database link]
#How to access DROBO [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/drobo link]
#Moving large files and directories around [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/file_move link]

===HPC Resources===
#Getting started and introduction to the HPC: [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Getting_started_on_the_HPC link]
#'''Hunt group HPC resources and run scripts''' [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link]
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link]
#Link to RCS (HPC) tips page [https://imperialcollegelondon.github.io/research-computing-tips/topics.html link]
#How to run jobs interactively [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/run_interactive link]
#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link]
#New gf script (more convenient job submitting) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/new_gf_script link]
#Retired: How to make qsub more comfortable (gfunc) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpQSUB link]
#Tired of entering your password all the time: set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link]
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link]
#Using VPN from home, for Sierra follow the college instructions [[link]]
#How to connect to HPC directory on desktop for file transfers [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_Directory_on_desktop link]
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link]
#How to use a slimmed down terminal on your IPhone [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/termius]

===Using evil Windows and PCs===
#Use Imperial Software Hub to access gaussview and gaussian [http://www.imperial.ac.uk/admin-services/ict/store/software/software-hub/ link]
#Using windows and setting up a connection to HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link]
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link]

===Key Papers, References and Resources===
*'''Papers'''
#Meta study on DFT functionals [https://pubs.acs.org/doi/abs/10.1021/ct401111c doi]
#M06 suite of DFT functionals [https://link.springer.com/article/10.1007/s00214-007-0310-x doi]
#SMD for ILs [https://pubs.acs.org/doi/abs/10.1021/jp304365v doi]
#Box size for MD simulations of ILs [https://dx.doi.org/10.1063/1.4748352 doi]
*'''Notes'''
#Solving the angular part of the Schrödinger equation for a hydrogen atom [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/angular_schrodinger link] (notes by Vincent)
#DFT Workshop Notes [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/DFT_Workshop]
#Cl- in water [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link]
#The use of Legendre time correlation functions to study reorientational dynamics in liquids [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/legendre link]

===Gaussian General===
#We are starting a database of common errors encountered when running Gaussian jobs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gaussian_errors link]
# Here is an already existing database of common errors [https://docs.computecanada.ca/wiki/Gaussian_error_messages link]
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#partial optimisations and scans [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/z-matrix link]
#General procedure for locating transition state structures [[link]]
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link]
#Basic ONIOM (Mechanical Embedding) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/basiconiom link]
#problems with scf convergence [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/scf_convergence link]
#manipulating checkpoint files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:usingchkfiles link]
#for NMR calculations look here: [http://cheshirenmr.info/index.htm Chemical Shift Repository]
#Population and charge analysis [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/population link]

===Gaussian Advanced===
#Systematic conformational scan for ion-pair dimers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ion_pair_scan link]
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link]
#generating natural transition orbitals [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/nto link]
#computing excited state polarisabilities [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_ES_alpha link]
#computing deuterated and/or anharmonic spectra [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_Danharm link]
#How to run at a higher temperature [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:high_temp link]
#Correcting the entropy due to low modes [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:low_modes_entropy link]
#Optimisation of charged molecules in an electric field [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Optimising_charged_molecules_in_electric_fields link]
#Multidimensional Scans of Internal Coordinates [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Multidimensional_Scans_of_Internal_Coordinates link]
#Conformational search of atomic and molecular clusters with ABCluster [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:ABCluster#.inp_file_on_the_HPC link]

===Solvation===
#Using the SMD model [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/solvent link]
#Using SMD on ILs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_Using_SMD_on_ILs link]
#Troublesome optimisations in SMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:troublesome_smd link]
#Atomic radii and solvent models [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/atomic_radii link]
#Molecular volume calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molecular_volume link]
#The cavity [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/solvent_cavity link]
#How to download and use GeomView to visualise solvation cavities [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/geomview link]
#Surfaces (Solvent-Accessible and Connolly) in Jmol [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/jmolsurfaces link]

===Codes to Help Gaussian Analysis===
====Python and Python codes====
# Using and installing python [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/python link]
# Python toolkit currently focussed towards gaussian analysis [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molLego link]
# Standalone python scripts and analysis:
#* List the energy for each step of a gaussian log file, find the lowest energy and produce a quick graph in kJ/mol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_energy link]
#* Build a frequency file from an optimisation file ready to submit, this will require editing for your particular job [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/build_freq link]
#* Extract last Standard Orientation structure of gaussian log file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_single_geom link]
#* Extract last structure of gaussian optimisation and build a freq com file for job with PP [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/build_freq_file link]
#* Extract each optimised step from a scan into xyz coordinate file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_scan_geom link]
#* Extract thermodynamic data and low frequencies from log files (python 2) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:simple_freq_script link]
#* Extract thermodynamic data and low frequencies from log files to enter into excel template provided for the database (python 3) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:model_freq_script link]
#* Extract geometry and charges (ESP) into a .pdb file for visualising in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ESP_charges_for_VMD link]
#* Codes to extract CHELPG and NBO charge values to excel [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/chelpg_extract link]
#* Extract ESP and NBO charges [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_ESP_charges link]
#* Script to pull thermodynamic data and low frequencies from log files AND evaluate to a reference [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:freq_script link]
#* Codes to extract frequency data from gaussian .log files and generate vibrational spectra [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:frequency_spectrum_script link]
#* Codes to visualise data matrices (correlation matrices/heatmaps)[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/heatmap link]
#* Python API for analysis of Gaussian computations [https://pygauss.readthedocs.org - Documentation]
#* Charge arm [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/charge_arm link]
#* Extract the MO orbital energies and concert to eV [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/MO_energies link]

====Other codes====
# Extract E2 Values (From NBO Calculations) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/NBO_Matlab_Code link]
# Calculate pDoS/XP spectra code (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Calc_XPS_Code link]
# Optimally Tuned Range Separated Hybrid Functionals [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/OTRSH_Funct link]
# Some G09 Parsers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Some_G09_Parsers link]

===QC Visualisation===
*'''Using AIMALL: density based visualisation'''
#download [http://aim.tkgristmill.com AIMALL]
#once downloaded and installed you need to send tricia your aimall-serialnumber.txt file, and she will arrange for a aimallpro.lic or license file for you
#basic instructions [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:aim_basics link]
#AimAll with pseudo potentials [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:aim_pseudopotentials link]
#AIMAll 19.10.12 on iMacs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:AIMAllQuickFix link]

*'''ESPs and manipulating gaussian cube files'''
#Instructions for visualizing electrostatic potentials (Gaussview)[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link]
#Electrostatic Potentials II (Molden) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials_2 link]
#Manipulating cube files [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/cube_files link]
#Format of cube files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/cube_format link]
#Using A. Stone's distributed multipole analysis [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/GDMA link]

*'''NCI plots'''
#get the program here: [http://www.lct.jussieu.fr/pagesperso/contrera/nciplot.html link]
#How to install NCIPlot on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/InstallNCIPlot link]
#Using NCIPlot [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/UseNCIPlot link]

*'''MOs'''
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link]

===Setup and Running Classical MD Simulations===
====dl_poly====
#DLPOLY_4.0 Installation for an IMac [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Installing_DL_POLY_4.09_on_MacOS_Mojave link]
#DLPOLY_Classic Installation for an IMac [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Installing_DL_POLY_classic link]

#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#some basics for getting started using DL_POLY [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dl_poly_basics link]
#control file basics [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/control_basics link]
*useful links
::[https://www.ccp5.ac.uk https://www.ccp5.ac.uk]
::[https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx]
::[ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/USRMAN4.pdf dlpoly4 user manual]
::[ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/JavaGUI.pdf javagui user manual]
::[ftp://ftp.dl.ac.uk/ccp5/DL_POLY/ dlpoly ftp server]
:::you can find test files in DL_POLY_4.0/DATA
:::more info about the dlpoly test files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/DL_POLY_test_files link]

====gromacs====
#GROMACS installing and getting started with gromacs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gromacs_1 link]
#using Agilio Padua force fields for ionic liquids [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/ilff link]
#Packmol installing and running to generate a starting box [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/packmol_1 link]
#initial rough relaxation [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Starting_MD link]
#GROMACS general run [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_run link]
#GROMACS viewing data [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_viewing_MD link]
#GROMACS control file [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_control_MD link]
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link]
====general====
#Getting the Force Field [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Wheretostart link]
#Choosing an Ensemble [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Ensembles link]
#Molten Salt Simulations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/MoltenSaltSimulation link]
#Common Errors [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/CommonErrors link]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link]

===MD Visualisation===
*'''VMD: a molecular dynamics visualisation package'''
#VMD can be installed from the [http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD VMD downloads page]
#Quick reminder [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDReminder link]
#Colour in VMD [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDColor link]
#Changing the graphical representation of your structures [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link]
#VMD indexing [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDindexing link]
#Using scripts in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScripts link]
#Dealing with periodic boundaries and bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsPeriodic link]
#Dealing with bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdBonding link]
#How to turn a Gaussian optimization into a VMD movie [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/VMDmovie link]
#Overlapping two structures [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdVisual link]
*'''Ovito: a molecular dynamics visualisation package'''
#Download Ovito [http://www.ovito.org/index.php/download]
#Using Ovito basics [//wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Ovito_basics link]
*'''SDFs'''
#How to generate SDFs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/sdfs_generate link]

===MD Post processing===
#Python script to convert a HISTORY file into a xyz file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/hist_to_xyz link]
#Python script to reduce the number of steps in a lammps traj file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/lam_to_xyz link]
#Python script to convert a lammps traj file to xyz coordinates and at the same time fold all atoms into a cell and center at the origin [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/lam_fold_xyz link]
#Center the trajectory at a particular atom ('''needs fixing''') [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Recenter link]
#How to generate SDFs with TRAVIS [[Talk:Mod:Hunt Research Group/How to draw SDFs with TRAVIS|link]]
#Tcl script to follow a particular atom [[Talk:Mod:Hunt Research Group/Traj_atom_following|link]]

===Coding===
*'''installing Xcode and other programming environments'''
#to use many programs you will need a compiler, this is not installed by default on your mac
#How to install Xcode on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/InstallXcode link]
#using MacPorts as code for managing other codes on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/MacPorts link]
#HomeBrew and Fink are other options (HomeBrew is not advised for us)
#gfortran on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Gfortran link]
#using python on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/python link]

*'''EMO Code'''
#How to use Ling's emo plot code[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emoplot link]
#How to plot EMOs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emo link]

*'''Jan's charge based analysis Code'''
#charge analysis [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Jan_charges link]
#Obtaining NBO, ESP, and RESP charges [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Charges link]

*'''Oxana's visualisation of ESPs Code'''
#Scripts for reading, saving, manipulating and visualising data from cube files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Python_scripts_for_cube_files link]

*'''Python Genereal'''
# General python recommendations and set up [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/PythonGeneral link]
# Analysis toolkit mainly geared towards processing Gaussian calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Python_Analysis_Tools link]

===Other Codes===
#ADF Submission script [http://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/ADF_sricpt link]
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link]
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/]
#Run SAPT calculations using Psi4 [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/SAPT link]

===Setup and Running Ab-Initio MD Simulations===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link]
#How to run CPMD to study aqueous solutions [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd_water link]
#How to run CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k_how link]

===Running QM/MM Simulations in ChemShell===

==Tcl-chemshell==
#ChemShell official website which contains the manual and a tutorial [http://www.stfc.ac.uk/CSE/randd/ccg/36254.aspx link]
#Introduction to ChemShell - Copper in water [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Introduction link]
#Defining the system: Cu2+ and its first 2 solvation shells [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_System_Aqeuous_Cu(II) link]
#Defining the force field parameters [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II) link]
#Single point QM/MM energy calculation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_SP_Aqeuous_Cu(II) link]
#QM/MM Optimisation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_OPT_Aqeuous_Cu(II) link]
#QM/MM Molecular Dynamics [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_MD_Aqeuous_Cu(II) link]
#Using MolCluster [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/MolCluster link]
#Running ChemShell [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell link]
#Explaining ChemShell files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files link]
#Step By Step [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Chemshell_Step_By_Step link]
==Py-chemshell==

# Compiling Chemshell and required programs []
# The DL_POLY_4 manual is available for download at this link [ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/USRMAN4.pdf]
# Molecular Mechanics computation with DL_POLY [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:_MM_Single_Point_computation]
# Basic QM/MM single point and optimisations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_QM/MM_Single_Point_and_optimisation]
# Visualise optimisation trajectories in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_Visualising_trajectories_with_VMD]
# Computing Mulliken charges and creating .wfn inputs for AIM analysis [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_Mulliken]

==Admin Stuff==
#Not used to writing a wiki, make your test runs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/testing on this page]
#How to set-up new macs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_setup link]
#How to switch the printer HP CP3525dn duplex on and off [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/printing link]

Mod:Hunt Research Group/hpc

2020-05-17T21:08:59Z

Phunt: /* Extra information/troubleshooting */

= General Resources =

== pqph ==

* You can check the current queue resources and staus here: [https://selfservice.rcs.imperial.ac.uk/pqs/nodes/pqph pqph queue status]
* Currently, pqph consists mainly of 40 proc/124GB nodes and a couple of 48 proc/256GB nodes in pqph.

==Express queue==

* We can also now submit jobs to the Express queue
* Use this for anytime our pqph is looking full or if you have a job you think will take more than a day or longer than 3 days

To run express jobs, use the command line input:

: <code>qsub -q express -P exp-00034 -lselect=1:ncpus=48:mem=126gb -lwalltime=72:00:00</code>

Or use this inside a PBS submit script:

<pre>
# batch processing commands
#PBS -l walltime=72:00:00
#PBS -lselect=1:ncpus=48:mem=126000MB
#PBS -j oe
#PBS -q express -P exp-00034
</pre>

* Don’t forget to call less memory in the gaussian com file say 125GB

= Gaussian jobs =
== Recommended job specifications ==
For running '''Gaussian''' jobs on '''pqph''' it is recommended to just use two job sizings. The sizings mean that either a full 40 proc node will be used or just half of the node, allowing for a second job to be run on the other half of the node. These are only applicable to Gaussian jobs which can't be run across nodes. You may want to use multiple nodes/alternate job sizings for codes which are parallelised.

'''Small/medium jobs:'''
* Run jobs using half of a 40 processor node and half the memory allowance (64GB).
* PBS script input:
:: <code>#PBS -l walltime=72:00:00</code>
:: <code>#PBS -lselect=1:ncpus=20:mem=64000MB</code>
* Gaussian .com file input:
:: <code>%nprocs=20</code>
:: <code>%mem=60000MB</code>

'''Medium/large jobs:'''
* Run jobs using a full 40 processor node and the full the memory allowance (128GB).
* PBS script input:
:: <code>#PBS -l walltime=72:00:00</code>
:: <code>#PBS -lselect=1:ncpus=40:mem=128000MB</code>
* Gaussian .com file input:
:: <code>%nprocs=40</code>
:: <code>%mem=122000MB</code>

If you need to use the larger (48 proc) nodes for more expensive calculations:
* Run jobs using a full 48 processor node and the full the memory allowance (256GB).
* PBS script input:
:: <code>#PBS -l walltime=72:00:00</code>
:: <code>#PBS -lselect=1:ncpus=48:mem=25000MB</code>
* Gaussian .com file input:
:: <code>%nprocs=48</code>
:: <code>%mem=256000MB</code>

==Runscripts==

=== Standard job script ===
An example gaussian runscript for a 20 processor job:

<pre>#!/bin/sh

# Submit jobs to the queue with this script using the following command:
#
# qsub -N jobname -v in=name rs20
#
# Where: rs20 is the name of this runscript
# jobname is a name you will see in the qstat command
# name is the actual file minus .com etc it is passed into this script as ${in%.com}

# batch processing commands
#PBS -l walltime=72:00:00
#PBS -lselect=1:ncpus=20:mem=64000MB
#PBS -j oe
#PBS -q pqph
#PBS -m a

# Load relevant modules

module load gaussian/g16-a03

# Check for a checkpoint file to copy to the temp directory
# variable PBS_O_WORKDIR=directory from which the job was submitted.
if [[ -e $PBS_O_WORKDIR/${in%.com}.chk ]]
then
echo "$PBS_O_WORKDIR/${in%.com}.chk located"
cp $PBS_O_WORKDIR/${in%.com}.chk $TMPDIR/.
else
echo "no checkpoint file $PBS_O_WORKDIR/${in%.com}.chk"
fi

# Execute Gaussian
#
g16 $PBS_O_WORKDIR/${in}

# Once job is finished copy across the .chk file
cp $TMPDIR/${in%.com}.chk /$PBS_O_WORKDIR/.

# exit
</pre>

* Edit the PBS lines to create runscripts for other job specifications.
* If you are not sure what the PBS commands are or on what the runscript does then check out the introduction to the hpc page: [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Getting_started_on_the_HPC Getting Started on the HPC]
* If you need to copy back any other output files you can either run the job in <code>${EPHERMAL}</code> instead of <code>${TMPDIR}</code> as all output files will remain in ephermal for a period of time. Or, if you know the extension of the additional desired output file you can use a modified version of the code:

<pre>
# Check for the existence of other possible output files and copy if located
if [[ -e $TMPDIR/*.extension ]]
then
cp $TMPDIR/*.extension /$PBS_O_WORKDIR/${in%.com}_*.extension
fi
</pre>

* Replace *.extension with the correct file extension that you want to copy back.

=== Array jobs ===

If you have a large number of small jobs which are only slightly different e.g. optimising a large number of conformers of a molecule/system that only vary in the input structure, then you should use an array job.

An example array job runscript for a 20 processor job is:

<pre>#!/bin/sh

# batch processing commands
#PBS -l walltime=72:00:00
#PBS -lselect=1:ncpus=20:mem=64000MB
#PBS -J 1-X
#PBS -j oe
#PBS -q pqph
#PBS -m a
#PBS -N arrayJobName

in=$( sed -n ${PBS_ARRAY_INDEX}p ${PBS_O_WORKDIR}/inputFiles.txt)

echo ${in}
# Load relevant modules
module load gaussian/g16-a03

# Check for a checkpoint file to copy to the temp directory
# variable PBS_O_WORKDIR=directory from which the job was submitted.
if [[ -e $PBS_O_WORKDIR/${in%.com}.chk ]]
then
echo "$PBS_O_WORKDIR/${in%.com}.chk located"
cp $PBS_O_WORKDIR/${in%.com}.chk $TMPDIR/.
fi

# Execute Gaussian
g16 $PBS_O_WORKDIR/${in}

# Once job is finished copy across the .chk file
cp $TMPDIR/${in%.com}.chk /$PBS_O_WORKDIR/.

# exit
</pre>

To use the script:
* Set up all your input .com files in the same directory
* Edit the line in the runscript that sets the number of jobs in the array: <code>#PBS -J 1-X</code>. Change X to the number of input files you have to run.
* The runscript works by running X separate jobs within the array. For each job, there is a PBS variable set ('''PBS_ARRAY_INDEX''') which is the jobs number within the array. E.g. for the first job to run, PBS_ARRAY_INDEX = 1.
* Change the job name using the -N flag in the script or by the command line option
* Save your changes to the runscript and exit
* Create a text file with the names of all the input .com files. An easy way to do this is by the command line:
: <code>ls *.com > inputFiles.txt</code>
* You will notice that the file inputFiles.txt is called in the line in the runscript which sets the variable '''in'''. It uses the array job number ('''PBS_ARRAY_INDEX''') as an index to reference the correct line in the text file, so each job will call a different input file.
* Submit the array job using the command:
: <code> qsub rs_ja </code>

* The job runs as a single job on the queue and gets a single job id number (e.g. 1096738), each of the separate jobs within the array job are then given an index (e.g. 1096738[4] for job 4 of the array)
* The qstat information for the array job now tells you how many jobs are in the array, how many are queued and how many are finished.

==Extra information/troubleshooting==

*add tmpspace=400 only for large disk jobs to ensure you are put on a node with enough disk!!
*Note that this requires you to include maxdisk=400gb in your gaussian input.
:NOTE the queuing system does not check disk allocations. When requesting large disk jobs remember to request all of the processors on a node even if you are not using all of the processors. For large jobs the maximum disk space you can request is '''800GB''' on the 12 processor nodes.

=== Memory needed to run ===

*Gaussian is greedy and will exceed the allocated memory

*Each proc needs a gaussian executable, which takes about 8MW (or 12 for MP2 frequencies)
::MW is megaword which is the unit gaussian allocates memory
::1MW is about 8.4MB
:::so each proc needs 1*8*8.4 approximately 68MB just to run
:::so 12 proc jobs require 12*68=816MB just to run
:::so 16 proc jobs require 16*68=1088MB just to run
:::so 20 proc jobs require 20*68=1360MB just to run
:::so 24 proc jobs require 24*68=1632MB just to run
:::so 40 proc jobs require 40*68=2720MB just to run
:::so 48 proc jobs require 48*68=3264MB just to run
::so when allocating memory inside the gaussian job you must reduce the memory by at least this amount
*thus best to reduce the memory by about 100MB*no.processors inside the gaussian script
*you also need some overhead within the PBS script

*the memory can be given in binary such as 251 GB (binary) is really 251 GB =251000*1,048,576 Bytes =264GB (decimal):newer notes

*Larger jobs, a good rule of thumb for >50 atoms or >500 basis functions is 4GB minimum per processor
::so 20proc is 80GB minimum
::for mp2 frequency and ccsd you should leave enough memory to buffer the large disk files
::so only give the gaussian job 50-70% of the total memory

=== More details for if you seem to be having memory or disk issues ===
*normal jobs
::will need 2*N^2 W *8.4 to get B (1,048,576B =1MB)
:: so 300 basis functions will need 180000W =0.18MW =1.5MB in addition to the above requirements
::require 2ON^2 W of disk to run where O=number of occupied orbitals, N=number of basis functions

*MP2 jobs
:: work best with %mem and maxdisk defined
:: in-core requires N^4/4 divided by 1,000,000 MW memory
:: so 400 basis functions will need 6400MW=53760MB=54GB memory per node, which is unlikely!
:: semi-direct requires 2*O(N^2) memory and N^3 disk
:: so N=476 basis functions O=56 occupied orbitals will need
::25.4MW=214MB of memory
::and 108MW=906MB disk (this is not actually true it will need much more probably around 1800MB disk per processor!)
::so total memory for MP2 freq 8proc will be
::12*8*8.4=807MB to run and 8*214=1712MB for calcs and some extra 400MB=3019MB=3.3GB
::gaussian does not like GB directive so give %mem in MB

=== Checkpoint and other files ===
: checkpoint files should be exactly the same name as the input file name
: for jobs that may exceed the wall time specify the full path of the checkpoint file, for example
::%chk=/work/phunt/tmp/filename.chk
:this means the checkpoint file will be written into your personal work directory, it may slow the job down
:this is also the reason /work is sometimes very slow on CX1 so only do this as an exception!

= Extra links =

The Imperial Research Computing service have a hpc wiki which has useful information including an intro to shell scripting, modules and job management information:
::https://wiki.imperial.ac.uk/display/HPC/High+Performance+Computing

The RCS also run several courses throughout the year, including intro to Linux, HPC, python and more advanced topics. Upcoming courses can be viewed from:
::https://www.imperial.ac.uk/admin-services/ict/self-service/research-support/rcs/training/

===Next steps===
Mount
Alias shortcut for logging in
Keypair page
Once you are comfortable and understand the job submission process then the automatic job script which ... can be used

== Other information (may be out of date) ==
:3.1 CPMD:
::https://www.ch.ic.ac.uk/wiki/index.php/Image:Runcpmd_md.sh
:3.2 DL-POLY:
::https://www.ch.ic.ac.uk/wiki/index.php/Image:Mpirun.sh
::Note: You´ll not be able to see the output until the job finishes : the directory /tmp/pb.XXX isn´t accessible to you because it is on the private disk of the node running the job.
::To get DLPOLY to terminate before the job hits the walltime limit and killed, you need to run it through a program called pbsexec, for example:
::pbsexec mpiexec DLPOLY.X
::This will kill DLPOLY 15 minutes before the walltime limit, giving your script time to transfer files back to $work.

Mod:Hunt Research Group/hpc

2020-05-17T21:08:07Z

Phunt: /* Memory needed to run */

= General Resources =

== pqph ==

* You can check the current queue resources and staus here: [https://selfservice.rcs.imperial.ac.uk/pqs/nodes/pqph pqph queue status]
* Currently, pqph consists mainly of 40 proc/124GB nodes and a couple of 48 proc/256GB nodes in pqph.

==Express queue==

* We can also now submit jobs to the Express queue
* Use this for anytime our pqph is looking full or if you have a job you think will take more than a day or longer than 3 days

To run express jobs, use the command line input:

: <code>qsub -q express -P exp-00034 -lselect=1:ncpus=48:mem=126gb -lwalltime=72:00:00</code>

Or use this inside a PBS submit script:

<pre>
# batch processing commands
#PBS -l walltime=72:00:00
#PBS -lselect=1:ncpus=48:mem=126000MB
#PBS -j oe
#PBS -q express -P exp-00034
</pre>

* Don’t forget to call less memory in the gaussian com file say 125GB

= Gaussian jobs =
== Recommended job specifications ==
For running '''Gaussian''' jobs on '''pqph''' it is recommended to just use two job sizings. The sizings mean that either a full 40 proc node will be used or just half of the node, allowing for a second job to be run on the other half of the node. These are only applicable to Gaussian jobs which can't be run across nodes. You may want to use multiple nodes/alternate job sizings for codes which are parallelised.

'''Small/medium jobs:'''
* Run jobs using half of a 40 processor node and half the memory allowance (64GB).
* PBS script input:
:: <code>#PBS -l walltime=72:00:00</code>
:: <code>#PBS -lselect=1:ncpus=20:mem=64000MB</code>
* Gaussian .com file input:
:: <code>%nprocs=20</code>
:: <code>%mem=60000MB</code>

'''Medium/large jobs:'''
* Run jobs using a full 40 processor node and the full the memory allowance (128GB).
* PBS script input:
:: <code>#PBS -l walltime=72:00:00</code>
:: <code>#PBS -lselect=1:ncpus=40:mem=128000MB</code>
* Gaussian .com file input:
:: <code>%nprocs=40</code>
:: <code>%mem=122000MB</code>

If you need to use the larger (48 proc) nodes for more expensive calculations:
* Run jobs using a full 48 processor node and the full the memory allowance (256GB).
* PBS script input:
:: <code>#PBS -l walltime=72:00:00</code>
:: <code>#PBS -lselect=1:ncpus=48:mem=25000MB</code>
* Gaussian .com file input:
:: <code>%nprocs=48</code>
:: <code>%mem=256000MB</code>

==Runscripts==

=== Standard job script ===
An example gaussian runscript for a 20 processor job:

<pre>#!/bin/sh

# Submit jobs to the queue with this script using the following command:
#
# qsub -N jobname -v in=name rs20
#
# Where: rs20 is the name of this runscript
# jobname is a name you will see in the qstat command
# name is the actual file minus .com etc it is passed into this script as ${in%.com}

# batch processing commands
#PBS -l walltime=72:00:00
#PBS -lselect=1:ncpus=20:mem=64000MB
#PBS -j oe
#PBS -q pqph
#PBS -m a

# Load relevant modules

module load gaussian/g16-a03

# Check for a checkpoint file to copy to the temp directory
# variable PBS_O_WORKDIR=directory from which the job was submitted.
if [[ -e $PBS_O_WORKDIR/${in%.com}.chk ]]
then
echo "$PBS_O_WORKDIR/${in%.com}.chk located"
cp $PBS_O_WORKDIR/${in%.com}.chk $TMPDIR/.
else
echo "no checkpoint file $PBS_O_WORKDIR/${in%.com}.chk"
fi

# Execute Gaussian
#
g16 $PBS_O_WORKDIR/${in}

# Once job is finished copy across the .chk file
cp $TMPDIR/${in%.com}.chk /$PBS_O_WORKDIR/.

# exit
</pre>

* Edit the PBS lines to create runscripts for other job specifications.
* If you are not sure what the PBS commands are or on what the runscript does then check out the introduction to the hpc page: [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Getting_started_on_the_HPC Getting Started on the HPC]
* If you need to copy back any other output files you can either run the job in <code>${EPHERMAL}</code> instead of <code>${TMPDIR}</code> as all output files will remain in ephermal for a period of time. Or, if you know the extension of the additional desired output file you can use a modified version of the code:

<pre>
# Check for the existence of other possible output files and copy if located
if [[ -e $TMPDIR/*.extension ]]
then
cp $TMPDIR/*.extension /$PBS_O_WORKDIR/${in%.com}_*.extension
fi
</pre>

* Replace *.extension with the correct file extension that you want to copy back.

=== Array jobs ===

If you have a large number of small jobs which are only slightly different e.g. optimising a large number of conformers of a molecule/system that only vary in the input structure, then you should use an array job.

An example array job runscript for a 20 processor job is:

<pre>#!/bin/sh

# batch processing commands
#PBS -l walltime=72:00:00
#PBS -lselect=1:ncpus=20:mem=64000MB
#PBS -J 1-X
#PBS -j oe
#PBS -q pqph
#PBS -m a
#PBS -N arrayJobName

in=$( sed -n ${PBS_ARRAY_INDEX}p ${PBS_O_WORKDIR}/inputFiles.txt)

echo ${in}
# Load relevant modules
module load gaussian/g16-a03

# Check for a checkpoint file to copy to the temp directory
# variable PBS_O_WORKDIR=directory from which the job was submitted.
if [[ -e $PBS_O_WORKDIR/${in%.com}.chk ]]
then
echo "$PBS_O_WORKDIR/${in%.com}.chk located"
cp $PBS_O_WORKDIR/${in%.com}.chk $TMPDIR/.
fi

# Execute Gaussian
g16 $PBS_O_WORKDIR/${in}

# Once job is finished copy across the .chk file
cp $TMPDIR/${in%.com}.chk /$PBS_O_WORKDIR/.

# exit
</pre>

To use the script:
* Set up all your input .com files in the same directory
* Edit the line in the runscript that sets the number of jobs in the array: <code>#PBS -J 1-X</code>. Change X to the number of input files you have to run.
* The runscript works by running X separate jobs within the array. For each job, there is a PBS variable set ('''PBS_ARRAY_INDEX''') which is the jobs number within the array. E.g. for the first job to run, PBS_ARRAY_INDEX = 1.
* Change the job name using the -N flag in the script or by the command line option
* Save your changes to the runscript and exit
* Create a text file with the names of all the input .com files. An easy way to do this is by the command line:
: <code>ls *.com > inputFiles.txt</code>
* You will notice that the file inputFiles.txt is called in the line in the runscript which sets the variable '''in'''. It uses the array job number ('''PBS_ARRAY_INDEX''') as an index to reference the correct line in the text file, so each job will call a different input file.
* Submit the array job using the command:
: <code> qsub rs_ja </code>

* The job runs as a single job on the queue and gets a single job id number (e.g. 1096738), each of the separate jobs within the array job are then given an index (e.g. 1096738[4] for job 4 of the array)
* The qstat information for the array job now tells you how many jobs are in the array, how many are queued and how many are finished.

==Extra information/troubleshooting==

*add tmpspace=400 only for large disk jobs to ensure you are put on a node with enough disk!!
*Note that this requires you to include maxdisk=400gb in your gaussian input.
:NOTE the queuing system does not check disk allocations. When requesting large disk jobs remember to request all of the processors on a node even if you are not using all of the processors. For large jobs the maximum disk space you can request is '''800GB''' on the 12 processor nodes.

=== More details for if you seem to be having memory or disk issues ===
*normal jobs
::will need 2*N^2 W *8.4 to get B (1,048,576B =1MB)
:: so 300 basis functions will need 180000W =0.18MW =1.5MB in addition to the above requirements
::require 2ON^2 W of disk to run where O=number of occupied orbitals, N=number of basis functions

*MP2 jobs
:: work best with %mem and maxdisk defined
:: in-core requires N^4/4 divided by 1,000,000 MW memory
:: so 400 basis functions will need 6400MW=53760MB=54GB memory per node, which is unlikely!
:: semi-direct requires 2*O(N^2) memory and N^3 disk
:: so N=476 basis functions O=56 occupied orbitals will need
::25.4MW=214MB of memory
::and 108MW=906MB disk (this is not actually true it will need much more probably around 1800MB disk per processor!)
::so total memory for MP2 freq 8proc will be
::12*8*8.4=807MB to run and 8*214=1712MB for calcs and some extra 400MB=3019MB=3.3GB
::gaussian does not like GB directive so give %mem in MB

=== Checkpoint and other files ===
: checkpoint files should be exactly the same name as the input file name
: for jobs that may exceed the wall time specify the full path of the checkpoint file, for example
::%chk=/work/phunt/tmp/filename.chk
:this means the checkpoint file will be written into your personal work directory, it may slow the job down
:this is also the reason /work is sometimes very slow on CX1 so only do this as an exception!

=== Memory needed to run ===

*Gaussian is greedy and will exceed the allocated memory

*Each proc needs a gaussian executable, which takes about 8MW (or 12 for MP2 frequencies)
::MW is megaword which is the unit gaussian allocates memory
::1MW is about 8.4MB
:::so each proc needs 1*8*8.4 approximately 68MB just to run
:::so 12 proc jobs require 12*68=816MB just to run
:::so 16 proc jobs require 16*68=1088MB just to run
:::so 20 proc jobs require 20*68=1360MB just to run
:::so 24 proc jobs require 24*68=1632MB just to run
:::so 40 proc jobs require 40*68=2720MB just to run
:::so 48 proc jobs require 48*68=3264MB just to run
::so when allocating memory inside the gaussian job you must reduce the memory by at least this amount
*thus best to reduce the memory by about 100MB*no.processors inside the gaussian script
*you also need some overhead within the PBS script

*the memory can be given in binary such as 251 GB (binary) is really 251 GB =251000*1,048,576 Bytes =264GB (decimal):newer notes

*Larger jobs, a good rule of thumb for >50 atoms or >500 basis functions is 4GB minimum per processor
::so 20proc is 80GB minimum
::for mp2 frequency and ccsd you should leave enough memory to buffer the large disk files
::so only give the gaussian job 50-70% of the total memory

= Extra links =

The Imperial Research Computing service have a hpc wiki which has useful information including an intro to shell scripting, modules and job management information:
::https://wiki.imperial.ac.uk/display/HPC/High+Performance+Computing

The RCS also run several courses throughout the year, including intro to Linux, HPC, python and more advanced topics. Upcoming courses can be viewed from:
::https://www.imperial.ac.uk/admin-services/ict/self-service/research-support/rcs/training/

===Next steps===
Mount
Alias shortcut for logging in
Keypair page
Once you are comfortable and understand the job submission process then the automatic job script which ... can be used

== Other information (may be out of date) ==
:3.1 CPMD:
::https://www.ch.ic.ac.uk/wiki/index.php/Image:Runcpmd_md.sh
:3.2 DL-POLY:
::https://www.ch.ic.ac.uk/wiki/index.php/Image:Mpirun.sh
::Note: You´ll not be able to see the output until the job finishes : the directory /tmp/pb.XXX isn´t accessible to you because it is on the private disk of the node running the job.
::To get DLPOLY to terminate before the job hits the walltime limit and killed, you need to run it through a program called pbsexec, for example:
::pbsexec mpiexec DLPOLY.X
::This will kill DLPOLY 15 minutes before the walltime limit, giving your script time to transfer files back to $work.

Mod:Hunt Research Group/hpc

2020-05-17T21:07:31Z

Phunt: /* Memory needed to run */

= General Resources =

== pqph ==

* You can check the current queue resources and staus here: [https://selfservice.rcs.imperial.ac.uk/pqs/nodes/pqph pqph queue status]
* Currently, pqph consists mainly of 40 proc/124GB nodes and a couple of 48 proc/256GB nodes in pqph.

==Express queue==

* We can also now submit jobs to the Express queue
* Use this for anytime our pqph is looking full or if you have a job you think will take more than a day or longer than 3 days

To run express jobs, use the command line input:

: <code>qsub -q express -P exp-00034 -lselect=1:ncpus=48:mem=126gb -lwalltime=72:00:00</code>

Or use this inside a PBS submit script:

<pre>
# batch processing commands
#PBS -l walltime=72:00:00
#PBS -lselect=1:ncpus=48:mem=126000MB
#PBS -j oe
#PBS -q express -P exp-00034
</pre>

* Don’t forget to call less memory in the gaussian com file say 125GB

= Gaussian jobs =
== Recommended job specifications ==
For running '''Gaussian''' jobs on '''pqph''' it is recommended to just use two job sizings. The sizings mean that either a full 40 proc node will be used or just half of the node, allowing for a second job to be run on the other half of the node. These are only applicable to Gaussian jobs which can't be run across nodes. You may want to use multiple nodes/alternate job sizings for codes which are parallelised.

'''Small/medium jobs:'''
* Run jobs using half of a 40 processor node and half the memory allowance (64GB).
* PBS script input:
:: <code>#PBS -l walltime=72:00:00</code>
:: <code>#PBS -lselect=1:ncpus=20:mem=64000MB</code>
* Gaussian .com file input:
:: <code>%nprocs=20</code>
:: <code>%mem=60000MB</code>

'''Medium/large jobs:'''
* Run jobs using a full 40 processor node and the full the memory allowance (128GB).
* PBS script input:
:: <code>#PBS -l walltime=72:00:00</code>
:: <code>#PBS -lselect=1:ncpus=40:mem=128000MB</code>
* Gaussian .com file input:
:: <code>%nprocs=40</code>
:: <code>%mem=122000MB</code>

If you need to use the larger (48 proc) nodes for more expensive calculations:
* Run jobs using a full 48 processor node and the full the memory allowance (256GB).
* PBS script input:
:: <code>#PBS -l walltime=72:00:00</code>
:: <code>#PBS -lselect=1:ncpus=48:mem=25000MB</code>
* Gaussian .com file input:
:: <code>%nprocs=48</code>
:: <code>%mem=256000MB</code>

==Runscripts==

=== Standard job script ===
An example gaussian runscript for a 20 processor job:

<pre>#!/bin/sh

# Submit jobs to the queue with this script using the following command:
#
# qsub -N jobname -v in=name rs20
#
# Where: rs20 is the name of this runscript
# jobname is a name you will see in the qstat command
# name is the actual file minus .com etc it is passed into this script as ${in%.com}

# batch processing commands
#PBS -l walltime=72:00:00
#PBS -lselect=1:ncpus=20:mem=64000MB
#PBS -j oe
#PBS -q pqph
#PBS -m a

# Load relevant modules

module load gaussian/g16-a03

# Check for a checkpoint file to copy to the temp directory
# variable PBS_O_WORKDIR=directory from which the job was submitted.
if [[ -e $PBS_O_WORKDIR/${in%.com}.chk ]]
then
echo "$PBS_O_WORKDIR/${in%.com}.chk located"
cp $PBS_O_WORKDIR/${in%.com}.chk $TMPDIR/.
else
echo "no checkpoint file $PBS_O_WORKDIR/${in%.com}.chk"
fi

# Execute Gaussian
#
g16 $PBS_O_WORKDIR/${in}

# Once job is finished copy across the .chk file
cp $TMPDIR/${in%.com}.chk /$PBS_O_WORKDIR/.

# exit
</pre>

* Edit the PBS lines to create runscripts for other job specifications.
* If you are not sure what the PBS commands are or on what the runscript does then check out the introduction to the hpc page: [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Getting_started_on_the_HPC Getting Started on the HPC]
* If you need to copy back any other output files you can either run the job in <code>${EPHERMAL}</code> instead of <code>${TMPDIR}</code> as all output files will remain in ephermal for a period of time. Or, if you know the extension of the additional desired output file you can use a modified version of the code:

<pre>
# Check for the existence of other possible output files and copy if located
if [[ -e $TMPDIR/*.extension ]]
then
cp $TMPDIR/*.extension /$PBS_O_WORKDIR/${in%.com}_*.extension
fi
</pre>

* Replace *.extension with the correct file extension that you want to copy back.

=== Array jobs ===

If you have a large number of small jobs which are only slightly different e.g. optimising a large number of conformers of a molecule/system that only vary in the input structure, then you should use an array job.

An example array job runscript for a 20 processor job is:

<pre>#!/bin/sh

# batch processing commands
#PBS -l walltime=72:00:00
#PBS -lselect=1:ncpus=20:mem=64000MB
#PBS -J 1-X
#PBS -j oe
#PBS -q pqph
#PBS -m a
#PBS -N arrayJobName

in=$( sed -n ${PBS_ARRAY_INDEX}p ${PBS_O_WORKDIR}/inputFiles.txt)

echo ${in}
# Load relevant modules
module load gaussian/g16-a03

# Check for a checkpoint file to copy to the temp directory
# variable PBS_O_WORKDIR=directory from which the job was submitted.
if [[ -e $PBS_O_WORKDIR/${in%.com}.chk ]]
then
echo "$PBS_O_WORKDIR/${in%.com}.chk located"
cp $PBS_O_WORKDIR/${in%.com}.chk $TMPDIR/.
fi

# Execute Gaussian
g16 $PBS_O_WORKDIR/${in}

# Once job is finished copy across the .chk file
cp $TMPDIR/${in%.com}.chk /$PBS_O_WORKDIR/.

# exit
</pre>

To use the script:
* Set up all your input .com files in the same directory
* Edit the line in the runscript that sets the number of jobs in the array: <code>#PBS -J 1-X</code>. Change X to the number of input files you have to run.
* The runscript works by running X separate jobs within the array. For each job, there is a PBS variable set ('''PBS_ARRAY_INDEX''') which is the jobs number within the array. E.g. for the first job to run, PBS_ARRAY_INDEX = 1.
* Change the job name using the -N flag in the script or by the command line option
* Save your changes to the runscript and exit
* Create a text file with the names of all the input .com files. An easy way to do this is by the command line:
: <code>ls *.com > inputFiles.txt</code>
* You will notice that the file inputFiles.txt is called in the line in the runscript which sets the variable '''in'''. It uses the array job number ('''PBS_ARRAY_INDEX''') as an index to reference the correct line in the text file, so each job will call a different input file.
* Submit the array job using the command:
: <code> qsub rs_ja </code>

* The job runs as a single job on the queue and gets a single job id number (e.g. 1096738), each of the separate jobs within the array job are then given an index (e.g. 1096738[4] for job 4 of the array)
* The qstat information for the array job now tells you how many jobs are in the array, how many are queued and how many are finished.

==Extra information/troubleshooting==

*add tmpspace=400 only for large disk jobs to ensure you are put on a node with enough disk!!
*Note that this requires you to include maxdisk=400gb in your gaussian input.
:NOTE the queuing system does not check disk allocations. When requesting large disk jobs remember to request all of the processors on a node even if you are not using all of the processors. For large jobs the maximum disk space you can request is '''800GB''' on the 12 processor nodes.

=== More details for if you seem to be having memory or disk issues ===
*normal jobs
::will need 2*N^2 W *8.4 to get B (1,048,576B =1MB)
:: so 300 basis functions will need 180000W =0.18MW =1.5MB in addition to the above requirements
::require 2ON^2 W of disk to run where O=number of occupied orbitals, N=number of basis functions

*MP2 jobs
:: work best with %mem and maxdisk defined
:: in-core requires N^4/4 divided by 1,000,000 MW memory
:: so 400 basis functions will need 6400MW=53760MB=54GB memory per node, which is unlikely!
:: semi-direct requires 2*O(N^2) memory and N^3 disk
:: so N=476 basis functions O=56 occupied orbitals will need
::25.4MW=214MB of memory
::and 108MW=906MB disk (this is not actually true it will need much more probably around 1800MB disk per processor!)
::so total memory for MP2 freq 8proc will be
::12*8*8.4=807MB to run and 8*214=1712MB for calcs and some extra 400MB=3019MB=3.3GB
::gaussian does not like GB directive so give %mem in MB

=== Checkpoint and other files ===
: checkpoint files should be exactly the same name as the input file name
: for jobs that may exceed the wall time specify the full path of the checkpoint file, for example
::%chk=/work/phunt/tmp/filename.chk
:this means the checkpoint file will be written into your personal work directory, it may slow the job down
:this is also the reason /work is sometimes very slow on CX1 so only do this as an exception!

=== Memory needed to run ===

*Gaussian is greedy and will exceed the allocated memory

:older notes
:: each proc needs a gaussian executable, which takes about 8MW (or 12 for MP2 frequencies)
::MW is megaword which is the unit gaussian allocates memory
::1MW is about 8.4MB
:::so each proc needs 1*8*8.4 approximately 68MB just to run
:::so 12 proc jobs require 12*68=816MB just to run
:::so 16 proc jobs require 16*68=1088MB just to run
:::so 20 proc jobs require 20*68=1360MB just to run
:::so 24 proc jobs require 24*68=1632MB just to run
:::so 40 proc jobs require 40*68=2720MB just to run
:::so 48 proc jobs require 48*68=3264MB just to run
::so when allocating memory inside the gaussian job you must reduce the memory by at least this amount
*thus best to reduce the memory by about 100MB*no.processors inside the gaussian script
*you also need some overhead within the PBS script

*the memory can be given in binary such as 251 GB (binary) is really 251 GB =251000*1,048,576 Bytes =264GB (decimal):newer notes

*a good rule of thumb for >50 atoms or >500 basis functions is 4GB minimum per processor
::so 20proc is 80GB minimum
::for mp2 frequency and ccsd you should leave enough memory to buffer the large disk files
::so only give the gaussian job 50-70% of the total memory

= Extra links =

The Imperial Research Computing service have a hpc wiki which has useful information including an intro to shell scripting, modules and job management information:
::https://wiki.imperial.ac.uk/display/HPC/High+Performance+Computing

The RCS also run several courses throughout the year, including intro to Linux, HPC, python and more advanced topics. Upcoming courses can be viewed from:
::https://www.imperial.ac.uk/admin-services/ict/self-service/research-support/rcs/training/

===Next steps===
Mount
Alias shortcut for logging in
Keypair page
Once you are comfortable and understand the job submission process then the automatic job script which ... can be used

== Other information (may be out of date) ==
:3.1 CPMD:
::https://www.ch.ic.ac.uk/wiki/index.php/Image:Runcpmd_md.sh
:3.2 DL-POLY:
::https://www.ch.ic.ac.uk/wiki/index.php/Image:Mpirun.sh
::Note: You´ll not be able to see the output until the job finishes : the directory /tmp/pb.XXX isn´t accessible to you because it is on the private disk of the node running the job.
::To get DLPOLY to terminate before the job hits the walltime limit and killed, you need to run it through a program called pbsexec, for example:
::pbsexec mpiexec DLPOLY.X
::This will kill DLPOLY 15 minutes before the walltime limit, giving your script time to transfer files back to $work.

Mod:Hunt Research Group/hpc

2020-05-17T21:02:30Z

Phunt: /* Memory needed to run */

= General Resources =

== pqph ==

* You can check the current queue resources and staus here: [https://selfservice.rcs.imperial.ac.uk/pqs/nodes/pqph pqph queue status]
* Currently, pqph consists mainly of 40 proc/124GB nodes and a couple of 48 proc/256GB nodes in pqph.

==Express queue==

* We can also now submit jobs to the Express queue
* Use this for anytime our pqph is looking full or if you have a job you think will take more than a day or longer than 3 days

To run express jobs, use the command line input:

: <code>qsub -q express -P exp-00034 -lselect=1:ncpus=48:mem=126gb -lwalltime=72:00:00</code>

Or use this inside a PBS submit script:

<pre>
# batch processing commands
#PBS -l walltime=72:00:00
#PBS -lselect=1:ncpus=48:mem=126000MB
#PBS -j oe
#PBS -q express -P exp-00034
</pre>

* Don’t forget to call less memory in the gaussian com file say 125GB

= Gaussian jobs =
== Recommended job specifications ==
For running '''Gaussian''' jobs on '''pqph''' it is recommended to just use two job sizings. The sizings mean that either a full 40 proc node will be used or just half of the node, allowing for a second job to be run on the other half of the node. These are only applicable to Gaussian jobs which can't be run across nodes. You may want to use multiple nodes/alternate job sizings for codes which are parallelised.

'''Small/medium jobs:'''
* Run jobs using half of a 40 processor node and half the memory allowance (64GB).
* PBS script input:
:: <code>#PBS -l walltime=72:00:00</code>
:: <code>#PBS -lselect=1:ncpus=20:mem=64000MB</code>
* Gaussian .com file input:
:: <code>%nprocs=20</code>
:: <code>%mem=60000MB</code>

'''Medium/large jobs:'''
* Run jobs using a full 40 processor node and the full the memory allowance (128GB).
* PBS script input:
:: <code>#PBS -l walltime=72:00:00</code>
:: <code>#PBS -lselect=1:ncpus=40:mem=128000MB</code>
* Gaussian .com file input:
:: <code>%nprocs=40</code>
:: <code>%mem=122000MB</code>

If you need to use the larger (48 proc) nodes for more expensive calculations:
* Run jobs using a full 48 processor node and the full the memory allowance (256GB).
* PBS script input:
:: <code>#PBS -l walltime=72:00:00</code>
:: <code>#PBS -lselect=1:ncpus=48:mem=25000MB</code>
* Gaussian .com file input:
:: <code>%nprocs=48</code>
:: <code>%mem=256000MB</code>

==Runscripts==

=== Standard job script ===
An example gaussian runscript for a 20 processor job:

<pre>#!/bin/sh

# Submit jobs to the queue with this script using the following command:
#
# qsub -N jobname -v in=name rs20
#
# Where: rs20 is the name of this runscript
# jobname is a name you will see in the qstat command
# name is the actual file minus .com etc it is passed into this script as ${in%.com}

# batch processing commands
#PBS -l walltime=72:00:00
#PBS -lselect=1:ncpus=20:mem=64000MB
#PBS -j oe
#PBS -q pqph
#PBS -m a

# Load relevant modules

module load gaussian/g16-a03

# Check for a checkpoint file to copy to the temp directory
# variable PBS_O_WORKDIR=directory from which the job was submitted.
if [[ -e $PBS_O_WORKDIR/${in%.com}.chk ]]
then
echo "$PBS_O_WORKDIR/${in%.com}.chk located"
cp $PBS_O_WORKDIR/${in%.com}.chk $TMPDIR/.
else
echo "no checkpoint file $PBS_O_WORKDIR/${in%.com}.chk"
fi

# Execute Gaussian
#
g16 $PBS_O_WORKDIR/${in}

# Once job is finished copy across the .chk file
cp $TMPDIR/${in%.com}.chk /$PBS_O_WORKDIR/.

# exit
</pre>

* Edit the PBS lines to create runscripts for other job specifications.
* If you are not sure what the PBS commands are or on what the runscript does then check out the introduction to the hpc page: [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Getting_started_on_the_HPC Getting Started on the HPC]
* If you need to copy back any other output files you can either run the job in <code>${EPHERMAL}</code> instead of <code>${TMPDIR}</code> as all output files will remain in ephermal for a period of time. Or, if you know the extension of the additional desired output file you can use a modified version of the code:

<pre>
# Check for the existence of other possible output files and copy if located
if [[ -e $TMPDIR/*.extension ]]
then
cp $TMPDIR/*.extension /$PBS_O_WORKDIR/${in%.com}_*.extension
fi
</pre>

* Replace *.extension with the correct file extension that you want to copy back.

=== Array jobs ===

If you have a large number of small jobs which are only slightly different e.g. optimising a large number of conformers of a molecule/system that only vary in the input structure, then you should use an array job.

An example array job runscript for a 20 processor job is:

<pre>#!/bin/sh

# batch processing commands
#PBS -l walltime=72:00:00
#PBS -lselect=1:ncpus=20:mem=64000MB
#PBS -J 1-X
#PBS -j oe
#PBS -q pqph
#PBS -m a
#PBS -N arrayJobName

in=$( sed -n ${PBS_ARRAY_INDEX}p ${PBS_O_WORKDIR}/inputFiles.txt)

echo ${in}
# Load relevant modules
module load gaussian/g16-a03

# Check for a checkpoint file to copy to the temp directory
# variable PBS_O_WORKDIR=directory from which the job was submitted.
if [[ -e $PBS_O_WORKDIR/${in%.com}.chk ]]
then
echo "$PBS_O_WORKDIR/${in%.com}.chk located"
cp $PBS_O_WORKDIR/${in%.com}.chk $TMPDIR/.
fi

# Execute Gaussian
g16 $PBS_O_WORKDIR/${in}

# Once job is finished copy across the .chk file
cp $TMPDIR/${in%.com}.chk /$PBS_O_WORKDIR/.

# exit
</pre>

To use the script:
* Set up all your input .com files in the same directory
* Edit the line in the runscript that sets the number of jobs in the array: <code>#PBS -J 1-X</code>. Change X to the number of input files you have to run.
* The runscript works by running X separate jobs within the array. For each job, there is a PBS variable set ('''PBS_ARRAY_INDEX''') which is the jobs number within the array. E.g. for the first job to run, PBS_ARRAY_INDEX = 1.
* Change the job name using the -N flag in the script or by the command line option
* Save your changes to the runscript and exit
* Create a text file with the names of all the input .com files. An easy way to do this is by the command line:
: <code>ls *.com > inputFiles.txt</code>
* You will notice that the file inputFiles.txt is called in the line in the runscript which sets the variable '''in'''. It uses the array job number ('''PBS_ARRAY_INDEX''') as an index to reference the correct line in the text file, so each job will call a different input file.
* Submit the array job using the command:
: <code> qsub rs_ja </code>

* The job runs as a single job on the queue and gets a single job id number (e.g. 1096738), each of the separate jobs within the array job are then given an index (e.g. 1096738[4] for job 4 of the array)
* The qstat information for the array job now tells you how many jobs are in the array, how many are queued and how many are finished.

==Extra information/troubleshooting==

*add tmpspace=400 only for large disk jobs to ensure you are put on a node with enough disk!!
*Note that this requires you to include maxdisk=400gb in your gaussian input.
:NOTE the queuing system does not check disk allocations. When requesting large disk jobs remember to request all of the processors on a node even if you are not using all of the processors. For large jobs the maximum disk space you can request is '''800GB''' on the 12 processor nodes.

=== More details for if you seem to be having memory or disk issues ===
*normal jobs
::will need 2*N^2 W *8.4 to get B (1,048,576B =1MB)
:: so 300 basis functions will need 180000W =0.18MW =1.5MB in addition to the above requirements
::require 2ON^2 W of disk to run where O=number of occupied orbitals, N=number of basis functions

*MP2 jobs
:: work best with %mem and maxdisk defined
:: in-core requires N^4/4 divided by 1,000,000 MW memory
:: so 400 basis functions will need 6400MW=53760MB=54GB memory per node, which is unlikely!
:: semi-direct requires 2*O(N^2) memory and N^3 disk
:: so N=476 basis functions O=56 occupied orbitals will need
::25.4MW=214MB of memory
::and 108MW=906MB disk (this is not actually true it will need much more probably around 1800MB disk per processor!)
::so total memory for MP2 freq 8proc will be
::12*8*8.4=807MB to run and 8*214=1712MB for calcs and some extra 400MB=3019MB=3.3GB
::gaussian does not like GB directive so give %mem in MB

=== Checkpoint and other files ===
: checkpoint files should be exactly the same name as the input file name
: for jobs that may exceed the wall time specify the full path of the checkpoint file, for example
::%chk=/work/phunt/tmp/filename.chk
:this means the checkpoint file will be written into your personal work directory, it may slow the job down
:this is also the reason /work is sometimes very slow on CX1 so only do this as an exception!

=== Memory needed to run ===

*Gaussian is greedy and will exceed the allocated memory
:newer notes
::a good rule of thumb for >50 atoms or >500 basis functions is 4GB minimum per processor
::so 20proc is 80GB minimum
::for mp2 frequency and ccsd you should leave enough memory to buffer the large disk files
::so only give the gaussian job 50-70% of the total memory

:older notes
:: each proc needs a gaussian executable, which takes about 8MW (or 12 for MP2 frequencies)
::MW is megaword which is the unit gaussian allocates memory
::1MW is about 8.4MB
:::so each proc needs 1*8*8.4 approximately 68MB just to run
:::so 12 proc jobs require 12*68=816MB just to run
:::so 16 proc jobs require 16*68=1088MB just to run
:::so 20 proc jobs require 20*68=1360MB just to run
:::so 24 proc jobs require 24*68=1632MB just to run
:::so 40 proc jobs require 40*68=2720MB just to run
:::so 48 proc jobs require 48*68=3264MB just to run
::so when allocating memory inside the gaussian job you must reduce the memory by at least this amount
*thus best to reduce the memory by about 100MB*no.processors inside the gaussian script
*you also need some overhead within the PBS script

*the memory can be given in binary such as 251 GB (binary) is really 251 GB =251000*1,048,576 Bytes =264GB (decimal)

= Extra links =

The Imperial Research Computing service have a hpc wiki which has useful information including an intro to shell scripting, modules and job management information:
::https://wiki.imperial.ac.uk/display/HPC/High+Performance+Computing

The RCS also run several courses throughout the year, including intro to Linux, HPC, python and more advanced topics. Upcoming courses can be viewed from:
::https://www.imperial.ac.uk/admin-services/ict/self-service/research-support/rcs/training/

===Next steps===
Mount
Alias shortcut for logging in
Keypair page
Once you are comfortable and understand the job submission process then the automatic job script which ... can be used

== Other information (may be out of date) ==
:3.1 CPMD:
::https://www.ch.ic.ac.uk/wiki/index.php/Image:Runcpmd_md.sh
:3.2 DL-POLY:
::https://www.ch.ic.ac.uk/wiki/index.php/Image:Mpirun.sh
::Note: You´ll not be able to see the output until the job finishes : the directory /tmp/pb.XXX isn´t accessible to you because it is on the private disk of the node running the job.
::To get DLPOLY to terminate before the job hits the walltime limit and killed, you need to run it through a program called pbsexec, for example:
::pbsexec mpiexec DLPOLY.X
::This will kill DLPOLY 15 minutes before the walltime limit, giving your script time to transfer files back to $work.

Mod:Hunt Research Group/hpc

2020-05-17T20:59:58Z

Phunt: /* Memory needed to run */

= General Resources =

== pqph ==

* You can check the current queue resources and staus here: [https://selfservice.rcs.imperial.ac.uk/pqs/nodes/pqph pqph queue status]
* Currently, pqph consists mainly of 40 proc/124GB nodes and a couple of 48 proc/256GB nodes in pqph.

==Express queue==

* We can also now submit jobs to the Express queue
* Use this for anytime our pqph is looking full or if you have a job you think will take more than a day or longer than 3 days

To run express jobs, use the command line input:

: <code>qsub -q express -P exp-00034 -lselect=1:ncpus=48:mem=126gb -lwalltime=72:00:00</code>

Or use this inside a PBS submit script:

<pre>
# batch processing commands
#PBS -l walltime=72:00:00
#PBS -lselect=1:ncpus=48:mem=126000MB
#PBS -j oe
#PBS -q express -P exp-00034
</pre>

* Don’t forget to call less memory in the gaussian com file say 125GB

= Gaussian jobs =
== Recommended job specifications ==
For running '''Gaussian''' jobs on '''pqph''' it is recommended to just use two job sizings. The sizings mean that either a full 40 proc node will be used or just half of the node, allowing for a second job to be run on the other half of the node. These are only applicable to Gaussian jobs which can't be run across nodes. You may want to use multiple nodes/alternate job sizings for codes which are parallelised.

'''Small/medium jobs:'''
* Run jobs using half of a 40 processor node and half the memory allowance (64GB).
* PBS script input:
:: <code>#PBS -l walltime=72:00:00</code>
:: <code>#PBS -lselect=1:ncpus=20:mem=64000MB</code>
* Gaussian .com file input:
:: <code>%nprocs=20</code>
:: <code>%mem=60000MB</code>

'''Medium/large jobs:'''
* Run jobs using a full 40 processor node and the full the memory allowance (128GB).
* PBS script input:
:: <code>#PBS -l walltime=72:00:00</code>
:: <code>#PBS -lselect=1:ncpus=40:mem=128000MB</code>
* Gaussian .com file input:
:: <code>%nprocs=40</code>
:: <code>%mem=122000MB</code>

If you need to use the larger (48 proc) nodes for more expensive calculations:
* Run jobs using a full 48 processor node and the full the memory allowance (256GB).
* PBS script input:
:: <code>#PBS -l walltime=72:00:00</code>
:: <code>#PBS -lselect=1:ncpus=48:mem=25000MB</code>
* Gaussian .com file input:
:: <code>%nprocs=48</code>
:: <code>%mem=256000MB</code>

==Runscripts==

=== Standard job script ===
An example gaussian runscript for a 20 processor job:

<pre>#!/bin/sh

# Submit jobs to the queue with this script using the following command:
#
# qsub -N jobname -v in=name rs20
#
# Where: rs20 is the name of this runscript
# jobname is a name you will see in the qstat command
# name is the actual file minus .com etc it is passed into this script as ${in%.com}

# batch processing commands
#PBS -l walltime=72:00:00
#PBS -lselect=1:ncpus=20:mem=64000MB
#PBS -j oe
#PBS -q pqph
#PBS -m a

# Load relevant modules

module load gaussian/g16-a03

# Check for a checkpoint file to copy to the temp directory
# variable PBS_O_WORKDIR=directory from which the job was submitted.
if [[ -e $PBS_O_WORKDIR/${in%.com}.chk ]]
then
echo "$PBS_O_WORKDIR/${in%.com}.chk located"
cp $PBS_O_WORKDIR/${in%.com}.chk $TMPDIR/.
else
echo "no checkpoint file $PBS_O_WORKDIR/${in%.com}.chk"
fi

# Execute Gaussian
#
g16 $PBS_O_WORKDIR/${in}

# Once job is finished copy across the .chk file
cp $TMPDIR/${in%.com}.chk /$PBS_O_WORKDIR/.

# exit
</pre>

* Edit the PBS lines to create runscripts for other job specifications.
* If you are not sure what the PBS commands are or on what the runscript does then check out the introduction to the hpc page: [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Getting_started_on_the_HPC Getting Started on the HPC]
* If you need to copy back any other output files you can either run the job in <code>${EPHERMAL}</code> instead of <code>${TMPDIR}</code> as all output files will remain in ephermal for a period of time. Or, if you know the extension of the additional desired output file you can use a modified version of the code:

<pre>
# Check for the existence of other possible output files and copy if located
if [[ -e $TMPDIR/*.extension ]]
then
cp $TMPDIR/*.extension /$PBS_O_WORKDIR/${in%.com}_*.extension
fi
</pre>

* Replace *.extension with the correct file extension that you want to copy back.

=== Array jobs ===

If you have a large number of small jobs which are only slightly different e.g. optimising a large number of conformers of a molecule/system that only vary in the input structure, then you should use an array job.

An example array job runscript for a 20 processor job is:

<pre>#!/bin/sh

# batch processing commands
#PBS -l walltime=72:00:00
#PBS -lselect=1:ncpus=20:mem=64000MB
#PBS -J 1-X
#PBS -j oe
#PBS -q pqph
#PBS -m a
#PBS -N arrayJobName

in=$( sed -n ${PBS_ARRAY_INDEX}p ${PBS_O_WORKDIR}/inputFiles.txt)

echo ${in}
# Load relevant modules
module load gaussian/g16-a03

# Check for a checkpoint file to copy to the temp directory
# variable PBS_O_WORKDIR=directory from which the job was submitted.
if [[ -e $PBS_O_WORKDIR/${in%.com}.chk ]]
then
echo "$PBS_O_WORKDIR/${in%.com}.chk located"
cp $PBS_O_WORKDIR/${in%.com}.chk $TMPDIR/.
fi

# Execute Gaussian
g16 $PBS_O_WORKDIR/${in}

# Once job is finished copy across the .chk file
cp $TMPDIR/${in%.com}.chk /$PBS_O_WORKDIR/.

# exit
</pre>

To use the script:
* Set up all your input .com files in the same directory
* Edit the line in the runscript that sets the number of jobs in the array: <code>#PBS -J 1-X</code>. Change X to the number of input files you have to run.
* The runscript works by running X separate jobs within the array. For each job, there is a PBS variable set ('''PBS_ARRAY_INDEX''') which is the jobs number within the array. E.g. for the first job to run, PBS_ARRAY_INDEX = 1.
* Change the job name using the -N flag in the script or by the command line option
* Save your changes to the runscript and exit
* Create a text file with the names of all the input .com files. An easy way to do this is by the command line:
: <code>ls *.com > inputFiles.txt</code>
* You will notice that the file inputFiles.txt is called in the line in the runscript which sets the variable '''in'''. It uses the array job number ('''PBS_ARRAY_INDEX''') as an index to reference the correct line in the text file, so each job will call a different input file.
* Submit the array job using the command:
: <code> qsub rs_ja </code>

* The job runs as a single job on the queue and gets a single job id number (e.g. 1096738), each of the separate jobs within the array job are then given an index (e.g. 1096738[4] for job 4 of the array)
* The qstat information for the array job now tells you how many jobs are in the array, how many are queued and how many are finished.

