ChemWiki - User contributions [en]

Mod:Hunt Research Group

2013-03-01T16:28:54Z

Lge: /* Setup and Running MD Simulations */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===Resources===

#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link] (notes by Tricia)

===Gaussian General===
#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] (notes by Everyone!)
#Instructions for visualizing electrostatic potentials [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link] (notes by Flo)
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#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] (notes by Heiko)
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link] (notes by Richard)
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link] (notes by Bryan & Richard)

===Unix and HPC===
#Setting up a connection to HPC if you have a PC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link] (notes by Hieu)
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link] (notes by Heiko)
#HPC servers and run scripts [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link] (notes by Tricia and Ling)]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link] (notes by Heiko)
#How to set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link] (notes by Heiko)
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link] (notes by Heiko)
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link] (notes by Heiko)
#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] (notes by Rachael, Weihong and Ling)
#How to set up cx2 [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cx2 link] (notes by Ling)

===Installing and using packages===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link] (notes by Ling)
#Beginners guide to VMD: a molecular dynamics visualisation package [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link] (notes by Ling & Bryan)
#DLPOLY a MD simulation package, Installation on an IMac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link] (notes by Ling)
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link] (notes by Tricia)
#How to install Geomview [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/geomview link] (notes by Tricia)
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/] (Ling)
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link] (notes by Bryan)

===Setup and Running MD Simulations===
#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] (notes by Ling)
#How to run CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k_how link] (notes by Ling)
#How to plot EMOs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emo link] (notes by Ling)
#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#Packmol for generating starting configurations [http://www.ime.unicamp.br/~martinez/packmol/] from Packmol webpage.
#Getting the Force Field [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Wheretostart link] (notes by Richard)
#Choosing an Ensemble [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Ensembles link] (notes by Richard)
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link] (notes by Richard)
#Visualising your Simulation [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VisualisingyourSimulation link] (notes by Richard)
#Voids in ILs[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids link] (notes by Ling)
#How to equilibrate an MD run[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/equilibration link] (notes by Tricia and Ling)]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link] (notes by Ling)]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link] (notes by Ling and Tricia)]

===Research Notes===
#Cl- in water [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link] (notes by Ling)]
#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] (notes by Yannis)
#Functional for ILs using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/IL_cpmd_functional link] (notes by Ling)
#[bmim]Cl using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cpmd link] (notes by Ling)
#[bmim]Cl using CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cp2k link] (notes by Ling)
#mman using CPMD and Gaussian [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/mman link] (notes by Ling)
#[emim]SCN using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emimscn link] (notes by Ling)
#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] (notes by Ling)
#CP2K Donts [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k link] (notes by Ling)
#How to make VMD trajectory repeated periodically [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/vmd link] (notes by Ling)
#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)

===CDT records===
#Activities record [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/CDT_records records]

===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] (notes by Tricia)
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link] (notes by Tricia)
#[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/calendar Calendar] (notes by Tricia)
#Demonstrating in the 3rd year computational chemistry lab [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/compchemlab Timetable] (notes by Tricia)
#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] notes by Tricia

Talk:Mod:Hunt Research Group/emo

2013-03-01T16:28:05Z

Lge:

wc2emo1.f90 is my original code to plot EMOs. Different versions of the code:

Use [wc2emo2.f90] for water and Cl-; use [wc2emo2_28.f90] for bmim+.

We need the following files presented in the same directory:
<pre>
[WANNIER_1.x.cube]
[Wfindex.dat]
the indices of Wannier functions
[EMOindices.dat]
the indices of EMO
[TM.dat]
trasformation matrix is the 'MO_vectors_in_wannier_basis' in [MO_DATA]
sed -n '252592,504311p' MO_DATA > TM.dat
</pre>
For example, we want to plot the EMO of Cl#35 from 10 ps:
* Find out which wannier functions belong to the molecule. (2 approaches)
** [LOG_DATA] stamp 11 're-ordered in terms of the molecular units' (L6874-7741)
<pre>
type
sed -n '6874,7741p' LOG_DATA > WAN_MOL
</pre>
** Visualise [IONs.xyz] and [CENTERS.xyz] in VMD to see which Wannier functions associated with the Cl-. Note: the index of VMD starts from 0, but WANNIER_1.x starts from 1)
* Put the Wannier functions indices in [Wfindex.dat] and the EMO indices in [EMOindices.dat].
In this case, Wfindex=200,789,796,809 and EMOindix=785,786,787,788.
* Copy the "MO_vectors_in_wannier_basis" in [MO_DATA] to a new file called [TM.dat].
* Use cpmd2cube.x to generate the Wannier cube files.
* Type: 'gfortran wc2emo2.f90' to generate the excutable file [a.out].
* Type: './a.out' to generate the EMO cube files.

Talk:Mod:Hunt Research Group/emo

2013-03-01T16:27:41Z

Lge:

wc2emo1.f90 is my original code to plot EMOs. Different versions of the code:

Use [wc2emo2.f90] for water and Cl-; use [wc2emo2_28.f90] for bmim+.

We need the following files presented in the same directory:
<pre>
[WANNIER_1.x.cube]
[Wfindex.dat]
the indices of Wannier functions
[EMOindices.dat]
the indices of EMO
[TM.dat]
trasformation matrix is the 'MO_vectors_in_wannier_basis' in [MO_DATA]
sed -n '252592,504311p' MO_DATA > TM.dat
</pre>
For example, we want to plot the EMO of Cl#35 from 10 ps:
* Find out which wannier functions belong to the molecule. (2 approaches)
** [LOG_DATA] stamp 11 're-ordered in terms of the molecular units' (L6874-7741)

sed -n '6874,7741p' LOG_DATA > WAN_MOL

** Visualise [IONs.xyz] and [CENTERS.xyz] in VMD to see which Wannier functions associated with the Cl-. Note: the index of VMD starts from 0, but WANNIER_1.x starts from 1)
* Put the Wannier functions indices in [Wfindex.dat] and the EMO indices in [EMOindices.dat].
In this case, Wfindex=200,789,796,809 and EMOindix=785,786,787,788.
* Copy the "MO_vectors_in_wannier_basis" in [MO_DATA] to a new file called [TM.dat].
* Use cpmd2cube.x to generate the Wannier cube files.
* Type: 'gfortran wc2emo2.f90' to generate the excutable file [a.out].
* Type: './a.out' to generate the EMO cube files.

Talk:Mod:Hunt Research Group/emo

2013-03-01T16:27:08Z

Lge:

wc2emo1.f90 is my original code to plot EMOs. Different versions of the code:

Use [wc2emo2.f90] for water and Cl-; use [wc2emo2_28.f90] for bmim+.

We need the following files presented in the same directory:
<pre>
[WANNIER_1.x.cube]
[Wfindex.dat]
the indices of Wannier functions
[EMOindices.dat]
the indices of EMO
[TM.dat]
trasformation matrix is the 'MO_vectors_in_wannier_basis' in [MO_DATA]
sed -n '252592,504311p' MO_DATA > TM.dat
</pre>
For example, we want to plot the EMO of Cl#35 from 10 ps:
* Find out which wannier functions belong to the molecule. (2 approaches)
** [LOG_DATA] stamp 11 're-ordered in terms of the molecular units' (L6874-7741)
<pre>
sed -n '6874,7741p' LOG_DATA > WAN_MOL
</pre>
** Visualise [IONs.xyz] and [CENTERS.xyz] in VMD to see which Wannier functions associated with the Cl-. Note: the index of VMD starts from 0, but WANNIER_1.x starts from 1)
* Put the Wannier functions indices in [Wfindex.dat] and the EMO indices in [EMOindices.dat].
In this case, Wfindex=200,789,796,809 and EMOindix=785,786,787,788.
* Copy the "MO_vectors_in_wannier_basis" in [MO_DATA] to a new file called [TM.dat].
* Use cpmd2cube.x to generate the Wannier cube files.
* Type: 'gfortran wc2emo2.f90' to generate the excutable file [a.out].
* Type: './a.out' to generate the EMO cube files.

Talk:Mod:Hunt Research Group/emo

2013-03-01T16:26:37Z

Lge:

wc2emo1.f90 is my original code to plot EMOs. Different versions of the code:

Use [wc2emo2.f90] for water and Cl-; use [wc2emo2_28.f90] for bmim+.

We need the following files presented in the same directory:
<pre>
[WANNIER_1.x.cube]
[Wfindex.dat]
the indices of Wannier functions
[EMOindices.dat]
the indices of EMO
[TM.dat]
trasformation matrix is the 'MO_vectors_in_wannier_basis' in [MO_DATA]
sed -n '252592,504311p' MO_DATA > TM.dat
</pre>
For example, we want to plot the EMO of Cl#35 from 10 ps:
# Find out which wannier functions belong to the molecule. (2 approaches)
** [LOG_DATA] stamp 11 're-ordered in terms of the molecular units' (L6874-7741)
<pre>
sed -n '6874,7741p' LOG_DATA > WAN_MOL
</pre>
** Visualise [IONs.xyz] and [CENTERS.xyz] in VMD to see which Wannier functions associated with the Cl-. Note: the index of VMD starts from 0, but WANNIER_1.x starts from 1)
# Put the Wannier functions indices in [Wfindex.dat] and the EMO indices in [EMOindices.dat].
In this case, Wfindex=200,789,796,809 and EMOindix=785,786,787,788.
# Copy the "MO_vectors_in_wannier_basis" in [MO_DATA] to a new file called [TM.dat].
# Use cpmd2cube.x to generate the Wannier cube files.
# Type: 'gfortran wc2emo2.f90' to generate the excutable file [a.out].
# Type: './a.out' to generate the EMO cube files.

Talk:Mod:Hunt Research Group/emo

2013-03-01T16:26:10Z

Lge:

wc2emo1.f90 is my original code to plot EMOs. Different versions of the code:

Use [wc2emo2.f90] for water and Cl-; use [wc2emo2_28.f90] for bmim+.

We need the following files presented in the same directory:
<pre>
[WANNIER_1.x.cube]
[Wfindex.dat]
the indices of Wannier functions
[EMOindices.dat]
the indices of EMO
[TM.dat]
trasformation matrix is the 'MO_vectors_in_wannier_basis' in [MO_DATA]
sed -n '252592,504311p' MO_DATA > TM.dat
</pre>
For example, we want to plot the EMO of Cl#35 from 10 ps:
# Find out which wannier functions belong to the molecule. (2 approaches)
## [LOG_DATA] stamp 11 're-ordered in terms of the molecular units' (L6874-7741)
<pre>
sed -n '6874,7741p' LOG_DATA > WAN_MOL
</pre>
## Visualise [IONs.xyz] and [CENTERS.xyz] in VMD to see which Wannier functions associated with the Cl-. Note: the index of VMD starts from 0, but WANNIER_1.x starts from 1)
# Put the Wannier functions indices in [Wfindex.dat] and the EMO indices in [EMOindices.dat].
In this case, Wfindex=200,789,796,809 and EMOindix=785,786,787,788.
# Copy the "MO_vectors_in_wannier_basis" in [MO_DATA] to a new file called [TM.dat].
# Use cpmd2cube.x to generate the Wannier cube files.
# Type: 'gfortran wc2emo2.f90' to generate the excutable file [a.out].
# Type: './a.out' to generate the EMO cube files.

Talk:Mod:Hunt Research Group/emo

2013-03-01T16:23:44Z

Lge:

wc2emo1.f90 is my original code to plot EMOs. Different versions of the code:

Use [wc2emo2.f90] for water and Cl-; use [wc2emo2_28.f90] for bmim+.

We need the following files presented in the same directory:
<pre>
[WANNIER_1.x.cube]
[Wfindex.dat]
the indices of Wannier functions
[EMOindices.dat]
the indices of EMO
[TM.dat]
trasformation matrix is the 'MO_vectors_in_wannier_basis' in [MO_DATA]
sed -n '252592,504311p' MO_DATA > TM.dat
</pre>
For example, we want to plot the EMO of Cl#35 from 10 ps:
#Find out which wannier functions belong to the molecule. (2 approaches)
(1)[LOG_DATA] stamp 11 're-ordered in terms of the molecular units' (L6874-7741)
<pre>
sed -n '6874,7741p' LOG_DATA > WAN_MOL
</pre>
(2)Visualise [IONs.xyz] and [CENTERS.xyz] in VMD to see which Wannier functions associated with the Cl-. Note: the index of VMD starts from 0, but WANNIER_1.x starts from 1)
#Put the Wannier functions indices in [Wfindex.dat] and the EMO indices in [EMOindices.dat].
In this case, Wfindex=200,789,796,809 and EMOindix=785,786,787,788.
#Copy the "MO_vectors_in_wannier_basis" in [MO_DATA] to a new file called [TM.dat].
#Use cpmd2cube.x to generate the Wannier cube files.
#Type: 'gfortran wc2emo2.f90' to generate the excutable file [a.out].
#Type: './a.out' to generate the EMO cube files.

Talk:Mod:Hunt Research Group/emo

2013-03-01T16:23:17Z

Lge:

wc2emo1.f90 is my original code to plot EMOs. Different versions of the code:

Use [wc2emo2.f90] for water and Cl-; use [wc2emo2_28.f90] for bmim+.

We need the following files presented in the same directory:
<pre>
[WANNIER_1.x.cube]
[Wfindex.dat]
the indices of Wannier functions
[EMOindices.dat]
the indices of EMO
[TM.dat]
trasformation matrix is the 'MO_vectors_in_wannier_basis' in [MO_DATA]
sed -n '252592,504311p' MO_DATA > TM.dat
</pre>
For example, we want to plot the EMO of Cl#35 from 10 ps:
#Find out which wannier functions belong to the molecule. (2 approaches)
(1)[LOG_DATA] stamp 11 're-ordered in terms of the molecular units' (L6874-7741)
<pre>
sed -n '6874,7741p' LOG_DATA > WAN_MOL
</pre>
(2)Visualise [IONs.xyz] and [CENTERS.xyz] in VMD to see which Wannier functions associated with the Cl-.(remember that the index of VMD starts from 0, but WANNIER_1.x starts from 1)
#Put the Wannier functions indices in [Wfindex.dat] and the EMO indices in [EMOindices.dat].
In this case, Wfindex=200,789,796,809 and EMOindix=785,786,787,788.
#Copy the "MO_vectors_in_wannier_basis" in [MO_DATA] to a new file called [TM.dat].
#Use cpmd2cube.x to generate the Wannier cube files.
#Type: 'gfortran wc2emo2.f90' to generate the excutable file [a.out].
#Type: './a.out' to generate the EMO cube files.

Talk:Mod:Hunt Research Group/emo

2013-03-01T16:22:44Z

Lge:

wc2emo1.f90 is my original code to plot EMOs. Different versions of the code:

Use [wc2emo2.f90] for water and Cl-; use [wc2emo2_28.f90] for bmim+.

We need the following files presented in the same directory:
<pre>
[WANNIER_1.x.cube]
[Wfindex.dat]
the indices of Wannier functions
[EMOindices.dat]
the indices of EMO
[TM.dat]
trasformation matrix is the 'MO_vectors_in_wannier_basis' in [MO_DATA]
sed -n '252592,504311p' MO_DATA > TM.dat
</pre>
For example, we want to plot the EMO of Cl#35 from 10 ps:
#Find out which wannier functions belong to the molecule. (2 approaches)
##[LOG_DATA] stamp 11 're-ordered in terms of the molecular units' (L6874-7741)
<pre>
sed -n '6874,7741p' LOG_DATA > WAN_MOL
</pre>
##Visualise [IONs.xyz] and [CENTERS.xyz] in VMD to see which Wannier functions associated with the Cl-.(remember that the index of VMD starts from 0, but WANNIER_1.x starts from 1)
#Put the Wannier functions indices in [Wfindex.dat] and the EMO indices in [EMOindices.dat].
In this case, Wfindex=200,789,796,809 and EMOindix=785,786,787,788.
#Copy the "MO_vectors_in_wannier_basis" in [MO_DATA] to a new file called [TM.dat].
#Use cpmd2cube.x to generate the Wannier cube files.
#Type: 'gfortran wc2emo2.f90' to generate the excutable file [a.out].
#Type: './a.out' to generate the EMO cube files.

Talk:Mod:Hunt Research Group/emo

2013-03-01T16:21:56Z

Lge:

wc2emo1.f90 is my original code to plot EMOs. Different versions of the code:

Use [wc2emo2.f90] for water and Cl-; use [wc2emo2_28.f90] for bmim+.

We need the following files presented in the same directory:
<pre>
[WANNIER_1.x.cube]
[Wfindex.dat]
the indices of Wannier functions
[EMOindices.dat]
the indices of EMO
[TM.dat]
trasformation matrix is the 'MO_vectors_in_wannier_basis' in [MO_DATA]
sed -n '252592,504311p' MO_DATA > TM.dat
</pre>
For example, we want to plot the EMO of Cl#35 from 10 ps:
#Find out which wannier functions belong to the molecule. (2 approaches)
##[LOG_DATA] stamp 11 're-ordered in terms of the molecular units' (L6874-7741)
<pre>
sed -n '6874,7741p' LOG_DATA > WAN_MOL
</pre>
##Visualise [IONs.xyz] and [CENTERS.xyz] in VMD to see which Wannier functions associated with the Cl-.(remember that the index of VMD starts from 0, but WANNIER_1.x starts from 1)

#Put the Wannier functions indices in [Wfindex.dat] and the EMO indices in [EMOindices.dat].
In this case, Wfindex=200,789,796,809 and EMOindix=785,786,787,788.

#Copy the "MO_vectors_in_wannier_basis" in [MO_DATA] to a new file called [TM.dat].

#Use cpmd2cube.x to generate the Wannier cube files.

#Type: 'gfortran wc2emo2.f90' to generate the excutable file [a.out].

#Type: './a.out' to generate the EMO cube files.

Talk:Mod:Hunt Research Group/emo

2013-03-01T16:20:43Z

Lge:

wc2emo1.f90 is my original code to plot EMOs. Different versions of the code:

Use [wc2emo2.f90] for water and Cl-; use [wc2emo2_28.f90] for bmim+.

We need the following files presented in the same directory:
<pre>
[WANNIER_1.x.cube]
[Wfindex.dat]
the indices of Wannier functions
[EMOindices.dat]
the indices of EMO
[TM.dat]
trasformation matrix is the 'MO_vectors_in_wannier_basis' in [MO_DATA]
sed -n '252592,504311p' MO_DATA > TM.dat
</pre>
For example, we want to plot the EMO of Cl#35 from 10 ps:
1. Find out which wannier functions belong to the molecule. (2 approaches)
1.1 [LOG_DATA] stamp 11 're-ordered in terms of the molecular units' (L6874-7741)
<pre>
sed -n '6874,7741p' LOG_DATA > WAN_MOL
</pre>
1.2 Visualise [IONs.xyz] and [CENTERS.xyz] in VMD to see which Wannier functions associated with the Cl-.(remember that the index of VMD starts from 0, but WANNIER_1.x starts from 1)

2. Put the Wannier functions indices in [Wfindex.dat] and the EMO indices in [EMOindices.dat].
In this case, Wfindex=200,789,796,809 and EMOindix=785,786,787,788.

3. Copy the "MO_vectors_in_wannier_basis" in [MO_DATA] to a new file called [TM.dat].

4. Use cpmd2cube.x to generate the Wannier cube files.

5. Type: 'gfortran wc2emo2.f90' to generate the excutable file [a.out].

6. Type: './a.out' to generate the EMO cube files.

Talk:Mod:Hunt Research Group/emo

2013-03-01T16:19:36Z

Lge: Created page with "wc2emo1.f90 is my original code to plot EMOs. Different versions of the code: Use [wc2emo2.f90] for water and Cl-; use [wc2emo2_28.f90] for bmim+. We need the following file..."

wc2emo1.f90 is my original code to plot EMOs. Different versions of the code:

Use [wc2emo2.f90] for water and Cl-; use [wc2emo2_28.f90] for bmim+.

We need the following files presented in the same directory:

[WANNIER_1.x.cube]

[Wfindex.dat]

the indices of Wannier functions

[EMOindices.dat]

the indices of EMO

[TM.dat]

trasformation matrix is the 'MO_vectors_in_wannier_basis' in [MO_DATA]

sed -n '252592,504311p' MO_DATA > TM.dat

For example, we want to plot the EMO of Cl#35 from 10 ps:

1. Find out which wannier functions belong to the molecule. (2 approaches)

1.1 [LOG_DATA] stamp 11 're-ordered in terms of the molecular units' (L6874-7741)

<pre>

sed -n '6874,7741p' LOG_DATA > WAN_MOL

</pre>

1.2 Visualise [IONs.xyz] and [CENTERS.xyz] in VMD to see which Wannier functions associated with the Cl-.

(remember that the index of VMD starts from 0, but WANNIER_1.x starts from 1)

2. Put the Wannier functions indices in [Wfindex.dat] and the EMO indices in [EMOindices.dat].

In this case, Wfindex=200,789,796,809 and EMOindix=785,786,787,788.

3. Copy the "MO_vectors_in_wannier_basis" in [MO_DATA] to a new file called [TM.dat].

4. Use cpmd2cube.x to generate the Wannier cube files.

5. Type: 'gfortran wc2emo2.f90' to generate the excutable file [a.out].

6. Type: './a.out' to generate the EMO cube files.

Mod:Hunt Research Group

2013-03-01T16:16:07Z

Lge: /* Setup and Running MD Simulations */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===Resources===

#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link] (notes by Tricia)

===Gaussian General===
#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] (notes by Everyone!)
#Instructions for visualizing electrostatic potentials [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link] (notes by Flo)
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#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] (notes by Heiko)
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link] (notes by Richard)
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link] (notes by Bryan & Richard)

===Unix and HPC===
#Setting up a connection to HPC if you have a PC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link] (notes by Hieu)
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link] (notes by Heiko)
#HPC servers and run scripts [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link] (notes by Tricia and Ling)]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link] (notes by Heiko)
#How to set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link] (notes by Heiko)
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link] (notes by Heiko)
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link] (notes by Heiko)
#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] (notes by Rachael, Weihong and Ling)
#How to set up cx2 [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cx2 link] (notes by Ling)

===Installing and using packages===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link] (notes by Ling)
#Beginners guide to VMD: a molecular dynamics visualisation package [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link] (notes by Ling & Bryan)
#DLPOLY a MD simulation package, Installation on an IMac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link] (notes by Ling)
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link] (notes by Tricia)
#How to install Geomview [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/geomview link] (notes by Tricia)
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/] (Ling)
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link] (notes by Bryan)

===Setup and Running MD Simulations===
#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#Packmol for generating starting configurations [http://www.ime.unicamp.br/~martinez/packmol/] from Packmol webpage.
#Getting the Force Field [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Wheretostart link] (notes by Richard)
#Choosing an Ensemble [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Ensembles link] (notes by Richard)
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link] (notes by Richard)
#Visualising your Simulation [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VisualisingyourSimulation link] (notes by Richard)
#Voids in ILs[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids link] (notes by Ling)
#How to equilibrate an MD run[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/equilibration link] (notes by Tricia and Ling)]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link] (notes by Ling)]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link] (notes by Ling and Tricia)]
#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] (notes by Ling)
#How to run CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k_how link] (notes by Ling)
#How to plot EMOs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emo link] (notes by Ling)

===Research Notes===
#Cl- in water [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link] (notes by Ling)]
#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] (notes by Yannis)
#Functional for ILs using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/IL_cpmd_functional link] (notes by Ling)
#[bmim]Cl using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cpmd link] (notes by Ling)
#[bmim]Cl using CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cp2k link] (notes by Ling)
#mman using CPMD and Gaussian [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/mman link] (notes by Ling)
#[emim]SCN using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emimscn link] (notes by Ling)
#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] (notes by Ling)
#CP2K Donts [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k link] (notes by Ling)
#How to make VMD trajectory repeated periodically [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/vmd link] (notes by Ling)
#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)

===CDT records===
#Activities record [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/CDT_records records]

===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] (notes by Tricia)
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link] (notes by Tricia)
#[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/calendar Calendar] (notes by Tricia)
#Demonstrating in the 3rd year computational chemistry lab [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/compchemlab Timetable] (notes by Tricia)
#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] notes by Tricia

Talk:Mod:Hunt Research Group/cp2k how

2013-03-01T13:07:53Z

Lge:

1. Website:
http://manual.cp2k.org/trunk/

2. Lecture notes:
http://www.cecam.org/workshop-4-529.html

3. Files you need:

Basis/Potential Files (can be downloaded together with the CP2K package):
<pre>
BASIS_SET
BASIS_MOLOPT
POTENTIAL
</pre>
runscript:
<pre>
runcp2k
runcp2krestart
</pre>
Input/output files (in directory on drobo: /Ling_project_2013/Rio-Tinto/cp2kcuwater/input_output_files/):
<pre>
cp2k_cuwater.inp
cp2k_cuwater.out
</pre>
4. Annotation of input files:

4.1 Example of [bmim]Cl:
<pre>
&GLOBAL --> Section that contains general information about the simulation and parameters for the whole program.
PROJECT bmimcl --> Name of the project, used to determine the name of the files generated by the program.
PRINT_LEVEL MEDIUM --> How much output is written out.
RUN_TYPE MD --> Type of run that to perform (e.g. MD, GeoOpt, MC).
&END --> End of section.

&FORCE_EVAL --> Parameters used to calculate energy and forces and to describe the system.
METHOD Quickstep --> Method used to compute forces. (Quickstep is for electronic structure methods, e.g. DFT).
&DFT --> Parameters for DFT.
BASIS_SET_FILE_NAME /work/lge/cp2ktest/BASIS_MOLOPT --> Path of basis set file.
POTENTIAL_FILE_NAME /work/lge/cp2ktest/POTENTIAL --> Path of pseudopotential file.
&XC --> Parameters to calculate the xc (exchange-correlation) potential.
&XC_FUNCTIONAL BLYP --> The xc functional to be used.
&END XC_FUNCTIONAL
&XC_GRID --> xc parameters used when calculating the xc on the grid.
XC_DERIV NN10_SMOOTH --> Method used to compute the derivatives.
XC_SMOOTH_RHO NN10 --> Density smoothing used for the xc calculation.
&END XC_GRID
&vdW_POTENTIAL --> Section for all additional dispersion corrections to the xc functionals.
DISPERSION_FUNCTIONAL PAIR_POTENTIAL --> (or POTENTIAL_TYPE, specifies the type of dispersion functional or potential to use).
&PAIR_POTENTIAL --> Info on the pair potential used to calculate dispersion.
TYPE DFTD3 --> Type of potential.
REFERENCE_FUNCTIONAL BLYP --> Use parameters for this specific density functional
&END PAIR_POTENTIAL
&END vdW_POTENTIAL
&END XC
&MGRID --> Multigrid information
CUTOFF 280 --> Cutoff of the finest grid level in Ry.
NGRIDS 5 --> Number of multigrids.
&END
&SCF --> Parameters for the SCF run.
SCF_GUESS ATOMIC --> Initial guess for the wavefunction (ATOMIC generates an atomic density using the atomic code).
MAX_SCF 300 --> Maximum number of SCF iterations for one optimisation.
&OT --> Various options for the orbtial transformation (OT) method.
PRECONDITIONER FULL_SINGLE_INVERSE --> Type of preconditioner to be used with all minimisation schemes (FULL_SINGLE_INVERSE based on H-eS cholesky inversion).
MINIMIZER DIIS --> Minimiser to be used with the OT method (e.g. CG, SD).
&END OT
&END SCF
&END SECTION DFT
&SUBSYS --> Defines a subsystem: coordinates, topology, molecules and cell.
&CELL --> Input parameters needed to set up the cell.
ABC 19.522 19.522 19.522 --> Specifies the lengths of the cell vectors A, B and C in Angstroms.
&END CELL
&KIND H --> Description of H atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q1 --> Name of pseudopotential.
&END
&KIND C --> Description of C atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q4 --> Name of pseudopotential.
&END
&KIND N --> Description of N atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q5 --> Name of pseudopotential.
&END
&KIND CL --> Description of Cl atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q7 --> Name of pseudopotential.
&END
&COORD --> Coordinates of the atoms in xyz format, in Angstroms (by default).
.....
&END
&END SUBSYS
&END FORCE_EVAL
&MOTION --> Defines tools connected with motion of the nuclei.
&MD --> Parameters to perform an MD run.
ENSEMBLE NVT --> Ensemble to be used.
STEPS 2000 --> Number of MD steps
TIMESTEP 0.5 --> Length of integration step in fs.
&THERMOSTAT --> Specify the thermostat and related parameters.
TYPE NOSE --> Thermostat to be used (NOSE is for the Nose-Hoover thermostat).
&NOSE --> Parameters of the Nose-Hoover thermostat chain.
TIMECON 100 --> Time constant of the thermostat chain in fs.
&END NOSE
&END THERMOSTAT
TEMPERATURE 353 --> Temperature in K used to initialise the velocities with init and pos restart, and in the NPT/NVT simulations.
&END MD
&END MOTION
</pre>
4.2 Example of Cu water (Cu(II)+64H2O):
<pre>
&GLOBAL --> Section that contains general information about the simulation and parameters for the whole program.
PROJECT cuwater --> Name of the project, used to determine the name of the files generated by the program.
PRINT_LEVEL MEDIUM --> How much output is written out.
RUN_TYPE MD --> Type of run that to perform (e.g. MD, GeoOpt, MC).
&END --> End of section.

&FORCE_EVAL --> Parameters used to calculate energy and forces and to describe the system.
METHOD Quickstep --> Method used to compute forces. (Quickstep is for electronic structure methods, e.g. DFT).
&DFT --> Parameters for DFT.
BASIS_SET_FILE_NAME /work/lge/cp2kcuwater/BASIS_MOLOPT --> Path of basis set file.
POTENTIAL_FILE_NAME /work/lge/cp2kcuwater/POTENTIAL --> Path of pseudopotential file.
LSD --> or UKS, requests a spin-polarised calculation using alpha and beta orbtials, i.e. no spin restriction is applied.
CHARGE 2 --> Total charge of the system
MULTIPLICITY 2 --> Two times the total spin plus one.
&PRINT --> Printing options.
&LOCALIZATION --> Printing options related to the Wannier centers and properties computed with Wannier centers.
&WANNIER_CENTERS --> Controls the printing of the wannier functions.
IONS+CENTERS --> Prints out the wannier centers together with the particles.
&END
&END
&END
&MGRID --> Multigrid information
CUTOFF 280 --> Cutoff of the finest grid level in Ry.
&END MGRID
&QS --> Parameters needed to set up the Quickstep framework
EXTRAPOLATION PS --> Extrapolation strategy for the wavefunction during e.g. MD (PS is higher order extrapolation of the density matrix times the overlap matrix).
EXTRAPOLATION_ORDER 2 --> Order for the PS or ASPC extrapolation.
&END QS
&SCF --> Parameters for the SCF run.
CHOLESKY OFF --> If the cholesky method should be used for computing the inverse of S, and in this case calling which Lapack routines (OFF means do not use cholesky).
SCF_GUESS ATOMIC --> Initial guess for the wavefunction (ATOMIC generates an atomic density using the atomic code).
EPS_SCF 3.0E-6 --> Target accuracy for the scf convergence.
MAX_SCF 20 --> Maximum number of SCF iterations for one optimisation.
&OUTER_SCF --> Parameters controlling the outer SCF loop.
EPS_SCF 3.0E-6 --> Target gradient (not accuracy?) of the outer SCF variables. Notice that the EPS_SCF of the inner loop also determines the value that can be reached in the outer loop, typically EPS_SCF of the outer loop must be smaller than the EPS_SCF of the inner loop.
MAX_SCF 20 --> The maximum number of outer loops.
&END
&OT --> Various options for the orbtial transformation (OT) method.
MINIMIZER DIIS --> Minimiser to be used with the OT method (e.g. CG, SD).
PRECONDITIONER FULL_ALL --> Type of preconditioner to be used with all minimisation schemes (FULL_ALL is the most effective state selective preconditioner based on diagonalisation, requires the ENERGY_GAP parameters to be an underestimate of the HOMO-LUMO gap).
ENERGY_GAP 0.01 --> Should be an estimate for the HOMO-LUMO energy gap in a.u. and is used in preconditioning.
&END OT
&END SCF
&XC --> Parameters to calculate the xc (exchange-correlation) potential.
&XC_FUNCTIONAL BLYP --> The xc functional to be used.
&END XC_FUNCTIONAL
&END XC
&END DFT
&SUBSYS --> Defines a subsystem: coordinates, topology, molecules and cell.
&CELL --> Input parameters needed to set up the cell.
ABC 12.535 12.535 12.535 --> Specifies the lengths of the cell vectors A, B and C in Angstroms.
&END CELL
&KIND H --> Description of H atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q1 --> Name of pseudopotential.
&END
&KIND O --> Description of O atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q6 --> Name of pseudopotential.
&END
&KIND Cu --> Description of Cu atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q11 --> Name of pseudopotential.
&END
&COORD --> Coordinates of the atoms in xyz format, in Angstroms (by default).
.....
&END
&END SUBSYS
&END FORCE_EVAL
&MOTION --> Defines tools connected with motion of the nuclei.
&MD --> Parameters to perform an MD run.
ENSEMBLE NVT --> Ensemble to be used.
STEPS 2000 --> Number of MD steps
TIMESTEP 0.5 --> Length of integration step in fs.
&THERMOSTAT --> Specify the thermostat and related parameters.
TYPE NOSE --> Thermostat to be used (NOSE is for the Nose-Hoover thermostat).
&NOSE --> Parameters of the Nose-Hoover thermostat chain.
TIMECON 100 --> Time constant of the thermostat chain in fs.
&END NOSE
&END THERMOSTAT
TEMPERATURE 298 --> Temperature in K used to initialise the velocities with init and pos restart, and in the NPT/NVT simulations.
&END MD
&END MOTION
</pre>

Talk:Mod:Hunt Research Group/cp2k how

2013-03-01T13:06:31Z

Lge:

1. Website:
http://manual.cp2k.org/trunk/

2. Lecture notes:
http://www.cecam.org/workshop-4-529.html

3. Files you need:

Basis/Potential Files (can be downloaded together with the CP2K package):
<pre>
BASIS_SET
BASIS_MOLOPT
POTENTIAL
</pre>
runscript:
<pre>
runcp2k
runcp2krestart
</pre>
Input/output files (in directory on drobo: /Ling_project_2013/Rio-Tinto/cp2kcuwater/input_output_files/):
<pre>
cp2k_cuwater.inp
cp2k_cuwater.out
</pre>
4. Annotation of input files:

4.1 Example of [bmim]Cl:
<pre>
&GLOBAL --> Section that contains general information about the simulation and parameters for the whole program.
PROJECT bmimcl --> Name of the project, used to determine the name of the files generated by the program.
PRINT_LEVEL MEDIUM --> How much output is written out.
RUN_TYPE MD --> Type of run that to perform (e.g. MD, GeoOpt, MC).
&END --> End of section.

&FORCE_EVAL --> Parameters used to calculate energy and forces and to describe the system.
METHOD Quickstep --> Method used to compute forces. (Quickstep is for electronic structure methods, e.g. DFT).
&DFT --> Parameters for DFT.
BASIS_SET_FILE_NAME /work/lge/cp2ktest/BASIS_MOLOPT --> Path of basis set file.
POTENTIAL_FILE_NAME /work/lge/cp2ktest/POTENTIAL --> Path of pseudopotential file.
&XC --> Parameters to calculate the xc (exchange-correlation) potential.
&XC_FUNCTIONAL BLYP --> The xc functional to be used.
&END XC_FUNCTIONAL
&XC_GRID --> xc parameters used when calculating the xc on the grid.
XC_DERIV NN10_SMOOTH --> Method used to compute the derivatives.
XC_SMOOTH_RHO NN10 --> Density smoothing used for the xc calculation.
&END XC_GRID
&vdW_POTENTIAL --> Section for all additional dispersion corrections to the xc functionals.
DISPERSION_FUNCTIONAL PAIR_POTENTIAL --> (or POTENTIAL_TYPE, specifies the type of dispersion functional or potential to use).
&PAIR_POTENTIAL --> Info on the pair potential used to calculate dispersion.
TYPE DFTD3 --> Type of potential.
REFERENCE_FUNCTIONAL BLYP --> Use parameters for this specific density functional
&END PAIR_POTENTIAL
&END vdW_POTENTIAL
&END XC
&MGRID --> Multigrid information
CUTOFF 280 --> Cutoff of the finest grid level in Ry.
NGRIDS 5 --> Number of multigrids.
&END
&SCF --> Parameters for the SCF run.
SCF_GUESS ATOMIC --> Initial guess for the wavefunction (ATOMIC generates an atomic density using the atomic code).
MAX_SCF 300 --> Maximum number of SCF iterations for one optimisation.
&OT --> Various options for the orbtial transformation (OT) method.
PRECONDITIONER FULL_SINGLE_INVERSE --> Type of preconditioner to be used with all minimisation schemes (FULL_SINGLE_INVERSE based on H-eS cholesky inversion).
MINIMIZER DIIS --> Minimiser to be used with the OT method (e.g. CG, SD).
&END OT
&END SCF
&END SECTION DFT
&SUBSYS --> Defines a subsystem: coordinates, topology, molecules and cell.
&CELL --> Input parameters needed to set up the cell.
ABC 19.522 19.522 19.522 --> Specifies the lengths of the cell vectors A, B and C in Angstroms.
&END CELL
&KIND H --> Description of H atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q1 --> Name of pseudopotential.
&END
&KIND C --> Description of C atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q4 --> Name of pseudopotential.
&END
&KIND N --> Description of N atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q5 --> Name of pseudopotential.
&END
&KIND CL --> Description of Cl atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q7 --> Name of pseudopotential.
&END
&COORD --> Coordinates of the atoms in xyz format, in Angstroms (by default).
.....
&END
&END SUBSYS
&END FORCE_EVAL
&MOTION --> Defines tools connected with motion of the nuclei.
&MD --> Parameters to perform an MD run.
ENSEMBLE NVT --> Ensemble to be used.
STEPS 2000 --> Number of MD steps
TIMESTEP 0.5 --> Length of integration step in fs.
&THERMOSTAT --> Specify the thermostat and related parameters.
TYPE NOSE --> Thermostat to be used (NOSE is for the Nose-Hoover thermostat).
&NOSE --> Parameters of the Nose-Hoover thermostat chain.
TIMECON 100 --> Time constant of the thermostat chain in fs.
&END NOSE
&END THERMOSTAT
TEMPERATURE 353 --> Temperature in K used to initialise the velocities with init and pos restart, and in the NPT/NVT simulations.
&END MD
&END MOTION
</pre>
4.2 Example of Cu water:
<pre>
&GLOBAL --> Section that contains general information about the simulation and parameters for the whole program.
PROJECT cuwater --> Name of the project, used to determine the name of the files generated by the program.
PRINT_LEVEL MEDIUM --> How much output is written out.
RUN_TYPE MD --> Type of run that to perform (e.g. MD, GeoOpt, MC).
&END --> End of section.