==Extra information/troubleshooting==

*add tmpspace=400 only for large disk jobs to ensure you are put on a node with enough disk!!
*Note that this requires you to include maxdisk=400gb in your gaussian input.
:NOTE the queuing system does not check disk allocations. When requesting large disk jobs remember to request all of the processors on a node even if you are not using all of the processors. For large jobs the maximum disk space you can request is '''800GB''' on the 12 processor nodes.

=== More details for if you seem to be having memory or disk issues ===
*normal jobs
::will need 2*N^2 W *8.4 to get B (1,048,576B =1MB)
:: so 300 basis functions will need 180000W =0.18MW =1.5MB in addition to the above requirements
::require 2ON^2 W of disk to run where O=number of occupied orbitals, N=number of basis functions

*MP2 jobs
:: work best with %mem and maxdisk defined
:: in-core requires N^4/4 divided by 1,000,000 MW memory
:: so 400 basis functions will need 6400MW=53760MB=54GB memory per node, which is unlikely!
:: semi-direct requires 2*O(N^2) memory and N^3 disk
:: so N=476 basis functions O=56 occupied orbitals will need
::25.4MW=214MB of memory
::and 108MW=906MB disk (this is not actually true it will need much more probably around 1800MB disk per processor!)
::so total memory for MP2 freq 8proc will be
::12*8*8.4=807MB to run and 8*214=1712MB for calcs and some extra 400MB=3019MB=3.3GB
::gaussian does not like GB directive so give %mem in MB

=== Checkpoint and other files ===
: checkpoint files should be exactly the same name as the input file name
: for jobs that may exceed the wall time specify the full path of the checkpoint file, for example
::%chk=/work/phunt/tmp/filename.chk
:this means the checkpoint file will be written into your personal work directory, it may slow the job down
:this is also the reason /work is sometimes very slow on CX1 so only do this as an exception!

=== Memory needed to run ===

*Gaussian is greedy and will exceed the allocated memory
:newer notes
::a good rule of thumb for >50 atoms or >500 basis functions is 4GB minimum per processor
:so 20proc is 80GB minimum
::for mp2 frequency and ccsd you should leave enough memory to buffer the large disk files, so only give the gaussian job 50-70% of the total memory

:older notes
:: each proc needs a gaussian executable, which takes about 8MW (or 12 for MP2 frequencies)
::MW is megaword which is the unit gaussian allocates memory
::1MW is about 8.4MB
:::so each proc needs 1*8*8.4 approximately 68MB just to run
:::so 12 proc jobs require 12*68=816MB just to run
:::so 16 proc jobs require 16*68=1088MB just to run
:::so 20 proc jobs require 20*68=1360MB just to run
:::so 24 proc jobs require 24*68=1632MB just to run
:::so 40 proc jobs require 40*68=2720MB just to run
:::so 48 proc jobs require 48*68=3264MB just to run
::so when allocating memory inside the gaussian job you must reduce the memory by at least this amount
*thus best to reduce the memory by about 100MB*no.processors inside the gaussian script
*you also need some overhead within the PBS script

*the memory can be given in binary such as 251 GB (binary) is really 251 GB =251000*1,048,576 Bytes =264GB (decimal)

= Extra links =

The Imperial Research Computing service have a hpc wiki which has useful information including an intro to shell scripting, modules and job management information:
::https://wiki.imperial.ac.uk/display/HPC/High+Performance+Computing

The RCS also run several courses throughout the year, including intro to Linux, HPC, python and more advanced topics. Upcoming courses can be viewed from:
::https://www.imperial.ac.uk/admin-services/ict/self-service/research-support/rcs/training/

===Next steps===
Mount
Alias shortcut for logging in
Keypair page
Once you are comfortable and understand the job submission process then the automatic job script which ... can be used

== Other information (may be out of date) ==
:3.1 CPMD:
::https://www.ch.ic.ac.uk/wiki/index.php/Image:Runcpmd_md.sh
:3.2 DL-POLY:
::https://www.ch.ic.ac.uk/wiki/index.php/Image:Mpirun.sh
::Note: You´ll not be able to see the output until the job finishes : the directory /tmp/pb.XXX isn´t accessible to you because it is on the private disk of the node running the job.
::To get DLPOLY to terminate before the job hits the walltime limit and killed, you need to run it through a program called pbsexec, for example:
::pbsexec mpiexec DLPOLY.X
::This will kill DLPOLY 15 minutes before the walltime limit, giving your script time to transfer files back to $work.

Talk:Mod:Hunt Research Group/build freq

2020-02-16T07:27:06Z

Phunt: /* python script to build frequency file from optimisation output */

===python script to build frequency file from optimisation output===
*copy the code into a script called "energy.py"
*to execute the script type "python build_freq.py file_name step
*if you have your execute directory in your path, you can alter the first line to your python executable and then you can just type "build_freq.py filename step"
*if step is not given the last structure from the optimisation file will be used
*if step is given the geometry from that step will be used
*NOTE: you will need to alter the string which prints the job key words into the gaussian input file

<pre>
#!/opt/local/bin/python3
#
# build_freq.py
#
# python script to extract a given step structure, or the last structure from a gaussian log file and build a frequency input file
# to run the script type:
#
# python build_freq.py input_file_name step_no
#
# if no step_no is given the last geometry will be used
#
import sys
import os
dir=os.getcwd()

#==set up FILES ==

# if there are 2 arguments to use the last step (of the optimisation)
# if there are 3 arguments then use a specific step_no from the optimisation
if len(sys.argv) == 2:
infile=str(sys.argv[1])
step_no=int(0)
elif len(sys.argv) == 3:
infile=str(sys.argv[1])
step_no=int(sys.argv[2])
#since counting starts from zero
step_no=step_no-1
#endif

# if there is less or more arguments something is wrong
else:
print('to run the script please type: python build_freq.py input_file_name step_no')
sys.exit()
#endif

# check to see if the user has used the .log extenion or not
# find returns -1 if the sub-string is not found, or the index of where the sub-string starts
# we cut out the .log part if .log is found
i_infile=infile.find('.log')
if (i_infile == -1):
base=infile
else:
base=infile[:i_infile]
#endif

# now set up the base file names
log_file=base+'.log'
geom_file=base+'.xyz'
# if opt is not in the filename add freq to the filename
# if opt is already in the file change this to freq
i_opt=base.find('opt')
i_optf=base.find('optf')
if 'opt' in base:
print ('yes')
if 'optf' in base:
base2=base.replace('optf','freq')
else:
base2=base.replace('opt','freq')
# endif
else:
base2=base + '_freq'
#endif
com_file=base2+'.com'

# print out some reference information
s='directory is '
print('{0:}{1:}'.format(s,dir))
s='input file is '
print('{0:}{1:}'.format(s,infile))
s='output file is '
print('{0:}{1:}'.format(s,com_file))
#sys.exit()
#
#==set some DEFAULTS ==
col_num=[]
col_atom=[]
col_type=[]
col_x=[]
col_y=[]
col_z=[]
rep=0
n=0
go=False
atom_total=0
geom_count=0
#
#==start READING THE FILE ==

# open file and read lines one by one
f=open(log_file,"r")

# line is a variable which contains the line
line =f.readline()
while line :
line =f.readline()
# print('{0:}'.format(line))

#==extract GEOMETRY ==
# check for standard orientation text set 'go' if the text appears
# geom_count is the number of the geometry stored
# atom_total will be the number of atoms
# n will be stepping through the lines in std orientation section so set to zero for each time through
# if this is the first geometry print that a geometry is found
if 'Standard orientation:' in line:
go=True
s='Structure in standard orientation found '
n=1
geom_count=geom_count+1
if geom_count == 1 : print('{0:}'.format(s))
s='geometry count= '
# print('{0:}{1:}'.format(s,geom_count))
# endif
#
# if go is on then we need to extract and store the structure
# skip the next 4 lines, on the 5th start collecting structure
# m is our switch to stop, we stop once we get to the Rotational constants line
# m is also our switch to not print the lines of dashes
# we need to know how many atoms there are in total as well
# we simply append each data list into the arrays col which has components num,atom,type,x,y,z
while go:
n = n+1
m = 0
line =f.readline()
if 'Rotational constants (GHZ):' in line: m=-1
if '---------' in line: m=1
if n > 4 and m == 0 :
# print('line: {0:}'.format(line))
if geom_count == 1 : atom_total=atom_total+1
a1,b1,c1,d1,e1,f1=line.rstrip().split()
col_num.append(int(a1))
col_atom.append(int(b1))
col_type.append(int(c1))
col_x.append(float(d1))
col_y.append(float(e1))
col_z.append(float(f1))
if m == -1 : go=False
# close while
#close while

#== build COM FILE ==

# first give all the comp details
c=open(com_file,"w")
s="%nprocshared=48\n%mem=122000MB\n"
c.write('{0:}'.format(s))
s='%chk='+base2+'.chk\n'
c.write('{0:}'.format(s))
s="# freq m06/6-311G(d,p) geom=cartesian int=ultrafine scf=conver=10 \n\n"
c.write('{0:}'.format(s))
s="Title Card Required\n\n0 1\n"
c.write('{0:}'.format(s))

#other options are
#s="# freq b3lyp/gen pseudo=cards empiricaldispersion=gd3bj geom=cartesian \n "
#s="gfinput int=ultrafine scf=conver=10 test\n\n"

# now put in the coordinates
# if step_no is zero we only use the last geometry
# if step_no is given, we use that geometry
# geom_count is the number of geometries
# atom_total is the numer of atoms
# if taking the last geometry count backwards
# n is the internal counter
# n_start defines where to start printing
# n_stop defines wher to stop printing
#
n=0
n_start=0
n_stop=0
#print ('{0:}{1:}'.format('step_no=',step_no))
#print ('{0:}{1:}'.format('atom_total=',atom_total))
#print ('{0:}{1:}'.format('geom_count=',geom_count))
if step_no == 0 :
n_start=len(col_num)-atom_total
n_stop=len(col_num)
s=' structures found only the last is used'
print('{0:}{1:}'.format(geom_count,s))
else:
n_start=atom_total*step_no
n_stop=n_start+atom_total
print('{0:}{1:}{2:}{3:}'.format('using structure ',step_no+1,' of ',geom_count))
# endif
#print ('{0:}{1:}'.format('n_start=',n_start))
#print ('{0:}{1:}'.format('n_stop=',n_stop))
n=n_start
while n >= n_start and n < n_stop:
c.write('{0:>4d} {1: 09.6f} {2: 09.6f} {3: 09.6f} \n'.format(col_atom[n],col_x[n],col_y[n],col_z[n]))
# print('{0:>4d} {1:>4d} {2: 09.6f} {3: 09.6f} {4: 09.6f}'.format(col_num[n],col_atom[n],col_x[n],col_y[n],col_z[n]))
n=n + 1
#close while

# now put in the gen information
#s="\nCl 0\n6-311+G(d,p)\n****\n"
#t="In 0\nLANL2DZ\n****\n\n"
#u="In 0\nLANL2DZ\n\n\n"
#c.write('{0:}{1:}{2:}'.format(s,t,u))

# and add the last blank lines
s=" \n\n"
c.write('{0:}'.format(s))

# close all open files
f.close()
c.close()
#
</pre>

Talk:Mod:Hunt Research Group/extract energy

2020-02-16T07:25:59Z

Phunt: /* python script to print energies */

===python script to print energies===
*copy the code into a script called "get_energy.py"
*to execute the script type "python energy.py file_name
*if you have given the path to your python executable at the front of the file, and this script is in your path
*you can simply execute with "get_energy.py filename"
*this will print to terminal the energy for each step, find the lowest energy and plot a quick graph relative to the lowest energy in kJ/mol
*NOTE: press "q" to close the graph (or click the red button on the graph)

<pre>
#!/opt/local/bin/python3
#
# energy.py
#
# python script to extract the SCF energy for each step, find the lowest energy step
# and produce a quick graph showing the change in energy in kJ/mol
# to run the script type
# python energy.py input_file_name
# NOTE you can close the graph by pressing "q" on keyboard
#
import sys
import numpy as np
import matplotlib.pyplot as plt
import os
dir=os.getcwd()
#
# setup files to read
if len(sys.argv) == 1:
print('to run the script please type: python energy.py input_file_name')
sys.exit()
else:
log_file=str(sys.argv[1])
s='directory is '
print('{0:}{1:}'.format(s,dir))
s='input file is '
print('{0:}{1:}'.format(s,log_file))
#close if

# open the file
f = open(log_file,'r')

# set some basic parameters
energy=[]
new_energy=[]
x_axis=[]
en_search_string='SCF Done:'

# read the if there is a first line, then read the file line by line
# if energy is given split the line into array tmp and extract the energy number
# and extract the energy and store in an array
count=0
line=f.readline()
while line:
line =f.readline()
# print('{0:}'.format(line))
if en_search_string in line:
tmp=line.rstrip().split()
energy.append(float(tmp[4]))
count1=count+1
print('{0:}{1:<3}{2:<.8f}'.format('step: ',count1,energy[count]))
count=count+1
# endif
#endwhile

total_steps=count
#print(total_steps)

# find the lowest energy
min_energy=min(energy)
min_index=energy.index(min(energy))
print('{0:}{1:}{2:}{3:}'.format('lowest energy is step: ',min_index+1,' energy: ',min_energy))

# convert to kJ/mol relative to lowest energy
# create x_axis which starts numbering at 1, remember python starts at zero
x=0
while x < total_steps :
temp=(energy[x] - min_energy) * 2625.5
new_energy.append(temp)
x=x+1
x_axis.append(x)
#endwhile

# plot the energy
plt.plot(x_axis,new_energy,'b-')
plt.plot(x_axis,new_energy,'bo')
plt.plot(min_index+1,new_energy[min_index],'rs',markersize=8)
plt.ylabel('energy kJ/mol')
plt.xlabel('step')
plt.show()

# close file
f.close()
#sys.exit()
#end
</pre>

Mod:Hunt Research Group/file move

2020-02-13T18:08:44Z

Phunt: Created page with "==Moving large files, or directories around== *Use dropbox if they are not too large, otherwise *Use the "tar" command ::If you have not used this command before **practice**..."

==Moving large files, or directories around==
*Use dropbox if they are not too large, otherwise
*Use the "tar" command
::If you have not used this command before **practice** (make up a directory with some test files in it) since you can '''destroy the WHOLE directory''' if you do it wrong.
*for example, for a directory called "jobs"
<pre>
tar -cvfz jobs.tar.gz jobs
</pre>
::the -c command means concatonate all files
::the -v is for verbose output
::the -f is to create a file
::the -z is to compress or gzip the whole lot

*to uncompress and expand out
<pre>
gunzip jobs.tar.gz
tar -xvf jobs.tar
</pre>
::we need to uncompress first using the gzip utility
::then use the tar command to expand the decompressed file
::the -x is to expand

Mod:Hunt Research Group

2020-02-13T18:04:59Z

Phunt: /* Group Admin */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===Report and Paper Writing===
#procedures [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/report_procedures link]
#advice [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/report_writing link]
#report components [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/report_components link]
#files to provide when writing a paper [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/paper link]

===Group Admin===
#Which files to store on the database and database template [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/database link]
#How to access DROBO [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/drobo link]
#Moving large files and directories around [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/file_move link]

===HPC Resources===
#'''Hunt group HPC servers and run scripts''' [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link]
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link]
#How to run jobs interactively [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/run_interactive link]
#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link]
#New gf script (more convenient job submitting) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/new_gf_script link]
#Retired: How to make qsub more comfortable (gfunc) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpQSUB link]
#Tired of entering your password all the time: set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link]
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link]
#Using VPN from home, for Sierra follow the college instructions [[link]]
#How to connect to HPC directory on desktop for file transfers [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_Directory_on_desktop link]
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link]
#How to use a slimmed down terminal on your IPhone [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/termius]

===Using evil Windows and PCs===
#Use Imperial Software Hub to access gaussview and gaussian [http://www.imperial.ac.uk/admin-services/ict/store/software/software-hub/ link]
#Using windows and setting up a connection to HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link]
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link]

===Key Papers, References and Resources===
*'''Papers'''
#Meta study on DFT functionals [https://pubs.acs.org/doi/abs/10.1021/ct401111c doi]
#M06 suite of DFT functionals [https://link.springer.com/article/10.1007/s00214-007-0310-x doi]
#SMD for ILs [https://pubs.acs.org/doi/abs/10.1021/jp304365v doi]
#Box size for MD simulations of ILs [https://dx.doi.org/10.1063/1.4748352 doi]
*'''Notes'''
#Solving the angular part of the Schrödinger equation for a hydrogen atom [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/angular_schrodinger link] (notes by Vincent)
#DFT Workshop Notes [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/DFT_Workshop]
#Cl- in water [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link]
#The use of Legendre time correlation functions to study reorientational dynamics in liquids [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/legendre link]

===Gaussian General===
#We are starting a database of common errors encountered when running Gaussian jobs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gaussian_errors link]
# Here is an already existing database of common errors [https://docs.computecanada.ca/wiki/Gaussian_error_messages link]
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#partial optimisations and scans [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/z-matrix link]
#General procedure for locating transition state structures [[link]]
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link]
#Basic ONIOM (Mechanical Embedding) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/basiconiom link]
#problems with scf convergence [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/scf_convergence link]
#manipulating checkpoint files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:usingchkfiles link]
#for NMR calculations look here: [http://cheshirenmr.info/index.htm Chemical Shift Repository]
#Population and charge analysis [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/population link]

===Gaussian Advanced===
#Systematic conformational scan for ion-pair dimers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ion_pair_scan link]
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link]
#generating natural transition orbitals [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/nto link]
#computing excited state polarisabilities [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_ES_alpha link]
#computing deuterated and/or anharmonic spectra [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_Danharm link]
#How to run at a higher temperature [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:high_temp link]
#Correcting the entropy due to low modes [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:low_modes_entropy link]
#Optimisation of charged molecules in an electric field [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Optimising_charged_molecules_in_electric_fields link]
#Multidimensional Scans of Internal Coordinates [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Multidimensional_Scans_of_Internal_Coordinates link]
#Conformational search of atomic and molecular clusters with ABCluster [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:ABCluster#.inp_file_on_the_HPC link]

===Solvation===
#Using the SMD model [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/solvent link]
#Using SMD on ILs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_Using_SMD_on_ILs link]
#Troublesome optimisations in SMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:troublesome_smd link]
#Atomic radii and solvent models [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/atomic_radii link]
#Molecular volume calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molecular_volume link]
#The cavity [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/solvent_cavity link]
#How to download and use GeomView to visualise solvation cavities [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/geomview link]
#Surfaces (Solvent-Accessible and Connolly) in Jmol [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/jmolsurfaces link]

===Codes to Help Gaussian Analysis===
====Python and Python codes====
# Using and installing python [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/python link]
# Python toolkit currently focussed towards gaussian analysis [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molLego link]
# Standalone python scripts and analysis:
#* List the energy for each step of a gaussian log file, find the lowest energy and produce a quick graph in kJ/mol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_energy link]
#* Build a frequency file from an optimisation file ready to submit, this will require editing for your particular job [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/build_freq link]
#* Extract last Standard Orientation structure of gaussian log file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_single_geom link]
#* Extract last structure of gaussian optimisation and build a freq com file for job with PP [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/build_freq_file link]
#* Extract each optimised step from a scan into xyz coordinate file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_scan_geom link]
#* Extract thermodynamic data and low frequencies from log files (python 2) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:simple_freq_script link]
#* Extract thermodynamic data and low frequencies from log files to enter into excel template provided for the database (python 3) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:model_freq_script link]
#* Extract geometry and charges (ESP) into a .pdb file for visualising in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ESP_charges_for_VMD link]
#* Codes to extract CHELPG and NBO charge values to excel [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/chelpg_extract link]
#* Extract ESP and NBO charges [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_ESP_charges link]
#* Script to pull thermodynamic data and low frequencies from log files AND evaluate to a reference [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:freq_script link]
#* Codes to extract frequency data from gaussian .log files and generate vibrational spectra [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:frequency_spectrum_script link]
#* Codes to visualise data matrices (correlation matrices/heatmaps)[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/heatmap link]
#* Python API for analysis of Gaussian computations [https://pygauss.readthedocs.org - Documentation]
#* Charge arm [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/charge_arm link]
#* Extract the MO orbital energies and concert to eV [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/MO_energies link]

====Other codes====
# Extract E2 Values (From NBO Calculations) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/NBO_Matlab_Code link]
# Calculate pDoS/XP spectra code (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Calc_XPS_Code link]
# Optimally Tuned Range Separated Hybrid Functionals [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/OTRSH_Funct link]
# Some G09 Parsers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Some_G09_Parsers link]

===QC Visualisation===
*'''Using AIMALL: density based visualisation'''
#download [http://aim.tkgristmill.com AIMALL]
#once downloaded and installed you need to send tricia your aimall-serialnumber.txt file, and she will arrange for a aimallpro.lic or license file for you
#basic instructions [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:aim_basics link]
#AimAll with pseudo potentials [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:aim_pseudopotentials link]
#AIMAll 19.10.12 on iMacs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:AIMAllQuickFix link]

*'''ESPs and manipulating gaussian cube files'''
#Instructions for visualizing electrostatic potentials (Gaussview)[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link]
#Electrostatic Potentials II (Molden) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials_2 link]
#Manipulating cube files [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/cube_files link]
#Format of cube files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/cube_format link]
#Using A. Stone's distributed multipole analysis [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/GDMA link]

*'''NCI plots'''
#get the program here: [http://www.lct.jussieu.fr/pagesperso/contrera/nciplot.html link]
#How to install NCIPlot on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/InstallNCIPlot link]
#Using NCIPlot [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/UseNCIPlot link]

*'''MOs'''
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link]

===Setup and Running Classical MD Simulations===
====dl_poly====
#DLPOLY_4.0 Installation for an IMac [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Installing_DL_POLY_4.09_on_MacOS_Mojave link]
#DLPOLY_Classic Installation for an IMac [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Installing_DL_POLY_classic link]

#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#some basics for getting started using DL_POLY [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dl_poly_basics link]
#control file basics [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/control_basics link]
*useful links
::[https://www.ccp5.ac.uk https://www.ccp5.ac.uk]
::[https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx]
::[ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/USRMAN4.pdf dlpoly4 user manual]
::[ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/JavaGUI.pdf javagui user manual]
::[ftp://ftp.dl.ac.uk/ccp5/DL_POLY/ dlpoly ftp server]
:::you can find test files in DL_POLY_4.0/DATA
:::more info about the dlpoly test files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/DL_POLY_test_files link]

====gromacs====
#GROMACS installing and getting started with gromacs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gromacs_1 link]
#using Agilio Padua force fields for ionic liquids [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/ilff link]
#Packmol installing and running to generate a starting box [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/packmol_1 link]
#initial rough relaxation [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Starting_MD link]
#GROMACS general run [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_run link]
#GROMACS viewing data [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_viewing_MD link]
#GROMACS control file [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_control_MD link]
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link]
====general====
#Getting the Force Field [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Wheretostart link]
#Choosing an Ensemble [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Ensembles link]
#Molten Salt Simulations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/MoltenSaltSimulation link]
#Common Errors [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/CommonErrors link]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link]

===MD Visualisation===
*'''VMD: a molecular dynamics visualisation package'''
#VMD can be installed from the [http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD VMD downloads page]
#Quick reminder [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDReminder link]
#Colour in VMD [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDColor link]
#Changing the graphical representation of your structures [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link]
#VMD indexing [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDindexing link]
#Using scripts in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScripts link]
#Dealing with periodic boundaries and bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsPeriodic link]
#Dealing with bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdBonding link]
#How to turn a Gaussian optimization into a VMD movie [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/VMDmovie link]
#Overlapping two structures [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdVisual link]
*'''Ovito: a molecular dynamics visualisation package'''
#Download Ovito [http://www.ovito.org/index.php/download]
#Using Ovito basics [//wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Ovito_basics link]
*'''SDFs'''
#How to generate SDFs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/sdfs_generate link]

===MD Post processing===
#Python script to convert a HISTORY file into a xyz file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/hist_to_xyz link]
#Python script to reduce the number of steps in a lammps traj file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/lam_to_xyz link]
#Python script to convert a lammps traj file to xyz coordinates and at the same time fold all atoms into a cell and center at the origin [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/lam_fold_xyz link]
#Center the trajectory at a particular atom ('''needs fixing''') [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Recenter link]
#How to generate SDFs with TRAVIS [[Talk:Mod:Hunt Research Group/How to draw SDFs with TRAVIS|link]]
#Tcl script to follow a particular atom [[Talk:Mod:Hunt Research Group/Traj_atom_following|link]]

===Coding===
*'''installing Xcode and other programming environments'''
#to use many programs you will need a compiler, this is not installed by default on your mac
#How to install Xcode on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/InstallXcode link]
#using MacPorts as code for managing other codes on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/MacPorts link]
#HomeBrew and Fink are other options (HomeBrew is not advised for us)
#gfortran on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Gfortran link]
#using python on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/python link]

*'''EMO Code'''
#How to use Ling's emo plot code[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emoplot link]
#How to plot EMOs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emo link]

*'''Jan's charge based analysis Code'''
#charge analysis [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Jan_charges link]
#Obtaining NBO, ESP, and RESP charges [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Charges link]

*'''Oxana's visualisation of ESPs Code'''
#Scripts for reading, saving, manipulating and visualising data from cube files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Python_scripts_for_cube_files link]

*'''Python Genereal'''
# General python recommendations and set up [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/PythonGeneral link]
# Analysis toolkit mainly geared towards processing Gaussian calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Python_Analysis_Tools link]

===Other Codes===
#ADF Submission script [http://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/ADF_sricpt link]
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link]
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/]

===Setup and Running Ab-Initio MD Simulations===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link]
#How to run CPMD to study aqueous solutions [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd_water link]
#How to run CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k_how link]

===Running QM/MM Simulations in ChemShell===

==Tcl-chemshell==
#ChemShell official website which contains the manual and a tutorial [http://www.stfc.ac.uk/CSE/randd/ccg/36254.aspx link]
#Introduction to ChemShell - Copper in water [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Introduction link]
#Defining the system: Cu2+ and its first 2 solvation shells [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_System_Aqeuous_Cu(II) link]
#Defining the force field parameters [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II) link]
#Single point QM/MM energy calculation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_SP_Aqeuous_Cu(II) link]
#QM/MM Optimisation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_OPT_Aqeuous_Cu(II) link]
#QM/MM Molecular Dynamics [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_MD_Aqeuous_Cu(II) link]
#Using MolCluster [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/MolCluster link]
#Running ChemShell [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell link]
#Explaining ChemShell files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files link]
#Step By Step [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Chemshell_Step_By_Step link]
==Py-chemshell==

# Compiling Chemshell and required programs []
# The DL_POLY_4 manual is available for download at this link [ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/USRMAN4.pdf]
# Molecular Mechanics computation with DL_POLY [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:_MM_Single_Point_computation]
# Basic QM/MM single point and optimisations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_QM/MM_Single_Point_and_optimisation]
# Visualise optimisation trajectories in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_Visualising_trajectories_with_VMD]
# Computing Mulliken charges and creating .wfn inputs for AIM analysis [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_Mulliken]

==Admin Stuff==
#Not used to writing a wiki, make your test runs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/testing on this page]
#How to set-up new macs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_setup link]
#How to switch the printer HP CP3525dn duplex on and off [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/printing link]

Mod:Hunt Research Group/MO energies

2020-02-04T13:51:29Z

Phunt: Created page with "==python script to extract MO energies == <pre> #!/opt/local/bin/python3 # # get_MOenergy.py # # python3 script to # extract key data from gaussian log files for input int..."

==python script to extract MO energies ==
<pre>
#!/opt/local/bin/python3
#
# get_MOenergy.py
#
# python3 script to
# extract key data from gaussian log files for input into
# excell spreadsheets for our database
#
# to run the script type
# python3 get_MOenergy.py file.log
#
import sys
import os
#
# check to see if the user has used the .log extenion or not
# find returns -1 if the sub-string is not found, or the index of where the sub-string starts
# we cut out the .log part if .log is found
infile=str(sys.argv[1])
i_infile=infile.find('.log')
if (i_infile == -1):
base=infile
else:
base=infile[:i_infile]
#endif
log_file=base+'.log'
f = open(log_file,'r')

s='input file is '
print('{0:}{1:}'.format(s,log_file))

# set some basic parameters
MOenergy = []
MOevenergy = []
MOnumber = []
MOenergy_search_string = 'Orbital energies and kinetic energies (alpha):'
MOenergy_end_string = 'Total kinetic energy from orbitals='
go=False

# read the file
count=0
line=f.readline()
#print('{0:}'.format(line))
while line:
line=f.readline()

# find where energies are
if MOenergy_search_string in line:
# print ('found txt')
line=f.readline()
go=True
# endif

# if MO energies are found
while go:
line=f.readline()
# print('{0:}'.format(line))
if MOenergy_end_string in line:
# print('stop')
go=False
else:
tmp=line.rstrip().split()
MOnumber.append(int(tmp[0]))
MOenergy.append(float(tmp[2]))
# print('{0:} {1:3d} {2:09.6f}'.format('step: ',MOnumber[count],MOenergy[count]))
count=count+1
# endif
# endif
#endwhile

s='total no MOs is '
print('{0:}{1:} \n'.format(s,count))

s='MO energy in au and eV'
print('{0:}'.format(s))

x=0
while x < count :
temp=MOenergy[x] * 27.2113
MOevenergy.append(temp)
# print('{0:3d},{1:9.6f},{2:9.6f}'.format(MOnumber[x],MOenergy[x],MOevenergy[x]))
x=x+1
#endwhile

#s='\n suitable for copying to excel:'
#print('{0:} \n'.format(s))

x=0
while x < count :
print(' {0:3d}, {1:9.6f}, {2:9.6f}'.format(MOnumber[x],MOenergy[x],MOevenergy[x]))
x=x+1
#endwhile

# finish up
f.close()
sys.exit()
</pre>

Mod:Hunt Research Group

2020-02-04T13:50:41Z

Phunt: /* Python and Python codes */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===Report and Paper Writing===
#procedures [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/report_procedures link]
#advice [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/report_writing link]
#report components [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/report_components link]
#files to provide when writing a paper [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/paper link]

===Group Admin===
#Which files to store on the database and database template [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/database link]
#How to access DROBO [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/drobo link]

===HPC Resources===
#'''Hunt group HPC servers and run scripts''' [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link]
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link]
#How to run jobs interactively [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/run_interactive link]
#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link]
#New gf script (more convenient job submitting) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/new_gf_script link]
#Retired: How to make qsub more comfortable (gfunc) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpQSUB link]
#Tired of entering your password all the time: set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link]
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link]
#Using VPN from home, for Sierra follow the college instructions [[link]]
#How to connect to HPC directory on desktop for file transfers [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_Directory_on_desktop link]
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link]
#How to use a slimmed down terminal on your IPhone [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/termius]

===Using evil Windows and PCs===
#Use Imperial Software Hub to access gaussview and gaussian [http://www.imperial.ac.uk/admin-services/ict/store/software/software-hub/ link]
#Using windows and setting up a connection to HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link]
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link]

===Key Papers, References and Resources===
*'''Papers'''
#Meta study on DFT functionals [https://pubs.acs.org/doi/abs/10.1021/ct401111c doi]
#M06 suite of DFT functionals [https://link.springer.com/article/10.1007/s00214-007-0310-x doi]
#SMD for ILs [https://pubs.acs.org/doi/abs/10.1021/jp304365v doi]
#Box size for MD simulations of ILs [https://dx.doi.org/10.1063/1.4748352 doi]
*'''Notes'''
#Solving the angular part of the Schrödinger equation for a hydrogen atom [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/angular_schrodinger link] (notes by Vincent)
#DFT Workshop Notes [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/DFT_Workshop]
#Cl- in water [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link]
#The use of Legendre time correlation functions to study reorientational dynamics in liquids [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/legendre link]

===Gaussian General===
#We are starting a database of common errors encountered when running Gaussian jobs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gaussian_errors link]
# Here is an already existing database of common errors [https://docs.computecanada.ca/wiki/Gaussian_error_messages link]
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#partial optimisations and scans [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/z-matrix link]
#General procedure for locating transition state structures [[link]]
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link]
#Basic ONIOM (Mechanical Embedding) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/basiconiom link]
#problems with scf convergence [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/scf_convergence link]
#manipulating checkpoint files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:usingchkfiles link]
#for NMR calculations look here: [http://cheshirenmr.info/index.htm Chemical Shift Repository]
#Population and charge analysis [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/population link]

===Gaussian Advanced===
#Systematic conformational scan for ion-pair dimers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ion_pair_scan link]
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link]
#generating natural transition orbitals [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/nto link]
#computing excited state polarisabilities [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_ES_alpha link]
#computing deuterated and/or anharmonic spectra [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_Danharm link]
#How to run at a higher temperature [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:high_temp link]
#Correcting the entropy due to low modes [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:low_modes_entropy link]
#Optimisation of charged molecules in an electric field [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Optimising_charged_molecules_in_electric_fields link]
#Multidimensional Scans of Internal Coordinates [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Multidimensional_Scans_of_Internal_Coordinates link]
#Conformational search of atomic and molecular clusters with ABCluster [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:ABCluster#.inp_file_on_the_HPC link]

===Solvation===
#Using the SMD model [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/solvent link]
#Using SMD on ILs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_Using_SMD_on_ILs link]
#Troublesome optimisations in SMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:troublesome_smd link]
#Atomic radii and solvent models [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/atomic_radii link]
#Molecular volume calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molecular_volume link]
#The cavity [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/solvent_cavity link]
#How to download and use GeomView to visualise solvation cavities [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/geomview link]
#Surfaces (Solvent-Accessible and Connolly) in Jmol [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/jmolsurfaces link]

===Codes to Help Gaussian Analysis===
====Python and Python codes====
# Using and installing python [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/python link]
# Python toolkit currently focussed towards gaussian analysis [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molLego link]
# Standalone python scripts and analysis:
#* List the energy for each step of a gaussian log file, find the lowest energy and produce a quick graph in kJ/mol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_energy link]
#* Build a frequency file from an optimisation file ready to submit, this will require editing for your particular job [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/build_freq link]
#* Extract last Standard Orientation structure of gaussian log file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_single_geom link]
#* Extract last structure of gaussian optimisation and build a freq com file for job with PP [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/build_freq_file link]
#* Extract each optimised step from a scan into xyz coordinate file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_scan_geom link]
#* Extract thermodynamic data and low frequencies from log files (python 2) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:simple_freq_script link]
#* Extract thermodynamic data and low frequencies from log files to enter into excel template provided for the database (python 3) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:model_freq_script link]
#* Extract geometry and charges (ESP) into a .pdb file for visualising in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ESP_charges_for_VMD link]
#* Codes to extract CHELPG and NBO charge values to excel [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/chelpg_extract link]
#* Extract ESP and NBO charges [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_ESP_charges link]
#* Script to pull thermodynamic data and low frequencies from log files AND evaluate to a reference [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:freq_script link]
#* Codes to extract frequency data from gaussian .log files and generate vibrational spectra [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:frequency_spectrum_script link]
#* Codes to visualise data matrices (correlation matrices/heatmaps)[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/heatmap link]
#* Python API for analysis of Gaussian computations [https://pygauss.readthedocs.org - Documentation]
#* Charge arm [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/charge_arm link]
#* Extract the MO orbital energies and concert to eV [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/MO_energies link]

====Other codes====
# Extract E2 Values (From NBO Calculations) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/NBO_Matlab_Code link]
# Calculate pDoS/XP spectra code (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Calc_XPS_Code link]
# Optimally Tuned Range Separated Hybrid Functionals [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/OTRSH_Funct link]
# Some G09 Parsers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Some_G09_Parsers link]

===QC Visualisation===
*'''Using AIMALL: density based visualisation'''
#download [http://aim.tkgristmill.com AIMALL]
#once downloaded and installed you need to send tricia your aimall-serialnumber.txt file, and she will arrange for a aimallpro.lic or license file for you
#basic instructions [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:aim_basics link]
#AimAll with pseudo potentials [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:aim_pseudopotentials link]
#AIMAll 19.10.12 on iMacs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:AIMAllQuickFix link]

*'''ESPs and manipulating gaussian cube files'''
#Instructions for visualizing electrostatic potentials (Gaussview)[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link]
#Electrostatic Potentials II (Molden) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials_2 link]
#Manipulating cube files [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/cube_files link]
#Format of cube files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/cube_format link]
#Using A. Stone's distributed multipole analysis [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/GDMA link]

*'''NCI plots'''
#get the program here: [http://www.lct.jussieu.fr/pagesperso/contrera/nciplot.html link]
#How to install NCIPlot on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/InstallNCIPlot link]
#Using NCIPlot [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/UseNCIPlot link]

*'''MOs'''
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link]

===Setup and Running Classical MD Simulations===
====dl_poly====
#DLPOLY_4.0 Installation for an IMac [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Installing_DL_POLY_4.09_on_MacOS_Mojave link]
#DLPOLY_Classic Installation for an IMac [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Installing_DL_POLY_classic link]

#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#some basics for getting started using DL_POLY [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dl_poly_basics link]
#control file basics [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/control_basics link]
*useful links
::[https://www.ccp5.ac.uk https://www.ccp5.ac.uk]
::[https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx]
::[ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/USRMAN4.pdf dlpoly4 user manual]
::[ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/JavaGUI.pdf javagui user manual]
::[ftp://ftp.dl.ac.uk/ccp5/DL_POLY/ dlpoly ftp server]
:::you can find test files in DL_POLY_4.0/DATA
:::more info about the dlpoly test files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/DL_POLY_test_files link]

====gromacs====
#GROMACS installing and getting started with gromacs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gromacs_1 link]
#using Agilio Padua force fields for ionic liquids [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/ilff link]
#Packmol installing and running to generate a starting box [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/packmol_1 link]
#initial rough relaxation [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Starting_MD link]
#GROMACS general run [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_run link]
#GROMACS viewing data [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_viewing_MD link]
#GROMACS control file [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_control_MD link]
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link]
====general====
#Getting the Force Field [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Wheretostart link]
#Choosing an Ensemble [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Ensembles link]
#Molten Salt Simulations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/MoltenSaltSimulation link]
#Common Errors [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/CommonErrors link]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link]

===MD Visualisation===
*'''VMD: a molecular dynamics visualisation package'''
#VMD can be installed from the [http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD VMD downloads page]
#Quick reminder [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDReminder link]
#Colour in VMD [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDColor link]
#Changing the graphical representation of your structures [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link]
#VMD indexing [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDindexing link]
#Using scripts in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScripts link]
#Dealing with periodic boundaries and bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsPeriodic link]
#Dealing with bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdBonding link]
#How to turn a Gaussian optimization into a VMD movie [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/VMDmovie link]
#Overlapping two structures [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdVisual link]
*'''Ovito: a molecular dynamics visualisation package'''
#Download Ovito [http://www.ovito.org/index.php/download]
#Using Ovito basics [//wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Ovito_basics link]
*'''SDFs'''
#How to generate SDFs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/sdfs_generate link]

===MD Post processing===
#Python script to convert a HISTORY file into a xyz file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/hist_to_xyz link]
#Python script to reduce the number of steps in a lammps traj file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/lam_to_xyz link]
#Python script to convert a lammps traj file to xyz coordinates and at the same time fold all atoms into a cell and center at the origin [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/lam_fold_xyz link]
#Center the trajectory at a particular atom ('''needs fixing''') [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Recenter link]
#How to generate SDFs with TRAVIS [[Talk:Mod:Hunt Research Group/How to draw SDFs with TRAVIS|link]]
#Tcl script to follow a particular atom [[Talk:Mod:Hunt Research Group/Traj_atom_following|link]]

===Coding===
*'''installing Xcode and other programming environments'''
#to use many programs you will need a compiler, this is not installed by default on your mac
#How to install Xcode on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/InstallXcode link]
#using MacPorts as code for managing other codes on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/MacPorts link]
#HomeBrew and Fink are other options (HomeBrew is not advised for us)
#gfortran on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Gfortran link]
#using python on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/python link]

*'''EMO Code'''
#How to use Ling's emo plot code[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emoplot link]
#How to plot EMOs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emo link]

*'''Jan's charge based analysis Code'''
#charge analysis [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Jan_charges link]
#Obtaining NBO, ESP, and RESP charges [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Charges link]

*'''Oxana's visualisation of ESPs Code'''
#Scripts for reading, saving, manipulating and visualising data from cube files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Python_scripts_for_cube_files link]

*'''Python Genereal'''
# General python recommendations and set up [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/PythonGeneral link]
# Analysis toolkit mainly geared towards processing Gaussian calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Python_Analysis_Tools link]

===Other Codes===
#ADF Submission script [http://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/ADF_sricpt link]
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link]
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/]

===Setup and Running Ab-Initio MD Simulations===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link]
#How to run CPMD to study aqueous solutions [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd_water link]
#How to run CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k_how link]

===Running QM/MM Simulations in ChemShell===

==Tcl-chemshell==
#ChemShell official website which contains the manual and a tutorial [http://www.stfc.ac.uk/CSE/randd/ccg/36254.aspx link]
#Introduction to ChemShell - Copper in water [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Introduction link]
#Defining the system: Cu2+ and its first 2 solvation shells [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_System_Aqeuous_Cu(II) link]
#Defining the force field parameters [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II) link]
#Single point QM/MM energy calculation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_SP_Aqeuous_Cu(II) link]
#QM/MM Optimisation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_OPT_Aqeuous_Cu(II) link]
#QM/MM Molecular Dynamics [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_MD_Aqeuous_Cu(II) link]
#Using MolCluster [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/MolCluster link]
#Running ChemShell [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell link]
#Explaining ChemShell files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files link]
#Step By Step [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Chemshell_Step_By_Step link]
==Py-chemshell==

# Compiling Chemshell and required programs []
# The DL_POLY_4 manual is available for download at this link [ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/USRMAN4.pdf]
# Molecular Mechanics computation with DL_POLY [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:_MM_Single_Point_computation]
# Basic QM/MM single point and optimisations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_QM/MM_Single_Point_and_optimisation]
# Visualise optimisation trajectories in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_Visualising_trajectories_with_VMD]
# Computing Mulliken charges and creating .wfn inputs for AIM analysis [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_Mulliken]

==Admin Stuff==
#Not used to writing a wiki, make your test runs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/testing on this page]
#How to set-up new macs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_setup link]
#How to switch the printer HP CP3525dn duplex on and off [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/printing link]

Mod:Hunt Research Group

2020-02-04T13:48:46Z

Phunt: /* Python and Python codes */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===Report and Paper Writing===
#procedures [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/report_procedures link]
#advice [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/report_writing link]
#report components [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/report_components link]
#files to provide when writing a paper [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/paper link]

===Group Admin===
#Which files to store on the database and database template [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/database link]
#How to access DROBO [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/drobo link]

===HPC Resources===
#'''Hunt group HPC servers and run scripts''' [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link]
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link]
#How to run jobs interactively [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/run_interactive link]
#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link]
#New gf script (more convenient job submitting) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/new_gf_script link]
#Retired: How to make qsub more comfortable (gfunc) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpQSUB link]
#Tired of entering your password all the time: set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link]
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link]
#Using VPN from home, for Sierra follow the college instructions [[link]]
#How to connect to HPC directory on desktop for file transfers [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_Directory_on_desktop link]
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link]
#How to use a slimmed down terminal on your IPhone [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/termius]

===Using evil Windows and PCs===
#Use Imperial Software Hub to access gaussview and gaussian [http://www.imperial.ac.uk/admin-services/ict/store/software/software-hub/ link]
#Using windows and setting up a connection to HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link]
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link]

===Key Papers, References and Resources===
*'''Papers'''
#Meta study on DFT functionals [https://pubs.acs.org/doi/abs/10.1021/ct401111c doi]
#M06 suite of DFT functionals [https://link.springer.com/article/10.1007/s00214-007-0310-x doi]
#SMD for ILs [https://pubs.acs.org/doi/abs/10.1021/jp304365v doi]
#Box size for MD simulations of ILs [https://dx.doi.org/10.1063/1.4748352 doi]
*'''Notes'''
#Solving the angular part of the Schrödinger equation for a hydrogen atom [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/angular_schrodinger link] (notes by Vincent)
#DFT Workshop Notes [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/DFT_Workshop]
#Cl- in water [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link]
#The use of Legendre time correlation functions to study reorientational dynamics in liquids [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/legendre link]

===Gaussian General===
#We are starting a database of common errors encountered when running Gaussian jobs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gaussian_errors link]
# Here is an already existing database of common errors [https://docs.computecanada.ca/wiki/Gaussian_error_messages link]
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#partial optimisations and scans [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/z-matrix link]
#General procedure for locating transition state structures [[link]]
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link]
#Basic ONIOM (Mechanical Embedding) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/basiconiom link]
#problems with scf convergence [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/scf_convergence link]
#manipulating checkpoint files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:usingchkfiles link]
#for NMR calculations look here: [http://cheshirenmr.info/index.htm Chemical Shift Repository]
#Population and charge analysis [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/population link]

===Gaussian Advanced===
#Systematic conformational scan for ion-pair dimers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ion_pair_scan link]
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link]
#generating natural transition orbitals [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/nto link]
#computing excited state polarisabilities [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_ES_alpha link]
#computing deuterated and/or anharmonic spectra [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_Danharm link]
#How to run at a higher temperature [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:high_temp link]
#Correcting the entropy due to low modes [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:low_modes_entropy link]
#Optimisation of charged molecules in an electric field [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Optimising_charged_molecules_in_electric_fields link]
#Multidimensional Scans of Internal Coordinates [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Multidimensional_Scans_of_Internal_Coordinates link]
#Conformational search of atomic and molecular clusters with ABCluster [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:ABCluster#.inp_file_on_the_HPC link]

===Solvation===
#Using the SMD model [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/solvent link]
#Using SMD on ILs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_Using_SMD_on_ILs link]
#Troublesome optimisations in SMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:troublesome_smd link]
#Atomic radii and solvent models [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/atomic_radii link]
#Molecular volume calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molecular_volume link]
#The cavity [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/solvent_cavity link]
#How to download and use GeomView to visualise solvation cavities [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/geomview link]
#Surfaces (Solvent-Accessible and Connolly) in Jmol [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/jmolsurfaces link]

===Codes to Help Gaussian Analysis===
====Python and Python codes====
# Using and installing python [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/python link]
# Python toolkit currently focussed towards gaussian analysis [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molLego link]
# Standalone python scripts and analysis:
#* List the energy for each step of a gaussian log file, find the lowest energy and produce a quick graph in kJ/mol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_energy link]
#* Build a frequency file from an optimisation file ready to submit, this will require editing for your particular job [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/build_freq link]
#* Extract last Standard Orientation structure of gaussian log file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_single_geom link]
#* Extract last structure of gaussian optimisation and build a freq com file for job with PP [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/build_freq_file link]
#* Extract each optimised step from a scan into xyz coordinate file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_scan_geom link]
#* Extract thermodynamic data and low frequencies from log files (python 2) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:simple_freq_script link]
#* Extract thermodynamic data and low frequencies from log files to enter into excel template provided for the database (python 3) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:model_freq_script link]
#* Extract geometry and charges (ESP) into a .pdb file for visualising in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ESP_charges_for_VMD link]
#* Codes to extract CHELPG and NBO charge values to excel [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/chelpg_extract link]
#* Extract ESP and NBO charges [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_ESP_charges link]
#* Script to pull thermodynamic data and low frequencies from log files AND evaluate to a reference [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:freq_script link]
#* Codes to extract frequency data from gaussian .log files and generate vibrational spectra [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:frequency_spectrum_script link]
#* Codes to visualise data matrices (correlation matrices/heatmaps)[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/heatmap link]
#* Python API for analysis of Gaussian computations [https://pygauss.readthedocs.org - Documentation]
#* Charge arm [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/charge_arm link]
#* Extract the MO orbital energies and concert to eV [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/MO_energies]

====Other codes====
# Extract E2 Values (From NBO Calculations) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/NBO_Matlab_Code link]
# Calculate pDoS/XP spectra code (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Calc_XPS_Code link]
# Optimally Tuned Range Separated Hybrid Functionals [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/OTRSH_Funct link]
# Some G09 Parsers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Some_G09_Parsers link]

===QC Visualisation===
*'''Using AIMALL: density based visualisation'''
#download [http://aim.tkgristmill.com AIMALL]
#once downloaded and installed you need to send tricia your aimall-serialnumber.txt file, and she will arrange for a aimallpro.lic or license file for you
#basic instructions [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:aim_basics link]
#AimAll with pseudo potentials [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:aim_pseudopotentials link]
#AIMAll 19.10.12 on iMacs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:AIMAllQuickFix link]

*'''ESPs and manipulating gaussian cube files'''
#Instructions for visualizing electrostatic potentials (Gaussview)[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link]
#Electrostatic Potentials II (Molden) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials_2 link]
#Manipulating cube files [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/cube_files link]
#Format of cube files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/cube_format link]
#Using A. Stone's distributed multipole analysis [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/GDMA link]

*'''NCI plots'''
#get the program here: [http://www.lct.jussieu.fr/pagesperso/contrera/nciplot.html link]
#How to install NCIPlot on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/InstallNCIPlot link]
#Using NCIPlot [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/UseNCIPlot link]

*'''MOs'''
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link]

===Setup and Running Classical MD Simulations===
====dl_poly====
#DLPOLY_4.0 Installation for an IMac [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Installing_DL_POLY_4.09_on_MacOS_Mojave link]
#DLPOLY_Classic Installation for an IMac [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Installing_DL_POLY_classic link]

#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#some basics for getting started using DL_POLY [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dl_poly_basics link]
#control file basics [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/control_basics link]
*useful links
::[https://www.ccp5.ac.uk https://www.ccp5.ac.uk]
::[https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx]
::[ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/USRMAN4.pdf dlpoly4 user manual]
::[ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/JavaGUI.pdf javagui user manual]
::[ftp://ftp.dl.ac.uk/ccp5/DL_POLY/ dlpoly ftp server]
:::you can find test files in DL_POLY_4.0/DATA
:::more info about the dlpoly test files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/DL_POLY_test_files link]

====gromacs====
#GROMACS installing and getting started with gromacs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gromacs_1 link]
#using Agilio Padua force fields for ionic liquids [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/ilff link]
#Packmol installing and running to generate a starting box [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/packmol_1 link]
#initial rough relaxation [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Starting_MD link]
#GROMACS general run [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_run link]
#GROMACS viewing data [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_viewing_MD link]
#GROMACS control file [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_control_MD link]
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link]
====general====
#Getting the Force Field [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Wheretostart link]
#Choosing an Ensemble [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Ensembles link]
#Molten Salt Simulations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/MoltenSaltSimulation link]
#Common Errors [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/CommonErrors link]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link]

===MD Visualisation===
*'''VMD: a molecular dynamics visualisation package'''
#VMD can be installed from the [http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD VMD downloads page]
#Quick reminder [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDReminder link]
#Colour in VMD [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDColor link]
#Changing the graphical representation of your structures [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link]
#VMD indexing [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDindexing link]
#Using scripts in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScripts link]
#Dealing with periodic boundaries and bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsPeriodic link]
#Dealing with bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdBonding link]
#How to turn a Gaussian optimization into a VMD movie [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/VMDmovie link]
#Overlapping two structures [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdVisual link]
*'''Ovito: a molecular dynamics visualisation package'''
#Download Ovito [http://www.ovito.org/index.php/download]
#Using Ovito basics [//wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Ovito_basics link]
*'''SDFs'''
#How to generate SDFs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/sdfs_generate link]

===MD Post processing===
#Python script to convert a HISTORY file into a xyz file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/hist_to_xyz link]
#Python script to reduce the number of steps in a lammps traj file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/lam_to_xyz link]
#Python script to convert a lammps traj file to xyz coordinates and at the same time fold all atoms into a cell and center at the origin [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/lam_fold_xyz link]
#Center the trajectory at a particular atom ('''needs fixing''') [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Recenter link]
#How to generate SDFs with TRAVIS [[Talk:Mod:Hunt Research Group/How to draw SDFs with TRAVIS|link]]
#Tcl script to follow a particular atom [[Talk:Mod:Hunt Research Group/Traj_atom_following|link]]

===Coding===
*'''installing Xcode and other programming environments'''
#to use many programs you will need a compiler, this is not installed by default on your mac
#How to install Xcode on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/InstallXcode link]
#using MacPorts as code for managing other codes on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/MacPorts link]
#HomeBrew and Fink are other options (HomeBrew is not advised for us)
#gfortran on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Gfortran link]
#using python on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/python link]

*'''EMO Code'''
#How to use Ling's emo plot code[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emoplot link]
#How to plot EMOs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emo link]

*'''Jan's charge based analysis Code'''
#charge analysis [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Jan_charges link]
#Obtaining NBO, ESP, and RESP charges [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Charges link]

*'''Oxana's visualisation of ESPs Code'''
#Scripts for reading, saving, manipulating and visualising data from cube files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Python_scripts_for_cube_files link]

*'''Python Genereal'''
# General python recommendations and set up [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/PythonGeneral link]
# Analysis toolkit mainly geared towards processing Gaussian calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Python_Analysis_Tools link]

===Other Codes===
#ADF Submission script [http://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/ADF_sricpt link]
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link]
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/]

===Setup and Running Ab-Initio MD Simulations===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link]
#How to run CPMD to study aqueous solutions [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd_water link]
#How to run CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k_how link]

===Running QM/MM Simulations in ChemShell===

==Tcl-chemshell==
#ChemShell official website which contains the manual and a tutorial [http://www.stfc.ac.uk/CSE/randd/ccg/36254.aspx link]
#Introduction to ChemShell - Copper in water [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Introduction link]
#Defining the system: Cu2+ and its first 2 solvation shells [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_System_Aqeuous_Cu(II) link]
#Defining the force field parameters [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II) link]
#Single point QM/MM energy calculation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_SP_Aqeuous_Cu(II) link]
#QM/MM Optimisation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_OPT_Aqeuous_Cu(II) link]
#QM/MM Molecular Dynamics [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_MD_Aqeuous_Cu(II) link]
#Using MolCluster [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/MolCluster link]
#Running ChemShell [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell link]
#Explaining ChemShell files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files link]
#Step By Step [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Chemshell_Step_By_Step link]
==Py-chemshell==

# Compiling Chemshell and required programs []
# The DL_POLY_4 manual is available for download at this link [ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/USRMAN4.pdf]
# Molecular Mechanics computation with DL_POLY [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:_MM_Single_Point_computation]
# Basic QM/MM single point and optimisations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_QM/MM_Single_Point_and_optimisation]
# Visualise optimisation trajectories in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_Visualising_trajectories_with_VMD]
# Computing Mulliken charges and creating .wfn inputs for AIM analysis [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_Mulliken]

==Admin Stuff==
#Not used to writing a wiki, make your test runs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/testing on this page]
#How to set-up new macs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_setup link]
#How to switch the printer HP CP3525dn duplex on and off [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/printing link]

Mod:Hunt Research Group/MacPorts

2020-01-20T07:19:25Z

Phunt: /* MacPorts */

===MacPorts===
*'''installing MacPorts'''
:*find installation information here [https://www.macports.org/install.php link]
:*find general information here [https://guide.macports.org link]
:*download and follow the instructions
:*macport installs in /opt/local so add to your path "export PATH=/opt/local/bin:/opt/local/sbin:$PATH"
:*see information on next wikipage if gcc is using mac version and not macports
:*see information on following wikipage regarding python
:*see information on folloing wikipage regarding fortran
;*after a major OS upgrade you will need to install a new MacPorts

*'''using MacPorts''' basic commands
:*you will need to run all commands as '''sudo'''
:*general commands to update macports
::sudo port version
::sudo port selfupdate
::sudo port outdated
::sudo port upgrade name
::sudo port -u upgrade outdated
:*find out what is installed
::sudo port installed
::sudo port select --list name
::sudo port uninstall --follow-dependents name
::sudo port uninstall name
::sudo port clean name
:*find out what you could install
::sudo port installed '*name*'
::port search --name --line --glob '*name*'
:*activate new install
::sudo port activate name
::sudo port deactivate name
::sudo port select --set python python37 or which ever version you want
::sudo port select --set python none removes the assignment
:*things are a bit bloated and you need to clean-up
::sudo port -f clean --all all
::sudo port -f uninstall inactive
::If you want to do more explicitly, but the above should suffice!
::Remove leftover build files (this is done automatically by default):
:::sudo rm -rf /opt/local/var/macports/build/*
::Remove download files:
:::sudo rm -rf /opt/local/var/macports/distfiles/*
::Remove archives (these aren't created by default):
:::sudo rm -rf /opt/local/var/macports/packages/*

Talk:Mod:Hunt Research Group/extract energy

2020-01-13T06:46:28Z

Phunt: /* python script to print energies */

===python script to print energies===
*copy the code into a script called "get_energy.py"
*to execute the script type "python energy.py file_name
*if you have given the path to your python executable at the front of the file, and this script is in your path
*you can simply execute with "get_energy.py filename"
*this will print to terminal the energy for each step, find the lowest energy and plot a quick graph relative to the lowest energy in kJ/mol
*NOTE: press "q" to close the graph (or click the red button on the graph)

<pre>
#
# get_energy.py
#
# python script to extract the SCF energy for each step, find the lowest energy step
# and produce a quick graph showing the change in energy in kJ/mol
# to run the script type
# python energy.py input_file_name
# NOTE you can close the graph by pressing "q" on keyboard
#
import sys
import numpy as np
import matplotlib.pyplot as plt
import os
dir=os.getcwd()
#
# setup files to read
if len(sys.argv) == 1:
print('to run the script please type: python energy.py input_file_name')
sys.exit()
else:
log_file=str(sys.argv[1])
s='directory is '
print('{0:}{1:}'.format(s,dir))
s='input file is '
print('{0:}{1:}'.format(s,log_file))
#close if

# open the file
f = open(log_file,'r')

# set some basic parameters
energy=[]
new_energy=[]
x_axis=[]
en_search_string='SCF Done:'

# read the if there is a first line, then read the file line by line
# if energy is given split the line into array tmp and extract the energy number
# and extract the energy and store in an array
count=0
line=f.readline()
while line:
line =f.readline()
# print('{0:}'.format(line))
if en_search_string in line:
tmp=line.rstrip().split()
energy.append(float(tmp[4]))
count1=count+1
print('{0:}{1:<3}{2:<.8f}'.format('step: ',count1,energy[count]))
count=count+1
# endif
#endwhile

total_steps=count
#print(total_steps)

# find the lowest energy
min_energy=min(energy)
min_index=energy.index(min(energy))
min_index=min_index+1
print('{0:}{1:}{2:}{3:}'.format('lowest energy is step: ',min_index,' energy: ',min_energy))

# re-align to start at one, and in kJ/mol relative to lowest energy
# remember python starts at zero
x=0
while x < total_steps-1 :
temp=(energy[x] - min_energy) * 2625.5
# print(temp)
new_energy.append(temp)
x=x+1
x_axis.append(x)
#endwhile

# plot the energy
plt.plot(x_axis,new_energy,'b-')
plt.plot(x_axis,new_energy,'bo')
plt.plot(min_index,new_energy[min_index],'rs',markersize=8)
plt.ylabel('energy kJ/mol')
plt.xlabel('step')
plt.show()

# close file
f.close()
#end
</pre>

Talk:Mod:Hunt Research Group/extract energy

2020-01-13T06:46:18Z

Phunt: /* python script to print energies */

===python script to print energies===
*copy the code into a script called "get_energy.py"
*to execute the script type "python energy.py file_name
*if you have given the path to your python executable at the front of the file, and this script is in your path
*you can simply execute with "get_energy.py filename"
*this will print to terminal the energy for each step, find the lowest energy and plot a quick graph relative to the lowest energy in kJ/mol
*NOTE: press "q" to close the graph (or click the red button on the graph)

<pre>
#
# energy.py
#
# python script to extract the SCF energy for each step, find the lowest energy step
# and produce a quick graph showing the change in energy in kJ/mol
# to run the script type
# python energy.py input_file_name
# NOTE you can close the graph by pressing "q" on keyboard
#
import sys
import numpy as np
import matplotlib.pyplot as plt
import os
dir=os.getcwd()
#
# setup files to read
if len(sys.argv) == 1:
print('to run the script please type: python energy.py input_file_name')
sys.exit()
else:
log_file=str(sys.argv[1])
s='directory is '
print('{0:}{1:}'.format(s,dir))
s='input file is '
print('{0:}{1:}'.format(s,log_file))
#close if

# open the file
f = open(log_file,'r')

# set some basic parameters
energy=[]
new_energy=[]
x_axis=[]
en_search_string='SCF Done:'

# read the if there is a first line, then read the file line by line
# if energy is given split the line into array tmp and extract the energy number
# and extract the energy and store in an array
count=0
line=f.readline()
while line:
line =f.readline()
# print('{0:}'.format(line))
if en_search_string in line:
tmp=line.rstrip().split()
energy.append(float(tmp[4]))
count1=count+1
print('{0:}{1:<3}{2:<.8f}'.format('step: ',count1,energy[count]))
count=count+1
# endif
#endwhile

total_steps=count
#print(total_steps)

# find the lowest energy
min_energy=min(energy)
min_index=energy.index(min(energy))
min_index=min_index+1
print('{0:}{1:}{2:}{3:}'.format('lowest energy is step: ',min_index,' energy: ',min_energy))

# re-align to start at one, and in kJ/mol relative to lowest energy
# remember python starts at zero
x=0
while x < total_steps-1 :
temp=(energy[x] - min_energy) * 2625.5
# print(temp)
new_energy.append(temp)
x=x+1
x_axis.append(x)
#endwhile

# plot the energy
plt.plot(x_axis,new_energy,'b-')
plt.plot(x_axis,new_energy,'bo')
plt.plot(min_index,new_energy[min_index],'rs',markersize=8)
plt.ylabel('energy kJ/mol')
plt.xlabel('step')
plt.show()

# close file
f.close()
#end
</pre>

Talk:Mod:Hunt Research Group/build freq

2020-01-13T06:37:51Z

Phunt: /* python script to build frequency file from optimisation output */

===python script to build frequency file from optimisation output===
*copy the code into a script called "energy.py"
*to execute the script type "python build_freq.py file_name step
*if you have your execute directory in your path, you can alter the first line to your python executable and then you can just type "build_freq.py filename step"
*if step is not given the last structure from the optimisation file will be used
*if step is given the geometry from that step will be used
*NOTE: you will need to alter the string which prints the job key words into the gaussian input file

<pre>
#!/opt/local/bin/python3
#
# build_freq.py
#
# python script to extract the final structure from a gaussian log file and build a frequency input file
# to run the script type:
#
# python build_freq.py input_file_name step_no
#
# if no step_no is given the last geometry will be used
#
import sys
import os
dir=os.getcwd()

#==set up FILES ==

# if there are 2 arguments to use the last step (of the optimisation)
# if there are 3 arguments then use a specific step_no from the optimisation
if len(sys.argv) == 2:
infile=str(sys.argv[1])
step_no=int(0)
elif len(sys.argv) == 3:
infile=str(sys.argv[1])
step_no=int(sys.argv[2])
#endif

# if there is less or more arguments something is wrong
else:
print('to run the script please type: python build_freq.py input_file_name step_no')
sys.exit()
#endif

# check to see if the user has used the .log extenion or not
# find returns -1 if the sub-string is not found, or the index of where the sub-string starts
# we cut out the .log part if .log is found
i_infile=infile.find('.log')
if (i_infile == -1):
base=infile
else:
base=infile[:i_infile]
#endif

# now set up the base file names
log_file=base+'.log'
geom_file=base+'.xyz'
# if opt is not in the filename add freq to the filename
# if opt is already in the file change this to freq
i_opt=base.find('opt')
if (i_infile == -1):
base2=base + '_freq'
else:
base2=base.replace('opt','freq')
#endif
com_file=base2+'.com'

# print out some reference information
s='directory is '
print('{0:}{1:}'.format(s,dir))
s='input file is '
print('{0:}{1:}'.format(s,infile))
s='output file is '
print('{0:}{1:}'.format(s,com_file))
#
#==set some DEFAULTS ==
col_num=[]
col_atom=[]
col_type=[]
col_x=[]
col_y=[]
col_z=[]
rep=0
n=0
go=False
atom_total=0
geom_count=0
#
#==start READING THE FILE ==

# open file and read lines one by one
f=open(log_file,"r")

# line is a variable which contains the line
line =f.readline()
while line :
line =f.readline()
# print('{0:}'.format(line))

#==extract GEOMETRY ==
# check for standard orientation text set 'go' if the text appears
# geom_count is the number of the geometry stored
# atom_total will be the number of atoms
# n will be stepping through the lines in std orientation section so set to zero for each time through
# if this is the first geometry print that a geometry is found
if 'Standard orientation:' in line:
go=True
s='Structure in standard orientation found '
n=1
geom_count=geom_count+1
if geom_count == 1 : print('{0:}'.format(s))
s='geometry count= '
# print('{0:}{1:}'.format(s,geom_count))
# endif
#
# if go is on then we need to extract and store the structure
# skip the next 4 lines, on the 5th start collecting structure
# m is our switch to stop, we stop once we get to the Rotational constants line
# m is also our switch to not print the lines of dashes
# we need to know how many atoms there are in total as well
# we simply append each data list into the arrays col which has components num,atom,type,x,y,z
while go:
n = n+1
m = 0
line =f.readline()
if 'Rotational constants (GHZ):' in line: m=-1
if '---------' in line: m=1
if n > 4 and m == 0 :
# print('line: {0:}'.format(line))
if geom_count == 1 : atom_total=atom_total+1
a1,b1,c1,d1,e1,f1=line.rstrip().split()
col_num.append(int(a1))
col_atom.append(int(b1))
col_type.append(int(c1))
col_x.append(float(d1))
col_y.append(float(e1))
col_z.append(float(f1))
if m == -1 : go=False
# close while
#close while

#== build COM FILE ==

# first give all the comp details
c=open(com_file,"w")
s="%nprocshared=40\n%mem=120000MB\n"
c.write('{0:}'.format(s))
s='%chk='+base2+'.chk\n'
c.write('{0:}'.format(s))
s="# freq m06/6-311G(d,p) geom=cartesian int=ultrafine scf=conver=9 \n\n"
c.write('{0:}'.format(s))
s="Title Card Required\n\n0 1\n"
c.write('{0:}'.format(s))

#other options are
#s="# freq b3lyp/gen pseudo=cards empiricaldispersion=gd3bj geom=cartesian \n "
#s="gfinput int=ultrafine scf=conver=9 test\n\n"

# now put in the coordinates
# if step_no is zero we only use the last geometry
# if step_no is given, we use that geometry
# geom_count is the number of geometries
# atom_total is the numer of atoms
# if taking the last geometry count backwards
# n is the internal counter
# n_start defines where to start printing
# n_stop defines wher to stop printing
#
n=0
n_start=0
n_stop=0
#print ('{0:}{1:}'.format('step_no=',step_no))
#print ('{0:}{1:}'.format('atom_total=',atom_total))
#print ('{0:}{1:}'.format('geom_count=',geom_count))
if step_no == 0 :
n_start=len(col_num)-atom_total
n_stop=len(col_num)
s=' structures found only the last is used'
print('{0:}{1:}'.format(geom_count,s))
else:
n_start=atom_total*step_no
n_stop=n_start+atom_total
print('{0:}{1:}{2:}{3:}'.format('using structure ',step_no,' of ',geom_count))
# endif
#print ('{0:}{1:}'.format('n_start=',n_start))
#print ('{0:}{1:}'.format('n_stop=',n_stop))
n=n_start
while n >= n_start and n < n_stop:
c.write('{0:>4d} {1: 09.6f} {2: 09.6f} {3: 09.6f} \n'.format(col_atom[n],col_x[n],col_y[n],col_z[n]))
# print('{0:>4d} {1:>4d} {2: 09.6f} {3: 09.6f} {4: 09.6f}'.format(col_num[n],col_atom[n],col_x[n],col_y[n],col_z[n]))
n=n + 1
#close while

# now put in the gen information
#s="\nC N H Cl 0\n6-311+G(d,p)\n****\n"
#t="Sn 0\nLANL2DZ\n****\n\n"
#u="Sn 0\nLANL2DZ\n\n\n"
#c.write('{0:}{1:}{2:}'.format(s,t,u))

# and add the last blank lines
s=" \n\n"
c.write('{0:}'.format(s))

# close all open files
f.close()
c.close()
#
</pre>

Talk:Mod:Hunt Research Group/build freq

2020-01-13T06:35:58Z

Phunt: /* python script to build frequency file from optimisation output */

===python script to build frequency file from optimisation output===
*copy the code into a script called "energy.py"
*to execute the script type "python build_freq.py file_name step
*if you have your execute directory in your path, you can alter the first line to your python executable and then you can just type "build_freq filename step"
*if step is not given the last structure from the optimisation file will be used
*if step is given the geometry from that step will be used
*NOTE: you will need to alter the string which prints the job key words into the gaussian input file

<pre>
#!/opt/local/bin/python3
#
# build_freq.py
#
# python script to extract the final structure from a gaussian log file and build a frequency input file
# to run the script type:
#
# python build_freq.py input_file_name step_no
#
# if no step_no is given the last geometry will be used
#
import sys
import os
dir=os.getcwd()

#==set up FILES ==

# if there are 2 arguments to use the last step (of the optimisation)
# if there are 3 arguments then use a specific step_no from the optimisation
if len(sys.argv) == 2:
infile=str(sys.argv[1])
step_no=int(0)
elif len(sys.argv) == 3:
infile=str(sys.argv[1])
step_no=int(sys.argv[2])
#endif

# if there is less or more arguments something is wrong
else:
print('to run the script please type: python build_freq.py input_file_name step_no')
sys.exit()
#endif

# check to see if the user has used the .log extenion or not
# find returns -1 if the sub-string is not found, or the index of where the sub-string starts
# we cut out the .log part if .log is found
i_infile=infile.find('.log')
if (i_infile == -1):
base=infile
else:
base=infile[:i_infile]
#endif

# now set up the base file names
log_file=base+'.log'
geom_file=base+'.xyz'
# if opt is not in the filename add freq to the filename
# if opt is already in the file change this to freq
i_opt=base.find('opt')
if (i_infile == -1):
base2=base + '_freq'
else:
base2=base.replace('opt','freq')
#endif
com_file=base2+'.com'

# print out some reference information
s='directory is '
print('{0:}{1:}'.format(s,dir))
s='input file is '
print('{0:}{1:}'.format(s,infile))
s='output file is '
print('{0:}{1:}'.format(s,com_file))
#
#==set some DEFAULTS ==
col_num=[]
col_atom=[]
col_type=[]
col_x=[]
col_y=[]
col_z=[]
rep=0
n=0
go=False
atom_total=0
geom_count=0
#
#==start READING THE FILE ==

# open file and read lines one by one
f=open(log_file,"r")

# line is a variable which contains the line
line =f.readline()
while line :
line =f.readline()
# print('{0:}'.format(line))

#==extract GEOMETRY ==
# check for standard orientation text set 'go' if the text appears
# geom_count is the number of the geometry stored
# atom_total will be the number of atoms
# n will be stepping through the lines in std orientation section so set to zero for each time through
# if this is the first geometry print that a geometry is found
if 'Standard orientation:' in line:
go=True
s='Structure in standard orientation found '
n=1
geom_count=geom_count+1
if geom_count == 1 : print('{0:}'.format(s))
s='geometry count= '
# print('{0:}{1:}'.format(s,geom_count))
# endif
#
# if go is on then we need to extract and store the structure
# skip the next 4 lines, on the 5th start collecting structure
# m is our switch to stop, we stop once we get to the Rotational constants line
# m is also our switch to not print the lines of dashes
# we need to know how many atoms there are in total as well
# we simply append each data list into the arrays col which has components num,atom,type,x,y,z
while go:
n = n+1
m = 0
line =f.readline()
if 'Rotational constants (GHZ):' in line: m=-1
if '---------' in line: m=1
if n > 4 and m == 0 :
# print('line: {0:}'.format(line))
if geom_count == 1 : atom_total=atom_total+1
a1,b1,c1,d1,e1,f1=line.rstrip().split()
col_num.append(int(a1))
col_atom.append(int(b1))
col_type.append(int(c1))
col_x.append(float(d1))
col_y.append(float(e1))
col_z.append(float(f1))
if m == -1 : go=False
# close while
#close while

#== build COM FILE ==

# first give all the comp details
c=open(com_file,"w")
s="%nprocshared=40\n%mem=120000MB\n"
c.write('{0:}'.format(s))
s='%chk='+base2+'.chk\n'
c.write('{0:}'.format(s))
s="# freq m06/6-311G(d,p) geom=cartesian int=ultrafine scf=conver=9 \n\n"
c.write('{0:}'.format(s))
s="Title Card Required\n\n0 1\n"
c.write('{0:}'.format(s))

#other options are
#s="# freq b3lyp/gen pseudo=cards empiricaldispersion=gd3bj geom=cartesian \n "
#s="gfinput int=ultrafine scf=conver=9 test\n\n"

# now put in the coordinates
# if step_no is zero we only use the last geometry
# if step_no is given, we use that geometry
# geom_count is the number of geometries
# atom_total is the numer of atoms
# if taking the last geometry count backwards
# n is the internal counter
# n_start defines where to start printing
# n_stop defines wher to stop printing
#
n=0
n_start=0
n_stop=0
#print ('{0:}{1:}'.format('step_no=',step_no))
#print ('{0:}{1:}'.format('atom_total=',atom_total))
#print ('{0:}{1:}'.format('geom_count=',geom_count))
if step_no == 0 :
n_start=len(col_num)-atom_total
n_stop=len(col_num)
s=' structures found only the last is used'
print('{0:}{1:}'.format(geom_count,s))
else:
n_start=atom_total*step_no
n_stop=n_start+atom_total
print('{0:}{1:}{2:}{3:}'.format('using structure ',step_no,' of ',geom_count))
# endif
#print ('{0:}{1:}'.format('n_start=',n_start))
#print ('{0:}{1:}'.format('n_stop=',n_stop))
n=n_start
while n >= n_start and n < n_stop:
c.write('{0:>4d} {1: 09.6f} {2: 09.6f} {3: 09.6f} \n'.format(col_atom[n],col_x[n],col_y[n],col_z[n]))
# print('{0:>4d} {1:>4d} {2: 09.6f} {3: 09.6f} {4: 09.6f}'.format(col_num[n],col_atom[n],col_x[n],col_y[n],col_z[n]))
n=n + 1
#close while

# now put in the gen information
#s="\nC N H Cl 0\n6-311+G(d,p)\n****\n"
#t="Sn 0\nLANL2DZ\n****\n\n"
#u="Sn 0\nLANL2DZ\n\n\n"
#c.write('{0:}{1:}{2:}'.format(s,t,u))

# and add the last blank lines
s=" \n\n"
c.write('{0:}'.format(s))

# close all open files
f.close()
c.close()
#
</pre>

Talk:Mod:Hunt Research Group/build freq

2020-01-13T06:35:31Z

Phunt: /* python script to build frequency file from optimisation output */

===python script to build frequency file from optimisation output===
*copy the code into a script called "energy.py"
*to execute the script type "python build_freq.py file_name step
*if you have your execute directory in your path, you can just type "build_freq filename step"
*if step is not given the last structure from the optimisation file will be used
*if step is given the geometry from that step will be used
*NOTE: you will need to alter the string which prints the job key words into the gaussian input file

<pre>
#!/opt/local/bin/python3
#
# build_freq.py
#
# python script to extract the final structure from a gaussian log file and build a frequency input file
# to run the script type:
#
# python build_freq.py input_file_name step_no
#
# if no step_no is given the last geometry will be used
#
import sys
import os
dir=os.getcwd()

#==set up FILES ==

# if there are 2 arguments to use the last step (of the optimisation)
# if there are 3 arguments then use a specific step_no from the optimisation
if len(sys.argv) == 2:
infile=str(sys.argv[1])
step_no=int(0)
elif len(sys.argv) == 3:
infile=str(sys.argv[1])
step_no=int(sys.argv[2])
#endif

# if there is less or more arguments something is wrong
else:
print('to run the script please type: python build_freq.py input_file_name step_no')
sys.exit()
#endif

# check to see if the user has used the .log extenion or not
# find returns -1 if the sub-string is not found, or the index of where the sub-string starts
# we cut out the .log part if .log is found
i_infile=infile.find('.log')
if (i_infile == -1):
base=infile
else:
base=infile[:i_infile]
#endif

# now set up the base file names
log_file=base+'.log'
geom_file=base+'.xyz'
# if opt is not in the filename add freq to the filename
# if opt is already in the file change this to freq
i_opt=base.find('opt')
if (i_infile == -1):
base2=base + '_freq'
else:
base2=base.replace('opt','freq')
#endif
com_file=base2+'.com'

# print out some reference information
s='directory is '
print('{0:}{1:}'.format(s,dir))
s='input file is '
print('{0:}{1:}'.format(s,infile))
s='output file is '
print('{0:}{1:}'.format(s,com_file))
#
#==set some DEFAULTS ==
col_num=[]
col_atom=[]
col_type=[]
col_x=[]
col_y=[]
col_z=[]
rep=0
n=0
go=False
atom_total=0
geom_count=0
#
#==start READING THE FILE ==

# open file and read lines one by one
f=open(log_file,"r")

# line is a variable which contains the line
line =f.readline()
while line :
line =f.readline()
# print('{0:}'.format(line))

#==extract GEOMETRY ==
# check for standard orientation text set 'go' if the text appears
# geom_count is the number of the geometry stored
# atom_total will be the number of atoms
# n will be stepping through the lines in std orientation section so set to zero for each time through
# if this is the first geometry print that a geometry is found
if 'Standard orientation:' in line:
go=True
s='Structure in standard orientation found '
n=1
geom_count=geom_count+1
if geom_count == 1 : print('{0:}'.format(s))
s='geometry count= '
# print('{0:}{1:}'.format(s,geom_count))
# endif
#
# if go is on then we need to extract and store the structure
# skip the next 4 lines, on the 5th start collecting structure
# m is our switch to stop, we stop once we get to the Rotational constants line
# m is also our switch to not print the lines of dashes
# we need to know how many atoms there are in total as well
# we simply append each data list into the arrays col which has components num,atom,type,x,y,z
while go:
n = n+1
m = 0
line =f.readline()
if 'Rotational constants (GHZ):' in line: m=-1
if '---------' in line: m=1
if n > 4 and m == 0 :
# print('line: {0:}'.format(line))
if geom_count == 1 : atom_total=atom_total+1
a1,b1,c1,d1,e1,f1=line.rstrip().split()
col_num.append(int(a1))
col_atom.append(int(b1))
col_type.append(int(c1))
col_x.append(float(d1))
col_y.append(float(e1))
col_z.append(float(f1))
if m == -1 : go=False
# close while
#close while

#== build COM FILE ==

# first give all the comp details
c=open(com_file,"w")
s="%nprocshared=40\n%mem=120000MB\n"
c.write('{0:}'.format(s))
s='%chk='+base2+'.chk\n'
c.write('{0:}'.format(s))
s="# freq m06/6-311G(d,p) geom=cartesian int=ultrafine scf=conver=9 \n\n"
c.write('{0:}'.format(s))
s="Title Card Required\n\n0 1\n"
c.write('{0:}'.format(s))

#other options are
#s="# freq b3lyp/gen pseudo=cards empiricaldispersion=gd3bj geom=cartesian \n "
#s="gfinput int=ultrafine scf=conver=9 test\n\n"

# now put in the coordinates
# if step_no is zero we only use the last geometry
# if step_no is given, we use that geometry
# geom_count is the number of geometries
# atom_total is the numer of atoms
# if taking the last geometry count backwards
# n is the internal counter
# n_start defines where to start printing
# n_stop defines wher to stop printing
#
n=0
n_start=0
n_stop=0
#print ('{0:}{1:}'.format('step_no=',step_no))
#print ('{0:}{1:}'.format('atom_total=',atom_total))
#print ('{0:}{1:}'.format('geom_count=',geom_count))
if step_no == 0 :
n_start=len(col_num)-atom_total
n_stop=len(col_num)
s=' structures found only the last is used'
print('{0:}{1:}'.format(geom_count,s))
else:
n_start=atom_total*step_no
n_stop=n_start+atom_total
print('{0:}{1:}{2:}{3:}'.format('using structure ',step_no,' of ',geom_count))
# endif
#print ('{0:}{1:}'.format('n_start=',n_start))
#print ('{0:}{1:}'.format('n_stop=',n_stop))
n=n_start
while n >= n_start and n < n_stop:
c.write('{0:>4d} {1: 09.6f} {2: 09.6f} {3: 09.6f} \n'.format(col_atom[n],col_x[n],col_y[n],col_z[n]))
# print('{0:>4d} {1:>4d} {2: 09.6f} {3: 09.6f} {4: 09.6f}'.format(col_num[n],col_atom[n],col_x[n],col_y[n],col_z[n]))
n=n + 1
#close while

# now put in the gen information
#s="\nC N H Cl 0\n6-311+G(d,p)\n****\n"
#t="Sn 0\nLANL2DZ\n****\n\n"
#u="Sn 0\nLANL2DZ\n\n\n"
#c.write('{0:}{1:}{2:}'.format(s,t,u))

# and add the last blank lines
s=" \n\n"
c.write('{0:}'.format(s))

# close all open files
f.close()
c.close()
#
</pre>

Talk:Mod:Hunt Research Group/build freq

2020-01-13T06:34:13Z

Phunt: /* python script to build frequency file from optimisation output */

===python script to build frequency file from optimisation output===
*copy the code into a script called "energy.py"
*to execute the script type "python build_freq.py file_name step
*if step is not given the last structure from the optimisation file will be used
*if step is given the geometry from that step will be used
*NOTE: you will need to alter the string which prints the job key words into the gaussian input file

<pre>
#!/opt/local/bin/python3
#
# build_freq.py
#
# python script to extract the final structure from a gaussian log file and build a frequency input file
# to run the script type:
#
# python build_freq.py input_file_name step_no
#
# if no step_no is given the last geometry will be used
#
import sys
import os
dir=os.getcwd()

#==set up FILES ==

# if there are 2 arguments to use the last step (of the optimisation)
# if there are 3 arguments then use a specific step_no from the optimisation
if len(sys.argv) == 2:
infile=str(sys.argv[1])
step_no=int(0)
elif len(sys.argv) == 3:
infile=str(sys.argv[1])
step_no=int(sys.argv[2])
#endif

# if there is less or more arguments something is wrong
else:
print('to run the script please type: python build_freq.py input_file_name step_no')
sys.exit()
#endif

# check to see if the user has used the .log extenion or not
# find returns -1 if the sub-string is not found, or the index of where the sub-string starts
# we cut out the .log part if .log is found
i_infile=infile.find('.log')
if (i_infile == -1):
base=infile
else:
base=infile[:i_infile]
#endif

# now set up the base file names
log_file=base+'.log'
geom_file=base+'.xyz'
# if opt is not in the filename add freq to the filename
# if opt is already in the file change this to freq
i_opt=base.find('opt')
if (i_infile == -1):
base2=base + '_freq'
else:
base2=base.replace('opt','freq')
#endif
com_file=base2+'.com'

# print out some reference information
s='directory is '
print('{0:}{1:}'.format(s,dir))
s='input file is '
print('{0:}{1:}'.format(s,infile))
s='output file is '
print('{0:}{1:}'.format(s,com_file))
#
#==set some DEFAULTS ==
col_num=[]
col_atom=[]
col_type=[]
col_x=[]
col_y=[]
col_z=[]
rep=0
n=0
go=False
atom_total=0
geom_count=0
#
#==start READING THE FILE ==

# open file and read lines one by one
f=open(log_file,"r")

# line is a variable which contains the line
line =f.readline()
while line :
line =f.readline()
# print('{0:}'.format(line))

#==extract GEOMETRY ==
# check for standard orientation text set 'go' if the text appears
# geom_count is the number of the geometry stored
# atom_total will be the number of atoms
# n will be stepping through the lines in std orientation section so set to zero for each time through
# if this is the first geometry print that a geometry is found
if 'Standard orientation:' in line:
go=True
s='Structure in standard orientation found '
n=1
geom_count=geom_count+1
if geom_count == 1 : print('{0:}'.format(s))
s='geometry count= '
# print('{0:}{1:}'.format(s,geom_count))
# endif
#
# if go is on then we need to extract and store the structure
# skip the next 4 lines, on the 5th start collecting structure
# m is our switch to stop, we stop once we get to the Rotational constants line
# m is also our switch to not print the lines of dashes
# we need to know how many atoms there are in total as well
# we simply append each data list into the arrays col which has components num,atom,type,x,y,z
while go:
n = n+1
m = 0
line =f.readline()
if 'Rotational constants (GHZ):' in line: m=-1
if '---------' in line: m=1
if n > 4 and m == 0 :
# print('line: {0:}'.format(line))
if geom_count == 1 : atom_total=atom_total+1
a1,b1,c1,d1,e1,f1=line.rstrip().split()
col_num.append(int(a1))
col_atom.append(int(b1))
col_type.append(int(c1))
col_x.append(float(d1))
col_y.append(float(e1))
col_z.append(float(f1))
if m == -1 : go=False
# close while
#close while

#== build COM FILE ==

# first give all the comp details
c=open(com_file,"w")
s="%nprocshared=40\n%mem=120000MB\n"
c.write('{0:}'.format(s))
s='%chk='+base2+'.chk\n'
c.write('{0:}'.format(s))
s="# freq m06/6-311G(d,p) geom=cartesian int=ultrafine scf=conver=9 \n\n"
c.write('{0:}'.format(s))
s="Title Card Required\n\n0 1\n"
c.write('{0:}'.format(s))

#other options are
#s="# freq b3lyp/gen pseudo=cards empiricaldispersion=gd3bj geom=cartesian \n "
#s="gfinput int=ultrafine scf=conver=9 test\n\n"

# now put in the coordinates
# if step_no is zero we only use the last geometry
# if step_no is given, we use that geometry
# geom_count is the number of geometries
# atom_total is the numer of atoms
# if taking the last geometry count backwards
# n is the internal counter
# n_start defines where to start printing
# n_stop defines wher to stop printing
#
n=0
n_start=0
n_stop=0
#print ('{0:}{1:}'.format('step_no=',step_no))
#print ('{0:}{1:}'.format('atom_total=',atom_total))
#print ('{0:}{1:}'.format('geom_count=',geom_count))
if step_no == 0 :
n_start=len(col_num)-atom_total
n_stop=len(col_num)
s=' structures found only the last is used'
print('{0:}{1:}'.format(geom_count,s))
else:
n_start=atom_total*step_no
n_stop=n_start+atom_total
print('{0:}{1:}{2:}{3:}'.format('using structure ',step_no,' of ',geom_count))
# endif
#print ('{0:}{1:}'.format('n_start=',n_start))
#print ('{0:}{1:}'.format('n_stop=',n_stop))
n=n_start
while n >= n_start and n < n_stop:
c.write('{0:>4d} {1: 09.6f} {2: 09.6f} {3: 09.6f} \n'.format(col_atom[n],col_x[n],col_y[n],col_z[n]))
# print('{0:>4d} {1:>4d} {2: 09.6f} {3: 09.6f} {4: 09.6f}'.format(col_num[n],col_atom[n],col_x[n],col_y[n],col_z[n]))
n=n + 1
#close while

# now put in the gen information
#s="\nC N H Cl 0\n6-311+G(d,p)\n****\n"
#t="Sn 0\nLANL2DZ\n****\n\n"
#u="Sn 0\nLANL2DZ\n\n\n"
#c.write('{0:}{1:}{2:}'.format(s,t,u))

# and add the last blank lines
s=" \n\n"
c.write('{0:}'.format(s))

# close all open files
f.close()
c.close()
#
</pre>

Talk:Mod:Hunt Research Group/build freq

2020-01-13T06:33:57Z

Phunt: Created page with "===python script to build frequency file from optimisation output=== *copy the code into a script called "energy.py" *to execute the script type "python build_freq.py file_nam..."

===python script to build frequency file from optimisation output===
*copy the code into a script called "energy.py"
*to execute the script type "python build_freq.py file_name step
*if step is not given the last structure from the optimisation file will be used
*if step is given the geometry from that step will be used
*NOTE: you will need to alter the string which prints the job key words into the gaussian input file

<pre>
#!/opt/local/bin/python3#
#
# build_freq.py
#
# python script to extract the final structure from a gaussian log file and build a frequency input file
# to run the script type:
#
# python build_freq.py input_file_name step_no
#
# if no step_no is given the last geometry will be used
#
import sys
import os
dir=os.getcwd()

#==set up FILES ==

# if there are 2 arguments to use the last step (of the optimisation)
# if there are 3 arguments then use a specific step_no from the optimisation
if len(sys.argv) == 2:
infile=str(sys.argv[1])
step_no=int(0)
elif len(sys.argv) == 3:
infile=str(sys.argv[1])
step_no=int(sys.argv[2])
#endif

# if there is less or more arguments something is wrong
else:
print('to run the script please type: python build_freq.py input_file_name step_no')
sys.exit()
#endif

# check to see if the user has used the .log extenion or not
# find returns -1 if the sub-string is not found, or the index of where the sub-string starts
# we cut out the .log part if .log is found
i_infile=infile.find('.log')
if (i_infile == -1):
base=infile
else:
base=infile[:i_infile]
#endif

# now set up the base file names
log_file=base+'.log'
geom_file=base+'.xyz'
# if opt is not in the filename add freq to the filename
# if opt is already in the file change this to freq
i_opt=base.find('opt')
if (i_infile == -1):
base2=base + '_freq'
else:
base2=base.replace('opt','freq')
#endif
com_file=base2+'.com'

# print out some reference information
s='directory is '
print('{0:}{1:}'.format(s,dir))
s='input file is '
print('{0:}{1:}'.format(s,infile))
s='output file is '
print('{0:}{1:}'.format(s,com_file))
#
#==set some DEFAULTS ==
col_num=[]
col_atom=[]
col_type=[]
col_x=[]
col_y=[]
col_z=[]
rep=0
n=0
go=False
atom_total=0
geom_count=0
#
#==start READING THE FILE ==

# open file and read lines one by one
f=open(log_file,"r")

# line is a variable which contains the line
line =f.readline()
while line :
line =f.readline()
# print('{0:}'.format(line))

#==extract GEOMETRY ==
# check for standard orientation text set 'go' if the text appears
# geom_count is the number of the geometry stored
# atom_total will be the number of atoms
# n will be stepping through the lines in std orientation section so set to zero for each time through
# if this is the first geometry print that a geometry is found
if 'Standard orientation:' in line:
go=True
s='Structure in standard orientation found '
n=1
geom_count=geom_count+1
if geom_count == 1 : print('{0:}'.format(s))
s='geometry count= '
# print('{0:}{1:}'.format(s,geom_count))
# endif
#
# if go is on then we need to extract and store the structure
# skip the next 4 lines, on the 5th start collecting structure
# m is our switch to stop, we stop once we get to the Rotational constants line
# m is also our switch to not print the lines of dashes
# we need to know how many atoms there are in total as well
# we simply append each data list into the arrays col which has components num,atom,type,x,y,z
while go:
n = n+1
m = 0
line =f.readline()
if 'Rotational constants (GHZ):' in line: m=-1
if '---------' in line: m=1
if n > 4 and m == 0 :
# print('line: {0:}'.format(line))
if geom_count == 1 : atom_total=atom_total+1
a1,b1,c1,d1,e1,f1=line.rstrip().split()
col_num.append(int(a1))
col_atom.append(int(b1))
col_type.append(int(c1))
col_x.append(float(d1))
col_y.append(float(e1))
col_z.append(float(f1))
if m == -1 : go=False
# close while
#close while

#== build COM FILE ==

# first give all the comp details
c=open(com_file,"w")
s="%nprocshared=40\n%mem=120000MB\n"
c.write('{0:}'.format(s))
s='%chk='+base2+'.chk\n'
c.write('{0:}'.format(s))
s="# freq m06/6-311G(d,p) geom=cartesian int=ultrafine scf=conver=9 \n\n"
c.write('{0:}'.format(s))
s="Title Card Required\n\n0 1\n"
c.write('{0:}'.format(s))

#other options are
#s="# freq b3lyp/gen pseudo=cards empiricaldispersion=gd3bj geom=cartesian \n "
#s="gfinput int=ultrafine scf=conver=9 test\n\n"

# now put in the coordinates
# if step_no is zero we only use the last geometry
# if step_no is given, we use that geometry
# geom_count is the number of geometries
# atom_total is the numer of atoms
# if taking the last geometry count backwards
# n is the internal counter
# n_start defines where to start printing
# n_stop defines wher to stop printing
#
n=0
n_start=0
n_stop=0
#print ('{0:}{1:}'.format('step_no=',step_no))
#print ('{0:}{1:}'.format('atom_total=',atom_total))
#print ('{0:}{1:}'.format('geom_count=',geom_count))
if step_no == 0 :
n_start=len(col_num)-atom_total
n_stop=len(col_num)
s=' structures found only the last is used'
print('{0:}{1:}'.format(geom_count,s))
else:
n_start=atom_total*step_no
n_stop=n_start+atom_total
print('{0:}{1:}{2:}{3:}'.format('using structure ',step_no,' of ',geom_count))
# endif
#print ('{0:}{1:}'.format('n_start=',n_start))
#print ('{0:}{1:}'.format('n_stop=',n_stop))
n=n_start
while n >= n_start and n < n_stop:
c.write('{0:>4d} {1: 09.6f} {2: 09.6f} {3: 09.6f} \n'.format(col_atom[n],col_x[n],col_y[n],col_z[n]))
# print('{0:>4d} {1:>4d} {2: 09.6f} {3: 09.6f} {4: 09.6f}'.format(col_num[n],col_atom[n],col_x[n],col_y[n],col_z[n]))
n=n + 1
#close while

# now put in the gen information
#s="\nC N H Cl 0\n6-311+G(d,p)\n****\n"
#t="Sn 0\nLANL2DZ\n****\n\n"
#u="Sn 0\nLANL2DZ\n\n\n"
#c.write('{0:}{1:}{2:}'.format(s,t,u))

# and add the last blank lines
s=" \n\n"
c.write('{0:}'.format(s))

# close all open files
f.close()
c.close()
#
</pre>

Mod:Hunt Research Group

2020-01-13T06:30:39Z

Phunt: /* Python and Python codes */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===Report and Paper Writing===
#procedures [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/report_procedures link]
#advice [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/report_writing link]
#report components [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/report_components link]
#files to provide when writing a paper [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/paper link]

===Group Admin===
#Which files to store on the database and database template [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/database link]
#How to access DROBO [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/drobo link]

===HPC Resources===
#'''Hunt group HPC servers and run scripts''' [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link]
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link]
#How to run jobs interactively [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/run_interactive link]
#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link]
#New gf script (more convenient job submitting) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/new_gf_script link]
#Retired: How to make qsub more comfortable (gfunc) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpQSUB link]
#Tired of entering your password all the time: set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link]
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link]
#Using VPN from home, for Sierra follow the college instructions [[link]]
#How to connect to HPC directory on desktop for file transfers [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_Directory_on_desktop link]
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link]
#How to use a slimmed down terminal on your IPhone [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/termius]

===Using evil Windows and PCs===
#Use Imperial Software Hub to access gaussview and gaussian [http://www.imperial.ac.uk/admin-services/ict/store/software/software-hub/ link]
#Using windows and setting up a connection to HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link]
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link]

===Key Papers, References and Resources===
*'''Papers'''
#Meta study on DFT functionals [https://pubs.acs.org/doi/abs/10.1021/ct401111c doi]
#M06 suite of DFT functionals [https://link.springer.com/article/10.1007/s00214-007-0310-x doi]
#SMD for ILs [https://pubs.acs.org/doi/abs/10.1021/jp304365v doi]
#Box size for MD simulations of ILs [https://dx.doi.org/10.1063/1.4748352 doi]
*'''Notes'''
#Solving the angular part of the Schrödinger equation for a hydrogen atom [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/angular_schrodinger link] (notes by Vincent)
#DFT Workshop Notes [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/DFT_Workshop]
#Cl- in water [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link]
#The use of Legendre time correlation functions to study reorientational dynamics in liquids [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/legendre link]

===Gaussian General===
#We are starting a database of common errors encountered when running Gaussian jobs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gaussian_errors link]
# Here is an already existing database of common errors [https://docs.computecanada.ca/wiki/Gaussian_error_messages link]
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#partial optimisations and scans [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/z-matrix link]
#General procedure for locating transition state structures [[link]]
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link]
#Basic ONIOM (Mechanical Embedding) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/basiconiom link]
#problems with scf convergence [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/scf_convergence link]
#manipulating checkpoint files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:usingchkfiles link]
#for NMR calculations look here: [http://cheshirenmr.info/index.htm Chemical Shift Repository]
#Population and charge analysis [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/population link]

===Gaussian Advanced===
#Systematic conformational scan for ion-pair dimers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ion_pair_scan link]
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link]
#generating natural transition orbitals [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/nto link]
#computing excited state polarisabilities [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_ES_alpha link]
#computing deuterated and/or anharmonic spectra [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_Danharm link]
#How to run at a higher temperature [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:high_temp link]
#Correcting the entropy due to low modes [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:low_modes_entropy link]
#Optimisation of charged molecules in an electric field [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Optimising_charged_molecules_in_electric_fields link]
#Multidimensional Scans of Internal Coordinates [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Multidimensional_Scans_of_Internal_Coordinates link]

===Solvation===
#Using the SMD model [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/solvent link]
#Using SMD on ILs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_Using_SMD_on_ILs link]
#Troublesome optimisations in SMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:troublesome_smd link]
#Atomic radii and solvent models [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/atomic_radii link]
#Molecular volume calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molecular_volume link]
#The cavity [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/solvent_cavity link]
#How to download and use GeomView to visualise solvation cavities [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/geomview link]
#Surfaces (Solvent-Accessible and Connolly) in Jmol [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/jmolsurfaces link]

===Codes to Help Gaussian Analysis===
====Python and Python codes====
# Using and installing python [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/python link]
# Python toolkit currently focussed towards gaussian analysis [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molLego link]
# Standalone python scripts and analysis:
#* List the energy for each step of a gaussian log file, find the lowest energy and produce a quick graph in kJ/mol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_energy link]
#* Build a frequency file from an optimisation file ready to submit, this will require editing for your particular job [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/build_freq link]
#* Extract last Standard Orientation structure of gaussian log file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_single_geom link]
#* Extract last structure of gaussian optimisation and build a freq com file for job with PP [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/build_freq_file link]
#* Extract each optimised step from a scan into xyz coordinate file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_scan_geom link]
#* Extract thermodynamic data and low frequencies from log files (python 2) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:simple_freq_script link]
#* Extract thermodynamic data and low frequencies from log files to enter into excel template provided for the database (python 3) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:model_freq_script link]
#* Extract geometry and charges (ESP) into a .pdb file for visualising in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ESP_charges_for_VMD link]
#* Codes to extract CHELPG and NBO charge values to excel [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/chelpg_extract link]
#* Extract ESP and NBO charges [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_ESP_charges link]
#* Script to pull thermodynamic data and low frequencies from log files AND evaluate to a reference [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:freq_script link]
#* Codes to extract frequency data from gaussian .log files and generate vibrational spectra [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:frequency_spectrum_script link]
#* Codes to visualise data matrices (correlation matrices/heatmaps)[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/heatmap link]
#* Python API for analysis of Gaussian computations [https://pygauss.readthedocs.org - Documentation]
#* Charge arm [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/charge_arm link]

====Other codes====
# Extract E2 Values (From NBO Calculations) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/NBO_Matlab_Code link]
# Calculate pDoS/XP spectra code (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Calc_XPS_Code link]
# Optimally Tuned Range Separated Hybrid Functionals [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/OTRSH_Funct link]
# Some G09 Parsers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Some_G09_Parsers link]

===QC Visualisation===
*'''Using AIMALL: density based visualisation'''
#download [http://aim.tkgristmill.com AIMALL]
#once downloaded and installed you need to send tricia your aimall-serialnumber.txt file, and she will arrange for a aimallpro.lic or license file for you
#basic instructions [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:aim_basics link]
#AimAll with pseudo potentials [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:aim_pseudopotentials link]
#AIMAll 19.10.12 on iMacs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:AIMAllQuickFix link]

*'''ESPs and manipulating gaussian cube files'''
#Instructions for visualizing electrostatic potentials (Gaussview)[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link]
#Electrostatic Potentials II (Molden) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials_2 link]
#Manipulating cube files [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/cube_files link]
#Format of cube files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/cube_format link]
#Using A. Stone's distributed multipole analysis [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/GDMA link]

*'''NCI plots'''
#get the program here: [http://www.lct.jussieu.fr/pagesperso/contrera/nciplot.html link]
#How to install NCIPlot on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/InstallNCIPlot link]
#Using NCIPlot [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/UseNCIPlot link]

*'''MOs'''
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link]

===Setup and Running Classical MD Simulations===
====dl_poly====
#DLPOLY_4.0 Installation for an IMac [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Installing_DL_POLY_4.09_on_MacOS_Mojave link]
#DLPOLY_Classic Installation for an IMac [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Installing_DL_POLY_classic link]

#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#some basics for getting started using DL_POLY [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dl_poly_basics link]
#control file basics [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/control_basics link]
*useful links
::[https://www.ccp5.ac.uk https://www.ccp5.ac.uk]
::[https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx]
::[ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/USRMAN4.pdf dlpoly4 user manual]
::[ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/JavaGUI.pdf javagui user manual]
::[ftp://ftp.dl.ac.uk/ccp5/DL_POLY/ dlpoly ftp server]
:::you can find test files in DL_POLY_4.0/DATA
:::more info about the dlpoly test files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/DL_POLY_test_files link]

====gromacs====
#GROMACS installing and getting started with gromacs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gromacs_1 link]
#using Agilio Padua force fields for ionic liquids [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/ilff link]
#Packmol installing and running to generate a starting box [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/packmol_1 link]
#initial rough relaxation [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Starting_MD link]
#GROMACS general run [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_run link]
#GROMACS viewing data [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_viewing_MD link]
#GROMACS control file [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_control_MD link]
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link]
====general====
#Getting the Force Field [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Wheretostart link]
#Choosing an Ensemble [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Ensembles link]
#Molten Salt Simulations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/MoltenSaltSimulation link]
#Common Errors [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/CommonErrors link]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link]

===MD Visualisation===
*'''VMD: a molecular dynamics visualisation package'''
#VMD can be installed from the [http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD VMD downloads page]
#Quick reminder [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDReminder link]
#Colour in VMD [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDColor link]
#Changing the graphical representation of your structures [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link]
#VMD indexing [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDindexing link]
#Using scripts in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScripts link]
#Dealing with periodic boundaries and bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsPeriodic link]
#Dealing with bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdBonding link]
#How to turn a Gaussian optimization into a VMD movie [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/VMDmovie link]
#Overlapping two structures [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdVisual link]
*'''Ovito: a molecular dynamics visualisation package'''
#Download Ovito [http://www.ovito.org/index.php/download]
#Using Ovito basics [//wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Ovito_basics link]
*'''SDFs'''
#How to generate SDFs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/sdfs_generate link]

===MD Post processing===
#Python script to convert a HISTORY file into a xyz file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/hist_to_xyz link]
#Python script to reduce the number of steps in a lammps traj file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/lam_to_xyz link]
#Python script to convert a lammps traj file to xyz coordinates and at the same time fold all atoms into a cell and center at the origin [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/lam_fold_xyz link]
#Center the trajectory at a particular atom ('''needs fixing''') [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Recenter link]
#How to generate SDFs with TRAVIS [[Talk:Mod:Hunt Research Group/How to draw SDFs with TRAVIS|link]]
#Tcl script to follow a particular atom [[Talk:Mod:Hunt Research Group/Traj_atom_following|link]]

===Coding===
*'''installing Xcode and other programming environments'''
#to use many programs you will need a compiler, this is not installed by default on your mac
#How to install Xcode on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/InstallXcode link]
#using MacPorts as code for managing other codes on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/MacPorts link]
#HomeBrew and Fink are other options (HomeBrew is not advised for us)
#gfortran on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Gfortran link]
#using python on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/python link]

*'''EMO Code'''
#How to use Ling's emo plot code[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emoplot link]
#How to plot EMOs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emo link]

*'''Jan's charge based analysis Code'''
#charge analysis [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Jan_charges link]
#Obtaining NBO, ESP, and RESP charges [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Charges link]

*'''Oxana's visualisation of ESPs Code'''
#Scripts for reading, saving, manipulating and visualising data from cube files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Python_scripts_for_cube_files link]

*'''Python Genereal'''
# General python recommendations and set up [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/PythonGeneral link]
# Analysis toolkit mainly geared towards processing Gaussian calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Python_Analysis_Tools link]

===Other Codes===
#ADF Submission script [http://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/ADF_sricpt link]
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link]
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/]

===Setup and Running Ab-Initio MD Simulations===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link]
#How to run CPMD to study aqueous solutions [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd_water link]
#How to run CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k_how link]

===Running QM/MM Simulations in ChemShell===

==Tcl-chemshell==
#ChemShell official website which contains the manual and a tutorial [http://www.stfc.ac.uk/CSE/randd/ccg/36254.aspx link]
#Introduction to ChemShell - Copper in water [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Introduction link]
#Defining the system: Cu2+ and its first 2 solvation shells [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_System_Aqeuous_Cu(II) link]
#Defining the force field parameters [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II) link]
#Single point QM/MM energy calculation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_SP_Aqeuous_Cu(II) link]
#QM/MM Optimisation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_OPT_Aqeuous_Cu(II) link]
#QM/MM Molecular Dynamics [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_MD_Aqeuous_Cu(II) link]
#Using MolCluster [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/MolCluster link]
#Running ChemShell [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell link]
#Explaining ChemShell files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files link]
#Step By Step [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Chemshell_Step_By_Step link]
==Py-chemshell==

# Compiling Chemshell and required programs []
# The DL_POLY_4 manual is available for download at this link [ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/USRMAN4.pdf]
# Molecular Mechanics computation with DL_POLY [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:_MM_Single_Point_computation]
# Basic QM/MM single point and optimisations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_QM/MM_Single_Point_and_optimisation]
# Visualise optimisation trajectories in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_Visualising_trajectories_with_VMD]
# Computing Mulliken charges and creating .wfn inputs for AIM analysis [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_Mulliken]

==Admin Stuff==
#Not used to writing a wiki, make your test runs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/testing on this page]
#How to set-up new macs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_setup link]
#How to switch the printer HP CP3525dn duplex on and off [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/printing link]

Talk:Mod:Hunt Research Group/extract energy

2020-01-12T12:08:41Z

Phunt:

===python script to print energies===
*copy the code into a script called "energy.py"
*to execute the script type "python energy.py file_name
*this will print to terminal the energy for each step, find the lowest energy and plot a quick graph relative to the lowest energy in kJ/mol
*NOTE: press "q" to close the graph (or click the red button on the graph)

<pre>
#
# energy.py
#
# python script to extract the SCF energy for each step, find the lowest energy step
# and produce a quick graph showing the change in energy in kJ/mol
# to run the script type
# python energy.py input_file_name
# NOTE you can close the graph by pressing "q" on keyboard
#
import sys
import numpy as np
import matplotlib.pyplot as plt
import os
dir=os.getcwd()
#
# setup files to read
if len(sys.argv) == 1:
print('to run the script please type: python energy.py input_file_name')
sys.exit()
else:
log_file=str(sys.argv[1])
s='directory is '
print('{0:}{1:}'.format(s,dir))
s='input file is '
print('{0:}{1:}'.format(s,log_file))
#close if

# open the file
f = open(log_file,'r')

# set some basic parameters
energy=[]
new_energy=[]
x_axis=[]
en_search_string='SCF Done:'

# read the if there is a first line, then read the file line by line
# if energy is given split the line into array tmp and extract the energy number
# and extract the energy and store in an array
count=0
line=f.readline()
while line:
line =f.readline()
# print('{0:}'.format(line))
if en_search_string in line:
tmp=line.rstrip().split()
energy.append(float(tmp[4]))
count1=count+1
print('{0:}{1:<3}{2:<.8f}'.format('step: ',count1,energy[count]))
count=count+1
# endif
#endwhile

total_steps=count
#print(total_steps)

# find the lowest energy
min_energy=min(energy)
min_index=energy.index(min(energy))
min_index=min_index+1
print('{0:}{1:}{2:}{3:}'.format('lowest energy is step: ',min_index,' energy: ',min_energy))

# re-align to start at one, and in kJ/mol relative to lowest energy
# remember python starts at zero
x=0
while x < total_steps-1 :
temp=(energy[x] - min_energy) * 2625.5
# print(temp)
new_energy.append(temp)
x=x+1
x_axis.append(x)
#endwhile

# plot the energy
plt.plot(x_axis,new_energy,'b-')
plt.plot(x_axis,new_energy,'bo')
plt.plot(min_index,new_energy[min_index],'rs',markersize=8)
plt.ylabel('energy kJ/mol')
plt.xlabel('step')
plt.show()

# close file
f.close()
#end
</pre>

Talk:Mod:Hunt Research Group/extract energy

2020-01-12T12:08:21Z

Phunt: /* python script to print energies */

===python script to print energies===
*copy the code into a script called "energy.py"
*to execute the script type "python energy.py file_name
*this will print to terminal the energy for each step, find the lowest energy and plot a quick graph relative to the lowest energy in kJ/mol
*NOTE:press "q" to close the graph

<pre>
#
# energy.py
#
# python script to extract the SCF energy for each step, find the lowest energy step
# and produce a quick graph showing the change in energy in kJ/mol
# to run the script type
# python energy.py input_file_name
# NOTE you can close the graph by pressing "q" on keyboard
#
import sys
import numpy as np
import matplotlib.pyplot as plt
import os
dir=os.getcwd()
#
# setup files to read
if len(sys.argv) == 1:
print('to run the script please type: python energy.py input_file_name')
sys.exit()
else:
log_file=str(sys.argv[1])
s='directory is '
print('{0:}{1:}'.format(s,dir))
s='input file is '
print('{0:}{1:}'.format(s,log_file))
#close if

# open the file
f = open(log_file,'r')

# set some basic parameters
energy=[]
new_energy=[]
x_axis=[]
en_search_string='SCF Done:'

# read the if there is a first line, then read the file line by line
# if energy is given split the line into array tmp and extract the energy number
# and extract the energy and store in an array
count=0
line=f.readline()
while line:
line =f.readline()
# print('{0:}'.format(line))
if en_search_string in line:
tmp=line.rstrip().split()
energy.append(float(tmp[4]))
count1=count+1
print('{0:}{1:<3}{2:<.8f}'.format('step: ',count1,energy[count]))
count=count+1
# endif
#endwhile

total_steps=count
#print(total_steps)

# find the lowest energy
min_energy=min(energy)
min_index=energy.index(min(energy))
min_index=min_index+1
print('{0:}{1:}{2:}{3:}'.format('lowest energy is step: ',min_index,' energy: ',min_energy))

# re-align to start at one, and in kJ/mol relative to lowest energy
# remember python starts at zero
x=0
while x < total_steps-1 :
temp=(energy[x] - min_energy) * 2625.5
# print(temp)
new_energy.append(temp)
x=x+1
x_axis.append(x)
#endwhile

# plot the energy
plt.plot(x_axis,new_energy,'b-')
plt.plot(x_axis,new_energy,'bo')
plt.plot(min_index,new_energy[min_index],'rs',markersize=8)
plt.ylabel('energy kJ/mol')
plt.xlabel('step')
plt.show()

# close file
f.close()
#end
</pre>

Talk:Mod:Hunt Research Group/extract energy

2020-01-12T12:07:44Z

Phunt: Created page with "===python script to print energies=== *copy the code into a script called "energy.py" *to execute the script type "python energy.py file_name *this will print to terminal the..."

===python script to print energies===
*copy the code into a script called "energy.py"
*to execute the script type "python energy.py file_name
*this will print to terminal the energy for each step, find the lowest energy and plot a quick graph, press "q" to close the graph

<pre>
#
# energy.py
#
# python script to extract the SCF energy for each step, find the lowest energy step
# and produce a quick graph showing the change in energy in kJ/mol
# to run the script type
# python energy.py input_file_name
# NOTE you can close the graph by pressing "q" on keyboard
#
import sys
import numpy as np
import matplotlib.pyplot as plt
import os
dir=os.getcwd()
#
# setup files to read
if len(sys.argv) == 1:
print('to run the script please type: python energy.py input_file_name')
sys.exit()
else:
log_file=str(sys.argv[1])
s='directory is '
print('{0:}{1:}'.format(s,dir))
s='input file is '
print('{0:}{1:}'.format(s,log_file))
#close if

# open the file
f = open(log_file,'r')

# set some basic parameters
energy=[]
new_energy=[]
x_axis=[]
en_search_string='SCF Done:'

# read the if there is a first line, then read the file line by line
# if energy is given split the line into array tmp and extract the energy number
# and extract the energy and store in an array
count=0
line=f.readline()
while line:
line =f.readline()
# print('{0:}'.format(line))
if en_search_string in line:
tmp=line.rstrip().split()
energy.append(float(tmp[4]))
count1=count+1
print('{0:}{1:<3}{2:<.8f}'.format('step: ',count1,energy[count]))
count=count+1
# endif
#endwhile

total_steps=count
#print(total_steps)

# find the lowest energy
min_energy=min(energy)
min_index=energy.index(min(energy))
min_index=min_index+1
print('{0:}{1:}{2:}{3:}'.format('lowest energy is step: ',min_index,' energy: ',min_energy))

# re-align to start at one, and in kJ/mol relative to lowest energy
# remember python starts at zero
x=0
while x < total_steps-1 :
temp=(energy[x] - min_energy) * 2625.5
# print(temp)
new_energy.append(temp)
x=x+1
x_axis.append(x)
#endwhile

# plot the energy
plt.plot(x_axis,new_energy,'b-')
plt.plot(x_axis,new_energy,'bo')
plt.plot(min_index,new_energy[min_index],'rs',markersize=8)
plt.ylabel('energy kJ/mol')
plt.xlabel('step')
plt.show()

# close file
f.close()
#end
</pre>

Mod:Hunt Research Group

2020-01-12T12:05:45Z

Phunt: /* Python and Python codes */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===Report and Paper Writing===
#procedures [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/report_procedures link]
#advice [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/report_writing link]
#report components [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/report_components link]
#files to provide when writing a paper [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/paper link]

===Group Admin===
#Which files to store on the database and database template [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/database link]
#How to access DROBO [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/drobo link]

===HPC Resources===
#'''Hunt group HPC servers and run scripts''' [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link]
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link]
#How to run jobs interactively [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/run_interactive link]
#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link]
#New gf script (more convenient job submitting) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/new_gf_script link]
#Retired: How to make qsub more comfortable (gfunc) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpQSUB link]
#Tired of entering your password all the time: set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link]
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link]
#Using VPN from home, for Sierra follow the college instructions [[link]]
#How to connect to HPC directory on desktop for file transfers [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_Directory_on_desktop link]
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link]
#How to use a slimmed down terminal on your IPhone [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/termius]

===Using evil Windows and PCs===
#Use Imperial Software Hub to access gaussview and gaussian [http://www.imperial.ac.uk/admin-services/ict/store/software/software-hub/ link]
#Using windows and setting up a connection to HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link]
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link]

===Key Papers, References and Resources===
*'''Papers'''
#Meta study on DFT functionals [https://pubs.acs.org/doi/abs/10.1021/ct401111c doi]
#M06 suite of DFT functionals [https://link.springer.com/article/10.1007/s00214-007-0310-x doi]
#SMD for ILs [https://pubs.acs.org/doi/abs/10.1021/jp304365v doi]
#Box size for MD simulations of ILs [https://dx.doi.org/10.1063/1.4748352 doi]
*'''Notes'''
#Solving the angular part of the Schrödinger equation for a hydrogen atom [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/angular_schrodinger link] (notes by Vincent)
#DFT Workshop Notes [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/DFT_Workshop]
#Cl- in water [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link]
#The use of Legendre time correlation functions to study reorientational dynamics in liquids [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/legendre link]

===Gaussian General===
#We are starting a database of common errors encountered when running Gaussian jobs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gaussian_errors link]
# Here is an already existing database of common errors [https://docs.computecanada.ca/wiki/Gaussian_error_messages link]
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#partial optimisations and scans [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/z-matrix link]
#General procedure for locating transition state structures [[link]]
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link]
#Basic ONIOM (Mechanical Embedding) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/basiconiom link]
#problems with scf convergence [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/scf_convergence link]
#manipulating checkpoint files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:usingchkfiles link]
#for NMR calculations look here: [http://cheshirenmr.info/index.htm Chemical Shift Repository]
#Population and charge analysis [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/population link]

===Gaussian Advanced===
#Systematic conformational scan for ion-pair dimers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ion_pair_scan link]
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link]
#generating natural transition orbitals [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/nto link]
#computing excited state polarisabilities [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_ES_alpha link]
#computing deuterated and/or anharmonic spectra [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_Danharm link]
#How to run at a higher temperature [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:high_temp link]
#Correcting the entropy due to low modes [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:low_modes_entropy link]
#Optimisation of charged molecules in an electric field [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Optimising_charged_molecules_in_electric_fields link]
#Multidimensional Scans of Internal Coordinates [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Multidimensional_Scans_of_Internal_Coordinates link]

===Solvation===
#Using the SMD model [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/solvent link]
#Using SMD on ILs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_Using_SMD_on_ILs link]
#Troublesome optimisations in SMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:troublesome_smd link]
#Atomic radii and solvent models [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/atomic_radii link]
#Molecular volume calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molecular_volume link]
#The cavity [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/solvent_cavity link]
#How to download and use GeomView to visualise solvation cavities [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/geomview link]
#Surfaces (Solvent-Accessible and Connolly) in Jmol [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/jmolsurfaces link]

===Codes to Help Gaussian Analysis===
====Python and Python codes====
# Using and installing python [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/python link]
# Python toolkit currently focussed towards gaussian analysis [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molLego link]
# Standalone python scripts and analysis:
#* list the energy for each step of a gaussian log file, find the lowest energy and produce a quick graph in kJ/mol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_energy link]
#* Extract last Standard Orientation structure of gaussian log file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_single_geom link]
#* Extract last structure of gaussian optimisation and build a freq com file for job with PP [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/build_freq_file link]
#* Extract each optimised step from a scan into xyz coordinate file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_scan_geom link]
#* Extract thermodynamic data and low frequencies from log files (python 2) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:simple_freq_script link]
#* Extract thermodynamic data and low frequencies from log files to enter into excel template provided for the database (python 3) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:model_freq_script link]
#* Extract geometry and charges (ESP) into a .pdb file for visualising in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ESP_charges_for_VMD link]
#* Codes to extract CHELPG and NBO charge values to excel [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/chelpg_extract link]
#* Extract ESP and NBO charges [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_ESP_charges link]
#* Script to pull thermodynamic data and low frequencies from log files AND evaluate to a reference [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:freq_script link]
#* Codes to extract frequency data from gaussian .log files and generate vibrational spectra [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:frequency_spectrum_script link]
#* Codes to visualise data matrices (correlation matrices/heatmaps)[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/heatmap link]
#* Python API for analysis of Gaussian computations [https://pygauss.readthedocs.org - Documentation]
#* Charge arm [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/charge_arm link]

====Other codes====
# Extract E2 Values (From NBO Calculations) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/NBO_Matlab_Code link]
# Calculate pDoS/XP spectra code (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Calc_XPS_Code link]
# Optimally Tuned Range Separated Hybrid Functionals [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/OTRSH_Funct link]
# Some G09 Parsers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Some_G09_Parsers link]

===QC Visualisation===
*'''Using AIMALL: density based visualisation'''
#download [http://aim.tkgristmill.com AIMALL]
#once downloaded and installed you need to send tricia your aimall-serialnumber.txt file, and she will arrange for a aimallpro.lic or license file for you
#basic instructions [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:aim_basics link]
#AimAll with pseudo potentials [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:aim_pseudopotentials link]
#AIMAll 19.10.12 on iMacs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:AIMAllQuickFix link]

*'''ESPs and manipulating gaussian cube files'''
#Instructions for visualizing electrostatic potentials (Gaussview)[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link]
#Electrostatic Potentials II (Molden) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials_2 link]
#Manipulating cube files [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/cube_files link]
#Format of cube files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/cube_format link]
#Using A. Stone's distributed multipole analysis [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/GDMA link]

*'''NCI plots'''
#get the program here: [http://www.lct.jussieu.fr/pagesperso/contrera/nciplot.html link]
#How to install NCIPlot on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/InstallNCIPlot link]
#Using NCIPlot [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/UseNCIPlot link]

*'''MOs'''
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link]

===Setup and Running Classical MD Simulations===
====dl_poly====
#DLPOLY_4.0 Installation for an IMac [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Installing_DL_POLY_4.09_on_MacOS_Mojave link]
#DLPOLY_Classic Installation for an IMac [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Installing_DL_POLY_classic link]

#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#some basics for getting started using DL_POLY [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dl_poly_basics link]
#control file basics [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/control_basics link]
*useful links
::[https://www.ccp5.ac.uk https://www.ccp5.ac.uk]
::[https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx]
::[ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/USRMAN4.pdf dlpoly4 user manual]
::[ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/JavaGUI.pdf javagui user manual]
::[ftp://ftp.dl.ac.uk/ccp5/DL_POLY/ dlpoly ftp server]
:::you can find test files in DL_POLY_4.0/DATA
:::more info about the dlpoly test files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/DL_POLY_test_files link]

====gromacs====
#GROMACS installing and getting started with gromacs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gromacs_1 link]
#using Agilio Padua force fields for ionic liquids [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/ilff link]
#Packmol installing and running to generate a starting box [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/packmol_1 link]
#initial rough relaxation [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Starting_MD link]
#GROMACS general run [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_run link]
#GROMACS viewing data [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_viewing_MD link]
#GROMACS control file [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_control_MD link]
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link]
====general====
#Getting the Force Field [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Wheretostart link]
#Choosing an Ensemble [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Ensembles link]
#Molten Salt Simulations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/MoltenSaltSimulation link]
#Common Errors [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/CommonErrors link]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link]

===MD Visualisation===
*'''VMD: a molecular dynamics visualisation package'''
#VMD can be installed from the [http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD VMD downloads page]
#Quick reminder [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDReminder link]
#Colour in VMD [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDColor link]
#Changing the graphical representation of your structures [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link]
#VMD indexing [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDindexing link]
#Using scripts in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScripts link]
#Dealing with periodic boundaries and bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsPeriodic link]
#Dealing with bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdBonding link]
#How to turn a Gaussian optimization into a VMD movie [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/VMDmovie link]
#Overlapping two structures [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdVisual link]
*'''Ovito: a molecular dynamics visualisation package'''
#Download Ovito [http://www.ovito.org/index.php/download]
#Using Ovito basics [//wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Ovito_basics link]
*'''SDFs'''
#How to generate SDFs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/sdfs_generate link]

===MD Post processing===
#Python script to convert a HISTORY file into a xyz file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/hist_to_xyz link]
#Python script to reduce the number of steps in a lammps traj file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/lam_to_xyz link]
#Python script to convert a lammps traj file to xyz coordinates and at the same time fold all atoms into a cell and center at the origin [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/lam_fold_xyz link]
#Center the trajectory at a particular atom ('''needs fixing''') [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Recenter link]
#How to generate SDFs with TRAVIS [[Talk:Mod:Hunt Research Group/How to draw SDFs with TRAVIS|link]]
#Tcl script to follow a particular atom [[Talk:Mod:Hunt Research Group/Traj_atom_following|link]]

===Coding===
*'''installing Xcode and other programming environments'''
#to use many programs you will need a compiler, this is not installed by default on your mac
#How to install Xcode on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/InstallXcode link]
#using MacPorts as code for managing other codes on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/MacPorts link]
#HomeBrew and Fink are other options (HomeBrew is not advised for us)
#gfortran on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Gfortran link]
#using python on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/python link]

*'''EMO Code'''
#How to use Ling's emo plot code[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emoplot link]
#How to plot EMOs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emo link]

*'''Jan's charge based analysis Code'''
#charge analysis [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Jan_charges link]
#Obtaining NBO, ESP, and RESP charges [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Charges link]

*'''Oxana's visualisation of ESPs Code'''
#Scripts for reading, saving, manipulating and visualising data from cube files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Python_scripts_for_cube_files link]

*'''Python Genereal'''
# General python recommendations and set up [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/PythonGeneral link]
# Analysis toolkit mainly geared towards processing Gaussian calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Python_Analysis_Tools link]

===Other Codes===
#ADF Submission script [http://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/ADF_sricpt link]
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link]
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/]

===Setup and Running Ab-Initio MD Simulations===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link]
#How to run CPMD to study aqueous solutions [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd_water link]
#How to run CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k_how link]

===Running QM/MM Simulations in ChemShell===

==Tcl-chemshell==
#ChemShell official website which contains the manual and a tutorial [http://www.stfc.ac.uk/CSE/randd/ccg/36254.aspx link]
#Introduction to ChemShell - Copper in water [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Introduction link]
#Defining the system: Cu2+ and its first 2 solvation shells [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_System_Aqeuous_Cu(II) link]
#Defining the force field parameters [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II) link]
#Single point QM/MM energy calculation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_SP_Aqeuous_Cu(II) link]
#QM/MM Optimisation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_OPT_Aqeuous_Cu(II) link]
#QM/MM Molecular Dynamics [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_MD_Aqeuous_Cu(II) link]
#Using MolCluster [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/MolCluster link]
#Running ChemShell [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell link]
#Explaining ChemShell files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files link]
#Step By Step [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Chemshell_Step_By_Step link]
==Py-chemshell==

# Compiling Chemshell and required programs []
# The DL_POLY_4 manual is available for download at this link [ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/USRMAN4.pdf]
# Molecular Mechanics computation with DL_POLY [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:_MM_Single_Point_computation]
# Basic QM/MM single point and optimisations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_QM/MM_Single_Point_and_optimisation]
# Visualise optimisation trajectories in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_Visualising_trajectories_with_VMD]
# Computing Mulliken charges and creating .wfn inputs for AIM analysis [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_Mulliken]

==Admin Stuff==
#Not used to writing a wiki, make your test runs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/testing on this page]
#How to set-up new macs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_setup link]
#How to switch the printer HP CP3525dn duplex on and off [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/printing link]

Mod:Hunt Research Group/mac setup

2020-01-08T13:25:20Z

Phunt:

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]

==== For NEW computers: make a group ====
::if you are a new user on an existing computer, the groups will already be set up!
::open accounts in system prefs
::click on the + button
::choose groups on pulldown menu
::type in a name and add those users you want to belong to the group
::in this case call the group "gaussian"
::exit

==== set-up the terminal ====
::you will find the terminal app in the Utilities folder in your Applications directory
::drag this app onto your Dock, you will be using it a lot!
::open a terminal
::check you are in your home directory type "ls" to list the files/folders

==== set-up your .bashrc_profile ====
::create the file ".bash_profile"
::copy and paste the following into it
<pre>
#echo "bash_profile"
. ~/.bashrc
</pre>

==== set-up your .bashrc ====
::create the file ".bashrc"
::copy and paste the following into it
<pre>
# .bashrc
# WARNING: had to make .bash_profile and added execute to this file
#
# important stuff
#
# tells the computer where to look for personal scripts
export PATH=$PATH:/Users/$USER/bin:/usr/local/bin
#
# change the prompt
export PS1="[\$USER@\h]\$PWD \$ "
#
# control-R lets you search backward through history
HISTSIZE=100
HISTCONTROL=erasedups
HISTIGNORE="cd:exit"
EDITOR=vi
export EDITOR
#
# gaussian
#
# where to fine the executable
export g16root="/Applications"
# set the default memory
export GAUSS_MEMDEF="500MB"
# where to put the LARGE temporary files when running gaussian
export GAUSS_SCRDIR="/Users/$USER/Work/Jobs/tmp"
# script which sets many variables for gaussian
source $g16root/g16/bsd/g16.profile
#
# gaussview
#
# where to find gaussview
export GV_DIR="/Applications/gv"
# libraries
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${GV_DIR}/lib
# allow start from the comand line in mac terminal
alias gv="open $GV_DIR/gview.app"
#
# alias definitions
#
alias home="cd"
alias force="grep -i 'Maximum Force'"
alias dist="grep -i 'Maximum Disp'"
#
</pre>

::edit key lines for the version of gaussian and gaussview that you have
::make sure you have a ~/Work/Jobs/tmp" directory
::type "source ~/.bashrc" into your terminal to active all the alias commands.
::if you are using visualisation tools you may want to add some of the following into your .bashrc
<pre>
#
# image magic
#
export PATH="$PATH:/Applications/ImageMagick-7.0.3/bin"
export MAGICK_HOME="/Applications/ImageMagick-7.0.3"
# export DYLD_LIBRARY_PATH="$MAGICK_HOME/lib/"
#
# multiwfn
#
export KMP_STACKSIZE=64000000
export Multiwfnpath="/Applications/Multiwfn_3.4_bin_Mac"
export DYLD_LIBRARY_PATH=$LD_LIBRARY_PATH:/Applications/Multiwfn
#
# nciplot
#
export NCIPLOT_HOME=/Applications/nciplot-3.0/src/nciplot
export OMP_NUM_THREADS=2
alias nciplot="/Applications/nciplot-3.0/src/nciplot"
#
# vmd
#
alias vmd="open /Applications/VMD_1.9.3.app"
#
</pre>
::again edit key lines for the version of gaussian and gaussview that you have

==== set-up your .login ====
::create the file ".login"
::this is needed because gaussview looks for csh stuff
::copy and paste the following into it
<pre>
setenv g16root /Applications
source $g16root/g16/bsd/g16.login
setenv GAUSS_SCRDIR /Users/$USER/Work/Jobs/tmp
setenv GV_DIR /Applications/gv
setenv GAUSS_EXEDIR /Applications/g16
</pre>
::of course you may need to change version specific information (or directory structure)
::the directory tmp should exist before you run any jobs.