&FORCE_EVAL --> Parameters used to calculate energy and forces and to describe the system.
METHOD Quickstep --> Method used to compute forces. (Quickstep is for electronic structure methods, e.g. DFT).
&DFT --> Parameters for DFT.
BASIS_SET_FILE_NAME /work/lge/cp2kcuwater/BASIS_MOLOPT --> Path of basis set file.
POTENTIAL_FILE_NAME /work/lge/cp2kcuwater/POTENTIAL --> Path of pseudopotential file.
LSD --> or UKS, requests a spin-polarised calculation using alpha and beta orbtials, i.e. no spin restriction is applied.
CHARGE 2 --> Total charge of the system
MULTIPLICITY 2 --> Two times the total spin plus one.
&PRINT --> Printing options.
&LOCALIZATION --> Printing options related to the Wannier centers and properties computed with Wannier centers.
&WANNIER_CENTERS --> Controls the printing of the wannier functions.
IONS+CENTERS --> Prints out the wannier centers together with the particles.
&END
&END
&END
&MGRID --> Multigrid information
CUTOFF 280 --> Cutoff of the finest grid level in Ry.
&END MGRID
&QS --> Parameters needed to set up the Quickstep framework
EXTRAPOLATION PS --> Extrapolation strategy for the wavefunction during e.g. MD (PS is higher order extrapolation of the density matrix times the overlap matrix).
EXTRAPOLATION_ORDER 2 --> Order for the PS or ASPC extrapolation.
&END QS
&SCF --> Parameters for the SCF run.
CHOLESKY OFF --> If the cholesky method should be used for computing the inverse of S, and in this case calling which Lapack routines (OFF means do not use cholesky).
SCF_GUESS ATOMIC --> Initial guess for the wavefunction (ATOMIC generates an atomic density using the atomic code).
EPS_SCF 3.0E-6 --> Target accuracy for the scf convergence.
MAX_SCF 20 --> Maximum number of SCF iterations for one optimisation.
&OUTER_SCF --> Parameters controlling the outer SCF loop.
EPS_SCF 3.0E-6 --> Target gradient (not accuracy?) of the outer SCF variables. Notice that the EPS_SCF of the inner loop also determines the value that can be reached in the outer loop, typically EPS_SCF of the outer loop must be smaller than the EPS_SCF of the inner loop.
MAX_SCF 20 --> The maximum number of outer loops.
&END
&OT --> Various options for the orbtial transformation (OT) method.
MINIMIZER DIIS --> Minimiser to be used with the OT method (e.g. CG, SD).
PRECONDITIONER FULL_ALL --> Type of preconditioner to be used with all minimisation schemes (FULL_ALL is the most effective state selective preconditioner based on diagonalisation, requires the ENERGY_GAP parameters to be an underestimate of the HOMO-LUMO gap).
ENERGY_GAP 0.01 --> Should be an estimate for the HOMO-LUMO energy gap in a.u. and is used in preconditioning.
&END OT
&END SCF
&XC --> Parameters to calculate the xc (exchange-correlation) potential.
&XC_FUNCTIONAL BLYP --> The xc functional to be used.
&END XC_FUNCTIONAL
&END XC
&END DFT
&SUBSYS --> Defines a subsystem: coordinates, topology, molecules and cell.
&CELL --> Input parameters needed to set up the cell.
ABC 12.535 12.535 12.535 --> Specifies the lengths of the cell vectors A, B and C in Angstroms.
&END CELL
&KIND H --> Description of H atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q1 --> Name of pseudopotential.
&END
&KIND O --> Description of O atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q6 --> Name of pseudopotential.
&END
&KIND Cu --> Description of Cu atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q11 --> Name of pseudopotential.
&END
&COORD --> Coordinates of the atoms in xyz format, in Angstroms (by default).
.....
&END
&END SUBSYS
&END FORCE_EVAL
&MOTION --> Defines tools connected with motion of the nuclei.
&MD --> Parameters to perform an MD run.
ENSEMBLE NVT --> Ensemble to be used.
STEPS 2000 --> Number of MD steps
TIMESTEP 0.5 --> Length of integration step in fs.
&THERMOSTAT --> Specify the thermostat and related parameters.
TYPE NOSE --> Thermostat to be used (NOSE is for the Nose-Hoover thermostat).
&NOSE --> Parameters of the Nose-Hoover thermostat chain.
TIMECON 100 --> Time constant of the thermostat chain in fs.
&END NOSE
&END THERMOSTAT
TEMPERATURE 298 --> Temperature in K used to initialise the velocities with init and pos restart, and in the NPT/NVT simulations.
&END MD
&END MOTION
</pre>

Talk:Mod:Hunt Research Group/cp2k how

2013-03-01T13:05:39Z

Lge:

1. Website:
http://manual.cp2k.org/trunk/

2. Lecture notes:
http://www.cecam.org/workshop-4-529.html

3. Files you need:

Basis/Potential Files (can be downloaded together with the CP2K package):
<pre>
BASIS_SET
BASIS_MOLOPT
POTENTIAL
</pre>
runscript:
<pre>
runcp2k
runcp2krestart
</pre>
Input/output files (in directory on drobo: /Ling_project_2013/Rio-Tinto/cp2kcuwater/input_output_files/):
<pre>
cp2k_cuwater.inp
cp2k_cuwater.out
</pre>
4. Annotation of input files:

4.1 Example of [bmim]Cl:
<pre>
&GLOBAL --> Section that contains general information about the simulation and parameters for the whole program.
PROJECT bmimcl --> Name of the project, used to determine the name of the files generated by the program.
PRINT_LEVEL MEDIUM --> How much output is written out.
RUN_TYPE MD --> Type of run that to perform (e.g. MD, GeoOpt, MC).
&END --> End of section.

&FORCE_EVAL --> Parameters used to calculate energy and forces and to describe the system.
METHOD Quickstep --> Method used to compute forces. (Quickstep is for electronic structure methods, e.g. DFT).
&DFT --> Parameters for DFT.
BASIS_SET_FILE_NAME /work/lge/cp2ktest/BASIS_MOLOPT --> Path of basis set file.
POTENTIAL_FILE_NAME /work/lge/cp2ktest/POTENTIAL --> Path of pseudopotential file.
&XC --> Parameters to calculate the xc (exchange-correlation) potential.
&XC_FUNCTIONAL BLYP --> The xc functional to be used.
&END XC_FUNCTIONAL
&XC_GRID --> xc parameters used when calculating the xc on the grid.
XC_DERIV NN10_SMOOTH --> Method used to compute the derivatives.
XC_SMOOTH_RHO NN10 --> Density smoothing used for the xc calculation.
&END XC_GRID
&vdW_POTENTIAL --> Section for all additional dispersion corrections to the xc functionals.
DISPERSION_FUNCTIONAL PAIR_POTENTIAL --> (or POTENTIAL_TYPE, specifies the type of dispersion functional or potential to use).
&PAIR_POTENTIAL --> Info on the pair potential used to calculate dispersion.
TYPE DFTD3 --> Type of potential.
REFERENCE_FUNCTIONAL BLYP --> Use parameters for this specific density functional
&END PAIR_POTENTIAL
&END vdW_POTENTIAL
&END XC
&MGRID --> Multigrid information
CUTOFF 280 --> Cutoff of the finest grid level in Ry.
NGRIDS 5 --> Number of multigrids.
&END
&SCF --> Parameters for the SCF run.
SCF_GUESS ATOMIC --> Initial guess for the wavefunction (ATOMIC generates an atomic density using the atomic code).
MAX_SCF 300 --> Maximum number of SCF iterations for one optimisation.
&OT --> Various options for the orbtial transformation (OT) method.
PRECONDITIONER FULL_SINGLE_INVERSE --> Type of preconditioner to be used with all minimisation schemes (FULL_SINGLE_INVERSE based on H-eS cholesky inversion).
MINIMIZER DIIS --> Minimiser to be used with the OT method (e.g. CG, SD).
&END OT
&END SCF
&END SECTION DFT
&SUBSYS --> Defines a subsystem: coordinates, topology, molecules and cell.
&CELL --> Input parameters needed to set up the cell.
ABC 19.522 19.522 19.522 --> Specifies the lengths of the cell vectors A, B and C in Angstroms.
&END CELL
&KIND H --> Description of H atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q1 --> Name of pseudopotential.
&END
&KIND C --> Description of C atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q4 --> Name of pseudopotential.
&END
&KIND N --> Description of N atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q5 --> Name of pseudopotential.
&END
&KIND CL --> Description of Cl atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q7 --> Name of pseudopotential.
&END
&COORD --> Coordinates of the atoms in xyz format, in Angstroms (by default).
.....
&END
&END SUBSYS
&END FORCE_EVAL
&MOTION --> Defines tools connected with motion of the nuclei.
&MD --> Parameters to perform an MD run.
ENSEMBLE NVT --> Ensemble to be used.
STEPS 2000 --> Number of MD steps
TIMESTEP 0.5 --> Length of integration step in fs.
&THERMOSTAT --> Specify the thermostat and related parameters.
TYPE NOSE --> Thermostat to be used (NOSE is for the Nose-Hoover thermostat).
&NOSE --> Parameters of the Nose-Hoover thermostat chain.
TIMECON 100 --> Time constant of the thermostat chain in fs.
&END NOSE
&END THERMOSTAT
TEMPERATURE 353 --> Temperature in K used to initialise the velocities with init and pos restart, and in the NPT/NVT simulations.
&END MD
&END MOTION
</pre>
4.2 Example of Cu water:

&GLOBAL --> Section that contains general information about the simulation and parameters for the whole program.
PROJECT cuwater --> Name of the project, used to determine the name of the files generated by the program.
PRINT_LEVEL MEDIUM --> How much output is written out.
RUN_TYPE MD --> Type of run that to perform (e.g. MD, GeoOpt, MC).
&END --> End of section.

&FORCE_EVAL --> Parameters used to calculate energy and forces and to describe the system.
METHOD Quickstep --> Method used to compute forces. (Quickstep is for electronic structure methods, e.g. DFT).
&DFT --> Parameters for DFT.
BASIS_SET_FILE_NAME /work/lge/cp2kcuwater/BASIS_MOLOPT --> Path of basis set file.
POTENTIAL_FILE_NAME /work/lge/cp2kcuwater/POTENTIAL --> Path of pseudopotential file.
LSD --> or UKS, requests a spin-polarised calculation using alpha and beta orbtials, i.e. no spin restriction is applied.
CHARGE 2 --> Total charge of the system
MULTIPLICITY 2 --> Two times the total spin plus one.
&PRINT --> Printing options.
&LOCALIZATION --> Printing options related to the Wannier centers and properties computed with Wannier centers.
&WANNIER_CENTERS --> Controls the printing of the wannier functions.
IONS+CENTERS --> Prints out the wannier centers together with the particles.
&END
&END
&END
&MGRID --> Multigrid information
CUTOFF 280 --> Cutoff of the finest grid level in Ry.
&END MGRID
&QS --> Parameters needed to set up the Quickstep framework
EXTRAPOLATION PS --> Extrapolation strategy for the wavefunction during e.g. MD (PS is higher order extrapolation of the density matrix times the overlap matrix).
EXTRAPOLATION_ORDER 2 --> Order for the PS or ASPC extrapolation.
&END QS
&SCF --> Parameters for the SCF run.
CHOLESKY OFF --> If the cholesky method should be used for computing the inverse of S, and in this case calling which Lapack routines (OFF means do not use cholesky).
SCF_GUESS ATOMIC --> Initial guess for the wavefunction (ATOMIC generates an atomic density using the atomic code).
EPS_SCF 3.0E-6 --> Target accuracy for the scf convergence.
MAX_SCF 20 --> Maximum number of SCF iterations for one optimisation.
&OUTER_SCF --> Parameters controlling the outer SCF loop.
EPS_SCF 3.0E-6 --> Target gradient (not accuracy?) of the outer SCF variables. Notice that the EPS_SCF of the inner loop also determines the value that can be reached in the outer loop, typically EPS_SCF of the outer loop must be smaller than the EPS_SCF of the inner loop.
MAX_SCF 20 --> The maximum number of outer loops.
&END
&OT --> Various options for the orbtial transformation (OT) method.
MINIMIZER DIIS --> Minimiser to be used with the OT method (e.g. CG, SD).
PRECONDITIONER FULL_ALL --> Type of preconditioner to be used with all minimisation schemes (FULL_ALL is the most effective state selective preconditioner based on diagonalisation, requires the ENERGY_GAP parameters to be an underestimate of the HOMO-LUMO gap).
ENERGY_GAP 0.01 --> Should be an estimate for the HOMO-LUMO energy gap in a.u. and is used in preconditioning.
&END OT
&END SCF
&XC --> Parameters to calculate the xc (exchange-correlation) potential.
&XC_FUNCTIONAL BLYP --> The xc functional to be used.
&END XC_FUNCTIONAL
&END XC
&END DFT
&SUBSYS --> Defines a subsystem: coordinates, topology, molecules and cell.
&CELL --> Input parameters needed to set up the cell.
ABC 12.535 12.535 12.535 --> Specifies the lengths of the cell vectors A, B and C in Angstroms.
&END CELL
&KIND H --> Description of H atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q1 --> Name of pseudopotential.
&END
&KIND O --> Description of O atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q6 --> Name of pseudopotential.
&END
&KIND Cu --> Description of Cu atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q11 --> Name of pseudopotential.
&END
&COORD --> Coordinates of the atoms in xyz format, in Angstroms (by default).
.....
&END
&END SUBSYS
&END FORCE_EVAL
&MOTION --> Defines tools connected with motion of the nuclei.
&MD --> Parameters to perform an MD run.
ENSEMBLE NVT --> Ensemble to be used.
STEPS 2000 --> Number of MD steps
TIMESTEP 0.5 --> Length of integration step in fs.
&THERMOSTAT --> Specify the thermostat and related parameters.
TYPE NOSE --> Thermostat to be used (NOSE is for the Nose-Hoover thermostat).
&NOSE --> Parameters of the Nose-Hoover thermostat chain.
TIMECON 100 --> Time constant of the thermostat chain in fs.
&END NOSE
&END THERMOSTAT
TEMPERATURE 298 --> Temperature in K used to initialise the velocities with init and pos restart, and in the NPT/NVT simulations.
&END MD
&END MOTION

Talk:Mod:Hunt Research Group/cp2k how

2013-03-01T13:04:47Z

Lge:

1. Website:
http://manual.cp2k.org/trunk/

2. Lecture notes:
http://www.cecam.org/workshop-4-529.html

3. Files you need:

Basis/Potential Files (can be downloaded together with the CP2K package):
<pre>
BASIS_SET
BASIS_MOLOPT
POTENTIAL
</pre>
runscript:
<pre>
runcp2k
runcp2krestart
</pre>
Input/output files (in directory on drobo: /Ling_project_2013/Rio-Tinto/cp2kcuwater/input_output_files/):
<pre>
cp2k_cuwater.inp
cp2k_cuwater.out
</pre>
4. Annotation of input files:

4.1 Example of [bmim]Cl:
<pre>
&GLOBAL --> Section that contains general information about the simulation and parameters for the whole program.
PROJECT bmimcl --> Name of the project, used to determine the name of the files generated by the program.
PRINT_LEVEL MEDIUM --> How much output is written out.
RUN_TYPE MD --> Type of run that to perform (e.g. MD, GeoOpt, MC).
&END --> End of section.

&FORCE_EVAL --> Parameters used to calculate energy and forces and to describe the system.
METHOD Quickstep --> Method used to compute forces. (Quickstep is for electronic structure methods, e.g. DFT).
&DFT --> Parameters for DFT.
BASIS_SET_FILE_NAME /work/lge/cp2ktest/BASIS_MOLOPT --> Path of basis set file.
POTENTIAL_FILE_NAME /work/lge/cp2ktest/POTENTIAL --> Path of pseudopotential file.
&XC --> Parameters to calculate the xc (exchange-correlation) potential.
&XC_FUNCTIONAL BLYP --> The xc functional to be used.
&END XC_FUNCTIONAL
&XC_GRID --> xc parameters used when calculating the xc on the grid.
XC_DERIV NN10_SMOOTH --> Method used to compute the derivatives.
XC_SMOOTH_RHO NN10 --> Density smoothing used for the xc calculation.
&END XC_GRID
&vdW_POTENTIAL --> Section for all additional dispersion corrections to the xc functionals.
DISPERSION_FUNCTIONAL PAIR_POTENTIAL --> (or POTENTIAL_TYPE, specifies the type of dispersion functional or potential to use).
&PAIR_POTENTIAL --> Info on the pair potential used to calculate dispersion.
TYPE DFTD2 --> Type of potential.
REFERENCE_FUNCTIONAL BLYP --> Use parameters for this specific density functional
&END PAIR_POTENTIAL
&END vdW_POTENTIAL
&END XC
&MGRID --> Multigrid information
CUTOFF 280 --> Cutoff of the finest grid level in Ry.
NGRIDS 5 --> Number of multigrids.
&END
&SCF --> Parameters for the SCF run.
SCF_GUESS ATOMIC --> Initial guess for the wavefunction (ATOMIC generates an atomic density using the atomic code).
MAX_SCF 300 --> Maximum number of SCF iterations for one optimisation.
&OT --> Various options for the orbtial transformation (OT) method.
PRECONDITIONER FULL_SINGLE_INVERSE --> Type of preconditioner to be used with all minimisation schemes (FULL_SINGLE_INVERSE based on H-eS cholesky inversion).
MINIMIZER DIIS --> Minimiser to be used with the OT method (e.g. CG, SD).
&END OT
&END SCF
&END SECTION DFT
&SUBSYS --> Defines a subsystem: coordinates, topology, molecules and cell.
&CELL --> Input parameters needed to set up the cell.
ABC 19.522 19.522 19.522 --> Specifies the lengths of the cell vectors A, B and C in Angstroms.
&END CELL
&KIND H --> Description of H atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q1 --> Name of pseudopotential.
&END
&KIND C --> Description of C atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q4 --> Name of pseudopotential.
&END
&KIND N --> Description of N atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q5 --> Name of pseudopotential.
&END
&KIND CL --> Description of Cl atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q7 --> Name of pseudopotential.
&END
&COORD --> Coordinates of the atoms in xyz format, in Angstroms (by default).
.....
&END
&END SUBSYS
&END FORCE_EVAL
&MOTION --> Defines tools connected with motion of the nuclei.
&MD --> Parameters to perform an MD run.
ENSEMBLE NVT --> Ensemble to be used.
STEPS 2000 --> Number of MD steps
TIMESTEP 0.5 --> Length of integration step in fs.
&THERMOSTAT --> Specify the thermostat and related parameters.
TYPE NOSE --> Thermostat to be used (NOSE is for the Nose-Hoover thermostat).
&NOSE --> Parameters of the Nose-Hoover thermostat chain.
TIMECON 100 --> Time constant of the thermostat chain in fs.
&END NOSE
&END THERMOSTAT
TEMPERATURE 353 --> Temperature in K used to initialise the velocities with init and pos restart, and in the NPT/NVT simulations.
&END MD
&END MOTION
</pre>
4.2 Example of Cu water:

&GLOBAL --> Section that contains general information about the simulation and parameters for the whole program.
PROJECT cuwater --> Name of the project, used to determine the name of the files generated by the program.
PRINT_LEVEL MEDIUM --> How much output is written out.
RUN_TYPE MD --> Type of run that to perform (e.g. MD, GeoOpt, MC).
&END --> End of section.

&FORCE_EVAL --> Parameters used to calculate energy and forces and to describe the system.
METHOD Quickstep --> Method used to compute forces. (Quickstep is for electronic structure methods, e.g. DFT).
&DFT --> Parameters for DFT.
BASIS_SET_FILE_NAME /work/lge/cp2kcuwater/BASIS_MOLOPT --> Path of basis set file.
POTENTIAL_FILE_NAME /work/lge/cp2kcuwater/POTENTIAL --> Path of pseudopotential file.
LSD --> or UKS, requests a spin-polarised calculation using alpha and beta orbtials, i.e. no spin restriction is applied.
CHARGE 2 --> Total charge of the system
MULTIPLICITY 2 --> Two times the total spin plus one.
&PRINT --> Printing options.
&LOCALIZATION --> Printing options related to the Wannier centers and properties computed with Wannier centers.
&WANNIER_CENTERS --> Controls the printing of the wannier functions.
IONS+CENTERS --> Prints out the wannier centers together with the particles.
&END
&END
&END
&MGRID --> Multigrid information
CUTOFF 280 --> Cutoff of the finest grid level in Ry.
&END MGRID
&QS --> Parameters needed to set up the Quickstep framework
EXTRAPOLATION PS --> Extrapolation strategy for the wavefunction during e.g. MD (PS is higher order extrapolation of the density matrix times the overlap matrix).
EXTRAPOLATION_ORDER 2 --> Order for the PS or ASPC extrapolation.
&END QS
&SCF --> Parameters for the SCF run.
CHOLESKY OFF --> If the cholesky method should be used for computing the inverse of S, and in this case calling which Lapack routines (OFF means do not use cholesky).
SCF_GUESS ATOMIC --> Initial guess for the wavefunction (ATOMIC generates an atomic density using the atomic code).
EPS_SCF 3.0E-6 --> Target accuracy for the scf convergence.
MAX_SCF 20 --> Maximum number of SCF iterations for one optimisation.
&OUTER_SCF --> Parameters controlling the outer SCF loop.
EPS_SCF 3.0E-6 --> Target gradient (not accuracy?) of the outer SCF variables. Notice that the EPS_SCF of the inner loop also determines the value that can be reached in the outer loop, typically EPS_SCF of the outer loop must be smaller than the EPS_SCF of the inner loop.
MAX_SCF 20 --> The maximum number of outer loops.
&END
&OT --> Various options for the orbtial transformation (OT) method.
MINIMIZER DIIS --> Minimiser to be used with the OT method (e.g. CG, SD).
PRECONDITIONER FULL_ALL --> Type of preconditioner to be used with all minimisation schemes (FULL_ALL is the most effective state selective preconditioner based on diagonalisation, requires the ENERGY_GAP parameters to be an underestimate of the HOMO-LUMO gap).
ENERGY_GAP 0.01 --> Should be an estimate for the HOMO-LUMO energy gap in a.u. and is used in preconditioning.
&END OT
&END SCF
&XC --> Parameters to calculate the xc (exchange-correlation) potential.
&XC_FUNCTIONAL BLYP --> The xc functional to be used.
&END XC_FUNCTIONAL
&END XC
&END DFT
&SUBSYS --> Defines a subsystem: coordinates, topology, molecules and cell.
&CELL --> Input parameters needed to set up the cell.
ABC 12.535 12.535 12.535 --> Specifies the lengths of the cell vectors A, B and C in Angstroms.
&END CELL
&KIND H --> Description of H atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q1 --> Name of pseudopotential.
&END
&KIND O --> Description of O atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q6 --> Name of pseudopotential.
&END
&KIND Cu --> Description of Cu atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q11 --> Name of pseudopotential.
&END
&COORD --> Coordinates of the atoms in xyz format, in Angstroms (by default).
.....
&END
&END SUBSYS
&END FORCE_EVAL
&MOTION --> Defines tools connected with motion of the nuclei.
&MD --> Parameters to perform an MD run.
ENSEMBLE NVT --> Ensemble to be used.
STEPS 2000 --> Number of MD steps
TIMESTEP 0.5 --> Length of integration step in fs.
&THERMOSTAT --> Specify the thermostat and related parameters.
TYPE NOSE --> Thermostat to be used (NOSE is for the Nose-Hoover thermostat).
&NOSE --> Parameters of the Nose-Hoover thermostat chain.
TIMECON 100 --> Time constant of the thermostat chain in fs.
&END NOSE
&END THERMOSTAT
TEMPERATURE 298 --> Temperature in K used to initialise the velocities with init and pos restart, and in the NPT/NVT simulations.
&END MD
&END MOTION

Talk:Mod:Hunt Research Group/cp2k how

2013-03-01T13:04:21Z

Lge:

1. Website:
http://manual.cp2k.org/trunk/

2. Lecture notes:
http://www.cecam.org/workshop-4-529.html

3. Files you need:

Basis/Potential Files (can be downloaded together with the CP2K package):
<pre>
BASIS_SET
BASIS_MOLOPT
POTENTIAL
</pre>
runscript:
<pre>

runcp2k
runcp2krestart
</pre>
Input/output files (in directory on drobo: /Ling_project_2013/Rio-Tinto/cp2kcuwater/input_output_files/):
<pre>cp2k_cuwater.inp
</pre> cp2k_cuwater.out

4. Annotation of input files:

4.1 Example of [bmim]Cl:
<pre>
&GLOBAL --> Section that contains general information about the simulation and parameters for the whole program.
PROJECT bmimcl --> Name of the project, used to determine the name of the files generated by the program.
PRINT_LEVEL MEDIUM --> How much output is written out.
RUN_TYPE MD --> Type of run that to perform (e.g. MD, GeoOpt, MC).
&END --> End of section.

&FORCE_EVAL --> Parameters used to calculate energy and forces and to describe the system.
METHOD Quickstep --> Method used to compute forces. (Quickstep is for electronic structure methods, e.g. DFT).
&DFT --> Parameters for DFT.
BASIS_SET_FILE_NAME /work/lge/cp2ktest/BASIS_MOLOPT --> Path of basis set file.
POTENTIAL_FILE_NAME /work/lge/cp2ktest/POTENTIAL --> Path of pseudopotential file.
&XC --> Parameters to calculate the xc (exchange-correlation) potential.
&XC_FUNCTIONAL BLYP --> The xc functional to be used.
&END XC_FUNCTIONAL
&XC_GRID --> xc parameters used when calculating the xc on the grid.
XC_DERIV NN10_SMOOTH --> Method used to compute the derivatives.
XC_SMOOTH_RHO NN10 --> Density smoothing used for the xc calculation.
&END XC_GRID
&vdW_POTENTIAL --> Section for all additional dispersion corrections to the xc functionals.
DISPERSION_FUNCTIONAL PAIR_POTENTIAL --> (or POTENTIAL_TYPE, specifies the type of dispersion functional or potential to use).
&PAIR_POTENTIAL --> Info on the pair potential used to calculate dispersion.
TYPE DFTD2 --> Type of potential.
REFERENCE_FUNCTIONAL BLYP --> Use parameters for this specific density functional
&END PAIR_POTENTIAL
&END vdW_POTENTIAL
&END XC
&MGRID --> Multigrid information
CUTOFF 280 --> Cutoff of the finest grid level in Ry.
NGRIDS 5 --> Number of multigrids.
&END
&SCF --> Parameters for the SCF run.
SCF_GUESS ATOMIC --> Initial guess for the wavefunction (ATOMIC generates an atomic density using the atomic code).
MAX_SCF 300 --> Maximum number of SCF iterations for one optimisation.
&OT --> Various options for the orbtial transformation (OT) method.
PRECONDITIONER FULL_SINGLE_INVERSE --> Type of preconditioner to be used with all minimisation schemes (FULL_SINGLE_INVERSE based on H-eS cholesky inversion).
MINIMIZER DIIS --> Minimiser to be used with the OT method (e.g. CG, SD).
&END OT
&END SCF
&END SECTION DFT
&SUBSYS --> Defines a subsystem: coordinates, topology, molecules and cell.
&CELL --> Input parameters needed to set up the cell.
ABC 19.522 19.522 19.522 --> Specifies the lengths of the cell vectors A, B and C in Angstroms.
&END CELL
&KIND H --> Description of H atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q1 --> Name of pseudopotential.
&END
&KIND C --> Description of C atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q4 --> Name of pseudopotential.
&END
&KIND N --> Description of N atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q5 --> Name of pseudopotential.
&END
&KIND CL --> Description of Cl atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q7 --> Name of pseudopotential.
&END
&COORD --> Coordinates of the atoms in xyz format, in Angstroms (by default).
.....
&END
&END SUBSYS
&END FORCE_EVAL
&MOTION --> Defines tools connected with motion of the nuclei.
&MD --> Parameters to perform an MD run.
ENSEMBLE NVT --> Ensemble to be used.
STEPS 2000 --> Number of MD steps
TIMESTEP 0.5 --> Length of integration step in fs.
&THERMOSTAT --> Specify the thermostat and related parameters.
TYPE NOSE --> Thermostat to be used (NOSE is for the Nose-Hoover thermostat).
&NOSE --> Parameters of the Nose-Hoover thermostat chain.
TIMECON 100 --> Time constant of the thermostat chain in fs.
&END NOSE
&END THERMOSTAT
TEMPERATURE 353 --> Temperature in K used to initialise the velocities with init and pos restart, and in the NPT/NVT simulations.
&END MD
&END MOTION
</pre>
4.2 Example of Cu water:

&GLOBAL --> Section that contains general information about the simulation and parameters for the whole program.
PROJECT cuwater --> Name of the project, used to determine the name of the files generated by the program.
PRINT_LEVEL MEDIUM --> How much output is written out.
RUN_TYPE MD --> Type of run that to perform (e.g. MD, GeoOpt, MC).
&END --> End of section.

&FORCE_EVAL --> Parameters used to calculate energy and forces and to describe the system.
METHOD Quickstep --> Method used to compute forces. (Quickstep is for electronic structure methods, e.g. DFT).
&DFT --> Parameters for DFT.
BASIS_SET_FILE_NAME /work/lge/cp2kcuwater/BASIS_MOLOPT --> Path of basis set file.
POTENTIAL_FILE_NAME /work/lge/cp2kcuwater/POTENTIAL --> Path of pseudopotential file.
LSD --> or UKS, requests a spin-polarised calculation using alpha and beta orbtials, i.e. no spin restriction is applied.
CHARGE 2 --> Total charge of the system
MULTIPLICITY 2 --> Two times the total spin plus one.
&PRINT --> Printing options.
&LOCALIZATION --> Printing options related to the Wannier centers and properties computed with Wannier centers.
&WANNIER_CENTERS --> Controls the printing of the wannier functions.
IONS+CENTERS --> Prints out the wannier centers together with the particles.
&END
&END
&END
&MGRID --> Multigrid information
CUTOFF 280 --> Cutoff of the finest grid level in Ry.
&END MGRID
&QS --> Parameters needed to set up the Quickstep framework
EXTRAPOLATION PS --> Extrapolation strategy for the wavefunction during e.g. MD (PS is higher order extrapolation of the density matrix times the overlap matrix).
EXTRAPOLATION_ORDER 2 --> Order for the PS or ASPC extrapolation.
&END QS
&SCF --> Parameters for the SCF run.
CHOLESKY OFF --> If the cholesky method should be used for computing the inverse of S, and in this case calling which Lapack routines (OFF means do not use cholesky).
SCF_GUESS ATOMIC --> Initial guess for the wavefunction (ATOMIC generates an atomic density using the atomic code).
EPS_SCF 3.0E-6 --> Target accuracy for the scf convergence.
MAX_SCF 20 --> Maximum number of SCF iterations for one optimisation.
&OUTER_SCF --> Parameters controlling the outer SCF loop.
EPS_SCF 3.0E-6 --> Target gradient (not accuracy?) of the outer SCF variables. Notice that the EPS_SCF of the inner loop also determines the value that can be reached in the outer loop, typically EPS_SCF of the outer loop must be smaller than the EPS_SCF of the inner loop.
MAX_SCF 20 --> The maximum number of outer loops.
&END
&OT --> Various options for the orbtial transformation (OT) method.
MINIMIZER DIIS --> Minimiser to be used with the OT method (e.g. CG, SD).
PRECONDITIONER FULL_ALL --> Type of preconditioner to be used with all minimisation schemes (FULL_ALL is the most effective state selective preconditioner based on diagonalisation, requires the ENERGY_GAP parameters to be an underestimate of the HOMO-LUMO gap).
ENERGY_GAP 0.01 --> Should be an estimate for the HOMO-LUMO energy gap in a.u. and is used in preconditioning.
&END OT
&END SCF
&XC --> Parameters to calculate the xc (exchange-correlation) potential.
&XC_FUNCTIONAL BLYP --> The xc functional to be used.
&END XC_FUNCTIONAL
&END XC
&END DFT
&SUBSYS --> Defines a subsystem: coordinates, topology, molecules and cell.
&CELL --> Input parameters needed to set up the cell.
ABC 12.535 12.535 12.535 --> Specifies the lengths of the cell vectors A, B and C in Angstroms.
&END CELL
&KIND H --> Description of H atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q1 --> Name of pseudopotential.
&END
&KIND O --> Description of O atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q6 --> Name of pseudopotential.
&END
&KIND Cu --> Description of Cu atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q11 --> Name of pseudopotential.
&END
&COORD --> Coordinates of the atoms in xyz format, in Angstroms (by default).
.....
&END
&END SUBSYS
&END FORCE_EVAL
&MOTION --> Defines tools connected with motion of the nuclei.
&MD --> Parameters to perform an MD run.
ENSEMBLE NVT --> Ensemble to be used.
STEPS 2000 --> Number of MD steps
TIMESTEP 0.5 --> Length of integration step in fs.
&THERMOSTAT --> Specify the thermostat and related parameters.
TYPE NOSE --> Thermostat to be used (NOSE is for the Nose-Hoover thermostat).
&NOSE --> Parameters of the Nose-Hoover thermostat chain.
TIMECON 100 --> Time constant of the thermostat chain in fs.
&END NOSE
&END THERMOSTAT
TEMPERATURE 298 --> Temperature in K used to initialise the velocities with init and pos restart, and in the NPT/NVT simulations.
&END MD
&END MOTION

Talk:Mod:Hunt Research Group/cpmd water

2013-03-01T12:47:52Z

Lge:

Car-Parrinello Molecular Dynamics Simulation of Aqueous Solutions

1. Introduction

1.1 Aqueous solutions

In this lab you are going to run CPMD calculations of systems containing water and chloride. The following paragraphs describe why these systems are interesting to study.

Solvation of the chloride anion in water solution has been the subject of a substantial amount of experimental and theoretical work, in view of the central importance of chloride solutions in biochemical and metabolic processes, geology, atmospheric chemistry, and the chemical industry. Indeed, it has been discovered that airborne aqueous sea-salt aerosols serve as a global source of molecular chlorine and bromine, both in the polluted and in the remote lower marine troposphere. A variety of experimental methods have been used to investigate the hydration structure of chloride ions in water, including neutron and X-ray diffraction techniques, X-ray absorption spectroscopy (XAS) and femtosecond mid-infrared nonlinear spectroscopy. Despite these efforts, a complete microscopic model of the hydration shell structure of aqueous Cl- and of its room temperature dynamics is still being debated.