==== set-up working directories ====
::make a directory called "work", keep ALL your files here
::inside work make a directory called "jobs", keep all your gaussian jobs here
::inside work make a directory called "testing" ie full path is /Users/name/work/jobs/testing
::inside work make a directory called tmp (this is where you should direct gaussview to put temporary files)

==== run a test job ====
::cd into your testing directory
::vi a file "test.com" and copy and paste the following into it
::ps don't forget the last line must be blank
<pre>
%chk=test.chk
%mem=500MB
%nproc=1
# hf/3-21g geom=connectivity

Title Card Required

0 1
C
H 1 B1
H 1 B2 2 A1
H 1 B3 3 A2 2 D1
H 1 B4 3 A3 2 D2

B1 1.07000000
B2 1.07000000
B3 1.07000000
B4 1.07000000
A1 109.47120255
A2 109.47125080
A3 109.47121829
D1 -119.99998525
D2 120.00000060

1 2 1.0 3 1.0 4 1.0 5 1.0
2
3
4
5

</pre>

==== For NEW computers: install gaussian ====
::if you are a new user on an existing computer, the groups will already be set up!
::goto the directory where the file is stored
<pre>
cd /Users/tricia/Work/Gaussian_Images/G16_A03_mac
</pre>
::read the "readme" file
::change to the cshell
<pre>
csh
</pre>
::tell the script where gaussian (G16) is to be installed
<pre>
setenv g16root "/Applications"
</pre>
::now goto the g16root directory
<pre>
cd $g16root
</pre>
::read and extract the files
<pre>
bzip2 -d -c /Users/tricia/Work/Gaussian_Images/G16_A03_mac/tar/*.tbz | tar xvf -
</pre>
::this will unpack and copy the contents of the tar file you should see a stream of file names, when this stops and the prompt returns
::ensure that the group permissions are set
<pre>
chgrp -R gaussian g16
</pre>
::check this has worked, type "ls -al"
::you should see a list with something like the following
<pre>
drwxr-x--- 195 tricia gaussian 6630 30 Dec 2016 g16
</pre>
::goto the gaussian directory and run the install script
<pre>
cd g16
./bsd/install
</pre>
::you are not quite ready to run as the variables g16root, GAUSS_SCRDIR and the g16.login script need to be set in your .bashrc file ... this was done in the terminal instructions above
:: you may also want to get rid of the pesky error "-bash: ulimit: open files: cannot modify limit: Invalid argument" which shows up because you have asked "source $g16root/g16/bsd/g16.profile" in your .bashrc
:::goto the direcotry g16/bsd
:::edit the file g16.profile, goto the end and hash out the following command
<pre>
#turned off by tricia to stop error message
#ulimit -n hard
</pre>
::now you are ready to run a test job
:::nohup means don't stop if you logout
:::the trailing & means run in the background
<pre>
cd work/jobs/testing
nohup g09 test &
</pre>
::ls to see that the job is running and that test.chk and test.log files are being generated.
::check that the job finishes ok

====For NEW computers: install gaussview ====
::assuming you are still in shell and that g16root is set
::goto the directory where the file is stored
<pre>
cd /Users/tricia/Mount/GV5_09_mac
cd cd /Users/tricia/Mount/GV6_17_mac
</pre>
::if you look inside these directories you will see the compressed gv files, they are compressed in different ways
::read the "readme" file for each version of gv
::then go back to the g16root directory, this is normally /Applications
::from there unpack the files
<pre>
tar -xvf tar -xvf /Users/tricia/Mount/GV5_09_mac/tar/*.tgz
</pre>
::move the gv directory to gv5
<pre>
bzip2 -d -c /Users/tricia/Mount/GV6_17_mac/*.tbz | tar xvf -
</pre>
::move the gv directory to gv5
::now change the group premisions to the same as those for g09/g16
<pre>
chgrp -R gaussian gv5
chgrp -R gaussian gv6
</pre>

::gaussview uses csh, so you need to have a .login if you want to run from the launcher
::check that you have the following in your .login
::you will need to manually change between gv5 and gv6!
::if you do change your .login you will need to re-execute the .login within csh
<pre>
csh
source .login
</pre>
<pre>
setenv g16root /Applications
source $g16root/g16/bsd/g16.login
setenv GAUSS_SCRDIR /Users/$USER/Work/tmp
setenv GV_DIR /Applications/gv6
#setenv GV_DIR /Applications/gv5
setenv GAUSS_EXEDIR /Applications/g16
#setenv GAUSS_EXEDIR /Applications/g09
</pre>

====For NEW computers: install GMMX ====
::assuming you are still in c-shell and that g16root is set
::goto the directory where the file is stored
<pre>
cd /Users/tricia/Mount/GMMX_MacOSX
</pre>
::double click on the file gmmx-m64.tbz
::this will be expanded into your downloads directory
::drag the gmmx file into the gv folder
::change the group to "gaussian" group (via appleI or via chmod)

====For OLD computers: setup for gaussian and gaussview====
::you will need to be added to the gaussian group on your computer before you have access to gaussview and gaussian
::goto System Preferences
::click on Users and Groups
::unlock this pane by entering an administrators name and password, if you are not an administrator come and see me
::click on Groups (appears after all the users)
::click on the group gaussian and then tick the box next to your name on the right hand panel
::lock and leave this panel
::reboot your computer (this step is required!)
::check to see that you have access to the gaussian and gaussview directories

=====set-up quick starting of gaussview=====
::goto the Applications folder and click on the gv folder
::drag the gaussview icon into the launcher
::double click to start gaussview
::if you get an error saying that it cannot find gaussian directories then
:::cd to the gv directory
:::cd into the data directory
:::edit the gpath.txt file (and give the correct path to the gaussian application)
<pre>
/Applications/g09
</pre>
:::quit gaussview and then restart it, your problem should be fixed

=====set-up preferences=====
::now we need to set some directories in the preferences of gaussview
::click on preferences
::choose the "File?Directory" option
::under the starting directory, choose Specify, click on the "..." button and pick your work/jobs directory
::under the scratch directory, choose "Use GAUSS_SCRDIR"
=====test run a job=====
::start a terminal
::type "gv" in the window (and press return)
::or start gaussview view by clicking on the icon in the Dock
::choose "open" and goto your /work/jobs/testing directory, open your test.com file
::submit it to run (save as test_1.com) so that you don't overwrite the other test job
::check that it finishes OK
::open your test molecule's com file

Mod:Hunt Research Group/mac setup

2020-01-08T13:18:11Z

Phunt:

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]

==== For NEW computers: make a group ====
::if you are a new user on an existing computer, the groups will already be set up!
::open accounts in system prefs
::click on the + button
::choose groups on pulldown menu
::type in a name and add those users you want to belong to the group
::in this case call the group "gaussian"
::exit

==== set-up the terminal ====
::you will find the terminal app in the Utilities folder in your Applications directory
::drag this app onto your Dock, you will be using it a lot!
::open a terminal
::check you are in your home directory type "ls" to list the files/folders

==== set-up your .bashrc_profile ====
::create the file ".bash_profile"
::copy and paste the following into it
<pre>
#echo "bash_profile"
. ~/.bashrc
</pre>

==== set-up your .bashrc ====
::create the file ".bashrc"
::copy and paste the following into it
<pre>
# .bashrc
# WARNING: had to make .bash_profile and added execute to this file
#
# important stuff
#
# tells the computer where to look for personal scripts
export PATH=$PATH:/Users/$USER/bin:/usr/local/bin
#
# change the prompt
export PS1="[\$USER@\h]\$PWD \$ "
#
# control-R lets you search backward through history
HISTSIZE=100
HISTCONTROL=erasedups
HISTIGNORE="cd:exit"
EDITOR=vi
export EDITOR
#
# gaussian
#
# where to fine the executable
export g16root="/Applications"
# set the default memory
export GAUSS_MEMDEF="500MB"
# where to put the LARGE temporary files when running gaussian
export GAUSS_SCRDIR="/Users/$USER/Work/Jobs/tmp"
# script which sets many variables for gaussian
source $g16root/g16/bsd/g16.profile
#
# gaussview
#
# where to find gaussview
export GV_DIR="/Applications/gv"
# libraries
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${GV_DIR}/lib
# allow start from the comand line in mac terminal
alias gv="open $GV_DIR/gview.app"
#
# alias definitions
#
alias home="cd"
alias force="grep -i 'Maximum Force'"
alias dist="grep -i 'Maximum Disp'"
#
</pre>

::edit key lines for the version of gaussian and gaussview that you have
::make sure you have a ~/Work/Jobs/tmp" directory
::type "source ~/.bashrc" into your terminal to active all the alias commands.
::if you are using visualisation tools you may want to add some of the following into your .bashrc
<pre>
#
# image magic
#
export PATH="$PATH:/Applications/ImageMagick-7.0.3/bin"
export MAGICK_HOME="/Applications/ImageMagick-7.0.3"
# export DYLD_LIBRARY_PATH="$MAGICK_HOME/lib/"
#
# multiwfn
#
export KMP_STACKSIZE=64000000
export Multiwfnpath="/Applications/Multiwfn_3.4_bin_Mac"
export DYLD_LIBRARY_PATH=$LD_LIBRARY_PATH:/Applications/Multiwfn
#
# nciplot
#
export NCIPLOT_HOME=/Applications/nciplot-3.0/src/nciplot
export OMP_NUM_THREADS=2
alias nciplot="/Applications/nciplot-3.0/src/nciplot"
#
# vmd
#
alias vmd="open /Applications/VMD_1.9.3.app"
#
</pre>
::again edit key lines for the version of gaussian and gaussview that you have

==== set-up your .login ====
::create the file ".login"
::this is needed because gaussview looks for csh stuff
::copy and paste the following into it
<pre>
setenv g16root /Applications
source $g16root/g16/bsd/g16.login
setenv GAUSS_SCRDIR /Users/$USER/Work/Jobs/tmp
setenv GV_DIR /Applications/gv
setenv GAUSS_EXEDIR /Applications/g16
</pre>
::of course you may need to change version specific information (or directory structure)
::the directory tmp should exist before you run any jobs.

==== set-up working directories ====
::make a directory called "work", keep ALL your files here
::inside work make a directory called "jobs", keep all your gaussian jobs here
::inside work make a directory called "testing" ie full path is /Users/name/work/jobs/testing
::inside work make a directory called tmp (this is where you should direct gaussview to put temporary files)

==== run a test job ====
::cd into your testing directory
::vi a file "test.com" and copy and paste the following into it
::ps don't forget the last line must be blank
<pre>
%chk=test.chk
%mem=500MB
%nproc=1
# hf/3-21g geom=connectivity

Title Card Required

0 1
C
H 1 B1
H 1 B2 2 A1
H 1 B3 3 A2 2 D1
H 1 B4 3 A3 2 D2

B1 1.07000000
B2 1.07000000
B3 1.07000000
B4 1.07000000
A1 109.47120255
A2 109.47125080
A3 109.47121829
D1 -119.99998525
D2 120.00000060

1 2 1.0 3 1.0 4 1.0 5 1.0
2
3
4
5

</pre>

==== For NEW computers: install gaussian ====
::if you are a new user on an existing computer, the groups will already be set up!
::goto the directory where the file is stored
<pre>
cd /Users/tricia/Work/Gaussian_Images/G16_A03_mac
</pre>
::read the "readme" file
::change to the cshell
<pre>
csh
</pre>
::tell the script where gaussian (G16) is to be installed
<pre>
setenv g16root "/Applications"
</pre>
::now goto the g16root directory
<pre>
cd $g16root
</pre>
::read and extract the files
<pre>
bzip2 -d -c /Users/tricia/Work/Gaussian_Images/G16_A03_mac/tar/*.tbz | tar xvf -
</pre>
::this will unpack and copy the contents of the tar file you should see a stream of file names, when this stops and the prompt returns
::ensure that the group permissions are set
<pre>
chgrp -R gaussian g16
</pre>
::check this has worked, type "ls -al"
::you should see a list with something like the following
<pre>
drwxr-x--- 195 tricia gaussian 6630 30 Dec 2016 g16
</pre>
::goto the gaussian directory and run the install script
<pre>
cd g16
./bsd/install
</pre>
::you are not quite ready to run as the variables g16root, GAUSS_SCRDIR and the g16.login script need to be set in your .bashrc file ... this was done in the terminal instructions above
:: you may also want to get rid of the pesky error "-bash: ulimit: open files: cannot modify limit: Invalid argument" which shows up because you have asked "source $g16root/g16/bsd/g16.profile" in your .bashrc
:::goto the direcotry g16/bsd
:::edit the file g16.profile, goto the end and hash out the following command
<pre>
#turned off by tricia to stop error message
#ulimit -n hard
</pre>
::now you are ready to run a test job
:::nohup means don't stop if you logout
:::the trailing & means run in the background
<pre>
cd work/jobs/testing
nohup g09 test &
</pre>
::ls to see that the job is running and that test.chk and test.log files are being generated.
::check that the job finishes ok

====For NEW computers: install gaussview ====
::assuming you are still in shell and that g16root is set
::goto the directory where the file is stored
<pre>
cd /Users/tricia/Mount/GV5_09_mac
cd cd /Users/tricia/Mount/GV6_17_mac
</pre>
::if you look inside these directories you will see the compressed gv files, they are compressed in different ways
::read the "readme" file for each version of gv
::then go back to the g16root directory, this is normally /Applications
::from there unpack the files
<pre>
tar -xvf tar -xvf /Users/tricia/Mount/GV5_09_mac/tar/*.tgz
</pre>
::move the gv directory to gv5
<pre>
bzip2 -d -c /Users/tricia/Mount/GV6_17_mac/*.tbz | tar xvf -
</pre>
::move the gv directory to gv5
::now change the group premisions to the same as those for g09/g16
<pre>
chgrp -R gaussian gv5
chgrp -R gaussian gv6
</pre>

::gaussview uses csh, so you need to have a .login if you want to run from the launcher
::check that you have the following in your .login
::you will need to manually change between gv5 and gv6!
::if you do change your .login you will need to re-execute the .login within csh
<pre>
csh
source .login
</pre>
<pre>
setenv g16root /Applications
source $g16root/g16/bsd/g16.login
setenv GAUSS_SCRDIR /Users/$USER/Work/tmp
setenv GV_DIR /Applications/gv6
#setenv GV_DIR /Applications/gv5
setenv GAUSS_EXEDIR /Applications/g16
#setenv GAUSS_EXEDIR /Applications/g09
</pre>

====For OLD computers: setup for gaussian and gaussview====
::you will need to be added to the gaussian group on your computer before you have access to gaussview and gaussian
::goto System Preferences
::click on Users and Groups
::unlock this pane by entering an administrators name and password, if you are not an administrator come and see me
::click on Groups (appears after all the users)
::click on the group gaussian and then tick the box next to your name on the right hand panel
::lock and leave this panel
::reboot your computer (this step is required!)
::check to see that you have access to the gaussian and gaussview directories

=====set-up quick starting of gaussview=====
::goto the Applications folder and click on the gv folder
::drag the gaussview icon into the launcher
::double click to start gaussview
::if you get an error saying that it cannot find gaussian directories then
:::cd to the gv directory
:::cd into the data directory
:::edit the gpath.txt file (and give the correct path to the gaussian application)
<pre>
/Applications/g09
</pre>
:::quit gaussview and then restart it, your problem should be fixed

=====set-up preferences=====
::now we need to set some directories in the preferences of gaussview
::click on preferences
::choose the "File?Directory" option
::under the starting directory, choose Specify, click on the "..." button and pick your work/jobs directory
::under the scratch directory, choose "Use GAUSS_SCRDIR"
=====test run a job=====
::start a terminal
::type "gv" in the window (and press return)
::or start gaussview view by clicking on the icon in the Dock
::choose "open" and goto your /work/jobs/testing directory, open your test.com file
::submit it to run (save as test_1.com) so that you don't overwrite the other test job
::check that it finishes OK
::open your test molecule's com file

Mod:Hunt Research Group/population

2019-12-28T08:12:24Z

Phunt: Created page with "==Population and Charge Analysis== ===ESP charges=== *using chelpg ::the internal radii are not present for transition metals or heavy elements ::you need to specify these ::m..."

==Population and Charge Analysis==
===ESP charges===
*using chelpg
::the internal radii are not present for transition metals or heavy elements
::you need to specify these
::most van der Waals radii refer back to an article by Bondi in 1964 doi:10.1021/j100785a001
::Batsnov compares radii in 2001 doi:10.1023/A:1011625728803
::Truhlar has improved these with new values for main group in 2009 doi:10.1021/jp8111556

Mod:Hunt Research Group

2019-12-28T07:49:27Z

Phunt: /* Gaussian General */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===Report and Paper Writing===
#procedures [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/report_procedures link]
#advice [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/report_writing link]
#report components [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/report_components link]
#files to provide when writing a paper [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/paper link]

===Group Admin===
#Which files to store on the database and database template [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/database link]
#How to access DROBO [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/drobo link]

===HPC Resources===
#'''Hunt group HPC servers and run scripts''' [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link]
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link]
#How to run jobs interactively [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/run_interactive link]
#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link]
#New gf script (more convenient job submitting) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/new_gf_script link]
#Retired: How to make qsub more comfortable (gfunc) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpQSUB link]
#Tired of entering your password all the time: set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link]
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link]
#Using VPN from home, for Sierra follow the college instructions [[link]]
#How to connect to HPC directory on desktop for file transfers [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_Directory_on_desktop link]
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link]
#How to use a slimmed down terminal on your IPhone [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/termius]

===Using evil Windows and PCs===
#Use Imperial Software Hub to access gaussview and gaussian [http://www.imperial.ac.uk/admin-services/ict/store/software/software-hub/ link]
#Using windows and setting up a connection to HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link]
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link]

===Key Papers, References and Resources===
*'''Papers'''
#Meta study on DFT functionals [https://pubs.acs.org/doi/abs/10.1021/ct401111c doi]
#M06 suite of DFT functionals [https://link.springer.com/article/10.1007/s00214-007-0310-x doi]
#SMD for ILs [https://pubs.acs.org/doi/abs/10.1021/jp304365v doi]
#Box size for MD simulations of ILs [https://dx.doi.org/10.1063/1.4748352 doi]
*'''Notes'''
#Solving the angular part of the Schrödinger equation for a hydrogen atom [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/angular_schrodinger link] (notes by Vincent)
#DFT Workshop Notes [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/DFT_Workshop]
#Cl- in water [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link]
#The use of Legendre time correlation functions to study reorientational dynamics in liquids [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/legendre link]

===Gaussian General===
#We are starting a database of common errors encountered when running Gaussian jobs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gaussian_errors link]
# Here is an already existing database of common errors [https://docs.computecanada.ca/wiki/Gaussian_error_messages link]
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#partial optimisations and scans [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/z-matrix link]
#General procedure for locating transition state structures [[link]]
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link]
#Basic ONIOM (Mechanical Embedding) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/basiconiom link]
#problems with scf convergence [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/scf_convergence link]
#manipulating checkpoint files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:usingchkfiles link]
#for NMR calculations look here: [http://cheshirenmr.info/index.htm Chemical Shift Repository]
#Population and charge analysis [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/population link]

===Gaussian Advanced===
#Systematic conformational scan for ion-pair dimers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ion_pair_scan link]
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link]
#generating natural transition orbitals [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/nto link]
#computing excited state polarisabilities [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_ES_alpha link]
#computing deuterated and/or anharmonic spectra [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_Danharm link]
#How to run at a higher temperature [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:high_temp link]
#Correcting the entropy due to low modes [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:low_modes_entropy link]
#Optimisation of charged molecules in an electric field [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Optimising_charged_molecules_in_electric_fields link]
#Multidimensional Scans of Internal Coordinates [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Multidimensional_Scans_of_Internal_Coordinates link]

===Solvation===
#Using the SMD model [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/solvent link]
#Using SMD on ILs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_Using_SMD_on_ILs link]
#Troublesome optimisations in SMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:troublesome_smd link]
#Atomic radii and solvent models [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/atomic_radii link]
#Molecular volume calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molecular_volume link]
#The cavity [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/solvent_cavity link]
#How to download and use GeomView to visualise solvation cavities [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/geomview link]
#Surfaces (Solvent-Accessible and Connolly) in Jmol [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/jmolsurfaces link]

===Codes to Help Gaussian Analysis===
# Extract last Standard Orientation structure of gaussian log file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_single_geom link]
# Extract last structure of gaussian optimisation and build a freq com file for job with PP [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/build_freq_file link]
# Extract each optimised step from a scan into xyz coordinate file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_scan_geom link]
# Extract geometry and charges (ESP) into a .pdb file for visualising in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ESP_charges_for_VMD link]
# Codes to extract CHELPG and NBO charge values to excel [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/chelpg_extract link]
# Extract ESP and NBO charges [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_ESP_charges link]
# Extract E2 Values (From NBO Calculations) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/NBO_Matlab_Code link]
# Calculate pDoS/XP spectra code (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Calc_XPS_Code link]
#Simple python2 script to simply pull thermodynamic data and low frequencies from log files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:simple_freq_script link]
#Simple python3 script which pulls thermodynamic data and low frequencies from log files to enter into excel template provided for the database [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:model_freq_script link]
#Script to pull thermodynamic data and low frequencies from log files AND evaluate to a reference [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:freq_script link]
# Codes to extract frequency data from gaussian .log files and generate vibrational spectra [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:frequency_spectrum_script link]
# Optimally Tuned Range Seperated Hybrid Functionals [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/OTRSH_Funct link]
# Some G09 Parsers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Some_G09_Parsers link]
# Codes to visualise data matrices (correlation matrices/heatmaps)[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/heatmap link]
#Python API for analysis of Gaussian compuations [https://pygauss.readthedocs.org - Documentation]
# Charge arm [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/charge_arm link]

===QC Visualisation===
*'''Using AIMALL: density based visualisation'''
#download [http://aim.tkgristmill.com AIMALL]
#once downloaded and installed you need to send tricia your aimall-serialnumber.txt file, and she will arrange for a aimallpro.lic or license file for you
#basic instructions [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:aim_basics link]
#AimAll with pseudo potentials [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:aim_pseudopotentials link]
#AIMAll 19.10.12 on iMacs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:AIMAllQuickFix link]

*'''ESPs and manipulating gaussian cube files'''
#Instructions for visualizing electrostatic potentials (Gaussview)[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link]
#Electrostatic Potentials II (Molden) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials_2 link]
#Manipulating cube files [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/cube_files link]
#Format of cube files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/cube_format link]
#Using A. Stone's distributed multipole analysis [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/GDMA link]

*'''NCI plots'''
#get the program here: [http://www.lct.jussieu.fr/pagesperso/contrera/nciplot.html link]
#How to install NCIPlot on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/InstallNCIPlot link]
#Using NCIPlot [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/UseNCIPlot link]

*'''MOs'''
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link]

===Setup and Running Classical MD Simulations===
====dl_poly====
#DLPOLY_4.0 Installation for an IMac [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Installing_DL_POLY_4.09_on_MacOS_Mojave link]
#DLPOLY_Classic Installation for an IMac [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Installing_DL_POLY_classic link]

#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#some basics for getting started using DL_POLY [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dl_poly_basics link]
#control file basics [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/control_basics link]
*useful links
::[https://www.ccp5.ac.uk https://www.ccp5.ac.uk]
::[https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx]
::[ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/USRMAN4.pdf dlpoly4 user manual]
::[ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/JavaGUI.pdf javagui user manual]
::[ftp://ftp.dl.ac.uk/ccp5/DL_POLY/ dlpoly ftp server]
:::you can find test files in DL_POLY_4.0/DATA
:::more info about the dlpoly test files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/DL_POLY_test_files link]

====gromacs====
#GROMACS installing and getting started with gromacs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gromacs_1 link]
#using Agilio Padua force fields for ionic liquids [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/ilff link]
#Packmol installing and running to generate a starting box [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/packmol_1 link]
#initial rough relaxation [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Starting_MD link]
#GROMACS general run [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_run link]
#GROMACS viewing data [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_viewing_MD link]
#GROMACS control file [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_control_MD link]
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link]
====general====
#Getting the Force Field [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Wheretostart link]
#Choosing an Ensemble [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Ensembles link]
#Molten Salt Simulations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/MoltenSaltSimulation link]
#Common Errors [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/CommonErrors link]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link]

===MD Visualisation===
*'''VMD: a molecular dynamics visualisation package'''
#VMD can be installed from the [http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD VMD downloads page]
#Quick reminder [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDReminder link]
#Colour in VMD [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDColor link]
#Changing the graphical representation of your structures [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link]
#VMD indexing [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDindexing link]
#Using scripts in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScripts link]
#Dealing with periodic boundaries and bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsPeriodic link]
#Dealing with bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdBonding link]
#How to turn a Gaussian optimization into a VMD movie [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/VMDmovie link]
#Overlapping two structures [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdVisual link]
*'''Ovito: a molecular dynamics visualisation package'''
#Download Ovito [http://www.ovito.org/index.php/download]
#Using Ovito basics [//wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Ovito_basics link]
*'''SDFs'''
#How to generate SDFs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/sdfs_generate link]

===MD Post processing===
#Python script to convert a HISTORY file into a xyz file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/hist_to_xyz link]
#Python script to reduce the number of steps in a lammps traj file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/lam_to_xyz link]
#Python script to convert a lammps traj file to xyz coordinates and at the same time fold all atoms into a cell and center at the origin [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/lam_fold_xyz link]
#Center the trajectory at a particular atom ('''needs fixing''') [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Recenter link]
#How to generate SDFs with TRAVIS [[Talk:Mod:Hunt Research Group/How to draw SDFs with TRAVIS|link]]
#Tcl script to follow a particular atom [[Talk:Mod:Hunt Research Group/Traj_atom_following|link]]

===Coding===
*'''installing Xcode and other programming environments'''
#to use many programs you will need a compiler, this is not installed by default on your mac
#How to install Xcode on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/InstallXcode link]
#using MacPorts as code for managing other codes on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/MacPorts link]
#HomeBrew and Fink are other options (HomeBrew is not advised for us)
#gfortran on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Gfortran link]
#using python on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/python link]

*'''EMO Code'''
#How to use Ling's emo plot code[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emoplot link]
#How to plot EMOs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emo link]

*'''Jan's charge based analysis Code'''
#charge analysis [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Jan_charges link]
#Obtaining NBO, ESP, and RESP charges [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Charges link]

*'''Oxana's visualisation of ESPs Code'''
#Scripts for reading, saving, manipulating and visualising data from cube files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Python_scripts_for_cube_files link]

*'''Python Genereal'''
# General python recommendations and set up [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/PythonGeneral link]
# Analysis toolkit mainly geared towards processing Gaussian calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Python_Analysis_Tools link]

===Other Codes===
#ADF Submission script [http://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/ADF_sricpt link]
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link]
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/]

===Setup and Running Ab-Initio MD Simulations===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link]
#How to run CPMD to study aqueous solutions [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd_water link]
#How to run CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k_how link]

===Running QM/MM Simulations in ChemShell===
==Tcl-chemshell==
#ChemShell official website which contains the manual and a tutorial [http://www.stfc.ac.uk/CSE/randd/ccg/36254.aspx link]
#Introduction to ChemShell - Copper in water [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Introduction link]
#Defining the system: Cu2+ and its first 2 solvation shells [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_System_Aqeuous_Cu(II) link]
#Defining the force field parameters [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II) link]
#Single point QM/MM energy calculation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_SP_Aqeuous_Cu(II) link]
#QM/MM Optimisation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_OPT_Aqeuous_Cu(II) link]
#QM/MM Molecular Dynamics [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_MD_Aqeuous_Cu(II) link]
#Using MolCluster [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/MolCluster link]
#Running ChemShell [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell link]
#Explaining ChemShell files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files link]
#Step By Step [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Chemshell_Step_By_Step link]
==Py-chemshell==

# Compiling Chemshell and required programs []
# The DL_POLY_4 manual is available for download at this link [ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/USRMAN4.pdf]
# Molecular Mechanics computation with DL_POLY [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:_MM_Single_Point_computation]
# Basic QM/MM single point and optimisations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_QM/MM_Single_Point_and_optimisation]
# Visualise optimisation trajectories in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_Visualising_trajectories_with_VMD]
# Computing Mulliken charges and creating .wfn inputs for AIM analysis [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_Mulliken]

==Admin Stuff==
#Not used to writing a wiki, make your test runs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/testing on this page]
#How to set-up new macs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_setup link]
#How to switch the printer HP CP3525dn duplex on and off [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/printing link]

Mod:Hunt Research Group

2019-12-28T07:48:31Z

Phunt: /* Solvation */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===Report and Paper Writing===
#procedures [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/report_procedures link]
#advice [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/report_writing link]
#report components [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/report_components link]
#files to provide when writing a paper [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/paper link]

===Group Admin===
#Which files to store on the database and database template [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/database link]
#How to access DROBO [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/drobo link]

===HPC Resources===
#'''Hunt group HPC servers and run scripts''' [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link]
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link]
#How to run jobs interactively [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/run_interactive link]
#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link]
#New gf script (more convenient job submitting) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/new_gf_script link]
#Retired: How to make qsub more comfortable (gfunc) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpQSUB link]
#Tired of entering your password all the time: set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link]
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link]
#Using VPN from home, for Sierra follow the college instructions [[link]]
#How to connect to HPC directory on desktop for file transfers [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_Directory_on_desktop link]
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link]
#How to use a slimmed down terminal on your IPhone [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/termius]

===Using evil Windows and PCs===
#Use Imperial Software Hub to access gaussview and gaussian [http://www.imperial.ac.uk/admin-services/ict/store/software/software-hub/ link]
#Using windows and setting up a connection to HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link]
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link]

===Key Papers, References and Resources===
*'''Papers'''
#Meta study on DFT functionals [https://pubs.acs.org/doi/abs/10.1021/ct401111c doi]
#M06 suite of DFT functionals [https://link.springer.com/article/10.1007/s00214-007-0310-x doi]
#SMD for ILs [https://pubs.acs.org/doi/abs/10.1021/jp304365v doi]
#Box size for MD simulations of ILs [https://dx.doi.org/10.1063/1.4748352 doi]
*'''Notes'''
#Solving the angular part of the Schrödinger equation for a hydrogen atom [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/angular_schrodinger link] (notes by Vincent)
#DFT Workshop Notes [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/DFT_Workshop]
#Cl- in water [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link]
#The use of Legendre time correlation functions to study reorientational dynamics in liquids [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/legendre link]

===Gaussian General===
#We are starting a database of common errors encountered when running Gaussian jobs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gaussian_errors link]
# Here is an already existing database of common errors [https://docs.computecanada.ca/wiki/Gaussian_error_messages link]
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#partial optimisations and scans [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/z-matrix link]
#General procedure for locating transition state structures [[link]]
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link]
#Basic ONIOM (Mechanical Embedding) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/basiconiom link]
#problems with scf convergence [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/scf_convergence link]
#manipulating checkpoint files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:usingchkfiles link]
#for NMR calculations look here: [http://cheshirenmr.info/index.htm Chemical Shift Repository]

===Gaussian Advanced===
#Systematic conformational scan for ion-pair dimers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ion_pair_scan link]
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link]
#generating natural transition orbitals [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/nto link]
#computing excited state polarisabilities [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_ES_alpha link]
#computing deuterated and/or anharmonic spectra [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_Danharm link]
#How to run at a higher temperature [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:high_temp link]
#Correcting the entropy due to low modes [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:low_modes_entropy link]
#Optimisation of charged molecules in an electric field [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Optimising_charged_molecules_in_electric_fields link]
#Multidimensional Scans of Internal Coordinates [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Multidimensional_Scans_of_Internal_Coordinates link]

===Solvation===
#Using the SMD model [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/solvent link]
#Using SMD on ILs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_Using_SMD_on_ILs link]
#Troublesome optimisations in SMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:troublesome_smd link]
#Atomic radii and solvent models [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/atomic_radii link]
#Molecular volume calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molecular_volume link]
#The cavity [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/solvent_cavity link]
#How to download and use GeomView to visualise solvation cavities [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/geomview link]
#Surfaces (Solvent-Accessible and Connolly) in Jmol [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/jmolsurfaces link]

===Codes to Help Gaussian Analysis===
# Extract last Standard Orientation structure of gaussian log file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_single_geom link]
# Extract last structure of gaussian optimisation and build a freq com file for job with PP [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/build_freq_file link]
# Extract each optimised step from a scan into xyz coordinate file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_scan_geom link]
# Extract geometry and charges (ESP) into a .pdb file for visualising in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ESP_charges_for_VMD link]
# Codes to extract CHELPG and NBO charge values to excel [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/chelpg_extract link]
# Extract ESP and NBO charges [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_ESP_charges link]
# Extract E2 Values (From NBO Calculations) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/NBO_Matlab_Code link]
# Calculate pDoS/XP spectra code (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Calc_XPS_Code link]
#Simple python2 script to simply pull thermodynamic data and low frequencies from log files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:simple_freq_script link]
#Simple python3 script which pulls thermodynamic data and low frequencies from log files to enter into excel template provided for the database [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:model_freq_script link]
#Script to pull thermodynamic data and low frequencies from log files AND evaluate to a reference [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:freq_script link]
# Codes to extract frequency data from gaussian .log files and generate vibrational spectra [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:frequency_spectrum_script link]
# Optimally Tuned Range Seperated Hybrid Functionals [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/OTRSH_Funct link]
# Some G09 Parsers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Some_G09_Parsers link]
# Codes to visualise data matrices (correlation matrices/heatmaps)[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/heatmap link]
#Python API for analysis of Gaussian compuations [https://pygauss.readthedocs.org - Documentation]
# Charge arm [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/charge_arm link]

===QC Visualisation===
*'''Using AIMALL: density based visualisation'''
#download [http://aim.tkgristmill.com AIMALL]
#once downloaded and installed you need to send tricia your aimall-serialnumber.txt file, and she will arrange for a aimallpro.lic or license file for you
#basic instructions [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:aim_basics link]
#AimAll with pseudo potentials [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:aim_pseudopotentials link]
#AIMAll 19.10.12 on iMacs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:AIMAllQuickFix link]

*'''ESPs and manipulating gaussian cube files'''
#Instructions for visualizing electrostatic potentials (Gaussview)[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link]
#Electrostatic Potentials II (Molden) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials_2 link]
#Manipulating cube files [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/cube_files link]
#Format of cube files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/cube_format link]
#Using A. Stone's distributed multipole analysis [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/GDMA link]

*'''NCI plots'''
#get the program here: [http://www.lct.jussieu.fr/pagesperso/contrera/nciplot.html link]
#How to install NCIPlot on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/InstallNCIPlot link]
#Using NCIPlot [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/UseNCIPlot link]

*'''MOs'''
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link]

===Setup and Running Classical MD Simulations===
====dl_poly====
#DLPOLY_4.0 Installation for an IMac [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Installing_DL_POLY_4.09_on_MacOS_Mojave link]
#DLPOLY_Classic Installation for an IMac [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Installing_DL_POLY_classic link]

#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#some basics for getting started using DL_POLY [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dl_poly_basics link]
#control file basics [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/control_basics link]
*useful links
::[https://www.ccp5.ac.uk https://www.ccp5.ac.uk]
::[https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx]
::[ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/USRMAN4.pdf dlpoly4 user manual]
::[ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/JavaGUI.pdf javagui user manual]
::[ftp://ftp.dl.ac.uk/ccp5/DL_POLY/ dlpoly ftp server]
:::you can find test files in DL_POLY_4.0/DATA
:::more info about the dlpoly test files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/DL_POLY_test_files link]

====gromacs====
#GROMACS installing and getting started with gromacs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gromacs_1 link]
#using Agilio Padua force fields for ionic liquids [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/ilff link]
#Packmol installing and running to generate a starting box [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/packmol_1 link]
#initial rough relaxation [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Starting_MD link]
#GROMACS general run [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_run link]
#GROMACS viewing data [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_viewing_MD link]
#GROMACS control file [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_control_MD link]
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link]
====general====
#Getting the Force Field [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Wheretostart link]
#Choosing an Ensemble [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Ensembles link]
#Molten Salt Simulations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/MoltenSaltSimulation link]
#Common Errors [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/CommonErrors link]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link]

===MD Visualisation===
*'''VMD: a molecular dynamics visualisation package'''
#VMD can be installed from the [http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD VMD downloads page]
#Quick reminder [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDReminder link]
#Colour in VMD [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDColor link]
#Changing the graphical representation of your structures [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link]
#VMD indexing [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDindexing link]
#Using scripts in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScripts link]
#Dealing with periodic boundaries and bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsPeriodic link]
#Dealing with bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdBonding link]
#How to turn a Gaussian optimization into a VMD movie [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/VMDmovie link]
#Overlapping two structures [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdVisual link]
*'''Ovito: a molecular dynamics visualisation package'''
#Download Ovito [http://www.ovito.org/index.php/download]
#Using Ovito basics [//wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Ovito_basics link]
*'''SDFs'''
#How to generate SDFs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/sdfs_generate link]

===MD Post processing===
#Python script to convert a HISTORY file into a xyz file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/hist_to_xyz link]
#Python script to reduce the number of steps in a lammps traj file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/lam_to_xyz link]
#Python script to convert a lammps traj file to xyz coordinates and at the same time fold all atoms into a cell and center at the origin [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/lam_fold_xyz link]
#Center the trajectory at a particular atom ('''needs fixing''') [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Recenter link]
#How to generate SDFs with TRAVIS [[Talk:Mod:Hunt Research Group/How to draw SDFs with TRAVIS|link]]
#Tcl script to follow a particular atom [[Talk:Mod:Hunt Research Group/Traj_atom_following|link]]

===Coding===
*'''installing Xcode and other programming environments'''
#to use many programs you will need a compiler, this is not installed by default on your mac
#How to install Xcode on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/InstallXcode link]
#using MacPorts as code for managing other codes on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/MacPorts link]
#HomeBrew and Fink are other options (HomeBrew is not advised for us)
#gfortran on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Gfortran link]
#using python on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/python link]

*'''EMO Code'''
#How to use Ling's emo plot code[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emoplot link]
#How to plot EMOs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emo link]

*'''Jan's charge based analysis Code'''
#charge analysis [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Jan_charges link]
#Obtaining NBO, ESP, and RESP charges [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Charges link]

*'''Oxana's visualisation of ESPs Code'''
#Scripts for reading, saving, manipulating and visualising data from cube files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Python_scripts_for_cube_files link]

*'''Python Genereal'''
# General python recommendations and set up [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/PythonGeneral link]
# Analysis toolkit mainly geared towards processing Gaussian calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Python_Analysis_Tools link]

===Other Codes===
#ADF Submission script [http://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/ADF_sricpt link]
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link]
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/]

===Setup and Running Ab-Initio MD Simulations===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link]
#How to run CPMD to study aqueous solutions [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd_water link]
#How to run CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k_how link]

===Running QM/MM Simulations in ChemShell===
==Tcl-chemshell==
#ChemShell official website which contains the manual and a tutorial [http://www.stfc.ac.uk/CSE/randd/ccg/36254.aspx link]
#Introduction to ChemShell - Copper in water [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Introduction link]
#Defining the system: Cu2+ and its first 2 solvation shells [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_System_Aqeuous_Cu(II) link]
#Defining the force field parameters [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II) link]
#Single point QM/MM energy calculation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_SP_Aqeuous_Cu(II) link]
#QM/MM Optimisation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_OPT_Aqeuous_Cu(II) link]
#QM/MM Molecular Dynamics [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_MD_Aqeuous_Cu(II) link]
#Using MolCluster [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/MolCluster link]
#Running ChemShell [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell link]
#Explaining ChemShell files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files link]
#Step By Step [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Chemshell_Step_By_Step link]
==Py-chemshell==

# Compiling Chemshell and required programs []
# The DL_POLY_4 manual is available for download at this link [ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/USRMAN4.pdf]
# Molecular Mechanics computation with DL_POLY [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:_MM_Single_Point_computation]
# Basic QM/MM single point and optimisations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_QM/MM_Single_Point_and_optimisation]
# Visualise optimisation trajectories in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_Visualising_trajectories_with_VMD]
# Computing Mulliken charges and creating .wfn inputs for AIM analysis [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_Mulliken]

==Admin Stuff==
#Not used to writing a wiki, make your test runs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/testing on this page]
#How to set-up new macs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_setup link]
#How to switch the printer HP CP3525dn duplex on and off [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/printing link]

Mod:Hunt Research Group

2019-12-24T14:16:53Z

Phunt: /* Key Papers, References and Resources */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===Report and Paper Writing===
#procedures [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/report_procedures link]
#advice [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/report_writing link]
#report components [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/report_components link]
#files to provide when writing a paper [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/paper link]

===Group Admin===
#Which files to store on the database and database template [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/database link]
#How to access DROBO [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/drobo link]

===HPC Resources===
#'''Hunt group HPC servers and run scripts''' [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link]
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link]
#How to run jobs interactively [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/run_interactive link]
#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link]
#New gf script (more convenient job submitting) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/new_gf_script link]
#Retired: How to make qsub more comfortable (gfunc) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpQSUB link]
#Tired of entering your password all the time: set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link]
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link]
#Using VPN from home, for Sierra follow the college instructions [[link]]
#How to connect to HPC directory on desktop for file transfers [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_Directory_on_desktop link]
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link]
#How to use a slimmed down terminal on your IPhone [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/termius]

===Using evil Windows and PCs===
#Use Imperial Software Hub to access gaussview and gaussian [http://www.imperial.ac.uk/admin-services/ict/store/software/software-hub/ link]
#Using windows and setting up a connection to HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link]
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link]

===Key Papers, References and Resources===
*'''Papers'''
#Meta study on DFT functionals [https://pubs.acs.org/doi/abs/10.1021/ct401111c doi]
#M06 suite of DFT functionals [https://link.springer.com/article/10.1007/s00214-007-0310-x doi]
#SMD for ILs [https://pubs.acs.org/doi/abs/10.1021/jp304365v doi]
#Box size for MD simulations of ILs [https://dx.doi.org/10.1063/1.4748352 doi]
*'''Notes'''
#Solving the angular part of the Schrödinger equation for a hydrogen atom [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/angular_schrodinger link] (notes by Vincent)
#DFT Workshop Notes [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/DFT_Workshop]
#Cl- in water [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link]
#The use of Legendre time correlation functions to study reorientational dynamics in liquids [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/legendre link]

===Gaussian General===
#We are starting a database of common errors encountered when running Gaussian jobs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gaussian_errors link]
# Here is an already existing database of common errors [https://docs.computecanada.ca/wiki/Gaussian_error_messages link]
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#partial optimisations and scans [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/z-matrix link]
#General procedure for locating transition state structures [[link]]
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link]
#Basic ONIOM (Mechanical Embedding) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/basiconiom link]
#problems with scf convergence [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/scf_convergence link]
#manipulating checkpoint files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:usingchkfiles link]
#for NMR calculations look here: [http://cheshirenmr.info/index.htm Chemical Shift Repository]

===Gaussian Advanced===
#Systematic conformational scan for ion-pair dimers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ion_pair_scan link]
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link]
#generating natural transition orbitals [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/nto link]
#computing excited state polarisabilities [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_ES_alpha link]
#computing deuterated and/or anharmonic spectra [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_Danharm link]
#How to run at a higher temperature [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:high_temp link]
#Correcting the entropy due to low modes [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:low_modes_entropy link]
#Optimisation of charged molecules in an electric field [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Optimising_charged_molecules_in_electric_fields link]
#Multidimensional Scans of Internal Coordinates [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Multidimensional_Scans_of_Internal_Coordinates link]

===Solvation===
#Using solvent models [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/solvent link]
#Using SMD on ILs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_Using_SMD_on_ILs link]
#Troublesome optimisations in SMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:troublesome_smd link]
#Atomic radii and solvent models [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/atomic_radii link]
#Molecular volume calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molecular_volume link]
#The cavity [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/solvent_cavity link]
#How to download and use GeomView to visualise solvation cavities [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/geomview link]
#Surfaces (Solvent-Accessible and Connolly) in Jmol [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/jmolsurfaces link]

===Codes to Help Gaussian Analysis===
# Extract last Standard Orientation structure of gaussian log file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_single_geom link]
# Extract last structure of gaussian optimisation and build a freq com file for job with PP [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/build_freq_file link]
# Extract each optimised step from a scan into xyz coordinate file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_scan_geom link]
# Extract geometry and charges (ESP) into a .pdb file for visualising in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ESP_charges_for_VMD link]
# Codes to extract CHELPG and NBO charge values to excel [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/chelpg_extract link]
# Extract ESP and NBO charges [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_ESP_charges link]
# Extract E2 Values (From NBO Calculations) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/NBO_Matlab_Code link]
# Calculate pDoS/XP spectra code (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Calc_XPS_Code link]
#Simple python2 script to simply pull thermodynamic data and low frequencies from log files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:simple_freq_script link]
#Simple python3 script which pulls thermodynamic data and low frequencies from log files to enter into excel template provided for the database [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:model_freq_script link]
#Script to pull thermodynamic data and low frequencies from log files AND evaluate to a reference [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:freq_script link]
# Codes to extract frequency data from gaussian .log files and generate vibrational spectra [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:frequency_spectrum_script link]
# Optimally Tuned Range Seperated Hybrid Functionals [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/OTRSH_Funct link]
# Some G09 Parsers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Some_G09_Parsers link]
# Codes to visualise data matrices (correlation matrices/heatmaps)[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/heatmap link]
#Python API for analysis of Gaussian compuations [https://pygauss.readthedocs.org - Documentation]
# Charge arm [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/charge_arm link]

===QC Visualisation===
*'''Using AIMALL: density based visualisation'''
#download [http://aim.tkgristmill.com AIMALL]
#once downloaded and installed you need to send tricia your aimall-serialnumber.txt file, and she will arrange for a aimallpro.lic or license file for you
#basic instructions [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:aim_basics link]
#AimAll with pseudo potentials [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:aim_pseudopotentials link]
#AIMAll 19.10.12 on iMacs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:AIMAllQuickFix link]

*'''ESPs and manipulating gaussian cube files'''
#Instructions for visualizing electrostatic potentials (Gaussview)[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link]
#Electrostatic Potentials II (Molden) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials_2 link]
#Manipulating cube files [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/cube_files link]
#Format of cube files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/cube_format link]
#Using A. Stone's distributed multipole analysis [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/GDMA link]

*'''NCI plots'''
#get the program here: [http://www.lct.jussieu.fr/pagesperso/contrera/nciplot.html link]
#How to install NCIPlot on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/InstallNCIPlot link]
#Using NCIPlot [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/UseNCIPlot link]

*'''MOs'''
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link]

===Setup and Running Classical MD Simulations===
====dl_poly====
#DLPOLY_4.0 Installation for an IMac [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Installing_DL_POLY_4.09_on_MacOS_Mojave link]
#DLPOLY_Classic Installation for an IMac [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Installing_DL_POLY_classic link]

#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#some basics for getting started using DL_POLY [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dl_poly_basics link]
#control file basics [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/control_basics link]
*useful links
::[https://www.ccp5.ac.uk https://www.ccp5.ac.uk]
::[https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx]
::[ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/USRMAN4.pdf dlpoly4 user manual]
::[ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/JavaGUI.pdf javagui user manual]
::[ftp://ftp.dl.ac.uk/ccp5/DL_POLY/ dlpoly ftp server]
:::you can find test files in DL_POLY_4.0/DATA
:::more info about the dlpoly test files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/DL_POLY_test_files link]

====gromacs====
#GROMACS installing and getting started with gromacs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gromacs_1 link]
#using Agilio Padua force fields for ionic liquids [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/ilff link]
#Packmol installing and running to generate a starting box [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/packmol_1 link]
#initial rough relaxation [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Starting_MD link]
#GROMACS general run [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_run link]
#GROMACS viewing data [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_viewing_MD link]
#GROMACS control file [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_control_MD link]
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link]
====general====
#Getting the Force Field [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Wheretostart link]
#Choosing an Ensemble [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Ensembles link]
#Molten Salt Simulations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/MoltenSaltSimulation link]
#Common Errors [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/CommonErrors link]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link]

===MD Visualisation===
*'''VMD: a molecular dynamics visualisation package'''
#VMD can be installed from the [http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD VMD downloads page]
#Quick reminder [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDReminder link]
#Colour in VMD [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDColor link]
#Changing the graphical representation of your structures [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link]
#VMD indexing [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDindexing link]
#Using scripts in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScripts link]
#Dealing with periodic boundaries and bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsPeriodic link]
#Dealing with bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdBonding link]
#How to turn a Gaussian optimization into a VMD movie [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/VMDmovie link]
#Overlapping two structures [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdVisual link]
*'''Ovito: a molecular dynamics visualisation package'''
#Download Ovito [http://www.ovito.org/index.php/download]
#Using Ovito basics [//wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Ovito_basics link]
*'''SDFs'''
#How to generate SDFs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/sdfs_generate link]

===MD Post processing===
#Python script to convert a HISTORY file into a xyz file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/hist_to_xyz link]
#Python script to reduce the number of steps in a lammps traj file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/lam_to_xyz link]
#Python script to convert a lammps traj file to xyz coordinates and at the same time fold all atoms into a cell and center at the origin [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/lam_fold_xyz link]
#Center the trajectory at a particular atom ('''needs fixing''') [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Recenter link]
#How to generate SDFs with TRAVIS [[Talk:Mod:Hunt Research Group/How to draw SDFs with TRAVIS|link]]
#Tcl script to follow a particular atom [[Talk:Mod:Hunt Research Group/Traj_atom_following|link]]

===Coding===
*'''installing Xcode and other programming environments'''
#to use many programs you will need a compiler, this is not installed by default on your mac
#How to install Xcode on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/InstallXcode link]
#using MacPorts as code for managing other codes on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/MacPorts link]
#HomeBrew and Fink are other options (HomeBrew is not advised for us)
#gfortran on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Gfortran link]
#using python on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/python link]

*'''EMO Code'''
#How to use Ling's emo plot code[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emoplot link]
#How to plot EMOs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emo link]

*'''Jan's charge based analysis Code'''
#charge analysis [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Jan_charges link]
#Obtaining NBO, ESP, and RESP charges [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Charges link]

*'''Oxana's visualisation of ESPs Code'''
#Scripts for reading, saving, manipulating and visualising data from cube files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Python_scripts_for_cube_files link]

*'''Python Genereal'''
# General python recommendations and set up [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/PythonGeneral link]
# Analysis toolkit mainly geared towards processing Gaussian calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Python_Analysis_Tools link]

===Other Codes===
#ADF Submission script [http://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/ADF_sricpt link]
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link]
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/]

===Setup and Running Ab-Initio MD Simulations===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link]
#How to run CPMD to study aqueous solutions [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd_water link]
#How to run CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k_how link]

===Running QM/MM Simulations in ChemShell===
==Tcl-chemshell==
#ChemShell official website which contains the manual and a tutorial [http://www.stfc.ac.uk/CSE/randd/ccg/36254.aspx link]
#Introduction to ChemShell - Copper in water [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Introduction link]
#Defining the system: Cu2+ and its first 2 solvation shells [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_System_Aqeuous_Cu(II) link]
#Defining the force field parameters [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II) link]
#Single point QM/MM energy calculation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_SP_Aqeuous_Cu(II) link]
#QM/MM Optimisation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_OPT_Aqeuous_Cu(II) link]
#QM/MM Molecular Dynamics [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_MD_Aqeuous_Cu(II) link]
#Using MolCluster [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/MolCluster link]
#Running ChemShell [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell link]
#Explaining ChemShell files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files link]
#Step By Step [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Chemshell_Step_By_Step link]
==Py-chemshell==

# Compiling Chemshell and required programs []
# The DL_POLY_4 manual is available for download at this link [ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/USRMAN4.pdf]
# Molecular Mechanics computation with DL_POLY [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:_MM_Single_Point_computation]
# Basic QM/MM single point and optimisations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_QM/MM_Single_Point_and_optimisation]
# Visualise optimisation trajectories in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_Visualising_trajectories_with_VMD]
# Computing Mulliken charges and creating .wfn inputs for AIM analysis [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_Mulliken]

==Admin Stuff==
#Not used to writing a wiki, make your test runs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/testing on this page]
#How to set-up new macs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_setup link]
#How to switch the printer HP CP3525dn duplex on and off [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/printing link]

Mod:Hunt Research Group: Using SMD on ILs

2019-12-23T11:43:24Z

Phunt:

This page explains how to use the SMD model to simulate an ionic liquid environment in Gaussian calculations. The SMD model is explained in detail in the original paper here.<ref name="Marenich"> Marenich 2009 http://pubs.acs.org/doi/abs/10.1021/jp810292n</ref> Its use on ILs is similarly explained here.<ref name="Bernales">Bernales 2012 http://pubs.acs.org/doi/abs/10.1021/jp304365v</ref> Many useful solvent parameters are also available in this paper.

== How to simulate a defined solvent environment ==
Gaussian has many previously defined solvent environments. A list is available at the bottom of this page.<ref>http://www.gaussian.com/g_tech/g_ur/k_scrf.htm</ref> For example to use the pre-defined water environment simply insert the following keyword into the method line of your input file. The rest of your method line should specify your functional, basis set, optimisation/other type of calculation as usual.
scrf=(smd,solvent=water)
To use a different solvent to water change the solvent=water part to solvent=something else in the list.

== How to simulate a generic solvent environment ==
The SMD model has many parameters. These are already defined inside Gaussian for the list of defined solvents. If you want to use a solvent not on the list e.g. an ionic liquid, you must define these parameters manually. In this case put the following into the method line:
scrf=(smd,solvent=generic)

===Solvent parameters===
{| class="wikitable"
!Parameter
!Symbol
!Name in Gaussian input file
|-
|Dielectric constant
|ε
|eps
|-
|Index of refraction, squared
|n2
|epsinf
|-
|Macroscopic surface tension /cal mol-1 Å-2
|γ
|SurfaceTensionAtInterface
|-
|Abraham hydrogen bond acidity parameter
|Σα2H
|HBondAcidity
|-
|Abraham hydrogen bond basicity parameter
|Σβ2H
|HBondBasicity
|-
|Fraction of non-hydrogen atoms which are aromatic carbon atoms
|φ
|CarbonAromaticity
|
|-
|Fraction of non-hydrogen atoms which are electronegative halogen atoms
|ψ
|ElectronegativeHalogenicity
|
|}

===Notes on parameters===
Surface tension
*surface tension is the only parameter with units, those used in SMD are non-standard cal mol-1Å-2
*the SI units are Jm-2 or Nm-1
*typical units are dyn cm-1 where 1 dyn = 1 g cm s-2
*as we tend to work in kJ/mol the energy part of this becomes not J but J/mol
*1 dyn cm-1 = 0.001N m-1 = 0.001J m-2
*1 m = 1*1010Å and 1J=0.239cal and 1 mol-1=6.022*1023
*1 dyn cm-1 = 0.001*0.239cal*6.022*1023mol-1/(1*102*10Å2
*and if you think about this 1023 on top line cancels with 1020 on bottom line leaving 103 which cancels with the 0.001=10-3 leaving us with 0.239*6.022=1.439
*1 dyn cm-1 = 1.439 cal mol-1 Å-2

Molar Volume
* MolarVolume=x.x in cm3/mol
* molecular volume in Å3 per molecule converted to cm3/mol
* 1cm = 1*108Å, 1Å = 1*10-8 cm
* x Å3 per molecule = x*6.022*1023mol-1 *103*-8cm3 = x*6.022*10-1cm3mol-1

Kamlet-Taft vs Abraham H-bonding parameters
*the SMD model requires Abraham H-bondonding parameters (Σα2H, Σβ2H)
*however Kamlet-Taft (α, β) measurements are more commonly reported for ILs
*a relationship between the parameters was investigated, giving the following equations:<ref name="Bernales" />

Σα2H = 0.4098α + 0.0064

Σβ2H = 0.6138β + 0.0890

Previously the group has developed a simple method for calculating Kamlet-Taft parameters, and the instructions are here.<ref>http://www.huntresearchgroup.org.uk/research/research_il_alpha_beta_intro.html</ref>

===Types of SMD model for ILs===
3 types of SMD for ILs have been defined.<ref name="Bernales" />
*SMD The standard SMD model. All parameters are determined for the particular IL (or a very similar one) being used as the solvent environment.
*SMD-GIL The generic ionic liquid model. The average values above are used for all parameters, except φ and ψ, which are simply calculated from the chemical formula of the IL.
*SMD-PGPThe partial generic parameters model. Any parameter which has been measured for that IL is used. For any parameters which you do not have values for, use the average values.

Example: [C4C1Im][NTf2] 
*All parameters for this IL have been measured, and can be found in reference 2.<ref name="Bernales" /> That means we can use the standard SMD method.
*To get a value for φ take the number of aromatic carbon atoms (3) and divide by the number of non-hydrogen atoms (25). φ = 0.12.
*To get a value for ψ take the number of electronegative halogen atoms (6) and divide by the number of non-hydrogen atoms (25). ψ = 0.24.
*To define these parameters place the following line at the bottom of the input file (include one blank line before and at least one blank line after):
* eps=11.52 epsinf=2.037 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.12 ElectronegativeHalogenicity=0.24
*see following data for other ILs

== SMD input database ==
Here we will keep a database of SMD parameters used by the group. Please add any IL you use, so no-one else has to re-do the research for the parameters! Please follow the template provided so that it is clear where you get each value from.

=== SMD-GIL ===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.50
|
|
|-
|epsinf (n2)
|2.0449
|
|
|-
|SurfaceTensionAtInterface
|61.24
|
|
|-
|HBondAcidity (α)
|0.229
|
|
|-
|HBondBasicity (β)
|0.265
|
|
|-
|CarbonAromaticity (φ)
|compute for your system
|
|
|-
|ElectronegativeHalogenicity (ψ)
|compute for your system
|
|
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][BF4]===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.70
|
|
|-
|epsinf n2)
|2.0207
|
|Value given in reference is n=1.4215, it has been squared to give epsinf=2.0207
|-
|SurfaceTensionAtInterface
|67.07
|
|
|-
|HBondAcidity (α)
|0.263
|
| Kamlet-Taft 0.627
|-
|HBondBasicity (β)
|0.320
|
| Kamlet-Taft 0.376
|-
|CarbonAromaticity (φ)
|0.2000
|
|There are 15 non-H atoms, 3 are aromatic C atoms, value=3/15=0.2000
|-
|ElectronegativeHalogenicity (ψ)
|0.2667
|
|There are 15 non-H atoms, 4 are electronegative halogen atoms, value =4/15=0.2667
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][PF6]===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.40
|
|
|-
|epsinf n2)
|1.9853
|
|Value given in reference is n=1.4090, it has been squared to give epsinf=1.9853
|-
|SurfaceTensionAtInterface
|70.24
|
|
|-
|HBondAcidity (α)
|0.266
|
| Kamlet-Taft 0.634
|-
|HBondBasicity (β)
|0.216
|
| Kamlet-Taft 0.207
|-
|CarbonAromaticity (φ)
|0.1765
|
|There are 17 non-H atoms, 3 are aromatic C atoms, value=3/17=0.1765
|-
|ElectronegativeHalogenicity (ψ)
|0.3529
|
|There are 17 non-H atoms, 4 are electronegative halogen atoms, value =6/17=0.3529
|-
| colspan="4" |<code>eps=11.40 epsinf=1.9853 SurfaceTensionAtInterface=70.24 HBondAcidity=0.266 HBondBasicity=0.216 CarbonAromaticity=0.1765 ElectronegativeHalogenicity=0.3529</code>
|}

=== [C4C1Im][NTf2] ===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.52
|<ref name="Daguenet">Daguenet 2006 http://pubs.acs.org/doi/abs/10.1021/jp0604903</ref>
|
|-
|epsinf n2)
|2.0366
|<ref name="Huddleston">Huddleston 2001 http://pubs.rsc.org/en/Content/ArticleLanding/2001/GC/b103275p</ref>
|Value given in reference is n=1.4271, it has been squared to give epsinf=2.0366
|-
|SurfaceTensionAtInterface
|53.97
|<ref name="Huddleston" />
|
|-
|HBondAcidity (α)
|0.259
|<ref name="Marenich"/>
| Kamlet-Taft 0.617
|-
|HBondBasicity (β)
|0.238
|<ref name="Marenich" />
| Kamlet-Taft 0.243
|-
|CarbonAromaticity
|0.1200
|
|There are 25 non-H atoms, 3 are aromatic C atoms, value =3/25=0.1200
|-
|ElectronegativeHalogenicity
|0.2400
|
|There are 25 non-H atoms, 6 are electronegative halogen atoms, value =6/25=0.2400
|-
| colspan="4" |<code>eps=11.52 epsinf=2.0366 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.1200 ElectronegativeHalogenicity=0.2400</code>
|}

=== [C4C1Im][OTf] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|12.90
|<ref name="Huang"> M. M. Huang, Y. P. Jiang, P. Sasisanker, G. W. Driver and H. Weingartner,  J. Chem. Eng. Data, 2011, 56, 1494–1499. http://pubs.acs.org/doi/abs/10.1021/je101184s</ref>
|Page 1495, number 11 on the list.
|-
|epsinf n2)
|2.0665
|<ref name="Gonzalez"> Gonzalez 2012 http://pubs.acs.org/doi/abs/10.1021/je201334p</ref>
|n=1.43755, has been squared to give epsinf=2.0665. Can be found in Table 1, 3rd row.
|-
|SurfaceTensionAtInterface
|unknown
|
|-
|HBondAcidity (α)
|0.263
|<ref name="Bernales" /> <ref name="Marenich" />
| Kamlet-Taft 0.625
|-
|HBondBasicity (β)
|0.374
|<ref name="Bernales" /> <ref name="Marenich" />
| Kamlet-Taft 0.464
|-
|CarbonAromaticity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are aromatic C atoms, value=3/18=0.1667.
|-
|ElectronegativeHalogenicity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are electronegative halogen atoms, value=3/18=0.1667.
|-
| colspan="4" |<code>eps=12.90 epsinf=2.0665 SurfaceTensionAtInterface'''=XX''' HBondAcidity=0.263 HBondBasicity=0.374 CarbonAromaticity=0.1667 ElectronegativeHalogenicity=0.1667</code>
|}

=== [C4C1Im][SCN] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|13.70
| <ref name="Huang" />
|
|-
|epsinf (n2)
|2.3691
| <ref name="Vakili">G. Vakili-Nezhaad, M. Vatani, M. Asghari and I. Ashour, J. Chem. Thermodyn., 2012, 54, 148–154. </ref>
|n=1.53921, has been squared to give epsinf=2.3691 (error in some database calcs with n=1.5436 n2=2.3827)
|-
|SurfaceTensionAtInterface
|68.34
| <ref name="Vakili" />
| η=45.41 (mN.m-1) converts to 45.41*1.439= cal mol-1 Å-2=65.34
|-
|HBondAcidity (α)
|0.18
|
| Kamlet-Taft 0.43
|-
|HBondBasicity (β)
|0.52
|
| Kamlet-Taft 0.71
|-
|CarbonAromaticity
|0.2308
|
|There are 13 non-H atoms, 3 are aromatic C atoms, value=3/13=0.2308
|-
|ElectronegativeHalogenicity
|0.0
|
|There are no electronegative halogen atoms, value=0.0
|-
| colspan="4" |<code>eps=13.70 epsinf=2.3691 SurfaceTensionAtInterface=68.34 HBondAcidity=0.18 HBondBasicity=0.52 CarbonAromaticity=0.2308 ElectronegativeHalogenicity=0.0</code>
|}

=== Molten salt [Li+,Na+,K+][CO32-] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|MolarVolume
|57
|<ref name="Janz" />
|molar volume Li2CO3 68 Na2CO3 92 K2CO3 124 Å3/molecule, average is 95 and 95*0.6022=57 at T=1.1Tm
|-
|Tabs
|900
|
|Absolute Temperature in K ie 298+600≈900
|-
|???
|
|
|ThermalExansionCoefficient estimate 20*10-6 K-1 at T=1.1Tm (this is not working!)
|-
|eps
|3
|<ref name="Janz"> G. Janz and M. Lorenz, <abbr>J. Electrochem. Soc.</abbr> 1961 volume 108, issue 11, 1052-1058 doi: 10.1149/1.2427946</ref>
|estimated value
|-
|epsinf n2)
|2.25
|
|refractive index Na2CO3 1.489-1.535,<ref><nowiki>https://pubchem.ncbi.nlm.nih.gov/compound/sodium_carbonate#section=Spectral-Properties&fullscreen=true</nowiki></ref> Li2CO3 1.428-1.572<ref>Weast, R.C. (ed.). Handbook of Chemistry and Physics. 60th ed. Boca Raton, Florida: CRC Press Inc., 1979., p. B-91</ref> K2CO3 1.426-1.541<ref><nowiki>http://cameo.mfa.org/wiki/Potassium_carbonate</nowiki></ref> taking a "mid" value 1.52=2.25
|-
|SurfaceTensionAtInterface
|273
|<ref name="Janz" />
|used surface tension of Na/K/CO3 mixture 50 mol % K2CO3 at 810 ºC , 190.0 dynes/cm
|-
|HBondAcidity (α)
|0.00
|<nowiki>-</nowiki>
| rowspan="2" |There are no H-atoms so H-bond acidity is zero
H-bond basicity computations result in proton transfer, NO3 ≈0.74-0.81, Cl ≈0.95-0.98, we assume it is even stronger due to -2 charge
|-
|HBondBasicity (β)
|0.99
|
|-
|CarbonAromaticity
|0.00
|<nowiki>-</nowiki>
|There are no aromatic C atoms
|-
|ElectronegativeHalogenicity
|0.00
|<nowiki>-</nowiki>
|There are no halogen atoms
|-
| colspan="4" |Stoichiometry=C2O62Li2Na2K2 MolarVolume=57.0 Tabs=900 eps=3.0 epsinf=2.25 SurfaceTensionAtInterface=273 HBondAcidity=0.0 HBondBasicity=0.99 CarbonAromaticity=0.0 ElectronegativeHalogenicity=0.0
|}

== Example table ==
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|
|
|
|-
|epsinf
|
|
|
|-
|SurfaceTensionAtInterface
|
|
|
|-
|HBondAcidity (α)
|
|
|
|-
|HBondBasicity (β)
|
|
|
|-
|CarbonAromaticity
|
|
|
|-
|ElectronegativeHalogenicity
|
|
|
|-
| colspan="4" |<code>eps= epsinf= SurfaceTensionAtInterface= HBondAcidity= HBondBasicity= CarbonAromaticity= ElectronegativeHalogenicity=</code>
|}

== References ==
<references />

Mod:Hunt Research Group: Using SMD on ILs

2019-12-23T11:18:12Z

Phunt: /* [C4C1Im][SCN] */

This page explains how to use the SMD model to simulate an ionic liquid environment in Gaussian calculations. The SMD model is explained in detail in the original paper here.<ref name="Marenich"> Marenich 2009 http://pubs.acs.org/doi/abs/10.1021/jp810292n</ref> Its use on ILs is similarly explained here.<ref name="Bernales">Bernales 2012 http://pubs.acs.org/doi/abs/10.1021/jp304365v</ref> Many useful solvent parameters are also available in this paper.

== How to simulate a defined solvent environment ==
Gaussian has many previously defined solvent environments. A list is available at the bottom of this page.<ref>http://www.gaussian.com/g_tech/g_ur/k_scrf.htm</ref> For example to use the pre-defined water environment simply insert the following keyword into the method line of your input file. The rest of your method line should specify your functional, basis set, optimisation/other type of calculation as usual.
scrf=(smd,solvent=water)
To use a different solvent to water change the solvent=water part to solvent=something else in the list.

== How to simulate a generic solvent environment ==
The SMD model has many parameters. These are already defined inside Gaussian for the list of defined solvents. If you want to use a solvent not on the list e.g. an ionic liquid, you must define these parameters manually. In this case put the following into the method line:
scrf=(smd,solvent=generic)

===Solvent parameters===
{| class="wikitable"
!Parameter
!Symbol
!Name in Gaussian input file
|-
|Dielectric constant
|ε
|eps
|-
|Index of refraction, squared
|n2
|epsinf
|-
|Macroscopic surface tension /cal mol-1 Å-2
|γ
|SurfaceTensionAtInterface
|-
|Abraham hydrogen bond acidity parameter
|Σα2H
|HBondAcidity
|-
|Abraham hydrogen bond basicity parameter
|Σβ2H
|HBondBasicity
|-
|Fraction of non-hydrogen atoms which are aromatic carbon atoms
|φ
|CarbonAromaticity
|
|-
|Fraction of non-hydrogen atoms which are electronegative halogen atoms
|ψ
|ElectronegativeHalogenicity
|
|}

===Notes on parameters===
Surface tension
*surface tension is the only parameter with units, those used in SMD are non-standard cal mol-1Å-2
*the SI units are Jm-2 or Nm-1
*typical units are dyn cm-1 where 1 dyn = 1 g cm s-2
*as we tend to work in kJ/mol the energy part of this becomes not J but J/mol
*1 dyn cm-1 = 0.001N m-1 = 0.001J m-2
*1 m = 1*1010Å and 1J=0.239cal and 1 mol-1=6.022*1023
*1 dyn cm-1 = 0.001*0.239cal*6.022*1023mol-1/(1*102*10Å2
*and if you think about this 1023 on top line cancels with 1020 on bottom line leaving 103 which cancels with the 0.001=10-3 leaving us with 0.239*6.022=1.439
*1 dyn cm-1 = 1.439 cal mol-1 Å-2

Molar Volume
* MolarVolume=x.x in cm3/mol
* molecular volume in Å3 per molecule converted to cm3/mol
* 1cm = 1*108Å, 1Å = 1*10-8 cm
* x Å3 per molecule = x*6.022*1023mol-1 *103*-8cm3 = x*6.022*10-1cm3mol-1

Kamlet-Taft vs Abraham H-bonding parameters
*the SMD model requires Abraham H-bondonding parameters (Σα2H, Σβ2H)
*however Kamlet-Taft (α, β) measurements are more commonly reported for ILs
*a relationship between the parameters was investigated, giving the following equations:<ref name="Bernales" />

Σα2H = 0.4098α + 0.0064

Σβ2H = 0.6138β + 0.0890

Previously the group has developed a simple method for calculating Kamlet-Taft parameters, and the instructions are here.<ref>http://www.huntresearchgroup.org.uk/research/research_il_alpha_beta_intro.html</ref>

===Types of SMD model for ILs===
3 types of SMD for ILs have been defined.<ref name="Bernales" />
*SMD The standard SMD model. All parameters are determined for the particular IL (or a very similar one) being used as the solvent environment.
*SMD-GIL The generic ionic liquid model. The average values above are used for all parameters, except φ and ψ, which are simply calculated from the chemical formula of the IL.
*SMD-PGPThe partial generic parameters model. Any parameter which has been measured for that IL is used. For any parameters which you do not have values for, use the average values.

Example: [C4C1Im][NTf2] 
*All parameters for this IL have been measured, and can be found in reference 2.<ref name="Bernales" /> That means we can use the standard SMD method.
*To get a value for φ take the number of aromatic carbon atoms (3) and divide by the number of non-hydrogen atoms (25). φ = 0.12.
*To get a value for ψ take the number of electronegative halogen atoms (6) and divide by the number of non-hydrogen atoms (25). ψ = 0.24.
*To define these parameters place the following line at the bottom of the input file (include one blank line before and at least one blank line after):
* eps=11.52 epsinf=2.037 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.12 ElectronegativeHalogenicity=0.24
*see following data for other ILs

== SMD input database ==
Here we will keep a database of SMD parameters used by the group. Please add any IL you use, so no-one else has to re-do the research for the parameters! Please follow the template provided so that it is clear where you get each value from.

=== SMD-GIL ===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.50
|
|
|-
|epsinf (n2)
|2.0449
|
|
|-
|SurfaceTensionAtInterface
|61.24
|
|
|-
|HBondAcidity (α)
|0.229
|
|
|-
|HBondBasicity (β)
|0.265
|
|
|-
|CarbonAromaticity (φ)
|compute for your system
|
|
|-
|ElectronegativeHalogenicity (ψ)
|compute for your system
|
|
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][BF4]===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.70
|
|
|-
|epsinf n2)
|2.0207
|
|Value given in reference is n=1.4215, it has been squared to give epsinf=2.0207
|-
|SurfaceTensionAtInterface
|67.07
|
|
|-
|HBondAcidity (α)
|0.263
|
| Kamlet-Taft 0.627
|-
|HBondBasicity (β)
|0.320
|
| Kamlet-Taft 0.376
|-
|CarbonAromaticity (φ)
|0.2000
|
|There are 15 non-H atoms, 3 are aromatic C atoms, value=3/15=0.2000
|-
|ElectronegativeHalogenicity (ψ)
|0.2667
|
|There are 15 non-H atoms, 4 are electronegative halogen atoms, value =4/15=0.2667
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][PF6]===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.40
|
|
|-
|epsinf n2)
|1.9853
|
|Value given in reference is n=1.4090, it has been squared to give epsinf=1.9853
|-
|SurfaceTensionAtInterface
|70.24
|
|
|-
|HBondAcidity (α)
|0.266
|
| Kamlet-Taft 0.634
|-
|HBondBasicity (β)
|0.216
|
| Kamlet-Taft 0.207
|-
|CarbonAromaticity (φ)
|0.1765
|
|There are 17 non-H atoms, 3 are aromatic C atoms, value=3/17=0.1765
|-
|ElectronegativeHalogenicity (ψ)
|0.3529
|
|There are 17 non-H atoms, 4 are electronegative halogen atoms, value =6/17=0.3529
|-
| colspan="4" |<code>eps=11.40 epsinf=1.9853 SurfaceTensionAtInterface=70.24 HBondAcidity=0.266 HBondBasicity=0.216 CarbonAromaticity=0.1765 ElectronegativeHalogenicity=0.3529</code>
|}

=== [C4C1Im][NTf2] ===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.52
|<ref name="Daguenet">Daguenet 2006 http://pubs.acs.org/doi/abs/10.1021/jp0604903</ref>
|
|-
|epsinf n2)
|2.0366
|<ref name="Huddleston">Huddleston 2001 http://pubs.rsc.org/en/Content/ArticleLanding/2001/GC/b103275p</ref>
|Value given in reference is n=1.4271, it has been squared to give epsinf=2.0366
|-
|SurfaceTensionAtInterface
|53.97
|<ref name="Huddleston" />
|
|-
|HBondAcidity (α)
|0.259
|<ref name="Marenich"/>
| Kamlet-Taft 0.617
|-
|HBondBasicity (β)
|0.238
|<ref name="Marenich" />
| Kamlet-Taft 0.243
|-
|CarbonAromaticity
|0.1200
|
|There are 25 non-H atoms, 3 are aromatic C atoms, value =3/25=0.1200
|-
|ElectronegativeHalogenicity
|0.2400
|
|There are 25 non-H atoms, 6 are electronegative halogen atoms, value =6/25=0.2400
|-
| colspan="4" |<code>eps=11.52 epsinf=2.0366 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.1200 ElectronegativeHalogenicity=0.2400</code>
|}

=== [C4C1Im][OTf] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|12.90
|<ref name="Huang"> M. M. Huang, Y. P. Jiang, P. Sasisanker, G. W. Driver and H. Weingartner,  J. Chem. Eng. Data, 2011, 56, 1494–1499. http://pubs.acs.org/doi/abs/10.1021/je101184s</ref>
|Page 1495, number 11 on the list.
|-
|epsinf n2)
|2.0665
|<ref name="Gonzalez"> Gonzalez 2012 http://pubs.acs.org/doi/abs/10.1021/je201334p</ref>
|n=1.43755, has been squared to give epsinf=2.0665. Can be found in Table 1, 3rd row.
|-
|SurfaceTensionAtInterface
|unknown
|
|-
|HBondAcidity (α)
|0.263
|<ref name="Bernales" /> <ref name="Marenich" />
| Kamlet-Taft 0.625
|-
|HBondBasicity (β)
|0.374
|<ref name="Bernales" /> <ref name="Marenich" />
| Kamlet-Taft 0.464
|-
|CarbonAromaticity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are aromatic C atoms, value=3/18=0.1667.
|-
|ElectronegativeHalogenicity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are electronegative halogen atoms, value=3/18=0.1667.
|-
| colspan="4" |<code>eps=12.90 epsinf=2.0665 SurfaceTensionAtInterface'''=XX''' HBondAcidity=0.263 HBondBasicity=0.374 CarbonAromaticity=0.1667 ElectronegativeHalogenicity=0.1667</code>
|}

=== [C4C1Im][SCN] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|13.70
| <ref name="Huang" />
|
|-
|epsinf (n2)
|2.3691
| <ref name="Vakili">G. Vakili-Nezhaad, M. Vatani, M. Asghari and I. Ashour, J. Chem. Thermodyn., 2012, 54, 148–154. </ref>
|n=1.53921, has been squared to give epsinf=2.3691 (error in some database calcs with n=1.5436 n2=2.3827)
|-
|SurfaceTensionAtInterface
|68.34
| <ref name="Vakili" />
| η=45.41 (mN.m-1) converts to 45.41*1.439= cal mol-1 Å-2=65.34
|-
|HBondAcidity (α)
|0.18
|
| Kamlet-Taft 0.43
|-
|HBondBasicity (β)
|0.52
|
| Kamlet-Taft 0.71
|-
|CarbonAromaticity
|0.2308
|
|There are 13 non-H atoms, 3 are aromatic C atoms, value=3/13=0.2308
|-
|ElectronegativeHalogenicity
|0.0
|
|There are no electronegative halogen atoms, value=0.0
|-
| colspan="4" |<code>eps=13.70 epsinf=2.3691 SurfaceTensionAtInterface=68.34 HBondAcidity=0.18 HBondBasicity=0.52 CarbonAromaticity=0.2308 ElectronegativeHalogenicity=0.0</code>
|}

=== Molten salt [Li+,Na+,K+][CO32-] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|MolarVolume
|57
|<ref name="Janz" />
|molar volume Li2CO3 68 Na2CO3 92 K2CO3 124 Å3/molecule, average is 95 and 95*0.6022=57 at T=1.1Tm
|-
|Tabs
|900
|
|Absolute Temperature in K ie 298+600≈900
|-
|???
|
|
|ThermalExansionCoefficient estimate 20*10-6 K-1 at T=1.1Tm (this is not working!)
|-
|eps
|3
|<ref name="Janz"> G. Janz and M. Lorenz, <abbr>J. Electrochem. Soc.</abbr> 1961 volume 108, issue 11, 1052-1058 doi: 10.1149/1.2427946</ref>
|estimated value
|-
|epsinf n2)
|2.25
|
|refractive index Na2CO3 1.489-1.535,<ref><nowiki>https://pubchem.ncbi.nlm.nih.gov/compound/sodium_carbonate#section=Spectral-Properties&fullscreen=true</nowiki></ref> Li2CO3 1.428-1.572<ref>Weast, R.C. (ed.). Handbook of Chemistry and Physics. 60th ed. Boca Raton, Florida: CRC Press Inc., 1979., p. B-91</ref> K2CO3 1.426-1.541<ref><nowiki>http://cameo.mfa.org/wiki/Potassium_carbonate</nowiki></ref> taking a "mid" value 1.52=2.25
|-
|SurfaceTensionAtInterface
|273
|<ref name="Janz" />
|used surface tension of Na/K/CO3 mixture 50 mol % K2CO3 at 810 ºC , 190.0 dynes/cm
|-
|HBondAcidity (α)
|0.00
|<nowiki>-</nowiki>
| rowspan="2" |There are no H-atoms so H-bond acidity is zero
H-bond basicity computations result in proton transfer, NO3 ≈0.74-0.81, Cl ≈0.95-0.98, we assume it is even stronger due to -2 charge
|-
|HBondBasicity (β)
|0.99
|
|-
|CarbonAromaticity
|0.00
|<nowiki>-</nowiki>
|There are no aromatic C atoms
|-
|ElectronegativeHalogenicity
|0.00
|<nowiki>-</nowiki>
|There are no halogen atoms
|-
| colspan="4" |Stoichiometry=C2O62Li2Na2K2 MolarVolume=57.0 Tabs=900 eps=3.0 epsinf=2.25 SurfaceTensionAtInterface=273 HBondAcidity=0.0 HBondBasicity=0.99 CarbonAromaticity=0.0 ElectronegativeHalogenicity=0.0
|}

=== Example IL-GIL (generic IL) ===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.50
|
|see ESI Table S2.1
|-
|epsinf n2)
|2.0449
|
|n=1.43, has been squared to give epsinf=2.0449
|-
|SurfaceTensionAtInterface
|61.24
|
|<code>see ESI Table S2.1</code>
|-
|HBondAcidity (α)
|0.229
|
|<code>see ESI Table S2.1</code>
|-
|HBondBasicity (β)
|0.265
|
|<code>see ESI Table S2.1</code>
|-
|CarbonAromaticity
|
|
|
|-
|ElectronegativeHalogenicity
|
|
|
|-
| colspan="4" |<code>eps=11.50 epsinf=2.0449 SurfaceTensionAtInterface=61.24 HBondAcidity=0.229 HBondBasicity=0.265 CarbonAromaticity=0.xxx ElectronegativeHalogenicity=0.xxx</code>
|}

== Example table ==
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|
|
|
|-
|epsinf
|
|
|
|-
|SurfaceTensionAtInterface
|
|
|
|-
|HBondAcidity (α)
|
|
|
|-
|HBondBasicity (β)
|
|
|
|-
|CarbonAromaticity
|
|
|
|-
|ElectronegativeHalogenicity
|
|
|
|-
| colspan="4" |<code>eps= epsinf= SurfaceTensionAtInterface= HBondAcidity= HBondBasicity= CarbonAromaticity= ElectronegativeHalogenicity=</code>
|}

== References ==
<references />

Mod:Hunt Research Group: Using SMD on ILs

2019-12-23T11:17:09Z

Phunt:

This page explains how to use the SMD model to simulate an ionic liquid environment in Gaussian calculations. The SMD model is explained in detail in the original paper here.<ref name="Marenich"> Marenich 2009 http://pubs.acs.org/doi/abs/10.1021/jp810292n</ref> Its use on ILs is similarly explained here.<ref name="Bernales">Bernales 2012 http://pubs.acs.org/doi/abs/10.1021/jp304365v</ref> Many useful solvent parameters are also available in this paper.

== How to simulate a defined solvent environment ==
Gaussian has many previously defined solvent environments. A list is available at the bottom of this page.<ref>http://www.gaussian.com/g_tech/g_ur/k_scrf.htm</ref> For example to use the pre-defined water environment simply insert the following keyword into the method line of your input file. The rest of your method line should specify your functional, basis set, optimisation/other type of calculation as usual.
scrf=(smd,solvent=water)
To use a different solvent to water change the solvent=water part to solvent=something else in the list.

== How to simulate a generic solvent environment ==
The SMD model has many parameters. These are already defined inside Gaussian for the list of defined solvents. If you want to use a solvent not on the list e.g. an ionic liquid, you must define these parameters manually. In this case put the following into the method line:
scrf=(smd,solvent=generic)

===Solvent parameters===
{| class="wikitable"
!Parameter
!Symbol
!Name in Gaussian input file
|-
|Dielectric constant
|ε
|eps
|-
|Index of refraction, squared
|n2
|epsinf
|-
|Macroscopic surface tension /cal mol-1 Å-2
|γ
|SurfaceTensionAtInterface
|-
|Abraham hydrogen bond acidity parameter
|Σα2H
|HBondAcidity
|-
|Abraham hydrogen bond basicity parameter
|Σβ2H
|HBondBasicity
|-
|Fraction of non-hydrogen atoms which are aromatic carbon atoms
|φ
|CarbonAromaticity
|
|-
|Fraction of non-hydrogen atoms which are electronegative halogen atoms
|ψ
|ElectronegativeHalogenicity
|
|}

===Notes on parameters===
Surface tension
*surface tension is the only parameter with units, those used in SMD are non-standard cal mol-1Å-2
*the SI units are Jm-2 or Nm-1
*typical units are dyn cm-1 where 1 dyn = 1 g cm s-2
*as we tend to work in kJ/mol the energy part of this becomes not J but J/mol
*1 dyn cm-1 = 0.001N m-1 = 0.001J m-2
*1 m = 1*1010Å and 1J=0.239cal and 1 mol-1=6.022*1023
*1 dyn cm-1 = 0.001*0.239cal*6.022*1023mol-1/(1*102*10Å2
*and if you think about this 1023 on top line cancels with 1020 on bottom line leaving 103 which cancels with the 0.001=10-3 leaving us with 0.239*6.022=1.439
*1 dyn cm-1 = 1.439 cal mol-1 Å-2

Molar Volume
* MolarVolume=x.x in cm3/mol
* molecular volume in Å3 per molecule converted to cm3/mol
* 1cm = 1*108Å, 1Å = 1*10-8 cm
* x Å3 per molecule = x*6.022*1023mol-1 *103*-8cm3 = x*6.022*10-1cm3mol-1

Kamlet-Taft vs Abraham H-bonding parameters
*the SMD model requires Abraham H-bondonding parameters (Σα2H, Σβ2H)
*however Kamlet-Taft (α, β) measurements are more commonly reported for ILs
*a relationship between the parameters was investigated, giving the following equations:<ref name="Bernales" />

Σα2H = 0.4098α + 0.0064

Σβ2H = 0.6138β + 0.0890

Previously the group has developed a simple method for calculating Kamlet-Taft parameters, and the instructions are here.<ref>http://www.huntresearchgroup.org.uk/research/research_il_alpha_beta_intro.html</ref>

===Types of SMD model for ILs===
3 types of SMD for ILs have been defined.<ref name="Bernales" />
*SMD The standard SMD model. All parameters are determined for the particular IL (or a very similar one) being used as the solvent environment.
*SMD-GIL The generic ionic liquid model. The average values above are used for all parameters, except φ and ψ, which are simply calculated from the chemical formula of the IL.
*SMD-PGPThe partial generic parameters model. Any parameter which has been measured for that IL is used. For any parameters which you do not have values for, use the average values.

Example: [C4C1Im][NTf2] 
*All parameters for this IL have been measured, and can be found in reference 2.<ref name="Bernales" /> That means we can use the standard SMD method.
*To get a value for φ take the number of aromatic carbon atoms (3) and divide by the number of non-hydrogen atoms (25). φ = 0.12.
*To get a value for ψ take the number of electronegative halogen atoms (6) and divide by the number of non-hydrogen atoms (25). ψ = 0.24.
*To define these parameters place the following line at the bottom of the input file (include one blank line before and at least one blank line after):
* eps=11.52 epsinf=2.037 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.12 ElectronegativeHalogenicity=0.24
*see following data for other ILs

== SMD input database ==
Here we will keep a database of SMD parameters used by the group. Please add any IL you use, so no-one else has to re-do the research for the parameters! Please follow the template provided so that it is clear where you get each value from.

=== SMD-GIL ===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.50
|
|
|-
|epsinf (n2)
|2.0449
|
|
|-
|SurfaceTensionAtInterface
|61.24
|
|
|-
|HBondAcidity (α)
|0.229
|
|
|-
|HBondBasicity (β)
|0.265
|
|
|-
|CarbonAromaticity (φ)
|compute for your system
|
|
|-
|ElectronegativeHalogenicity (ψ)
|compute for your system
|
|
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][BF4]===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.70
|
|
|-
|epsinf n2)
|2.0207
|
|Value given in reference is n=1.4215, it has been squared to give epsinf=2.0207
|-
|SurfaceTensionAtInterface
|67.07
|
|
|-
|HBondAcidity (α)
|0.263
|
| Kamlet-Taft 0.627
|-
|HBondBasicity (β)
|0.320
|
| Kamlet-Taft 0.376
|-
|CarbonAromaticity (φ)
|0.2000
|
|There are 15 non-H atoms, 3 are aromatic C atoms, value=3/15=0.2000
|-
|ElectronegativeHalogenicity (ψ)
|0.2667
|
|There are 15 non-H atoms, 4 are electronegative halogen atoms, value =4/15=0.2667
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][PF6]===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.40
|
|
|-
|epsinf n2)
|1.9853
|
|Value given in reference is n=1.4090, it has been squared to give epsinf=1.9853
|-
|SurfaceTensionAtInterface
|70.24
|
|
|-
|HBondAcidity (α)
|0.266
|
| Kamlet-Taft 0.634
|-
|HBondBasicity (β)
|0.216
|
| Kamlet-Taft 0.207
|-
|CarbonAromaticity (φ)
|0.1765
|
|There are 17 non-H atoms, 3 are aromatic C atoms, value=3/17=0.1765
|-
|ElectronegativeHalogenicity (ψ)
|0.3529
|
|There are 17 non-H atoms, 4 are electronegative halogen atoms, value =6/17=0.3529
|-
| colspan="4" |<code>eps=11.40 epsinf=1.9853 SurfaceTensionAtInterface=70.24 HBondAcidity=0.266 HBondBasicity=0.216 CarbonAromaticity=0.1765 ElectronegativeHalogenicity=0.3529</code>
|}

=== [C4C1Im][NTf2] ===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.52
|<ref name="Daguenet">Daguenet 2006 http://pubs.acs.org/doi/abs/10.1021/jp0604903</ref>
|
|-
|epsinf n2)
|2.0366
|<ref name="Huddleston">Huddleston 2001 http://pubs.rsc.org/en/Content/ArticleLanding/2001/GC/b103275p</ref>
|Value given in reference is n=1.4271, it has been squared to give epsinf=2.0366
|-
|SurfaceTensionAtInterface
|53.97
|<ref name="Huddleston" />
|
|-
|HBondAcidity (α)
|0.259
|<ref name="Marenich"/>
| Kamlet-Taft 0.617
|-
|HBondBasicity (β)
|0.238
|<ref name="Marenich" />
| Kamlet-Taft 0.243
|-
|CarbonAromaticity
|0.1200
|
|There are 25 non-H atoms, 3 are aromatic C atoms, value =3/25=0.1200
|-
|ElectronegativeHalogenicity
|0.2400
|
|There are 25 non-H atoms, 6 are electronegative halogen atoms, value =6/25=0.2400
|-
| colspan="4" |<code>eps=11.52 epsinf=2.0366 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.1200 ElectronegativeHalogenicity=0.2400</code>
|}

=== [C4C1Im][OTf] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|12.90
|<ref name="Huang"> M. M. Huang, Y. P. Jiang, P. Sasisanker, G. W. Driver and H. Weingartner,  J. Chem. Eng. Data, 2011, 56, 1494–1499. http://pubs.acs.org/doi/abs/10.1021/je101184s</ref>
|Page 1495, number 11 on the list.
|-
|epsinf n2)
|2.0665
|<ref name="Gonzalez"> Gonzalez 2012 http://pubs.acs.org/doi/abs/10.1021/je201334p</ref>
|n=1.43755, has been squared to give epsinf=2.0665. Can be found in Table 1, 3rd row.
|-
|SurfaceTensionAtInterface
|unknown
|
|-
|HBondAcidity (α)
|0.263
|<ref name="Bernales" /> <ref name="Marenich" />
| Kamlet-Taft 0.625
|-
|HBondBasicity (β)
|0.374
|<ref name="Bernales" /> <ref name="Marenich" />
| Kamlet-Taft 0.464
|-
|CarbonAromaticity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are aromatic C atoms, value=3/18=0.1667.
|-
|ElectronegativeHalogenicity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are electronegative halogen atoms, value=3/18=0.1667.
|-
| colspan="4" |<code>eps=12.90 epsinf=2.0665 SurfaceTensionAtInterface'''=XX''' HBondAcidity=0.263 HBondBasicity=0.374 CarbonAromaticity=0.1667 ElectronegativeHalogenicity=0.1667</code>
|}

=== [C4C1Im][SCN] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|13.70
| <ref name="Huang" />
|
|-
|epsinf (n2)
|2.3691
| <ref name="Vakili">G. Vakili-Nezhaad, M. Vatani, M. Asghari and I. Ashour, J. Chem. Thermodyn., 2012, 54, 148–154. </ref>
|n=1.53921, has been squared to give epsinf=2.3691 (error in some database calcs with n=1.5436 n2=2.3827)
|-
|SurfaceTensionAtInterface
|68.34
| <ref name="Vakili" />
| η=45.41 (mN.m-1) converts to 45.41*1.439= cal mol-1 Å-2=65.34
|-
|HBondAcidity (α)
|0.18
|
| Kamlet-Taft 0.43
|-
|HBondBasicity (β)
|0.52
|
| Kamlet-Taft 0.71
|-
|CarbonAromaticity
|0.2308
|
|There are 13 non-H atoms, 3 are aromatic C atoms, value=xx/xx=0.2308
|-
|ElectronegativeHalogenicity
|0.0
|
|There are no electronegative halogen atoms, value=0.0
|-
| colspan="4" |<code>eps=13.70 epsinf=2.3691 SurfaceTensionAtInterface=68.34 HBondAcidity=0.18 HBondBasicity=0.52 CarbonAromaticity=0.2308 ElectronegativeHalogenicity=0.0</code>
|}

=== Molten salt [Li+,Na+,K+][CO32-] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|MolarVolume
|57
|<ref name="Janz" />
|molar volume Li2CO3 68 Na2CO3 92 K2CO3 124 Å3/molecule, average is 95 and 95*0.6022=57 at T=1.1Tm
|-
|Tabs
|900
|
|Absolute Temperature in K ie 298+600≈900
|-
|???
|
|
|ThermalExansionCoefficient estimate 20*10-6 K-1 at T=1.1Tm (this is not working!)
|-
|eps
|3
|<ref name="Janz"> G. Janz and M. Lorenz, <abbr>J. Electrochem. Soc.</abbr> 1961 volume 108, issue 11, 1052-1058 doi: 10.1149/1.2427946</ref>
|estimated value
|-
|epsinf n2)
|2.25
|
|refractive index Na2CO3 1.489-1.535,<ref><nowiki>https://pubchem.ncbi.nlm.nih.gov/compound/sodium_carbonate#section=Spectral-Properties&fullscreen=true</nowiki></ref> Li2CO3 1.428-1.572<ref>Weast, R.C. (ed.). Handbook of Chemistry and Physics. 60th ed. Boca Raton, Florida: CRC Press Inc., 1979., p. B-91</ref> K2CO3 1.426-1.541<ref><nowiki>http://cameo.mfa.org/wiki/Potassium_carbonate</nowiki></ref> taking a "mid" value 1.52=2.25
|-
|SurfaceTensionAtInterface
|273
|<ref name="Janz" />
|used surface tension of Na/K/CO3 mixture 50 mol % K2CO3 at 810 ºC , 190.0 dynes/cm
|-
|HBondAcidity (α)
|0.00
|<nowiki>-</nowiki>
| rowspan="2" |There are no H-atoms so H-bond acidity is zero
H-bond basicity computations result in proton transfer, NO3 ≈0.74-0.81, Cl ≈0.95-0.98, we assume it is even stronger due to -2 charge
|-
|HBondBasicity (β)
|0.99
|
|-
|CarbonAromaticity
|0.00
|<nowiki>-</nowiki>
|There are no aromatic C atoms
|-
|ElectronegativeHalogenicity
|0.00
|<nowiki>-</nowiki>
|There are no halogen atoms
|-
| colspan="4" |Stoichiometry=C2O62Li2Na2K2 MolarVolume=57.0 Tabs=900 eps=3.0 epsinf=2.25 SurfaceTensionAtInterface=273 HBondAcidity=0.0 HBondBasicity=0.99 CarbonAromaticity=0.0 ElectronegativeHalogenicity=0.0
|}

=== Example IL-GIL (generic IL) ===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.50
|
|see ESI Table S2.1
|-
|epsinf n2)
|2.0449
|
|n=1.43, has been squared to give epsinf=2.0449
|-
|SurfaceTensionAtInterface
|61.24
|
|<code>see ESI Table S2.1</code>
|-
|HBondAcidity (α)
|0.229
|
|<code>see ESI Table S2.1</code>
|-
|HBondBasicity (β)
|0.265
|
|<code>see ESI Table S2.1</code>
|-
|CarbonAromaticity
|
|
|
|-
|ElectronegativeHalogenicity
|
|
|
|-
| colspan="4" |<code>eps=11.50 epsinf=2.0449 SurfaceTensionAtInterface=61.24 HBondAcidity=0.229 HBondBasicity=0.265 CarbonAromaticity=0.xxx ElectronegativeHalogenicity=0.xxx</code>
|}

== Example table ==
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|
|
|
|-
|epsinf
|
|
|
|-
|SurfaceTensionAtInterface
|
|
|
|-
|HBondAcidity (α)
|
|
|
|-
|HBondBasicity (β)
|
|
|
|-
|CarbonAromaticity
|
|
|
|-
|ElectronegativeHalogenicity
|
|
|
|-
| colspan="4" |<code>eps= epsinf= SurfaceTensionAtInterface= HBondAcidity= HBondBasicity= CarbonAromaticity= ElectronegativeHalogenicity=</code>
|}

== References ==
<references />

Mod:Hunt Research Group: Using SMD on ILs

2019-12-23T11:16:06Z

Phunt:

This page explains how to use the SMD model to simulate an ionic liquid environment in Gaussian calculations. The SMD model is explained in detail in the original paper here.<ref name="Marenich"> Marenich 2009 http://pubs.acs.org/doi/abs/10.1021/jp810292n</ref> Its use on ILs is similarly explained here.<ref name="Bernales">Bernales 2012 http://pubs.acs.org/doi/abs/10.1021/jp304365v</ref> Many useful solvent parameters are also available in this paper.

== How to simulate a defined solvent environment ==
Gaussian has many previously defined solvent environments. A list is available at the bottom of this page.<ref>http://www.gaussian.com/g_tech/g_ur/k_scrf.htm</ref> For example to use the pre-defined water environment simply insert the following keyword into the method line of your input file. The rest of your method line should specify your functional, basis set, optimisation/other type of calculation as usual.
scrf=(smd,solvent=water)
To use a different solvent to water change the solvent=water part to solvent=something else in the list.

== How to simulate a generic solvent environment ==
The SMD model has many parameters. These are already defined inside Gaussian for the list of defined solvents. If you want to use a solvent not on the list e.g. an ionic liquid, you must define these parameters manually. In this case put the following into the method line:
scrf=(smd,solvent=generic)

===Solvent parameters===
{| class="wikitable"
!Parameter
!Symbol
!Name in Gaussian input file
|-
|Dielectric constant
|ε
|eps
|-
|Index of refraction, squared
|n2
|epsinf
|-
|Macroscopic surface tension /cal mol-1 Å-2
|γ
|SurfaceTensionAtInterface
|-
|Abraham hydrogen bond acidity parameter
|Σα2H
|HBondAcidity
|-
|Abraham hydrogen bond basicity parameter
|Σβ2H
|HBondBasicity
|-
|Fraction of non-hydrogen atoms which are aromatic carbon atoms
|φ
|CarbonAromaticity
|
|-
|Fraction of non-hydrogen atoms which are electronegative halogen atoms
|ψ
|ElectronegativeHalogenicity
|
|}

===Notes on parameters===
Surface tension
*surface tension is the only parameter with units, those used in SMD are non-standard cal mol-1Å-2
*the SI units are Jm-2 or Nm-1
*typical units are dyn cm-1 where 1 dyn = 1 g cm s-2
*as we tend to work in kJ/mol the energy part of this becomes not J but J/mol
*1 dyn cm-1 = 0.001N m-1 = 0.001J m-2
*1 m = 1*1010Å and 1J=0.239cal and 1 mol-1=6.022*1023
*1 dyn cm-1 = 0.001*0.239cal*6.022*1023mol-1/(1*102*10Å2
*and if you think about this 1023 on top line cancels with 1020 on bottom line leaving 103 which cancels with the 0.001=10-3 leaving us with 0.239*6.022=1.439
*1 dyn cm-1 = 1.439 cal mol-1 Å-2

Molar Volume
* MolarVolume=x.x in cm3/mol
* molecular volume in Å3 per molecule converted to cm3/mol
* 1cm = 1*108Å, 1Å = 1*10-8 cm
* x Å3 per molecule = x*6.022*1023mol-1 *103*-8cm3 = x*6.022*10-1cm3mol-1

Kamlet-Taft vs Abraham H-bonding parameters
*the SMD model requires Abraham H-bondonding parameters (Σα2H, Σβ2H)
*however Kamlet-Taft (α, β) measurements are more commonly reported for ILs
*a relationship between the parameters was investigated, giving the following equations:<ref name="Bernales" />

Σα2H = 0.4098α + 0.0064

Σβ2H = 0.6138β + 0.0890

Previously the group has developed a simple method for calculating Kamlet-Taft parameters, and the instructions are here.<ref>http://www.huntresearchgroup.org.uk/research/research_il_alpha_beta_intro.html</ref>

===Types of SMD model for ILs===
3 types of SMD for ILs have been defined.<ref name="Bernales" />
*SMD The standard SMD model. All parameters are determined for the particular IL (or a very similar one) being used as the solvent environment.
*SMD-GIL The generic ionic liquid model. The average values above are used for all parameters, except φ and ψ, which are simply calculated from the chemical formula of the IL.
*SMD-PGPThe partial generic parameters model. Any parameter which has been measured for that IL is used. For any parameters which you do not have values for, use the average values.

Example: [C4C1Im][NTf2] 
*All parameters for this IL have been measured, and can be found in reference 2.<ref name="Bernales" /> That means we can use the standard SMD method.
*To get a value for φ take the number of aromatic carbon atoms (3) and divide by the number of non-hydrogen atoms (25). φ = 0.12.
*To get a value for ψ take the number of electronegative halogen atoms (6) and divide by the number of non-hydrogen atoms (25). ψ = 0.24.
*To define these parameters place the following line at the bottom of the input file (include one blank line before and at least one blank line after):
* eps=11.52 epsinf=2.037 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.12 ElectronegativeHalogenicity=0.24
*see following data for other ILs

== SMD input database ==
Here we will keep a database of SMD parameters used by the group. Please add any IL you use, so no-one else has to re-do the research for the parameters! Please follow the template provided so that it is clear where you get each value from.

=== SMD-GIL ===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.50
|
|
|-
|epsinf (n2)
|2.0449
|
|
|-
|SurfaceTensionAtInterface
|61.24
|
|
|-
|HBondAcidity (α)
|0.229
|
|
|-
|HBondBasicity (β)
|0.265
|
|
|-
|CarbonAromaticity (φ)
|compute for your system
|
|
|-
|ElectronegativeHalogenicity (ψ)
|compute for your system
|
|
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][BF4]===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.70
|
|
|-
|epsinf n2)
|2.0207
|
|Value given in reference is n=1.4215, it has been squared to give epsinf=2.0207
|-
|SurfaceTensionAtInterface
|67.07
|
|
|-
|HBondAcidity (α)
|0.263
|
| Kamlet-Taft 0.627
|-
|HBondBasicity (β)
|0.320
|
| Kamlet-Taft 0.376
|-
|CarbonAromaticity (φ)
|0.2000
|
|There are 15 non-H atoms, 3 are aromatic C atoms, value=3/15=0.2000
|-
|ElectronegativeHalogenicity (ψ)
|0.2667
|
|There are 15 non-H atoms, 4 are electronegative halogen atoms, value =4/15=0.2667
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][PF6]===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.40
|
|
|-
|epsinf n2)
|1.9853
|
|Value given in reference is n=1.4090, it has been squared to give epsinf=1.9853
|-
|SurfaceTensionAtInterface
|70.24
|
|
|-
|HBondAcidity (α)
|0.266
|
| Kamlet-Taft 0.634
|-
|HBondBasicity (β)
|0.216
|
| Kamlet-Taft 0.207
|-
|CarbonAromaticity (φ)
|0.1765
|
|There are 17 non-H atoms, 3 are aromatic C atoms, value=3/17=0.1765
|-
|ElectronegativeHalogenicity (ψ)
|0.3529
|
|There are 17 non-H atoms, 4 are electronegative halogen atoms, value =6/17=0.3529
|-
| colspan="4" |<code>eps=11.40 epsinf=1.9853 SurfaceTensionAtInterface=70.24 HBondAcidity=0.266 HBondBasicity=0.216 CarbonAromaticity=0.1765 ElectronegativeHalogenicity=0.3529</code>
|}

=== [C4C1Im][NTf2] ===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.52
|<ref name="Daguenet">Daguenet 2006 http://pubs.acs.org/doi/abs/10.1021/jp0604903</ref>
|
|-
|epsinf n2)
|2.0366
|<ref name="Huddleston">Huddleston 2001 http://pubs.rsc.org/en/Content/ArticleLanding/2001/GC/b103275p</ref>
|Value given in reference is n=1.4271, it has been squared to give epsinf=2.0366
|-
|SurfaceTensionAtInterface
|53.97
|<ref name="Huddleston" />
|
|-
|HBondAcidity (α)
|0.259
|<ref name="Marenich"/>
| Kamlet-Taft 0.617
|-
|HBondBasicity (β)
|0.238
|<ref name="Marenich" />
| Kamlet-Taft 0.243
|-
|CarbonAromaticity
|0.1200
|
|There are 25 non-H atoms, 3 are aromatic C atoms, value =3/25=0.1200
|-
|ElectronegativeHalogenicity
|0.2400
|
|There are 25 non-H atoms, 6 are electronegative halogen atoms, value =6/25=0.2400
|-
| colspan="4" |<code>eps=11.52 epsinf=2.0366 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.1200 ElectronegativeHalogenicity=0.2400</code>
|}

=== [C4C1Im][OTf] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|12.90
|<ref name="Huang"> M. M. Huang, Y. P. Jiang, P. Sasisanker, G. W. Driver and H. Weingartner,  J. Chem. Eng. Data, 2011, 56, 1494–1499. http://pubs.acs.org/doi/abs/10.1021/je101184s</ref>
|Page 1495, number 11 on the list.
|-
|epsinf n2)
|2.0665
|<ref name="Gonzalez"> Gonzalez 2012 http://pubs.acs.org/doi/abs/10.1021/je201334p</ref>
|n=1.43755, has been squared to give epsinf=2.0665. Can be found in Table 1, 3rd row.
|-
|SurfaceTensionAtInterface
|unknown
|
|-
|HBondAcidity (α)
|0.263
|<ref name="Bernales" /> <ref name="Marenich" />
| Kamlet-Taft 0.625
|-
|HBondBasicity (β)
|0.374
|<ref name="Bernales" /> <ref name="Marenich" />
| Kamlet-Taft 0.464
|-
|CarbonAromaticity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are aromatic C atoms, value=3/18=0.1667.
|-
|ElectronegativeHalogenicity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are electronegative halogen atoms, value=3/18=0.1667.
|-
| colspan="4" |<code>eps=12.90 epsinf=2.0665 SurfaceTensionAtInterface'''=XX''' HBondAcidity=0.263 HBondBasicity=0.374 CarbonAromaticity=0.1667 ElectronegativeHalogenicity=0.1667</code>
|}

=== [C4C1Im][SCN] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|13.70
| <ref name="Huang" />
|
|-
|epsinf (n2)
|2.3691
| <ref name="Vakili">G. Vakili-Nezhaad, M. Vatani, M. Asghari and I. Ashour, J. Chem. Thermodyn., 2012, 54, 148–154. </ref>
|n=1.53921, has been squared to give epsinf=2.3691 (error in some database calcs with n=1.5436 n2=2.3827)
|-
|SurfaceTensionAtInterface
|68.34
| <ref name="Vakili" />
| η=45.41 (mN.m-1) converts to 45.41*1.439= cal mol-1 Å-2=65.34
|-
|HBondAcidity (α)
|0.18
|
| Kamlet-Taft 0.43
|-
|HBondBasicity (β)
|0.52
|
| Kamlet-Taft 0.71
|-
|CarbonAromaticity
|0.2308
|
|There are 13 non-H atoms, 3 are aromatic C atoms, value=xx/xx=0.2308
|-
|ElectronegativeHalogenicity
|0.0
|
|There are no electronegative halogen atoms, value=0.0
|-
| colspan="4" |<code>eps=13.70 epsinf=2.3691 SurfaceTensionAtInterface=68.34 HBondAcidity=0.18 HBondBasicity=0.52 CarbonAromaticity=0.2308 ElectronegativeHalogenicity=0.0</code>
|}

=== Molten salt [Li+,Na+,K+][CO32-] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|MolarVolume
|57
|<ref name=":5" />
|molar volume Li2CO3 68 Na2CO3 92 K2CO3 124 Å3/molecule, average is 95 and 95*0.6022=57 at T=1.1Tm
|-
|Tabs
|900
|
|Absolute Temperature in K ie 298+600≈900
|-
|???
|
|
|ThermalExansionCoefficient estimate 20*10-6 K-1 at T=1.1Tm (this is not working!)
|-
|eps
|3
|<ref name="Janz"> G. Janz and M. Lorenz, <abbr>J. Electrochem. Soc.</abbr> 1961 volume 108, issue 11, 1052-1058 doi: 10.1149/1.2427946</ref>
|estimated value
|-
|epsinf n2)
|2.25
|
|refractive index Na2CO3 1.489-1.535,<ref><nowiki>https://pubchem.ncbi.nlm.nih.gov/compound/sodium_carbonate#section=Spectral-Properties&fullscreen=true</nowiki></ref> Li2CO3 1.428-1.572<ref>Weast, R.C. (ed.). Handbook of Chemistry and Physics. 60th ed. Boca Raton, Florida: CRC Press Inc., 1979., p. B-91</ref> K2CO3 1.426-1.541<ref><nowiki>http://cameo.mfa.org/wiki/Potassium_carbonate</nowiki></ref> taking a "mid" value 1.52=2.25
|-
|SurfaceTensionAtInterface
|273
|<ref name=":5" />
|used surface tension of Na/K/CO3 mixture 50 mol % K2CO3 at 810 ºC , 190.0 dynes/cm
|-
|HBondAcidity (α)
|0.00
|<nowiki>-</nowiki>
| rowspan="2" |There are no H-atoms so H-bond acidity is zero
H-bond basicity computations result in proton transfer, NO3 ≈0.74-0.81, Cl ≈0.95-0.98, we assume it is even stronger due to -2 charge
|-
|HBondBasicity (β)
|0.99
|
|-
|CarbonAromaticity
|0.00
|<nowiki>-</nowiki>
|There are no aromatic C atoms
|-
|ElectronegativeHalogenicity
|0.00
|<nowiki>-</nowiki>
|There are no halogen atoms
|-
| colspan="4" |Stoichiometry=C2O62Li2Na2K2 MolarVolume=57.0 Tabs=900 eps=3.0 epsinf=2.25 SurfaceTensionAtInterface=273 HBondAcidity=0.0 HBondBasicity=0.99 CarbonAromaticity=0.0 ElectronegativeHalogenicity=0.0
|}

=== Example IL-GIL (generic IL) ===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.50
|
|see ESI Table S2.1
|-
|epsinf n2)
|2.0449
|
|n=1.43, has been squared to give epsinf=2.0449
|-
|SurfaceTensionAtInterface
|61.24
|
|<code>see ESI Table S2.1</code>
|-
|HBondAcidity (α)
|0.229
|
|<code>see ESI Table S2.1</code>
|-
|HBondBasicity (β)
|0.265
|
|<code>see ESI Table S2.1</code>
|-
|CarbonAromaticity
|
|
|
|-
|ElectronegativeHalogenicity
|
|
|
|-
| colspan="4" |<code>eps=11.50 epsinf=2.0449 SurfaceTensionAtInterface=61.24 HBondAcidity=0.229 HBondBasicity=0.265 CarbonAromaticity=0.xxx ElectronegativeHalogenicity=0.xxx</code>
|}

== Example table ==
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|
|
|
|-
|epsinf
|
|
|
|-
|SurfaceTensionAtInterface
|
|
|
|-
|HBondAcidity (α)
|
|
|
|-
|HBondBasicity (β)
|
|
|
|-
|CarbonAromaticity
|
|
|
|-
|ElectronegativeHalogenicity
|
|
|
|-
| colspan="4" |<code>eps= epsinf= SurfaceTensionAtInterface= HBondAcidity= HBondBasicity= CarbonAromaticity= ElectronegativeHalogenicity=</code>
|}

== References ==
<references />

Mod:Hunt Research Group: Using SMD on ILs

2019-12-23T11:14:47Z

Phunt:

This page explains how to use the SMD model to simulate an ionic liquid environment in Gaussian calculations. The SMD model is explained in detail in the original paper here.<ref name="Marenich">Marenich 2009 http://pubs.acs.org/doi/abs/10.1021/jp810292n</ref> Its use on ILs is similarly explained here.<ref name="Bernales">Bernales 2012 http://pubs.acs.org/doi/abs/10.1021/jp304365v</ref> Many useful solvent parameters are also available in this paper.

== How to simulate a defined solvent environment ==
Gaussian has many previously defined solvent environments. A list is available at the bottom of this page.<ref>http://www.gaussian.com/g_tech/g_ur/k_scrf.htm</ref> For example to use the pre-defined water environment simply insert the following keyword into the method line of your input file. The rest of your method line should specify your functional, basis set, optimisation/other type of calculation as usual.
scrf=(smd,solvent=water)
To use a different solvent to water change the solvent=water part to solvent=something else in the list.

== How to simulate a generic solvent environment ==
The SMD model has many parameters. These are already defined inside Gaussian for the list of defined solvents. If you want to use a solvent not on the list e.g. an ionic liquid, you must define these parameters manually. In this case put the following into the method line:
scrf=(smd,solvent=generic)

===Solvent parameters===
{| class="wikitable"
!Parameter
!Symbol
!Name in Gaussian input file
|-
|Dielectric constant
|ε
|eps
|-
|Index of refraction, squared
|n2
|epsinf
|-
|Macroscopic surface tension /cal mol-1 Å-2
|γ
|SurfaceTensionAtInterface
|-
|Abraham hydrogen bond acidity parameter
|Σα2H
|HBondAcidity
|-
|Abraham hydrogen bond basicity parameter
|Σβ2H
|HBondBasicity
|-
|Fraction of non-hydrogen atoms which are aromatic carbon atoms
|φ
|CarbonAromaticity
|
|-
|Fraction of non-hydrogen atoms which are electronegative halogen atoms
|ψ
|ElectronegativeHalogenicity
|
|}

===Notes on parameters===
Surface tension
*surface tension is the only parameter with units, those used in SMD are non-standard cal mol-1Å-2
*the SI units are Jm-2 or Nm-1
*typical units are dyn cm-1 where 1 dyn = 1 g cm s-2
*as we tend to work in kJ/mol the energy part of this becomes not J but J/mol
*1 dyn cm-1 = 0.001N m-1 = 0.001J m-2
*1 m = 1*1010Å and 1J=0.239cal and 1 mol-1=6.022*1023
*1 dyn cm-1 = 0.001*0.239cal*6.022*1023mol-1/(1*102*10Å2
*and if you think about this 1023 on top line cancels with 1020 on bottom line leaving 103 which cancels with the 0.001=10-3 leaving us with 0.239*6.022=1.439
*1 dyn cm-1 = 1.439 cal mol-1 Å-2

Molar Volume
* MolarVolume=x.x in cm3/mol
* molecular volume in Å3 per molecule converted to cm3/mol
* 1cm = 1*108Å, 1Å = 1*10-8 cm
* x Å3 per molecule = x*6.022*1023mol-1 *103*-8cm3 = x*6.022*10-1cm3mol-1

Kamlet-Taft vs Abraham H-bonding parameters
*the SMD model requires Abraham H-bondonding parameters (Σα2H, Σβ2H)
*however Kamlet-Taft (α, β) measurements are more commonly reported for ILs
*a relationship between the parameters was investigated, giving the following equations:<ref name="Bernales" />

Σα2H = 0.4098α + 0.0064

Σβ2H = 0.6138β + 0.0890

Previously the group has developed a simple method for calculating Kamlet-Taft parameters, and the instructions are here.<ref>http://www.huntresearchgroup.org.uk/research/research_il_alpha_beta_intro.html</ref>

===Types of SMD model for ILs===
3 types of SMD for ILs have been defined.<ref name="Bernales" />
*SMD The standard SMD model. All parameters are determined for the particular IL (or a very similar one) being used as the solvent environment.
*SMD-GIL The generic ionic liquid model. The average values above are used for all parameters, except φ and ψ, which are simply calculated from the chemical formula of the IL.
*SMD-PGPThe partial generic parameters model. Any parameter which has been measured for that IL is used. For any parameters which you do not have values for, use the average values.

Example: [C4C1Im][NTf2] 
*All parameters for this IL have been measured, and can be found in reference 2.<ref name="Bernales" /> That means we can use the standard SMD method.
*To get a value for φ take the number of aromatic carbon atoms (3) and divide by the number of non-hydrogen atoms (25). φ = 0.12.
*To get a value for ψ take the number of electronegative halogen atoms (6) and divide by the number of non-hydrogen atoms (25). ψ = 0.24.
*To define these parameters place the following line at the bottom of the input file (include one blank line before and at least one blank line after):
* eps=11.52 epsinf=2.037 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.12 ElectronegativeHalogenicity=0.24
*see following data for other ILs

== SMD input database ==
Here we will keep a database of SMD parameters used by the group. Please add any IL you use, so no-one else has to re-do the research for the parameters! Please follow the template provided so that it is clear where you get each value from.

=== SMD-GIL ===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.50
|
|
|-
|epsinf (n2)
|2.0449
|
|
|-
|SurfaceTensionAtInterface
|61.24
|
|
|-
|HBondAcidity (α)
|0.229
|
|
|-
|HBondBasicity (β)
|0.265
|
|
|-
|CarbonAromaticity (φ)
|compute for your system
|
|
|-
|ElectronegativeHalogenicity (ψ)
|compute for your system
|
|
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][BF4]===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.70
|
|
|-
|epsinf n2)
|2.0207
|
|Value given in reference is n=1.4215, it has been squared to give epsinf=2.0207
|-
|SurfaceTensionAtInterface
|67.07
|
|
|-
|HBondAcidity (α)
|0.263
|
| Kamlet-Taft 0.627
|-
|HBondBasicity (β)
|0.320
|
| Kamlet-Taft 0.376
|-
|CarbonAromaticity (φ)
|0.2000
|
|There are 15 non-H atoms, 3 are aromatic C atoms, value=3/15=0.2000
|-
|ElectronegativeHalogenicity (ψ)
|0.2667
|
|There are 15 non-H atoms, 4 are electronegative halogen atoms, value =4/15=0.2667
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][PF6]===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.40
|
|
|-
|epsinf n2)
|1.9853
|
|Value given in reference is n=1.4090, it has been squared to give epsinf=1.9853
|-
|SurfaceTensionAtInterface
|70.24
|
|
|-
|HBondAcidity (α)
|0.266
|
| Kamlet-Taft 0.634
|-
|HBondBasicity (β)
|0.216
|
| Kamlet-Taft 0.207
|-
|CarbonAromaticity (φ)
|0.1765
|
|There are 17 non-H atoms, 3 are aromatic C atoms, value=3/17=0.1765
|-
|ElectronegativeHalogenicity (ψ)
|0.3529
|
|There are 17 non-H atoms, 4 are electronegative halogen atoms, value =6/17=0.3529
|-
| colspan="4" |<code>eps=11.40 epsinf=1.9853 SurfaceTensionAtInterface=70.24 HBondAcidity=0.266 HBondBasicity=0.216 CarbonAromaticity=0.1765 ElectronegativeHalogenicity=0.3529</code>
|}

=== [C4C1Im][NTf2] ===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.52
|<ref name="Daguenet">Daguenet 2006 http://pubs.acs.org/doi/abs/10.1021/jp0604903</ref>
|
|-
|epsinf n2)
|2.0366
|<ref name="Huddleston">Huddleston 2001 http://pubs.rsc.org/en/Content/ArticleLanding/2001/GC/b103275p</ref>
|Value given in reference is n=1.4271, it has been squared to give epsinf=2.0366
|-
|SurfaceTensionAtInterface
|53.97
|<ref name="Huddleston" />
|
|-
|HBondAcidity (α)
|0.259
|<ref name=":2" />
| Kamlet-Taft 0.617
|-
|HBondBasicity (β)
|0.238
|<ref name=":2" />
| Kamlet-Taft 0.243
|-
|CarbonAromaticity
|0.1200
|
|There are 25 non-H atoms, 3 are aromatic C atoms, value =3/25=0.1200
|-
|ElectronegativeHalogenicity
|0.2400
|
|There are 25 non-H atoms, 6 are electronegative halogen atoms, value =6/25=0.2400
|-
| colspan="4" |<code>eps=11.52 epsinf=2.0366 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.1200 ElectronegativeHalogenicity=0.2400</code>
|}

=== [C4C1Im][OTf] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|12.90
|<ref name="Huang"> M. M. Huang, Y. P. Jiang, P. Sasisanker, G. W. Driver and H. Weingartner,  J. Chem. Eng. Data, 2011, 56, 1494–1499. http://pubs.acs.org/doi/abs/10.1021/je101184s</ref>
|Page 1495, number 11 on the list.
|-
|epsinf n2)
|2.0665
|<ref name="Gonzalez"> Gonzalez 2012 http://pubs.acs.org/doi/abs/10.1021/je201334p</ref>
|n=1.43755, has been squared to give epsinf=2.0665. Can be found in Table 1, 3rd row.
|-
|SurfaceTensionAtInterface
|unknown
|
|-
|HBondAcidity (α)
|0.263
|<ref name="Bernales" /> <ref name=":2" />
| Kamlet-Taft 0.625
|-
|HBondBasicity (β)
|0.374
|<ref name="Bernales" /> <ref name=":2" />
| Kamlet-Taft 0.464
|-
|CarbonAromaticity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are aromatic C atoms, value=3/18=0.1667.
|-
|ElectronegativeHalogenicity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are electronegative halogen atoms, value=3/18=0.1667.
|-
| colspan="4" |<code>eps=12.90 epsinf=2.0665 SurfaceTensionAtInterface'''=XX''' HBondAcidity=0.263 HBondBasicity=0.374 CarbonAromaticity=0.1667 ElectronegativeHalogenicity=0.1667</code>
|}

=== [C4C1Im][SCN] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|13.70
| <ref name="Huang" />
|
|-
|epsinf (n2)
|2.3691
| <ref name="Vakili">G. Vakili-Nezhaad, M. Vatani, M. Asghari and I. Ashour, J. Chem. Thermodyn., 2012, 54, 148–154. </ref>
|n=1.53921, has been squared to give epsinf=2.3691 (error in some database calcs with n=1.5436 n2=2.3827)
|-
|SurfaceTensionAtInterface
|68.34
| <ref name="Vakili" />
| η=45.41 (mN.m-1) converts to 45.41*1.439= cal mol-1 Å-2=65.34
|-
|HBondAcidity (α)
|0.18
|
| Kamlet-Taft 0.43
|-
|HBondBasicity (β)
|0.52
|
| Kamlet-Taft 0.71
|-
|CarbonAromaticity
|0.2308
|
|There are 13 non-H atoms, 3 are aromatic C atoms, value=xx/xx=0.2308
|-
|ElectronegativeHalogenicity
|0.0
|
|There are no electronegative halogen atoms, value=0.0
|-
| colspan="4" |<code>eps=13.70 epsinf=2.3691 SurfaceTensionAtInterface=68.34 HBondAcidity=0.18 HBondBasicity=0.52 CarbonAromaticity=0.2308 ElectronegativeHalogenicity=0.0</code>
|}

=== Molten salt [Li+,Na+,K+][CO32-] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|MolarVolume
|57
|<ref name=":5" />
|molar volume Li2CO3 68 Na2CO3 92 K2CO3 124 Å3/molecule, average is 95 and 95*0.6022=57 at T=1.1Tm
|-
|Tabs
|900
|
|Absolute Temperature in K ie 298+600≈900
|-
|???
|
|
|ThermalExansionCoefficient estimate 20*10-6 K-1 at T=1.1Tm (this is not working!)
|-
|eps
|3
|<ref name="Janz"> G. Janz and M. Lorenz, <abbr>J. Electrochem. Soc.</abbr> 1961 volume 108, issue 11, 1052-1058 doi: 10.1149/1.2427946</ref>
|estimated value
|-
|epsinf n2)
|2.25
|
|refractive index Na2CO3 1.489-1.535,<ref><nowiki>https://pubchem.ncbi.nlm.nih.gov/compound/sodium_carbonate#section=Spectral-Properties&fullscreen=true</nowiki></ref> Li2CO3 1.428-1.572<ref>Weast, R.C. (ed.). Handbook of Chemistry and Physics. 60th ed. Boca Raton, Florida: CRC Press Inc., 1979., p. B-91</ref> K2CO3 1.426-1.541<ref><nowiki>http://cameo.mfa.org/wiki/Potassium_carbonate</nowiki></ref> taking a "mid" value 1.52=2.25
|-
|SurfaceTensionAtInterface
|273
|<ref name=":5" />
|used surface tension of Na/K/CO3 mixture 50 mol % K2CO3 at 810 ºC , 190.0 dynes/cm
|-
|HBondAcidity (α)
|0.00
|<nowiki>-</nowiki>
| rowspan="2" |There are no H-atoms so H-bond acidity is zero
H-bond basicity computations result in proton transfer, NO3 ≈0.74-0.81, Cl ≈0.95-0.98, we assume it is even stronger due to -2 charge
|-
|HBondBasicity (β)
|0.99
|
|-
|CarbonAromaticity
|0.00
|<nowiki>-</nowiki>
|There are no aromatic C atoms
|-
|ElectronegativeHalogenicity
|0.00
|<nowiki>-</nowiki>
|There are no halogen atoms
|-
| colspan="4" |Stoichiometry=C2O62Li2Na2K2 MolarVolume=57.0 Tabs=900 eps=3.0 epsinf=2.25 SurfaceTensionAtInterface=273 HBondAcidity=0.0 HBondBasicity=0.99 CarbonAromaticity=0.0 ElectronegativeHalogenicity=0.0
|}

=== Example IL-GIL (generic IL) ===
all values from <ref name="Bernales" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.50
|
|see ESI Table S2.1
|-
|epsinf n2)
|2.0449
|
|n=1.43, has been squared to give epsinf=2.0449
|-
|SurfaceTensionAtInterface
|61.24
|
|<code>see ESI Table S2.1</code>
|-
|HBondAcidity (α)
|0.229
|
|<code>see ESI Table S2.1</code>
|-
|HBondBasicity (β)
|0.265
|
|<code>see ESI Table S2.1</code>
|-
|CarbonAromaticity
|
|
|
|-
|ElectronegativeHalogenicity
|
|
|
|-
| colspan="4" |<code>eps=11.50 epsinf=2.0449 SurfaceTensionAtInterface=61.24 HBondAcidity=0.229 HBondBasicity=0.265 CarbonAromaticity=0.xxx ElectronegativeHalogenicity=0.xxx</code>
|}

== Example table ==
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|
|
|
|-
|epsinf
|
|
|
|-
|SurfaceTensionAtInterface
|
|
|
|-
|HBondAcidity (α)
|
|
|
|-
|HBondBasicity (β)
|
|
|
|-
|CarbonAromaticity
|
|
|
|-
|ElectronegativeHalogenicity
|
|
|
|-
| colspan="4" |<code>eps= epsinf= SurfaceTensionAtInterface= HBondAcidity= HBondBasicity= CarbonAromaticity= ElectronegativeHalogenicity=</code>
|}

== References ==
<references />

Mod:Hunt Research Group: Using SMD on ILs

2019-12-23T10:52:12Z

Phunt: /* [C4C1Im][XX] */

This page explains how to use the SMD model to simulate an ionic liquid environment in Gaussian calculations. The SMD model is explained in detail in the original paper here.<ref>Marenich 2009 http://pubs.acs.org/doi/abs/10.1021/jp810292n</ref> Its use on ILs is similarly explained here.<ref name=":0">Bernales 2012 http://pubs.acs.org/doi/abs/10.1021/jp304365v</ref> Many useful solvent parameters are also available in this paper.