Difficulties in determining the structure of the solvation environment arise because of the comparable magnitudes of the water-Cl- and water-water interaction energies. Established results from the literature, both experimental and theoretical, reveal a rather inhomogeneous picture of the hydrated ion solvation shell structure. Vibrational spectroscopy experiments indicate that a chloride ion is asymmetrically solvated in clusters containing up to five water molecules. This contrasts with older and less direct experiments based on mass spectroscopy and photoelectron spectroscopy from which a symmetrical solvent cage around the anion was inferred. Experimental measurements such as photoelectron spectroscopy, IR spectroscopy and a combined technique of XAS (extended X-ray absorption fine structure, EXAFS and X-ray absorption near-edge structure, XANES) yield coordination numbers that are significantly scattered, ranging from 3 to 8. The first peak of the Cl-O radial distribution function (RDF) is measured to be in the range of 3.10-3.36 A.

Uncertainty in the coordination number is also evinced from theoretical studies, with variations between 5.1 and 8.4 depending on the simulation techniques adopted. Classical molecular dynamics (MD) simulations have been found to depend strongly on the anion-water and water-water potentials used. On the other hand, the use of different parametrized potentials, i.e. with and without a treatment of molecular polarizability, gave different structural properties. Quantum mechanics / molecular mechanics (QM/MM) simulations of Cl− in water indicate that the hydration structure of the an- ion has considerable flexibility in consequence to the weakness of Cl--water interactions. This leads to a competition between solvation of the ion and hydrogen bonding among water molecules. The QM/MM results clearly indicate the importance of QM treatment in order to correctly describe such a delicate balance between Cl--water and water-water interactions.

Reference: Tongraar, A.; T-Thienprasert, J.; Rujirawat, S.; Limpijumnong, S. Phys. Chem. Chem. Phys. 2010, 12, 10876.

1.2 Car-Parrinello/Born-Oppenheimer molecular dynamics

The aim of this tutorial is to help you getting started using the CPMD program. CPMD is an ab initio electronic structure and molecular dynamics (MD) program using a plane wave/pseudopotential implementation of density functional theory (DFT). It is mainly targeted at Car-Parrinello MD simulations, but also supports geometry optimisations, Born-Oppenheimer MD, path integral MD, response functions, excited states and calculations of some electronic properties. For further information you may want to take a look at the CPMD consortium homepage at www.cpmd.org.

Born-Oppenheimer (BO) MD: at each step of atomic MD, one solves the DFT SCF problem for a fixed atomic configuration, computes the wavefunction, and from it the (quantum mechanical) forces acting on the nuclei. This allows it to propagate the atoms classically to the next configuration. (In simple words, one computes energy and forces, move the atoms, re-compute energy and forces for the new configuration, move the atoms, and so on.)

Car-Parrinello: One propagates simultaneously a set of atoms and a fictitious set of electrons. From the fictitious set of electrons, one can estimate the forces on the atoms and move the atoms. Atoms and fictitious electrons have to be independent, and their dynamics is described using a generalised Lagrangian formalism, rather than simply propagating the atoms using Newton's equations like in Born-Oppenheimer MD. In the CPMD manual, it is written:

“The basic idea of the Car-Parrinello approach can be viewed to exploit the time-scale separation of fast electronic and slow nuclear motion by transforming that into classical-mechanical adiabatic energy-scale separation in the framework of dynamical systems theory. In order to achieve this goal the two-component quantum / classical problem is mapped onto a two-component purely classical problem with two separate energy scales at the expense of loosing the explicit time-dependence of the quantum subsystem dynamics.”

Born-Oppenheimer MD is easier to implement in practice, but slower. Also it requires a very well converged calculation of the forces at each step of dynamics. The Car-Parrinello only requires a very accurate ground state at the first step. The rest of the dynamics sustains itself, provided it is carried out in the right way.

If you would like to know more about the theoretical background of CPMD or BOMD, please read CPMD manual Sections 6.6 and 6.7.

2. Code Running Environment

2.1 Before running the job

Before you run CPMD it is a good idea to copy all you need in your local directory.

- Copy the folder lab from the usb disk to your laptop.

- open the terminal application

- open two windows, one will be for your local mac and the other for the hpc cluster

- on one of them login to the hpc cluster by typing ssh yourname@login.cx1.hpc.ic.ac.uk

- the cluster has two key directories /WORK/yourname and /HOME/yourname do all the calculations from the WORK/yourname directory, from now on this directory will be referred to simply as work

- cd to your work directory and make a new directory called liquids, cd into the new directory, this is where you will run all your jobs from

- copy the file from your desktop to hpc:

scp filename yourname@login.cx1.hpc.ic.ac.uk:/work/yourname/foldername/.

- unzip the tar file

tar -xvf filename.tar

2.2 How to run the job

In the directory cpmd you should have two subdirectories: clw1 and clw63.

To run CPMD type qsub runcpmd_wf (or other run scripts depending on the type of calculation such as runcpmd_md) in the clw1 or clw63 directory.

2.3 Using VMD to analyse results

For visualisation of the results you may want to take a look at the tutorial on visualising results from CPMD with the VMD program under www.theochem.ruhr-uni-bochum.de/go/cpmd-vmd.html

3. CPMD

3.1 Theoretical background

3.1.1 Pseudopotentials (read CPMD manual section 4.2)

3.1.2 Kohn-Sham orbitals, Wannier orbitals and Effective molecular orbitals

The EMO method for analysing the electronic structure of solutes and solvents starts by considering the Kohn-Sham Hamiltonian and energy eigenvalues obtained from the ab initio molecular dynamics. A band structure similar to that obtained for solid state systems emerges. While the Kohn-Sham Hamiltonian is diagonal, and the Kohn-Sham orbital energies are uniquely defined, the Kohn-Sham orbitals are delocalised Bloch states which extend over all space and the molecular picture is lost, as shown in Figure 1 (a). This makes it very difficult to analyse interactions between an ion and the solvating water molecules. Maximally localized Wannier orbitals are local to atomic centers. However, the Wannier Hamiltonian is not diagonal and thus there is no unique energy eigenvalue that can be associated with each orbital, as shown in Figure 1 (c). An intermediate representation where orbitals are local to a molecule, but are delocalised within the molecule has been developed. The EMOs are obtained by assigning Wannier orbitals to a specific molecule, and block-diagonalising the Wannier Hamiltonian within the molecular subspace, as shown in Figure 1 (b). This analysis has been successfully applied to pure liquid water. An isolated water molecule has C2v symmetry and valence MOs 1a1, 1b2, 2a1 and 1b1. A liquid environment is disordered and there is no symmetry. However, Figure 1 (b) shows that the EMOs strongly resemble the standard MOs for a single water molecule in vacuum. This close resemblance is by no means predetermined and is a validation of the EMO method. For clarity, we will continue to use the isolated atomic or molecular symmetry labels when we refer to the individual atomic orbitals, MOs and bands in the aqueous system.

3.2 Functional

We will use a gradient corrected functional (BLYP) instead of LDA throughout the tutorial as this combination of generalized gradient approximations to exchange and correlation has been shown to give good results for the structure and dynamics of water.

Figure 1 Wavefunction diagrams from a CPMD simulation of pure liquid water related to graphical representations of the respective Hamiltonian matrices: (a) Kohn-Sham Hamiltonian, (b) EMO Hamiltonian and (c) Wannier Hamiltonian.

3.3 Generating input files and understanding output files

The first example will demonstrate some of the basic steps of performing a CPMD calculation with a very simple system: 1 water molecule+Cl-, and a very simple task: calculate the electronic structure. We will use that as an example to have a look at the input file format, and how to read the output.

- emacs filename

- and then look inside and follow the instructions below

3.3.1 Wavefunction optimisation

(a) Input File format

For nearly all CPMD calculations, you first have to optimise the wavefunction of your system, and use that as a base for further calculations. For our first calculation you’ll need the input file inp.clw_blyp_wf and the pseudopotential files H_MT_BLYP.psp, O_MT_BLYP.psp, Cl_MT_BLYP.psp.

Now let’s have a look at the input file. The input file is organised in sections which start with &NAME and end with &END. Everything outside those sections is ignored. All keywords have to be in upper case or else they will be ignored. The sequence of the sections does not matter, nor does the order of keywords. A minimal input file must have a &CPMD, &SYSTEM and an &ATOMS section.

<pre>
&CPMD
OPTIMIZE WAVEFUNCTION
CONVERGENCE ORBITALS
1.0d-7
&END
</pre>

This first part of the &CPMD section instructs the program to do a wavefunction optimization (i.e. a single point calculation) with a tight convergence criterion (the default is 1.0d-5).

Exercise: look up in the CPMD manual about the usage of the keywords ODIIS, STORE, TIMESTEP, EMASS, ISOLATED MOLECULE.

<pre>
&DFT
FUNCTIONAL BLYP
GC-CUTOFF
0.1D-06
&END
</pre>

The &DFT section is used to select the density functional and related parameters. In this case we go with the BLYP functional.
<pre>
&SYSTEM
ANGSTROM
SYMMETRY
0
CELL
11.800 1.0 1.0 0 0 0
CUTOFF
70.0
CHARGE
-1.0
&END
</pre>
The &SYSTEM section contains various parameters related to the simulation cell and the representation of the electronic structure. The keywords SYMMETRY, CELL and CUTOFF are required and define the (periodic) symmetry, shape, and size of the simulation cell, as well as the plane wave cutoff (i.e. the size of the basis set). The keyword Angstrom additionally indicates that all lengths and coordinates are given in angstrom (not in a.u.).

Exercise: look up in the CPMD manual about the usage of the keyword CHARGE.

Finally the &ATOMS section is needed to specify the atom coordinates and the pseudopotentials, that are used to represent them. The detailed syntax of the pseudopotential specification is a bit complicated and will not be needed nor discussed here. If you want to know more, please have a look at the Further details of the Input section of the CPMD manual (P222).

- To run, type: qsub runcpmd_wf,

The code will generate the following output files once the calculation is completed after a few minutes: log.clw_blyp_wf, GOMETRY., RESTART.. The purpose of the wavefunction optimisation is to generate the RESTART. file which is needed for further calculations.

(b) Output File Format

To start the calculation, which should be completed in less than a minute once the job starts running. The main output of the CPMD program is now in the file log.clw_blyp_wf. Let’s have a closer look at the contents of this file.
<pre>
PROGRAM CPMD STARTED AT: Thu Jan 20 16:23:24 2011
SETCNST| USING: CODATA 2006 UNITS
THE INPUT FILE IS: /work/lge/wannier/test/inp.clw_blyp_wf
THIS JOB RUNS ON: cx1-50-2-1.cx1.hpc.ic.ac.uk
THE CURRENT DIRECTORY IS:
/tmp/pbs.5020787.cx1
THE TEMPORARY DIRECTORY IS:
/tmp/pbs.5020787.cx1
THE PROCESS ID IS: 13680
</pre>
Here we have some technical information about the environment, where this job was run.
<pre>
SINGLE POINT DENSITY OPTIMIZATION
PATH TO THE RESTART FILES: ./
GRAM-SCHMIDT ORTHOGONALIZATION
MAXIMUM NUMBER OF STEPS: 1000 STEPS
MAXIMUM NUMBER OF ITERATIONS FOR SC: 1000 STEPS
PRINT INTERMEDIATE RESULTS EVERY 10001 STEPS
STORE INTERMEDIATE RESULTS EVERY 10 STEPS
NUMBER OF DISTINCT RESTART FILES: 1
TEMPERATURE IS CALCULATED ASSUMING AN ISOLATED MOLECULE
FICTITIOUS ELECTRON MASS: 500.0000
TIME STEP FOR ELECTRONS: 5.0000
TIME STEP FOR IONS: 5.0000
CONVERGENCE CRITERIA FOR WAVEFUNCTION OPTIMIZATION: 1.0000E-07
WAVEFUNCTION OPTIMIZATION BY PRECONDITIONED DIIS
THRESHOLD FOR THE WF-HESSIAN IS 0.5000
MAXIMUM NUMBER OF VECTORS RETAINED FOR DIIS: 5
STEPS UNTIL DIIS RESET ON POOR PROGRESS: 5
FULL ELECTRONIC GRADIENT IS USED
SPLINE INTERPOLATION IN G-SPACE FOR PSEUDOPOTENTIAL FUNCTIONS
NUMBER OF SPLINE POINTS: 5000
</pre>
This section now gives you a summary of the parameters read in from the &CPMD section, or their respective default settings.
<pre>
EXCHANGE CORRELATION FUNCTIONALS
LDA EXCHANGE: SLATER (ALPHA = 0.66667)
LDA CORRELATION: LEE, YANG & PARR
[C.L. LEE, W. YANG, AND R.G. PARR, PRB 37 785 (1988)]
GRADIENT CORRECTED FUNCTIONAL
DENSITY THRESHOLD: 1.00000E-07
EXCHANGE ENERGY
[A.D. BECKE, PHYS. REV. A 38, 3098 (1988)]
PARAMETER BETA: 0.004200
CORRELATION ENERGY
[LYP: C.L. LEE ET AL. PHYS. REV. B 37, 785 (1988)]
*** DETSP| SIZE OF THE PROGRAM IS 8748/ 110552 kBYTES ***
>>>>>>>> CENTER OF MASS HAS BEEN MOVED TO CENTER OF BOX <<<<<<<<
***************************** ATOMS ****************************
NR TYPE X(bohr) Y(bohr) Z(bohr) MBL
1 Cl 11.199323 11.186938 9.180419 3
2 O 10.970667 11.067318 15.135702 3
3 H 10.558139 11.108892 13.264684 3
4 H 12.820897 11.171631 15.013437 3
****************************************************************
NUMBER OF STATES: 8
NUMBER OF ELECTRONS: 16.00000
CHARGE: -1.00000
ELECTRON TEMPERATURE(KELVIN): 0.00000
OCCUPATION
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
</pre>
This part of the output tells you which and how many atoms and electrons are used, what functional and what pseudopotentials were used, and what the values of some related parameters are.
<pre>
POISSON EQUATION SOLVER : HOCKNEY
COULOMB SMOOTHING RADIUS : 1.593
SYMMETRY: SIMPLE CUBIC
LATTICE CONSTANT(a.u.): 22.29877
CELL DIMENSION: 22.2988 1.0000 1.0000 0.0000 0.0000 0.0000
VOLUME(OMEGA IN BOHR^3): 11087.72952
LATTICE VECTOR A1(BOHR): 22.2988 0.0000 0.0000
LATTICE VECTOR A2(BOHR): 0.0000 22.2988 0.0000
LATTICE VECTOR A3(BOHR): 0.0000 0.0000 22.2988
RECIP. LAT. VEC. B1(2Pi/BOHR): 0.0448 0.0000 0.0000
RECIP. LAT. VEC. B2(2Pi/BOHR): 0.0000 0.0448 0.0000
RECIP. LAT. VEC. B3(2Pi/BOHR): 0.0000 0.0000 0.0448
REAL SPACE MESH: 120 120 120
WAVEFUNCTION CUTOFF(RYDBERG): 70.00000
DENSITY CUTOFF(RYDBERG): (DUAL= 4.00) 280.00000
NUMBER OF PLANE WAVES FOR WAVEFUNCTION CUTOFF: 54804
NUMBER OF PLANE WAVES FOR DENSITY CUTOFF: 438632
</pre>
This part of the output presents the settings read in from the &SYSTEM section of the input file and some derived parameters.
[…]
<pre>
(K+E1+L+N+X) TOTAL ENERGY = -31.48398404 A.U.
(K) KINETIC ENERGY = 19.91015701 A.U.
(E1=A-S+R) ELECTROSTATIC ENERGY = -26.99115337 A.U.
(S) ESELF = 28.92331533 A.U.
(R) ESR = 0.74536593 A.U.
(L) LOCAL PSEUDOPOTENTIAL ENERGY = -19.20863875 A.U.
(N) N-L PSEUDOPOTENTIAL ENERGY = 2.63857242 A.U.
(X) EXCHANGE-CORRELATION ENERGY = -7.83292134 A.U.
GRADIENT CORRECTION ENERGY = -0.43675318 A.U.
</pre>
After some output to report the setup of the initial guess for the electronic structure, we now see a summary of the various energy contribution of the total energy of the system, based on the initial guess. Now the program is ready to start the wavefunction optimisation.

Starting from the initial guess based on atomic wavefunctions the wavefunction for the total system is now calculated with an optimisation procedure. You can follow the progress of the optimisation in the output file.
<pre>
NFI GEMAX CNORM ETOT DETOT TCPU
1 4.556E-02 4.038E-03 -31.483984 0.000E+00 5.88
2 1.580E-02 1.381E-03 -32.031355 -5.474E-01 5.90
3 1.347E-02 6.554E-04 -32.139961 -1.086E-01 5.93
4 7.667E-03 3.432E-04 -32.162687 -2.273E-02 5.95
5 3.490E-03 1.256E-04 -32.168927 -6.240E-03 5.97
6 2.655E-03 6.618E-05 -32.170107 -1.180E-03 5.98
7 1.888E-03 3.959E-05 -32.170488 -3.805E-04 5.99
8 1.004E-03 2.399E-05 -32.170647 -1.597E-04 5.97
9 6.207E-04 1.431E-05 -32.170689 -4.167E-05 5.96
10 4.309E-04 8.966E-06 -32.170703 -1.373E-05 5.96
</pre>

<pre>
NFI: Step number (number of finite iterations)
GEMAX: largest off-diagonal component
CNORM: average of the off-diagonal components
ETOT: total energy
DETOT: change in total energy to the previous step
TCPU: (CPU) time for this step
</pre>
And you can see that the calculation stops after the convergence of 1.0d-7 has been reached for the GEMAX value.
****************************************************************
* *
* FINAL RESULTS *
* *
****************************************************************
****************************************************************
* ATOMIC COORDINATES *
****************************************************************
1 Cl 11.199323 11.186938 9.180419
2 O 10.970667 11.067318 15.135702
3 H 10.558139 11.108892 13.264684
4 H 12.820897 11.171631 15.013437
****************************************************************
ELECTRONIC GRADIENT:
MAX. COMPONENT = 9.69721E-08 NORM = 8.07825E-10
TOTAL INTEGRATED ELECTRONIC DENSITY
IN G-SPACE = 16.000000
IN R-SPACE = 16.000000
(K+E1+L+N+X) TOTAL ENERGY = -32.17071373 A.U.
(K) KINETIC ENERGY = 18.31556847 A.U.
(E1=A-S+R) ELECTROSTATIC ENERGY = -26.97530784 A.U.
(S) ESELF = 28.92331533 A.U.
(R) ESR = 0.74536593 A.U.
(L) LOCAL PSEUDOPOTENTIAL ENERGY = -18.46114493 A.U.
(N) N-L PSEUDOPOTENTIAL ENERGY = 2.17769037 A.U.
(X) EXCHANGE-CORRELATION ENERGY = -7.22751980 A.U.
GRADIENT CORRECTION ENERGY = -0.41653735 A.U.
****************************************************************

Here we have the final summary of the results from our single point calculation. Please note that regardless of the input units, coordinates in the CPMD output are always in atomic units.

Other Output files:

Apart from the console output, our CPMD run created a few other files. Most importantly the restart file RESTART., which contains the final state of the system when the program terminated. This is needed to start other calculations, which need a converged wavefunction as a starting point. The file GEOMETRY. contains the coordinates of the atoms in atomic unit. This can be converted to a .xyz file.

3.3.2 Car-Parrinello Molecular dynamics

Based on the previously calculated electronic structure, we can now start a Car-Parrinello Molecular dynamics calculation. Note that although you can start a CP-MD run from a non-converged wavefunction (e.g. by not restarting from a pre-optimised wavefunction), you will be far away from the Born-Oppenheimer surface, and thus your result will be unphysical.

To run, type:
<pre>
cp RESTART. RESTART
qsub runcpmd_md
</pre>

3.3.2.1 Input for CP dynamics

For the CP-MD job you need a new input file, inp.clw_blyp_md, which should be copied into the same directory, where you started the wavefunction optimisation run. If you compare it to the previous input files, you will find, that the only changes are again only in the &CPMD section of the input files.
<pre>
&CPMD
MOLECULAR DYNAMICS CP
RESTART WAVEFUNCTION COORDINATES VELOCITIES NOSEP LATEST
QUENCH BO
MIRROR
CONVERGENCE ORBITAL
1.0D-7
ODIIS
5
MAXSTEP
3000
STORE
20
TIMESTEP
5
EMASS
500.0
NOSE IONS
298.0 1100
TRAJECTORY SAMPLE
10
ISOLATED MOLECULE
&END
</pre>
The keyword MOLECULAR DYNAMICS CP defines the job type. Furthermore we tell the CPMD program to pick up the previously calculated wavefunction and coordinates from the latest restart file (which is named RESTART by default). MAXSTEP limits the MD to 3000 steps and the equations of motion will be solved for a time step of 5 atomic units (~0.12 femtoseconds). The temperature of the system will be initialised to 298K via the NOSE IONS keyword with Nose thermostat.

- Now start the CPMD program once more: qsub runcpmd_md

This run should be completed in a few minutes.

3.3.2.2 CP dynamics output

The output of the CPMD program is now in the file log.clw_blyp_md. There are also some new files (TRAJECTORY, ENERGIES). We will have a look at the output file first.
<pre>
CAR-PARRINELLO MOLECULAR DYNAMICS
PATH TO THE RESTART FILES: ./
RESTART WITH OLD ORBITALS
RESTART WITH OLD ION POSITIONS
RESTART WITH OLD VELOCITIES
RESTART WITH OLD ION THERMOSTAT
RESTART WITH LATEST RESTART FILE
ITERATIVE ORTHOGONALIZATION
MAXIT: 30
EPS: 1.00E-06
MAXIMUM NUMBER OF STEPS: 3000 STEPS
</pre>
The header is unchanged up to the point where the settings from the &CPMD section are printed. As you can see, the program has recognised the RESTART and the MAXSTEP keywords. (NOTE: in the CPMD code atoms are sometimes referred to as ions. This is due to the pseudopotential approach, where you integrate the core electrons into the (pseudo)atom which then could also be described as an ion.)
<pre>
TIME STEP FOR ELECTRONS: 5.0000
TIME STEP FOR IONS: 5.0000
QUENCH SYSTEM TO THE BORN-OPPENHEIMER SURFACE
TRAJECTORIES ARE SAVED ON FILE EVERY 10 STEPS
ELECTRON DYNAMICS: THE TEMPERATURE IS NOT CONTROLLED
ION DYNAMICS: TEMPERATURE CONTROL (NOSE-HOOVER THERMOSTATS)
TARGET TEMPERATURE(KELVIN): 2.980000E+02
CHARACTERISTIC FREQUENCY(CM**-1): 1100.00
NOSE PARAMETERS
NUMBER OF THERMOSTATS (IONS) : 3
NUMBER OF THERMOSTATS (ELECTRONS) : 3
NUMBER OF THERMOSTATS (CELL) : 3
SCALING FOR ELEC. DOF : 6.00
NUMBER OF YOSHIDA-SUZUKI STEPS : 7
NUMBER OF INTEGRATION CYCLES (NIT): 1
</pre>
This part of the output tells us, that the TIMESTEP 5.0 keyword was recognised (which is the default timestep), that the trajectory will be recorded and that NOSE-HOOVER thermostat is used.
</pre>
RESTART INFORMATION READ ON FILE ./RESTART
</pre>
Here we get notified, that the program has read the requested data from the restart file.
<pre>
NFI EKINC TEMPP EKS ECLASSIC EHAM DIS TCPU
1 0.00000 0.0 -32.17071 -32.17010 -32.17010 0.458E-10 3.25
2 0.00000 0.0 -32.17071 -32.17010 -32.17010 0.727E-09 3.24
3 0.00000 0.0 -32.17071 -32.17010 -32.17010 0.365E-08 3.24
4 0.00000 0.0 -32.17071 -32.17010 -32.17010 0.114E-07 3.24
5 0.00000 0.1 -32.17071 -32.17010 -32.17010 0.275E-07 3.24
6 0.00000 0.1 -32.17071 -32.17010 -32.17010 0.565E-07 3.25
7 0.00000 0.1 -32.17071 -32.17010 -32.17010 0.104E-06 3.24
8 0.00000 0.2 -32.17072 -32.17010 -32.17010 0.175E-06 3.24
9 0.00000 0.2 -32.17072 -32.17010 -32.17010 0.279E-06 3.25
10 0.00000 0.3 -32.17072 -32.17010 -32.17010 0.422E-06 3.25
11 0.00000 0.3 -32.17072 -32.17010 -32.17010 0.614E-06 3.25
12 0.00000 0.4 -32.17072 -32.17010 -32.17010 0.865E-06 3.25
13 0.00000 0.4 -32.17072 -32.17010 -32.17010 0.119E-05 3.24
14 0.00000 0.5 -32.17072 -32.17010 -32.17010 0.159E-05 3.24
15 0.00000 0.6 -32.17072 -32.17010 -32.17010 0.209E-05 3.25
16 0.00000 0.6 -32.17072 -32.17010 -32.17010 0.269E-05 3.25
17 0.00000 0.7 -32.17072 -32.17010 -32.17010 0.343E-05 3.24
18 0.00000 0.8 -32.17072 -32.17010 -32.17010 0.429E-05 3.25
19 0.00000 0.9 -32.17072 -32.17010 -32.17010 0.532E-05 3.24
20 0.00000 1.0 -32.17072 -32.17010 -32.17010 0.652E-05 3.24
...
2981 0.00015 274.5 -32.16644 -32.17025 -32.17010 0.443E+01 3.25
2982 0.00015 268.3 -32.16638 -32.17025 -32.17010 0.444E+01 3.25
2983 0.00014 262.2 -32.16632 -32.17025 -32.17010 0.444E+01 3.26
2984 0.00014 256.0 -32.16627 -32.17024 -32.17010 0.445E+01 3.25
2985 0.00014 249.9 -32.16621 -32.17024 -32.17010 0.446E+01 3.26
2986 0.00013 243.8 -32.16615 -32.17024 -32.17010 0.446E+01 3.25
2987 0.00013 237.7 -32.16610 -32.17023 -32.17010 0.447E+01 3.25
2988 0.00013 231.7 -32.16604 -32.17023 -32.17010 0.447E+01 3.25
...
2997 0.00010 179.1 -32.16554 -32.17020 -32.17010 0.452E+01 3.25
2998 0.00010 173.6 -32.16549 -32.17020 -32.17010 0.452E+01 3.26
2999 0.00009 168.1 -32.16544 -32.17020 -32.17010 0.453E+01 3.26
3000 0.00009 162.6 -32.16539 -32.17019 -32.17010 0.453E+01 3.25
</pre>

After some more output, we already discussed for the wavefunction optimisation, this is now part of the energy summary for a Car-Parrinello-MD run.
<pre>
NFI: Step number (number of finite iterations)
EKINC: (fictitious) kinetic energy of the electron (sub-)system
TEMPP: Temerature (=kinetic energy / degrees of freedom) for atoms (ions)
EKS: Kohn-Sham Energy: equivalent to the potential energy in classical MD
ECLASSIC: Equivalent to the total energy in a classical MD (ECLASSIC = EHAM-EKINC)
EHAM: total energy, should be conserved
DIS: mean squared displacement of the atoms from the initial coordinates
TCPU: (CPU) time needed for this step
</pre>
To read about why do the MD part and how to analyse results, please read this CPMD paper on water.

Reference: Kuo et al, J. Phys. Chem. B 2004, 108, 12990-12998

Note: For a meaningful Car-Parrinello MD, EKINC has to be (and stay) very small (although for larger systems with more electrons, the absolute value of EKINC will be larger, i.e. no drift in EKINC.

Exercise: plot EKINC vs NFI, TEMPP vs NFI, EKS vs NFI, ECLASSIC vs NFI, EHAM vs NFI. Discuss the trend of these curves.

<pre>
MEAN VALUE +/- RMS DEVIATION
<x> [<x^2>-<x>^2]**(1/2)
ELECTRON KINETIC ENERGY 0.000125 0.105171E-03
IONIC TEMPERATURE 233.0551 194.923
DENSITY FUNCTIONAL ENERGY -32.169126 0.152974E-02
CLASSICAL ENERGY -32.170228 0.105180E-03
CONSERVED ENERGY -32.170104 0.247772E-05
NOSE ENERGY ELECTRONS 0.000000 0.00000
NOSE ENERGY IONS -0.003317 0.200165E-02
CONSTRAINTS ENERGY 0.000000 0.00000
RESTRAINTS ENERGY 0.000000 0.00000
ION DISPLACEMENT 1.25973 1.33130
CPU TIME 3.2487
</pre>
Finally we get a summary of some averages and root mean squared deviations for some of the monitored quantities. This is quite useful to detect unwanted energy drifts or too large fluctuations in the simulation.

Exercise: visualise the motion of the system of (1 water + Cl-)

Type: ./traj2xyz.x < TRAJECTORY.clw_blyp_md > TRAJ.xyz

You can load the file TRAJ.xyz directly into the molecular visualisation program VMD.
<pre>
Launch VMD program
File -> Load files for: New Molecule
click ‘Browse’, choose the file TRAJ.xyz
click ‘Load’
</pre>
The trajectory file can be used to generate structural properties such as radial distribution functions and analyse the solvation shells such as Cl-O distances.

3.3.3 Kohn-Sham energies

Altogether the first part of the CPMD input (file name: inp.clw_blyp_ksl) now contains:
<pre>
&CPMD
RESTART WAVEFUNCTION VELOCITIES COORDINATES LATEST
KOHN-SHAM ENERGIES
0
MAXSTEP
1000
STORE
10
TIMESTEP
5.0
EMASS
500.0
ISOLATED MOLECULE
&END
</pre>
Output file (log.clw_blyp_ksl)
<pre>
EIGENVALUES(EV) AND OCCUPATION:
1 -19.9458449 2.00000000 2 -11.8998056 2.00000000
3 -7.3120943 2.00000000 4 -4.5277656 2.00000000
5 -2.2061693 2.00000000 6 -0.5375340 2.00000000
7 -0.3936740 2.00000000 8 -0.3633460 2.00000000
CHEMICAL POTENTIAL = -0.3633465899 EV
</pre>
This part lists the Kohn-Sham energies.

3.3.4 Kohn-Sham Orbitals

Altogether the first part of the CPMD input (file name: inp.clw_blyp_ksorb) now contains:
<pre>
&CPMD
KOHN-SHAM ENERGIES
8
RESTART WAVEFUNCTION COORDINATES LATEST
DAVIDSON DIAGNOALIZATION
RHOOUT BANDS
8
-1 -2 -3 -4 -5 -6 -7 -8
&END
</pre>
This generages a series of files with the names WAVEFUNCTION.1, WAVEFUNCTION.2, …, WAVEFUNCTION.8 which have to be converted to cube format with cpmd2cube.x -o clw1 WAVEFUNCTION.1

3.3.5 Wannier Analysis

To calculate the Wannier centers or orbitals for our system we need to do a properties calculation starting from the previously generated wavefunction.

For the Wannier orbitals the keywords LOCALIZE and WANNIER WFNOUT are required. This generates a series of files with the names WANNIER_1.* which have to be converted to cube format with cpmd2cube.x -o clw1 WANNIER_1.1.

Altogether the first and second parts of the CPMD input to calculate Wannier enters now contains:
<pre>
&CPMD
RESTART WAVEFUNCTION LATEST
PROPERTIES
WANNIER DOS
&END

&PROP
LOCALIZE
&END
</pre>
To plot all the WANNIER ORBITALS, replace the first part with:
<pre>
&CPMD
RESTART WAVEFUNCTION COORDINATES LATEST
PROPERTIES
WANNIER WFNOUT ALL
&END
</pre>
Exercise: use VMD to visualise the Kohn-Sham and Wannier orbitals. Describe the Kohn-Sham and Wannier Orbitals of the system. (Hint: One of the Kohn-Sham orbitals looks like this. Discuss delocalisation/localisation.)

Figure 2 Kohn-Sham Orbital

Note: Different phases can be visualised in VMD by creating two representations from the same data set and just using isovalues with opposite sign for each of them. The input and cube files used in this section are:

WAVEFUNCTION.* or WANNIER_1.*

clw1.*.cube (for Kohn-Sham orbitals) or clw11.*.cube (for Wannier orbitals)

VMD:
<pre>
-> Launch VMD program
-> File -> Load files for: New Molecule
-> click ‘Browse’, choose the file TRAJ.xyz
-> click ‘Load’
-> Graphics -> Representations -> Drawing Method -> Choose CPK
-> repeat the above procedure and load the cube file again but this time choose Isosurface as Drawing method and play around with Isovalues.

</pre>

To change colour of the background:

-> Graphics -> Colors -> Display -> Background -> Choose white

4. Exercises (63 water + Cl-)

The next step is a more typical (while ambitious) application of the CPMD code: a Car-Parrinello MD simulation of a bulk system with water and a chloride ion. In this specific example, we try to look at how the electronic structure changes when a chloride ion is solvated in liquid water. Our system will consist of 63 water molecules and one chloride ion (note the CHARGE keyword in the &SYSTEM section). To speed up the equilibration phase, we start from a restart configuration that has been equilibrated with classical MD for about 3 ns using the SPC/E water potential and CPMD for 31.56 ps. Since water has a dipole moment, you have to keep in mind, that we are calculating a system with periodic boundary conditions, so a water molecules ‘sees’ its images and interacts with them. There are methods implemented in CPMD to compensate this effect, but we won’t discuss them here.

Now run jobs to get data.

4.1 Run a wavefunction optimisation (use inp.w63Cl-wf).

4.2 We want to run the MD at 298 Kelvin, so now run a short MD with temperature rescaling for the atoms and no thermostat for the electrons (use inp.w63Cl-md)

4.3 Now you have your MD trajectory files, analyse them

4.4 Liquid water structure and hydrogen bonding

4.4.1 Generate a movie of trajectories using VMD which will read in the TRAJ.xyz file.

4.4.2 what to look at => Radial Distribution Functions

4.4.3 Compare your traj to the one we have made

4.4.4 Do you see water molecules entering and exiting solvation shell?

4.5 Plotting Kohn-Sham energies, Kohn-Sham orbitals, Wannier centers and Wannier orbitals

4.6 Follow the instructions above for clw1 but with your clw63 file (do it for last step of your trajectory) in reality we would want to examine 50-100 points sampled from the trajectory

4.7 Each student to look at one of the following:

4.7.1 Plot density of states for KS, KS orbitals

4.7.2 Plot Wannier orbitals and centers

4.7.3 Plot Cl-water distances over time

Talk:Mod:Hunt Research Group/cpmd water

2013-03-01T12:32:34Z

Lge:

Car-Parrinello Molecular Dynamics Simulation of Aqueous Solutions

1. Introduction

1.1 Aqueous solutions

In this lab you are going to run CPMD calculations of systems containing water and chloride. The following paragraphs describe why these systems are interesting to study.

Solvation of the chloride anion in water solution has been the subject of a substantial amount of experimental and theoretical work, in view of the central importance of chloride solutions in biochemical and metabolic processes, geology, atmospheric chemistry, and the chemical industry. Indeed, it has been discovered that airborne aqueous sea-salt aerosols serve as a global source of molecular chlorine and bromine, both in the polluted and in the remote lower marine troposphere. A variety of experimental methods have been used to investigate the hydration structure of chloride ions in water, including neutron and X-ray diffraction techniques, X-ray absorption spectroscopy (XAS) and femtosecond mid-infrared nonlinear spectroscopy. Despite these efforts, a complete microscopic model of the hydration shell structure of aqueous Cl- and of its room temperature dynamics is still being debated.

Difficulties in determining the structure of the solvation environment arise because of the comparable magnitudes of the water-Cl- and water-water interaction energies. Established results from the literature, both experimental and theoretical, reveal a rather inhomogeneous picture of the hydrated ion solvation shell structure. Vibrational spectroscopy experiments indicate that a chloride ion is asymmetrically solvated in clusters containing up to five water molecules. This contrasts with older and less direct experiments based on mass spectroscopy and photoelectron spectroscopy from which a symmetrical solvent cage around the anion was inferred. Experimental measurements such as photoelectron spectroscopy, IR spectroscopy and a combined technique of XAS (extended X-ray absorption fine structure, EXAFS and X-ray absorption near-edge structure, XANES) yield coordination numbers that are significantly scattered, ranging from 3 to 8. The first peak of the Cl-O radial distribution function (RDF) is measured to be in the range of 3.10-3.36 A.

Uncertainty in the coordination number is also evinced from theoretical studies, with variations between 5.1 and 8.4 depending on the simulation techniques adopted. Classical molecular dynamics (MD) simulations have been found to depend strongly on the anion-water and water-water potentials used. On the other hand, the use of different parametrized potentials, i.e. with and without a treatment of molecular polarizability, gave different structural properties. Quantum mechanics / molecular mechanics (QM/MM) simulations of Cl− in water indicate that the hydration structure of the an- ion has considerable flexibility in consequence to the weakness of Cl--water interactions. This leads to a competition between solvation of the ion and hydrogen bonding among water molecules. The QM/MM results clearly indicate the importance of QM treatment in order to correctly describe such a delicate balance between Cl--water and water-water interactions.

Reference: Tongraar, A.; T-Thienprasert, J.; Rujirawat, S.; Limpijumnong, S. Phys. Chem. Chem. Phys. 2010, 12, 10876.

1.2 Car-Parrinello/Born-Oppenheimer molecular dynamics

The aim of this tutorial is to help you getting started using the CPMD program. CPMD is an ab initio electronic structure and molecular dynamics (MD) program using a plane wave/pseudopotential implementation of density functional theory (DFT). It is mainly targeted at Car-Parrinello MD simulations, but also supports geometry optimisations, Born-Oppenheimer MD, path integral MD, response functions, excited states and calculations of some electronic properties. For further information you may want to take a look at the CPMD consortium homepage at www.cpmd.org.

Born-Oppenheimer (BO) MD: at each step of atomic MD, one solves the DFT SCF problem for a fixed atomic configuration, computes the wavefunction, and from it the (quantum mechanical) forces acting on the nuclei. This allows it to propagate the atoms classically to the next configuration. (In simple words, one computes energy and forces, move the atoms, re-compute energy and forces for the new configuration, move the atoms, and so on.)

Car-Parrinello: One propagates simultaneously a set of atoms and a fictitious set of electrons. From the fictitious set of electrons, one can estimate the forces on the atoms and move the atoms. Atoms and fictitious electrons have to be independent, and their dynamics is described using a generalised Lagrangian formalism, rather than simply propagating the atoms using Newton's equations like in Born-Oppenheimer MD. In the CPMD manual, it is written:

“The basic idea of the Car-Parrinello approach can be viewed to exploit the time-scale separation of fast electronic and slow nuclear motion by transforming that into classical-mechanical adiabatic energy-scale separation in the framework of dynamical systems theory. In order to achieve this goal the two-component quantum / classical problem is mapped onto a two-component purely classical problem with two separate energy scales at the expense of loosing the explicit time-dependence of the quantum subsystem dynamics.”

Born-Oppenheimer MD is easier to implement in practice, but slower. Also it requires a very well converged calculation of the forces at each step of dynamics. The Car-Parrinello only requires a very accurate ground state at the first step. The rest of the dynamics sustains itself, provided it is carried out in the right way.

If you would like to know more about the theoretical background of CPMD or BOMD, please read CPMD manual Sections 6.6 and 6.7.

2. Code Running Environment

2.1 Before running the job

Before you run CPMD it is a good idea to copy all you need in your local directory.

- Copy the folder lab from the usb disk to your laptop.

- open the terminal application

- open two windows, one will be for your local mac and the other for the hpc cluster

- on one of them login to the hpc cluster by typing ssh yourname@login.cx1.hpc.ic.ac.uk

- the cluster has two key directories /WORK/yourname and /HOME/yourname do all the calculations from the WORK/yourname directory, from now on this directory will be referred to simply as work

- cd to your work directory and make a new directory called liquids, cd into the new directory, this is where you will run all your jobs from

- copy the file from your desktop to hpc:

scp filename yourname@login.cx1.hpc.ic.ac.uk:/work/yourname/foldername/.

- unzip the tar file

tar -xvf filename.tar

2.2 How to run the job

In the directory cpmd you should have two subdirectories: clw1 and clw63.

To run CPMD type qsub runcpmd_wf (or other run scripts depending on the type of calculation such as runcpmd_md) in the clw1 or clw63 directory.

2.3 Using VMD to analyse results

For visualisation of the results you may want to take a look at the tutorial on visualising results from CPMD with the VMD program under www.theochem.ruhr-uni-bochum.de/go/cpmd-vmd.html

3. CPMD

3.1 Theoretical background

3.1.1 Pseudopotentials (read CPMD manual section 4.2)

3.1.2 Kohn-Sham orbitals, Wannier orbitals and Effective molecular orbitals

The EMO method for analysing the electronic structure of solutes and solvents starts by considering the Kohn-Sham Hamiltonian and energy eigenvalues obtained from the ab initio molecular dynamics. A band structure similar to that obtained for solid state systems emerges. While the Kohn-Sham Hamiltonian is diagonal, and the Kohn-Sham orbital energies are uniquely defined, the Kohn-Sham orbitals are delocalised Bloch states which extend over all space and the molecular picture is lost, as shown in Figure 1 (a). This makes it very difficult to analyse interactions between an ion and the solvating water molecules. Maximally localized Wannier orbitals are local to atomic centers. However, the Wannier Hamiltonian is not diagonal and thus there is no unique energy eigenvalue that can be associated with each orbital, as shown in Figure 1 (c). An intermediate representation where orbitals are local to a molecule, but are delocalised within the molecule has been developed. The EMOs are obtained by assigning Wannier orbitals to a specific molecule, and block-diagonalising the Wannier Hamiltonian within the molecular subspace, as shown in Figure 1 (b). This analysis has been successfully applied to pure liquid water. An isolated water molecule has C2v symmetry and valence MOs 1a1, 1b2, 2a1 and 1b1. A liquid environment is disordered and there is no symmetry. However, Figure 1 (b) shows that the EMOs strongly resemble the standard MOs for a single water molecule in vacuum. This close resemblance is by no means predetermined and is a validation of the EMO method. For clarity, we will continue to use the isolated atomic or molecular symmetry labels when we refer to the individual atomic orbitals, MOs and bands in the aqueous system.

3.2 Functional

We will use a gradient corrected functional (BLYP) instead of LDA throughout the tutorial as this combination of generalized gradient approximations to exchange and correlation has been shown to give good results for the structure and dynamics of water.

Figure 1 Wavefunction diagrams from a CPMD simulation of pure liquid water related to graphical representations of the respective Hamiltonian matrices: (a) Kohn-Sham Hamiltonian, (b) EMO Hamiltonian and (c) Wannier Hamiltonian.

3.3 Generating input files and understanding output files

The first example will demonstrate some of the basic steps of performing a CPMD calculation with a very simple system: 1 water molecule+Cl-, and a very simple task: calculate the electronic structure. We will use that as an example to have a look at the input file format, and how to read the output.

- emacs filename

- and then look inside and follow the instructions below

3.3.1 Wavefunction optimisation

(a) Input File format

For nearly all CPMD calculations, you first have to optimise the wavefunction of your system, and use that as a base for further calculations. For our first calculation you’ll need the input file inp.clw_blyp_wf and the pseudopotential files H_MT_BLYP.psp, O_MT_BLYP.psp, Cl_MT_BLYP.psp.

Now let’s have a look at the input file. The input file is organised in sections which start with &NAME and end with &END. Everything outside those sections is ignored. All keywords have to be in upper case or else they will be ignored. The sequence of the sections does not matter, nor does the order of keywords. A minimal input file must have a &CPMD, &SYSTEM and an &ATOMS section.

&CPMD

OPTIMIZE WAVEFUNCTION

CONVERGENCE ORBITALS

1.0d-7

&END

This first part of the &CPMD section instructs the program to do a wavefunction optimization (i.e. a single point calculation) with a tight convergence criterion (the default is 1.0d-5).

Exercise: look up in the CPMD manual about the usage of the keywords ODIIS, STORE, TIMESTEP, EMASS, ISOLATED MOLECULE.

&DFT

FUNCTIONAL BLYP

GC-CUTOFF

0.1D-06

&END

The &DFT section is used to select the density functional and related parameters. In this case we go with the BLYP functional.

&SYSTEM

ANGSTROM

SYMMETRY

0

CELL

11.800 1.0 1.0 0 0 0

CUTOFF

70.0

CHARGE

-1.0

&END

The &SYSTEM section contains various parameters related to the simulation cell and the representation of the electronic structure. The keywords SYMMETRY, CELL and CUTOFF are required and define the (periodic) symmetry, shape, and size of the simulation cell, as well as the plane wave cutoff (i.e. the size of the basis set). The keyword Angstrom additionally indicates that all lengths and coordinates are given in angstrom (not in a.u.).

Exercise: look up in the CPMD manual about the usage of the keyword CHARGE.

Finally the &ATOMS section is needed to specify the atom coordinates and the pseudopotentials, that are used to represent them. The detailed syntax of the pseudopotential specification is a bit complicated and will not be needed nor discussed here. If you want to know more, please have a look at the Further details of the Input section of the CPMD manual (P222).

- To run, type: qsub runcpmd_wf,

The code will generate the following output files once the calculation is completed after a few minutes: log.clw_blyp_wf, GOMETRY., RESTART.. The purpose of the wavefunction optimisation is to generate the RESTART. file which is needed for further calculations.

(b) Output File Format

To start the calculation, which should be completed in less than a minute once the job starts running. The main output of the CPMD program is now in the file log.clw_blyp_wf. Let’s have a closer look at the contents of this file.

PROGRAM CPMD STARTED AT: Thu Jan 20 16:23:24 2011
SETCNST| USING: CODATA 2006 UNITS
THE INPUT FILE IS: /work/lge/wannier/test/inp.clw_blyp_wf
THIS JOB RUNS ON: cx1-50-2-1.cx1.hpc.ic.ac.uk
THE CURRENT DIRECTORY IS:
/tmp/pbs.5020787.cx1
THE TEMPORARY DIRECTORY IS:
/tmp/pbs.5020787.cx1
THE PROCESS ID IS: 13680

Here we have some technical information about the environment, where this job was run.

SINGLE POINT DENSITY OPTIMIZATION
PATH TO THE RESTART FILES: ./
GRAM-SCHMIDT ORTHOGONALIZATION
MAXIMUM NUMBER OF STEPS: 1000 STEPS
MAXIMUM NUMBER OF ITERATIONS FOR SC: 1000 STEPS
PRINT INTERMEDIATE RESULTS EVERY 10001 STEPS
STORE INTERMEDIATE RESULTS EVERY 10 STEPS
NUMBER OF DISTINCT RESTART FILES: 1
TEMPERATURE IS CALCULATED ASSUMING AN ISOLATED MOLECULE
FICTITIOUS ELECTRON MASS: 500.0000
TIME STEP FOR ELECTRONS: 5.0000
TIME STEP FOR IONS: 5.0000
CONVERGENCE CRITERIA FOR WAVEFUNCTION OPTIMIZATION: 1.0000E-07
WAVEFUNCTION OPTIMIZATION BY PRECONDITIONED DIIS
THRESHOLD FOR THE WF-HESSIAN IS 0.5000
MAXIMUM NUMBER OF VECTORS RETAINED FOR DIIS: 5
STEPS UNTIL DIIS RESET ON POOR PROGRESS: 5
FULL ELECTRONIC GRADIENT IS USED
SPLINE INTERPOLATION IN G-SPACE FOR PSEUDOPOTENTIAL FUNCTIONS
NUMBER OF SPLINE POINTS: 5000

This section now gives you a summary of the parameters read in from the &CPMD section, or their respective default settings.

EXCHANGE CORRELATION FUNCTIONALS
LDA EXCHANGE: SLATER (ALPHA = 0.66667)
LDA CORRELATION: LEE, YANG & PARR
[C.L. LEE, W. YANG, AND R.G. PARR, PRB 37 785 (1988)]
GRADIENT CORRECTED FUNCTIONAL
DENSITY THRESHOLD: 1.00000E-07
EXCHANGE ENERGY
[A.D. BECKE, PHYS. REV. A 38, 3098 (1988)]
PARAMETER BETA: 0.004200
CORRELATION ENERGY
[LYP: C.L. LEE ET AL. PHYS. REV. B 37, 785 (1988)]
*** DETSP| SIZE OF THE PROGRAM IS 8748/ 110552 kBYTES ***
>>>>>>>> CENTER OF MASS HAS BEEN MOVED TO CENTER OF BOX <<<<<<<<
***************************** ATOMS ****************************
NR TYPE X(bohr) Y(bohr) Z(bohr) MBL
1 Cl 11.199323 11.186938 9.180419 3
2 O 10.970667 11.067318 15.135702 3
3 H 10.558139 11.108892 13.264684 3
4 H 12.820897 11.171631 15.013437 3
****************************************************************
NUMBER OF STATES: 8
NUMBER OF ELECTRONS: 16.00000
CHARGE: -1.00000
ELECTRON TEMPERATURE(KELVIN): 0.00000
OCCUPATION
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0

This part of the output tells you which and how many atoms and electrons are used, what functional and what pseudopotentials were used, and what the values of some related parameters are.

POISSON EQUATION SOLVER : HOCKNEY
COULOMB SMOOTHING RADIUS : 1.593
SYMMETRY: SIMPLE CUBIC
LATTICE CONSTANT(a.u.): 22.29877
CELL DIMENSION: 22.2988 1.0000 1.0000 0.0000 0.0000 0.0000
VOLUME(OMEGA IN BOHR^3): 11087.72952
LATTICE VECTOR A1(BOHR): 22.2988 0.0000 0.0000
LATTICE VECTOR A2(BOHR): 0.0000 22.2988 0.0000
LATTICE VECTOR A3(BOHR): 0.0000 0.0000 22.2988
RECIP. LAT. VEC. B1(2Pi/BOHR): 0.0448 0.0000 0.0000
RECIP. LAT. VEC. B2(2Pi/BOHR): 0.0000 0.0448 0.0000
RECIP. LAT. VEC. B3(2Pi/BOHR): 0.0000 0.0000 0.0448
REAL SPACE MESH: 120 120 120
WAVEFUNCTION CUTOFF(RYDBERG): 70.00000
DENSITY CUTOFF(RYDBERG): (DUAL= 4.00) 280.00000
NUMBER OF PLANE WAVES FOR WAVEFUNCTION CUTOFF: 54804
NUMBER OF PLANE WAVES FOR DENSITY CUTOFF: 438632
****************************************************************

This part of the output presents the settings read in from the &SYSTEM section of the input file and some derived parameters.
[…]

(K+E1+L+N+X) TOTAL ENERGY = -31.48398404 A.U.
(K) KINETIC ENERGY = 19.91015701 A.U.
(E1=A-S+R) ELECTROSTATIC ENERGY = -26.99115337 A.U.
(S) ESELF = 28.92331533 A.U.
(R) ESR = 0.74536593 A.U.
(L) LOCAL PSEUDOPOTENTIAL ENERGY = -19.20863875 A.U.
(N) N-L PSEUDOPOTENTIAL ENERGY = 2.63857242 A.U.
(X) EXCHANGE-CORRELATION ENERGY = -7.83292134 A.U.
GRADIENT CORRECTION ENERGY = -0.43675318 A.U.

After some output to report the setup of the initial guess for the electronic structure, we now see a summary of the various energy contribution of the total energy of the system, based on the initial guess. Now the program is ready to start the wavefunction optimisation.

Starting from the initial guess based on atomic wavefunctions the wavefunction for the total system is now calculated with an optimisation procedure. You can follow the progress of the optimisation in the output file.

NFI GEMAX CNORM ETOT DETOT TCPU
1 4.556E-02 4.038E-03 -31.483984 0.000E+00 5.88
2 1.580E-02 1.381E-03 -32.031355 -5.474E-01 5.90
3 1.347E-02 6.554E-04 -32.139961 -1.086E-01 5.93
4 7.667E-03 3.432E-04 -32.162687 -2.273E-02 5.95
5 3.490E-03 1.256E-04 -32.168927 -6.240E-03 5.97
6 2.655E-03 6.618E-05 -32.170107 -1.180E-03 5.98
7 1.888E-03 3.959E-05 -32.170488 -3.805E-04 5.99
8 1.004E-03 2.399E-05 -32.170647 -1.597E-04 5.97
9 6.207E-04 1.431E-05 -32.170689 -4.167E-05 5.96
10 4.309E-04 8.966E-06 -32.170703 -1.373E-05 5.96

NFI: Step number (number of finite iterations)

GEMAX: largest off-diagonal component

CNORM: average of the off-diagonal components

ETOT: total energy

DETOT: change in total energy to the previous step

TCPU: (CPU) time for this step

And you can see that the calculation stops after the convergence of 1.0d-7 has been reached for the GEMAX value.
****************************************************************
* *
* FINAL RESULTS *
* *
****************************************************************
****************************************************************
* ATOMIC COORDINATES *
****************************************************************
1 Cl 11.199323 11.186938 9.180419
2 O 10.970667 11.067318 15.135702
3 H 10.558139 11.108892 13.264684
4 H 12.820897 11.171631 15.013437
****************************************************************
ELECTRONIC GRADIENT:
MAX. COMPONENT = 9.69721E-08 NORM = 8.07825E-10
TOTAL INTEGRATED ELECTRONIC DENSITY
IN G-SPACE = 16.000000
IN R-SPACE = 16.000000
(K+E1+L+N+X) TOTAL ENERGY = -32.17071373 A.U.
(K) KINETIC ENERGY = 18.31556847 A.U.
(E1=A-S+R) ELECTROSTATIC ENERGY = -26.97530784 A.U.
(S) ESELF = 28.92331533 A.U.
(R) ESR = 0.74536593 A.U.
(L) LOCAL PSEUDOPOTENTIAL ENERGY = -18.46114493 A.U.
(N) N-L PSEUDOPOTENTIAL ENERGY = 2.17769037 A.U.
(X) EXCHANGE-CORRELATION ENERGY = -7.22751980 A.U.
GRADIENT CORRECTION ENERGY = -0.41653735 A.U.
****************************************************************

Here we have the final summary of the results from our single point calculation. Please note that regardless of the input units, coordinates in the CPMD output are always in atomic units.

Other Output files:

Apart from the console output, our CPMD run created a few other files. Most importantly the restart file RESTART., which contains the final state of the system when the program terminated. This is needed to start other calculations, which need a converged wavefunction as a starting point. The file GEOMETRY. contains the coordinates of the atoms in atomic unit. This can be converted to a .xyz file.

3.3.2 Car-Parrinello Molecular dynamics

Based on the previously calculated electronic structure, we can now start a Car-Parrinello Molecular dynamics calculation. Note that although you can start a CP-MD run from a non-converged wavefunction (e.g. by not restarting from a pre-optimised wavefunction), you will be far away from the Born-Oppenheimer surface, and thus your result will be unphysical.

To run, type:

cp RESTART. RESTART

qsub runcpmd_md

3.3.2.1 Input for CP dynamics

For the CP-MD job you need a new input file, inp.clw_blyp_md, which should be copied into the same directory, where you started the wavefunction optimisation run. If you compare it to the previous input files, you will find, that the only changes are again only in the &CPMD section of the input files.

&CPMD
MOLECULAR DYNAMICS CP
RESTART WAVEFUNCTION COORDINATES VELOCITIES NOSEP LATEST
QUENCH BO
MIRROR
CONVERGENCE ORBITAL
1.0D-7
ODIIS
5
MAXSTEP
3000
STORE
20
TIMESTEP
5
EMASS
500.0
NOSE IONS
298.0 1100
TRAJECTORY SAMPLE
10
ISOLATED MOLECULE
&END

The keyword MOLECULAR DYNAMICS CP defines the job type. Furthermore we tell the CPMD program to pick up the previously calculated wavefunction and coordinates from the latest restart file (which is named RESTART by default). MAXSTEP limits the MD to 3000 steps and the equations of motion will be solved for a time step of 5 atomic units (~0.12 femtoseconds). The temperature of the system will be initialised to 298K via the NOSE IONS keyword with Nose thermostat.

- Now start the CPMD program once more: qsub runcpmd_md

This run should be completed in a few minutes.

3.3.2.2 CP dynamics output

The output of the CPMD program is now in the file log.clw_blyp_md. There are also some new files (TRAJECTORY, ENERGIES). We will have a look at the output file first.

CAR-PARRINELLO MOLECULAR DYNAMICS
PATH TO THE RESTART FILES: ./
RESTART WITH OLD ORBITALS
RESTART WITH OLD ION POSITIONS
RESTART WITH OLD VELOCITIES
RESTART WITH OLD ION THERMOSTAT
RESTART WITH LATEST RESTART FILE
ITERATIVE ORTHOGONALIZATION
MAXIT: 30
EPS: 1.00E-06
MAXIMUM NUMBER OF STEPS: 3000 STEPS

The header is unchanged up to the point where the settings from the &CPMD section are printed. As you can see, the program has recognised the RESTART and the MAXSTEP keywords. (NOTE: in the CPMD code atoms are sometimes referred to as ions. This is due to the pseudopotential approach, where you integrate the core electrons into the (pseudo)atom which then could also be described as an ion.)

TIME STEP FOR ELECTRONS: 5.0000
TIME STEP FOR IONS: 5.0000
QUENCH SYSTEM TO THE BORN-OPPENHEIMER SURFACE
TRAJECTORIES ARE SAVED ON FILE EVERY 10 STEPS
ELECTRON DYNAMICS: THE TEMPERATURE IS NOT CONTROLLED
ION DYNAMICS: TEMPERATURE CONTROL (NOSE-HOOVER THERMOSTATS)
TARGET TEMPERATURE(KELVIN): 2.980000E+02
CHARACTERISTIC FREQUENCY(CM**-1): 1100.00
NOSE PARAMETERS
NUMBER OF THERMOSTATS (IONS) : 3
NUMBER OF THERMOSTATS (ELECTRONS) : 3
NUMBER OF THERMOSTATS (CELL) : 3
SCALING FOR ELEC. DOF : 6.00
NUMBER OF YOSHIDA-SUZUKI STEPS : 7
NUMBER OF INTEGRATION CYCLES (NIT): 1

This part of the output tells us, that the TIMESTEP 5.0 keyword was recognised (which is the default timestep), that the trajectory will be recorded and that NOSE-HOOVER thermostat is used.

RESTART INFORMATION READ ON FILE ./RESTART

Here we get notified, that the program has read the requested data from the restart file.

NFI EKINC TEMPP EKS ECLASSIC EHAM DIS TCPU
1 0.00000 0.0 -32.17071 -32.17010 -32.17010 0.458E-10 3.25
2 0.00000 0.0 -32.17071 -32.17010 -32.17010 0.727E-09 3.24
3 0.00000 0.0 -32.17071 -32.17010 -32.17010 0.365E-08 3.24
4 0.00000 0.0 -32.17071 -32.17010 -32.17010 0.114E-07 3.24
5 0.00000 0.1 -32.17071 -32.17010 -32.17010 0.275E-07 3.24
6 0.00000 0.1 -32.17071 -32.17010 -32.17010 0.565E-07 3.25
7 0.00000 0.1 -32.17071 -32.17010 -32.17010 0.104E-06 3.24
8 0.00000 0.2 -32.17072 -32.17010 -32.17010 0.175E-06 3.24
9 0.00000 0.2 -32.17072 -32.17010 -32.17010 0.279E-06 3.25
10 0.00000 0.3 -32.17072 -32.17010 -32.17010 0.422E-06 3.25
11 0.00000 0.3 -32.17072 -32.17010 -32.17010 0.614E-06 3.25
12 0.00000 0.4 -32.17072 -32.17010 -32.17010 0.865E-06 3.25
13 0.00000 0.4 -32.17072 -32.17010 -32.17010 0.119E-05 3.24
14 0.00000 0.5 -32.17072 -32.17010 -32.17010 0.159E-05 3.24
15 0.00000 0.6 -32.17072 -32.17010 -32.17010 0.209E-05 3.25
16 0.00000 0.6 -32.17072 -32.17010 -32.17010 0.269E-05 3.25
17 0.00000 0.7 -32.17072 -32.17010 -32.17010 0.343E-05 3.24
18 0.00000 0.8 -32.17072 -32.17010 -32.17010 0.429E-05 3.25
19 0.00000 0.9 -32.17072 -32.17010 -32.17010 0.532E-05 3.24
20 0.00000 1.0 -32.17072 -32.17010 -32.17010 0.652E-05 3.24
...
2981 0.00015 274.5 -32.16644 -32.17025 -32.17010 0.443E+01 3.25
2982 0.00015 268.3 -32.16638 -32.17025 -32.17010 0.444E+01 3.25
2983 0.00014 262.2 -32.16632 -32.17025 -32.17010 0.444E+01 3.26
2984 0.00014 256.0 -32.16627 -32.17024 -32.17010 0.445E+01 3.25
2985 0.00014 249.9 -32.16621 -32.17024 -32.17010 0.446E+01 3.26
2986 0.00013 243.8 -32.16615 -32.17024 -32.17010 0.446E+01 3.25
2987 0.00013 237.7 -32.16610 -32.17023 -32.17010 0.447E+01 3.25
2988 0.00013 231.7 -32.16604 -32.17023 -32.17010 0.447E+01 3.25
...
2997 0.00010 179.1 -32.16554 -32.17020 -32.17010 0.452E+01 3.25
2998 0.00010 173.6 -32.16549 -32.17020 -32.17010 0.452E+01 3.26
2999 0.00009 168.1 -32.16544 -32.17020 -32.17010 0.453E+01 3.26
3000 0.00009 162.6 -32.16539 -32.17019 -32.17010 0.453E+01 3.25

After some more output, we already discussed for the wavefunction optimisation, this is now part of the energy summary for a Car-Parrinello-MD run.

NFI: Step number (number of finite iterations)

EKINC: (fictitious) kinetic energy of the electron (sub-)system

TEMPP: Temerature (=kinetic energy / degrees of freedom) for atoms (ions)

EKS: Kohn-Sham Energy: equivalent to the potential energy in classical MD

ECLASSIC: Equivalent to the total energy in a classical MD (ECLASSIC = EHAM-EKINC)

EHAM: total energy, should be conserved

DIS: mean squared displacement of the atoms from the initial coordinates

TCPU: (CPU) time needed for this step

To read about why do the MD part and how to analyse results, please read this CPMD paper on water.

Reference: Kuo et al, J. Phys. Chem. B 2004, 108, 12990-12998

Note: For a meaningful Car-Parrinello MD, EKINC has to be (and stay) very small (although for larger systems with more electrons, the absolute value of EKINC will be larger, i.e. no drift in EKINC.

Exercise: plot EKINC vs NFI, TEMPP vs NFI, EKS vs NFI, ECLASSIC vs NFI, EHAM vs NFI. Discuss the trend of these curves.

MEAN VALUE +/- RMS DEVIATION
<x> [<x^2>-<x>^2]**(1/2)
ELECTRON KINETIC ENERGY 0.000125 0.105171E-03
IONIC TEMPERATURE 233.0551 194.923
DENSITY FUNCTIONAL ENERGY -32.169126 0.152974E-02
CLASSICAL ENERGY -32.170228 0.105180E-03
CONSERVED ENERGY -32.170104 0.247772E-05
NOSE ENERGY ELECTRONS 0.000000 0.00000
NOSE ENERGY IONS -0.003317 0.200165E-02
CONSTRAINTS ENERGY 0.000000 0.00000
RESTRAINTS ENERGY 0.000000 0.00000
ION DISPLACEMENT 1.25973 1.33130
CPU TIME 3.2487

Finally we get a summary of some averages and root mean squared deviations for some of the monitored quantities. This is quite useful to detect unwanted energy drifts or too large fluctuations in the simulation.

Exercise: visualise the motion of the system of (1 water + Cl-)

Type: ./traj2xyz.x < TRAJECTORY.clw_blyp_md > TRAJ.xyz

You can load the file TRAJ.xyz directly into the molecular visualisation program VMD.

-> Launch VMD program

-> File -> Load files for: New Molecule

-> click ‘Browse’, choose the file TRAJ.xyz

-> click ‘Load’

The trajectory file can be used to generate structural properties such as radial distribution functions and analyse the solvation shells such as Cl-O distances.

3.3.3 Kohn-Sham energies

Altogether the first part of the CPMD input (file name: inp.clw_blyp_ksl) now contains:

&CPMD
RESTART WAVEFUNCTION VELOCITIES COORDINATES LATEST
KOHN-SHAM ENERGIES
0
MAXSTEP
1000
STORE
10
TIMESTEP
5.0
EMASS
500.0
ISOLATED MOLECULE
&END

Output file (log.clw_blyp_ksl)

EIGENVALUES(EV) AND OCCUPATION:
1 -19.9458449 2.00000000 2 -11.8998056 2.00000000
3 -7.3120943 2.00000000 4 -4.5277656 2.00000000
5 -2.2061693 2.00000000 6 -0.5375340 2.00000000
7 -0.3936740 2.00000000 8 -0.3633460 2.00000000
CHEMICAL POTENTIAL = -0.3633465899 EV

This part lists the Kohn-Sham energies.

3.3.4 Kohn-Sham Orbitals

Altogether the first part of the CPMD input (file name: inp.clw_blyp_ksorb) now contains:

&CPMD
KOHN-SHAM ENERGIES
8
RESTART WAVEFUNCTION COORDINATES LATEST
DAVIDSON DIAGNOALIZATION
RHOOUT BANDS
8
-1 -2 -3 -4 -5 -6 -7 -8
&END

This generages a series of files with the names WAVEFUNCTION.1, WAVEFUNCTION.2, …, WAVEFUNCTION.8 which have to be converted to cube format with cpmd2cube.x -o clw1 WAVEFUNCTION.1

3.3.5 Wannier Analysis

To calculate the Wannier centers or orbitals for our system we need to do a properties calculation starting from the previously generated wavefunction.

For the Wannier orbitals the keywords LOCALIZE and WANNIER WFNOUT are required. This generates a series of files with the names WANNIER_1.* which have to be converted to cube format with cpmd2cube.x –o clw1 WANNIER_1.1.

Altogether the first and second parts of the CPMD input to calculate Wannier enters now contains:

&CPMD
RESTART WAVEFUNCTION LATEST
PROPERTIES
WANNIER DOS
&END

&PROP
LOCALIZE
&END

To plot all the WANNIER ORBITALS, replace the first part with:

&CPMD
RESTART WAVEFUNCTION COORDINATES LATEST
PROPERTIES
WANNIER WFNOUT ALL
&END

Exercise: use VMD to visualise the Kohn-Sham and Wannier orbitals. Describe the Kohn-Sham and Wannier Orbitals of the system. (Hint: One of the Kohn-Sham orbitals looks like this. Discuss delocalisation/localisation.)

Figure 2 Kohn-Sham Orbital

Note: Different phases can be visualised in VMD by creating two representations from the same data set and just using isovalues with opposite sign for each of them. The input and cube files used in this section are:

WAVEFUNCTION.* or WANNIER_1.*

clw1.*.cube (for Kohn-Sham orbitals) or clw11.*.cube (for Wannier orbitals)

VMD:

-> Launch VMD program

-> File -> Load files for: New Molecule

-> click ‘Browse’, choose the file TRAJ.xyz

-> click ‘Load’

-> Graphics -> Representations -> Drawing Method -> Choose CPK

-> repeat the above procedure and load the cube file again but this time choose Isosurface as Drawing method and play around with Isovalues.

To change colour of the background:

-> Graphics -> Colors -> Display -> Background -> Choose white

4. Exercises (63 water + Cl-)

The next step is a more typical (while ambitious) application of the CPMD code: a Car-Parrinello MD simulation of a bulk system with water and a chloride ion. In this specific example, we try to look at how the electronic structure changes when a chloride ion is solvated in liquid water. Our system will consist of 63 water molecules and one chloride ion (note the CHARGE keyword in the &SYSTEM section). To speed up the equilibration phase, we start from a restart configuration that has been equilibrated with classical MD for about 3 ns using the SPC/E water potential and CPMD for 31.56 ps. Since water has a dipole moment, you have to keep in mind, that we are calculating a system with periodic boundary conditions, so a water molecules ‘sees’ its images and interacts with them. There are methods implemented in CPMD to compensate this effect, but we won’t discuss them here.

Now run jobs to get data.

4.1 Run a wavefunction optimisation (use inp.w63Cl-wf).

4.2 We want to run the MD at 298 Kelvin, so now run a short MD with temperature rescaling for the atoms and no thermostat for the electrons (use inp.w63Cl-md)

4.3 Now you have your MD trajectory files, analyse them

4.4 Liquid water structure and hydrogen bonding

4.4.1 Generate a movie of trajectories using VMD which will read in the TRAJ.xyz file.

4.4.2 what to look at => Radial Distribution Functions

4.4.3 Compare your traj to the one we have made

4.4.4 Do you see water molecules entering and exiting solvation shell?

4.5 Plotting Kohn-Sham energies, Kohn-Sham orbitals, Wannier centers and Wannier orbitals

4.6 Follow the instructions above for clw1 but with your clw63 file (do it for last step of your trajectory) in reality we would want to examine 50-100 points sampled from the trajectory

4.7 Each student to look at one of the following:

4.7.1 Plot density of states for KS, KS orbitals

4.7.2 Plot Wannier orbitals and centers

4.7.3 Plot Cl-water distances over time

Talk:Mod:Hunt Research Group/cpmd water

2013-03-01T12:32:04Z

Lge:

Car-Parrinello Molecular Dynamics Simulation of Aqueous Solutions

1. Introduction

1.1 Aqueous solutions

In this lab you are going to run CPMD calculations of systems containing water and chloride. The following paragraphs describe why these systems are interesting to study.

Solvation of the chloride anion in water solution has been the subject of a substantial amount of experimental and theoretical work, in view of the central importance of chloride solutions in biochemical and metabolic processes, geology, atmospheric chemistry, and the chemical industry. Indeed, it has been discovered that airborne aqueous sea-salt aerosols serve as a global source of molecular chlorine and bromine, both in the polluted and in the remote lower marine troposphere. A variety of experimental methods have been used to investigate the hydration structure of chloride ions in water, including neutron and X-ray diffraction techniques, X-ray absorption spectroscopy (XAS) and femtosecond mid-infrared nonlinear spectroscopy. Despite these efforts, a complete microscopic model of the hydration shell structure of aqueous Cl- and of its room temperature dynamics is still being debated.

Difficulties in determining the structure of the solvation environment arise because of the comparable magnitudes of the water-Cl- and water-water interaction energies. Established results from the literature, both experimental and theoretical, reveal a rather inhomogeneous picture of the hydrated ion solvation shell structure. Vibrational spectroscopy experiments indicate that a chloride ion is asymmetrically solvated in clusters containing up to five water molecules. This contrasts with older and less direct experiments based on mass spectroscopy and photoelectron spectroscopy from which a symmetrical solvent cage around the anion was inferred. Experimental measurements such as photoelectron spectroscopy, IR spectroscopy and a combined technique of XAS (extended X-ray absorption fine structure, EXAFS and X-ray absorption near-edge structure, XANES) yield coordination numbers that are significantly scattered, ranging from 3 to 8. The first peak of the Cl-O radial distribution function (RDF) is measured to be in the range of 3.10-3.36 A.

Uncertainty in the coordination number is also evinced from theoretical studies, with variations between 5.1 and 8.4 depending on the simulation techniques adopted. Classical molecular dynamics (MD) simulations have been found to depend strongly on the anion-water and water-water potentials used. On the other hand, the use of different parametrized potentials, i.e. with and without a treatment of molecular polarizability, gave different structural properties. Quantum mechanics / molecular mechanics (QM/MM) simulations of Cl− in water indicate that the hydration structure of the an- ion has considerable flexibility in consequence to the weakness of Cl--water interactions. This leads to a competition between solvation of the ion and hydrogen bonding among water molecules. The QM/MM results clearly indicate the importance of QM treatment in order to correctly describe such a delicate balance between Cl--water and water-water interactions.

Reference: Tongraar, A.; T-Thienprasert, J.; Rujirawat, S.; Limpijumnong, S. Phys. Chem. Chem. Phys. 2010, 12, 10876.

1.2 Car-Parrinello/Born-Oppenheimer molecular dynamics

The aim of this tutorial is to help you getting started using the CPMD program. CPMD is an ab initio electronic structure and molecular dynamics (MD) program using a plane wave/pseudopotential implementation of density functional theory (DFT). It is mainly targeted at Car-Parrinello MD simulations, but also supports geometry optimisations, Born-Oppenheimer MD, path integral MD, response functions, excited states and calculations of some electronic properties. For further information you may want to take a look at the CPMD consortium homepage at www.cpmd.org.

Born-Oppenheimer (BO) MD: at each step of atomic MD, one solves the DFT SCF problem for a fixed atomic configuration, computes the wavefunction, and from it the (quantum mechanical) forces acting on the nuclei. This allows it to propagate the atoms classically to the next configuration. (In simple words, one computes energy and forces, move the atoms, re-compute energy and forces for the new configuration, move the atoms, and so on.)

Car-Parrinello: One propagates simultaneously a set of atoms and a fictitious set of electrons. From the fictitious set of electrons, one can estimate the forces on the atoms and move the atoms. Atoms and fictitious electrons have to be independent, and their dynamics is described using a generalised Lagrangian formalism, rather than simply propagating the atoms using Newton's equations like in Born-Oppenheimer MD. In the CPMD manual, it is written:

“The basic idea of the Car-Parrinello approach can be viewed to exploit the time-scale separation of fast electronic and slow nuclear motion by transforming that into classical-mechanical adiabatic energy-scale separation in the framework of dynamical systems theory. In order to achieve this goal the two-component quantum / classical problem is mapped onto a two-component purely classical problem with two separate energy scales at the expense of loosing the explicit time-dependence of the quantum subsystem dynamics.”

Born-Oppenheimer MD is easier to implement in practice, but slower. Also it requires a very well converged calculation of the forces at each step of dynamics. The Car-Parrinello only requires a very accurate ground state at the first step. The rest of the dynamics sustains itself, provided it is carried out in the right way.