== How to simulate a defined solvent environment ==
Gaussian has many previously defined solvent environments. A list is available at the bottom of this page.<ref>http://www.gaussian.com/g_tech/g_ur/k_scrf.htm</ref> For example to use the pre-defined water environment simply insert the following keyword into the method line of your input file. The rest of your method line should specify your functional, basis set, optimisation/other type of calculation as usual.
scrf=(smd,solvent=water)
To use a different solvent to water change the solvent=water part to solvent=something else in the list.

== How to simulate a generic solvent environment ==
The SMD model has many parameters. These are already defined inside Gaussian for the list of defined solvents. If you want to use a solvent not on the list e.g. an ionic liquid, you must define these parameters manually. In this case put the following into the method line:
scrf=(smd,solvent=generic)

===Solvent parameters===
{| class="wikitable"
!Parameter
!Symbol
!Name in Gaussian input file
|-
|Dielectric constant
|ε
|eps
|-
|Index of refraction, squared
|n2
|epsinf
|-
|Macroscopic surface tension /cal mol-1 Å-2
|γ
|SurfaceTensionAtInterface
|-
|Abraham hydrogen bond acidity parameter
|Σα2H
|HBondAcidity
|-
|Abraham hydrogen bond basicity parameter
|Σβ2H
|HBondBasicity
|-
|Fraction of non-hydrogen atoms which are aromatic carbon atoms
|φ
|CarbonAromaticity
|
|-
|Fraction of non-hydrogen atoms which are electronegative halogen atoms
|ψ
|ElectronegativeHalogenicity
|
|}

===Notes on parameters===
Surface tension
*surface tension is the only parameter with units, those used in SMD are non-standard cal mol-1Å-2
*the SI units are Jm-2 or Nm-1
*typical units are dyn cm-1 where 1 dyn = 1 g cm s-2
*as we tend to work in kJ/mol the energy part of this becomes not J but J/mol
*1 dyn cm-1 = 0.001N m-1 = 0.001J m-2
*1 m = 1*1010Å and 1J=0.239cal and 1 mol-1=6.022*1023
*1 dyn cm-1 = 0.001*0.239cal*6.022*1023mol-1/(1*102*10Å2
*and if you think about this 1023 on top line cancels with 1020 on bottom line leaving 103 which cancels with the 0.001=10-3 leaving us with 0.239*6.022=1.439
*1 dyn cm-1 = 1.439 cal mol-1 Å-2

Molar Volume
* MolarVolume=x.x in cm3/mol
* molecular volume in Å3 per molecule converted to cm3/mol
* 1cm = 1*108Å, 1Å = 1*10-8 cm
* x Å3 per molecule = x*6.022*1023mol-1 *103*-8cm3 = x*6.022*10-1cm3mol-1

Kamlet-Taft vs Abraham H-bonding parameters
*the SMD model requires Abraham H-bondonding parameters (Σα2H, Σβ2H)
*however Kamlet-Taft (α, β) measurements are more commonly reported for ILs
*a relationship between the parameters was investigated, giving the following equations:<ref name=":0" />

Σα2H = 0.4098α + 0.0064

Σβ2H = 0.6138β + 0.0890

Previously the group has developed a simple method for calculating Kamlet-Taft parameters, and the instructions are here.<ref>http://www.huntresearchgroup.org.uk/research/research_il_alpha_beta_intro.html</ref>

===Types of SMD model for ILs===
3 types of SMD for ILs have been defined.<ref name=":0" />
*SMD The standard SMD model. All parameters are determined for the particular IL (or a very similar one) being used as the solvent environment.
*SMD-GIL The generic ionic liquid model. The average values above are used for all parameters, except φ and ψ, which are simply calculated from the chemical formula of the IL.
*SMD-PGPThe partial generic parameters model. Any parameter which has been measured for that IL is used. For any parameters which you do not have values for, use the average values.

Example: [C4C1Im][NTf2] 
*All parameters for this IL have been measured, and can be found in reference 2.<ref name=":0" /> That means we can use the standard SMD method.
*To get a value for φ take the number of aromatic carbon atoms (3) and divide by the number of non-hydrogen atoms (25). φ = 0.12.
*To get a value for ψ take the number of electronegative halogen atoms (6) and divide by the number of non-hydrogen atoms (25). ψ = 0.24.
*To define these parameters place the following line at the bottom of the input file (include one blank line before and at least one blank line after):
* eps=11.52 epsinf=2.037 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.12 ElectronegativeHalogenicity=0.24
*see following data for other ILs

== SMD input database ==
Here we will keep a database of SMD parameters used by the group. Please add any IL you use, so no-one else has to re-do the research for the parameters! Please follow the template provided so that it is clear where you get each value from.

=== SMD-GIL ===
all values from <ref name=":0" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.50
|<ref name=":0" />
|
|-
|epsinf (n2)
|2.0449
|<ref name=":0" />
|
|-
|SurfaceTensionAtInterface
|61.24
|<ref name=":0" />
|
|-
|HBondAcidity (α)
|0.229
|<ref name=":0" />
|
|-
|HBondBasicity (β)
|0.265
|<ref name=":0" />
|
|-
|CarbonAromaticity (φ)
|compute for your system
|
|
|-
|ElectronegativeHalogenicity (ψ)
|compute for your system
|
|
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][BF4]===
all values from <ref name=":0" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.70
|<ref name=":0" />
|
|-
|epsinf n2)
|2.0207
|<ref name=":0" />
|Value given in reference is n=1.4215, it has been squared to give epsinf=2.0207
|-
|SurfaceTensionAtInterface
|67.07
|<ref name=":0" />
|
|-
|HBondAcidity (α)
|0.263
|<ref name=":0" />
| Kamlet-Taft 0.627
|-
|HBondBasicity (β)
|0.320
|<ref name=":0" />
| Kamlet-Taft 0.376
|-
|CarbonAromaticity (φ)
|0.2000
|
|There are 15 non-H atoms, 3 are aromatic C atoms, value=3/15=0.2000
|-
|ElectronegativeHalogenicity (ψ)
|0.2667
|
|There are 15 non-H atoms, 4 are electronegative halogen atoms, value =4/15=0.2667
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][PF6]===
all values from <ref name=":0" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.40
|<ref name=":0" />
|
|-
|epsinf n2)
|1.9853
|<ref name=":0" />
|Value given in reference is n=1.4090, it has been squared to give epsinf=1.9853
|-
|SurfaceTensionAtInterface
|70.24
|<ref name=":0" />
|
|-
|HBondAcidity (α)
|0.266
|<ref name=":0" />
| Kamlet-Taft 0.634
|-
|HBondBasicity (β)
|0.216
|<ref name=":0" />
| Kamlet-Taft 0.207
|-
|CarbonAromaticity (φ)
|0.1765
|
|There are 17 non-H atoms, 3 are aromatic C atoms, value=3/17=0.1765
|-
|ElectronegativeHalogenicity (ψ)
|0.3529
|
|There are 17 non-H atoms, 4 are electronegative halogen atoms, value =6/17=0.3529
|-
| colspan="4" |<code>eps=11.40 epsinf=1.9853 SurfaceTensionAtInterface=70.24 HBondAcidity=0.266 HBondBasicity=0.216 CarbonAromaticity=0.1765 ElectronegativeHalogenicity=0.3529</code>
|}

=== [C4C1Im][NTf2] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.52
|<ref name=":0" /> <ref name=":6">Daguenet 2006 http://pubs.acs.org/doi/abs/10.1021/jp0604903</ref>
|
|-
|epsinf n2)
|2.0366
|<ref name=":0" /> <ref name=":1">Huddleston 2001 http://pubs.rsc.org/en/Content/ArticleLanding/2001/GC/b103275p</ref>
|Value given in reference is n=1.4271, it has been squared to give epsinf=2.0366
|-
|SurfaceTensionAtInterface
|53.97
|<ref name=":0" /> <ref name=":1" />
|
|-
|HBondAcidity (α)
|0.259
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.617
|-
|HBondBasicity (β)
|0.238
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.243
|-
|CarbonAromaticity
|0.1200
|
|There are 25 non-H atoms, 3 are aromatic C atoms, value =3/25=0.1200
|-
|ElectronegativeHalogenicity
|0.2400
|
|There are 25 non-H atoms, 6 are electronegative halogen atoms, value =6/25=0.2400
|-
| colspan="4" |<code>eps=11.52 epsinf=2.0366 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.1200 ElectronegativeHalogenicity=0.2400</code>
|}

=== [C4C1Im][OTf] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|12.90
|<ref name=":3">Huang 2011 http://pubs.acs.org/doi/abs/10.1021/je101184s</ref>
|Page 1495, number 11 on the list.
|-
|epsinf n2)
|2.0665
|<ref name=":4">Gonzalez 2012 http://pubs.acs.org/doi/abs/10.1021/je201334p</ref>
|n=1.43755, has been squared to give epsinf=2.0665. Can be found in Table 1, 3rd row.
|-
|SurfaceTensionAtInterface
|unknown
|
|-
|HBondAcidity (α)
|0.263
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.625
|-
|HBondBasicity (β)
|0.374
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.464
|-
|CarbonAromaticity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are aromatic C atoms, value=3/18=0.1667.
|-
|ElectronegativeHalogenicity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are electronegative halogen atoms, value=3/18=0.1667.
|-
| colspan="4" |<code>eps=12.90 epsinf=2.0665 SurfaceTensionAtInterface'''=XX''' HBondAcidity=0.263 HBondBasicity=0.374 CarbonAromaticity=0.1667 ElectronegativeHalogenicity=0.1667</code>
|}

=== [C4C1Im][SCN] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|13.70
| M. M. Huang, Y. P. Jiang, P. Sasisanker, G. W. Driver and H. Weingartner,  J. Chem. Eng. Data, 2011, 56, 1494–1499.
|
|-
|epsinf (n2)
|2.3691
| G. Vakili-Nezhaad, M. Vatani, M. Asghari and I. Ashour, J. Chem. Thermodyn., 2012, 54, 148–154.
|n=1.53921, has been squared to give epsinf=2.3691 (error in some database calcs with n=1.5436 n2=2.3827)
|-
|SurfaceTensionAtInterface
|68.34
| G. Vakili-Nezhaad, M. Vatani, M. Asghari and I. Ashour, J. Chem. Thermodyn., 2012, 54, 148–154.
| η=45.41 (mN.m-1) converts to 45.41*1.439= cal mol-1 Å-2=65.34
|-
|HBondAcidity (α)
|0.18
|
| Kamlet-Taft 0.43
|-
|HBondBasicity (β)
|0.52
|
| Kamlet-Taft 0.71
|-
|CarbonAromaticity
|0.2308
|
|There are 13 non-H atoms, 3 are aromatic C atoms, value=xx/xx=0.2308
|-
|ElectronegativeHalogenicity
|0.0
|
|There are no electronegative halogen atoms, value=0.0
|-
| colspan="4" |<code>eps=13.70 epsinf=2.3691 SurfaceTensionAtInterface=68.34 HBondAcidity=0.18 HBondBasicity=0.52 CarbonAromaticity=0.2308 ElectronegativeHalogenicity=0.0</code>
|}

=== Molten salt [Li+,Na+,K+][CO32-] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|MolarVolume
|57
|<ref name=":5" />
|molar volume Li2CO3 68 Na2CO3 92 K2CO3 124 Å3/molecule, average is 95 and 95*0.6022=57 at T=1.1Tm
|-
|Tabs
|900
|
|Absolute Temperature in K ie 298+600≈900
|-
|???
|
|
|ThermalExansionCoefficient estimate 20*10-6 K-1 at T=1.1Tm (this is not working!)
|-
|eps
|3
|<ref name=":5">G. Janz and M. Lorenz, <abbr>J. Electrochem. Soc.</abbr> 1961 volume 108, issue 11, 1052-1058 doi: 10.1149/1.2427946</ref>
|estimated value
|-
|epsinf n2)
|2.25
|
|refractive index Na2CO3 1.489-1.535,<ref><nowiki>https://pubchem.ncbi.nlm.nih.gov/compound/sodium_carbonate#section=Spectral-Properties&fullscreen=true</nowiki></ref> Li2CO3 1.428-1.572<ref>Weast, R.C. (ed.). Handbook of Chemistry and Physics. 60th ed. Boca Raton, Florida: CRC Press Inc., 1979., p. B-91</ref> K2CO3 1.426-1.541<ref><nowiki>http://cameo.mfa.org/wiki/Potassium_carbonate</nowiki></ref> taking a "mid" value 1.52=2.25
|-
|SurfaceTensionAtInterface
|273
|<ref name=":5" />
|used surface tension of Na/K/CO3 mixture 50 mol % K2CO3 at 810 ºC , 190.0 dynes/cm
|-
|HBondAcidity (α)
|0.00
|<nowiki>-</nowiki>
| rowspan="2" |There are no H-atoms so H-bond acidity is zero
H-bond basicity computations result in proton transfer, NO3 ≈0.74-0.81, Cl ≈0.95-0.98, we assume it is even stronger due to -2 charge
|-
|HBondBasicity (β)
|0.99
|
|-
|CarbonAromaticity
|0.00
|<nowiki>-</nowiki>
|There are no aromatic C atoms
|-
|ElectronegativeHalogenicity
|0.00
|<nowiki>-</nowiki>
|There are no halogen atoms
|-
| colspan="4" |Stoichiometry=C2O62Li2Na2K2 MolarVolume=57.0 Tabs=900 eps=3.0 epsinf=2.25 SurfaceTensionAtInterface=273 HBondAcidity=0.0 HBondBasicity=0.99 CarbonAromaticity=0.0 ElectronegativeHalogenicity=0.0
|}

=== Example IL-GIL (generic IL) ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.50
|<ref name=":0" />
|see ESI Table S2.1
|-
|epsinf n2)
|2.0449
|<ref name=":0" />
|n=1.43, has been squared to give epsinf=2.0449
|-
|SurfaceTensionAtInterface
|61.24
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|HBondAcidity (α)
|0.229
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|HBondBasicity (β)
|0.265
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|CarbonAromaticity
|
|<ref name=":0" />
|
|-
|ElectronegativeHalogenicity
|
|<ref name=":0" />
|
|-
| colspan="4" |<code>eps=11.50 epsinf=2.0449 SurfaceTensionAtInterface=61.24 HBondAcidity=0.229 HBondBasicity=0.265 CarbonAromaticity=0.xxx ElectronegativeHalogenicity=0.xxx</code>
|}

== Example table ==
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|
|
|
|-
|epsinf
|
|
|
|-
|SurfaceTensionAtInterface
|
|
|
|-
|HBondAcidity (α)
|
|
|
|-
|HBondBasicity (β)
|
|
|
|-
|CarbonAromaticity
|
|
|
|-
|ElectronegativeHalogenicity
|
|
|
|-
| colspan="4" |<code>eps= epsinf= SurfaceTensionAtInterface= HBondAcidity= HBondBasicity= CarbonAromaticity= ElectronegativeHalogenicity=</code>
|}

== References ==
<references />

Mod:Hunt Research Group: Using SMD on ILs

2019-12-23T10:50:42Z

Phunt: /* SMD input database */

This page explains how to use the SMD model to simulate an ionic liquid environment in Gaussian calculations. The SMD model is explained in detail in the original paper here.<ref>Marenich 2009 http://pubs.acs.org/doi/abs/10.1021/jp810292n</ref> Its use on ILs is similarly explained here.<ref name=":0">Bernales 2012 http://pubs.acs.org/doi/abs/10.1021/jp304365v</ref> Many useful solvent parameters are also available in this paper.

== How to simulate a defined solvent environment ==
Gaussian has many previously defined solvent environments. A list is available at the bottom of this page.<ref>http://www.gaussian.com/g_tech/g_ur/k_scrf.htm</ref> For example to use the pre-defined water environment simply insert the following keyword into the method line of your input file. The rest of your method line should specify your functional, basis set, optimisation/other type of calculation as usual.
scrf=(smd,solvent=water)
To use a different solvent to water change the solvent=water part to solvent=something else in the list.

== How to simulate a generic solvent environment ==
The SMD model has many parameters. These are already defined inside Gaussian for the list of defined solvents. If you want to use a solvent not on the list e.g. an ionic liquid, you must define these parameters manually. In this case put the following into the method line:
scrf=(smd,solvent=generic)

===Solvent parameters===
{| class="wikitable"
!Parameter
!Symbol
!Name in Gaussian input file
|-
|Dielectric constant
|ε
|eps
|-
|Index of refraction, squared
|n2
|epsinf
|-
|Macroscopic surface tension /cal mol-1 Å-2
|γ
|SurfaceTensionAtInterface
|-
|Abraham hydrogen bond acidity parameter
|Σα2H
|HBondAcidity
|-
|Abraham hydrogen bond basicity parameter
|Σβ2H
|HBondBasicity
|-
|Fraction of non-hydrogen atoms which are aromatic carbon atoms
|φ
|CarbonAromaticity
|
|-
|Fraction of non-hydrogen atoms which are electronegative halogen atoms
|ψ
|ElectronegativeHalogenicity
|
|}

===Notes on parameters===
Surface tension
*surface tension is the only parameter with units, those used in SMD are non-standard cal mol-1Å-2
*the SI units are Jm-2 or Nm-1
*typical units are dyn cm-1 where 1 dyn = 1 g cm s-2
*as we tend to work in kJ/mol the energy part of this becomes not J but J/mol
*1 dyn cm-1 = 0.001N m-1 = 0.001J m-2
*1 m = 1*1010Å and 1J=0.239cal and 1 mol-1=6.022*1023
*1 dyn cm-1 = 0.001*0.239cal*6.022*1023mol-1/(1*102*10Å2
*and if you think about this 1023 on top line cancels with 1020 on bottom line leaving 103 which cancels with the 0.001=10-3 leaving us with 0.239*6.022=1.439
*1 dyn cm-1 = 1.439 cal mol-1 Å-2

Molar Volume
* MolarVolume=x.x in cm3/mol
* molecular volume in Å3 per molecule converted to cm3/mol
* 1cm = 1*108Å, 1Å = 1*10-8 cm
* x Å3 per molecule = x*6.022*1023mol-1 *103*-8cm3 = x*6.022*10-1cm3mol-1

Kamlet-Taft vs Abraham H-bonding parameters
*the SMD model requires Abraham H-bondonding parameters (Σα2H, Σβ2H)
*however Kamlet-Taft (α, β) measurements are more commonly reported for ILs
*a relationship between the parameters was investigated, giving the following equations:<ref name=":0" />

Σα2H = 0.4098α + 0.0064

Σβ2H = 0.6138β + 0.0890

Previously the group has developed a simple method for calculating Kamlet-Taft parameters, and the instructions are here.<ref>http://www.huntresearchgroup.org.uk/research/research_il_alpha_beta_intro.html</ref>

===Types of SMD model for ILs===
3 types of SMD for ILs have been defined.<ref name=":0" />
*SMD The standard SMD model. All parameters are determined for the particular IL (or a very similar one) being used as the solvent environment.
*SMD-GIL The generic ionic liquid model. The average values above are used for all parameters, except φ and ψ, which are simply calculated from the chemical formula of the IL.
*SMD-PGPThe partial generic parameters model. Any parameter which has been measured for that IL is used. For any parameters which you do not have values for, use the average values.

Example: [C4C1Im][NTf2] 
*All parameters for this IL have been measured, and can be found in reference 2.<ref name=":0" /> That means we can use the standard SMD method.
*To get a value for φ take the number of aromatic carbon atoms (3) and divide by the number of non-hydrogen atoms (25). φ = 0.12.
*To get a value for ψ take the number of electronegative halogen atoms (6) and divide by the number of non-hydrogen atoms (25). ψ = 0.24.
*To define these parameters place the following line at the bottom of the input file (include one blank line before and at least one blank line after):
* eps=11.52 epsinf=2.037 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.12 ElectronegativeHalogenicity=0.24
*see following data for other ILs

== SMD input database ==
Here we will keep a database of SMD parameters used by the group. Please add any IL you use, so no-one else has to re-do the research for the parameters! Please follow the template provided so that it is clear where you get each value from.

=== SMD-GIL ===
all values from <ref name=":0" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.50
|<ref name=":0" />
|
|-
|epsinf (n2)
|2.0449
|<ref name=":0" />
|
|-
|SurfaceTensionAtInterface
|61.24
|<ref name=":0" />
|
|-
|HBondAcidity (α)
|0.229
|<ref name=":0" />
|
|-
|HBondBasicity (β)
|0.265
|<ref name=":0" />
|
|-
|CarbonAromaticity (φ)
|compute for your system
|
|
|-
|ElectronegativeHalogenicity (ψ)
|compute for your system
|
|
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][BF4]===
all values from <ref name=":0" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.70
|<ref name=":0" />
|
|-
|epsinf n2)
|2.0207
|<ref name=":0" />
|Value given in reference is n=1.4215, it has been squared to give epsinf=2.0207
|-
|SurfaceTensionAtInterface
|67.07
|<ref name=":0" />
|
|-
|HBondAcidity (α)
|0.263
|<ref name=":0" />
| Kamlet-Taft 0.627
|-
|HBondBasicity (β)
|0.320
|<ref name=":0" />
| Kamlet-Taft 0.376
|-
|CarbonAromaticity (φ)
|0.2000
|
|There are 15 non-H atoms, 3 are aromatic C atoms, value=3/15=0.2000
|-
|ElectronegativeHalogenicity (ψ)
|0.2667
|
|There are 15 non-H atoms, 4 are electronegative halogen atoms, value =4/15=0.2667
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][PF6]===
all values from <ref name=":0" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.40
|<ref name=":0" />
|
|-
|epsinf n2)
|1.9853
|<ref name=":0" />
|Value given in reference is n=1.4090, it has been squared to give epsinf=1.9853
|-
|SurfaceTensionAtInterface
|70.24
|<ref name=":0" />
|
|-
|HBondAcidity (α)
|0.266
|<ref name=":0" />
| Kamlet-Taft 0.634
|-
|HBondBasicity (β)
|0.216
|<ref name=":0" />
| Kamlet-Taft 0.207
|-
|CarbonAromaticity (φ)
|0.1765
|
|There are 17 non-H atoms, 3 are aromatic C atoms, value=3/17=0.1765
|-
|ElectronegativeHalogenicity (ψ)
|0.3529
|
|There are 17 non-H atoms, 4 are electronegative halogen atoms, value =6/17=0.3529
|-
| colspan="4" |<code>eps=11.40 epsinf=1.9853 SurfaceTensionAtInterface=70.24 HBondAcidity=0.266 HBondBasicity=0.216 CarbonAromaticity=0.1765 ElectronegativeHalogenicity=0.3529</code>
|}

=== [C4C1Im][NTf2] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.52
|<ref name=":0" /> <ref name=":6">Daguenet 2006 http://pubs.acs.org/doi/abs/10.1021/jp0604903</ref>
|
|-
|epsinf n2)
|2.0366
|<ref name=":0" /> <ref name=":1">Huddleston 2001 http://pubs.rsc.org/en/Content/ArticleLanding/2001/GC/b103275p</ref>
|Value given in reference is n=1.4271, it has been squared to give epsinf=2.0366
|-
|SurfaceTensionAtInterface
|53.97
|<ref name=":0" /> <ref name=":1" />
|
|-
|HBondAcidity (α)
|0.259
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.617
|-
|HBondBasicity (β)
|0.238
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.243
|-
|CarbonAromaticity
|0.1200
|
|There are 25 non-H atoms, 3 are aromatic C atoms, value =3/25=0.1200
|-
|ElectronegativeHalogenicity
|0.2400
|
|There are 25 non-H atoms, 6 are electronegative halogen atoms, value =6/25=0.2400
|-
| colspan="4" |<code>eps=11.52 epsinf=2.0366 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.1200 ElectronegativeHalogenicity=0.2400</code>
|}

=== [C4C1Im][OTf] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|12.90
|<ref name=":3">Huang 2011 http://pubs.acs.org/doi/abs/10.1021/je101184s</ref>
|Page 1495, number 11 on the list.
|-
|epsinf n2)
|2.0665
|<ref name=":4">Gonzalez 2012 http://pubs.acs.org/doi/abs/10.1021/je201334p</ref>
|n=1.43755, has been squared to give epsinf=2.0665. Can be found in Table 1, 3rd row.
|-
|SurfaceTensionAtInterface
|unknown
|
|-
|HBondAcidity (α)
|0.263
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.625
|-
|HBondBasicity (β)
|0.374
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.464
|-
|CarbonAromaticity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are aromatic C atoms, value=3/18=0.1667.
|-
|ElectronegativeHalogenicity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are electronegative halogen atoms, value=3/18=0.1667.
|-
| colspan="4" |<code>eps=12.90 epsinf=2.0665 SurfaceTensionAtInterface'''=XX''' HBondAcidity=0.263 HBondBasicity=0.374 CarbonAromaticity=0.1667 ElectronegativeHalogenicity=0.1667</code>
|}

=== [C4C1Im][XX] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|13.70
| M. M. Huang, Y. P. Jiang, P. Sasisanker, G. W. Driver and H. Weingartner,  J. Chem. Eng. Data, 2011, 56, 1494–1499.
|
|-
|epsinf (n2)
|2.3691
| G. Vakili-Nezhaad, M. Vatani, M. Asghari and I. Ashour, J. Chem. Thermodyn., 2012, 54, 148–154.
|n=1.53921, has been squared to give epsinf=2.3691 (error in some database calcs with n=1.5436 n2=2.3827)
|-
|SurfaceTensionAtInterface
|68.34
| G. Vakili-Nezhaad, M. Vatani, M. Asghari and I. Ashour, J. Chem. Thermodyn., 2012, 54, 148–154.
| η=45.41 (mN.m-1) converts to 45.41*1.439= cal mol-1 Å-2=65.34
|-
|HBondAcidity (α)
|0.18
|
| Kamlet-Taft 0.43
|-
|HBondBasicity (β)
|0.52
|
| Kamlet-Taft 0.71
|-
|CarbonAromaticity
|0.2308
|
|There are 13 non-H atoms, 3 are aromatic C atoms, value=xx/xx=0.2308
|-
|ElectronegativeHalogenicity
|0.0
|
|There are no electronegative halogen atoms, value=0.0
|-
| colspan="4" |<code>eps=13.70 epsinf=2.3691 SurfaceTensionAtInterface=68.34 HBondAcidity=0.18 HBondBasicity=0.52 CarbonAromaticity=0.2308 ElectronegativeHalogenicity=0.0</code>
|}

=== Molten salt [Li+,Na+,K+][CO32-] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|MolarVolume
|57
|<ref name=":5" />
|molar volume Li2CO3 68 Na2CO3 92 K2CO3 124 Å3/molecule, average is 95 and 95*0.6022=57 at T=1.1Tm
|-
|Tabs
|900
|
|Absolute Temperature in K ie 298+600≈900
|-
|???
|
|
|ThermalExansionCoefficient estimate 20*10-6 K-1 at T=1.1Tm (this is not working!)
|-
|eps
|3
|<ref name=":5">G. Janz and M. Lorenz, <abbr>J. Electrochem. Soc.</abbr> 1961 volume 108, issue 11, 1052-1058 doi: 10.1149/1.2427946</ref>
|estimated value
|-
|epsinf n2)
|2.25
|
|refractive index Na2CO3 1.489-1.535,<ref><nowiki>https://pubchem.ncbi.nlm.nih.gov/compound/sodium_carbonate#section=Spectral-Properties&fullscreen=true</nowiki></ref> Li2CO3 1.428-1.572<ref>Weast, R.C. (ed.). Handbook of Chemistry and Physics. 60th ed. Boca Raton, Florida: CRC Press Inc., 1979., p. B-91</ref> K2CO3 1.426-1.541<ref><nowiki>http://cameo.mfa.org/wiki/Potassium_carbonate</nowiki></ref> taking a "mid" value 1.52=2.25
|-
|SurfaceTensionAtInterface
|273
|<ref name=":5" />
|used surface tension of Na/K/CO3 mixture 50 mol % K2CO3 at 810 ºC , 190.0 dynes/cm
|-
|HBondAcidity (α)
|0.00
|<nowiki>-</nowiki>
| rowspan="2" |There are no H-atoms so H-bond acidity is zero
H-bond basicity computations result in proton transfer, NO3 ≈0.74-0.81, Cl ≈0.95-0.98, we assume it is even stronger due to -2 charge
|-
|HBondBasicity (β)
|0.99
|
|-
|CarbonAromaticity
|0.00
|<nowiki>-</nowiki>
|There are no aromatic C atoms
|-
|ElectronegativeHalogenicity
|0.00
|<nowiki>-</nowiki>
|There are no halogen atoms
|-
| colspan="4" |Stoichiometry=C2O62Li2Na2K2 MolarVolume=57.0 Tabs=900 eps=3.0 epsinf=2.25 SurfaceTensionAtInterface=273 HBondAcidity=0.0 HBondBasicity=0.99 CarbonAromaticity=0.0 ElectronegativeHalogenicity=0.0
|}

=== Example IL-GIL (generic IL) ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.50
|<ref name=":0" />
|see ESI Table S2.1
|-
|epsinf n2)
|2.0449
|<ref name=":0" />
|n=1.43, has been squared to give epsinf=2.0449
|-
|SurfaceTensionAtInterface
|61.24
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|HBondAcidity (α)
|0.229
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|HBondBasicity (β)
|0.265
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|CarbonAromaticity
|
|<ref name=":0" />
|
|-
|ElectronegativeHalogenicity
|
|<ref name=":0" />
|
|-
| colspan="4" |<code>eps=11.50 epsinf=2.0449 SurfaceTensionAtInterface=61.24 HBondAcidity=0.229 HBondBasicity=0.265 CarbonAromaticity=0.xxx ElectronegativeHalogenicity=0.xxx</code>
|}

== Example table ==
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|
|
|
|-
|epsinf
|
|
|
|-
|SurfaceTensionAtInterface
|
|
|
|-
|HBondAcidity (α)
|
|
|
|-
|HBondBasicity (β)
|
|
|
|-
|CarbonAromaticity
|
|
|
|-
|ElectronegativeHalogenicity
|
|
|
|-
| colspan="4" |<code>eps= epsinf= SurfaceTensionAtInterface= HBondAcidity= HBondBasicity= CarbonAromaticity= ElectronegativeHalogenicity=</code>
|}

== References ==
<references />

Mod:Hunt Research Group: Using SMD on ILs

2019-12-23T10:44:09Z

Phunt: /* How to simulate a generic solvent environment */

This page explains how to use the SMD model to simulate an ionic liquid environment in Gaussian calculations. The SMD model is explained in detail in the original paper here.<ref>Marenich 2009 http://pubs.acs.org/doi/abs/10.1021/jp810292n</ref> Its use on ILs is similarly explained here.<ref name=":0">Bernales 2012 http://pubs.acs.org/doi/abs/10.1021/jp304365v</ref> Many useful solvent parameters are also available in this paper.

== How to simulate a defined solvent environment ==
Gaussian has many previously defined solvent environments. A list is available at the bottom of this page.<ref>http://www.gaussian.com/g_tech/g_ur/k_scrf.htm</ref> For example to use the pre-defined water environment simply insert the following keyword into the method line of your input file. The rest of your method line should specify your functional, basis set, optimisation/other type of calculation as usual.
scrf=(smd,solvent=water)
To use a different solvent to water change the solvent=water part to solvent=something else in the list.

== How to simulate a generic solvent environment ==
The SMD model has many parameters. These are already defined inside Gaussian for the list of defined solvents. If you want to use a solvent not on the list e.g. an ionic liquid, you must define these parameters manually. In this case put the following into the method line:
scrf=(smd,solvent=generic)

===Solvent parameters===
{| class="wikitable"
!Parameter
!Symbol
!Name in Gaussian input file
|-
|Dielectric constant
|ε
|eps
|-
|Index of refraction, squared
|n2
|epsinf
|-
|Macroscopic surface tension /cal mol-1 Å-2
|γ
|SurfaceTensionAtInterface
|-
|Abraham hydrogen bond acidity parameter
|Σα2H
|HBondAcidity
|-
|Abraham hydrogen bond basicity parameter
|Σβ2H
|HBondBasicity
|-
|Fraction of non-hydrogen atoms which are aromatic carbon atoms
|φ
|CarbonAromaticity
|
|-
|Fraction of non-hydrogen atoms which are electronegative halogen atoms
|ψ
|ElectronegativeHalogenicity
|
|}

===Notes on parameters===
Surface tension
*surface tension is the only parameter with units, those used in SMD are non-standard cal mol-1Å-2
*the SI units are Jm-2 or Nm-1
*typical units are dyn cm-1 where 1 dyn = 1 g cm s-2
*as we tend to work in kJ/mol the energy part of this becomes not J but J/mol
*1 dyn cm-1 = 0.001N m-1 = 0.001J m-2
*1 m = 1*1010Å and 1J=0.239cal and 1 mol-1=6.022*1023
*1 dyn cm-1 = 0.001*0.239cal*6.022*1023mol-1/(1*102*10Å2
*and if you think about this 1023 on top line cancels with 1020 on bottom line leaving 103 which cancels with the 0.001=10-3 leaving us with 0.239*6.022=1.439
*1 dyn cm-1 = 1.439 cal mol-1 Å-2

Molar Volume
* MolarVolume=x.x in cm3/mol
* molecular volume in Å3 per molecule converted to cm3/mol
* 1cm = 1*108Å, 1Å = 1*10-8 cm
* x Å3 per molecule = x*6.022*1023mol-1 *103*-8cm3 = x*6.022*10-1cm3mol-1

Kamlet-Taft vs Abraham H-bonding parameters
*the SMD model requires Abraham H-bondonding parameters (Σα2H, Σβ2H)
*however Kamlet-Taft (α, β) measurements are more commonly reported for ILs
*a relationship between the parameters was investigated, giving the following equations:<ref name=":0" />

Σα2H = 0.4098α + 0.0064

Σβ2H = 0.6138β + 0.0890

Previously the group has developed a simple method for calculating Kamlet-Taft parameters, and the instructions are here.<ref>http://www.huntresearchgroup.org.uk/research/research_il_alpha_beta_intro.html</ref>

===Types of SMD model for ILs===
3 types of SMD for ILs have been defined.<ref name=":0" />
*SMD The standard SMD model. All parameters are determined for the particular IL (or a very similar one) being used as the solvent environment.
*SMD-GIL The generic ionic liquid model. The average values above are used for all parameters, except φ and ψ, which are simply calculated from the chemical formula of the IL.
*SMD-PGPThe partial generic parameters model. Any parameter which has been measured for that IL is used. For any parameters which you do not have values for, use the average values.

Example: [C4C1Im][NTf2] 
*All parameters for this IL have been measured, and can be found in reference 2.<ref name=":0" /> That means we can use the standard SMD method.
*To get a value for φ take the number of aromatic carbon atoms (3) and divide by the number of non-hydrogen atoms (25). φ = 0.12.
*To get a value for ψ take the number of electronegative halogen atoms (6) and divide by the number of non-hydrogen atoms (25). ψ = 0.24.
*To define these parameters place the following line at the bottom of the input file (include one blank line before and at least one blank line after):
* eps=11.52 epsinf=2.037 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.12 ElectronegativeHalogenicity=0.24
*see following data for other ILs

== SMD input database ==
Here we will keep a database of SMD parameters used by the group. Please add any IL you use, so no-one else has to re-do the research for the parameters! Please follow the template provided so that it is clear where you get each value from.

===[C4C1Im][BF4]===
all values from <ref name=":0" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.70
|<ref name=":0" />
|
|-
|epsinf
|2.0207
|<ref name=":0" />
|Value given in reference is n=1.4215, it has been squared to give epsinf=2.0207
|-
|SurfaceTensionAtInterface
|67.07
|<ref name=":0" />
|
|-
|HBondAcidity (α)
|0.263
|<ref name=":0" />
| Kamlet-Taft 0.627
|-
|HBondBasicity (β)
|0.320
|<ref name=":0" />
| Kamlet-Taft 0.376
|-
|CarbonAromaticity (φ)
|0.2000
|
|There are 15 non-H atoms, 3 are aromatic C atoms, value=3/15=0.2000
|-
|ElectronegativeHalogenicity (ψ)
|0.2667
|
|There are 15 non-H atoms, 4 are electronegative halogen atoms, value =4/15=0.2667
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][PF6]===
all values from <ref name=":0" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.40
|<ref name=":0" />
|
|-
|epsinf
|1.9853
|<ref name=":0" />
|Value given in reference is n=1.4090, it has been squared to give epsinf=1.9853
|-
|SurfaceTensionAtInterface
|70.24
|<ref name=":0" />
|
|-
|HBondAcidity (α)
|0.266
|<ref name=":0" />
| Kamlet-Taft 0.634
|-
|HBondBasicity (β)
|0.216
|<ref name=":0" />
| Kamlet-Taft 0.207
|-
|CarbonAromaticity (φ)
|0.1765
|
|There are 17 non-H atoms, 3 are aromatic C atoms, value=3/17=0.1765
|-
|ElectronegativeHalogenicity (ψ)
|0.3529
|
|There are 17 non-H atoms, 4 are electronegative halogen atoms, value =6/17=0.3529
|-
| colspan="4" |<code>eps=11.40 epsinf=1.9853 SurfaceTensionAtInterface=70.24 HBondAcidity=0.266 HBondBasicity=0.216 CarbonAromaticity=0.1765 ElectronegativeHalogenicity=0.3529</code>
|}

=== [C4C1Im][NTf2] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.52
|<ref name=":0" /> <ref name=":6">Daguenet 2006 http://pubs.acs.org/doi/abs/10.1021/jp0604903</ref>
|
|-
|epsinf
|2.0366
|<ref name=":0" /> <ref name=":1">Huddleston 2001 http://pubs.rsc.org/en/Content/ArticleLanding/2001/GC/b103275p</ref>
|Value given in reference is n=1.4271, it has been squared to give epsinf=2.0366
|-
|SurfaceTensionAtInterface
|53.97
|<ref name=":0" /> <ref name=":1" />
|
|-
|HBondAcidity (α)
|0.259
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.617
|-
|HBondBasicity (β)
|0.238
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.243
|-
|CarbonAromaticity
|0.1200
|
|There are 25 non-H atoms, 3 are aromatic C atoms, value =3/25=0.1200
|-
|ElectronegativeHalogenicity
|0.2400
|
|There are 25 non-H atoms, 6 are electronegative halogen atoms, value =6/25=0.2400
|-
| colspan="4" |<code>eps=11.52 epsinf=2.0366 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.1200 ElectronegativeHalogenicity=0.2400</code>
|}

=== [C4C1Im][OTf] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|12.90
|<ref name=":3">Huang 2011 http://pubs.acs.org/doi/abs/10.1021/je101184s</ref>
|Page 1495, number 11 on the list.
|-
|epsinf
|2.0665
|<ref name=":4">Gonzalez 2012 http://pubs.acs.org/doi/abs/10.1021/je201334p</ref>
|n=1.43755, has been squared to give epsinf=2.0665. Can be found in Table 1, 3rd row.
|-
|SurfaceTensionAtInterface
|unknown
|
|-
|HBondAcidity (α)
|0.263
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.625
|-
|HBondBasicity (β)
|0.374
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.464
|-
|CarbonAromaticity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are aromatic C atoms, value=3/18=0.1667.
|-
|ElectronegativeHalogenicity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are electronegative halogen atoms, value=3/18=0.1667.
|-
| colspan="4" |<code>eps=12.90 epsinf=2.0665 SurfaceTensionAtInterface'''=XX''' HBondAcidity=0.263 HBondBasicity=0.374 CarbonAromaticity=0.1667 ElectronegativeHalogenicity=0.1667</code>
|}

=== [C4C1Im][XX] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|13.70
| M. M. Huang, Y. P. Jiang, P. Sasisanker, G. W. Driver and H. Weingartner,  J. Chem. Eng. Data, 2011, 56, 1494–1499.
|
|-
|epsinf (n2)
|2.3691
| G. Vakili-Nezhaad, M. Vatani, M. Asghari and I. Ashour, J. Chem. Thermodyn., 2012, 54, 148–154.
|n=1.53921, has been squared to give epsinf=2.3691 (error in some database calcs with n=1.5436 n2=2.3827)
|-
|SurfaceTensionAtInterface
|68.34
| G. Vakili-Nezhaad, M. Vatani, M. Asghari and I. Ashour, J. Chem. Thermodyn., 2012, 54, 148–154.
| η=45.41 (mN.m-1) converts to 45.41*1.439= cal mol-1 Å-2=65.34
|-
|HBondAcidity (α)
|0.18
|
| Kamlet-Taft 0.43
|-
|HBondBasicity (β)
|0.52
|
| Kamlet-Taft 0.71
|-
|CarbonAromaticity
|0.2308
|
|There are 13 non-H atoms, 3 are aromatic C atoms, value=xx/xx=0.2308
|-
|ElectronegativeHalogenicity
|0.0
|
|There are no electronegative halogen atoms, value=0.0
|-
| colspan="4" |<code>eps=13.70 epsinf=2.3691 SurfaceTensionAtInterface=68.34 HBondAcidity=0.18 HBondBasicity=0.52 CarbonAromaticity=0.2308 ElectronegativeHalogenicity=0.0</code>
|}

=== Molten salt [Li+,Na+,K+][CO32-] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|MolarVolume
|57
|<ref name=":5" />
|molar volume Li2CO3 68 Na2CO3 92 K2CO3 124 Å3/molecule, average is 95 and 95*0.6022=57 at T=1.1Tm
|-
|Tabs
|900
|
|Absolute Temperature in K ie 298+600≈900
|-
|???
|
|
|ThermalExansionCoefficient estimate 20*10-6 K-1 at T=1.1Tm (this is not working!)
|-
|eps
|3
|<ref name=":5">G. Janz and M. Lorenz, <abbr>J. Electrochem. Soc.</abbr> 1961 volume 108, issue 11, 1052-1058 doi: 10.1149/1.2427946</ref>
|estimated value
|-
|epsinf
|2.25
|
|refractive index Na2CO3 1.489-1.535,<ref><nowiki>https://pubchem.ncbi.nlm.nih.gov/compound/sodium_carbonate#section=Spectral-Properties&fullscreen=true</nowiki></ref> Li2CO3 1.428-1.572<ref>Weast, R.C. (ed.). Handbook of Chemistry and Physics. 60th ed. Boca Raton, Florida: CRC Press Inc., 1979., p. B-91</ref> K2CO3 1.426-1.541<ref><nowiki>http://cameo.mfa.org/wiki/Potassium_carbonate</nowiki></ref> taking a "mid" value 1.52=2.25
|-
|SurfaceTensionAtInterface
|273
|<ref name=":5" />
|used surface tension of Na/K/CO3 mixture 50 mol % K2CO3 at 810 ºC , 190.0 dynes/cm
|-
|HBondAcidity (α)
|0.00
|<nowiki>-</nowiki>
| rowspan="2" |There are no H-atoms so H-bond acidity is zero
H-bond basicity computations result in proton transfer, NO3 ≈0.74-0.81, Cl ≈0.95-0.98, we assume it is even stronger due to -2 charge
|-
|HBondBasicity (β)
|0.99
|
|-
|CarbonAromaticity
|0.00
|<nowiki>-</nowiki>
|There are no aromatic C atoms
|-
|ElectronegativeHalogenicity
|0.00
|<nowiki>-</nowiki>
|There are no halogen atoms
|-
| colspan="4" |Stoichiometry=C2O62Li2Na2K2 MolarVolume=57.0 Tabs=900 eps=3.0 epsinf=2.25 SurfaceTensionAtInterface=273 HBondAcidity=0.0 HBondBasicity=0.99 CarbonAromaticity=0.0 ElectronegativeHalogenicity=0.0
|}

=== Example IL-GIL (generic IL) ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.50
|<ref name=":0" />
|see ESI Table S2.1
|-
|epsinf
|2.0449
|<ref name=":0" />
|n=1.43, has been squared to give epsinf=2.0449
|-
|SurfaceTensionAtInterface
|61.24
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|HBondAcidity (α)
|0.229
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|HBondBasicity (β)
|0.265
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|CarbonAromaticity
|
|<ref name=":0" />
|
|-
|ElectronegativeHalogenicity
|
|<ref name=":0" />
|
|-
| colspan="4" |<code>eps=11.50 epsinf=2.0449 SurfaceTensionAtInterface=61.24 HBondAcidity=0.229 HBondBasicity=0.265 CarbonAromaticity=0.xxx ElectronegativeHalogenicity=0.xxx</code>
|}

== Example table ==
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|
|
|
|-
|epsinf
|
|
|
|-
|SurfaceTensionAtInterface
|
|
|
|-
|HBondAcidity (α)
|
|
|
|-
|HBondBasicity (β)
|
|
|
|-
|CarbonAromaticity
|
|
|
|-
|ElectronegativeHalogenicity
|
|
|
|-
| colspan="4" |<code>eps= epsinf= SurfaceTensionAtInterface= HBondAcidity= HBondBasicity= CarbonAromaticity= ElectronegativeHalogenicity=</code>
|}

== References ==
<references />

Mod:Hunt Research Group: Using SMD on ILs

2019-12-23T10:34:58Z

Phunt: /* Types of SMD model */

This page explains how to use the SMD model to simulate an ionic liquid environment in Gaussian calculations. The SMD model is explained in detail in the original paper here.<ref>Marenich 2009 http://pubs.acs.org/doi/abs/10.1021/jp810292n</ref> Its use on ILs is similarly explained here.<ref name=":0">Bernales 2012 http://pubs.acs.org/doi/abs/10.1021/jp304365v</ref> Many useful solvent parameters are also available in this paper.

== How to simulate a defined solvent environment ==
Gaussian has many previously defined solvent environments. A list is available at the bottom of this page.<ref>http://www.gaussian.com/g_tech/g_ur/k_scrf.htm</ref> For example to use the pre-defined water environment simply insert the following keyword into the method line of your input file. The rest of your method line should specify your functional, basis set, optimisation/other type of calculation as usual.
scrf=(smd,solvent=water)
To use a different solvent to water change the solvent=water part to solvent=something else in the list.

== How to simulate a generic solvent environment ==
The SMD model has many parameters. These are already defined inside Gaussian for the list of defined solvents. If you want to use a solvent not on the list e.g. an ionic liquid, you must define these parameters manually. In this case put the following into the method line:
scrf=(smd,solvent=generic)

=== Types of SMD model ===
3 types of SMD for ILs have been defined.<ref name=":0" />
*SMD The standard SMD model. All parameters are determined for the particular IL (or a very similar one) being used as the solvent environment.
*SMD-GIL The generic ionic liquid model. The average values above are used for all parameters, except φ and ψ, which are simply calculated from the chemical formula of the IL.
*SMD-PGPThe partial generic parameters model. Any parameter which has been measured for that IL is used. For any parameters which you do not have values for, use the average values.

=== Solvent parameters and SMD-GIL ===
The parameters are defined at the bottom of the input file, these parameters are listed in the table below:
{| class="wikitable"
!Parameter
!Symbol
!Name in Gaussian input file
!Average value for ILs<ref name=":0" />
|-
|Dielectric constant
|ε
|eps
|11.50
|-
|Index of refraction, squared
|n2
|epsinf
|2.0449
|-
|Macroscopic surface tension /cal mol-1 Å-2
|γ
|SurfaceTensionAtInterface
|61.24
|-
|Abraham hydrogen bond acidity parameter
|Σα2H
|HBondAcidity
|0.229
|-
|Abraham hydrogen bond basicity parameter
|Σβ2H
|HBondBasicity
|0.265
|-
|Fraction of non-hydrogen atoms which are aromatic carbon atoms
|φ
|CarbonAromaticity
|<nowiki>-</nowiki>
|-
|Fraction of non-hydrogen atoms which are electronegative halogen atoms
|ψ
|ElectronegativeHalogenicity
|<nowiki>-</nowiki>
|}

=== Note on parameters ===
Surface tension
*surface tension is the only parameter with units, those used in SMD are non-standard cal mol-1Å-2
*the SI units are Jm-2 or Nm-1
*typical units are dyn cm-1 where 1 dyn = 1 g cm s-2
*as we tend to work in kJ/mol the energy part of this becomes not J but J/mol
*1 dyn cm-1 = 0.001N m-1 = 0.001J m-2
*1 m = 1*1010Å and 1J=0.239cal and 1 mol-1=6.022*1023
*1 dyn cm-1 = 0.001*0.239cal*6.022*1023mol-1/(1*102*10Å2
*and if you think about this 1023 on top line cancels with 1020 on bottom line leaving 103 which cancels with the 0.001=10-3 leaving us with 0.239*6.022=1.439
*1 dyn cm-1 = 1.439 cal mol-1 Å-2
Molar Volume
* MolarVolume=x.x in cm3/mol
* molecular volume in Å3 per molecule converted to cm3/mol
* 1cm = 1*108Å, 1Å = 1*10-8 cm
* x Å3 per molecule = x*6.022*1023mol-1 *103*-8cm3 = x*6.022*10-1cm3mol-1

=== Example: [C4C1Im][NTf2] ===
All parameters for this IL have been measured, and can be found in reference 2.<ref name=":0" /> That means we can use the standard SMD method.

To get a value for φ take the number of aromatic carbon atoms (3) and divide by the number of non-hydrogen atoms (25). φ = 0.12.

To get a value for ψ take the number of electronegative halogen atoms (6) and divide by the number of non-hydrogen atoms (25). ψ = 0.24.

To define these parameters place the following line at the bottom of the input file (include one blank line before and at least one blank line after):
eps=11.52 epsinf=2.037 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.12 ElectronegativeHalogenicity=0.24

=== Kamlet-Taft vs Abraham H-bonding parameters ===
The SMD model requires Abraham H-bondonding parameters (Σα2H, Σβ2H), however Kamlet-Taft (α, β) measurements are more commonly reported for ILs. To alleviate this problem a relationship between the parameters was investigated, giving the following equations:<ref name=":0" />

Σα2H = 0.4098α + 0.0064

Σβ2H = 0.6138β + 0.0890

Previously the group has developed a simple method for calculating Kamlet-Taft parameters, and the instructions are here.<ref>http://www.huntresearchgroup.org.uk/research/research_il_alpha_beta_intro.html</ref>

== SMD input database ==
Here we will keep a database of SMD parameters used by the group. Please add any IL you use, so no-one else has to re-do the research for the parameters! Please follow the template provided so that it is clear where you get each value from.

===[C4C1Im][BF4]===
all values from <ref name=":0" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.70
|<ref name=":0" />
|
|-
|epsinf
|2.0207
|<ref name=":0" />
|Value given in reference is n=1.4215, it has been squared to give epsinf=2.0207
|-
|SurfaceTensionAtInterface
|67.07
|<ref name=":0" />
|
|-
|HBondAcidity (α)
|0.263
|<ref name=":0" />
| Kamlet-Taft 0.627
|-
|HBondBasicity (β)
|0.320
|<ref name=":0" />
| Kamlet-Taft 0.376
|-
|CarbonAromaticity (φ)
|0.2000
|
|There are 15 non-H atoms, 3 are aromatic C atoms, value=3/15=0.2000
|-
|ElectronegativeHalogenicity (ψ)
|0.2667
|
|There are 15 non-H atoms, 4 are electronegative halogen atoms, value =4/15=0.2667
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][PF6]===
all values from <ref name=":0" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.40
|<ref name=":0" />
|
|-
|epsinf
|1.9853
|<ref name=":0" />
|Value given in reference is n=1.4090, it has been squared to give epsinf=1.9853
|-
|SurfaceTensionAtInterface
|70.24
|<ref name=":0" />
|
|-
|HBondAcidity (α)
|0.266
|<ref name=":0" />
| Kamlet-Taft 0.634
|-
|HBondBasicity (β)
|0.216
|<ref name=":0" />
| Kamlet-Taft 0.207
|-
|CarbonAromaticity (φ)
|0.1765
|
|There are 17 non-H atoms, 3 are aromatic C atoms, value=3/17=0.1765
|-
|ElectronegativeHalogenicity (ψ)
|0.3529
|
|There are 17 non-H atoms, 4 are electronegative halogen atoms, value =6/17=0.3529
|-
| colspan="4" |<code>eps=11.40 epsinf=1.9853 SurfaceTensionAtInterface=70.24 HBondAcidity=0.266 HBondBasicity=0.216 CarbonAromaticity=0.1765 ElectronegativeHalogenicity=0.3529</code>
|}

=== [C4C1Im][NTf2] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.52
|<ref name=":0" /> <ref name=":6">Daguenet 2006 http://pubs.acs.org/doi/abs/10.1021/jp0604903</ref>
|
|-
|epsinf
|2.0366
|<ref name=":0" /> <ref name=":1">Huddleston 2001 http://pubs.rsc.org/en/Content/ArticleLanding/2001/GC/b103275p</ref>
|Value given in reference is n=1.4271, it has been squared to give epsinf=2.0366
|-
|SurfaceTensionAtInterface
|53.97
|<ref name=":0" /> <ref name=":1" />
|
|-
|HBondAcidity (α)
|0.259
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.617
|-
|HBondBasicity (β)
|0.238
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.243
|-
|CarbonAromaticity
|0.1200
|
|There are 25 non-H atoms, 3 are aromatic C atoms, value =3/25=0.1200
|-
|ElectronegativeHalogenicity
|0.2400
|
|There are 25 non-H atoms, 6 are electronegative halogen atoms, value =6/25=0.2400
|-
| colspan="4" |<code>eps=11.52 epsinf=2.0366 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.1200 ElectronegativeHalogenicity=0.2400</code>
|}

=== [C4C1Im][OTf] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|12.90
|<ref name=":3">Huang 2011 http://pubs.acs.org/doi/abs/10.1021/je101184s</ref>
|Page 1495, number 11 on the list.
|-
|epsinf
|2.0665
|<ref name=":4">Gonzalez 2012 http://pubs.acs.org/doi/abs/10.1021/je201334p</ref>
|n=1.43755, has been squared to give epsinf=2.0665. Can be found in Table 1, 3rd row.
|-
|SurfaceTensionAtInterface
|unknown
|
|-
|HBondAcidity (α)
|0.263
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.625
|-
|HBondBasicity (β)
|0.374
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.464
|-
|CarbonAromaticity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are aromatic C atoms, value=3/18=0.1667.
|-
|ElectronegativeHalogenicity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are electronegative halogen atoms, value=3/18=0.1667.
|-
| colspan="4" |<code>eps=12.90 epsinf=2.0665 SurfaceTensionAtInterface'''=XX''' HBondAcidity=0.263 HBondBasicity=0.374 CarbonAromaticity=0.1667 ElectronegativeHalogenicity=0.1667</code>
|}

=== [C4C1Im][XX] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|13.70
| M. M. Huang, Y. P. Jiang, P. Sasisanker, G. W. Driver and H. Weingartner,  J. Chem. Eng. Data, 2011, 56, 1494–1499.
|
|-
|epsinf (n2)
|2.3691
| G. Vakili-Nezhaad, M. Vatani, M. Asghari and I. Ashour, J. Chem. Thermodyn., 2012, 54, 148–154.
|n=1.53921, has been squared to give epsinf=2.3691 (error in some database calcs with n=1.5436 n2=2.3827)
|-
|SurfaceTensionAtInterface
|68.34
| G. Vakili-Nezhaad, M. Vatani, M. Asghari and I. Ashour, J. Chem. Thermodyn., 2012, 54, 148–154.
| η=45.41 (mN.m-1) converts to 45.41*1.439= cal mol-1 Å-2=65.34
|-
|HBondAcidity (α)
|0.18
|
| Kamlet-Taft 0.43
|-
|HBondBasicity (β)
|0.52
|
| Kamlet-Taft 0.71
|-
|CarbonAromaticity
|0.2308
|
|There are 13 non-H atoms, 3 are aromatic C atoms, value=xx/xx=0.2308
|-
|ElectronegativeHalogenicity
|0.0
|
|There are no electronegative halogen atoms, value=0.0
|-
| colspan="4" |<code>eps=13.70 epsinf=2.3691 SurfaceTensionAtInterface=68.34 HBondAcidity=0.18 HBondBasicity=0.52 CarbonAromaticity=0.2308 ElectronegativeHalogenicity=0.0</code>
|}

=== Molten salt [Li+,Na+,K+][CO32-] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|MolarVolume
|57
|<ref name=":5" />
|molar volume Li2CO3 68 Na2CO3 92 K2CO3 124 Å3/molecule, average is 95 and 95*0.6022=57 at T=1.1Tm
|-
|Tabs
|900
|
|Absolute Temperature in K ie 298+600≈900
|-
|???
|
|
|ThermalExansionCoefficient estimate 20*10-6 K-1 at T=1.1Tm (this is not working!)
|-
|eps
|3
|<ref name=":5">G. Janz and M. Lorenz, <abbr>J. Electrochem. Soc.</abbr> 1961 volume 108, issue 11, 1052-1058 doi: 10.1149/1.2427946</ref>
|estimated value
|-
|epsinf
|2.25
|
|refractive index Na2CO3 1.489-1.535,<ref><nowiki>https://pubchem.ncbi.nlm.nih.gov/compound/sodium_carbonate#section=Spectral-Properties&fullscreen=true</nowiki></ref> Li2CO3 1.428-1.572<ref>Weast, R.C. (ed.). Handbook of Chemistry and Physics. 60th ed. Boca Raton, Florida: CRC Press Inc., 1979., p. B-91</ref> K2CO3 1.426-1.541<ref><nowiki>http://cameo.mfa.org/wiki/Potassium_carbonate</nowiki></ref> taking a "mid" value 1.52=2.25
|-
|SurfaceTensionAtInterface
|273
|<ref name=":5" />
|used surface tension of Na/K/CO3 mixture 50 mol % K2CO3 at 810 ºC , 190.0 dynes/cm
|-
|HBondAcidity (α)
|0.00
|<nowiki>-</nowiki>
| rowspan="2" |There are no H-atoms so H-bond acidity is zero
H-bond basicity computations result in proton transfer, NO3 ≈0.74-0.81, Cl ≈0.95-0.98, we assume it is even stronger due to -2 charge
|-
|HBondBasicity (β)
|0.99
|
|-
|CarbonAromaticity
|0.00
|<nowiki>-</nowiki>
|There are no aromatic C atoms
|-
|ElectronegativeHalogenicity
|0.00
|<nowiki>-</nowiki>
|There are no halogen atoms
|-
| colspan="4" |Stoichiometry=C2O62Li2Na2K2 MolarVolume=57.0 Tabs=900 eps=3.0 epsinf=2.25 SurfaceTensionAtInterface=273 HBondAcidity=0.0 HBondBasicity=0.99 CarbonAromaticity=0.0 ElectronegativeHalogenicity=0.0
|}

=== Example IL-GIL (generic IL) ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.50
|<ref name=":0" />
|see ESI Table S2.1
|-
|epsinf
|2.0449
|<ref name=":0" />
|n=1.43, has been squared to give epsinf=2.0449
|-
|SurfaceTensionAtInterface
|61.24
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|HBondAcidity (α)
|0.229
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|HBondBasicity (β)
|0.265
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|CarbonAromaticity
|
|<ref name=":0" />
|
|-
|ElectronegativeHalogenicity
|
|<ref name=":0" />
|
|-
| colspan="4" |<code>eps=11.50 epsinf=2.0449 SurfaceTensionAtInterface=61.24 HBondAcidity=0.229 HBondBasicity=0.265 CarbonAromaticity=0.xxx ElectronegativeHalogenicity=0.xxx</code>
|}

== Example table ==
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|
|
|
|-
|epsinf
|
|
|
|-
|SurfaceTensionAtInterface
|
|
|
|-
|HBondAcidity (α)
|
|
|
|-
|HBondBasicity (β)
|
|
|
|-
|CarbonAromaticity
|
|
|
|-
|ElectronegativeHalogenicity
|
|
|
|-
| colspan="4" |<code>eps= epsinf= SurfaceTensionAtInterface= HBondAcidity= HBondBasicity= CarbonAromaticity= ElectronegativeHalogenicity=</code>
|}

== References ==
<references />

Mod:Hunt Research Group: Using SMD on ILs

2019-12-23T10:34:35Z

Phunt: /* How to simulate a generic solvent environment */

This page explains how to use the SMD model to simulate an ionic liquid environment in Gaussian calculations. The SMD model is explained in detail in the original paper here.<ref>Marenich 2009 http://pubs.acs.org/doi/abs/10.1021/jp810292n</ref> Its use on ILs is similarly explained here.<ref name=":0">Bernales 2012 http://pubs.acs.org/doi/abs/10.1021/jp304365v</ref> Many useful solvent parameters are also available in this paper.

== How to simulate a defined solvent environment ==
Gaussian has many previously defined solvent environments. A list is available at the bottom of this page.<ref>http://www.gaussian.com/g_tech/g_ur/k_scrf.htm</ref> For example to use the pre-defined water environment simply insert the following keyword into the method line of your input file. The rest of your method line should specify your functional, basis set, optimisation/other type of calculation as usual.
scrf=(smd,solvent=water)
To use a different solvent to water change the solvent=water part to solvent=something else in the list.

== How to simulate a generic solvent environment ==
The SMD model has many parameters. These are already defined inside Gaussian for the list of defined solvents. If you want to use a solvent not on the list e.g. an ionic liquid, you must define these parameters manually. In this case put the following into the method line:
scrf=(smd,solvent=generic)

=== Types of SMD model ===
3 types of SMD for ILs have been defined.<ref name=":0" />
•SMD The standard SMD model. All parameters are determined for the particular IL (or a very similar one) being used as the solvent environment.
•SMD-GIL The generic ionic liquid model. The average values above are used for all parameters, except φ and ψ, which are simply calculated from the chemical formula of the IL.
•SMD-PGPThe partial generic parameters model. Any parameter which has been measured for that IL is used. For any parameters which you do not have values for, use the average values.

=== Solvent parameters and SMD-GIL ===
The parameters are defined at the bottom of the input file, these parameters are listed in the table below:
{| class="wikitable"
!Parameter
!Symbol
!Name in Gaussian input file
!Average value for ILs<ref name=":0" />
|-
|Dielectric constant
|ε
|eps
|11.50
|-
|Index of refraction, squared
|n2
|epsinf
|2.0449
|-
|Macroscopic surface tension /cal mol-1 Å-2
|γ
|SurfaceTensionAtInterface
|61.24
|-
|Abraham hydrogen bond acidity parameter
|Σα2H
|HBondAcidity
|0.229
|-
|Abraham hydrogen bond basicity parameter
|Σβ2H
|HBondBasicity
|0.265
|-
|Fraction of non-hydrogen atoms which are aromatic carbon atoms
|φ
|CarbonAromaticity
|<nowiki>-</nowiki>
|-
|Fraction of non-hydrogen atoms which are electronegative halogen atoms
|ψ
|ElectronegativeHalogenicity
|<nowiki>-</nowiki>
|}

=== Note on parameters ===
Surface tension
*surface tension is the only parameter with units, those used in SMD are non-standard cal mol-1Å-2
*the SI units are Jm-2 or Nm-1
*typical units are dyn cm-1 where 1 dyn = 1 g cm s-2
*as we tend to work in kJ/mol the energy part of this becomes not J but J/mol
*1 dyn cm-1 = 0.001N m-1 = 0.001J m-2
*1 m = 1*1010Å and 1J=0.239cal and 1 mol-1=6.022*1023
*1 dyn cm-1 = 0.001*0.239cal*6.022*1023mol-1/(1*102*10Å2
*and if you think about this 1023 on top line cancels with 1020 on bottom line leaving 103 which cancels with the 0.001=10-3 leaving us with 0.239*6.022=1.439
*1 dyn cm-1 = 1.439 cal mol-1 Å-2
Molar Volume
* MolarVolume=x.x in cm3/mol
* molecular volume in Å3 per molecule converted to cm3/mol
* 1cm = 1*108Å, 1Å = 1*10-8 cm
* x Å3 per molecule = x*6.022*1023mol-1 *103*-8cm3 = x*6.022*10-1cm3mol-1

=== Example: [C4C1Im][NTf2] ===
All parameters for this IL have been measured, and can be found in reference 2.<ref name=":0" /> That means we can use the standard SMD method.

To get a value for φ take the number of aromatic carbon atoms (3) and divide by the number of non-hydrogen atoms (25). φ = 0.12.

To get a value for ψ take the number of electronegative halogen atoms (6) and divide by the number of non-hydrogen atoms (25). ψ = 0.24.