If you would like to know more about the theoretical background of CPMD or BOMD, please read CPMD manual Sections 6.6 and 6.7.

2. Code Running Environment

2.1 Before running the job

Before you run CPMD it is a good idea to copy all you need in your local directory.

- Copy the folder lab from the usb disk to your laptop.

- open the terminal application

- open two windows, one will be for your local mac and the other for the hpc cluster

- on one of them login to the hpc cluster by typing ssh yourname@login.cx1.hpc.ic.ac.uk

- the cluster has two key directories /WORK/yourname and /HOME/yourname do all the calculations from the WORK/yourname directory, from now on this directory will be referred to simply as work

- cd to your work directory and make a new directory called liquids, cd into the new directory, this is where you will run all your jobs from

- copy the file from your desktop to hpc:

scp filename yourname@login.cx1.hpc.ic.ac.uk:/work/yourname/foldername/.

- unzip the tar file

tar -xvf filename.tar

2.2 How to run the job

In the directory cpmd you should have two subdirectories: clw1 and clw63.

To run CPMD type qsub runcpmd_wf (or other run scripts depending on the type of calculation such as runcpmd_md) in the clw1 or clw63 directory.

2.3 Using VMD to analyse results

For visualisation of the results you may want to take a look at the tutorial on visualising results from CPMD with the VMD program under www.theochem.ruhr-uni-bochum.de/go/cpmd-vmd.html

3. CPMD

3.1 Theoretical background

3.1.1 Pseudopotentials (read CPMD manual section 4.2)

3.1.2 Kohn-Sham orbitals, Wannier orbitals and Effective molecular orbitals

The EMO method for analysing the electronic structure of solutes and solvents starts by considering the Kohn-Sham Hamiltonian and energy eigenvalues obtained from the ab initio molecular dynamics. A band structure similar to that obtained for solid state systems emerges. While the Kohn-Sham Hamiltonian is diagonal, and the Kohn-Sham orbital energies are uniquely defined, the Kohn-Sham orbitals are delocalised Bloch states which extend over all space and the molecular picture is lost, as shown in Figure 1 (a). This makes it very difficult to analyse interactions between an ion and the solvating water molecules. Maximally localized Wannier orbitals are local to atomic centers. However, the Wannier Hamiltonian is not diagonal and thus there is no unique energy eigenvalue that can be associated with each orbital, as shown in Figure 1 (c). An intermediate representation where orbitals are local to a molecule, but are delocalised within the molecule has been developed. The EMOs are obtained by assigning Wannier orbitals to a specific molecule, and block-diagonalising the Wannier Hamiltonian within the molecular subspace, as shown in Figure 1 (b). This analysis has been successfully applied to pure liquid water. An isolated water molecule has C2v symmetry and valence MOs 1a1, 1b2, 2a1 and 1b1. A liquid environment is disordered and there is no symmetry. However, Figure 1 (b) shows that the EMOs strongly resemble the standard MOs for a single water molecule in vacuum. This close resemblance is by no means predetermined and is a validation of the EMO method. For clarity, we will continue to use the isolated atomic or molecular symmetry labels when we refer to the individual atomic orbitals, MOs and bands in the aqueous system.

3.2 Functional

We will use a gradient corrected functional (BLYP) instead of LDA throughout the tutorial as this combination of generalized gradient approximations to exchange and correlation has been shown to give good results for the structure and dynamics of water.

Figure 1 Wavefunction diagrams from a CPMD simulation of pure liquid water related to graphical representations of the respective Hamiltonian matrices: (a) Kohn-Sham Hamiltonian, (b) EMO Hamiltonian and (c) Wannier Hamiltonian.

3.3 Generating input files and understanding output files

The first example will demonstrate some of the basic steps of performing a CPMD calculation with a very simple system: 1 water molecule+Cl-, and a very simple task: calculate the electronic structure. We will use that as an example to have a look at the input file format, and how to read the output.

- emacs filename

- and then look inside and follow the instructions below

3.3.1 Wavefunction optimisation

(a) Input File format

For nearly all CPMD calculations, you first have to optimise the wavefunction of your system, and use that as a base for further calculations. For our first calculation you’ll need the input file inp.clw_blyp_wf and the pseudopotential files H_MT_BLYP.psp, O_MT_BLYP.psp, Cl_MT_BLYP.psp.

Now let’s have a look at the input file. The input file is organised in sections which start with &NAME and end with &END. Everything outside those sections is ignored. All keywords have to be in upper case or else they will be ignored. The sequence of the sections does not matter, nor does the order of keywords. A minimal input file must have a &CPMD, &SYSTEM and an &ATOMS section.

&CPMD

OPTIMIZE WAVEFUNCTION

CONVERGENCE ORBITALS

1.0d-7

&END

This first part of the &CPMD section instructs the program to do a wavefunction optimization (i.e. a single point calculation) with a tight convergence criterion (the default is 1.0d-5).

Exercise: look up in the CPMD manual about the usage of the keywords ODIIS, STORE, TIMESTEP, EMASS, ISOLATED MOLECULE.

&DFT

FUNCTIONAL BLYP

GC-CUTOFF

0.1D-06

&END

The &DFT section is used to select the density functional and related parameters. In this case we go with the BLYP functional.

&SYSTEM

ANGSTROM

SYMMETRY

0

CELL

11.800 1.0 1.0 0 0 0

CUTOFF

70.0

CHARGE

-1.0

&END

The &SYSTEM section contains various parameters related to the simulation cell and the representation of the electronic structure. The keywords SYMMETRY, CELL and CUTOFF are required and define the (periodic) symmetry, shape, and size of the simulation cell, as well as the plane wave cutoff (i.e. the size of the basis set). The keyword Angstrom additionally indicates that all lengths and coordinates are given in angstrom (not in a.u.).

Exercise: look up in the CPMD manual about the usage of the keyword CHARGE.

Finally the &ATOMS section is needed to specify the atom coordinates and the pseudopotentials, that are used to represent them. The detailed syntax of the pseudopotential specification is a bit complicated and will not be needed nor discussed here. If you want to know more, please have a look at the Further details of the Input section of the CPMD manual (P222).

- To run, type: qsub runcpmd_wf,

The code will generate the following output files once the calculation is completed after a few minutes: log.clw_blyp_wf, GOMETRY., RESTART.. The purpose of the wavefunction optimisation is to generate the RESTART. file which is needed for further calculations.

(b) Output File Format

To start the calculation, which should be completed in less than a minute once the job starts running. The main output of the CPMD program is now in the file log.clw_blyp_wf. Let’s have a closer look at the contents of this file.

PROGRAM CPMD STARTED AT: Thu Jan 20 16:23:24 2011
SETCNST| USING: CODATA 2006 UNITS
THE INPUT FILE IS: /work/lge/wannier/test/inp.clw_blyp_wf
THIS JOB RUNS ON: cx1-50-2-1.cx1.hpc.ic.ac.uk
THE CURRENT DIRECTORY IS:
/tmp/pbs.5020787.cx1
THE TEMPORARY DIRECTORY IS:
/tmp/pbs.5020787.cx1
THE PROCESS ID IS: 13680

Here we have some technical information about the environment, where this job was run.

SINGLE POINT DENSITY OPTIMIZATION
PATH TO THE RESTART FILES: ./
GRAM-SCHMIDT ORTHOGONALIZATION
MAXIMUM NUMBER OF STEPS: 1000 STEPS
MAXIMUM NUMBER OF ITERATIONS FOR SC: 1000 STEPS
PRINT INTERMEDIATE RESULTS EVERY 10001 STEPS
STORE INTERMEDIATE RESULTS EVERY 10 STEPS
NUMBER OF DISTINCT RESTART FILES: 1
TEMPERATURE IS CALCULATED ASSUMING AN ISOLATED MOLECULE
FICTITIOUS ELECTRON MASS: 500.0000
TIME STEP FOR ELECTRONS: 5.0000
TIME STEP FOR IONS: 5.0000
CONVERGENCE CRITERIA FOR WAVEFUNCTION OPTIMIZATION: 1.0000E-07
WAVEFUNCTION OPTIMIZATION BY PRECONDITIONED DIIS
THRESHOLD FOR THE WF-HESSIAN IS 0.5000
MAXIMUM NUMBER OF VECTORS RETAINED FOR DIIS: 5
STEPS UNTIL DIIS RESET ON POOR PROGRESS: 5
FULL ELECTRONIC GRADIENT IS USED
SPLINE INTERPOLATION IN G-SPACE FOR PSEUDOPOTENTIAL FUNCTIONS
NUMBER OF SPLINE POINTS: 5000

This section now gives you a summary of the parameters read in from the &CPMD section, or their respective default settings.

EXCHANGE CORRELATION FUNCTIONALS
LDA EXCHANGE: SLATER (ALPHA = 0.66667)
LDA CORRELATION: LEE, YANG & PARR
[C.L. LEE, W. YANG, AND R.G. PARR, PRB 37 785 (1988)]
GRADIENT CORRECTED FUNCTIONAL
DENSITY THRESHOLD: 1.00000E-07
EXCHANGE ENERGY
[A.D. BECKE, PHYS. REV. A 38, 3098 (1988)]
PARAMETER BETA: 0.004200
CORRELATION ENERGY
[LYP: C.L. LEE ET AL. PHYS. REV. B 37, 785 (1988)]
*** DETSP| SIZE OF THE PROGRAM IS 8748/ 110552 kBYTES ***
>>>>>>>> CENTER OF MASS HAS BEEN MOVED TO CENTER OF BOX <<<<<<<<
***************************** ATOMS ****************************
NR TYPE X(bohr) Y(bohr) Z(bohr) MBL
1 Cl 11.199323 11.186938 9.180419 3
2 O 10.970667 11.067318 15.135702 3
3 H 10.558139 11.108892 13.264684 3
4 H 12.820897 11.171631 15.013437 3
****************************************************************
NUMBER OF STATES: 8
NUMBER OF ELECTRONS: 16.00000
CHARGE: -1.00000
ELECTRON TEMPERATURE(KELVIN): 0.00000
OCCUPATION
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0

This part of the output tells you which and how many atoms and electrons are used, what functional and what pseudopotentials were used, and what the values of some related parameters are.

POISSON EQUATION SOLVER : HOCKNEY
COULOMB SMOOTHING RADIUS : 1.593
SYMMETRY: SIMPLE CUBIC
LATTICE CONSTANT(a.u.): 22.29877
CELL DIMENSION: 22.2988 1.0000 1.0000 0.0000 0.0000 0.0000
VOLUME(OMEGA IN BOHR^3): 11087.72952
LATTICE VECTOR A1(BOHR): 22.2988 0.0000 0.0000
LATTICE VECTOR A2(BOHR): 0.0000 22.2988 0.0000
LATTICE VECTOR A3(BOHR): 0.0000 0.0000 22.2988
RECIP. LAT. VEC. B1(2Pi/BOHR): 0.0448 0.0000 0.0000
RECIP. LAT. VEC. B2(2Pi/BOHR): 0.0000 0.0448 0.0000
RECIP. LAT. VEC. B3(2Pi/BOHR): 0.0000 0.0000 0.0448
REAL SPACE MESH: 120 120 120
WAVEFUNCTION CUTOFF(RYDBERG): 70.00000
DENSITY CUTOFF(RYDBERG): (DUAL= 4.00) 280.00000
NUMBER OF PLANE WAVES FOR WAVEFUNCTION CUTOFF: 54804
NUMBER OF PLANE WAVES FOR DENSITY CUTOFF: 438632
****************************************************************

This part of the output presents the settings read in from the &SYSTEM section of the input file and some derived parameters.
[…]

(K+E1+L+N+X) TOTAL ENERGY = -31.48398404 A.U.
(K) KINETIC ENERGY = 19.91015701 A.U.
(E1=A-S+R) ELECTROSTATIC ENERGY = -26.99115337 A.U.
(S) ESELF = 28.92331533 A.U.
(R) ESR = 0.74536593 A.U.
(L) LOCAL PSEUDOPOTENTIAL ENERGY = -19.20863875 A.U.
(N) N-L PSEUDOPOTENTIAL ENERGY = 2.63857242 A.U.
(X) EXCHANGE-CORRELATION ENERGY = -7.83292134 A.U.
GRADIENT CORRECTION ENERGY = -0.43675318 A.U.

After some output to report the setup of the initial guess for the electronic structure, we now see a summary of the various energy contribution of the total energy of the system, based on the initial guess. Now the program is ready to start the wavefunction optimisation.

Starting from the initial guess based on atomic wavefunctions the wavefunction for the total system is now calculated with an optimisation procedure. You can follow the progress of the optimisation in the output file.

NFI GEMAX CNORM ETOT DETOT TCPU
1 4.556E-02 4.038E-03 -31.483984 0.000E+00 5.88
2 1.580E-02 1.381E-03 -32.031355 -5.474E-01 5.90
3 1.347E-02 6.554E-04 -32.139961 -1.086E-01 5.93
4 7.667E-03 3.432E-04 -32.162687 -2.273E-02 5.95
5 3.490E-03 1.256E-04 -32.168927 -6.240E-03 5.97
6 2.655E-03 6.618E-05 -32.170107 -1.180E-03 5.98
7 1.888E-03 3.959E-05 -32.170488 -3.805E-04 5.99
8 1.004E-03 2.399E-05 -32.170647 -1.597E-04 5.97
9 6.207E-04 1.431E-05 -32.170689 -4.167E-05 5.96
10 4.309E-04 8.966E-06 -32.170703 -1.373E-05 5.96

NFI: Step number (number of finite iterations)

GEMAX: largest off-diagonal component

CNORM: average of the off-diagonal components

ETOT: total energy

DETOT: change in total energy to the previous step

TCPU: (CPU) time for this step

And you can see that the calculation stops after the convergence of 1.0d-7 has been reached for the GEMAX value.
****************************************************************
* *
* FINAL RESULTS *
* *
****************************************************************
****************************************************************
* ATOMIC COORDINATES *
****************************************************************
1 Cl 11.199323 11.186938 9.180419
2 O 10.970667 11.067318 15.135702
3 H 10.558139 11.108892 13.264684
4 H 12.820897 11.171631 15.013437
****************************************************************
ELECTRONIC GRADIENT:
MAX. COMPONENT = 9.69721E-08 NORM = 8.07825E-10
TOTAL INTEGRATED ELECTRONIC DENSITY
IN G-SPACE = 16.000000
IN R-SPACE = 16.000000
(K+E1+L+N+X) TOTAL ENERGY = -32.17071373 A.U.
(K) KINETIC ENERGY = 18.31556847 A.U.
(E1=A-S+R) ELECTROSTATIC ENERGY = -26.97530784 A.U.
(S) ESELF = 28.92331533 A.U.
(R) ESR = 0.74536593 A.U.
(L) LOCAL PSEUDOPOTENTIAL ENERGY = -18.46114493 A.U.
(N) N-L PSEUDOPOTENTIAL ENERGY = 2.17769037 A.U.
(X) EXCHANGE-CORRELATION ENERGY = -7.22751980 A.U.
GRADIENT CORRECTION ENERGY = -0.41653735 A.U.
****************************************************************

Here we have the final summary of the results from our single point calculation. Please note that regardless of the input units, coordinates in the CPMD output are always in atomic units.

Other Output files:

Apart from the console output, our CPMD run created a few other files. Most importantly the restart file RESTART., which contains the final state of the system when the program terminated. This is needed to start other calculations, which need a converged wavefunction as a starting point. The file GEOMETRY. contains the coordinates of the atoms in atomic unit. This can be converted to a .xyz file.

3.3.2 Car-Parrinello Molecular dynamics

Based on the previously calculated electronic structure, we can now start a Car-Parrinello Molecular dynamics calculation. Note that although you can start a CP-MD run from a non-converged wavefunction (e.g. by not restarting from a pre-optimised wavefunction), you will be far away from the Born-Oppenheimer surface, and thus your result will be unphysical.

To run, type:

cp RESTART. RESTART

qsub runcpmd_md

3.3.2.1 Input for CP dynamics

For the CP-MD job you need a new input file, inp.clw_blyp_md, which should be copied into the same directory, where you started the wavefunction optimisation run. If you compare it to the previous input files, you will find, that the only changes are again only in the &CPMD section of the input files.

&CPMD
MOLECULAR DYNAMICS CP
RESTART WAVEFUNCTION COORDINATES VELOCITIES NOSEP LATEST
QUENCH BO
MIRROR
CONVERGENCE ORBITAL
1.0D-7
ODIIS
5
MAXSTEP
3000
STORE
20
TIMESTEP
5
EMASS
500.0
NOSE IONS
298.0 1100
TRAJECTORY SAMPLE
10
ISOLATED MOLECULE
&END

The keyword MOLECULAR DYNAMICS CP defines the job type. Furthermore we tell the CPMD program to pick up the previously calculated wavefunction and coordinates from the latest restart file (which is named RESTART by default). MAXSTEP limits the MD to 3000 steps and the equations of motion will be solved for a time step of 5 atomic units (~0.12 femtoseconds). The temperature of the system will be initialised to 298K via the NOSE IONS keyword with Nose thermostat.

- Now start the CPMD program once more: qsub runcpmd_md

This run should be completed in a few minutes.

3.3.2.2 CP dynamics output

The output of the CPMD program is now in the file log.clw_blyp_md. There are also some new files (TRAJECTORY, ENERGIES). We will have a look at the output file first.

CAR-PARRINELLO MOLECULAR DYNAMICS
PATH TO THE RESTART FILES: ./
RESTART WITH OLD ORBITALS
RESTART WITH OLD ION POSITIONS
RESTART WITH OLD VELOCITIES
RESTART WITH OLD ION THERMOSTAT
RESTART WITH LATEST RESTART FILE
ITERATIVE ORTHOGONALIZATION
MAXIT: 30
EPS: 1.00E-06
MAXIMUM NUMBER OF STEPS: 3000 STEPS

The header is unchanged up to the point where the settings from the &CPMD section are printed. As you can see, the program has recognised the RESTART and the MAXSTEP keywords. (NOTE: in the CPMD code atoms are sometimes referred to as ions. This is due to the pseudopotential approach, where you integrate the core electrons into the (pseudo)atom which then could also be described as an ion.)

TIME STEP FOR ELECTRONS: 5.0000
TIME STEP FOR IONS: 5.0000
QUENCH SYSTEM TO THE BORN-OPPENHEIMER SURFACE
TRAJECTORIES ARE SAVED ON FILE EVERY 10 STEPS
ELECTRON DYNAMICS: THE TEMPERATURE IS NOT CONTROLLED
ION DYNAMICS: TEMPERATURE CONTROL (NOSE-HOOVER THERMOSTATS)
TARGET TEMPERATURE(KELVIN): 2.980000E+02
CHARACTERISTIC FREQUENCY(CM**-1): 1100.00
NOSE PARAMETERS
NUMBER OF THERMOSTATS (IONS) : 3
NUMBER OF THERMOSTATS (ELECTRONS) : 3
NUMBER OF THERMOSTATS (CELL) : 3
SCALING FOR ELEC. DOF : 6.00
NUMBER OF YOSHIDA-SUZUKI STEPS : 7
NUMBER OF INTEGRATION CYCLES (NIT): 1

This part of the output tells us, that the TIMESTEP 5.0 keyword was recognised (which is the default timestep), that the trajectory will be recorded and that NOSE-HOOVER thermostat is used.

RESTART INFORMATION READ ON FILE ./RESTART

Here we get notified, that the program has read the requested data from the restart file.

NFI EKINC TEMPP EKS ECLASSIC EHAM DIS TCPU
1 0.00000 0.0 -32.17071 -32.17010 -32.17010 0.458E-10 3.25
2 0.00000 0.0 -32.17071 -32.17010 -32.17010 0.727E-09 3.24
3 0.00000 0.0 -32.17071 -32.17010 -32.17010 0.365E-08 3.24
4 0.00000 0.0 -32.17071 -32.17010 -32.17010 0.114E-07 3.24
5 0.00000 0.1 -32.17071 -32.17010 -32.17010 0.275E-07 3.24
6 0.00000 0.1 -32.17071 -32.17010 -32.17010 0.565E-07 3.25
7 0.00000 0.1 -32.17071 -32.17010 -32.17010 0.104E-06 3.24
8 0.00000 0.2 -32.17072 -32.17010 -32.17010 0.175E-06 3.24
9 0.00000 0.2 -32.17072 -32.17010 -32.17010 0.279E-06 3.25
10 0.00000 0.3 -32.17072 -32.17010 -32.17010 0.422E-06 3.25
11 0.00000 0.3 -32.17072 -32.17010 -32.17010 0.614E-06 3.25
12 0.00000 0.4 -32.17072 -32.17010 -32.17010 0.865E-06 3.25
13 0.00000 0.4 -32.17072 -32.17010 -32.17010 0.119E-05 3.24
14 0.00000 0.5 -32.17072 -32.17010 -32.17010 0.159E-05 3.24
15 0.00000 0.6 -32.17072 -32.17010 -32.17010 0.209E-05 3.25
16 0.00000 0.6 -32.17072 -32.17010 -32.17010 0.269E-05 3.25
17 0.00000 0.7 -32.17072 -32.17010 -32.17010 0.343E-05 3.24
18 0.00000 0.8 -32.17072 -32.17010 -32.17010 0.429E-05 3.25
19 0.00000 0.9 -32.17072 -32.17010 -32.17010 0.532E-05 3.24
20 0.00000 1.0 -32.17072 -32.17010 -32.17010 0.652E-05 3.24
...
2981 0.00015 274.5 -32.16644 -32.17025 -32.17010 0.443E+01 3.25
2982 0.00015 268.3 -32.16638 -32.17025 -32.17010 0.444E+01 3.25
2983 0.00014 262.2 -32.16632 -32.17025 -32.17010 0.444E+01 3.26
2984 0.00014 256.0 -32.16627 -32.17024 -32.17010 0.445E+01 3.25
2985 0.00014 249.9 -32.16621 -32.17024 -32.17010 0.446E+01 3.26
2986 0.00013 243.8 -32.16615 -32.17024 -32.17010 0.446E+01 3.25
2987 0.00013 237.7 -32.16610 -32.17023 -32.17010 0.447E+01 3.25
2988 0.00013 231.7 -32.16604 -32.17023 -32.17010 0.447E+01 3.25
...
2997 0.00010 179.1 -32.16554 -32.17020 -32.17010 0.452E+01 3.25
2998 0.00010 173.6 -32.16549 -32.17020 -32.17010 0.452E+01 3.26
2999 0.00009 168.1 -32.16544 -32.17020 -32.17010 0.453E+01 3.26
3000 0.00009 162.6 -32.16539 -32.17019 -32.17010 0.453E+01 3.25

After some more output, we already discussed for the wavefunction optimisation, this is now part of the energy summary for a Car-Parrinello-MD run.

NFI: Step number (number of finite iterations)

EKINC: (fictitious) kinetic energy of the electron (sub-)system

TEMPP: Temerature (=kinetic energy / degrees of freedom) for atoms (ions)

EKS: Kohn-Sham Energy: equivalent to the potential energy in classical MD

ECLASSIC: Equivalent to the total energy in a classical MD (ECLASSIC = EHAM-EKINC)

EHAM: total energy, should be conserved

DIS: mean squared displacement of the atoms from the initial coordinates

TCPU: (CPU) time needed for this step

To read about why do the MD part and how to analyse results, please read this CPMD paper on water.

Reference: Kuo et al, J. Phys. Chem. B 2004, 108, 12990-12998

Note: For a meaningful Car-Parrinello MD, EKINC has to be (and stay) very small (although for larger systems with more electrons, the absolute value of EKINC will be larger, i.e. no drift in EKINC.

Exercise: plot EKINC vs NFI, TEMPP vs NFI, EKS vs NFI, ECLASSIC vs NFI, EHAM vs NFI. Discuss the trend of these curves.

MEAN VALUE +/- RMS DEVIATION
<x> [<x^2>-<x>^2]**(1/2)
ELECTRON KINETIC ENERGY 0.000125 0.105171E-03
IONIC TEMPERATURE 233.0551 194.923
DENSITY FUNCTIONAL ENERGY -32.169126 0.152974E-02
CLASSICAL ENERGY -32.170228 0.105180E-03
CONSERVED ENERGY -32.170104 0.247772E-05
NOSE ENERGY ELECTRONS 0.000000 0.00000
NOSE ENERGY IONS -0.003317 0.200165E-02
CONSTRAINTS ENERGY 0.000000 0.00000
RESTRAINTS ENERGY 0.000000 0.00000
ION DISPLACEMENT 1.25973 1.33130
CPU TIME 3.2487

Finally we get a summary of some averages and root mean squared deviations for some of the monitored quantities. This is quite useful to detect unwanted energy drifts or too large fluctuations in the simulation.

Exercise: visualise the motion of the system of (1 water + Cl-)

Type: ./traj2xyz.x < TRAJECTORY.clw_blyp_md > TRAJ.xyz

You can load the file TRAJ.xyz directly into the molecular visualisation program VMD.

-> Launch VMD program

-> File -> Load files for: New Molecule

-> click ‘Browse’, choose the file TRAJ.xyz

-> click ‘Load’

The trajectory file can be used to generate structural properties such as radial distribution functions and analyse the solvation shells such as Cl-O distances.

3.3.3 Kohn-Sham energies

Altogether the first part of the CPMD input (file name: inp.clw_blyp_ksl) now contains:

&CPMD
RESTART WAVEFUNCTION VELOCITIES COORDINATES LATEST
KOHN-SHAM ENERGIES
0
MAXSTEP
1000
STORE
10
TIMESTEP
5.0
EMASS
500.0
ISOLATED MOLECULE
&END

Output file (log.clw_blyp_ksl)

EIGENVALUES(EV) AND OCCUPATION:
1 -19.9458449 2.00000000 2 -11.8998056 2.00000000
3 -7.3120943 2.00000000 4 -4.5277656 2.00000000
5 -2.2061693 2.00000000 6 -0.5375340 2.00000000
7 -0.3936740 2.00000000 8 -0.3633460 2.00000000
CHEMICAL POTENTIAL = -0.3633465899 EV

This part lists the Kohn-Sham energies.

3.3.4 Kohn-Sham Orbitals

Altogether the first part of the CPMD input (file name: inp.clw_blyp_ksorb) now contains:

&CPMD
KOHN-SHAM ENERGIES
8
RESTART WAVEFUNCTION COORDINATES LATEST
DAVIDSON DIAGNOALIZATION
RHOOUT BANDS
8
-1 -2 -3 -4 -5 -6 -7 -8
&END

This generages a series of files with the names WAVEFUNCTION.1, WAVEFUNCTION.2, …, WAVEFUNCTION.8 which have to be converted to cube format with cpmd2cube.x -o clw1 WAVEFUNCTION.1

3.3.5 Wannier Analysis

To calculate the Wannier centers or orbitals for our system we need to do a properties calculation starting from the previously generated wavefunction.

For the Wannier orbitals the keywords LOCALIZE and WANNIER WFNOUT are required. This generates a series of files with the names WANNIER_1.* which have to be converted to cube format with cpmd2cube.x –o clw1 WANNIER_1.1.

Altogether the first and second parts of the CPMD input to calculate Wannier enters now contains:

&CPMD
RESTART WAVEFUNCTION LATEST
PROPERTIES
WANNIER DOS
&END

&PROP
LOCALIZE
&END

To plot all the WANNIER ORBITALS, replace the first part with:

&CPMD
RESTART WAVEFUNCTION COORDINATES LATEST
PROPERTIES
WANNIER WFNOUT ALL
&END

Exercise: use VMD to visualise the Kohn-Sham and Wannier orbitals. Describe the Kohn-Sham and Wannier Orbitals of the system. (Hint: One of the Kohn-Sham orbitals looks like this. Discuss delocalisation/localisation.)

Figure 2 Kohn-Sham Orbital

Note: Different phases can be visualised in VMD by creating two representations from the same data set and just using isovalues with opposite sign for each of them. The input and cube files used in this section are:

WAVEFUNCTION.* or WANNIER_1.*

clw1.*.cube (for Kohn-Sham orbitals) or clw11.*.cube (for Wannier orbitals)

VMD:

-> Launch VMD program

-> File -> Load files for: New Molecule

-> click ‘Browse’, choose the file TRAJ.xyz

-> click ‘Load’

-> Graphics -> Representations -> Drawing Method -> Choose CPK

-> repeat the above procedure and load the cube file again but this time choose Isosurface as Drawing method and play around with Isovalues.

To change colour of the background:

-> Graphics -> Colors -> Display -> Background -> Choose white

4. Exercises (63 water + Cl-)

The next step is a more typical (while ambitious) application of the CPMD code: a Car-Parrinello MD simulation of a bulk system with water and a chloride ion. In this specific example, we try to look at how the electronic structure changes when a chloride ion is solvated in liquid water. Our system will consist of 63 water molecules and one chloride ion (note the CHARGE keyword in the &SYSTEM section). To speed up the equilibration phase, we start from a restart configuration that has been equilibrated with classical MD for about 3 ns using the SPC/E water potential and CPMD for 31.56 ps. Since water has a dipole moment, you have to keep in mind, that we are calculating a system with periodic boundary conditions, so a water molecules ‘sees’ its images and interacts with them. There are methods implemented in CPMD to compensate this effect, but we won’t discuss them here.

Now run jobs to get data.

4.1 Run a wavefunction optimisation (use inp.w63Cl-wf).

4.2 We want to run the MD at 298 Kelvin, so now run a short MD with temperature rescaling for the atoms and no thermostat for the electrons (use inp.w63Cl-md)

4.3 Now you have your MD trajectory files, analyse them

4.4 Liquid water structure and hydrogen bonding

4.4.1 Generate a movie of trajectories using VMD which will read in the TRAJ.xyz file.

4.4.2 what to look at => Radial Distribution Functions

4.4.3 Compare your traj to the one we have made

4.4.4 Do you see water molecules entering and exiting solvation shell?

4.5 Plotting Kohn-Sham energies, Kohn-Sham orbitals, Wannier centers and Wannier orbitals

4.6 Follow the instructions above for clw1 but with your clw63 file (do it for last step of your trajectory) in reality we would want to examine 50-100 points sampled from the trajectory

4.7 Each student to look at one of the following:

4.7.1 Plot density of states for KS, KS orbitals

4.7.2 Plot Wannier orbitals and centers

4.7.3 Plot Cl-water distances over time

Mod:Hunt Research Group

2013-02-28T18:18:24Z

Lge: /* Setup and Running MD Simulations */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===Resources===

#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link] (notes by Tricia)

===Gaussian General===
#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] (notes by Everyone!)
#Instructions for visualizing electrostatic potentials [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link] (notes by Flo)
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#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] (notes by Heiko)
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link] (notes by Richard)
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link] (notes by Bryan & Richard)

===Unix and HPC===
#Setting up a connection to HPC if you have a PC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link] (notes by Hieu)
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link] (notes by Heiko)
#HPC servers and run scripts [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link] (notes by Tricia and Ling)]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link] (notes by Heiko)
#How to set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link] (notes by Heiko)
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link] (notes by Heiko)
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link] (notes by Heiko)
#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] (notes by Rachael, Weihong and Ling)
#How to set up cx2 [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cx2 link] (notes by Ling)

===Installing and using packages===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link] (notes by Ling)
#Beginners guide to VMD: a molecular dynamics visualisation package [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link] (notes by Ling & Bryan)
#DLPOLY a MD simulation package, Installation on an IMac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link] (notes by Ling)
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link] (notes by Tricia)
#How to install Geomview [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/geomview link] (notes by Tricia)
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/] (Ling)
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link] (notes by Bryan)

===Setup and Running MD Simulations===
#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#Packmol for generating starting configurations [http://www.ime.unicamp.br/~martinez/packmol/] from Packmol webpage.
#Getting the Force Field [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Wheretostart link] (notes by Richard)
#Choosing an Ensemble [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Ensembles link] (notes by Richard)
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link] (notes by Richard)
#Visualising your Simulation [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VisualisingyourSimulation link] (notes by Richard)
#Voids in ILs[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids link] (notes by Ling)
#How to equilibrate an MD run[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/equilibration link] (notes by Tricia and Ling)]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link] (notes by Ling)]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link] (notes by Ling and Tricia)]
#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] (notes by Ling)
#How to run CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k_how link] (notes by Ling)

===Research Notes===
#Cl- in water [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link] (notes by Ling)]
#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] (notes by Yannis)
#Functional for ILs using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/IL_cpmd_functional link] (notes by Ling)
#[bmim]Cl using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cpmd link] (notes by Ling)
#[bmim]Cl using CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cp2k link] (notes by Ling)
#mman using CPMD and Gaussian [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/mman link] (notes by Ling)
#[emim]SCN using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emimscn link] (notes by Ling)
#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] (notes by Ling)
#CP2K Donts [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k link] (notes by Ling)
#How to make VMD trajectory repeated periodically [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/vmd link] (notes by Ling)
#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)

===CDT records===
#Activities record [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/CDT_records records]

===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] (notes by Tricia)
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link] (notes by Tricia)
#[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/calendar Calendar] (notes by Tricia)
#Demonstrating in the 3rd year computational chemistry lab [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/compchemlab Timetable] (notes by Tricia)
#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] notes by Tricia

Mod:Hunt Research Group

2013-02-28T18:18:15Z

Lge: /* Research Notes */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===Resources===

#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link] (notes by Tricia)

===Gaussian General===
#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] (notes by Everyone!)
#Instructions for visualizing electrostatic potentials [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link] (notes by Flo)
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#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] (notes by Heiko)
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link] (notes by Richard)
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link] (notes by Bryan & Richard)

===Unix and HPC===
#Setting up a connection to HPC if you have a PC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link] (notes by Hieu)
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link] (notes by Heiko)
#HPC servers and run scripts [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link] (notes by Tricia and Ling)]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link] (notes by Heiko)
#How to set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link] (notes by Heiko)
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link] (notes by Heiko)
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link] (notes by Heiko)
#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] (notes by Rachael, Weihong and Ling)
#How to set up cx2 [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cx2 link] (notes by Ling)

===Installing and using packages===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link] (notes by Ling)
#Beginners guide to VMD: a molecular dynamics visualisation package [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link] (notes by Ling & Bryan)
#DLPOLY a MD simulation package, Installation on an IMac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link] (notes by Ling)
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link] (notes by Tricia)
#How to install Geomview [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/geomview link] (notes by Tricia)
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/] (Ling)
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link] (notes by Bryan)

===Setup and Running MD Simulations===
#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#Packmol for generating starting configurations [http://www.ime.unicamp.br/~martinez/packmol/] from Packmol webpage.
#Getting the Force Field [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Wheretostart link] (notes by Richard)
#Choosing an Ensemble [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Ensembles link] (notes by Richard)
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link] (notes by Richard)
#Visualising your Simulation [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VisualisingyourSimulation link] (notes by Richard)
#Voids in ILs[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids link] (notes by Ling)
#How to equilibrate an MD run[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/equilibration link] (notes by Tricia and Ling)]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link] (notes by Ling)]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link] (notes by Ling and Tricia)]
#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] (notes by Ling)

===Research Notes===
#Cl- in water [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link] (notes by Ling)]
#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] (notes by Yannis)
#Functional for ILs using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/IL_cpmd_functional link] (notes by Ling)
#[bmim]Cl using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cpmd link] (notes by Ling)
#[bmim]Cl using CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cp2k link] (notes by Ling)
#mman using CPMD and Gaussian [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/mman link] (notes by Ling)
#[emim]SCN using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emimscn link] (notes by Ling)
#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] (notes by Ling)
#CP2K Donts [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k link] (notes by Ling)
#How to make VMD trajectory repeated periodically [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/vmd link] (notes by Ling)
#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)

===CDT records===
#Activities record [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/CDT_records records]

===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] (notes by Tricia)
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link] (notes by Tricia)
#[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/calendar Calendar] (notes by Tricia)
#Demonstrating in the 3rd year computational chemistry lab [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/compchemlab Timetable] (notes by Tricia)
#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] notes by Tricia

Mod:Hunt Research Group

2013-02-28T18:17:54Z

Lge: /* Research Notes */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===Resources===

#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link] (notes by Tricia)

===Gaussian General===
#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] (notes by Everyone!)
#Instructions for visualizing electrostatic potentials [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link] (notes by Flo)
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#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] (notes by Heiko)
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link] (notes by Richard)
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link] (notes by Bryan & Richard)

===Unix and HPC===
#Setting up a connection to HPC if you have a PC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link] (notes by Hieu)
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link] (notes by Heiko)
#HPC servers and run scripts [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link] (notes by Tricia and Ling)]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link] (notes by Heiko)
#How to set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link] (notes by Heiko)
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link] (notes by Heiko)
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link] (notes by Heiko)
#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] (notes by Rachael, Weihong and Ling)
#How to set up cx2 [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cx2 link] (notes by Ling)

===Installing and using packages===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link] (notes by Ling)
#Beginners guide to VMD: a molecular dynamics visualisation package [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link] (notes by Ling & Bryan)
#DLPOLY a MD simulation package, Installation on an IMac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link] (notes by Ling)
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link] (notes by Tricia)
#How to install Geomview [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/geomview link] (notes by Tricia)
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/] (Ling)
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link] (notes by Bryan)

===Setup and Running MD Simulations===
#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#Packmol for generating starting configurations [http://www.ime.unicamp.br/~martinez/packmol/] from Packmol webpage.
#Getting the Force Field [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Wheretostart link] (notes by Richard)
#Choosing an Ensemble [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Ensembles link] (notes by Richard)
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link] (notes by Richard)
#Visualising your Simulation [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VisualisingyourSimulation link] (notes by Richard)
#Voids in ILs[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids link] (notes by Ling)
#How to equilibrate an MD run[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/equilibration link] (notes by Tricia and Ling)]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link] (notes by Ling)]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link] (notes by Ling and Tricia)]
#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] (notes by Ling)

===Research Notes===
#Cl- in water [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link] (notes by Ling)]
#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] (notes by Yannis)
#Functional for ILs using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/IL_cpmd_functional link] (notes by Ling)
#[bmim]Cl using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cpmd link] (notes by Ling)
#[bmim]Cl using CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cp2k link] (notes by Ling)
#mman using CPMD and Gaussian [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/mman link] (notes by Ling)
#[emim]SCN using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emimscn link] (notes by Ling)
#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] (notes by Ling)
#CP2K Donts [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k link] (notes by Ling)
#How to make VMD trajectory repeated periodically [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/vmd link] (notes by Ling)
#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)
#How to run CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k_how link] (notes by Ling)

===CDT records===
#Activities record [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/CDT_records records]

===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] (notes by Tricia)
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link] (notes by Tricia)
#[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/calendar Calendar] (notes by Tricia)
#Demonstrating in the 3rd year computational chemistry lab [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/compchemlab Timetable] (notes by Tricia)
#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] notes by Tricia

Talk:Mod:Hunt Research Group/cp2k how

2013-02-28T18:14:04Z

Lge: Created page with "1. Website: http://manual.cp2k.org/trunk/ 2. Lecture notes: http://www.cecam.org/workshop-4-529.html 3. Files you need: Basis/Potential Files (can be downloaded together wit..."

1. Website:
http://manual.cp2k.org/trunk/

2. Lecture notes:
http://www.cecam.org/workshop-4-529.html

3. Files you need:

Basis/Potential Files (can be downloaded together with the CP2K package):
-BASIS_SET
-BASIS_MOLOPT
-POTENTIAL

runscript:
-runcp2k

-runcp2krestart

Input/output files (in directory on drobo: /Ling_project_2013/Rio-Tinto/cp2kcuwater/input_output_files/):
- cp2k_cuwater.inp
- cp2k_cuwater.out

4. Annotation of input files:

4.1 Example of [bmim]Cl:

&GLOBAL --> Section that contains general information about the simulation and parameters for the whole program.
PROJECT bmimcl --> Name of the project, used to determine the name of the files generated by the program.
PRINT_LEVEL MEDIUM --> How much output is written out.
RUN_TYPE MD --> Type of run that to perform (e.g. MD, GeoOpt, MC).
&END --> End of section.

&FORCE_EVAL --> Parameters used to calculate energy and forces and to describe the system.
METHOD Quickstep --> Method used to compute forces. (Quickstep is for electronic structure methods, e.g. DFT).
&DFT --> Parameters for DFT.
BASIS_SET_FILE_NAME /work/lge/cp2ktest/BASIS_MOLOPT --> Path of basis set file.
POTENTIAL_FILE_NAME /work/lge/cp2ktest/POTENTIAL --> Path of pseudopotential file.
&XC --> Parameters to calculate the xc (exchange-correlation) potential.
&XC_FUNCTIONAL BLYP --> The xc functional to be used.
&END XC_FUNCTIONAL
&XC_GRID --> xc parameters used when calculating the xc on the grid.
XC_DERIV NN10_SMOOTH --> Method used to compute the derivatives.
XC_SMOOTH_RHO NN10 --> Density smoothing used for the xc calculation.
&END XC_GRID
&vdW_POTENTIAL --> Section for all additional dispersion corrections to the xc functionals.
DISPERSION_FUNCTIONAL PAIR_POTENTIAL --> (or POTENTIAL_TYPE, specifies the type of dispersion functional or potential to use).
&PAIR_POTENTIAL --> Info on the pair potential used to calculate dispersion.
TYPE DFTD2 --> Type of potential.
REFERENCE_FUNCTIONAL BLYP --> Use parameters for this specific density functional
&END PAIR_POTENTIAL
&END vdW_POTENTIAL
&END XC
&MGRID --> Multigrid information
CUTOFF 280 --> Cutoff of the finest grid level in Ry.
NGRIDS 5 --> Number of multigrids.
&END
&SCF --> Parameters for the SCF run.
SCF_GUESS ATOMIC --> Initial guess for the wavefunction (ATOMIC generates an atomic density using the atomic code).
MAX_SCF 300 --> Maximum number of SCF iterations for one optimisation.
&OT --> Various options for the orbtial transformation (OT) method.
PRECONDITIONER FULL_SINGLE_INVERSE --> Type of preconditioner to be used with all minimisation schemes (FULL_SINGLE_INVERSE based on H-eS cholesky inversion).
MINIMIZER DIIS --> Minimiser to be used with the OT method (e.g. CG, SD).
&END OT
&END SCF
&END SECTION DFT
&SUBSYS --> Defines a subsystem: coordinates, topology, molecules and cell.
&CELL --> Input parameters needed to set up the cell.
ABC 19.522 19.522 19.522 --> Specifies the lengths of the cell vectors A, B and C in Angstroms.
&END CELL
&KIND H --> Description of H atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q1 --> Name of pseudopotential.
&END
&KIND C --> Description of C atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q4 --> Name of pseudopotential.
&END
&KIND N --> Description of N atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q5 --> Name of pseudopotential.
&END
&KIND CL --> Description of Cl atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q7 --> Name of pseudopotential.
&END
&COORD --> Coordinates of the atoms in xyz format, in Angstroms (by default).
.....
&END
&END SUBSYS
&END FORCE_EVAL
&MOTION --> Defines tools connected with motion of the nuclei.
&MD --> Parameters to perform an MD run.
ENSEMBLE NVT --> Ensemble to be used.
STEPS 2000 --> Number of MD steps
TIMESTEP 0.5 --> Length of integration step in fs.
&THERMOSTAT --> Specify the thermostat and related parameters.
TYPE NOSE --> Thermostat to be used (NOSE is for the Nose-Hoover thermostat).
&NOSE --> Parameters of the Nose-Hoover thermostat chain.
TIMECON 100 --> Time constant of the thermostat chain in fs.
&END NOSE
&END THERMOSTAT
TEMPERATURE 353 --> Temperature in K used to initialise the velocities with init and pos restart, and in the NPT/NVT simulations.
&END MD
&END MOTION

4.2 Example of Cu water:

&GLOBAL --> Section that contains general information about the simulation and parameters for the whole program.
PROJECT cuwater --> Name of the project, used to determine the name of the files generated by the program.
PRINT_LEVEL MEDIUM --> How much output is written out.
RUN_TYPE MD --> Type of run that to perform (e.g. MD, GeoOpt, MC).
&END --> End of section.

&FORCE_EVAL --> Parameters used to calculate energy and forces and to describe the system.
METHOD Quickstep --> Method used to compute forces. (Quickstep is for electronic structure methods, e.g. DFT).
&DFT --> Parameters for DFT.
BASIS_SET_FILE_NAME /work/lge/cp2kcuwater/BASIS_MOLOPT --> Path of basis set file.
POTENTIAL_FILE_NAME /work/lge/cp2kcuwater/POTENTIAL --> Path of pseudopotential file.
LSD --> or UKS, requests a spin-polarised calculation using alpha and beta orbtials, i.e. no spin restriction is applied.
CHARGE 2 --> Total charge of the system
MULTIPLICITY 2 --> Two times the total spin plus one.
&PRINT --> Printing options.
&LOCALIZATION --> Printing options related to the Wannier centers and properties computed with Wannier centers.
&WANNIER_CENTERS --> Controls the printing of the wannier functions.
IONS+CENTERS --> Prints out the wannier centers together with the particles.
&END
&END
&END
&MGRID --> Multigrid information
CUTOFF 280 --> Cutoff of the finest grid level in Ry.
&END MGRID
&QS --> Parameters needed to set up the Quickstep framework
EXTRAPOLATION PS --> Extrapolation strategy for the wavefunction during e.g. MD (PS is higher order extrapolation of the density matrix times the overlap matrix).
EXTRAPOLATION_ORDER 2 --> Order for the PS or ASPC extrapolation.
&END QS
&SCF --> Parameters for the SCF run.
CHOLESKY OFF --> If the cholesky method should be used for computing the inverse of S, and in this case calling which Lapack routines (OFF means do not use cholesky).
SCF_GUESS ATOMIC --> Initial guess for the wavefunction (ATOMIC generates an atomic density using the atomic code).
EPS_SCF 3.0E-6 --> Target accuracy for the scf convergence.
MAX_SCF 20 --> Maximum number of SCF iterations for one optimisation.
&OUTER_SCF --> Parameters controlling the outer SCF loop.
EPS_SCF 3.0E-6 --> Target gradient (not accuracy?) of the outer SCF variables. Notice that the EPS_SCF of the inner loop also determines the value that can be reached in the outer loop, typically EPS_SCF of the outer loop must be smaller than the EPS_SCF of the inner loop.
MAX_SCF 20 --> The maximum number of outer loops.
&END
&OT --> Various options for the orbtial transformation (OT) method.
MINIMIZER DIIS --> Minimiser to be used with the OT method (e.g. CG, SD).
PRECONDITIONER FULL_ALL --> Type of preconditioner to be used with all minimisation schemes (FULL_ALL is the most effective state selective preconditioner based on diagonalisation, requires the ENERGY_GAP parameters to be an underestimate of the HOMO-LUMO gap).
ENERGY_GAP 0.01 --> Should be an estimate for the HOMO-LUMO energy gap in a.u. and is used in preconditioning.
&END OT
&END SCF
&XC --> Parameters to calculate the xc (exchange-correlation) potential.
&XC_FUNCTIONAL BLYP --> The xc functional to be used.
&END XC_FUNCTIONAL
&END XC
&END DFT
&SUBSYS --> Defines a subsystem: coordinates, topology, molecules and cell.
&CELL --> Input parameters needed to set up the cell.
ABC 12.535 12.535 12.535 --> Specifies the lengths of the cell vectors A, B and C in Angstroms.
&END CELL
&KIND H --> Description of H atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q1 --> Name of pseudopotential.
&END
&KIND O --> Description of O atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q6 --> Name of pseudopotential.
&END
&KIND Cu --> Description of Cu atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q11 --> Name of pseudopotential.
&END
&COORD --> Coordinates of the atoms in xyz format, in Angstroms (by default).
.....
&END
&END SUBSYS
&END FORCE_EVAL
&MOTION --> Defines tools connected with motion of the nuclei.
&MD --> Parameters to perform an MD run.
ENSEMBLE NVT --> Ensemble to be used.
STEPS 2000 --> Number of MD steps
TIMESTEP 0.5 --> Length of integration step in fs.
&THERMOSTAT --> Specify the thermostat and related parameters.
TYPE NOSE --> Thermostat to be used (NOSE is for the Nose-Hoover thermostat).
&NOSE --> Parameters of the Nose-Hoover thermostat chain.
TIMECON 100 --> Time constant of the thermostat chain in fs.
&END NOSE
&END THERMOSTAT
TEMPERATURE 298 --> Temperature in K used to initialise the velocities with init and pos restart, and in the NPT/NVT simulations.
&END MD
&END MOTION

Mod:Hunt Research Group

2013-02-28T18:03:11Z

Lge: /* Research Notes */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===Resources===

#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link] (notes by Tricia)

===Gaussian General===
#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] (notes by Everyone!)
#Instructions for visualizing electrostatic potentials [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link] (notes by Flo)
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#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] (notes by Heiko)
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link] (notes by Richard)
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link] (notes by Bryan & Richard)

===Unix and HPC===
#Setting up a connection to HPC if you have a PC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link] (notes by Hieu)
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link] (notes by Heiko)
#HPC servers and run scripts [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link] (notes by Tricia and Ling)]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link] (notes by Heiko)
#How to set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link] (notes by Heiko)
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link] (notes by Heiko)
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link] (notes by Heiko)
#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] (notes by Rachael, Weihong and Ling)
#How to set up cx2 [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cx2 link] (notes by Ling)

===Installing and using packages===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link] (notes by Ling)
#Beginners guide to VMD: a molecular dynamics visualisation package [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link] (notes by Ling & Bryan)
#DLPOLY a MD simulation package, Installation on an IMac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link] (notes by Ling)
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link] (notes by Tricia)
#How to install Geomview [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/geomview link] (notes by Tricia)
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/] (Ling)
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link] (notes by Bryan)

===Setup and Running MD Simulations===
#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#Packmol for generating starting configurations [http://www.ime.unicamp.br/~martinez/packmol/] from Packmol webpage.
#Getting the Force Field [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Wheretostart link] (notes by Richard)
#Choosing an Ensemble [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Ensembles link] (notes by Richard)
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link] (notes by Richard)
#Visualising your Simulation [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VisualisingyourSimulation link] (notes by Richard)
#Voids in ILs[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids link] (notes by Ling)
#How to equilibrate an MD run[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/equilibration link] (notes by Tricia and Ling)]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link] (notes by Ling)]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link] (notes by Ling and Tricia)]
#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] (notes by Ling)

===Research Notes===
#Cl- in water[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link] (notes by Ling)]
#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] (notes by Yannis)
#Functional for ILs using CPMD[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/IL_cpmd_functional link] (notes by Ling)
#[bmim]Cl using CPMD[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cpmd link] (notes by Ling)
#[bmim]Cl using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cp2k link] (notes by Ling)
#mman using CPMD and Gaussian [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/mman link] (notes by Ling)
#[emim]SCN using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emimscn link] (notes by Ling)
#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] (notes by Ling)
#CP2K Donts [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k link] (notes by Ling)
#How to make VMD trajectory repeated periodically [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/vmd link] (notes by Ling)
#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)
#How to run CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k_how link] (notes by Ling)

===CDT records===
#Activities record [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/CDT_records records]

===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] (notes by Tricia)
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link] (notes by Tricia)
#[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/calendar Calendar] (notes by Tricia)
#Demonstrating in the 3rd year computational chemistry lab [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/compchemlab Timetable] (notes by Tricia)
#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] notes by Tricia

Talk:Mod:Hunt Research Group/cpmd water

2013-02-28T17:58:17Z

Lge: Created page with "Car-Parrinello Molecular Dynamics Simulation of Aqueous Solutions 1. Introduction 1.1 Aqueous solutions In this lab you are going to run CPMD calculations of systems contai..."

Car-Parrinello Molecular Dynamics Simulation of Aqueous Solutions

1. Introduction

1.1 Aqueous solutions

In this lab you are going to run CPMD calculations of systems containing water and chloride. The following paragraphs describe why these systems are interesting to study.

Solvation of the chloride anion in water solution has been the subject of a substantial amount of experimental and theoretical work, in view of the central importance of chloride solutions in biochemical and metabolic processes, geology, atmospheric chemistry, and the chemical industry. Indeed, it has been discovered that airborne aqueous sea-salt aerosols serve as a global source of molecular chlorine and bromine, both in the polluted and in the remote lower marine troposphere. A variety of experimental methods have been used to investigate the hydration structure of chloride ions in water, including neutron and X-ray diffraction techniques, X-ray absorption spectroscopy (XAS) and femtosecond mid-infrared nonlinear spectroscopy. Despite these efforts, a complete microscopic model of the hydration shell structure of aqueous Cl- and of its room temperature dynamics is still being debated.

Difficulties in determining the structure of the solvation environment arise because of the comparable magnitudes of the water-Cl- and water-water interaction energies. Established results from the literature, both experimental and theoretical, reveal a rather inhomogeneous picture of the hydrated ion solvation shell structure. Vibrational spectroscopy experiments indicate that a chloride ion is asymmetrically solvated in clusters containing up to five water molecules. This contrasts with older and less direct experiments based on mass spectroscopy and photoelectron spectroscopy from which a symmetrical solvent cage around the anion was inferred. Experimental measurements such as photoelectron spectroscopy, IR spectroscopy and a combined technique of XAS (extended X-ray absorption fine structure, EXAFS and X-ray absorption near-edge structure, XANES) yield coordination numbers that are significantly scattered, ranging from 3 to 8. The first peak of the Cl-O radial distribution function (RDF) is measured to be in the range of 3.10-3.36 A.

Uncertainty in the coordination number is also evinced from theoretical studies, with variations between 5.1 and 8.4 depending on the simulation techniques adopted. Classical molecular dynamics (MD) simulations have been found to depend strongly on the anion-water and water-water potentials used. On the other hand, the use of different parametrized potentials, i.e. with and without a treatment of molecular polarizability, gave different structural properties. Quantum mechanics / molecular mechanics (QM/MM) simulations of Cl− in water indicate that the hydration structure of the an- ion has considerable flexibility in consequence to the weakness of Cl--water interactions. This leads to a competition between solvation of the ion and hydrogen bonding among water molecules. The QM/MM results clearly indicate the importance of QM treatment in order to correctly describe such a delicate balance between Cl--water and water-water interactions.

Reference: Tongraar, A.; T-Thienprasert, J.; Rujirawat, S.; Limpijumnong, S. Phys. Chem. Chem. Phys. 2010, 12, 10876.

1.2 Car-Parrinello/Born-Oppenheimer molecular dynamics

The aim of this tutorial is to help you getting started using the CPMD program. CPMD is an ab initio electronic structure and molecular dynamics (MD) program using a plane wave/pseudopotential implementation of density functional theory (DFT). It is mainly targeted at Car-Parrinello MD simulations, but also supports geometry optimisations, Born-Oppenheimer MD, path integral MD, response functions, excited states and calculations of some electronic properties. For further information you may want to take a look at the CPMD consortium homepage at www.cpmd.org.

Born-Oppenheimer (BO) MD: at each step of atomic MD, one solves the DFT SCF problem for a fixed atomic configuration, computes the wavefunction, and from it the (quantum mechanical) forces acting on the nuclei. This allows it to propagate the atoms classically to the next configuration. (In simple words, one computes energy and forces, move the atoms, re-compute energy and forces for the new configuration, move the atoms, and so on.)

Car-Parrinello: One propagates simultaneously a set of atoms and a fictitious set of electrons. From the fictitious set of electrons, one can estimate the forces on the atoms and move the atoms. Atoms and fictitious electrons have to be independent, and their dynamics is described using a generalised Lagrangian formalism, rather than simply propagating the atoms using Newton's equations like in Born-Oppenheimer MD. In the CPMD manual, it is written:

“The basic idea of the Car-Parrinello approach can be viewed to exploit the time-scale separation of fast electronic and slow nuclear motion by transforming that into classical-mechanical adiabatic energy-scale separation in the framework of dynamical systems theory. In order to achieve this goal the two-component quantum / classical problem is mapped onto a two-component purely classical problem with two separate energy scales at the expense of loosing the explicit time-dependence of the quantum subsystem dynamics.”

Born-Oppenheimer MD is easier to implement in practice, but slower. Also it requires a very well converged calculation of the forces at each step of dynamics. The Car-Parrinello only requires a very accurate ground state at the first step. The rest of the dynamics sustains itself, provided it is carried out in the right way.

If you would like to know more about the theoretical background of CPMD or BOMD, please read CPMD manual Sections 6.6 and 6.7.

2. Code Running Environment

2.1 Before running the job

Before you run CPMD it is a good idea to copy all you need in your local directory.

- Copy the folder lab from the usb disk to your laptop.

- open the terminal application

- open two windows, one will be for your local mac and the other for the hpc cluster

- on one of them login to the hpc cluster by typing ssh yourname@login.cx1.hpc.ic.ac.uk

- the cluster has two key directories /WORK/yourname and /HOME/yourname do all the calculations from the WORK/yourname directory, from now on this directory will be referred to simply as work

- cd to your work directory and make a new directory called liquids, cd into the new directory, this is where you will run all your jobs from

- copy the file from your desktop to hpc:

scp filename yourname@login.cx1.hpc.ic.ac.uk:/work/yourname/foldername/.

- unzip the tar file

tar -xvf filename.tar

2.2 How to run the job

In the directory cpmd you should have two subdirectories: clw1 and clw63.

To run CPMD type qsub runcpmd_wf (or other run scripts depending on the type of calculation such as runcpmd_md) in the clw1 or clw63 directory.

2.3 Using VMD to analyse results

For visualisation of the results you may want to take a look at the tutorial on visualising results from CPMD with the VMD program under www.theochem.ruhr-uni-bochum.de/go/cpmd-vmd.html

3. CPMD

3.1 Theoretical background

3.1.1 Pseudopotentials (read CPMD manual section 4.2)

3.1.2 Kohn-Sham orbitals, Wannier orbitals and Effective molecular orbitals

The EMO method for analysing the electronic structure of solutes and solvents starts by considering the Kohn-Sham Hamiltonian and energy eigenvalues obtained from the ab initio molecular dynamics. A band structure similar to that obtained for solid state systems emerges. While the Kohn-Sham Hamiltonian is diagonal, and the Kohn-Sham orbital energies are uniquely defined, the Kohn-Sham orbitals are delocalised Bloch states which extend over all space and the molecular picture is lost, as shown in Figure 1 (a). This makes it very difficult to analyse interactions between an ion and the solvating water molecules. Maximally localized Wannier orbitals are local to atomic centers. However, the Wannier Hamiltonian is not diagonal and thus there is no unique energy eigenvalue that can be associated with each orbital, as shown in Figure 1 (c). An intermediate representation where orbitals are local to a molecule, but are delocalised within the molecule has been developed. The EMOs are obtained by assigning Wannier orbitals to a specific molecule, and block-diagonalising the Wannier Hamiltonian within the molecular subspace, as shown in Figure 1 (b). This analysis has been successfully applied to pure liquid water. An isolated water molecule has C2v symmetry and valence MOs 1a1, 1b2, 2a1 and 1b1. A liquid environment is disordered and there is no symmetry. However, Figure 1 (b) shows that the EMOs strongly resemble the standard MOs for a single water molecule in vacuum. This close resemblance is by no means predetermined and is a validation of the EMO method. For clarity, we will continue to use the isolated atomic or molecular symmetry labels when we refer to the individual atomic orbitals, MOs and bands in the aqueous system.

3.2 Functional

We will use a gradient corrected functional (BLYP) instead of LDA throughout the tutorial as this combination of generalized gradient approximations to exchange and correlation has been shown to give good results for the structure and dynamics of water.

Figure 1 Wavefunction diagrams from a CPMD simulation of pure liquid water related to graphical representations of the respective Hamiltonian matrices: (a) Kohn-Sham Hamiltonian, (b) EMO Hamiltonian and (c) Wannier Hamiltonian.

3.3 Generating input files and understanding output files

The first example will demonstrate some of the basic steps of performing a CPMD calculation with a very simple system: 1 water molecule+Cl-, and a very simple task: calculate the electronic structure. We will use that as an example to have a look at the input file format, and how to read the output.

- emacs filename

- and then look inside and follow the instructions below

3.3.1 Wavefunction optimisation

(a) Input File format

For nearly all CPMD calculations, you first have to optimise the wavefunction of your system, and use that as a base for further calculations. For our first calculation you’ll need the input file inp.clw_blyp_wf and the pseudopotential files H_MT_BLYP.psp, O_MT_BLYP.psp, Cl_MT_BLYP.psp.

Now let’s have a look at the input file. The input file is organised in sections which start with &NAME and end with &END. Everything outside those sections is ignored. All keywords have to be in upper case or else they will be ignored. The sequence of the sections does not matter, nor does the order of keywords. A minimal input file must have a &CPMD, &SYSTEM and an &ATOMS section.

&CPMD

OPTIMIZE WAVEFUNCTION

CONVERGENCE ORBITALS

1.0d-7

&END

This first part of the &CPMD section instructs the program to do a wavefunction optimization (i.e. a single point calculation) with a tight convergence criterion (the default is 1.0d-5).

Exercise: look up in the CPMD manual about the usage of the keywords ODIIS, STORE, TIMESTEP, EMASS, ISOLATED MOLECULE.

&DFT

FUNCTIONAL BLYP

GC-CUTOFF

0.1D-06

&END

The &DFT section is used to select the density functional and related parameters. In this case we go with the BLYP functional.

&SYSTEM

ANGSTROM

SYMMETRY

0

CELL

11.800 1.0 1.0 0 0 0

CUTOFF

70.0

CHARGE

-1.0

&END

The &SYSTEM section contains various parameters related to the simulation cell and the representation of the electronic structure. The keywords SYMMETRY, CELL and CUTOFF are required and define the (periodic) symmetry, shape, and size of the simulation cell, as well as the plane wave cutoff (i.e. the size of the basis set). The keyword Angstrom additionally indicates that all lengths and coordinates are given in angstrom (not in a.u.).

Exercise: look up in the CPMD manual about the usage of the keyword CHARGE.

Finally the &ATOMS section is needed to specify the atom coordinates and the pseudopotentials, that are used to represent them. The detailed syntax of the pseudopotential specification is a bit complicated and will not be needed nor discussed here. If you want to know more, please have a look at the Further details of the Input section of the CPMD manual (P222).

- To run, type: qsub runcpmd_wf,

The code will generate the following output files once the calculation is completed after a few minutes: log.clw_blyp_wf, GOMETRY., RESTART.. The purpose of the wavefunction optimisation is to generate the RESTART. file which is needed for further calculations.

(b) Output File Format

To start the calculation, which should be completed in less than a minute once the job starts running. The main output of the CPMD program is now in the file log.clw_blyp_wf. Let’s have a closer look at the contents of this file.

PROGRAM CPMD STARTED AT: Thu Jan 20 16:23:24 2011
SETCNST| USING: CODATA 2006 UNITS
THE INPUT FILE IS: /work/lge/wannier/test/inp.clw_blyp_wf
THIS JOB RUNS ON: cx1-50-2-1.cx1.hpc.ic.ac.uk
THE CURRENT DIRECTORY IS:
/tmp/pbs.5020787.cx1
THE TEMPORARY DIRECTORY IS:
/tmp/pbs.5020787.cx1
THE PROCESS ID IS: 13680

Here we have some technical information about the environment, where this job was run.

SINGLE POINT DENSITY OPTIMIZATION
PATH TO THE RESTART FILES: ./
GRAM-SCHMIDT ORTHOGONALIZATION
MAXIMUM NUMBER OF STEPS: 1000 STEPS
MAXIMUM NUMBER OF ITERATIONS FOR SC: 1000 STEPS
PRINT INTERMEDIATE RESULTS EVERY 10001 STEPS
STORE INTERMEDIATE RESULTS EVERY 10 STEPS
NUMBER OF DISTINCT RESTART FILES: 1
TEMPERATURE IS CALCULATED ASSUMING AN ISOLATED MOLECULE
FICTITIOUS ELECTRON MASS: 500.0000
TIME STEP FOR ELECTRONS: 5.0000
TIME STEP FOR IONS: 5.0000
CONVERGENCE CRITERIA FOR WAVEFUNCTION OPTIMIZATION: 1.0000E-07
WAVEFUNCTION OPTIMIZATION BY PRECONDITIONED DIIS
THRESHOLD FOR THE WF-HESSIAN IS 0.5000
MAXIMUM NUMBER OF VECTORS RETAINED FOR DIIS: 5
STEPS UNTIL DIIS RESET ON POOR PROGRESS: 5
FULL ELECTRONIC GRADIENT IS USED
SPLINE INTERPOLATION IN G-SPACE FOR PSEUDOPOTENTIAL FUNCTIONS
NUMBER OF SPLINE POINTS: 5000

This section now gives you a summary of the parameters read in from the &CPMD section, or their respective default settings.

EXCHANGE CORRELATION FUNCTIONALS
LDA EXCHANGE: SLATER (ALPHA = 0.66667)
LDA CORRELATION: LEE, YANG & PARR
[C.L. LEE, W. YANG, AND R.G. PARR, PRB 37 785 (1988)]
GRADIENT CORRECTED FUNCTIONAL
DENSITY THRESHOLD: 1.00000E-07
EXCHANGE ENERGY
[A.D. BECKE, PHYS. REV. A 38, 3098 (1988)]
PARAMETER BETA: 0.004200
CORRELATION ENERGY
[LYP: C.L. LEE ET AL. PHYS. REV. B 37, 785 (1988)]
*** DETSP| SIZE OF THE PROGRAM IS 8748/ 110552 kBYTES ***
>>>>>>>> CENTER OF MASS HAS BEEN MOVED TO CENTER OF BOX <<<<<<<<
***************************** ATOMS ****************************
NR TYPE X(bohr) Y(bohr) Z(bohr) MBL
1 Cl 11.199323 11.186938 9.180419 3
2 O 10.970667 11.067318 15.135702 3
3 H 10.558139 11.108892 13.264684 3
4 H 12.820897 11.171631 15.013437 3
****************************************************************
NUMBER OF STATES: 8
NUMBER OF ELECTRONS: 16.00000
CHARGE: -1.00000
ELECTRON TEMPERATURE(KELVIN): 0.00000
OCCUPATION
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0

This part of the output tells you which and how many atoms and electrons are used, what functional and what pseudopotentials were used, and what the values of some related parameters are.

POISSON EQUATION SOLVER : HOCKNEY
COULOMB SMOOTHING RADIUS : 1.593
SYMMETRY: SIMPLE CUBIC
LATTICE CONSTANT(a.u.): 22.29877
CELL DIMENSION: 22.2988 1.0000 1.0000 0.0000 0.0000 0.0000
VOLUME(OMEGA IN BOHR^3): 11087.72952
LATTICE VECTOR A1(BOHR): 22.2988 0.0000 0.0000
LATTICE VECTOR A2(BOHR): 0.0000 22.2988 0.0000
LATTICE VECTOR A3(BOHR): 0.0000 0.0000 22.2988
RECIP. LAT. VEC. B1(2Pi/BOHR): 0.0448 0.0000 0.0000
RECIP. LAT. VEC. B2(2Pi/BOHR): 0.0000 0.0448 0.0000
RECIP. LAT. VEC. B3(2Pi/BOHR): 0.0000 0.0000 0.0448
REAL SPACE MESH: 120 120 120
WAVEFUNCTION CUTOFF(RYDBERG): 70.00000
DENSITY CUTOFF(RYDBERG): (DUAL= 4.00) 280.00000
NUMBER OF PLANE WAVES FOR WAVEFUNCTION CUTOFF: 54804
NUMBER OF PLANE WAVES FOR DENSITY CUTOFF: 438632
****************************************************************

This part of the output presents the settings read in from the &SYSTEM section of the input file and some derived parameters.
[…]

(K+E1+L+N+X) TOTAL ENERGY = -31.48398404 A.U.
(K) KINETIC ENERGY = 19.91015701 A.U.
(E1=A-S+R) ELECTROSTATIC ENERGY = -26.99115337 A.U.
(S) ESELF = 28.92331533 A.U.
(R) ESR = 0.74536593 A.U.
(L) LOCAL PSEUDOPOTENTIAL ENERGY = -19.20863875 A.U.
(N) N-L PSEUDOPOTENTIAL ENERGY = 2.63857242 A.U.
(X) EXCHANGE-CORRELATION ENERGY = -7.83292134 A.U.
GRADIENT CORRECTION ENERGY = -0.43675318 A.U.

After some output to report the setup of the initial guess for the electronic structure, we now see a summary of the various energy contribution of the total energy of the system, based on the initial guess. Now the program is ready to start the wavefunction optimisation.

Starting from the initial guess based on atomic wavefunctions the wavefunction for the total system is now calculated with an optimisation procedure. You can follow the progress of the optimisation in the output file.

NFI GEMAX CNORM ETOT DETOT TCPU
1 4.556E-02 4.038E-03 -31.483984 0.000E+00 5.88
2 1.580E-02 1.381E-03 -32.031355 -5.474E-01 5.90
3 1.347E-02 6.554E-04 -32.139961 -1.086E-01 5.93
4 7.667E-03 3.432E-04 -32.162687 -2.273E-02 5.95
5 3.490E-03 1.256E-04 -32.168927 -6.240E-03 5.97
6 2.655E-03 6.618E-05 -32.170107 -1.180E-03 5.98
7 1.888E-03 3.959E-05 -32.170488 -3.805E-04 5.99
8 1.004E-03 2.399E-05 -32.170647 -1.597E-04 5.97
9 6.207E-04 1.431E-05 -32.170689 -4.167E-05 5.96
10 4.309E-04 8.966E-06 -32.170703 -1.373E-05 5.96

NFI: Step number (number of finite iterations)

GEMAX: largest off-diagonal component

CNORM: average of the off-diagonal components

ETOT: total energy

DETOT: change in total energy to the previous step

TCPU: (CPU) time for this step

And you can see that the calculation stops after the convergence of 1.0d-7 has been reached for the GEMAX value.
****************************************************************
* *
* FINAL RESULTS *
* *
****************************************************************
****************************************************************
* ATOMIC COORDINATES *
****************************************************************
1 Cl 11.199323 11.186938 9.180419
2 O 10.970667 11.067318 15.135702
3 H 10.558139 11.108892 13.264684
4 H 12.820897 11.171631 15.013437
****************************************************************
ELECTRONIC GRADIENT:
MAX. COMPONENT = 9.69721E-08 NORM = 8.07825E-10
TOTAL INTEGRATED ELECTRONIC DENSITY
IN G-SPACE = 16.000000
IN R-SPACE = 16.000000
(K+E1+L+N+X) TOTAL ENERGY = -32.17071373 A.U.
(K) KINETIC ENERGY = 18.31556847 A.U.
(E1=A-S+R) ELECTROSTATIC ENERGY = -26.97530784 A.U.
(S) ESELF = 28.92331533 A.U.
(R) ESR = 0.74536593 A.U.
(L) LOCAL PSEUDOPOTENTIAL ENERGY = -18.46114493 A.U.
(N) N-L PSEUDOPOTENTIAL ENERGY = 2.17769037 A.U.
(X) EXCHANGE-CORRELATION ENERGY = -7.22751980 A.U.
GRADIENT CORRECTION ENERGY = -0.41653735 A.U.
****************************************************************

Here we have the final summary of the results from our single point calculation. Please note that regardless of the input units, coordinates in the CPMD output are always in atomic units.

Other Output files:

Apart from the console output, our CPMD run created a few other files. Most importantly the restart file RESTART., which contains the final state of the system when the program terminated. This is needed to start other calculations, which need a converged wavefunction as a starting point. The file GEOMETRY. contains the coordinates of the atoms in atomic unit. This can be converted to a .xyz file.

3.3.2 Car-Parrinello Molecular dynamics

Based on the previously calculated electronic structure, we can now start a Car-Parrinello Molecular dynamics calculation. Note that although you can start a CP-MD run from a non-converged wavefunction (e.g. by not restarting from a pre-optimised wavefunction), you will be far away from the Born-Oppenheimer surface, and thus your result will be unphysical.

To run, type:

cp RESTART. RESTART

qsub runcpmd_md

3.3.2.1 Input for CP dynamics

For the CP-MD job you need a new input file, inp.clw_blyp_md, which should be copied into the same directory, where you started the wavefunction optimisation run. If you compare it to the previous input files, you will find, that the only changes are again only in the &CPMD section of the input files.

&CPMD
MOLECULAR DYNAMICS CP
RESTART WAVEFUNCTION COORDINATES VELOCITIES NOSEP LATEST
QUENCH BO
MIRROR
CONVERGENCE ORBITAL
1.0D-7
ODIIS
5
MAXSTEP
3000
STORE
20
TIMESTEP
5
EMASS
500.0
NOSE IONS
298.0 1100
TRAJECTORY SAMPLE
10
ISOLATED MOLECULE
&END

The keyword MOLECULAR DYNAMICS CP defines the job type. Furthermore we tell the CPMD program to pick up the previously calculated wavefunction and coordinates from the latest restart file (which is named RESTART by default). MAXSTEP limits the MD to 3000 steps and the equations of motion will be solved for a time step of 5 atomic units (~0.12 femtoseconds). The temperature of the system will be initialised to 298K via the NOSE IONS keyword with Nose thermostat.

- Now start the CPMD program once more: qsub runcpmd_md

This run should be completed in a few minutes.

3.3.2.2 CP dynamics output

The output of the CPMD program is now in the file log.clw_blyp_md. There are also some new files (TRAJECTORY, ENERGIES). We will have a look at the output file first.