To define these parameters place the following line at the bottom of the input file (include one blank line before and at least one blank line after):
eps=11.52 epsinf=2.037 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.12 ElectronegativeHalogenicity=0.24

=== Kamlet-Taft vs Abraham H-bonding parameters ===
The SMD model requires Abraham H-bondonding parameters (Σα2H, Σβ2H), however Kamlet-Taft (α, β) measurements are more commonly reported for ILs. To alleviate this problem a relationship between the parameters was investigated, giving the following equations:<ref name=":0" />

Σα2H = 0.4098α + 0.0064

Σβ2H = 0.6138β + 0.0890

Previously the group has developed a simple method for calculating Kamlet-Taft parameters, and the instructions are here.<ref>http://www.huntresearchgroup.org.uk/research/research_il_alpha_beta_intro.html</ref>

== SMD input database ==
Here we will keep a database of SMD parameters used by the group. Please add any IL you use, so no-one else has to re-do the research for the parameters! Please follow the template provided so that it is clear where you get each value from.

===[C4C1Im][BF4]===
all values from <ref name=":0" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.70
|<ref name=":0" />
|
|-
|epsinf
|2.0207
|<ref name=":0" />
|Value given in reference is n=1.4215, it has been squared to give epsinf=2.0207
|-
|SurfaceTensionAtInterface
|67.07
|<ref name=":0" />
|
|-
|HBondAcidity (α)
|0.263
|<ref name=":0" />
| Kamlet-Taft 0.627
|-
|HBondBasicity (β)
|0.320
|<ref name=":0" />
| Kamlet-Taft 0.376
|-
|CarbonAromaticity (φ)
|0.2000
|
|There are 15 non-H atoms, 3 are aromatic C atoms, value=3/15=0.2000
|-
|ElectronegativeHalogenicity (ψ)
|0.2667
|
|There are 15 non-H atoms, 4 are electronegative halogen atoms, value =4/15=0.2667
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][PF6]===
all values from <ref name=":0" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.40
|<ref name=":0" />
|
|-
|epsinf
|1.9853
|<ref name=":0" />
|Value given in reference is n=1.4090, it has been squared to give epsinf=1.9853
|-
|SurfaceTensionAtInterface
|70.24
|<ref name=":0" />
|
|-
|HBondAcidity (α)
|0.266
|<ref name=":0" />
| Kamlet-Taft 0.634
|-
|HBondBasicity (β)
|0.216
|<ref name=":0" />
| Kamlet-Taft 0.207
|-
|CarbonAromaticity (φ)
|0.1765
|
|There are 17 non-H atoms, 3 are aromatic C atoms, value=3/17=0.1765
|-
|ElectronegativeHalogenicity (ψ)
|0.3529
|
|There are 17 non-H atoms, 4 are electronegative halogen atoms, value =6/17=0.3529
|-
| colspan="4" |<code>eps=11.40 epsinf=1.9853 SurfaceTensionAtInterface=70.24 HBondAcidity=0.266 HBondBasicity=0.216 CarbonAromaticity=0.1765 ElectronegativeHalogenicity=0.3529</code>
|}

=== [C4C1Im][NTf2] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.52
|<ref name=":0" /> <ref name=":6">Daguenet 2006 http://pubs.acs.org/doi/abs/10.1021/jp0604903</ref>
|
|-
|epsinf
|2.0366
|<ref name=":0" /> <ref name=":1">Huddleston 2001 http://pubs.rsc.org/en/Content/ArticleLanding/2001/GC/b103275p</ref>
|Value given in reference is n=1.4271, it has been squared to give epsinf=2.0366
|-
|SurfaceTensionAtInterface
|53.97
|<ref name=":0" /> <ref name=":1" />
|
|-
|HBondAcidity (α)
|0.259
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.617
|-
|HBondBasicity (β)
|0.238
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.243
|-
|CarbonAromaticity
|0.1200
|
|There are 25 non-H atoms, 3 are aromatic C atoms, value =3/25=0.1200
|-
|ElectronegativeHalogenicity
|0.2400
|
|There are 25 non-H atoms, 6 are electronegative halogen atoms, value =6/25=0.2400
|-
| colspan="4" |<code>eps=11.52 epsinf=2.0366 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.1200 ElectronegativeHalogenicity=0.2400</code>
|}

=== [C4C1Im][OTf] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|12.90
|<ref name=":3">Huang 2011 http://pubs.acs.org/doi/abs/10.1021/je101184s</ref>
|Page 1495, number 11 on the list.
|-
|epsinf
|2.0665
|<ref name=":4">Gonzalez 2012 http://pubs.acs.org/doi/abs/10.1021/je201334p</ref>
|n=1.43755, has been squared to give epsinf=2.0665. Can be found in Table 1, 3rd row.
|-
|SurfaceTensionAtInterface
|unknown
|
|-
|HBondAcidity (α)
|0.263
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.625
|-
|HBondBasicity (β)
|0.374
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.464
|-
|CarbonAromaticity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are aromatic C atoms, value=3/18=0.1667.
|-
|ElectronegativeHalogenicity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are electronegative halogen atoms, value=3/18=0.1667.
|-
| colspan="4" |<code>eps=12.90 epsinf=2.0665 SurfaceTensionAtInterface'''=XX''' HBondAcidity=0.263 HBondBasicity=0.374 CarbonAromaticity=0.1667 ElectronegativeHalogenicity=0.1667</code>
|}

=== [C4C1Im][XX] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|13.70
| M. M. Huang, Y. P. Jiang, P. Sasisanker, G. W. Driver and H. Weingartner,  J. Chem. Eng. Data, 2011, 56, 1494–1499.
|
|-
|epsinf (n2)
|2.3691
| G. Vakili-Nezhaad, M. Vatani, M. Asghari and I. Ashour, J. Chem. Thermodyn., 2012, 54, 148–154.
|n=1.53921, has been squared to give epsinf=2.3691 (error in some database calcs with n=1.5436 n2=2.3827)
|-
|SurfaceTensionAtInterface
|68.34
| G. Vakili-Nezhaad, M. Vatani, M. Asghari and I. Ashour, J. Chem. Thermodyn., 2012, 54, 148–154.
| η=45.41 (mN.m-1) converts to 45.41*1.439= cal mol-1 Å-2=65.34
|-
|HBondAcidity (α)
|0.18
|
| Kamlet-Taft 0.43
|-
|HBondBasicity (β)
|0.52
|
| Kamlet-Taft 0.71
|-
|CarbonAromaticity
|0.2308
|
|There are 13 non-H atoms, 3 are aromatic C atoms, value=xx/xx=0.2308
|-
|ElectronegativeHalogenicity
|0.0
|
|There are no electronegative halogen atoms, value=0.0
|-
| colspan="4" |<code>eps=13.70 epsinf=2.3691 SurfaceTensionAtInterface=68.34 HBondAcidity=0.18 HBondBasicity=0.52 CarbonAromaticity=0.2308 ElectronegativeHalogenicity=0.0</code>
|}

=== Molten salt [Li+,Na+,K+][CO32-] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|MolarVolume
|57
|<ref name=":5" />
|molar volume Li2CO3 68 Na2CO3 92 K2CO3 124 Å3/molecule, average is 95 and 95*0.6022=57 at T=1.1Tm
|-
|Tabs
|900
|
|Absolute Temperature in K ie 298+600≈900
|-
|???
|
|
|ThermalExansionCoefficient estimate 20*10-6 K-1 at T=1.1Tm (this is not working!)
|-
|eps
|3
|<ref name=":5">G. Janz and M. Lorenz, <abbr>J. Electrochem. Soc.</abbr> 1961 volume 108, issue 11, 1052-1058 doi: 10.1149/1.2427946</ref>
|estimated value
|-
|epsinf
|2.25
|
|refractive index Na2CO3 1.489-1.535,<ref><nowiki>https://pubchem.ncbi.nlm.nih.gov/compound/sodium_carbonate#section=Spectral-Properties&fullscreen=true</nowiki></ref> Li2CO3 1.428-1.572<ref>Weast, R.C. (ed.). Handbook of Chemistry and Physics. 60th ed. Boca Raton, Florida: CRC Press Inc., 1979., p. B-91</ref> K2CO3 1.426-1.541<ref><nowiki>http://cameo.mfa.org/wiki/Potassium_carbonate</nowiki></ref> taking a "mid" value 1.52=2.25
|-
|SurfaceTensionAtInterface
|273
|<ref name=":5" />
|used surface tension of Na/K/CO3 mixture 50 mol % K2CO3 at 810 ºC , 190.0 dynes/cm
|-
|HBondAcidity (α)
|0.00
|<nowiki>-</nowiki>
| rowspan="2" |There are no H-atoms so H-bond acidity is zero
H-bond basicity computations result in proton transfer, NO3 ≈0.74-0.81, Cl ≈0.95-0.98, we assume it is even stronger due to -2 charge
|-
|HBondBasicity (β)
|0.99
|
|-
|CarbonAromaticity
|0.00
|<nowiki>-</nowiki>
|There are no aromatic C atoms
|-
|ElectronegativeHalogenicity
|0.00
|<nowiki>-</nowiki>
|There are no halogen atoms
|-
| colspan="4" |Stoichiometry=C2O62Li2Na2K2 MolarVolume=57.0 Tabs=900 eps=3.0 epsinf=2.25 SurfaceTensionAtInterface=273 HBondAcidity=0.0 HBondBasicity=0.99 CarbonAromaticity=0.0 ElectronegativeHalogenicity=0.0
|}

=== Example IL-GIL (generic IL) ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.50
|<ref name=":0" />
|see ESI Table S2.1
|-
|epsinf
|2.0449
|<ref name=":0" />
|n=1.43, has been squared to give epsinf=2.0449
|-
|SurfaceTensionAtInterface
|61.24
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|HBondAcidity (α)
|0.229
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|HBondBasicity (β)
|0.265
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|CarbonAromaticity
|
|<ref name=":0" />
|
|-
|ElectronegativeHalogenicity
|
|<ref name=":0" />
|
|-
| colspan="4" |<code>eps=11.50 epsinf=2.0449 SurfaceTensionAtInterface=61.24 HBondAcidity=0.229 HBondBasicity=0.265 CarbonAromaticity=0.xxx ElectronegativeHalogenicity=0.xxx</code>
|}

== Example table ==
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|
|
|
|-
|epsinf
|
|
|
|-
|SurfaceTensionAtInterface
|
|
|
|-
|HBondAcidity (α)
|
|
|
|-
|HBondBasicity (β)
|
|
|
|-
|CarbonAromaticity
|
|
|
|-
|ElectronegativeHalogenicity
|
|
|
|-
| colspan="4" |<code>eps= epsinf= SurfaceTensionAtInterface= HBondAcidity= HBondBasicity= CarbonAromaticity= ElectronegativeHalogenicity=</code>
|}

== References ==
<references />

Mod:Hunt Research Group: Using SMD on ILs

2019-12-23T10:33:07Z

Phunt: /* Note on parameters */

This page explains how to use the SMD model to simulate an ionic liquid environment in Gaussian calculations. The SMD model is explained in detail in the original paper here.<ref>Marenich 2009 http://pubs.acs.org/doi/abs/10.1021/jp810292n</ref> Its use on ILs is similarly explained here.<ref name=":0">Bernales 2012 http://pubs.acs.org/doi/abs/10.1021/jp304365v</ref> Many useful solvent parameters are also available in this paper.

== How to simulate a defined solvent environment ==
Gaussian has many previously defined solvent environments. A list is available at the bottom of this page.<ref>http://www.gaussian.com/g_tech/g_ur/k_scrf.htm</ref> For example to use the pre-defined water environment simply insert the following keyword into the method line of your input file. The rest of your method line should specify your functional, basis set, optimisation/other type of calculation as usual.
scrf=(smd,solvent=water)
To use a different solvent to water change the solvent=water part to solvent=something else in the list.

== How to simulate a generic solvent environment ==
The SMD model has many parameters. These are already defined inside Gaussian for the list of defined solvents. If you want to use a solvent not on the list e.g. an ionic liquid, you must define these parameters manually. In this case put the following into the method line:
scrf=(smd,solvent=generic)

=== Types of SMD model ===
3 types of SMD for ILs have been defined.<ref name=":0" />

==== SMD ====
The standard SMD model. All parameters are determined for the particular IL (or a very similar one) being used as the solvent environment.

==== SMD-GIL ====
The generic ionic liquid model. The average values above are used for all parameters, except φ and ψ, which are simply calculated from the chemical formula of the IL.

==== SMD-PGP ====
The partial generic parameters model. Any parameter which has been measured for that IL is used. For any parameters which you do not have values for, use the average values.

=== Solvent parameters and SMD-GIL ===
The parameters are defined at the bottom of the input file, these parameters are listed in the table below:
{| class="wikitable"
!Parameter
!Symbol
!Name in Gaussian input file
!Average value for ILs<ref name=":0" />
|-
|Dielectric constant
|ε
|eps
|11.50
|-
|Index of refraction, squared
|n2
|epsinf
|2.0449
|-
|Macroscopic surface tension /cal mol-1 Å-2
|γ
|SurfaceTensionAtInterface
|61.24
|-
|Abraham hydrogen bond acidity parameter
|Σα2H
|HBondAcidity
|0.229
|-
|Abraham hydrogen bond basicity parameter
|Σβ2H
|HBondBasicity
|0.265
|-
|Fraction of non-hydrogen atoms which are aromatic carbon atoms
|φ
|CarbonAromaticity
|<nowiki>-</nowiki>
|-
|Fraction of non-hydrogen atoms which are electronegative halogen atoms
|ψ
|ElectronegativeHalogenicity
|<nowiki>-</nowiki>
|}

=== Note on parameters ===
Surface tension
*surface tension is the only parameter with units, those used in SMD are non-standard cal mol-1Å-2
*the SI units are Jm-2 or Nm-1
*typical units are dyn cm-1 where 1 dyn = 1 g cm s-2
*as we tend to work in kJ/mol the energy part of this becomes not J but J/mol
*1 dyn cm-1 = 0.001N m-1 = 0.001J m-2
*1 m = 1*1010Å and 1J=0.239cal and 1 mol-1=6.022*1023
*1 dyn cm-1 = 0.001*0.239cal*6.022*1023mol-1/(1*102*10Å2
*and if you think about this 1023 on top line cancels with 1020 on bottom line leaving 103 which cancels with the 0.001=10-3 leaving us with 0.239*6.022=1.439
*1 dyn cm-1 = 1.439 cal mol-1 Å-2
Molar Volume
* MolarVolume=x.x in cm3/mol
* molecular volume in Å3 per molecule converted to cm3/mol
* 1cm = 1*108Å, 1Å = 1*10-8 cm
* x Å3 per molecule = x*6.022*1023mol-1 *103*-8cm3 = x*6.022*10-1cm3mol-1

=== Example: [C4C1Im][NTf2] ===
All parameters for this IL have been measured, and can be found in reference 2.<ref name=":0" /> That means we can use the standard SMD method.

To get a value for φ take the number of aromatic carbon atoms (3) and divide by the number of non-hydrogen atoms (25). φ = 0.12.

To get a value for ψ take the number of electronegative halogen atoms (6) and divide by the number of non-hydrogen atoms (25). ψ = 0.24.

To define these parameters place the following line at the bottom of the input file (include one blank line before and at least one blank line after):
eps=11.52 epsinf=2.037 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.12 ElectronegativeHalogenicity=0.24

=== Kamlet-Taft vs Abraham H-bonding parameters ===
The SMD model requires Abraham H-bondonding parameters (Σα2H, Σβ2H), however Kamlet-Taft (α, β) measurements are more commonly reported for ILs. To alleviate this problem a relationship between the parameters was investigated, giving the following equations:<ref name=":0" />

Σα2H = 0.4098α + 0.0064

Σβ2H = 0.6138β + 0.0890

Previously the group has developed a simple method for calculating Kamlet-Taft parameters, and the instructions are here.<ref>http://www.huntresearchgroup.org.uk/research/research_il_alpha_beta_intro.html</ref>

== SMD input database ==
Here we will keep a database of SMD parameters used by the group. Please add any IL you use, so no-one else has to re-do the research for the parameters! Please follow the template provided so that it is clear where you get each value from.

===[C4C1Im][BF4]===
all values from <ref name=":0" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.70
|<ref name=":0" />
|
|-
|epsinf
|2.0207
|<ref name=":0" />
|Value given in reference is n=1.4215, it has been squared to give epsinf=2.0207
|-
|SurfaceTensionAtInterface
|67.07
|<ref name=":0" />
|
|-
|HBondAcidity (α)
|0.263
|<ref name=":0" />
| Kamlet-Taft 0.627
|-
|HBondBasicity (β)
|0.320
|<ref name=":0" />
| Kamlet-Taft 0.376
|-
|CarbonAromaticity (φ)
|0.2000
|
|There are 15 non-H atoms, 3 are aromatic C atoms, value=3/15=0.2000
|-
|ElectronegativeHalogenicity (ψ)
|0.2667
|
|There are 15 non-H atoms, 4 are electronegative halogen atoms, value =4/15=0.2667
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][PF6]===
all values from <ref name=":0" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.40
|<ref name=":0" />
|
|-
|epsinf
|1.9853
|<ref name=":0" />
|Value given in reference is n=1.4090, it has been squared to give epsinf=1.9853
|-
|SurfaceTensionAtInterface
|70.24
|<ref name=":0" />
|
|-
|HBondAcidity (α)
|0.266
|<ref name=":0" />
| Kamlet-Taft 0.634
|-
|HBondBasicity (β)
|0.216
|<ref name=":0" />
| Kamlet-Taft 0.207
|-
|CarbonAromaticity (φ)
|0.1765
|
|There are 17 non-H atoms, 3 are aromatic C atoms, value=3/17=0.1765
|-
|ElectronegativeHalogenicity (ψ)
|0.3529
|
|There are 17 non-H atoms, 4 are electronegative halogen atoms, value =6/17=0.3529
|-
| colspan="4" |<code>eps=11.40 epsinf=1.9853 SurfaceTensionAtInterface=70.24 HBondAcidity=0.266 HBondBasicity=0.216 CarbonAromaticity=0.1765 ElectronegativeHalogenicity=0.3529</code>
|}

=== [C4C1Im][NTf2] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.52
|<ref name=":0" /> <ref name=":6">Daguenet 2006 http://pubs.acs.org/doi/abs/10.1021/jp0604903</ref>
|
|-
|epsinf
|2.0366
|<ref name=":0" /> <ref name=":1">Huddleston 2001 http://pubs.rsc.org/en/Content/ArticleLanding/2001/GC/b103275p</ref>
|Value given in reference is n=1.4271, it has been squared to give epsinf=2.0366
|-
|SurfaceTensionAtInterface
|53.97
|<ref name=":0" /> <ref name=":1" />
|
|-
|HBondAcidity (α)
|0.259
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.617
|-
|HBondBasicity (β)
|0.238
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.243
|-
|CarbonAromaticity
|0.1200
|
|There are 25 non-H atoms, 3 are aromatic C atoms, value =3/25=0.1200
|-
|ElectronegativeHalogenicity
|0.2400
|
|There are 25 non-H atoms, 6 are electronegative halogen atoms, value =6/25=0.2400
|-
| colspan="4" |<code>eps=11.52 epsinf=2.0366 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.1200 ElectronegativeHalogenicity=0.2400</code>
|}

=== [C4C1Im][OTf] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|12.90
|<ref name=":3">Huang 2011 http://pubs.acs.org/doi/abs/10.1021/je101184s</ref>
|Page 1495, number 11 on the list.
|-
|epsinf
|2.0665
|<ref name=":4">Gonzalez 2012 http://pubs.acs.org/doi/abs/10.1021/je201334p</ref>
|n=1.43755, has been squared to give epsinf=2.0665. Can be found in Table 1, 3rd row.
|-
|SurfaceTensionAtInterface
|unknown
|
|-
|HBondAcidity (α)
|0.263
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.625
|-
|HBondBasicity (β)
|0.374
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.464
|-
|CarbonAromaticity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are aromatic C atoms, value=3/18=0.1667.
|-
|ElectronegativeHalogenicity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are electronegative halogen atoms, value=3/18=0.1667.
|-
| colspan="4" |<code>eps=12.90 epsinf=2.0665 SurfaceTensionAtInterface'''=XX''' HBondAcidity=0.263 HBondBasicity=0.374 CarbonAromaticity=0.1667 ElectronegativeHalogenicity=0.1667</code>
|}

=== [C4C1Im][XX] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|13.70
| M. M. Huang, Y. P. Jiang, P. Sasisanker, G. W. Driver and H. Weingartner,  J. Chem. Eng. Data, 2011, 56, 1494–1499.
|
|-
|epsinf (n2)
|2.3691
| G. Vakili-Nezhaad, M. Vatani, M. Asghari and I. Ashour, J. Chem. Thermodyn., 2012, 54, 148–154.
|n=1.53921, has been squared to give epsinf=2.3691 (error in some database calcs with n=1.5436 n2=2.3827)
|-
|SurfaceTensionAtInterface
|68.34
| G. Vakili-Nezhaad, M. Vatani, M. Asghari and I. Ashour, J. Chem. Thermodyn., 2012, 54, 148–154.
| η=45.41 (mN.m-1) converts to 45.41*1.439= cal mol-1 Å-2=65.34
|-
|HBondAcidity (α)
|0.18
|
| Kamlet-Taft 0.43
|-
|HBondBasicity (β)
|0.52
|
| Kamlet-Taft 0.71
|-
|CarbonAromaticity
|0.2308
|
|There are 13 non-H atoms, 3 are aromatic C atoms, value=xx/xx=0.2308
|-
|ElectronegativeHalogenicity
|0.0
|
|There are no electronegative halogen atoms, value=0.0
|-
| colspan="4" |<code>eps=13.70 epsinf=2.3691 SurfaceTensionAtInterface=68.34 HBondAcidity=0.18 HBondBasicity=0.52 CarbonAromaticity=0.2308 ElectronegativeHalogenicity=0.0</code>
|}

=== Molten salt [Li+,Na+,K+][CO32-] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|MolarVolume
|57
|<ref name=":5" />
|molar volume Li2CO3 68 Na2CO3 92 K2CO3 124 Å3/molecule, average is 95 and 95*0.6022=57 at T=1.1Tm
|-
|Tabs
|900
|
|Absolute Temperature in K ie 298+600≈900
|-
|???
|
|
|ThermalExansionCoefficient estimate 20*10-6 K-1 at T=1.1Tm (this is not working!)
|-
|eps
|3
|<ref name=":5">G. Janz and M. Lorenz, <abbr>J. Electrochem. Soc.</abbr> 1961 volume 108, issue 11, 1052-1058 doi: 10.1149/1.2427946</ref>
|estimated value
|-
|epsinf
|2.25
|
|refractive index Na2CO3 1.489-1.535,<ref><nowiki>https://pubchem.ncbi.nlm.nih.gov/compound/sodium_carbonate#section=Spectral-Properties&fullscreen=true</nowiki></ref> Li2CO3 1.428-1.572<ref>Weast, R.C. (ed.). Handbook of Chemistry and Physics. 60th ed. Boca Raton, Florida: CRC Press Inc., 1979., p. B-91</ref> K2CO3 1.426-1.541<ref><nowiki>http://cameo.mfa.org/wiki/Potassium_carbonate</nowiki></ref> taking a "mid" value 1.52=2.25
|-
|SurfaceTensionAtInterface
|273
|<ref name=":5" />
|used surface tension of Na/K/CO3 mixture 50 mol % K2CO3 at 810 ºC , 190.0 dynes/cm
|-
|HBondAcidity (α)
|0.00
|<nowiki>-</nowiki>
| rowspan="2" |There are no H-atoms so H-bond acidity is zero
H-bond basicity computations result in proton transfer, NO3 ≈0.74-0.81, Cl ≈0.95-0.98, we assume it is even stronger due to -2 charge
|-
|HBondBasicity (β)
|0.99
|
|-
|CarbonAromaticity
|0.00
|<nowiki>-</nowiki>
|There are no aromatic C atoms
|-
|ElectronegativeHalogenicity
|0.00
|<nowiki>-</nowiki>
|There are no halogen atoms
|-
| colspan="4" |Stoichiometry=C2O62Li2Na2K2 MolarVolume=57.0 Tabs=900 eps=3.0 epsinf=2.25 SurfaceTensionAtInterface=273 HBondAcidity=0.0 HBondBasicity=0.99 CarbonAromaticity=0.0 ElectronegativeHalogenicity=0.0
|}

=== Example IL-GIL (generic IL) ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.50
|<ref name=":0" />
|see ESI Table S2.1
|-
|epsinf
|2.0449
|<ref name=":0" />
|n=1.43, has been squared to give epsinf=2.0449
|-
|SurfaceTensionAtInterface
|61.24
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|HBondAcidity (α)
|0.229
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|HBondBasicity (β)
|0.265
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|CarbonAromaticity
|
|<ref name=":0" />
|
|-
|ElectronegativeHalogenicity
|
|<ref name=":0" />
|
|-
| colspan="4" |<code>eps=11.50 epsinf=2.0449 SurfaceTensionAtInterface=61.24 HBondAcidity=0.229 HBondBasicity=0.265 CarbonAromaticity=0.xxx ElectronegativeHalogenicity=0.xxx</code>
|}

== Example table ==
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|
|
|
|-
|epsinf
|
|
|
|-
|SurfaceTensionAtInterface
|
|
|
|-
|HBondAcidity (α)
|
|
|
|-
|HBondBasicity (β)
|
|
|
|-
|CarbonAromaticity
|
|
|
|-
|ElectronegativeHalogenicity
|
|
|
|-
| colspan="4" |<code>eps= epsinf= SurfaceTensionAtInterface= HBondAcidity= HBondBasicity= CarbonAromaticity= ElectronegativeHalogenicity=</code>
|}

== References ==
<references />

Mod:Hunt Research Group: Using SMD on ILs

2019-12-23T10:32:30Z

Phunt: /* [C4C1Im][XX] */

This page explains how to use the SMD model to simulate an ionic liquid environment in Gaussian calculations. The SMD model is explained in detail in the original paper here.<ref>Marenich 2009 http://pubs.acs.org/doi/abs/10.1021/jp810292n</ref> Its use on ILs is similarly explained here.<ref name=":0">Bernales 2012 http://pubs.acs.org/doi/abs/10.1021/jp304365v</ref> Many useful solvent parameters are also available in this paper.

== How to simulate a defined solvent environment ==
Gaussian has many previously defined solvent environments. A list is available at the bottom of this page.<ref>http://www.gaussian.com/g_tech/g_ur/k_scrf.htm</ref> For example to use the pre-defined water environment simply insert the following keyword into the method line of your input file. The rest of your method line should specify your functional, basis set, optimisation/other type of calculation as usual.
scrf=(smd,solvent=water)
To use a different solvent to water change the solvent=water part to solvent=something else in the list.

== How to simulate a generic solvent environment ==
The SMD model has many parameters. These are already defined inside Gaussian for the list of defined solvents. If you want to use a solvent not on the list e.g. an ionic liquid, you must define these parameters manually. In this case put the following into the method line:
scrf=(smd,solvent=generic)

=== Types of SMD model ===
3 types of SMD for ILs have been defined.<ref name=":0" />

==== SMD ====
The standard SMD model. All parameters are determined for the particular IL (or a very similar one) being used as the solvent environment.

==== SMD-GIL ====
The generic ionic liquid model. The average values above are used for all parameters, except φ and ψ, which are simply calculated from the chemical formula of the IL.

==== SMD-PGP ====
The partial generic parameters model. Any parameter which has been measured for that IL is used. For any parameters which you do not have values for, use the average values.

=== Solvent parameters and SMD-GIL ===
The parameters are defined at the bottom of the input file, these parameters are listed in the table below:
{| class="wikitable"
!Parameter
!Symbol
!Name in Gaussian input file
!Average value for ILs<ref name=":0" />
|-
|Dielectric constant
|ε
|eps
|11.50
|-
|Index of refraction, squared
|n2
|epsinf
|2.0449
|-
|Macroscopic surface tension /cal mol-1 Å-2
|γ
|SurfaceTensionAtInterface
|61.24
|-
|Abraham hydrogen bond acidity parameter
|Σα2H
|HBondAcidity
|0.229
|-
|Abraham hydrogen bond basicity parameter
|Σβ2H
|HBondBasicity
|0.265
|-
|Fraction of non-hydrogen atoms which are aromatic carbon atoms
|φ
|CarbonAromaticity
|<nowiki>-</nowiki>
|-
|Fraction of non-hydrogen atoms which are electronegative halogen atoms
|ψ
|ElectronegativeHalogenicity
|<nowiki>-</nowiki>
|}

=== Note on parameters ===
Surface tension
*surface tension is the only parameter with units, those used in SMD are non-standard cal mol-1Å-2
*the SI units are Jm-2 or Nm-1
*typical units are dyn cm-1 where 1 dyn = 1 g cm s-2
*as we tend to work in kJ/mol the energy part of this becomes not J but J/mol
*1 dyn cm-1 = 0.001N m-1 = 0.001J m-2
*1 m = 1*1010Å and 1J=0.239cal and 1 mol-1=6.022*1023
*1 dyn cm-1 = 0.001*0.239cal*6.022*1023mol-1/(1*102*10Å2
*and if you think about this 1023 on top line cancels with 1020 on bottom line leaving 103 which cancels with the 0.001=10-3 leaving us with 0.239*6.022=1.439
*1 dyn cm-1 = 1.439 cal mol-1 Å-2
Molar Volume
* MolarVolume=x.x in cm3/mol
* molecular volume in Å3 per molecule converted to cm3/mol
* 1cm = 1*108Å, 1Å = 1*10-8 cm
* x Å3 per molecule = x*6.022*1023mol-1 *103*-8cm3 = x*6.022*10-1cm3mol-1

=== Example: [C4C1Im][NTf2] ===
All parameters for this IL have been measured, and can be found in reference 2.<ref name=":0" /> That means we can use the standard SMD method.

To get a value for φ take the number of aromatic carbon atoms (3) and divide by the number of non-hydrogen atoms (25). φ = 0.12.

To get a value for ψ take the number of electronegative halogen atoms (6) and divide by the number of non-hydrogen atoms (25). ψ = 0.24.

To define these parameters place the following line at the bottom of the input file (include one blank line before and at least one blank line after):
eps=11.52 epsinf=2.037 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.12 ElectronegativeHalogenicity=0.24

=== Kamlet-Taft vs Abraham H-bonding parameters ===
The SMD model requires Abraham H-bondonding parameters (Σα2H, Σβ2H), however Kamlet-Taft (α, β) measurements are more commonly reported for ILs. To alleviate this problem a relationship between the parameters was investigated, giving the following equations:<ref name=":0" />

Σα2H = 0.4098α + 0.0064

Σβ2H = 0.6138β + 0.0890

Previously the group has developed a simple method for calculating Kamlet-Taft parameters, and the instructions are here.<ref>http://www.huntresearchgroup.org.uk/research/research_il_alpha_beta_intro.html</ref>

== SMD input database ==
Here we will keep a database of SMD parameters used by the group. Please add any IL you use, so no-one else has to re-do the research for the parameters! Please follow the template provided so that it is clear where you get each value from.

===[C4C1Im][BF4]===
all values from <ref name=":0" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.70
|<ref name=":0" />
|
|-
|epsinf
|2.0207
|<ref name=":0" />
|Value given in reference is n=1.4215, it has been squared to give epsinf=2.0207
|-
|SurfaceTensionAtInterface
|67.07
|<ref name=":0" />
|
|-
|HBondAcidity (α)
|0.263
|<ref name=":0" />
| Kamlet-Taft 0.627
|-
|HBondBasicity (β)
|0.320
|<ref name=":0" />
| Kamlet-Taft 0.376
|-
|CarbonAromaticity (φ)
|0.2000
|
|There are 15 non-H atoms, 3 are aromatic C atoms, value=3/15=0.2000
|-
|ElectronegativeHalogenicity (ψ)
|0.2667
|
|There are 15 non-H atoms, 4 are electronegative halogen atoms, value =4/15=0.2667
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][PF6]===
all values from <ref name=":0" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.40
|<ref name=":0" />
|
|-
|epsinf
|1.9853
|<ref name=":0" />
|Value given in reference is n=1.4090, it has been squared to give epsinf=1.9853
|-
|SurfaceTensionAtInterface
|70.24
|<ref name=":0" />
|
|-
|HBondAcidity (α)
|0.266
|<ref name=":0" />
| Kamlet-Taft 0.634
|-
|HBondBasicity (β)
|0.216
|<ref name=":0" />
| Kamlet-Taft 0.207
|-
|CarbonAromaticity (φ)
|0.1765
|
|There are 17 non-H atoms, 3 are aromatic C atoms, value=3/17=0.1765
|-
|ElectronegativeHalogenicity (ψ)
|0.3529
|
|There are 17 non-H atoms, 4 are electronegative halogen atoms, value =6/17=0.3529
|-
| colspan="4" |<code>eps=11.40 epsinf=1.9853 SurfaceTensionAtInterface=70.24 HBondAcidity=0.266 HBondBasicity=0.216 CarbonAromaticity=0.1765 ElectronegativeHalogenicity=0.3529</code>
|}

=== [C4C1Im][NTf2] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.52
|<ref name=":0" /> <ref name=":6">Daguenet 2006 http://pubs.acs.org/doi/abs/10.1021/jp0604903</ref>
|
|-
|epsinf
|2.0366
|<ref name=":0" /> <ref name=":1">Huddleston 2001 http://pubs.rsc.org/en/Content/ArticleLanding/2001/GC/b103275p</ref>
|Value given in reference is n=1.4271, it has been squared to give epsinf=2.0366
|-
|SurfaceTensionAtInterface
|53.97
|<ref name=":0" /> <ref name=":1" />
|
|-
|HBondAcidity (α)
|0.259
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.617
|-
|HBondBasicity (β)
|0.238
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.243
|-
|CarbonAromaticity
|0.1200
|
|There are 25 non-H atoms, 3 are aromatic C atoms, value =3/25=0.1200
|-
|ElectronegativeHalogenicity
|0.2400
|
|There are 25 non-H atoms, 6 are electronegative halogen atoms, value =6/25=0.2400
|-
| colspan="4" |<code>eps=11.52 epsinf=2.0366 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.1200 ElectronegativeHalogenicity=0.2400</code>
|}

=== [C4C1Im][OTf] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|12.90
|<ref name=":3">Huang 2011 http://pubs.acs.org/doi/abs/10.1021/je101184s</ref>
|Page 1495, number 11 on the list.
|-
|epsinf
|2.0665
|<ref name=":4">Gonzalez 2012 http://pubs.acs.org/doi/abs/10.1021/je201334p</ref>
|n=1.43755, has been squared to give epsinf=2.0665. Can be found in Table 1, 3rd row.
|-
|SurfaceTensionAtInterface
|unknown
|
|-
|HBondAcidity (α)
|0.263
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.625
|-
|HBondBasicity (β)
|0.374
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.464
|-
|CarbonAromaticity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are aromatic C atoms, value=3/18=0.1667.
|-
|ElectronegativeHalogenicity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are electronegative halogen atoms, value=3/18=0.1667.
|-
| colspan="4" |<code>eps=12.90 epsinf=2.0665 SurfaceTensionAtInterface'''=XX''' HBondAcidity=0.263 HBondBasicity=0.374 CarbonAromaticity=0.1667 ElectronegativeHalogenicity=0.1667</code>
|}

=== [C4C1Im][XX] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|13.70
| M. M. Huang, Y. P. Jiang, P. Sasisanker, G. W. Driver and H. Weingartner,  J. Chem. Eng. Data, 2011, 56, 1494–1499.
|
|-
|epsinf (n2)
|2.3691
| G. Vakili-Nezhaad, M. Vatani, M. Asghari and I. Ashour, J. Chem. Thermodyn., 2012, 54, 148–154.
|n=1.53921, has been squared to give epsinf=2.3691 (error in some database calcs with n=1.5436 n2=2.3827)
|-
|SurfaceTensionAtInterface
|68.34
| G. Vakili-Nezhaad, M. Vatani, M. Asghari and I. Ashour, J. Chem. Thermodyn., 2012, 54, 148–154.
| η=45.41 (mN.m-1) converts to 45.41*1.439= cal mol-1 Å-2=65.34
|-
|HBondAcidity (α)
|0.18
|
| Kamlet-Taft 0.43
|-
|HBondBasicity (β)
|0.52
|
| Kamlet-Taft 0.71
|-
|CarbonAromaticity
|0.2308
|
|There are 13 non-H atoms, 3 are aromatic C atoms, value=xx/xx=0.2308
|-
|ElectronegativeHalogenicity
|0.0
|
|There are no electronegative halogen atoms, value=0.0
|-
| colspan="4" |<code>eps=13.70 epsinf=2.3691 SurfaceTensionAtInterface=68.34 HBondAcidity=0.18 HBondBasicity=0.52 CarbonAromaticity=0.2308 ElectronegativeHalogenicity=0.0</code>
|}

=== Molten salt [Li+,Na+,K+][CO32-] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|MolarVolume
|57
|<ref name=":5" />
|molar volume Li2CO3 68 Na2CO3 92 K2CO3 124 Å3/molecule, average is 95 and 95*0.6022=57 at T=1.1Tm
|-
|Tabs
|900
|
|Absolute Temperature in K ie 298+600≈900
|-
|???
|
|
|ThermalExansionCoefficient estimate 20*10-6 K-1 at T=1.1Tm (this is not working!)
|-
|eps
|3
|<ref name=":5">G. Janz and M. Lorenz, <abbr>J. Electrochem. Soc.</abbr> 1961 volume 108, issue 11, 1052-1058 doi: 10.1149/1.2427946</ref>
|estimated value
|-
|epsinf
|2.25
|
|refractive index Na2CO3 1.489-1.535,<ref><nowiki>https://pubchem.ncbi.nlm.nih.gov/compound/sodium_carbonate#section=Spectral-Properties&fullscreen=true</nowiki></ref> Li2CO3 1.428-1.572<ref>Weast, R.C. (ed.). Handbook of Chemistry and Physics. 60th ed. Boca Raton, Florida: CRC Press Inc., 1979., p. B-91</ref> K2CO3 1.426-1.541<ref><nowiki>http://cameo.mfa.org/wiki/Potassium_carbonate</nowiki></ref> taking a "mid" value 1.52=2.25
|-
|SurfaceTensionAtInterface
|273
|<ref name=":5" />
|used surface tension of Na/K/CO3 mixture 50 mol % K2CO3 at 810 ºC , 190.0 dynes/cm
|-
|HBondAcidity (α)
|0.00
|<nowiki>-</nowiki>
| rowspan="2" |There are no H-atoms so H-bond acidity is zero
H-bond basicity computations result in proton transfer, NO3 ≈0.74-0.81, Cl ≈0.95-0.98, we assume it is even stronger due to -2 charge
|-
|HBondBasicity (β)
|0.99
|
|-
|CarbonAromaticity
|0.00
|<nowiki>-</nowiki>
|There are no aromatic C atoms
|-
|ElectronegativeHalogenicity
|0.00
|<nowiki>-</nowiki>
|There are no halogen atoms
|-
| colspan="4" |Stoichiometry=C2O62Li2Na2K2 MolarVolume=57.0 Tabs=900 eps=3.0 epsinf=2.25 SurfaceTensionAtInterface=273 HBondAcidity=0.0 HBondBasicity=0.99 CarbonAromaticity=0.0 ElectronegativeHalogenicity=0.0
|}

=== Example IL-GIL (generic IL) ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.50
|<ref name=":0" />
|see ESI Table S2.1
|-
|epsinf
|2.0449
|<ref name=":0" />
|n=1.43, has been squared to give epsinf=2.0449
|-
|SurfaceTensionAtInterface
|61.24
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|HBondAcidity (α)
|0.229
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|HBondBasicity (β)
|0.265
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|CarbonAromaticity
|
|<ref name=":0" />
|
|-
|ElectronegativeHalogenicity
|
|<ref name=":0" />
|
|-
| colspan="4" |<code>eps=11.50 epsinf=2.0449 SurfaceTensionAtInterface=61.24 HBondAcidity=0.229 HBondBasicity=0.265 CarbonAromaticity=0.xxx ElectronegativeHalogenicity=0.xxx</code>
|}

== Example table ==
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|
|
|
|-
|epsinf
|
|
|
|-
|SurfaceTensionAtInterface
|
|
|
|-
|HBondAcidity (α)
|
|
|
|-
|HBondBasicity (β)
|
|
|
|-
|CarbonAromaticity
|
|
|
|-
|ElectronegativeHalogenicity
|
|
|
|-
| colspan="4" |<code>eps= epsinf= SurfaceTensionAtInterface= HBondAcidity= HBondBasicity= CarbonAromaticity= ElectronegativeHalogenicity=</code>
|}

== References ==
<references />

Mod:Hunt Research Group: Using SMD on ILs

2019-12-23T10:24:51Z

Phunt: /* [C4C1Im][XX] */

This page explains how to use the SMD model to simulate an ionic liquid environment in Gaussian calculations. The SMD model is explained in detail in the original paper here.<ref>Marenich 2009 http://pubs.acs.org/doi/abs/10.1021/jp810292n</ref> Its use on ILs is similarly explained here.<ref name=":0">Bernales 2012 http://pubs.acs.org/doi/abs/10.1021/jp304365v</ref> Many useful solvent parameters are also available in this paper.

== How to simulate a defined solvent environment ==
Gaussian has many previously defined solvent environments. A list is available at the bottom of this page.<ref>http://www.gaussian.com/g_tech/g_ur/k_scrf.htm</ref> For example to use the pre-defined water environment simply insert the following keyword into the method line of your input file. The rest of your method line should specify your functional, basis set, optimisation/other type of calculation as usual.
scrf=(smd,solvent=water)
To use a different solvent to water change the solvent=water part to solvent=something else in the list.

== How to simulate a generic solvent environment ==
The SMD model has many parameters. These are already defined inside Gaussian for the list of defined solvents. If you want to use a solvent not on the list e.g. an ionic liquid, you must define these parameters manually. In this case put the following into the method line:
scrf=(smd,solvent=generic)

=== Types of SMD model ===
3 types of SMD for ILs have been defined.<ref name=":0" />

==== SMD ====
The standard SMD model. All parameters are determined for the particular IL (or a very similar one) being used as the solvent environment.

==== SMD-GIL ====
The generic ionic liquid model. The average values above are used for all parameters, except φ and ψ, which are simply calculated from the chemical formula of the IL.

==== SMD-PGP ====
The partial generic parameters model. Any parameter which has been measured for that IL is used. For any parameters which you do not have values for, use the average values.

=== Solvent parameters and SMD-GIL ===
The parameters are defined at the bottom of the input file, these parameters are listed in the table below:
{| class="wikitable"
!Parameter
!Symbol
!Name in Gaussian input file
!Average value for ILs<ref name=":0" />
|-
|Dielectric constant
|ε
|eps
|11.50
|-
|Index of refraction, squared
|n2
|epsinf
|2.0449
|-
|Macroscopic surface tension /cal mol-1 Å-2
|γ
|SurfaceTensionAtInterface
|61.24
|-
|Abraham hydrogen bond acidity parameter
|Σα2H
|HBondAcidity
|0.229
|-
|Abraham hydrogen bond basicity parameter
|Σβ2H
|HBondBasicity
|0.265
|-
|Fraction of non-hydrogen atoms which are aromatic carbon atoms
|φ
|CarbonAromaticity
|<nowiki>-</nowiki>
|-
|Fraction of non-hydrogen atoms which are electronegative halogen atoms
|ψ
|ElectronegativeHalogenicity
|<nowiki>-</nowiki>
|}

=== Note on parameters ===
Surface tension
*surface tension is the only parameter with units, those used in SMD are non-standard cal mol-1Å-2
*the SI units are Jm-2 or Nm-1
*typical units are dyn cm-1 where 1 dyn = 1 g cm s-2
*as we tend to work in kJ/mol the energy part of this becomes not J but J/mol
*1 dyn cm-1 = 0.001N m-1 = 0.001J m-2
*1 m = 1*1010Å and 1J=0.239cal and 1 mol-1=6.022*1023
*1 dyn cm-1 = 0.001*0.239cal*6.022*1023mol-1/(1*102*10Å2
*and if you think about this 1023 on top line cancels with 1020 on bottom line leaving 103 which cancels with the 0.001=10-3 leaving us with 0.239*6.022=1.439
*1 dyn cm-1 = 1.439 cal mol-1 Å-2
Molar Volume
* MolarVolume=x.x in cm3/mol
* molecular volume in Å3 per molecule converted to cm3/mol
* 1cm = 1*108Å, 1Å = 1*10-8 cm
* x Å3 per molecule = x*6.022*1023mol-1 *103*-8cm3 = x*6.022*10-1cm3mol-1

=== Example: [C4C1Im][NTf2] ===
All parameters for this IL have been measured, and can be found in reference 2.<ref name=":0" /> That means we can use the standard SMD method.

To get a value for φ take the number of aromatic carbon atoms (3) and divide by the number of non-hydrogen atoms (25). φ = 0.12.

To get a value for ψ take the number of electronegative halogen atoms (6) and divide by the number of non-hydrogen atoms (25). ψ = 0.24.

To define these parameters place the following line at the bottom of the input file (include one blank line before and at least one blank line after):
eps=11.52 epsinf=2.037 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.12 ElectronegativeHalogenicity=0.24

=== Kamlet-Taft vs Abraham H-bonding parameters ===
The SMD model requires Abraham H-bondonding parameters (Σα2H, Σβ2H), however Kamlet-Taft (α, β) measurements are more commonly reported for ILs. To alleviate this problem a relationship between the parameters was investigated, giving the following equations:<ref name=":0" />

Σα2H = 0.4098α + 0.0064

Σβ2H = 0.6138β + 0.0890

Previously the group has developed a simple method for calculating Kamlet-Taft parameters, and the instructions are here.<ref>http://www.huntresearchgroup.org.uk/research/research_il_alpha_beta_intro.html</ref>

== SMD input database ==
Here we will keep a database of SMD parameters used by the group. Please add any IL you use, so no-one else has to re-do the research for the parameters! Please follow the template provided so that it is clear where you get each value from.

===[C4C1Im][BF4]===
all values from <ref name=":0" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.70
|<ref name=":0" />
|
|-
|epsinf
|2.0207
|<ref name=":0" />
|Value given in reference is n=1.4215, it has been squared to give epsinf=2.0207
|-
|SurfaceTensionAtInterface
|67.07
|<ref name=":0" />
|
|-
|HBondAcidity (α)
|0.263
|<ref name=":0" />
| Kamlet-Taft 0.627
|-
|HBondBasicity (β)
|0.320
|<ref name=":0" />
| Kamlet-Taft 0.376
|-
|CarbonAromaticity (φ)
|0.2000
|
|There are 15 non-H atoms, 3 are aromatic C atoms, value=3/15=0.2000
|-
|ElectronegativeHalogenicity (ψ)
|0.2667
|
|There are 15 non-H atoms, 4 are electronegative halogen atoms, value =4/15=0.2667
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][PF6]===
all values from <ref name=":0" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.40
|<ref name=":0" />
|
|-
|epsinf
|1.9853
|<ref name=":0" />
|Value given in reference is n=1.4090, it has been squared to give epsinf=1.9853
|-
|SurfaceTensionAtInterface
|70.24
|<ref name=":0" />
|
|-
|HBondAcidity (α)
|0.266
|<ref name=":0" />
| Kamlet-Taft 0.634
|-
|HBondBasicity (β)
|0.216
|<ref name=":0" />
| Kamlet-Taft 0.207
|-
|CarbonAromaticity (φ)
|0.1765
|
|There are 17 non-H atoms, 3 are aromatic C atoms, value=3/17=0.1765
|-
|ElectronegativeHalogenicity (ψ)
|0.3529
|
|There are 17 non-H atoms, 4 are electronegative halogen atoms, value =6/17=0.3529
|-
| colspan="4" |<code>eps=11.40 epsinf=1.9853 SurfaceTensionAtInterface=70.24 HBondAcidity=0.266 HBondBasicity=0.216 CarbonAromaticity=0.1765 ElectronegativeHalogenicity=0.3529</code>
|}

=== [C4C1Im][NTf2] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.52
|<ref name=":0" /> <ref name=":6">Daguenet 2006 http://pubs.acs.org/doi/abs/10.1021/jp0604903</ref>
|
|-
|epsinf
|2.0366
|<ref name=":0" /> <ref name=":1">Huddleston 2001 http://pubs.rsc.org/en/Content/ArticleLanding/2001/GC/b103275p</ref>
|Value given in reference is n=1.4271, it has been squared to give epsinf=2.0366
|-
|SurfaceTensionAtInterface
|53.97
|<ref name=":0" /> <ref name=":1" />
|
|-
|HBondAcidity (α)
|0.259
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.617
|-
|HBondBasicity (β)
|0.238
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.243
|-
|CarbonAromaticity
|0.1200
|
|There are 25 non-H atoms, 3 are aromatic C atoms, value =3/25=0.1200
|-
|ElectronegativeHalogenicity
|0.2400
|
|There are 25 non-H atoms, 6 are electronegative halogen atoms, value =6/25=0.2400
|-
| colspan="4" |<code>eps=11.52 epsinf=2.0366 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.1200 ElectronegativeHalogenicity=0.2400</code>
|}

=== [C4C1Im][OTf] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|12.90
|<ref name=":3">Huang 2011 http://pubs.acs.org/doi/abs/10.1021/je101184s</ref>
|Page 1495, number 11 on the list.
|-
|epsinf
|2.0665
|<ref name=":4">Gonzalez 2012 http://pubs.acs.org/doi/abs/10.1021/je201334p</ref>
|n=1.43755, has been squared to give epsinf=2.0665. Can be found in Table 1, 3rd row.
|-
|SurfaceTensionAtInterface
|unknown
|
|-
|HBondAcidity (α)
|0.263
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.625
|-
|HBondBasicity (β)
|0.374
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.464
|-
|CarbonAromaticity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are aromatic C atoms, value=3/18=0.1667.
|-
|ElectronegativeHalogenicity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are electronegative halogen atoms, value=3/18=0.1667.
|-
| colspan="4" |<code>eps=12.90 epsinf=2.0665 SurfaceTensionAtInterface'''=XX''' HBondAcidity=0.263 HBondBasicity=0.374 CarbonAromaticity=0.1667 ElectronegativeHalogenicity=0.1667</code>
|}

=== [C4C1Im][XX] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|13.70
| M. M. Huang, Y. P. Jiang, P. Sasisanker, G. W. Driver and H. Weingartner,  J. Chem. Eng. Data, 2011, 56, 1494–1499.
|
|-
|epsinf (n2)
|2.3691
| G. Vakili-Nezhaad, M. Vatani, M. Asghari and I. Ashour, J. Chem. Thermodyn., 2012, 54, 148–154.
|n=1.53921, has been squared to give epsinf=2.3691 (error in some database calcs with n=1.5436 n2=2.3827)
|-
|SurfaceTensionAtInterface
|68.29
| G. Vakili-Nezhaad, M. Vatani, M. Asghari and I. Ashour, J. Chem. Thermodyn., 2012, 54, 148–154.
| η=45.41 (mN.m-1) converts to
|-
|HBondAcidity (α)
|0.18
|
| Kamlet-Taft
|-
|HBondBasicity (β)
|0.52
|
| Kamlet-Taft
|-
|CarbonAromaticity
|0.308
|
|There are xx non-H atoms, xx are aromatic C atoms, value=xx/xx=0.308
|-
|ElectronegativeHalogenicity
|0.0
|
|There are no electronegative halogen atoms, value=0.0
|-
| colspan="4" |<code>eps=13.70 epsinf=2.36917 SurfaceTensionAtInterface=68.29 HBondAcidity=0.18 HBondBasicity=0.52 CarbonAromaticity=0.3080 ElectronegativeHalogenicity=0.0</code>
|}

=== Molten salt [Li+,Na+,K+][CO32-] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|MolarVolume
|57
|<ref name=":5" />
|molar volume Li2CO3 68 Na2CO3 92 K2CO3 124 Å3/molecule, average is 95 and 95*0.6022=57 at T=1.1Tm
|-
|Tabs
|900
|
|Absolute Temperature in K ie 298+600≈900
|-
|???
|
|
|ThermalExansionCoefficient estimate 20*10-6 K-1 at T=1.1Tm (this is not working!)
|-
|eps
|3
|<ref name=":5">G. Janz and M. Lorenz, <abbr>J. Electrochem. Soc.</abbr> 1961 volume 108, issue 11, 1052-1058 doi: 10.1149/1.2427946</ref>
|estimated value
|-
|epsinf
|2.25
|
|refractive index Na2CO3 1.489-1.535,<ref><nowiki>https://pubchem.ncbi.nlm.nih.gov/compound/sodium_carbonate#section=Spectral-Properties&fullscreen=true</nowiki></ref> Li2CO3 1.428-1.572<ref>Weast, R.C. (ed.). Handbook of Chemistry and Physics. 60th ed. Boca Raton, Florida: CRC Press Inc., 1979., p. B-91</ref> K2CO3 1.426-1.541<ref><nowiki>http://cameo.mfa.org/wiki/Potassium_carbonate</nowiki></ref> taking a "mid" value 1.52=2.25
|-
|SurfaceTensionAtInterface
|273
|<ref name=":5" />
|used surface tension of Na/K/CO3 mixture 50 mol % K2CO3 at 810 ºC , 190.0 dynes/cm
|-
|HBondAcidity (α)
|0.00
|<nowiki>-</nowiki>
| rowspan="2" |There are no H-atoms so H-bond acidity is zero
H-bond basicity computations result in proton transfer, NO3 ≈0.74-0.81, Cl ≈0.95-0.98, we assume it is even stronger due to -2 charge
|-
|HBondBasicity (β)
|0.99
|
|-
|CarbonAromaticity
|0.00
|<nowiki>-</nowiki>
|There are no aromatic C atoms
|-
|ElectronegativeHalogenicity
|0.00
|<nowiki>-</nowiki>
|There are no halogen atoms
|-
| colspan="4" |Stoichiometry=C2O62Li2Na2K2 MolarVolume=57.0 Tabs=900 eps=3.0 epsinf=2.25 SurfaceTensionAtInterface=273 HBondAcidity=0.0 HBondBasicity=0.99 CarbonAromaticity=0.0 ElectronegativeHalogenicity=0.0
|}

=== Example IL-GIL (generic IL) ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.50
|<ref name=":0" />
|see ESI Table S2.1
|-
|epsinf
|2.0449
|<ref name=":0" />
|n=1.43, has been squared to give epsinf=2.0449
|-
|SurfaceTensionAtInterface
|61.24
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|HBondAcidity (α)
|0.229
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|HBondBasicity (β)
|0.265
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|CarbonAromaticity
|
|<ref name=":0" />
|
|-
|ElectronegativeHalogenicity
|
|<ref name=":0" />
|
|-
| colspan="4" |<code>eps=11.50 epsinf=2.0449 SurfaceTensionAtInterface=61.24 HBondAcidity=0.229 HBondBasicity=0.265 CarbonAromaticity=0.xxx ElectronegativeHalogenicity=0.xxx</code>
|}

== Example table ==
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|
|
|
|-
|epsinf
|
|
|
|-
|SurfaceTensionAtInterface
|
|
|
|-
|HBondAcidity (α)
|
|
|
|-
|HBondBasicity (β)
|
|
|
|-
|CarbonAromaticity
|
|
|
|-
|ElectronegativeHalogenicity
|
|
|
|-
| colspan="4" |<code>eps= epsinf= SurfaceTensionAtInterface= HBondAcidity= HBondBasicity= CarbonAromaticity= ElectronegativeHalogenicity=</code>
|}

== References ==
<references />

Mod:Hunt Research Group: Using SMD on ILs

2019-12-23T09:55:03Z

Phunt: /* [C4C1Im][XX] */

This page explains how to use the SMD model to simulate an ionic liquid environment in Gaussian calculations. The SMD model is explained in detail in the original paper here.<ref>Marenich 2009 http://pubs.acs.org/doi/abs/10.1021/jp810292n</ref> Its use on ILs is similarly explained here.<ref name=":0">Bernales 2012 http://pubs.acs.org/doi/abs/10.1021/jp304365v</ref> Many useful solvent parameters are also available in this paper.

== How to simulate a defined solvent environment ==
Gaussian has many previously defined solvent environments. A list is available at the bottom of this page.<ref>http://www.gaussian.com/g_tech/g_ur/k_scrf.htm</ref> For example to use the pre-defined water environment simply insert the following keyword into the method line of your input file. The rest of your method line should specify your functional, basis set, optimisation/other type of calculation as usual.
scrf=(smd,solvent=water)
To use a different solvent to water change the solvent=water part to solvent=something else in the list.

== How to simulate a generic solvent environment ==
The SMD model has many parameters. These are already defined inside Gaussian for the list of defined solvents. If you want to use a solvent not on the list e.g. an ionic liquid, you must define these parameters manually. In this case put the following into the method line:
scrf=(smd,solvent=generic)

=== Types of SMD model ===
3 types of SMD for ILs have been defined.<ref name=":0" />

==== SMD ====
The standard SMD model. All parameters are determined for the particular IL (or a very similar one) being used as the solvent environment.

==== SMD-GIL ====
The generic ionic liquid model. The average values above are used for all parameters, except φ and ψ, which are simply calculated from the chemical formula of the IL.

==== SMD-PGP ====
The partial generic parameters model. Any parameter which has been measured for that IL is used. For any parameters which you do not have values for, use the average values.

=== Solvent parameters and SMD-GIL ===
The parameters are defined at the bottom of the input file, these parameters are listed in the table below:
{| class="wikitable"
!Parameter
!Symbol
!Name in Gaussian input file
!Average value for ILs<ref name=":0" />
|-
|Dielectric constant
|ε
|eps
|11.50
|-
|Index of refraction, squared
|n2
|epsinf
|2.0449
|-
|Macroscopic surface tension /cal mol-1 Å-2
|γ
|SurfaceTensionAtInterface
|61.24
|-
|Abraham hydrogen bond acidity parameter
|Σα2H
|HBondAcidity
|0.229
|-
|Abraham hydrogen bond basicity parameter
|Σβ2H
|HBondBasicity
|0.265
|-
|Fraction of non-hydrogen atoms which are aromatic carbon atoms
|φ
|CarbonAromaticity
|<nowiki>-</nowiki>
|-
|Fraction of non-hydrogen atoms which are electronegative halogen atoms
|ψ
|ElectronegativeHalogenicity
|<nowiki>-</nowiki>
|}

=== Note on parameters ===
Surface tension
*surface tension is the only parameter with units, those used in SMD are non-standard cal mol-1Å-2
*the SI units are Jm-2 or Nm-1
*typical units are dyn cm-1 where 1 dyn = 1 g cm s-2
*as we tend to work in kJ/mol the energy part of this becomes not J but J/mol
*1 dyn cm-1 = 0.001N m-1 = 0.001J m-2
*1 m = 1*1010Å and 1J=0.239cal and 1 mol-1=6.022*1023
*1 dyn cm-1 = 0.001*0.239cal*6.022*1023mol-1/(1*102*10Å2
*and if you think about this 1023 on top line cancels with 1020 on bottom line leaving 103 which cancels with the 0.001=10-3 leaving us with 0.239*6.022=1.439
*1 dyn cm-1 = 1.439 cal mol-1 Å-2
Molar Volume
* MolarVolume=x.x in cm3/mol
* molecular volume in Å3 per molecule converted to cm3/mol
* 1cm = 1*108Å, 1Å = 1*10-8 cm
* x Å3 per molecule = x*6.022*1023mol-1 *103*-8cm3 = x*6.022*10-1cm3mol-1

=== Example: [C4C1Im][NTf2] ===
All parameters for this IL have been measured, and can be found in reference 2.<ref name=":0" /> That means we can use the standard SMD method.

To get a value for φ take the number of aromatic carbon atoms (3) and divide by the number of non-hydrogen atoms (25). φ = 0.12.

To get a value for ψ take the number of electronegative halogen atoms (6) and divide by the number of non-hydrogen atoms (25). ψ = 0.24.

To define these parameters place the following line at the bottom of the input file (include one blank line before and at least one blank line after):
eps=11.52 epsinf=2.037 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.12 ElectronegativeHalogenicity=0.24

=== Kamlet-Taft vs Abraham H-bonding parameters ===
The SMD model requires Abraham H-bondonding parameters (Σα2H, Σβ2H), however Kamlet-Taft (α, β) measurements are more commonly reported for ILs. To alleviate this problem a relationship between the parameters was investigated, giving the following equations:<ref name=":0" />

Σα2H = 0.4098α + 0.0064

Σβ2H = 0.6138β + 0.0890

Previously the group has developed a simple method for calculating Kamlet-Taft parameters, and the instructions are here.<ref>http://www.huntresearchgroup.org.uk/research/research_il_alpha_beta_intro.html</ref>

== SMD input database ==
Here we will keep a database of SMD parameters used by the group. Please add any IL you use, so no-one else has to re-do the research for the parameters! Please follow the template provided so that it is clear where you get each value from.