CAR-PARRINELLO MOLECULAR DYNAMICS
PATH TO THE RESTART FILES: ./
RESTART WITH OLD ORBITALS
RESTART WITH OLD ION POSITIONS
RESTART WITH OLD VELOCITIES
RESTART WITH OLD ION THERMOSTAT
RESTART WITH LATEST RESTART FILE
ITERATIVE ORTHOGONALIZATION
MAXIT: 30
EPS: 1.00E-06
MAXIMUM NUMBER OF STEPS: 3000 STEPS

The header is unchanged up to the point where the settings from the &CPMD section are printed. As you can see, the program has recognised the RESTART and the MAXSTEP keywords. (NOTE: in the CPMD code atoms are sometimes referred to as ions. This is due to the pseudopotential approach, where you integrate the core electrons into the (pseudo)atom which then could also be described as an ion.)

TIME STEP FOR ELECTRONS: 5.0000
TIME STEP FOR IONS: 5.0000
QUENCH SYSTEM TO THE BORN-OPPENHEIMER SURFACE
TRAJECTORIES ARE SAVED ON FILE EVERY 10 STEPS
ELECTRON DYNAMICS: THE TEMPERATURE IS NOT CONTROLLED
ION DYNAMICS: TEMPERATURE CONTROL (NOSE-HOOVER THERMOSTATS)
TARGET TEMPERATURE(KELVIN): 2.980000E+02
CHARACTERISTIC FREQUENCY(CM**-1): 1100.00
NOSE PARAMETERS
NUMBER OF THERMOSTATS (IONS) : 3
NUMBER OF THERMOSTATS (ELECTRONS) : 3
NUMBER OF THERMOSTATS (CELL) : 3
SCALING FOR ELEC. DOF : 6.00
NUMBER OF YOSHIDA-SUZUKI STEPS : 7
NUMBER OF INTEGRATION CYCLES (NIT): 1

This part of the output tells us, that the TIMESTEP 5.0 keyword was recognised (which is the default timestep), that the trajectory will be recorded and that NOSE-HOOVER thermostat is used.

RESTART INFORMATION READ ON FILE ./RESTART

Here we get notified, that the program has read the requested data from the restart file.

NFI EKINC TEMPP EKS ECLASSIC EHAM DIS TCPU
1 0.00000 0.0 -32.17071 -32.17010 -32.17010 0.458E-10 3.25
2 0.00000 0.0 -32.17071 -32.17010 -32.17010 0.727E-09 3.24
3 0.00000 0.0 -32.17071 -32.17010 -32.17010 0.365E-08 3.24
4 0.00000 0.0 -32.17071 -32.17010 -32.17010 0.114E-07 3.24
5 0.00000 0.1 -32.17071 -32.17010 -32.17010 0.275E-07 3.24
6 0.00000 0.1 -32.17071 -32.17010 -32.17010 0.565E-07 3.25
7 0.00000 0.1 -32.17071 -32.17010 -32.17010 0.104E-06 3.24
8 0.00000 0.2 -32.17072 -32.17010 -32.17010 0.175E-06 3.24
9 0.00000 0.2 -32.17072 -32.17010 -32.17010 0.279E-06 3.25
10 0.00000 0.3 -32.17072 -32.17010 -32.17010 0.422E-06 3.25
11 0.00000 0.3 -32.17072 -32.17010 -32.17010 0.614E-06 3.25
12 0.00000 0.4 -32.17072 -32.17010 -32.17010 0.865E-06 3.25
13 0.00000 0.4 -32.17072 -32.17010 -32.17010 0.119E-05 3.24
14 0.00000 0.5 -32.17072 -32.17010 -32.17010 0.159E-05 3.24
15 0.00000 0.6 -32.17072 -32.17010 -32.17010 0.209E-05 3.25
16 0.00000 0.6 -32.17072 -32.17010 -32.17010 0.269E-05 3.25
17 0.00000 0.7 -32.17072 -32.17010 -32.17010 0.343E-05 3.24
18 0.00000 0.8 -32.17072 -32.17010 -32.17010 0.429E-05 3.25
19 0.00000 0.9 -32.17072 -32.17010 -32.17010 0.532E-05 3.24
20 0.00000 1.0 -32.17072 -32.17010 -32.17010 0.652E-05 3.24
...
2981 0.00015 274.5 -32.16644 -32.17025 -32.17010 0.443E+01 3.25
2982 0.00015 268.3 -32.16638 -32.17025 -32.17010 0.444E+01 3.25
2983 0.00014 262.2 -32.16632 -32.17025 -32.17010 0.444E+01 3.26
2984 0.00014 256.0 -32.16627 -32.17024 -32.17010 0.445E+01 3.25
2985 0.00014 249.9 -32.16621 -32.17024 -32.17010 0.446E+01 3.26
2986 0.00013 243.8 -32.16615 -32.17024 -32.17010 0.446E+01 3.25
2987 0.00013 237.7 -32.16610 -32.17023 -32.17010 0.447E+01 3.25
2988 0.00013 231.7 -32.16604 -32.17023 -32.17010 0.447E+01 3.25
...
2997 0.00010 179.1 -32.16554 -32.17020 -32.17010 0.452E+01 3.25
2998 0.00010 173.6 -32.16549 -32.17020 -32.17010 0.452E+01 3.26
2999 0.00009 168.1 -32.16544 -32.17020 -32.17010 0.453E+01 3.26
3000 0.00009 162.6 -32.16539 -32.17019 -32.17010 0.453E+01 3.25

After some more output, we already discussed for the wavefunction optimisation, this is now part of the energy summary for a Car-Parrinello-MD run.

NFI: Step number (number of finite iterations)

EKINC: (fictitious) kinetic energy of the electron (sub-)system

TEMPP: Temerature (=kinetic energy / degrees of freedom) for atoms (ions)

EKS: Kohn-Sham Energy: equivalent to the potential energy in classical MD

ECLASSIC: Equivalent to the total energy in a classical MD (ECLASSIC = EHAM-EKINC)

EHAM: total energy, should be conserved

DIS: mean squared displacement of the atoms from the initial coordinates

TCPU: (CPU) time needed for this step

To read about why do the MD part and how to analyse results, please read this CPMD paper on water.

Reference: Kuo et al, J. Phys. Chem. B 2004, 108, 12990-12998

Note: For a meaningful Car-Parrinello MD, EKINC has to be (and stay) very small (although for larger systems with more electrons, the absolute value of EKINC will be larger, i.e. no drift in EKINC.

Exercise: plot EKINC vs NFI, TEMPP vs NFI, EKS vs NFI, ECLASSIC vs NFI, EHAM vs NFI. Discuss the trend of these curves.

MEAN VALUE +/- RMS DEVIATION
<x> [<x^2>-<x>^2]**(1/2)
ELECTRON KINETIC ENERGY 0.000125 0.105171E-03
IONIC TEMPERATURE 233.0551 194.923
DENSITY FUNCTIONAL ENERGY -32.169126 0.152974E-02
CLASSICAL ENERGY -32.170228 0.105180E-03
CONSERVED ENERGY -32.170104 0.247772E-05
NOSE ENERGY ELECTRONS 0.000000 0.00000
NOSE ENERGY IONS -0.003317 0.200165E-02
CONSTRAINTS ENERGY 0.000000 0.00000
RESTRAINTS ENERGY 0.000000 0.00000
ION DISPLACEMENT 1.25973 1.33130
CPU TIME 3.2487

Finally we get a summary of some averages and root mean squared deviations for some of the monitored quantities. This is quite useful to detect unwanted energy drifts or too large fluctuations in the simulation.

Exercise: visualise the motion of the system of (1 water + Cl-)

Type: ./traj2xyz.x < TRAJECTORY.clw_blyp_md > TRAJ.xyz

You can load the file TRAJ.xyz directly into the molecular visualisation program VMD.

-> Launch VMD program

-> File -> Load files for: New Molecule

-> click ‘Browse’, choose the file TRAJ.xyz

-> click ‘Load’

The trajectory file can be used to generate structural properties such as radial distribution functions and analyse the solvation shells such as Cl-O distances.

3.3.3 Kohn-Sham energies

Altogether the first part of the CPMD input (file name: inp.clw_blyp_ksl) now contains:

&CPMD
RESTART WAVEFUNCTION VELOCITIES COORDINATES LATEST
KOHN-SHAM ENERGIES
0
MAXSTEP
1000
STORE
10
TIMESTEP
5.0
EMASS
500.0
ISOLATED MOLECULE
&END

Output file (log.clw_blyp_ksl)

EIGENVALUES(EV) AND OCCUPATION:
1 -19.9458449 2.00000000 2 -11.8998056 2.00000000
3 -7.3120943 2.00000000 4 -4.5277656 2.00000000
5 -2.2061693 2.00000000 6 -0.5375340 2.00000000
7 -0.3936740 2.00000000 8 -0.3633460 2.00000000
CHEMICAL POTENTIAL = -0.3633465899 EV

This part lists the Kohn-Sham energies.

3.3.4 Kohn-Sham Orbitals

Altogether the first part of the CPMD input (file name: inp.clw_blyp_ksorb) now contains:

&CPMD
KOHN-SHAM ENERGIES
8
RESTART WAVEFUNCTION COORDINATES LATEST
DAVIDSON DIAGNOALIZATION
RHOOUT BANDS
8
-1 -2 -3 -4 -5 -6 -7 -8
&END

This generages a series of files with the names WAVEFUNCTION.1, WAVEFUNCTION.2, …, WAVEFUNCTION.8 which have to be converted to cube format with cpmd2cube.x -o clw1 WAVEFUNCTION.1

3.3.5 Wannier Analysis

To calculate the Wannier centers or orbitals for our system we need to do a properties calculation starting from the previously generated wavefunction.

For the Wannier orbitals the keywords LOCALIZE and WANNIER WFNOUT are required. This generates a series of files with the names WANNIER_1.* which have to be converted to cube format with cpmd2cube.x –o clw1 WANNIER_1.1.

Altogether the first and second parts of the CPMD input to calculate Wannier enters now contains:

&CPMD
RESTART WAVEFUNCTION LATEST
PROPERTIES
WANNIER DOS
&END

&PROP
LOCALIZE
&END

To plot all the WANNIER ORBITALS, replace the first part with:

&CPMD
RESTART WAVEFUNCTION COORDINATES LATEST
PROPERTIES
WANNIER WFNOUT ALL
&END

Exercise: use VMD to visualise the Kohn-Sham and Wannier orbitals. Describe the Kohn-Sham and Wannier Orbitals of the system. (Hint: One of the Kohn-Sham orbitals looks like this. Discuss delocalisation/localisation.)

Figure 2 Kohn-Sham Orbital

Note: Different phases can be visualised in VMD by creating two representations from the same data set and just using isovalues with opposite sign for each of them. The input and cube files used in this section are:

WAVEFUNCTION.* or WANNIER_1.*

clw1.*.cube (for Kohn-Sham orbitals) or clw11.*.cube (for Wannier orbitals)

VMD:

-> Launch VMD program

-> File -> Load files for: New Molecule

-> click ‘Browse’, choose the file TRAJ.xyz

-> click ‘Load’

-> Graphics -> Representations -> Drawing Method -> Choose CPK

-> repeat the above procedure and load the cube file again but this time choose Isosurface as Drawing method and play around with Isovalues.

To change colour of the background:

-> Graphics -> Colors -> Display -> Background -> Choose white

4. Exercises (63 water + Cl-)

The next step is a more typical (while ambitious) application of the CPMD code: a Car-Parrinello MD simulation of a bulk system with water and a chloride ion. In this specific example, we try to look at how the electronic structure changes when a chloride ion is solvated in liquid water. Our system will consist of 63 water molecules and one chloride ion (note the CHARGE keyword in the &SYSTEM section). To speed up the equilibration phase, we start from a restart configuration that has been equilibrated with classical MD for about 3 ns using the SPC/E water potential and CPMD for 31.56 ps. Since water has a dipole moment, you have to keep in mind, that we are calculating a system with periodic boundary conditions, so a water molecules ‘sees’ its images and interacts with them. There are methods implemented in CPMD to compensate this effect, but we won’t discuss them here.

Now run jobs to get data.

4.1 Run a wavefunction optimisation (use inp.w63Cl-wf).

4.2 We want to run the MD at 298 Kelvin, so now run a short MD with temperature rescaling for the atoms and no thermostat for the electrons (use inp.w63Cl-md)

4.3 Now you have your MD trajectory files, analyse them

4.4 Liquid water structure and hydrogen bonding

4.4.1 Generate a movie of trajectories using VMD which will read in the TRAJ.xyz file.

4.4.2 what to look at => Radial Distribution Functions

4.4.3 Compare your traj to the one we have made

4.4.4 Do you see water molecules entering and exiting solvation shell?

4.5 Plotting Kohn-Sham energies, Kohn-Sham orbitals, Wannier centers and Wannier orbitals

4.6 Follow the instructions above for clw1 but with your clw63 file (do it for last step of your trajectory) in reality we would want to examine 50-100 points sampled from the trajectory

4.7 Each student to look at one of the following:

4.7.1 Plot density of states for KS, KS orbitals

4.7.2 Plot Wannier orbitals and centers

4.7.3 Plot Cl-water distances over time

Mod:Hunt Research Group

2013-02-28T17:33:08Z

Lge: /* Setup and Running MD Simulations */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===Resources===

#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link] (notes by Tricia)

===Gaussian General===
#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] (notes by Everyone!)
#Instructions for visualizing electrostatic potentials [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link] (notes by Flo)
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#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] (notes by Heiko)
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link] (notes by Richard)
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link] (notes by Bryan & Richard)

===Unix and HPC===
#Setting up a connection to HPC if you have a PC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link] (notes by Hieu)
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link] (notes by Heiko)
#HPC servers and run scripts [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link] (notes by Tricia and Ling)]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link] (notes by Heiko)
#How to set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link] (notes by Heiko)
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link] (notes by Heiko)
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link] (notes by Heiko)
#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] (notes by Rachael, Weihong and Ling)
#How to set up cx2 [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cx2 link] (notes by Ling)

===Installing and using packages===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link] (notes by Ling)
#Beginners guide to VMD: a molecular dynamics visualisation package [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link] (notes by Ling & Bryan)
#DLPOLY a MD simulation package, Installation on an IMac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link] (notes by Ling)
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link] (notes by Tricia)
#How to install Geomview [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/geomview link] (notes by Tricia)
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/] (Ling)
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link] (notes by Bryan)

===Setup and Running MD Simulations===
#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#Packmol for generating starting configurations [http://www.ime.unicamp.br/~martinez/packmol/] from Packmol webpage.
#Getting the Force Field [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Wheretostart link] (notes by Richard)
#Choosing an Ensemble [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Ensembles link] (notes by Richard)
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link] (notes by Richard)
#Visualising your Simulation [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VisualisingyourSimulation link] (notes by Richard)
#Voids in ILs[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids link] (notes by Ling)
#How to equilibrate an MD run[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/equilibration link] (notes by Tricia and Ling)]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link] (notes by Ling)]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link] (notes by Ling and Tricia)]
#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] (notes by Ling)

===Research Notes===
#Cl- in water[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link] (notes by Ling)]
#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] (notes by Yannis)
#Functional for ILs using CPMD[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/IL_cpmd_functional link] (notes by Ling)
#[bmim]Cl using CPMD[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cpmd link] (notes by Ling)
#[bmim]Cl using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cp2k link] (notes by Ling)
#mman using CPMD and Gaussian [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/mman link] (notes by Ling)
#[emim]SCN using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emimscn link] (notes by Ling)
#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] (notes by Ling)
#CP2K Donts [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k link] (notes by Ling)
#How to make VMD trajectory repeated periodically [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/vmd link] (notes by Ling)
#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)

===CDT records===
#Activities record [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/CDT_records records]

===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] (notes by Tricia)
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link] (notes by Tricia)
#[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/calendar Calendar] (notes by Tricia)
#Demonstrating in the 3rd year computational chemistry lab [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/compchemlab Timetable] (notes by Tricia)
#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] notes by Tricia

Mod:Hunt Research Group/hpc Directory on desktop

2013-02-25T11:23:51Z

Lge:

[['''Mounting your HPC directories on your Mac Desktop''']]

NOTE1: Macfusion DOES NOT work on Leopard (OS X 10.5+). Read further down for an alternative (SSHFS GUI). To check your OS X version, click on the Apple logo on the top left of your screen and select "About This Mac".

NOTE2: Each drive/connection you mount creates a persistant connection between your computer and the HPC login server. And if you open too many connections, this could cause a lot of unhappy people in HPC if you forget to unmount these connections.

NOTE3: To unmount your drive, simply right click on the desktop icon and "Eject" the virtual drive.

'''For Lion Users (OS X 10.7+)''' - using Macfusion

Software required:

1. OSXFUSE (Latest build 2.5.4) - http://osxfuse.github.com

2. Macfusion (Latest build 2.0.4) - http://macfusionapp.org/

'''For Snow Leopard Users (OS X 10.6+)''' - using Macfusion

Software required:

1. MacFuse (Latest build 2.0.3,2) - http://code.google.com/p/macfuse/

2. Macfusion (Latest build 2.0.4) - http://macfusionapp.org/

Installation instructions:

1. Extract MacFuse (i.e. MacFUSE-2.0.3,2.dmg) and install MacFUSE.pkg (you will need Administrator access)

2. Extract Macfusion (i.e. Macfusion_2.0.4.zip) and copy/drag Macfusion.app into your ~/Applications folder

Using Macfusion:

1. Open Macfusion.app (in your ~/Applications folder)

2. To add a connection, click on the "+" button on the bottom left and select "SSHFS"

[[Image:MacFusion1.png]]

3. Enter the information required for your login

[[Image:MacFusion2.png]]

4. Keep the remaining settings as their default

5. Macfusion will mount each connection as a virtual drive. To change the name of the mounted drive, select the "Macfusion" tab and enter your desired name into "Volume Name:"

[[Image:MacFusion3.png]]

6. Click OK and you should see your newly added connection in the main window. Select the "Mount" option to mount your drive.

7. On your first attempt to mount the drive, MacFusion will ask for permission to access your password. Click "Always Allow" to avoid seeing this popup on subsequent connections.

[[Image:MacFusion4.png]]

8. When the drive is successfully mounted, it should turn green with the option to unmount it.

[[Image:MacFusion5.png]]

9. You can access your drive via the icon on your desktop.

[[Image:MacFusion6.png]]

'''For Leopard Users (OS X 10.5+)''' - using SSHFS

Software required:

1. MacFuse (Latest build 2.0.3,2) - http://code.google.com/p/macfuse/

2. SSHFS-GUI (Latest build 1.2) - http://code.google.com/p/sshfs-gui/

Installation instructions:

1. Extract MacFuse (i.e. MacFUSE-2.0.3,2.dmg) and install MacFUSE.pkg (you will need Administrator access)

2. Extract SSHFS-GUI (i.e. sshfs-gui.1.2.dmg) and copy/drag SSHFS GUI.app into your ~/Applications folder

Using SSHFS GUI:

1. Open SSHFS GUI.app (in your ~/Applications folder)

2. Enter the relevant information and click on the "Mount" button on the lower right to mount your connection. SSHFS mounts each connection as a virtual drive.

[[Image:SSHFS1.png]]

3. SSHFS stores your login information and you should see your current connection stored under "Recent servers"

[[Image:SSHFS2.png]]

4. You can access your drive via the icon on the desktop

[[Image:SSHFS3.png]]

'''Accessing your virtual drive via Finder'''

1. Your drive is located under your root directory

[[Image:Finder1.png]]

2. To make your life easier, you can drag it under "devices" so it will appear there every time you mount your drive.

[[Image:Finder2.png]]

Mod:Hunt Research Group/hpc Directory on desktop

2013-02-25T11:23:43Z

Lge:

Mod:Hunt Research Group/hpc Directory on desktop

2013-02-25T11:23:28Z

Lge:

[['''Mounting your HPC directories on your Mac Desktop''']]

NOTE1: Macfusion DOES NOT work on Leopard (OS X 10.5+). Read further down for an alternative (SSHFS GUI). To check your OS X version, click on the Apple logo on the top left of your screen and select "About This Mac".

NOTE2: Each drive/connection you mount creates a persistant connection between your computer and the HPC login server. And if you open too many connections, this could cause a lot of unhappy people in HPC if you forget to unmount these connections.

NOTE3: To unmount your drive, simply right click on the desktop icon and "Eject" the virtual drive.

'''For Lion Users (OS X 10.7+)''' - using Macfusion
Software required:
1. OSXFUSE (Latest build 2.5.4) - http://osxfuse.github.com

2. Macfusion (Latest build 2.0.4) - http://macfusionapp.org/

'''For Snow Leopard Users (OS X 10.6+)''' - using Macfusion

Software required:

1. MacFuse (Latest build 2.0.3,2) - http://code.google.com/p/macfuse/

2. Macfusion (Latest build 2.0.4) - http://macfusionapp.org/

Installation instructions:

1. Extract MacFuse (i.e. MacFUSE-2.0.3,2.dmg) and install MacFUSE.pkg (you will need Administrator access)

2. Extract Macfusion (i.e. Macfusion_2.0.4.zip) and copy/drag Macfusion.app into your ~/Applications folder

Using Macfusion:

1. Open Macfusion.app (in your ~/Applications folder)

2. To add a connection, click on the "+" button on the bottom left and select "SSHFS"

[[Image:MacFusion1.png]]

3. Enter the information required for your login

[[Image:MacFusion2.png]]

4. Keep the remaining settings as their default

5. Macfusion will mount each connection as a virtual drive. To change the name of the mounted drive, select the "Macfusion" tab and enter your desired name into "Volume Name:"

[[Image:MacFusion3.png]]

6. Click OK and you should see your newly added connection in the main window. Select the "Mount" option to mount your drive.

7. On your first attempt to mount the drive, MacFusion will ask for permission to access your password. Click "Always Allow" to avoid seeing this popup on subsequent connections.

[[Image:MacFusion4.png]]

8. When the drive is successfully mounted, it should turn green with the option to unmount it.

[[Image:MacFusion5.png]]

9. You can access your drive via the icon on your desktop.

[[Image:MacFusion6.png]]

'''For Leopard Users (OS X 10.5+)''' - using SSHFS

Software required:

1. MacFuse (Latest build 2.0.3,2) - http://code.google.com/p/macfuse/

2. SSHFS-GUI (Latest build 1.2) - http://code.google.com/p/sshfs-gui/

Installation instructions:

1. Extract MacFuse (i.e. MacFUSE-2.0.3,2.dmg) and install MacFUSE.pkg (you will need Administrator access)

2. Extract SSHFS-GUI (i.e. sshfs-gui.1.2.dmg) and copy/drag SSHFS GUI.app into your ~/Applications folder

Using SSHFS GUI:

1. Open SSHFS GUI.app (in your ~/Applications folder)

2. Enter the relevant information and click on the "Mount" button on the lower right to mount your connection. SSHFS mounts each connection as a virtual drive.

[[Image:SSHFS1.png]]

3. SSHFS stores your login information and you should see your current connection stored under "Recent servers"

[[Image:SSHFS2.png]]

4. You can access your drive via the icon on the desktop

[[Image:SSHFS3.png]]

'''Accessing your virtual drive via Finder'''

1. Your drive is located under your root directory

[[Image:Finder1.png]]

2. To make your life easier, you can drag it under "devices" so it will appear there every time you mount your drive.

[[Image:Finder2.png]]

Mod:Hunt Research Group/hpc Directory on desktop

2013-02-25T11:23:07Z

Lge:

[['''Mounting your HPC directories on your Mac Desktop''']]

NOTE1: Macfusion DOES NOT work on Leopard (OS X 10.5+). Read further down for an alternative (SSHFS GUI). To check your OS X version, click on the Apple logo on the top left of your screen and select "About This Mac".

NOTE2: Each drive/connection you mount creates a persistant connection between your computer and the HPC login server. And if you open too many connections, this could cause a lot of unhappy people in HPC if you forget to unmount these connections.

NOTE3: To unmount your drive, simply right click on the desktop icon and "Eject" the virtual drive.

'''For Lion Users (OS X 10.7+)''' - using Macfusion

1. OSXFUSE (Latest build 2.5.4) - http://osxfuse.github.com

2. Macfusion (Latest build 2.0.4) - http://macfusionapp.org/

'''For Snow Leopard Users (OS X 10.6+)''' - using Macfusion

Software required:

1. MacFuse (Latest build 2.0.3,2) - http://code.google.com/p/macfuse/

2. Macfusion (Latest build 2.0.4) - http://macfusionapp.org/

Installation instructions:

1. Extract MacFuse (i.e. MacFUSE-2.0.3,2.dmg) and install MacFUSE.pkg (you will need Administrator access)

2. Extract Macfusion (i.e. Macfusion_2.0.4.zip) and copy/drag Macfusion.app into your ~/Applications folder

Using Macfusion:

1. Open Macfusion.app (in your ~/Applications folder)

2. To add a connection, click on the "+" button on the bottom left and select "SSHFS"

[[Image:MacFusion1.png]]

3. Enter the information required for your login

[[Image:MacFusion2.png]]

4. Keep the remaining settings as their default

5. Macfusion will mount each connection as a virtual drive. To change the name of the mounted drive, select the "Macfusion" tab and enter your desired name into "Volume Name:"

[[Image:MacFusion3.png]]

6. Click OK and you should see your newly added connection in the main window. Select the "Mount" option to mount your drive.

7. On your first attempt to mount the drive, MacFusion will ask for permission to access your password. Click "Always Allow" to avoid seeing this popup on subsequent connections.

[[Image:MacFusion4.png]]

8. When the drive is successfully mounted, it should turn green with the option to unmount it.

[[Image:MacFusion5.png]]

9. You can access your drive via the icon on your desktop.

[[Image:MacFusion6.png]]

'''For Leopard Users (OS X 10.5+)''' - using SSHFS

Software required:

1. MacFuse (Latest build 2.0.3,2) - http://code.google.com/p/macfuse/

2. SSHFS-GUI (Latest build 1.2) - http://code.google.com/p/sshfs-gui/

Installation instructions:

1. Extract MacFuse (i.e. MacFUSE-2.0.3,2.dmg) and install MacFUSE.pkg (you will need Administrator access)

2. Extract SSHFS-GUI (i.e. sshfs-gui.1.2.dmg) and copy/drag SSHFS GUI.app into your ~/Applications folder

Using SSHFS GUI:

1. Open SSHFS GUI.app (in your ~/Applications folder)

2. Enter the relevant information and click on the "Mount" button on the lower right to mount your connection. SSHFS mounts each connection as a virtual drive.

[[Image:SSHFS1.png]]

3. SSHFS stores your login information and you should see your current connection stored under "Recent servers"

[[Image:SSHFS2.png]]

4. You can access your drive via the icon on the desktop

[[Image:SSHFS3.png]]

'''Accessing your virtual drive via Finder'''

1. Your drive is located under your root directory

[[Image:Finder1.png]]

2. To make your life easier, you can drag it under "devices" so it will appear there every time you mount your drive.

[[Image:Finder2.png]]

Mod:Hunt Research Group

2013-02-25T11:22:51Z

Lge: /* Unix and HPC */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===Resources===

#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link] (notes by Tricia)

===Gaussian General===
#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] (notes by Everyone!)
#Instructions for visualizing electrostatic potentials [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link] (notes by Flo)
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#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] (notes by Heiko)
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link] (notes by Richard)
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link] (notes by Bryan & Richard)

===Unix and HPC===
#Setting up a connection to HPC if you have a PC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link] (notes by Hieu)
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link] (notes by Heiko)
#HPC servers and run scripts [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link] (notes by Tricia and Ling)]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link] (notes by Heiko)
#How to set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link] (notes by Heiko)
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link] (notes by Heiko)
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link] (notes by Heiko)
#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] (notes by Rachael, Weihong and Ling)
#How to set up cx2 [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cx2 link] (notes by Ling)

===Installing and using packages===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link] (notes by Ling)
#Beginners guide to VMD: a molecular dynamics visualisation package [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link] (notes by Ling & Bryan)
#DLPOLY a MD simulation package, Installation on an IMac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link] (notes by Ling)
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link] (notes by Tricia)
#How to install Geomview [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/geomview link] (notes by Tricia)
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/] (Ling)
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link] (notes by Bryan)

===Setup and Running MD Simulations===
#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#Packmol for generating starting configurations [http://www.ime.unicamp.br/~martinez/packmol/] from Packmol webpage.
#Getting the Force Field [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Wheretostart link] (notes by Richard)
#Choosing an Ensemble [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Ensembles link] (notes by Richard)
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link] (notes by Richard)
#Visualising your Simulation [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VisualisingyourSimulation link] (notes by Richard)
#Voids in ILs[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids link] (notes by Ling)
#How to equilibrate an MD run[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/equilibration link] (notes by Tricia and Ling)]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link] (notes by Ling)]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link] (notes by Ling and Tricia)]

===Research Notes===
#Cl- in water[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link] (notes by Ling)]
#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] (notes by Yannis)
#Functional for ILs using CPMD[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/IL_cpmd_functional link] (notes by Ling)
#[bmim]Cl using CPMD[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cpmd link] (notes by Ling)
#[bmim]Cl using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cp2k link] (notes by Ling)
#mman using CPMD and Gaussian [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/mman link] (notes by Ling)
#[emim]SCN using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emimscn link] (notes by Ling)
#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] (notes by Ling)
#CP2K Donts [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k link] (notes by Ling)
#How to make VMD trajectory repeated periodically [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/vmd link] (notes by Ling)
#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)

===CDT records===
#Activities record [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/CDT_records records]

===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] (notes by Tricia)
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link] (notes by Tricia)
#[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/calendar Calendar] (notes by Tricia)
#Demonstrating in the 3rd year computational chemistry lab [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/compchemlab Timetable] (notes by Tricia)
#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] notes by Tricia

Mod:Hunt Research Group/hpc Directory on desktop

2013-02-25T11:21:41Z

Lge:

[['''Mounting your HPC directories on your Mac Desktop''']]

NOTE1: Macfusion DOES NOT work on Leopard (OS X 10.5+). Read further down for an alternative (SSHFS GUI). To check your OS X version, click on the Apple logo on the top left of your screen and select "About This Mac".

NOTE2: Each drive/connection you mount creates a persistant connection between your computer and the HPC login server. And if you open too many connections, this could cause a lot of unhappy people in HPC if you forget to unmount these connections.

NOTE3: To unmount your drive, simply right click on the desktop icon and "Eject" the virtual drive.

'''For Lion Users (OS X 10.7+)''' - using Macfusion

1. OSXFUSE (Latest build 2.5.4) - http://osxfuse.github.com

2. Macfusion (Latest build 2.0.4) - http://macfusionapp.org/

'''For Snow Leopard Users (OS X 10.6+)''' - using Macfusion

Software required:

1. MacFuse (Latest build 2.0.3,2) - http://code.google.com/p/macfuse/

2. Macfusion (Latest build 2.0.4) - http://macfusionapp.org/

Installation instructions:

1. Extract MacFuse (i.e. MacFUSE-2.0.3,2.dmg) and install MacFUSE.pkg (you will need Administrator access)

2. Extract Macfusion (i.e. Macfusion_2.0.4.zip) and copy/drag Macfusion.app into your ~/Applications folder

Using Macfusion:

1. Open Macfusion.app (in your ~/Applications folder)

2. To add a connection, click on the "+" button on the bottom left and select "SSHFS"

[[Image:MacFusion1.png]]

3. Enter the information required for your login

[[Image:MacFusion2.png]]

4. Keep the remaining settings as their default

5. Macfusion will mount each connection as a virtual drive. To change the name of the mounted drive, select the "Macfusion" tab and enter your desired name into "Volume Name:"

[[Image:MacFusion3.png]]

6. Click OK and you should see your newly added connection in the main window. Select the "Mount" option to mount your drive.

7. On your first attempt to mount the drive, MacFusion will ask for permission to access your password. Click "Always Allow" to avoid seeing this popup on subsequent connections.

[[Image:MacFusion4.png]]

8. When the drive is successfully mounted, it should turn green with the option to unmount it.

[[Image:MacFusion5.png]]

9. You can access your drive via the icon on your desktop.

[[Image:MacFusion6.png]]

'''For Leopard Users (OS X 10.5+)''' - using SSHFS

Software required:

1. MacFuse (Latest build 2.0.3,2) - http://code.google.com/p/macfuse/

2. SSHFS-GUI (Latest build 1.2) - http://code.google.com/p/sshfs-gui/

Installation instructions:

1. Extract MacFuse (i.e. MacFUSE-2.0.3,2.dmg) and install MacFUSE.pkg (you will need Administrator access)

2. Extract SSHFS-GUI (i.e. sshfs-gui.1.2.dmg) and copy/drag SSHFS GUI.app into your ~/Applications folder

Using SSHFS GUI:

1. Open SSHFS GUI.app (in your ~/Applications folder)

2. Enter the relevant information and click on the "Mount" button on the lower right to mount your connection. SSHFS mounts each connection as a virtual drive.