===[C4C1Im][BF4]===
all values from <ref name=":0" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.70
|<ref name=":0" />
|
|-
|epsinf
|2.0207
|<ref name=":0" />
|Value given in reference is n=1.4215, it has been squared to give epsinf=2.0207
|-
|SurfaceTensionAtInterface
|67.07
|<ref name=":0" />
|
|-
|HBondAcidity (α)
|0.263
|<ref name=":0" />
| Kamlet-Taft 0.627
|-
|HBondBasicity (β)
|0.320
|<ref name=":0" />
| Kamlet-Taft 0.376
|-
|CarbonAromaticity (φ)
|0.2000
|
|There are 15 non-H atoms, 3 are aromatic C atoms, value=3/15=0.2000
|-
|ElectronegativeHalogenicity (ψ)
|0.2667
|
|There are 15 non-H atoms, 4 are electronegative halogen atoms, value =4/15=0.2667
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][PF6]===
all values from <ref name=":0" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.40
|<ref name=":0" />
|
|-
|epsinf
|1.9853
|<ref name=":0" />
|Value given in reference is n=1.4090, it has been squared to give epsinf=1.9853
|-
|SurfaceTensionAtInterface
|70.24
|<ref name=":0" />
|
|-
|HBondAcidity (α)
|0.266
|<ref name=":0" />
| Kamlet-Taft 0.634
|-
|HBondBasicity (β)
|0.216
|<ref name=":0" />
| Kamlet-Taft 0.207
|-
|CarbonAromaticity (φ)
|0.1765
|
|There are 17 non-H atoms, 3 are aromatic C atoms, value=3/17=0.1765
|-
|ElectronegativeHalogenicity (ψ)
|0.3529
|
|There are 17 non-H atoms, 4 are electronegative halogen atoms, value =6/17=0.3529
|-
| colspan="4" |<code>eps=11.40 epsinf=1.9853 SurfaceTensionAtInterface=70.24 HBondAcidity=0.266 HBondBasicity=0.216 CarbonAromaticity=0.1765 ElectronegativeHalogenicity=0.3529</code>
|}

=== [C4C1Im][NTf2] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.52
|<ref name=":0" /> <ref name=":6">Daguenet 2006 http://pubs.acs.org/doi/abs/10.1021/jp0604903</ref>
|
|-
|epsinf
|2.0366
|<ref name=":0" /> <ref name=":1">Huddleston 2001 http://pubs.rsc.org/en/Content/ArticleLanding/2001/GC/b103275p</ref>
|Value given in reference is n=1.4271, it has been squared to give epsinf=2.0366
|-
|SurfaceTensionAtInterface
|53.97
|<ref name=":0" /> <ref name=":1" />
|
|-
|HBondAcidity (α)
|0.259
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.617
|-
|HBondBasicity (β)
|0.238
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.243
|-
|CarbonAromaticity
|0.1200
|
|There are 25 non-H atoms, 3 are aromatic C atoms, value =3/25=0.1200
|-
|ElectronegativeHalogenicity
|0.2400
|
|There are 25 non-H atoms, 6 are electronegative halogen atoms, value =6/25=0.2400
|-
| colspan="4" |<code>eps=11.52 epsinf=2.0366 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.1200 ElectronegativeHalogenicity=0.2400</code>
|}

=== [C4C1Im][OTf] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|12.90
|<ref name=":3">Huang 2011 http://pubs.acs.org/doi/abs/10.1021/je101184s</ref>
|Page 1495, number 11 on the list.
|-
|epsinf
|2.0665
|<ref name=":4">Gonzalez 2012 http://pubs.acs.org/doi/abs/10.1021/je201334p</ref>
|n=1.43755, has been squared to give epsinf=2.0665. Can be found in Table 1, 3rd row.
|-
|SurfaceTensionAtInterface
|unknown
|
|-
|HBondAcidity (α)
|0.263
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.625
|-
|HBondBasicity (β)
|0.374
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.464
|-
|CarbonAromaticity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are aromatic C atoms, value=3/18=0.1667.
|-
|ElectronegativeHalogenicity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are electronegative halogen atoms, value=3/18=0.1667.
|-
| colspan="4" |<code>eps=12.90 epsinf=2.0665 SurfaceTensionAtInterface'''=XX''' HBondAcidity=0.263 HBondBasicity=0.374 CarbonAromaticity=0.1667 ElectronegativeHalogenicity=0.1667</code>
|}

=== [C4C1Im][XX] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|13.70
|
|
|-
|epsinf
|1.5392
|
|n=1.5392, has been squared to give epsinf=2.36917
|-
|SurfaceTensionAtInterface
|68.29
|
|
|-
|HBondAcidity (α)
|0.18
|
| Kamlet-Taft
|-
|HBondBasicity (β)
|0.52
|
| Kamlet-Taft
|-
|CarbonAromaticity
|0.308
|
|There are xx non-H atoms, xx are aromatic C atoms, value=xx/xx=0.308
|-
|ElectronegativeHalogenicity
|0.0
|
|There are no electronegative halogen atoms, value=0.0
|-
| colspan="4" |<code>eps=13.70 epsinf=2.36917 SurfaceTensionAtInterface=68.29 HBondAcidity=0.18 HBondBasicity=0.52 CarbonAromaticity=0.3080 ElectronegativeHalogenicity=0.0</code>
|}

=== Molten salt [Li+,Na+,K+][CO32-] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|MolarVolume
|57
|<ref name=":5" />
|molar volume Li2CO3 68 Na2CO3 92 K2CO3 124 Å3/molecule, average is 95 and 95*0.6022=57 at T=1.1Tm
|-
|Tabs
|900
|
|Absolute Temperature in K ie 298+600≈900
|-
|???
|
|
|ThermalExansionCoefficient estimate 20*10-6 K-1 at T=1.1Tm (this is not working!)
|-
|eps
|3
|<ref name=":5">G. Janz and M. Lorenz, <abbr>J. Electrochem. Soc.</abbr> 1961 volume 108, issue 11, 1052-1058 doi: 10.1149/1.2427946</ref>
|estimated value
|-
|epsinf
|2.25
|
|refractive index Na2CO3 1.489-1.535,<ref><nowiki>https://pubchem.ncbi.nlm.nih.gov/compound/sodium_carbonate#section=Spectral-Properties&fullscreen=true</nowiki></ref> Li2CO3 1.428-1.572<ref>Weast, R.C. (ed.). Handbook of Chemistry and Physics. 60th ed. Boca Raton, Florida: CRC Press Inc., 1979., p. B-91</ref> K2CO3 1.426-1.541<ref><nowiki>http://cameo.mfa.org/wiki/Potassium_carbonate</nowiki></ref> taking a "mid" value 1.52=2.25
|-
|SurfaceTensionAtInterface
|273
|<ref name=":5" />
|used surface tension of Na/K/CO3 mixture 50 mol % K2CO3 at 810 ºC , 190.0 dynes/cm
|-
|HBondAcidity (α)
|0.00
|<nowiki>-</nowiki>
| rowspan="2" |There are no H-atoms so H-bond acidity is zero
H-bond basicity computations result in proton transfer, NO3 ≈0.74-0.81, Cl ≈0.95-0.98, we assume it is even stronger due to -2 charge
|-
|HBondBasicity (β)
|0.99
|
|-
|CarbonAromaticity
|0.00
|<nowiki>-</nowiki>
|There are no aromatic C atoms
|-
|ElectronegativeHalogenicity
|0.00
|<nowiki>-</nowiki>
|There are no halogen atoms
|-
| colspan="4" |Stoichiometry=C2O62Li2Na2K2 MolarVolume=57.0 Tabs=900 eps=3.0 epsinf=2.25 SurfaceTensionAtInterface=273 HBondAcidity=0.0 HBondBasicity=0.99 CarbonAromaticity=0.0 ElectronegativeHalogenicity=0.0
|}

=== Example IL-GIL (generic IL) ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.50
|<ref name=":0" />
|see ESI Table S2.1
|-
|epsinf
|2.0449
|<ref name=":0" />
|n=1.43, has been squared to give epsinf=2.0449
|-
|SurfaceTensionAtInterface
|61.24
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|HBondAcidity (α)
|0.229
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|HBondBasicity (β)
|0.265
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|CarbonAromaticity
|
|<ref name=":0" />
|
|-
|ElectronegativeHalogenicity
|
|<ref name=":0" />
|
|-
| colspan="4" |<code>eps=11.50 epsinf=2.0449 SurfaceTensionAtInterface=61.24 HBondAcidity=0.229 HBondBasicity=0.265 CarbonAromaticity=0.xxx ElectronegativeHalogenicity=0.xxx</code>
|}

== Example table ==
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|
|
|
|-
|epsinf
|
|
|
|-
|SurfaceTensionAtInterface
|
|
|
|-
|HBondAcidity (α)
|
|
|
|-
|HBondBasicity (β)
|
|
|
|-
|CarbonAromaticity
|
|
|
|-
|ElectronegativeHalogenicity
|
|
|
|-
| colspan="4" |<code>eps= epsinf= SurfaceTensionAtInterface= HBondAcidity= HBondBasicity= CarbonAromaticity= ElectronegativeHalogenicity=</code>
|}

== References ==
<references />

Mod:Hunt Research Group: Using SMD on ILs

2019-12-23T09:54:13Z

Phunt: /* [C4C1Im][NTf2] */

This page explains how to use the SMD model to simulate an ionic liquid environment in Gaussian calculations. The SMD model is explained in detail in the original paper here.<ref>Marenich 2009 http://pubs.acs.org/doi/abs/10.1021/jp810292n</ref> Its use on ILs is similarly explained here.<ref name=":0">Bernales 2012 http://pubs.acs.org/doi/abs/10.1021/jp304365v</ref> Many useful solvent parameters are also available in this paper.

== How to simulate a defined solvent environment ==
Gaussian has many previously defined solvent environments. A list is available at the bottom of this page.<ref>http://www.gaussian.com/g_tech/g_ur/k_scrf.htm</ref> For example to use the pre-defined water environment simply insert the following keyword into the method line of your input file. The rest of your method line should specify your functional, basis set, optimisation/other type of calculation as usual.
scrf=(smd,solvent=water)
To use a different solvent to water change the solvent=water part to solvent=something else in the list.

== How to simulate a generic solvent environment ==
The SMD model has many parameters. These are already defined inside Gaussian for the list of defined solvents. If you want to use a solvent not on the list e.g. an ionic liquid, you must define these parameters manually. In this case put the following into the method line:
scrf=(smd,solvent=generic)

=== Types of SMD model ===
3 types of SMD for ILs have been defined.<ref name=":0" />

==== SMD ====
The standard SMD model. All parameters are determined for the particular IL (or a very similar one) being used as the solvent environment.

==== SMD-GIL ====
The generic ionic liquid model. The average values above are used for all parameters, except φ and ψ, which are simply calculated from the chemical formula of the IL.

==== SMD-PGP ====
The partial generic parameters model. Any parameter which has been measured for that IL is used. For any parameters which you do not have values for, use the average values.

=== Solvent parameters and SMD-GIL ===
The parameters are defined at the bottom of the input file, these parameters are listed in the table below:
{| class="wikitable"
!Parameter
!Symbol
!Name in Gaussian input file
!Average value for ILs<ref name=":0" />
|-
|Dielectric constant
|ε
|eps
|11.50
|-
|Index of refraction, squared
|n2
|epsinf
|2.0449
|-
|Macroscopic surface tension /cal mol-1 Å-2
|γ
|SurfaceTensionAtInterface
|61.24
|-
|Abraham hydrogen bond acidity parameter
|Σα2H
|HBondAcidity
|0.229
|-
|Abraham hydrogen bond basicity parameter
|Σβ2H
|HBondBasicity
|0.265
|-
|Fraction of non-hydrogen atoms which are aromatic carbon atoms
|φ
|CarbonAromaticity
|<nowiki>-</nowiki>
|-
|Fraction of non-hydrogen atoms which are electronegative halogen atoms
|ψ
|ElectronegativeHalogenicity
|<nowiki>-</nowiki>
|}

=== Note on parameters ===
Surface tension
*surface tension is the only parameter with units, those used in SMD are non-standard cal mol-1Å-2
*the SI units are Jm-2 or Nm-1
*typical units are dyn cm-1 where 1 dyn = 1 g cm s-2
*as we tend to work in kJ/mol the energy part of this becomes not J but J/mol
*1 dyn cm-1 = 0.001N m-1 = 0.001J m-2
*1 m = 1*1010Å and 1J=0.239cal and 1 mol-1=6.022*1023
*1 dyn cm-1 = 0.001*0.239cal*6.022*1023mol-1/(1*102*10Å2
*and if you think about this 1023 on top line cancels with 1020 on bottom line leaving 103 which cancels with the 0.001=10-3 leaving us with 0.239*6.022=1.439
*1 dyn cm-1 = 1.439 cal mol-1 Å-2
Molar Volume
* MolarVolume=x.x in cm3/mol
* molecular volume in Å3 per molecule converted to cm3/mol
* 1cm = 1*108Å, 1Å = 1*10-8 cm
* x Å3 per molecule = x*6.022*1023mol-1 *103*-8cm3 = x*6.022*10-1cm3mol-1

=== Example: [C4C1Im][NTf2] ===
All parameters for this IL have been measured, and can be found in reference 2.<ref name=":0" /> That means we can use the standard SMD method.

To get a value for φ take the number of aromatic carbon atoms (3) and divide by the number of non-hydrogen atoms (25). φ = 0.12.

To get a value for ψ take the number of electronegative halogen atoms (6) and divide by the number of non-hydrogen atoms (25). ψ = 0.24.

To define these parameters place the following line at the bottom of the input file (include one blank line before and at least one blank line after):
eps=11.52 epsinf=2.037 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.12 ElectronegativeHalogenicity=0.24

=== Kamlet-Taft vs Abraham H-bonding parameters ===
The SMD model requires Abraham H-bondonding parameters (Σα2H, Σβ2H), however Kamlet-Taft (α, β) measurements are more commonly reported for ILs. To alleviate this problem a relationship between the parameters was investigated, giving the following equations:<ref name=":0" />

Σα2H = 0.4098α + 0.0064

Σβ2H = 0.6138β + 0.0890

Previously the group has developed a simple method for calculating Kamlet-Taft parameters, and the instructions are here.<ref>http://www.huntresearchgroup.org.uk/research/research_il_alpha_beta_intro.html</ref>

== SMD input database ==
Here we will keep a database of SMD parameters used by the group. Please add any IL you use, so no-one else has to re-do the research for the parameters! Please follow the template provided so that it is clear where you get each value from.

===[C4C1Im][BF4]===
all values from <ref name=":0" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.70
|<ref name=":0" />
|
|-
|epsinf
|2.0207
|<ref name=":0" />
|Value given in reference is n=1.4215, it has been squared to give epsinf=2.0207
|-
|SurfaceTensionAtInterface
|67.07
|<ref name=":0" />
|
|-
|HBondAcidity (α)
|0.263
|<ref name=":0" />
| Kamlet-Taft 0.627
|-
|HBondBasicity (β)
|0.320
|<ref name=":0" />
| Kamlet-Taft 0.376
|-
|CarbonAromaticity (φ)
|0.2000
|
|There are 15 non-H atoms, 3 are aromatic C atoms, value=3/15=0.2000
|-
|ElectronegativeHalogenicity (ψ)
|0.2667
|
|There are 15 non-H atoms, 4 are electronegative halogen atoms, value =4/15=0.2667
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][PF6]===
all values from <ref name=":0" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.40
|<ref name=":0" />
|
|-
|epsinf
|1.9853
|<ref name=":0" />
|Value given in reference is n=1.4090, it has been squared to give epsinf=1.9853
|-
|SurfaceTensionAtInterface
|70.24
|<ref name=":0" />
|
|-
|HBondAcidity (α)
|0.266
|<ref name=":0" />
| Kamlet-Taft 0.634
|-
|HBondBasicity (β)
|0.216
|<ref name=":0" />
| Kamlet-Taft 0.207
|-
|CarbonAromaticity (φ)
|0.1765
|
|There are 17 non-H atoms, 3 are aromatic C atoms, value=3/17=0.1765
|-
|ElectronegativeHalogenicity (ψ)
|0.3529
|
|There are 17 non-H atoms, 4 are electronegative halogen atoms, value =6/17=0.3529
|-
| colspan="4" |<code>eps=11.40 epsinf=1.9853 SurfaceTensionAtInterface=70.24 HBondAcidity=0.266 HBondBasicity=0.216 CarbonAromaticity=0.1765 ElectronegativeHalogenicity=0.3529</code>
|}

=== [C4C1Im][NTf2] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.52
|<ref name=":0" /> <ref name=":6">Daguenet 2006 http://pubs.acs.org/doi/abs/10.1021/jp0604903</ref>
|
|-
|epsinf
|2.0366
|<ref name=":0" /> <ref name=":1">Huddleston 2001 http://pubs.rsc.org/en/Content/ArticleLanding/2001/GC/b103275p</ref>
|Value given in reference is n=1.4271, it has been squared to give epsinf=2.0366
|-
|SurfaceTensionAtInterface
|53.97
|<ref name=":0" /> <ref name=":1" />
|
|-
|HBondAcidity (α)
|0.259
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.617
|-
|HBondBasicity (β)
|0.238
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.243
|-
|CarbonAromaticity
|0.1200
|
|There are 25 non-H atoms, 3 are aromatic C atoms, value =3/25=0.1200
|-
|ElectronegativeHalogenicity
|0.2400
|
|There are 25 non-H atoms, 6 are electronegative halogen atoms, value =6/25=0.2400
|-
| colspan="4" |<code>eps=11.52 epsinf=2.0366 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.1200 ElectronegativeHalogenicity=0.2400</code>
|}

=== [C4C1Im][OTf] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|12.90
|<ref name=":3">Huang 2011 http://pubs.acs.org/doi/abs/10.1021/je101184s</ref>
|Page 1495, number 11 on the list.
|-
|epsinf
|2.0665
|<ref name=":4">Gonzalez 2012 http://pubs.acs.org/doi/abs/10.1021/je201334p</ref>
|n=1.43755, has been squared to give epsinf=2.0665. Can be found in Table 1, 3rd row.
|-
|SurfaceTensionAtInterface
|unknown
|
|-
|HBondAcidity (α)
|0.263
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.625
|-
|HBondBasicity (β)
|0.374
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.464
|-
|CarbonAromaticity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are aromatic C atoms, value=3/18=0.1667.
|-
|ElectronegativeHalogenicity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are electronegative halogen atoms, value=3/18=0.1667.
|-
| colspan="4" |<code>eps=12.90 epsinf=2.0665 SurfaceTensionAtInterface'''=XX''' HBondAcidity=0.263 HBondBasicity=0.374 CarbonAromaticity=0.1667 ElectronegativeHalogenicity=0.1667</code>
|}

=== [C4C1Im][XX] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|13.70
|
|
|-
|epsinf
|1.5392
|
|n=1.5392, has been squared to give epsinf=2.36917
|-
|SurfaceTensionAtInterface
|68.29
|
|
|-
|HBondAcidity (α)
|0.18
|
| Kamlet-Taft
|-
|HBondBasicity (β)
|0.52
|
| Kamlet-Taft
|-
|CarbonAromaticity
|0.308
|
|There are xx non-H atoms, xx are aromatic C atoms, value=xx/xx=0.308
|-
|ElectronegativeHalogenicity
|0.0
|
|There are xx non-H atoms, xx are electronegative halogen atoms, value=xx/xx=xx
|-
| colspan="4" |<code>eps=13.70 epsinf=2.36917 SurfaceTensionAtInterface=68.29 HBondAcidity=0.18 HBondBasicity=0.52 CarbonAromaticity=0.3080 ElectronegativeHalogenicity=0.0000</code>
|}

=== Molten salt [Li+,Na+,K+][CO32-] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|MolarVolume
|57
|<ref name=":5" />
|molar volume Li2CO3 68 Na2CO3 92 K2CO3 124 Å3/molecule, average is 95 and 95*0.6022=57 at T=1.1Tm
|-
|Tabs
|900
|
|Absolute Temperature in K ie 298+600≈900
|-
|???
|
|
|ThermalExansionCoefficient estimate 20*10-6 K-1 at T=1.1Tm (this is not working!)
|-
|eps
|3
|<ref name=":5">G. Janz and M. Lorenz, <abbr>J. Electrochem. Soc.</abbr> 1961 volume 108, issue 11, 1052-1058 doi: 10.1149/1.2427946</ref>
|estimated value
|-
|epsinf
|2.25
|
|refractive index Na2CO3 1.489-1.535,<ref><nowiki>https://pubchem.ncbi.nlm.nih.gov/compound/sodium_carbonate#section=Spectral-Properties&fullscreen=true</nowiki></ref> Li2CO3 1.428-1.572<ref>Weast, R.C. (ed.). Handbook of Chemistry and Physics. 60th ed. Boca Raton, Florida: CRC Press Inc., 1979., p. B-91</ref> K2CO3 1.426-1.541<ref><nowiki>http://cameo.mfa.org/wiki/Potassium_carbonate</nowiki></ref> taking a "mid" value 1.52=2.25
|-
|SurfaceTensionAtInterface
|273
|<ref name=":5" />
|used surface tension of Na/K/CO3 mixture 50 mol % K2CO3 at 810 ºC , 190.0 dynes/cm
|-
|HBondAcidity (α)
|0.00
|<nowiki>-</nowiki>
| rowspan="2" |There are no H-atoms so H-bond acidity is zero
H-bond basicity computations result in proton transfer, NO3 ≈0.74-0.81, Cl ≈0.95-0.98, we assume it is even stronger due to -2 charge
|-
|HBondBasicity (β)
|0.99
|
|-
|CarbonAromaticity
|0.00
|<nowiki>-</nowiki>
|There are no aromatic C atoms
|-
|ElectronegativeHalogenicity
|0.00
|<nowiki>-</nowiki>
|There are no halogen atoms
|-
| colspan="4" |Stoichiometry=C2O62Li2Na2K2 MolarVolume=57.0 Tabs=900 eps=3.0 epsinf=2.25 SurfaceTensionAtInterface=273 HBondAcidity=0.0 HBondBasicity=0.99 CarbonAromaticity=0.0 ElectronegativeHalogenicity=0.0
|}

=== Example IL-GIL (generic IL) ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.50
|<ref name=":0" />
|see ESI Table S2.1
|-
|epsinf
|2.0449
|<ref name=":0" />
|n=1.43, has been squared to give epsinf=2.0449
|-
|SurfaceTensionAtInterface
|61.24
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|HBondAcidity (α)
|0.229
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|HBondBasicity (β)
|0.265
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|CarbonAromaticity
|
|<ref name=":0" />
|
|-
|ElectronegativeHalogenicity
|
|<ref name=":0" />
|
|-
| colspan="4" |<code>eps=11.50 epsinf=2.0449 SurfaceTensionAtInterface=61.24 HBondAcidity=0.229 HBondBasicity=0.265 CarbonAromaticity=0.xxx ElectronegativeHalogenicity=0.xxx</code>
|}

== Example table ==
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|
|
|
|-
|epsinf
|
|
|
|-
|SurfaceTensionAtInterface
|
|
|
|-
|HBondAcidity (α)
|
|
|
|-
|HBondBasicity (β)
|
|
|
|-
|CarbonAromaticity
|
|
|
|-
|ElectronegativeHalogenicity
|
|
|
|-
| colspan="4" |<code>eps= epsinf= SurfaceTensionAtInterface= HBondAcidity= HBondBasicity= CarbonAromaticity= ElectronegativeHalogenicity=</code>
|}

== References ==
<references />

Mod:Hunt Research Group: Using SMD on ILs

2019-12-23T09:15:09Z

Phunt: /* [C4C1Im][XX] */

This page explains how to use the SMD model to simulate an ionic liquid environment in Gaussian calculations. The SMD model is explained in detail in the original paper here.<ref>Marenich 2009 http://pubs.acs.org/doi/abs/10.1021/jp810292n</ref> Its use on ILs is similarly explained here.<ref name=":0">Bernales 2012 http://pubs.acs.org/doi/abs/10.1021/jp304365v</ref> Many useful solvent parameters are also available in this paper.

== How to simulate a defined solvent environment ==
Gaussian has many previously defined solvent environments. A list is available at the bottom of this page.<ref>http://www.gaussian.com/g_tech/g_ur/k_scrf.htm</ref> For example to use the pre-defined water environment simply insert the following keyword into the method line of your input file. The rest of your method line should specify your functional, basis set, optimisation/other type of calculation as usual.
scrf=(smd,solvent=water)
To use a different solvent to water change the solvent=water part to solvent=something else in the list.

== How to simulate a generic solvent environment ==
The SMD model has many parameters. These are already defined inside Gaussian for the list of defined solvents. If you want to use a solvent not on the list e.g. an ionic liquid, you must define these parameters manually. In this case put the following into the method line:
scrf=(smd,solvent=generic)

=== Types of SMD model ===
3 types of SMD for ILs have been defined.<ref name=":0" />

==== SMD ====
The standard SMD model. All parameters are determined for the particular IL (or a very similar one) being used as the solvent environment.

==== SMD-GIL ====
The generic ionic liquid model. The average values above are used for all parameters, except φ and ψ, which are simply calculated from the chemical formula of the IL.

==== SMD-PGP ====
The partial generic parameters model. Any parameter which has been measured for that IL is used. For any parameters which you do not have values for, use the average values.

=== Solvent parameters and SMD-GIL ===
The parameters are defined at the bottom of the input file, these parameters are listed in the table below:
{| class="wikitable"
!Parameter
!Symbol
!Name in Gaussian input file
!Average value for ILs<ref name=":0" />
|-
|Dielectric constant
|ε
|eps
|11.50
|-
|Index of refraction, squared
|n2
|epsinf
|2.0449
|-
|Macroscopic surface tension /cal mol-1 Å-2
|γ
|SurfaceTensionAtInterface
|61.24
|-
|Abraham hydrogen bond acidity parameter
|Σα2H
|HBondAcidity
|0.229
|-
|Abraham hydrogen bond basicity parameter
|Σβ2H
|HBondBasicity
|0.265
|-
|Fraction of non-hydrogen atoms which are aromatic carbon atoms
|φ
|CarbonAromaticity
|<nowiki>-</nowiki>
|-
|Fraction of non-hydrogen atoms which are electronegative halogen atoms
|ψ
|ElectronegativeHalogenicity
|<nowiki>-</nowiki>
|}

=== Note on parameters ===
Surface tension
*surface tension is the only parameter with units, those used in SMD are non-standard cal mol-1Å-2
*the SI units are Jm-2 or Nm-1
*typical units are dyn cm-1 where 1 dyn = 1 g cm s-2
*as we tend to work in kJ/mol the energy part of this becomes not J but J/mol
*1 dyn cm-1 = 0.001N m-1 = 0.001J m-2
*1 m = 1*1010Å and 1J=0.239cal and 1 mol-1=6.022*1023
*1 dyn cm-1 = 0.001*0.239cal*6.022*1023mol-1/(1*102*10Å2
*and if you think about this 1023 on top line cancels with 1020 on bottom line leaving 103 which cancels with the 0.001=10-3 leaving us with 0.239*6.022=1.439
*1 dyn cm-1 = 1.439 cal mol-1 Å-2
Molar Volume
* MolarVolume=x.x in cm3/mol
* molecular volume in Å3 per molecule converted to cm3/mol
* 1cm = 1*108Å, 1Å = 1*10-8 cm
* x Å3 per molecule = x*6.022*1023mol-1 *103*-8cm3 = x*6.022*10-1cm3mol-1

=== Example: [C4C1Im][NTf2] ===
All parameters for this IL have been measured, and can be found in reference 2.<ref name=":0" /> That means we can use the standard SMD method.

To get a value for φ take the number of aromatic carbon atoms (3) and divide by the number of non-hydrogen atoms (25). φ = 0.12.

To get a value for ψ take the number of electronegative halogen atoms (6) and divide by the number of non-hydrogen atoms (25). ψ = 0.24.

To define these parameters place the following line at the bottom of the input file (include one blank line before and at least one blank line after):
eps=11.52 epsinf=2.037 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.12 ElectronegativeHalogenicity=0.24

=== Kamlet-Taft vs Abraham H-bonding parameters ===
The SMD model requires Abraham H-bondonding parameters (Σα2H, Σβ2H), however Kamlet-Taft (α, β) measurements are more commonly reported for ILs. To alleviate this problem a relationship between the parameters was investigated, giving the following equations:<ref name=":0" />

Σα2H = 0.4098α + 0.0064

Σβ2H = 0.6138β + 0.0890

Previously the group has developed a simple method for calculating Kamlet-Taft parameters, and the instructions are here.<ref>http://www.huntresearchgroup.org.uk/research/research_il_alpha_beta_intro.html</ref>

== SMD input database ==
Here we will keep a database of SMD parameters used by the group. Please add any IL you use, so no-one else has to re-do the research for the parameters! Please follow the template provided so that it is clear where you get each value from.

===[C4C1Im][BF4]===
all values from <ref name=":0" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.70
|<ref name=":0" />
|
|-
|epsinf
|2.0207
|<ref name=":0" />
|Value given in reference is n=1.4215, it has been squared to give epsinf=2.0207
|-
|SurfaceTensionAtInterface
|67.07
|<ref name=":0" />
|
|-
|HBondAcidity (α)
|0.263
|<ref name=":0" />
| Kamlet-Taft 0.627
|-
|HBondBasicity (β)
|0.320
|<ref name=":0" />
| Kamlet-Taft 0.376
|-
|CarbonAromaticity (φ)
|0.2000
|
|There are 15 non-H atoms, 3 are aromatic C atoms, value=3/15=0.2000
|-
|ElectronegativeHalogenicity (ψ)
|0.2667
|
|There are 15 non-H atoms, 4 are electronegative halogen atoms, value =4/15=0.2667
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][PF6]===
all values from <ref name=":0" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.40
|<ref name=":0" />
|
|-
|epsinf
|1.9853
|<ref name=":0" />
|Value given in reference is n=1.4090, it has been squared to give epsinf=1.9853
|-
|SurfaceTensionAtInterface
|70.24
|<ref name=":0" />
|
|-
|HBondAcidity (α)
|0.266
|<ref name=":0" />
| Kamlet-Taft 0.634
|-
|HBondBasicity (β)
|0.216
|<ref name=":0" />
| Kamlet-Taft 0.207
|-
|CarbonAromaticity (φ)
|0.1765
|
|There are 17 non-H atoms, 3 are aromatic C atoms, value=3/17=0.1765
|-
|ElectronegativeHalogenicity (ψ)
|0.3529
|
|There are 17 non-H atoms, 4 are electronegative halogen atoms, value =6/17=0.3529
|-
| colspan="4" |<code>eps=11.40 epsinf=1.9853 SurfaceTensionAtInterface=70.24 HBondAcidity=0.266 HBondBasicity=0.216 CarbonAromaticity=0.1765 ElectronegativeHalogenicity=0.3529</code>
|}

=== [C4C1Im][NTf2] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.52
|<ref name=":0" /> <ref name=":6">Daguenet 2006 http://pubs.acs.org/doi/abs/10.1021/jp0604903</ref>
|
|-
|epsinf
|2.0366|<ref name=":0" /> <ref name=":1">Huddleston 2001 http://pubs.rsc.org/en/Content/ArticleLanding/2001/GC/b103275p</ref>
|Value given in reference is n=1.4271, it has been squared to give epsinf=2.0366
|-
|SurfaceTensionAtInterface
|53.97
|<ref name=":0" /> <ref name=":1" />
|
|-
|HBondAcidity (α)
|0.259
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.617
|-
|HBondBasicity (β)
|0.238
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.243
|-
|CarbonAromaticity
|0.1200
|
|There are 25 non-H atoms, 3 are aromatic C atoms, value =3/25=0.1200
|-
|ElectronegativeHalogenicity
|0.2400
|
|There are 25 non-H atoms, 6 are electronegative halogen atoms, value =6/25=0.2400
|-
| colspan="4" |<code>eps=11.52 epsinf=2.0366 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.1200 ElectronegativeHalogenicity=0.2400</code>
|}

=== [C4C1Im][OTf] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|12.90
|<ref name=":3">Huang 2011 http://pubs.acs.org/doi/abs/10.1021/je101184s</ref>
|Page 1495, number 11 on the list.
|-
|epsinf
|2.0665
|<ref name=":4">Gonzalez 2012 http://pubs.acs.org/doi/abs/10.1021/je201334p</ref>
|n=1.43755, has been squared to give epsinf=2.0665. Can be found in Table 1, 3rd row.
|-
|SurfaceTensionAtInterface
|unknown
|
|-
|HBondAcidity (α)
|0.263
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.625
|-
|HBondBasicity (β)
|0.374
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.464
|-
|CarbonAromaticity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are aromatic C atoms, value=3/18=0.1667.
|-
|ElectronegativeHalogenicity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are electronegative halogen atoms, value=3/18=0.1667.
|-
| colspan="4" |<code>eps=12.90 epsinf=2.0665 SurfaceTensionAtInterface'''=XX''' HBondAcidity=0.263 HBondBasicity=0.374 CarbonAromaticity=0.1667 ElectronegativeHalogenicity=0.1667</code>
|}

=== [C4C1Im][XX] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|13.70
|
|
|-
|epsinf
|1.5392
|
|n=1.5392, has been squared to give epsinf=2.36917
|-
|SurfaceTensionAtInterface
|68.29
|
|
|-
|HBondAcidity (α)
|0.18
|
| Kamlet-Taft
|-
|HBondBasicity (β)
|0.52
|
| Kamlet-Taft
|-
|CarbonAromaticity
|0.308
|
|There are xx non-H atoms, xx are aromatic C atoms, value=xx/xx=0.308
|-
|ElectronegativeHalogenicity
|0.0
|
|There are xx non-H atoms, xx are electronegative halogen atoms, value=xx/xx=xx
|-
| colspan="4" |<code>eps=13.70 epsinf=2.36917 SurfaceTensionAtInterface=68.29 HBondAcidity=0.18 HBondBasicity=0.52 CarbonAromaticity=0.3080 ElectronegativeHalogenicity=0.0000</code>
|}

=== Molten salt [Li+,Na+,K+][CO32-] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|MolarVolume
|57
|<ref name=":5" />
|molar volume Li2CO3 68 Na2CO3 92 K2CO3 124 Å3/molecule, average is 95 and 95*0.6022=57 at T=1.1Tm
|-
|Tabs
|900
|
|Absolute Temperature in K ie 298+600≈900
|-
|???
|
|
|ThermalExansionCoefficient estimate 20*10-6 K-1 at T=1.1Tm (this is not working!)
|-
|eps
|3
|<ref name=":5">G. Janz and M. Lorenz, <abbr>J. Electrochem. Soc.</abbr> 1961 volume 108, issue 11, 1052-1058 doi: 10.1149/1.2427946</ref>
|estimated value
|-
|epsinf
|2.25
|
|refractive index Na2CO3 1.489-1.535,<ref><nowiki>https://pubchem.ncbi.nlm.nih.gov/compound/sodium_carbonate#section=Spectral-Properties&fullscreen=true</nowiki></ref> Li2CO3 1.428-1.572<ref>Weast, R.C. (ed.). Handbook of Chemistry and Physics. 60th ed. Boca Raton, Florida: CRC Press Inc., 1979., p. B-91</ref> K2CO3 1.426-1.541<ref><nowiki>http://cameo.mfa.org/wiki/Potassium_carbonate</nowiki></ref> taking a "mid" value 1.52=2.25
|-
|SurfaceTensionAtInterface
|273
|<ref name=":5" />
|used surface tension of Na/K/CO3 mixture 50 mol % K2CO3 at 810 ºC , 190.0 dynes/cm
|-
|HBondAcidity (α)
|0.00
|<nowiki>-</nowiki>
| rowspan="2" |There are no H-atoms so H-bond acidity is zero
H-bond basicity computations result in proton transfer, NO3 ≈0.74-0.81, Cl ≈0.95-0.98, we assume it is even stronger due to -2 charge
|-
|HBondBasicity (β)
|0.99
|
|-
|CarbonAromaticity
|0.00
|<nowiki>-</nowiki>
|There are no aromatic C atoms
|-
|ElectronegativeHalogenicity
|0.00
|<nowiki>-</nowiki>
|There are no halogen atoms
|-
| colspan="4" |Stoichiometry=C2O62Li2Na2K2 MolarVolume=57.0 Tabs=900 eps=3.0 epsinf=2.25 SurfaceTensionAtInterface=273 HBondAcidity=0.0 HBondBasicity=0.99 CarbonAromaticity=0.0 ElectronegativeHalogenicity=0.0
|}

=== Example IL-GIL (generic IL) ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.50
|<ref name=":0" />
|see ESI Table S2.1
|-
|epsinf
|2.0449
|<ref name=":0" />
|n=1.43, has been squared to give epsinf=2.0449
|-
|SurfaceTensionAtInterface
|61.24
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|HBondAcidity (α)
|0.229
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|HBondBasicity (β)
|0.265
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|CarbonAromaticity
|
|<ref name=":0" />
|
|-
|ElectronegativeHalogenicity
|
|<ref name=":0" />
|
|-
| colspan="4" |<code>eps=11.50 epsinf=2.0449 SurfaceTensionAtInterface=61.24 HBondAcidity=0.229 HBondBasicity=0.265 CarbonAromaticity=0.xxx ElectronegativeHalogenicity=0.xxx</code>
|}

== Example table ==
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|
|
|
|-
|epsinf
|
|
|
|-
|SurfaceTensionAtInterface
|
|
|
|-
|HBondAcidity (α)
|
|
|
|-
|HBondBasicity (β)
|
|
|
|-
|CarbonAromaticity
|
|
|
|-
|ElectronegativeHalogenicity
|
|
|
|-
| colspan="4" |<code>eps= epsinf= SurfaceTensionAtInterface= HBondAcidity= HBondBasicity= CarbonAromaticity= ElectronegativeHalogenicity=</code>
|}

== References ==
<references />

Mod:Hunt Research Group: Using SMD on ILs

2019-12-23T09:11:21Z

Phunt: /* [C4C1Im][OTf] */

This page explains how to use the SMD model to simulate an ionic liquid environment in Gaussian calculations. The SMD model is explained in detail in the original paper here.<ref>Marenich 2009 http://pubs.acs.org/doi/abs/10.1021/jp810292n</ref> Its use on ILs is similarly explained here.<ref name=":0">Bernales 2012 http://pubs.acs.org/doi/abs/10.1021/jp304365v</ref> Many useful solvent parameters are also available in this paper.

== How to simulate a defined solvent environment ==
Gaussian has many previously defined solvent environments. A list is available at the bottom of this page.<ref>http://www.gaussian.com/g_tech/g_ur/k_scrf.htm</ref> For example to use the pre-defined water environment simply insert the following keyword into the method line of your input file. The rest of your method line should specify your functional, basis set, optimisation/other type of calculation as usual.
scrf=(smd,solvent=water)
To use a different solvent to water change the solvent=water part to solvent=something else in the list.

== How to simulate a generic solvent environment ==
The SMD model has many parameters. These are already defined inside Gaussian for the list of defined solvents. If you want to use a solvent not on the list e.g. an ionic liquid, you must define these parameters manually. In this case put the following into the method line:
scrf=(smd,solvent=generic)

=== Types of SMD model ===
3 types of SMD for ILs have been defined.<ref name=":0" />

==== SMD ====
The standard SMD model. All parameters are determined for the particular IL (or a very similar one) being used as the solvent environment.

==== SMD-GIL ====
The generic ionic liquid model. The average values above are used for all parameters, except φ and ψ, which are simply calculated from the chemical formula of the IL.

==== SMD-PGP ====
The partial generic parameters model. Any parameter which has been measured for that IL is used. For any parameters which you do not have values for, use the average values.

=== Solvent parameters and SMD-GIL ===
The parameters are defined at the bottom of the input file, these parameters are listed in the table below:
{| class="wikitable"
!Parameter
!Symbol
!Name in Gaussian input file
!Average value for ILs<ref name=":0" />
|-
|Dielectric constant
|ε
|eps
|11.50
|-
|Index of refraction, squared
|n2
|epsinf
|2.0449
|-
|Macroscopic surface tension /cal mol-1 Å-2
|γ
|SurfaceTensionAtInterface
|61.24
|-
|Abraham hydrogen bond acidity parameter
|Σα2H
|HBondAcidity
|0.229
|-
|Abraham hydrogen bond basicity parameter
|Σβ2H
|HBondBasicity
|0.265
|-
|Fraction of non-hydrogen atoms which are aromatic carbon atoms
|φ
|CarbonAromaticity
|<nowiki>-</nowiki>
|-
|Fraction of non-hydrogen atoms which are electronegative halogen atoms
|ψ
|ElectronegativeHalogenicity
|<nowiki>-</nowiki>
|}

=== Note on parameters ===
Surface tension
*surface tension is the only parameter with units, those used in SMD are non-standard cal mol-1Å-2
*the SI units are Jm-2 or Nm-1
*typical units are dyn cm-1 where 1 dyn = 1 g cm s-2
*as we tend to work in kJ/mol the energy part of this becomes not J but J/mol
*1 dyn cm-1 = 0.001N m-1 = 0.001J m-2
*1 m = 1*1010Å and 1J=0.239cal and 1 mol-1=6.022*1023
*1 dyn cm-1 = 0.001*0.239cal*6.022*1023mol-1/(1*102*10Å2
*and if you think about this 1023 on top line cancels with 1020 on bottom line leaving 103 which cancels with the 0.001=10-3 leaving us with 0.239*6.022=1.439
*1 dyn cm-1 = 1.439 cal mol-1 Å-2
Molar Volume
* MolarVolume=x.x in cm3/mol
* molecular volume in Å3 per molecule converted to cm3/mol
* 1cm = 1*108Å, 1Å = 1*10-8 cm
* x Å3 per molecule = x*6.022*1023mol-1 *103*-8cm3 = x*6.022*10-1cm3mol-1

=== Example: [C4C1Im][NTf2] ===
All parameters for this IL have been measured, and can be found in reference 2.<ref name=":0" /> That means we can use the standard SMD method.

To get a value for φ take the number of aromatic carbon atoms (3) and divide by the number of non-hydrogen atoms (25). φ = 0.12.

To get a value for ψ take the number of electronegative halogen atoms (6) and divide by the number of non-hydrogen atoms (25). ψ = 0.24.

To define these parameters place the following line at the bottom of the input file (include one blank line before and at least one blank line after):
eps=11.52 epsinf=2.037 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.12 ElectronegativeHalogenicity=0.24

=== Kamlet-Taft vs Abraham H-bonding parameters ===
The SMD model requires Abraham H-bondonding parameters (Σα2H, Σβ2H), however Kamlet-Taft (α, β) measurements are more commonly reported for ILs. To alleviate this problem a relationship between the parameters was investigated, giving the following equations:<ref name=":0" />

Σα2H = 0.4098α + 0.0064

Σβ2H = 0.6138β + 0.0890

Previously the group has developed a simple method for calculating Kamlet-Taft parameters, and the instructions are here.<ref>http://www.huntresearchgroup.org.uk/research/research_il_alpha_beta_intro.html</ref>

== SMD input database ==
Here we will keep a database of SMD parameters used by the group. Please add any IL you use, so no-one else has to re-do the research for the parameters! Please follow the template provided so that it is clear where you get each value from.

===[C4C1Im][BF4]===
all values from <ref name=":0" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.70
|<ref name=":0" />
|
|-
|epsinf
|2.0207
|<ref name=":0" />
|Value given in reference is n=1.4215, it has been squared to give epsinf=2.0207
|-
|SurfaceTensionAtInterface
|67.07
|<ref name=":0" />
|
|-
|HBondAcidity (α)
|0.263
|<ref name=":0" />
| Kamlet-Taft 0.627
|-
|HBondBasicity (β)
|0.320
|<ref name=":0" />
| Kamlet-Taft 0.376
|-
|CarbonAromaticity (φ)
|0.2000
|
|There are 15 non-H atoms, 3 are aromatic C atoms, value=3/15=0.2000
|-
|ElectronegativeHalogenicity (ψ)
|0.2667
|
|There are 15 non-H atoms, 4 are electronegative halogen atoms, value =4/15=0.2667
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][PF6]===
all values from <ref name=":0" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.40
|<ref name=":0" />
|
|-
|epsinf
|1.9853
|<ref name=":0" />
|Value given in reference is n=1.4090, it has been squared to give epsinf=1.9853
|-
|SurfaceTensionAtInterface
|70.24
|<ref name=":0" />
|
|-
|HBondAcidity (α)
|0.266
|<ref name=":0" />
| Kamlet-Taft 0.634
|-
|HBondBasicity (β)
|0.216
|<ref name=":0" />
| Kamlet-Taft 0.207
|-
|CarbonAromaticity (φ)
|0.1765
|
|There are 17 non-H atoms, 3 are aromatic C atoms, value=3/17=0.1765
|-
|ElectronegativeHalogenicity (ψ)
|0.3529
|
|There are 17 non-H atoms, 4 are electronegative halogen atoms, value =6/17=0.3529
|-
| colspan="4" |<code>eps=11.40 epsinf=1.9853 SurfaceTensionAtInterface=70.24 HBondAcidity=0.266 HBondBasicity=0.216 CarbonAromaticity=0.1765 ElectronegativeHalogenicity=0.3529</code>
|}

=== [C4C1Im][NTf2] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.52
|<ref name=":0" /> <ref name=":6">Daguenet 2006 http://pubs.acs.org/doi/abs/10.1021/jp0604903</ref>
|
|-
|epsinf
|2.0366|<ref name=":0" /> <ref name=":1">Huddleston 2001 http://pubs.rsc.org/en/Content/ArticleLanding/2001/GC/b103275p</ref>
|Value given in reference is n=1.4271, it has been squared to give epsinf=2.0366
|-
|SurfaceTensionAtInterface
|53.97
|<ref name=":0" /> <ref name=":1" />
|
|-
|HBondAcidity (α)
|0.259
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.617
|-
|HBondBasicity (β)
|0.238
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.243
|-
|CarbonAromaticity
|0.1200
|
|There are 25 non-H atoms, 3 are aromatic C atoms, value =3/25=0.1200
|-
|ElectronegativeHalogenicity
|0.2400
|
|There are 25 non-H atoms, 6 are electronegative halogen atoms, value =6/25=0.2400
|-
| colspan="4" |<code>eps=11.52 epsinf=2.0366 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.1200 ElectronegativeHalogenicity=0.2400</code>
|}

=== [C4C1Im][OTf] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|12.90
|<ref name=":3">Huang 2011 http://pubs.acs.org/doi/abs/10.1021/je101184s</ref>
|Page 1495, number 11 on the list.
|-
|epsinf
|2.0665
|<ref name=":4">Gonzalez 2012 http://pubs.acs.org/doi/abs/10.1021/je201334p</ref>
|n=1.43755, has been squared to give epsinf=2.0665. Can be found in Table 1, 3rd row.
|-
|SurfaceTensionAtInterface
|unknown
|
|-
|HBondAcidity (α)
|0.263
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.625
|-
|HBondBasicity (β)
|0.374
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.464
|-
|CarbonAromaticity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are aromatic C atoms, value=3/18=0.1667.
|-
|ElectronegativeHalogenicity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are electronegative halogen atoms, value=3/18=0.1667.
|-
| colspan="4" |<code>eps=12.90 epsinf=2.0665 SurfaceTensionAtInterface'''=XX''' HBondAcidity=0.263 HBondBasicity=0.374 CarbonAromaticity=0.1667 ElectronegativeHalogenicity=0.1667</code>
|}

=== [C4C1Im][XX] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|13.7
|<ref name=":3">Huang 2011 http://pubs.acs.org/doi/abs/10.1021/je101184s</ref>
|Page 1495, number 11 on the list.
|-
|epsinf
|1.5392
|<ref name=":4">Gonzalez 2012 http://pubs.acs.org/doi/abs/10.1021/je201334p</ref>
|n=1.5392, has been squared to give epsinf=2.36917
|-
|SurfaceTensionAtInterface
|68.29
|
|XX
|-
|HBondAcidity (α)
|0.18
|<ref name=":0" /> <ref name=":2" />
| rowspan="2" |Kamlet and Taft measurements were reported in ref.<ref name=":2" /> Conversion to Abraham values was done using the equations above.<ref name=":0" />
|-
|HBondBasicity (β)
|0.52
|<ref name=":0" /> <ref name=":2" />
|-
|CarbonAromaticity
|0.308
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are aromatic C atoms.
|-
|ElectronegativeHalogenicity
|0.0
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are electronegative halogen atoms.
|-
| colspan="4" |eps=13.7 epsinf=2.36917 SurfaceTensionAtInterface=68.29 HBondAcidity=0.18 HBondBasicity=0.52 CarbonAromaticity=0.308 ElectronegativeHalogenicity=0.0
|}

=== Molten salt [Li+,Na+,K+][CO32-] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|MolarVolume
|57
|<ref name=":5" />
|molar volume Li2CO3 68 Na2CO3 92 K2CO3 124 Å3/molecule, average is 95 and 95*0.6022=57 at T=1.1Tm
|-
|Tabs
|900
|
|Absolute Temperature in K ie 298+600≈900
|-
|???
|
|
|ThermalExansionCoefficient estimate 20*10-6 K-1 at T=1.1Tm (this is not working!)
|-
|eps
|3
|<ref name=":5">G. Janz and M. Lorenz, <abbr>J. Electrochem. Soc.</abbr> 1961 volume 108, issue 11, 1052-1058 doi: 10.1149/1.2427946</ref>
|estimated value
|-
|epsinf
|2.25
|
|refractive index Na2CO3 1.489-1.535,<ref><nowiki>https://pubchem.ncbi.nlm.nih.gov/compound/sodium_carbonate#section=Spectral-Properties&fullscreen=true</nowiki></ref> Li2CO3 1.428-1.572<ref>Weast, R.C. (ed.). Handbook of Chemistry and Physics. 60th ed. Boca Raton, Florida: CRC Press Inc., 1979., p. B-91</ref> K2CO3 1.426-1.541<ref><nowiki>http://cameo.mfa.org/wiki/Potassium_carbonate</nowiki></ref> taking a "mid" value 1.52=2.25
|-
|SurfaceTensionAtInterface
|273
|<ref name=":5" />
|used surface tension of Na/K/CO3 mixture 50 mol % K2CO3 at 810 ºC , 190.0 dynes/cm
|-
|HBondAcidity (α)
|0.00
|<nowiki>-</nowiki>
| rowspan="2" |There are no H-atoms so H-bond acidity is zero
H-bond basicity computations result in proton transfer, NO3 ≈0.74-0.81, Cl ≈0.95-0.98, we assume it is even stronger due to -2 charge
|-
|HBondBasicity (β)
|0.99
|
|-
|CarbonAromaticity
|0.00
|<nowiki>-</nowiki>
|There are no aromatic C atoms
|-
|ElectronegativeHalogenicity
|0.00
|<nowiki>-</nowiki>
|There are no halogen atoms
|-
| colspan="4" |Stoichiometry=C2O62Li2Na2K2 MolarVolume=57.0 Tabs=900 eps=3.0 epsinf=2.25 SurfaceTensionAtInterface=273 HBondAcidity=0.0 HBondBasicity=0.99 CarbonAromaticity=0.0 ElectronegativeHalogenicity=0.0
|}

=== Example IL-GIL (generic IL) ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.50
|<ref name=":0" />
|see ESI Table S2.1
|-
|epsinf
|2.0449
|<ref name=":0" />
|n=1.43, has been squared to give epsinf=2.0449
|-
|SurfaceTensionAtInterface
|61.24
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|HBondAcidity (α)
|0.229
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|HBondBasicity (β)
|0.265
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|CarbonAromaticity
|
|<ref name=":0" />
|
|-
|ElectronegativeHalogenicity
|
|<ref name=":0" />
|
|-
| colspan="4" |<code>eps=11.50 epsinf=2.0449 SurfaceTensionAtInterface=61.24 HBondAcidity=0.229 HBondBasicity=0.265 CarbonAromaticity=0.xxx ElectronegativeHalogenicity=0.xxx</code>
|}

== Example table ==
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|
|
|
|-
|epsinf
|
|
|
|-
|SurfaceTensionAtInterface
|
|
|
|-
|HBondAcidity (α)
|
|
|
|-
|HBondBasicity (β)
|
|
|
|-
|CarbonAromaticity
|
|
|
|-
|ElectronegativeHalogenicity
|
|
|
|-
| colspan="4" |<code>eps= epsinf= SurfaceTensionAtInterface= HBondAcidity= HBondBasicity= CarbonAromaticity= ElectronegativeHalogenicity=</code>
|}

== References ==
<references />

Mod:Hunt Research Group: Using SMD on ILs

2019-12-23T09:10:35Z

Phunt: /* [C4C1Im][OTf] */

This page explains how to use the SMD model to simulate an ionic liquid environment in Gaussian calculations. The SMD model is explained in detail in the original paper here.<ref>Marenich 2009 http://pubs.acs.org/doi/abs/10.1021/jp810292n</ref> Its use on ILs is similarly explained here.<ref name=":0">Bernales 2012 http://pubs.acs.org/doi/abs/10.1021/jp304365v</ref> Many useful solvent parameters are also available in this paper.

== How to simulate a defined solvent environment ==
Gaussian has many previously defined solvent environments. A list is available at the bottom of this page.<ref>http://www.gaussian.com/g_tech/g_ur/k_scrf.htm</ref> For example to use the pre-defined water environment simply insert the following keyword into the method line of your input file. The rest of your method line should specify your functional, basis set, optimisation/other type of calculation as usual.
scrf=(smd,solvent=water)
To use a different solvent to water change the solvent=water part to solvent=something else in the list.

== How to simulate a generic solvent environment ==
The SMD model has many parameters. These are already defined inside Gaussian for the list of defined solvents. If you want to use a solvent not on the list e.g. an ionic liquid, you must define these parameters manually. In this case put the following into the method line:
scrf=(smd,solvent=generic)

=== Types of SMD model ===
3 types of SMD for ILs have been defined.<ref name=":0" />

==== SMD ====
The standard SMD model. All parameters are determined for the particular IL (or a very similar one) being used as the solvent environment.

==== SMD-GIL ====
The generic ionic liquid model. The average values above are used for all parameters, except φ and ψ, which are simply calculated from the chemical formula of the IL.

==== SMD-PGP ====
The partial generic parameters model. Any parameter which has been measured for that IL is used. For any parameters which you do not have values for, use the average values.

=== Solvent parameters and SMD-GIL ===
The parameters are defined at the bottom of the input file, these parameters are listed in the table below:
{| class="wikitable"
!Parameter
!Symbol
!Name in Gaussian input file
!Average value for ILs<ref name=":0" />
|-
|Dielectric constant
|ε
|eps
|11.50
|-
|Index of refraction, squared
|n2
|epsinf
|2.0449
|-
|Macroscopic surface tension /cal mol-1 Å-2
|γ
|SurfaceTensionAtInterface
|61.24
|-
|Abraham hydrogen bond acidity parameter
|Σα2H
|HBondAcidity
|0.229
|-
|Abraham hydrogen bond basicity parameter
|Σβ2H
|HBondBasicity
|0.265
|-
|Fraction of non-hydrogen atoms which are aromatic carbon atoms
|φ
|CarbonAromaticity
|<nowiki>-</nowiki>
|-
|Fraction of non-hydrogen atoms which are electronegative halogen atoms
|ψ
|ElectronegativeHalogenicity
|<nowiki>-</nowiki>
|}

=== Note on parameters ===
Surface tension
*surface tension is the only parameter with units, those used in SMD are non-standard cal mol-1Å-2
*the SI units are Jm-2 or Nm-1
*typical units are dyn cm-1 where 1 dyn = 1 g cm s-2
*as we tend to work in kJ/mol the energy part of this becomes not J but J/mol
*1 dyn cm-1 = 0.001N m-1 = 0.001J m-2
*1 m = 1*1010Å and 1J=0.239cal and 1 mol-1=6.022*1023
*1 dyn cm-1 = 0.001*0.239cal*6.022*1023mol-1/(1*102*10Å2
*and if you think about this 1023 on top line cancels with 1020 on bottom line leaving 103 which cancels with the 0.001=10-3 leaving us with 0.239*6.022=1.439
*1 dyn cm-1 = 1.439 cal mol-1 Å-2
Molar Volume
* MolarVolume=x.x in cm3/mol
* molecular volume in Å3 per molecule converted to cm3/mol
* 1cm = 1*108Å, 1Å = 1*10-8 cm
* x Å3 per molecule = x*6.022*1023mol-1 *103*-8cm3 = x*6.022*10-1cm3mol-1

=== Example: [C4C1Im][NTf2] ===
All parameters for this IL have been measured, and can be found in reference 2.<ref name=":0" /> That means we can use the standard SMD method.

To get a value for φ take the number of aromatic carbon atoms (3) and divide by the number of non-hydrogen atoms (25). φ = 0.12.

To get a value for ψ take the number of electronegative halogen atoms (6) and divide by the number of non-hydrogen atoms (25). ψ = 0.24.

To define these parameters place the following line at the bottom of the input file (include one blank line before and at least one blank line after):
eps=11.52 epsinf=2.037 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.12 ElectronegativeHalogenicity=0.24

=== Kamlet-Taft vs Abraham H-bonding parameters ===
The SMD model requires Abraham H-bondonding parameters (Σα2H, Σβ2H), however Kamlet-Taft (α, β) measurements are more commonly reported for ILs. To alleviate this problem a relationship between the parameters was investigated, giving the following equations:<ref name=":0" />

Σα2H = 0.4098α + 0.0064

Σβ2H = 0.6138β + 0.0890

Previously the group has developed a simple method for calculating Kamlet-Taft parameters, and the instructions are here.<ref>http://www.huntresearchgroup.org.uk/research/research_il_alpha_beta_intro.html</ref>

== SMD input database ==
Here we will keep a database of SMD parameters used by the group. Please add any IL you use, so no-one else has to re-do the research for the parameters! Please follow the template provided so that it is clear where you get each value from.

===[C4C1Im][BF4]===
all values from <ref name=":0" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.70
|<ref name=":0" />
|
|-
|epsinf
|2.0207
|<ref name=":0" />
|Value given in reference is n=1.4215, it has been squared to give epsinf=2.0207
|-
|SurfaceTensionAtInterface
|67.07
|<ref name=":0" />
|
|-
|HBondAcidity (α)
|0.263
|<ref name=":0" />
| Kamlet-Taft 0.627
|-
|HBondBasicity (β)
|0.320
|<ref name=":0" />
| Kamlet-Taft 0.376
|-
|CarbonAromaticity (φ)
|0.2000
|
|There are 15 non-H atoms, 3 are aromatic C atoms, value=3/15=0.2000
|-
|ElectronegativeHalogenicity (ψ)
|0.2667
|
|There are 15 non-H atoms, 4 are electronegative halogen atoms, value =4/15=0.2667
|-
| colspan="4" |<code>eps=11.70 epsinf=2.0207 SurfaceTensionAtInterface=67.07 HBondAcidity=0.263 HBondBasicity=0.320 CarbonAromaticity=0.2000 ElectronegativeHalogenicity=0.2667</code>
|}

===[C4C1Im][PF6]===
all values from <ref name=":0" />
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.40
|<ref name=":0" />
|
|-
|epsinf
|1.9853
|<ref name=":0" />
|Value given in reference is n=1.4090, it has been squared to give epsinf=1.9853
|-
|SurfaceTensionAtInterface
|70.24
|<ref name=":0" />
|
|-
|HBondAcidity (α)
|0.266
|<ref name=":0" />
| Kamlet-Taft 0.634
|-
|HBondBasicity (β)
|0.216
|<ref name=":0" />
| Kamlet-Taft 0.207
|-
|CarbonAromaticity (φ)
|0.1765
|
|There are 17 non-H atoms, 3 are aromatic C atoms, value=3/17=0.1765
|-
|ElectronegativeHalogenicity (ψ)
|0.3529
|
|There are 17 non-H atoms, 4 are electronegative halogen atoms, value =6/17=0.3529
|-
| colspan="4" |<code>eps=11.40 epsinf=1.9853 SurfaceTensionAtInterface=70.24 HBondAcidity=0.266 HBondBasicity=0.216 CarbonAromaticity=0.1765 ElectronegativeHalogenicity=0.3529</code>
|}

=== [C4C1Im][NTf2] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.52
|<ref name=":0" /> <ref name=":6">Daguenet 2006 http://pubs.acs.org/doi/abs/10.1021/jp0604903</ref>
|
|-
|epsinf
|2.0366|<ref name=":0" /> <ref name=":1">Huddleston 2001 http://pubs.rsc.org/en/Content/ArticleLanding/2001/GC/b103275p</ref>
|Value given in reference is n=1.4271, it has been squared to give epsinf=2.0366
|-
|SurfaceTensionAtInterface
|53.97
|<ref name=":0" /> <ref name=":1" />
|
|-
|HBondAcidity (α)
|0.259
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.617
|-
|HBondBasicity (β)
|0.238
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.243
|-
|CarbonAromaticity
|0.1200
|
|There are 25 non-H atoms, 3 are aromatic C atoms, value =3/25=0.1200
|-
|ElectronegativeHalogenicity
|0.2400
|
|There are 25 non-H atoms, 6 are electronegative halogen atoms, value =6/25=0.2400
|-
| colspan="4" |<code>eps=11.52 epsinf=2.0366 SurfaceTensionAtInterface=53.97 HBondAcidity=0.259 HBondBasicity=0.238 CarbonAromaticity=0.1200 ElectronegativeHalogenicity=0.2400</code>
|}

=== [C4C1Im][OTf] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|12.9
|<ref name=":3">Huang 2011 http://pubs.acs.org/doi/abs/10.1021/je101184s</ref>
|Page 1495, number 11 on the list.
|-
|epsinf
|2.0665
|<ref name=":4">Gonzalez 2012 http://pubs.acs.org/doi/abs/10.1021/je201334p</ref>
|n=1.43755, has been squared to give epsinf=2.0665. Can be found in Table 1, 3rd row.
|-
|SurfaceTensionAtInterface
|unknown
|
|-
|HBondAcidity (α)
|0.263
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.625
|-
|HBondBasicity (β)
|0.374
|<ref name=":0" /> <ref name=":2" />
| Kamlet-Taft 0.464
|-
|CarbonAromaticity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are aromatic C atoms, value=3/18=0.1667.
|-
|ElectronegativeHalogenicity
|0.1667
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are electronegative halogen atoms, value=3/18=0.1667.
|-
| colspan="4" |<code>eps=12.9 epsinf=2.0665 SurfaceTensionAtInterface'''=XX''' HBondAcidity=0.263 HBondBasicity=0.374 CarbonAromaticity=0.1667 ElectronegativeHalogenicity=0.1667</code>
|}

=== [C4C1Im][XX] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|13.7
|<ref name=":3">Huang 2011 http://pubs.acs.org/doi/abs/10.1021/je101184s</ref>
|Page 1495, number 11 on the list.
|-
|epsinf
|1.5392
|<ref name=":4">Gonzalez 2012 http://pubs.acs.org/doi/abs/10.1021/je201334p</ref>
|n=1.5392, has been squared to give epsinf=2.36917
|-
|SurfaceTensionAtInterface
|68.29
|
|XX
|-
|HBondAcidity (α)
|0.18
|<ref name=":0" /> <ref name=":2" />
| rowspan="2" |Kamlet and Taft measurements were reported in ref.<ref name=":2" /> Conversion to Abraham values was done using the equations above.<ref name=":0" />
|-
|HBondBasicity (β)
|0.52
|<ref name=":0" /> <ref name=":2" />
|-
|CarbonAromaticity
|0.308
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are aromatic C atoms.
|-
|ElectronegativeHalogenicity
|0.0
|<nowiki>-</nowiki>
|There are 18 non-H atoms, 3 are electronegative halogen atoms.
|-
| colspan="4" |eps=13.7 epsinf=2.36917 SurfaceTensionAtInterface=68.29 HBondAcidity=0.18 HBondBasicity=0.52 CarbonAromaticity=0.308 ElectronegativeHalogenicity=0.0
|}

=== Molten salt [Li+,Na+,K+][CO32-] ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|MolarVolume
|57
|<ref name=":5" />
|molar volume Li2CO3 68 Na2CO3 92 K2CO3 124 Å3/molecule, average is 95 and 95*0.6022=57 at T=1.1Tm
|-
|Tabs
|900
|
|Absolute Temperature in K ie 298+600≈900
|-
|???
|
|
|ThermalExansionCoefficient estimate 20*10-6 K-1 at T=1.1Tm (this is not working!)
|-
|eps
|3
|<ref name=":5">G. Janz and M. Lorenz, <abbr>J. Electrochem. Soc.</abbr> 1961 volume 108, issue 11, 1052-1058 doi: 10.1149/1.2427946</ref>
|estimated value
|-
|epsinf
|2.25
|
|refractive index Na2CO3 1.489-1.535,<ref><nowiki>https://pubchem.ncbi.nlm.nih.gov/compound/sodium_carbonate#section=Spectral-Properties&fullscreen=true</nowiki></ref> Li2CO3 1.428-1.572<ref>Weast, R.C. (ed.). Handbook of Chemistry and Physics. 60th ed. Boca Raton, Florida: CRC Press Inc., 1979., p. B-91</ref> K2CO3 1.426-1.541<ref><nowiki>http://cameo.mfa.org/wiki/Potassium_carbonate</nowiki></ref> taking a "mid" value 1.52=2.25
|-
|SurfaceTensionAtInterface
|273
|<ref name=":5" />
|used surface tension of Na/K/CO3 mixture 50 mol % K2CO3 at 810 ºC , 190.0 dynes/cm
|-
|HBondAcidity (α)
|0.00
|<nowiki>-</nowiki>
| rowspan="2" |There are no H-atoms so H-bond acidity is zero
H-bond basicity computations result in proton transfer, NO3 ≈0.74-0.81, Cl ≈0.95-0.98, we assume it is even stronger due to -2 charge
|-
|HBondBasicity (β)
|0.99
|
|-
|CarbonAromaticity
|0.00
|<nowiki>-</nowiki>
|There are no aromatic C atoms
|-
|ElectronegativeHalogenicity
|0.00
|<nowiki>-</nowiki>
|There are no halogen atoms
|-
| colspan="4" |Stoichiometry=C2O62Li2Na2K2 MolarVolume=57.0 Tabs=900 eps=3.0 epsinf=2.25 SurfaceTensionAtInterface=273 HBondAcidity=0.0 HBondBasicity=0.99 CarbonAromaticity=0.0 ElectronegativeHalogenicity=0.0
|}

=== Example IL-GIL (generic IL) ===
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|11.50
|<ref name=":0" />
|see ESI Table S2.1
|-
|epsinf
|2.0449
|<ref name=":0" />
|n=1.43, has been squared to give epsinf=2.0449
|-
|SurfaceTensionAtInterface
|61.24
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|HBondAcidity (α)
|0.229
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|HBondBasicity (β)
|0.265
|<ref name=":0" />
|<code>see ESI Table S2.1</code>
|-
|CarbonAromaticity
|
|<ref name=":0" />
|
|-
|ElectronegativeHalogenicity
|
|<ref name=":0" />
|
|-
| colspan="4" |<code>eps=11.50 epsinf=2.0449 SurfaceTensionAtInterface=61.24 HBondAcidity=0.229 HBondBasicity=0.265 CarbonAromaticity=0.xxx ElectronegativeHalogenicity=0.xxx</code>
|}

== Example table ==
{| class="wikitable"
!Name in Gaussian input file
!Value
!Reference
!Comments/calculations
|-
|eps
|
|
|
|-
|epsinf
|
|
|
|-
|SurfaceTensionAtInterface
|
|
|
|-
|HBondAcidity (α)
|
|
|
|-
|HBondBasicity (β)
|
|
|
|-
|CarbonAromaticity
|
|
|
|-
|ElectronegativeHalogenicity
|
|
|
|-
| colspan="4" |<code>eps= epsinf= SurfaceTensionAtInterface= HBondAcidity= HBondBasicity= CarbonAromaticity= ElectronegativeHalogenicity=</code>
|}

== References ==
<references />