[[Image:SSHFS1.png]]

3. SSHFS stores your login information and you should see your current connection stored under "Recent servers"

[[Image:SSHFS2.png]]

4. You can access your drive via the icon on the desktop

[[Image:SSHFS3.png]]

'''Accessing your virtual drive via Finder'''

1. Your drive is located under your root directory

[[Image:Finder1.png]]

2. To make your life easier, you can drag it under "devices" so it will appear there every time you mount your drive.

[[Image:Finder2.png]]

Mod:Hunt Research Group/calendar

2012-12-20T17:16:48Z

Lge:

== Calendar ==

*Tricia (Done)
*Abdihakim Hassan (Done)
*Bryan Ward (Done)
*Claire Ashworth (Done)
*Matthew Clough (Done)
*Dimitrios Katsikadakos (Not done)
*Ling Ge (Done)
*Precious Ugbomah (done)
*Richard Matthews (Done)
*Wendy Kuo (Not done)
*Vincent Chen (Done)
*Gabriel Lau (Done)
*Sarah Smith (Done)

 
<table border="1" cellpadding="5">
<tr bgcolor="#66CCFF">
<th width="115px">Mon</th>
<th width="115px">Tues</th>
<th width="115px">Wed</th>
<th width="115px">Thur</th>
<th width="115px">Fri</th>
<th width="115px" bgcolor="#CCCCCC">Sat</th>
<th width="115px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td bgcolor="#FFCCFF">14th End of Autumn Term </td>
<td bgcolor="#CCCCCC">15th </td>
<td bgcolor="#CCCCCC">16th </td>
</tr>
<tr valign="top">
<td>17th Tricia-CDT away day Bryan @ Oxford</td>
<td>18th Tricia-CDT away day Bryan @ Oxford '''{{fontcolor|red|Christmas dinner 6pm}}'''</td>
<td>19th Tricia-Home,Precious work from home </td>
<td>20th Tricia-at work!,Precious home</td>
<td>21st Tricia-Home</td>
<td bgcolor="#2E8B57">22nd ''College Closed'' </td>
<td bgcolor="#2E8B57">23rd ''College Closed'' </td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">24th ''College Closed'' </td>
<td bgcolor="#2E8B57">25th ''College Closed'' '''Christmas Day''' </td>
<td bgcolor="#2E8B57">26th ''College Closed'' '''Boxing Day''' </td>
<td bgcolor="#2E8B57">27th ''College Closed'' </td>
<td bgcolor="#2E8B57">28th ''College Closed'' </td>
<td bgcolor="#2E8B57">29th ''College Closed'' </td>
<td bgcolor="#2E8B57">30th ''College Closed'' </td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">31st ''College Closed'' '''New Year's Eve''' </td>
<td bgcolor="#4357CFF">1st January ''College Closed'' '''New Year's Day''' </td>
<td>2nd Tricia, Claire, Sarah, Richard, Bryan, Precious all Home</td>
<td>3rd Tricia, Sarah, Bryan, precious all home</td>
<td>4th Tricia, Matthew, Bryan, precious all home </td>
<td bgcolor="#FFCCFF">5th Start of Spring Term</td>
<td bgcolor="#CCCCCC">6th </td>
</tr>
<tr valign="top">
<td>7th Tricia at ETH</td>
<td>8th Tricia at ETH </td>
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td bgcolor="#CCCCCC"> 19th </td>
<td bgcolor="#CCCCCC"> 20th </td>
</tr>
<tr valign="top">
<td>21st Ling College Rep Away Day</td>
<td>22nd </td>
<td>23rd Claire Away</td>
<td>24th Claire Away</td>
<td>25th Claire Away</td>
<td bgcolor="#CCCCCC">26th Claire Away</td>
<td bgcolor="#CCCCCC">27th Claire Away </td>
</tr>
<tr valign="top">
<td>28th Claire Away</td>
<td>29th Claire Away</td>
<td>30th Claire Away</td>
<td>31st Claire Away</td>
<td bgcolor="#4357CFF">1st February Claire Away</td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td>4th </td>
<td>5th </td>
<td>6th </td>
<td>7th </td>
<td>8th </td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td>14th </td>
<td>15th </td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th </td>
<td>19th</td>
<td>20th </td>
<td>21st </td>
<td>22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td>25th </td>
<td>26th </td>
<td>27th </td>
<td>28th </td>
<td bgcolor="#4357CFF">1st March </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td >4th </td>
<td>5th </td>
<td>6th </td>
<td>7th </td>
<td>8th </td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td>14th </td>
<td>15th </td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td bgcolor="#FFCCFF">22nd End of Spring Term</td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td> 25th</td>
<td>26th </td>
<td>27th </td>
<td bgcolor="#2E8B57">28th College Closed</td>
<td bgcolor="#2E8B57">29th College Closed '''Good Friday'''</td>
<td bgcolor="#2E8B57">30th College Closed</td>
<td bgcolor="#2E8B57">31st College Closed '''Easter Sunday'''</td>
</tr>

<tr valign="top">
<td bgcolor="#4357CFF">1st April College Closed '''Easter Monday'''</td>
<td bgcolor="#2E8B57">2nd College Closed</td>
<td>3rd </td>
<td>4th </td>
<td>5th </td>
<td bgcolor="#CCCCCC">6th </td>
<td bgcolor="#CCCCCC">7th </td>
</tr>
</table>

Mod:Hunt Research Group

2012-11-21T17:45:29Z

Lge:

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===Resources===

#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link] (notes by Tricia)

===Gaussian General===
#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] (notes by Everyone!)
#Instructions for visualizing electrostatic potentials [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link] (notes by Flo)
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#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] (notes by Heiko)
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link] (notes by Richard)
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link] (notes by Bryan & Richard)

===Unix and HPC===
#Setting up a connection to HPC if you have a PC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link] (notes by Hieu)
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link] (notes by Heiko)
#HPC servers and run scripts [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link] (notes by Tricia and Ling)]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link] (notes by Heiko)
#How to set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link] (notes by Heiko)
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link] (notes by Heiko)
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link] (notes by Heiko)
#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] (notes by Rachael and Weihong)
#How to set up cx2 [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cx2 link] (notes by Ling)

===Installing and using packages===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link] (notes by Ling)
#Beginners guide to VMD: a molecular dynamics visualisation package [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link] (notes by Ling & Bryan)
#DLPOLY a MD simmulation package, Installation on an IMac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link] (notes by Ling)
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link] (notes by Tricia)
#How to install Geomview [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/geomview link] (notes by Tricia)
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/] (Ling)
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link] (notes by Bryan)

===Research Notes===
#Voids in ILs[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids link] (notes by Ling)
#How to equilibrate an MD run[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/equilibration link] (notes by Tricia and Ling)]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link] (notes by Ling)]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link] (notes by Ling and Tricia)]
#Cl- in water[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link] (notes by Ling)]
#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] (notes by Yannis)
#Functional for ILs using CPMD[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/IL_cpmd_functional link] (notes by Ling)
#[bmim]Cl using CPMD[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cpmd link] (notes by Ling)
#[bmim]Cl using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cp2k link] (notes by Ling)
#mman using CPMD and Gaussian [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/mman link] (notes by Ling)
#[emim]SCN using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emimscn link] (notes by Ling)
#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] (notes by Ling)
#CP2K Donts [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k link] (notes by Ling)
#How to make VMD trajectory repeated periodically [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/vmd link] (notes by Ling)

===CDT records===
#Activities record [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/CDT_records records]

===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] (notes by Tricia)
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link] (notes by Tricia)
#[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/calendar Calendar] (notes by Tricia)
#Demonstrating in the 3rd year computational chemistry lab [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/compchemlab Timetable] (notes by Tricia)
#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] notes by Tricia

Mod:Hunt Research Group/calendar

2012-11-21T17:41:48Z

Lge:

== Calendar ==

*Tricia (Not done)
*Abdihakim Hassan (Not done)
*Bryan Ward (Not done)
*Claire Ashworth (Done)
*Matthew Clough (Done)
*Dimitrios Katsikadakos (Not done)
*Ling Ge (Done)
*Precious Ugbomah (Not done)
*Richard Matthews (Not done)
*Wendy Kuo (Not done)
*Vincent Chen (Done)
*Gabriel Lau (Not done)
*Sarah Smith (Not done)

 
<table border="1" cellpadding="5">
<tr bgcolor="#66CCFF">
<th width="115px">Mon</th>
<th width="115px">Tues</th>
<th width="115px">Wed</th>
<th width="115px">Thur</th>
<th width="115px">Fri</th>
<th width="115px" bgcolor="#CCCCCC">Sat</th>
<th width="115px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td>26th November </td>
<td>27th </td>
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td bgcolor="#4357CFF">1st December </td>
<td bgcolor="#CCCCCC">2nd </td>
</tr>
<tr valign="top">
<td>3rd </td>
<td>4th </td>
<td>5th </td>
<td>6th </td>
<td>7th Matthew Away </td>
<td bgcolor="#CCCCCC">8th </td>
<td bgcolor="#CCCCCC">9th </td>
</tr>
<tr valign="top">
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td bgcolor="#FFCCFF">14th End of Autumn Term </td>
<td bgcolor="#CCCCCC">15th </td>
<td bgcolor="#CCCCCC">16th </td>
</tr>
<tr valign="top">
<td>17th </td>
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td bgcolor="#2E8B57">22nd ''College Closed'' Claire Home Sarah Home Matthew Home Vincent Home</td>
<td bgcolor="#2E8B57">23rd ''College Closed'' Claire Home Sarah Home Matthew Home Vincent Home</td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">24th ''College Closed'' Claire Home Sarah Home Matthew Home</td>
<td bgcolor="#2E8B57">25th ''College Closed'' '''Christmas Day''' Claire Home Sarah Home Matthew Home Vincent Home</td>
<td bgcolor="#2E8B57">26th ''College Closed'' '''Boxing Day''' Claire Home Sarah Home Matthew Home Vincent Home</td>
<td bgcolor="#2E8B57">27th ''College Closed'' Claire Home Sarah Home Matthew Home Vincent Home</td>
<td bgcolor="#2E8B57">28th ''College Closed'' Claire Home Sarah Home Matthew Home Vincent Home</td>
<td bgcolor="#2E8B57">29th ''College Closed'' Claire Home Sarah Home Matthew Home Vincent Home</td>
<td bgcolor="#2E8B57">30th ''College Closed'' Claire Home Sarah Home Matthew Home Vincent Home</td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">31st ''College Closed'' '''New Year's Eve''' Claire Home Sarah Home Matthew Home Vincent Home</td>
<td bgcolor="#4357CFF">1st January ''College Closed'' '''New Year's Day''' Claire Home Sarah Home Matthew Home Vincent Home</td>
<td>2nd Claire Home Sarah Home</td> <td>3rd Sarah Home</td>
<td>4th Matthew Home </td>
<td bgcolor="#FFCCFF">5th Start of Spring Term</td>
<td bgcolor="#CCCCCC">6th </td>
</tr>
<tr valign="top">
<td>7th </td>
<td>8th </td>
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td bgcolor="#CCCCCC"> 19th </td>
<td bgcolor="#CCCCCC"> 20th </td>
</tr>
<tr valign="top">
<td>21st </td>
<td>22nd </td>
<td>23rd Claire Away</td>
<td>24th Claire Away</td>
<td>25th Claire Away</td>
<td bgcolor="#CCCCCC">26th Claire Away</td>
<td bgcolor="#CCCCCC">27th Claire Away </td>
</tr>
<tr valign="top">
<td>28th Claire Away</td>
<td>29th Claire Away</td>
<td>30th Claire Away</td>
<td>31st Claire Away</td>
<td bgcolor="#4357CFF">1st February Claire Away</td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td>4th </td>
<td>5th </td>
<td>6th </td>
<td>7th </td>
<td>8th </td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td>14th </td>
<td>15th </td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th </td>
<td>19th</td>
<td>20th </td>
<td>21st </td>
<td>22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td>25th </td>
<td>26th </td>
<td>27th </td>
<td>28th </td>
<td bgcolor="#4357CFF">1st March </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td >4th </td>
<td>5th </td>
<td>6th </td>
<td>7th </td>
<td>8th </td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td>14th </td>
<td>15th </td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td bgcolor="#FFCCFF">22nd End of Spring Term</td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td> 25th</td>
<td>26th </td>
<td>27th </td>
<td bgcolor="#2E8B57">28th College Closed</td>
<td bgcolor="#2E8B57">29th College Closed '''Good Friday'''</td>
<td bgcolor="#2E8B57">30th College Closed</td>
<td bgcolor="#2E8B57">31st College Closed '''Easter Sunday'''</td>
</tr>

<tr valign="top">
<td bgcolor="#4357CFF">1st April College Closed '''Easter Monday'''</td>
<td bgcolor="#2E8B57">2nd College Closed</td>
<td>3rd </td>
<td>4th </td>
<td>5th </td>
<td bgcolor="#CCCCCC">6th </td>
<td bgcolor="#CCCCCC">7th </td>
</tr>
</table>

Talk:Mod:Hunt Research Group/vmd

2012-07-20T16:47:54Z

Lge:

Talk:Mod:Hunt Research Group/vmd

2012-07-20T16:47:07Z

Lge:

VMD (Notes by Ling)

1. VMD .xyz file format:

232
generated by VMD
O 0.362322 -4.33666 1.47307
O 0.270228 -4.78598 4.21874
O 1.65391 -1.59018 -1.22525

2. Load geometry file in VMD:

File => New Molecule => File name => File type (xyz), click 'Load'.

Or

File => New Molecule => File name (e.g. structure.xsf), click 'Load'.

3. Change representation:

Graphics => Representations => Coloring Method (Element) => Drawing Method (CPK).

CPK Coloring is a way to color atoms when visualizing molecular models, inspired by CPK plastic molecular model kits by Corey, Pauling and Koltun. The method uses the van der Waals radii to visualize atoms.

CPK coloring conventionally depicts:

hydrogen as white,

carbon as black or grey,

nitrogen as blue,

oxygen as red,

phosphorus as orange, and

sulfur as yellow.

Other colors that are not always standard include:

green for magnesium and / or chlorine,

orange for iron, and

pink for unknown elements or those with atomic numbers over 57.

4. How to read the coordinates of selected atom:

Mouse => Query => then click the atom and read the information (atom name, index, coordinates) of the atom in terminal window.

5. How to change colour:

Atoms:

Graphics => Colors => Name => X => blue, then click 'Apply' in the Graphic Representations window.

Background:

Graphics => Colors => Display => Background => White

6. Movie of DL-POLY trajectory:

File => New Molecule => File name (HISTORY) => File type (DLPOLY V2 History), click 'Load'.

(Note: need to have to keyword 'traj i j k' in CONTROL file of DLPOLY to produce HISTORY file.)

7. Movie of CPMD trajectory:

a. modify traj2xyz.f90 (no. of atoms and loops) for the new system.

b. use ./traj2xyz.x < TRAJECTORY > traj.xyz (./traj2xyz.x is in my home directory of my desktop).

c. use VMD to load traj.xyz

8. How to make a trajectory appear repeated in x,y,z directions:

Use tcl script vmd_periodic_xyz:

###############################################################
# #
# - pbc.tcl - #
# #
# Andrea Minoia, March 2010 #
# #
# Tcl script for VMD to set the size of the unit cell for #
# file formats that does not contain such information, e.g. #
# XYZ and TINKER arc files. #
# #
# Once the unit cell has been defined, periodic images can be #
# be displayed. #
# #
# Contacts: http://chembytes.wikidot.com #
# minoiaa@gmail.com #
# #
###############################################################
#pick ID for current molecule
set molid [molinfo top]

#pick the number of frames
set n [molinfo $molid get numframes]

puts -nonewline "\n Set length for a (angstrom): "
gets stdin a
puts -nonewline "\n Set length for b (angstrom): "
gets stdin b
puts -nonewline "\n Set length for c (angstrom): "
gets stdin c
puts -nonewline "\n Set angle alpha (if monoclinic cell press enter): "
gets stdin alpha
if { $alpha =="" } {
set alpha 90.000
set beta 90.000
set gamma 90.000
} else {
puts -nonewline "\n Set angle beta (degrees): "
gets stdin beta
puts -nonewline "\n Set angle gamma (degrees): "
gets stdin gamma
}

# Applying to all the frames
for {set i 0} {$i < $n} {incr i} {
molinfo $molid set frame $i
molinfo $molid set a $a
molinfo $molid set b $b
molinfo $molid set c $c
molinfo $molid set alpha $alpha
molinfo $molid set beta $beta
molinfo $molid set gamma $gamma
}
#rewind trajectory
animate goto start

a. Load the trajectory file and wait for it to finish loading.

b. In the VMD terminal type 'source vmd_periodic_xyz'

then type length for a, b, c cell size (angstrom) and the angles.

c. Graphical presentations -> Periodic

Mod:Hunt Research Group

2012-07-20T16:44:56Z

Lge: /* Hunt Group Wiki */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===Resources===

#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link] (notes by Tricia)

===Gaussian General===
#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] (notes by Everyone!)
#Instructions for visualizing electrostatic potentials [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link] (notes by Flo)
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#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] (notes by Heiko)
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9] (notes by Richard)

===Unix and HPC===
#Setting up a connection to HPC if you have a PC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link] (notes by Hieu)
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link] (notes by Heiko)
#HPC servers and run scripts [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link] (notes by Tricia and Ling)]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link] (notes by Heiko)
#How to set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link] (notes by Heiko)
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link] (notes by Heiko)
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link] (notes by Heiko)
#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] (notes by Rachael and Weihong)
#How to set up cx2 [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cx2 link] (notes by Ling)

===Installing packages===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link] (notes by Ling)
#VMD: a molecular dynamics visualisation package [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link] (notes by Ling)
#DLPOLY a MD simmulation package, Installation on an IMac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link] (notes by Ling)
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link] (notes by Tricia)
#How to install Geomview [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/geomview link] (notes by Tricia)
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/] (Ling)

===Research Notes===
#Voids in ILs[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids link] (notes by Ling)
#How to equilibrate an MD run[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/equilibration link] (notes by Tricia and Ling)]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link] (notes by Ling)]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link] (notes by Ling and Tricia)]
#Cl- in water[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link] (notes by Ling)]
#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] (notes by Yannis)
#Functional for ILs using CPMD[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/IL_cpmd_functional link] (notes by Ling)
#[bmim]Cl using CPMD[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cpmd link] (notes by Ling)
#[bmim]Cl using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cp2k link] (notes by Ling)
#mman using CPMD and Gaussian [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/mman link] (notes by Ling)
#[emim]SCN using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emimscn link] (notes by Ling)
#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] (notes by Ling)
#CP2K Donts [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k link] (nots by Ling)
#How to make VMD trajectory repeated periodically [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/vmd link] (nots by Ling)

===Teaching Stuff===
#Tutorial group A [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Tutorial_A notes]
#Tutorial group B [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Tutorial_B notes]

===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] (notes by Tricia)
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link] (notes by Tricia)
#[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/calendar Calendar] (notes by Tricia)
#Demonstrating in the 3rd year computational chemistry lab [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/compchemlab Timetable] (notes by Tricia)
#computational chemistry lab [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/comp_chem_results results] (notes by Yannis)
#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] notes by Tricia

Talk:Mod:Hunt Research Group/cp2k

2012-07-03T15:18:29Z

Lge: Created page with "1. Tabs are absolutely forbidden in CP2K input."

1. Tabs are absolutely forbidden in CP2K input.

Mod:Hunt Research Group

2012-07-03T15:18:00Z

Lge: /* Research Notes */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===Resources===

#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link] (notes by Tricia)

===Gaussian General===
#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] (notes by Everyone!)
#Instructions for visualizing electrostatic potentials [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link] (notes by Flo)
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#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] (notes by Heiko)
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9] (notes by Richard)

===Unix and HPC===
#Setting up a connection to HPC if you have a PC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link] (notes by Hieu)
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link] (notes by Heiko)
#HPC servers and run scripts [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link] (notes by Tricia and Ling)]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link] (notes by Heiko)
#How to set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link] (notes by Heiko)
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link] (notes by Heiko)
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link] (notes by Heiko)
#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] (notes by Rachael and Weihong)
#How to set up cx2 [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cx2 link] (notes by Ling)

===Installing packages===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link] (notes by Ling)
#VMD: a molecular dynamics visualisation package [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link] (notes by Ling)
#DLPOLY a MD simmulation package, Installation on an IMac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link] (notes by Ling)
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link] (notes by Tricia)
#How to install Geomview [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/geomview link] (notes by Tricia)
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/] (Ling)

===Research Notes===
#Voids in ILs[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids link] (notes by Ling)
#How to equilibrate an MD run[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/equilibration link] (notes by Tricia and Ling)]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link] (notes by Ling)]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link] (notes by Ling and Tricia)]
#Cl- in water[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link] (notes by Ling)]
#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] (notes by Yannis)
#Functional for ILs using CPMD[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/IL_cpmd_functional link] (notes by Ling)
#[bmim]Cl using CPMD[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cpmd link] (notes by Ling)
#[bmim]Cl using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cp2k link] (notes by Ling)
#mman using CPMD and Gaussian [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/mman link] (notes by Ling)
#[emim]SCN using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emimscn link] (notes by Ling)
#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] (notes by Ling)
#CP2K Donts [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k link] (nots by Ling)

===Teaching Stuff===
#Tutorial group A [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Tutorial_A notes]
#Tutorial group B [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Tutorial_B notes]

===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] (notes by Tricia)
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link] (notes by Tricia)
#[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/calendar Calendar] (notes by Tricia)
#Demonstrating in the 3rd year computational chemistry lab [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/compchemlab Timetable] (notes by Tricia)
#computational chemistry lab [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/comp_chem_results results] (notes by Yannis)
#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] notes by Tricia

Mod:Hunt Research Group/calendar

2012-06-08T13:07:14Z

Lge:

== Calendar ==

*Tricia (not done)
*Abdihakim Hassan (not done)
*Bryan Ward (not done)
*Claire Ashworth (not done)
*Matthew Clough (not done)
*Dimitrios Katsikadakos (not done)
*Ling Ge (not done)
*Precious Ugbomah (not done)
*Richard Matthews (Done)
*Wendy Kuo (not done)
 
<table border="1" cellpadding="5">
<tr bgcolor="#66CCFF">
<th width="90px">Mon</th>
<th width="90px">Tues</th>
<th width="90px">Wed</th>
<th width="90px">Thur</th>
<th width="90px">Fri</th>
<th width="90px" bgcolor="#CCCCCC">Sat</th>
<th width="90px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td bgcolor="#4357CFF">June 4 </td>
<td>5 </td>
<td>6 </td>
<td>7 </td>
<td>8 </td>
<td bgcolor="#CCCCCC">9 </td>
<td bgcolor="#CCCCCC">10 </td>
</tr>
<tr valign="top">
<td>11 </td>
<td>12 </td>
<td>13 Richard Workshop (Afternoon) </td>
<td>14 </td>
<td>15 Ling working from Home</td>
<td bgcolor="#CCCCCC">16 </td>
<td bgcolor="#CCCCCC">17 </td>
</tr>
<tr valign="top">
<td>18 Bryan Summer School </td>
<td>19 Bryan Summer School </td>
<td>20 Bryan Summer School </td>
<td>21 Bryan Summer School Richard Workshop </td>
<td>22 Bryan Summer School Ling working from Home</td>
<td bgcolor="#CCCCCC">23 </td>
<td bgcolor="#CCCCCC">24 Richard CMS2012 </td>
</tr>
<tr valign="top">
<td>25 Richard CMS2012 </td>
<td>26 Richard CMS2012 </td>
<td>27 Richard CMS2012 </td>
<td>28 </td>
<td bgcolor="#954645">29 Summer Term Ends Ling working from Home </td>
<td bgcolor="#CCCCCC">30 </td>
<td bgcolor="#4357CFF">July 1 </td>
</tr>
<tr valign="top">
<td>2 </td>
<td>3 </td>
<td>4 </td>
<td>5 </td>
<td>6 </td>
<td bgcolor="#CCCCCC">7 </td>
<td bgcolor="#CCCCCC">8 </td>
</tr>
<tr valign="top">
<td>9 </td>
<td>10 </td>
<td>11 </td>
<td>12 </td>
<td>13 </td>
<td bgcolor="#CCCCCC">14 </td>
<td bgcolor="#CCCCCC">15 </td>
</tr>
<tr valign="top">
<td>16 </td>
<td>17 Richard Away </td>
<td>18 Richard Away </td>
<td>19 Richard Away </td>
<td>20 Richard Away </td>
<td bgcolor="#CCCCCC">21 Richard Away </td>
<td bgcolor="#CCCCCC">22 Richard Away </td>
</tr>
<tr valign="top">
<td>23 Richard Away </td>
<td>24 Richard Away </td>
<td>25 </td>
<td>26 </td>
<td bgcolor="#2E8B57">27 Olympics </td>
<td bgcolor="#2E8B57">28 Olympics </td>
<td bgcolor="#2E8B57">29 Olympics </td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">30 Olympics </td>
<td bgcolor="#2E8B57">31 Olympics </td>
<td bgcolor="#2E8B57">August 1 Olympics </td>
<td bgcolor="#2E8B57">2 Olympics </td>
<td bgcolor="#2E8B57">3 Olympics </td>
<td bgcolor="#2E8B57">4 Olympics </td>
<td bgcolor="#2E8B57">5 Olympics </td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">6 Olympics </td>
<td bgcolor="#2E8B57">7 Olympics </td>
<td bgcolor="#2E8B57">8 Olympics </td>
<td bgcolor="#2E8B57">9 Olympics </td>
<td bgcolor="#2E8B57">10 Olympics </td>
<td bgcolor="#2E8B57">11 Olympics </td>
<td bgcolor="#2E8B57">12 Olympics </td>
<tr valign="top">
<td>13 </td>
<td>14 </td>
<td>15 </td>
<td>16 </td>
<td>17 </td>
<td bgcolor="#CCCCCC">18 </td>
<td bgcolor="#CCCCCC">19 </td>
<tr valign="top">
<td>20 Ling FT</td>
<td>21 Ling FT</td>
<td>22 Ling FT</td>
<td>23 Ling FT </td>
<td>24 Ling FT </td>
<td bgcolor="#CCCCCC">25 </td>
<td bgcolor="#CCCCCC">26 </td>
<tr valign="top">
<td>27 Ling FT</td>
<td>28 Ling FT</td>
<td>29 Ling FT</td>
<td>30 Ling FT </td>
<td>31 Ling FT </td>
<td bgcolor="#4357CFF">September 1 </td>
<td bgcolor="#CCCCCC">2 </td>
<tr valign="top">
<td>3 Ling FT</td>
<td>4 Ling Science Festival Aberdeen</td>
<td>5 Ling Science Festival Aberdeen</td>
<td>6 Ling Science Festival Aberdeen</td>
<td>7 Ling Science Festival Aberdeen</td>
<td bgcolor="#CCCCCC">8 Ling Science Festival Aberdeen</td>
<td bgcolor="#CCCCCC">9 Ling Science Festival Aberdeen</td>
<tr valign="top">
<td>10 Ling FT</td>
<td>11 Ling FT</td>
<td>12 Ling FT</td>
<td>13 Ling FT </td>
<td>14 Ling FT </td>
<td bgcolor="#CCCCCC">15 </td>
<td bgcolor="#CCCCCC">16 </td>

<tr valign="top">
<td>17 </td>
<td>18 </td>
<td>19 </td>
<td>20 </td>
<td>21 </td>
<td bgcolor="#CCCCCC">22 </td>
<td bgcolor="#CCCCCC">23 </td>

<tr valign="top">
<td>24 </td>
<td>25 </td>
<td>26 </td>
<td>27 </td>
<td>28 </td>
<td bgcolor="#954645">29 Autumn Term Starts </td>
<td bgcolor="#CCCCCC">30 </td>

<tr valign="top">
<td bgcolor="#4357CFF">October 1 </td>
<td>2 </td>
<td>3 </td>
<td>4 </td>
<td>5 </td>
<td bgcolor="#CCCCCC">6 </td>
<td bgcolor="#CCCCCC">7 </td>
<tr valign="top">
<td>8 </td>
<td>9 </td>
<td>10 </td>
<td>11 </td>
<td>12 </td>
<td bgcolor="#CCCCCC">13 </td>
<td bgcolor="#CCCCCC">14 </td>
<tr valign="top">
<td>15 </td>
<td>16 </td>
<td>17 </td>
<td>18 </td>
<td>19 </td>
<td bgcolor="#CCCCCC">20 </td>
<td bgcolor="#CCCCCC">21 </td>
<tr valign="top">
<td>22 </td>
<td>23 </td>
<td>24 </td>
<td>25 </td>
<td>26 </td>
<td bgcolor="#CCCCCC">27 </td>
<td bgcolor="#CCCCCC">28 </td>
<tr valign="top">
<td>29 </td>
<td>30 </td>
<td>31 </td>
<td bgcolor="#4357CFF">November 1 </td>
<td>2 </td>
<td bgcolor="#CCCCCC">3 </td>
<td bgcolor="#CCCCCC">4 </td>

</tr>
</table>

Mod:Hunt Research Group/calendar

2012-06-08T13:04:21Z

Lge:

== Calendar ==

*Tricia (not done)
*Abdihakim Hassan (not done)
*Bryan Ward (not done)
*Claire Ashworth (not done)
*Matthew Clough (not done)
*Dimitrios Katsikadakos (not done)
*Ling Ge (not done)
*Precious Ugbomah (not done)
*Richard Matthews (Done)
*Wendy Kuo (not done)
 
<table border="1" cellpadding="5">
<tr bgcolor="#66CCFF">
<th width="90px">Mon</th>
<th width="90px">Tues</th>
<th width="90px">Wed</th>
<th width="90px">Thur</th>
<th width="90px">Fri</th>
<th width="90px" bgcolor="#CCCCCC">Sat</th>
<th width="90px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td bgcolor="#4357CFF">June 4 </td>
<td>5 </td>
<td>6 </td>
<td>7 </td>
<td>8 </td>
<td bgcolor="#CCCCCC">9 </td>
<td bgcolor="#CCCCCC">10 </td>
</tr>
<tr valign="top">
<td>11 </td>
<td>12 </td>
<td>13 Richard Workshop (Afternoon) </td>
<td>14 </td>
<td>15 Ling working from Home</td>
<td bgcolor="#CCCCCC">16 </td>
<td bgcolor="#CCCCCC">17 </td>
</tr>
<tr valign="top">
<td>18 Bryan Summer School </td>
<td>19 Bryan Summer School </td>
<td>20 Bryan Summer School </td>
<td>21 Bryan Summer School Richard Workshop </td>
<td>22 Bryan Summer School </td>
<td bgcolor="#CCCCCC">23 </td>
<td bgcolor="#CCCCCC">24 Richard CMS2012 </td>
</tr>
<tr valign="top">
<td>25 Richard CMS2012 </td>
<td>26 Richard CMS2012 </td>
<td>27 Richard CMS2012 </td>
<td>28 </td>
<td bgcolor="#954645">29 Summer Term Ends </td>
<td bgcolor="#CCCCCC">30 </td>
<td bgcolor="#4357CFF">July 1 </td>
</tr>
<tr valign="top">
<td>2 </td>
<td>3 </td>
<td>4 </td>
<td>5 </td>
<td>6 </td>
<td bgcolor="#CCCCCC">7 </td>
<td bgcolor="#CCCCCC">8 </td>
</tr>
<tr valign="top">
<td>9 </td>
<td>10 </td>
<td>11 </td>
<td>12 </td>
<td>13 </td>
<td bgcolor="#CCCCCC">14 </td>
<td bgcolor="#CCCCCC">15 </td>
</tr>
<tr valign="top">
<td>16 </td>
<td>17 Richard Away </td>
<td>18 Richard Away </td>
<td>19 Richard Away </td>
<td>20 Richard Away </td>
<td bgcolor="#CCCCCC">21 Richard Away </td>
<td bgcolor="#CCCCCC">22 Richard Away </td>
</tr>
<tr valign="top">
<td>23 Richard Away </td>
<td>24 Richard Away </td>
<td>25 </td>
<td>26 </td>
<td bgcolor="#2E8B57">27 Olympics </td>
<td bgcolor="#2E8B57">28 Olympics </td>
<td bgcolor="#2E8B57">29 Olympics </td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">30 Olympics </td>
<td bgcolor="#2E8B57">31 Olympics </td>
<td bgcolor="#2E8B57">August 1 Olympics </td>
<td bgcolor="#2E8B57">2 Olympics </td>
<td bgcolor="#2E8B57">3 Olympics </td>
<td bgcolor="#2E8B57">4 Olympics </td>
<td bgcolor="#2E8B57">5 Olympics </td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">6 Olympics </td>
<td bgcolor="#2E8B57">7 Olympics </td>
<td bgcolor="#2E8B57">8 Olympics </td>
<td bgcolor="#2E8B57">9 Olympics </td>
<td bgcolor="#2E8B57">10 Olympics </td>
<td bgcolor="#2E8B57">11 Olympics </td>
<td bgcolor="#2E8B57">12 Olympics </td>
<tr valign="top">
<td>13 </td>
<td>14 </td>
<td>15 </td>
<td>16 </td>
<td>17 </td>
<td bgcolor="#CCCCCC">18 </td>
<td bgcolor="#CCCCCC">19 </td>
<tr valign="top">
<td>20 Ling FT</td>
<td>21 Ling FT</td>
<td>22 Ling FT</td>
<td>23 Ling FT </td>
<td>24 Ling FT </td>
<td bgcolor="#CCCCCC">25 </td>
<td bgcolor="#CCCCCC">26 </td>
<tr valign="top">
<td>27 Ling FT</td>
<td>28 Ling FT</td>
<td>29 Ling FT</td>
<td>30 Ling FT </td>
<td>31 Ling FT </td>
<td bgcolor="#4357CFF">September 1 </td>
<td bgcolor="#CCCCCC">2 </td>
<tr valign="top">
<td>3 Ling FT</td>
<td>4 Ling Science Festival Aberdeen</td>
<td>5 Ling Science Festival Aberdeen</td>
<td>6 Ling Science Festival Aberdeen</td>
<td>7 Ling Science Festival Aberdeen</td>
<td bgcolor="#CCCCCC">8 Ling Science Festival Aberdeen</td>
<td bgcolor="#CCCCCC">9 Ling Science Festival Aberdeen</td>
<tr valign="top">
<td>10 Ling FT</td>
<td>11 Ling FT</td>
<td>12 Ling FT</td>
<td>13 Ling FT </td>
<td>14 Ling FT </td>
<td bgcolor="#CCCCCC">15 </td>
<td bgcolor="#CCCCCC">16 </td>

<tr valign="top">
<td>17 </td>
<td>18 </td>
<td>19 </td>
<td>20 </td>
<td>21 </td>
<td bgcolor="#CCCCCC">22 </td>
<td bgcolor="#CCCCCC">23 </td>

<tr valign="top">
<td>24 </td>
<td>25 </td>
<td>26 </td>
<td>27 </td>
<td>28 </td>
<td bgcolor="#954645">29 Autumn Term Starts </td>
<td bgcolor="#CCCCCC">30 </td>

<tr valign="top">
<td bgcolor="#4357CFF">October 1 </td>
<td>2 </td>
<td>3 </td>
<td>4 </td>
<td>5 </td>
<td bgcolor="#CCCCCC">6 </td>
<td bgcolor="#CCCCCC">7 </td>
<tr valign="top">
<td>8 </td>
<td>9 </td>
<td>10 </td>
<td>11 </td>
<td>12 </td>
<td bgcolor="#CCCCCC">13 </td>
<td bgcolor="#CCCCCC">14 </td>
<tr valign="top">
<td>15 </td>
<td>16 </td>
<td>17 </td>
<td>18 </td>
<td>19 </td>
<td bgcolor="#CCCCCC">20 </td>
<td bgcolor="#CCCCCC">21 </td>
<tr valign="top">
<td>22 </td>
<td>23 </td>
<td>24 </td>
<td>25 </td>
<td>26 </td>
<td bgcolor="#CCCCCC">27 </td>
<td bgcolor="#CCCCCC">28 </td>
<tr valign="top">
<td>29 </td>
<td>30 </td>
<td>31 </td>
<td bgcolor="#4357CFF">November 1 </td>
<td>2 </td>
<td bgcolor="#CCCCCC">3 </td>
<td bgcolor="#CCCCCC">4 </td>

</tr>
</table>

Mod:Hunt Research Group/calendar

2012-06-08T12:58:47Z

Lge:

== Calendar ==

*Tricia (not done)
*Abdihakim Hassan (not done)
*Bryan Ward (not done)
*Claire Ashworth (not done)
*Matthew Clough (not done)
*Dimitrios Katsikadakos (not done)
*Ling Ge (not done)
*Precious Ugbomah (not done)
*Richard Matthews (Done)
*Wendy Kuo (not done)
 
<table border="1" cellpadding="5">
<tr bgcolor="#66CCFF">
<th width="90px">Mon</th>
<th width="90px">Tues</th>
<th width="90px">Wed</th>
<th width="90px">Thur</th>
<th width="90px">Fri</th>
<th width="90px" bgcolor="#CCCCCC">Sat</th>
<th width="90px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td bgcolor="#4357CFF">June 4 </td>
<td>5 </td>
<td>6 </td>
<td>7 </td>
<td>8 </td>
<td bgcolor="#CCCCCC">9 </td>
<td bgcolor="#CCCCCC">10 </td>
</tr>
<tr valign="top">
<td>11 </td>
<td>12 </td>
<td>13 Richard Workshop (Afternoon) </td>
<td>14 </td>
<td>15 Ling working from Home</td>
<td bgcolor="#CCCCCC">16 </td>
<td bgcolor="#CCCCCC">17 </td>
</tr>
<tr valign="top">
<td>18 Bryan Summer School </td>
<td>19 Bryan Summer School </td>
<td>20 Bryan Summer School </td>
<td>21 Bryan Summer School Richard Workshop </td>
<td>22 Bryan Summer School </td>
<td bgcolor="#CCCCCC">23 </td>
<td bgcolor="#CCCCCC">24 Richard CMS2012 </td>
</tr>
<tr valign="top">
<td>25 Richard CMS2012 </td>
<td>26 Richard CMS2012 </td>
<td>27 Richard CMS2012 </td>
<td>28 </td>
<td bgcolor="#954645">29 Summer Term Ends </td>
<td bgcolor="#CCCCCC">30 </td>
<td bgcolor="#4357CFF">July 1 </td>
</tr>
<tr valign="top">
<td>2 </td>
<td>3 </td>
<td>4 </td>
<td>5 </td>
<td>6 </td>
<td bgcolor="#CCCCCC">7 </td>
<td bgcolor="#CCCCCC">8 </td>
</tr>
<tr valign="top">
<td>9 </td>
<td>10 </td>
<td>11 </td>
<td>12 </td>
<td>13 </td>
<td bgcolor="#CCCCCC">14 </td>
<td bgcolor="#CCCCCC">15 </td>
</tr>
<tr valign="top">
<td>16 </td>
<td>17 Richard Away </td>
<td>18 Richard Away </td>
<td>19 Richard Away </td>
<td>20 Richard Away </td>
<td bgcolor="#CCCCCC">21 Richard Away </td>
<td bgcolor="#CCCCCC">22 Richard Away </td>
</tr>
<tr valign="top">
<td>23 Richard Away </td>
<td>24 Richard Away </td>
<td>25 </td>
<td>26 </td>
<td bgcolor="#2E8B57">27 Olympics </td>
<td bgcolor="#2E8B57">28 Olympics </td>
<td bgcolor="#2E8B57">29 Olympics </td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">30 Olympics </td>
<td bgcolor="#2E8B57">31 Olympics </td>
<td bgcolor="#2E8B57">August 1 Olympics </td>
<td bgcolor="#2E8B57">2 Olympics </td>
<td bgcolor="#2E8B57">3 Olympics </td>
<td bgcolor="#2E8B57">4 Olympics </td>
<td bgcolor="#2E8B57">5 Olympics </td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">6 Olympics </td>
<td bgcolor="#2E8B57">7 Olympics </td>
<td bgcolor="#2E8B57">8 Olympics </td>
<td bgcolor="#2E8B57">9 Olympics </td>
<td bgcolor="#2E8B57">10 Olympics </td>
<td bgcolor="#2E8B57">11 Olympics </td>
<td bgcolor="#2E8B57">12 Olympics </td>
<tr valign="top">
<td>13 </td>
<td>14 </td>
<td>15 </td>
<td>16 </td>
<td>17 </td>
<td bgcolor="#CCCCCC">18 </td>
<td bgcolor="#CCCCCC">19 </td>
<tr valign="top">
<td>20 Ling doing Media Fellowship</td>
<td>21 Ling doing Media Fellowship</td>
<td>22 Ling doing Media Fellowship</td>
<td>23 Ling doing Media Fellowship </td>
<td>24 Ling doing Media Fellowship </td>
<td bgcolor="#CCCCCC">25 </td>
<td bgcolor="#CCCCCC">26 </td>
<tr valign="top">
<td>27 Ling doing Media Fellowship</td>
<td>28 Ling doing Media Fellowship</td>
<td>29 Ling doing Media Fellowship</td>
<td>30 Ling doing Media Fellowship </td>
<td>31 Ling doing Media Fellowship </td>
<td bgcolor="#4357CFF">September 1 </td>
<td bgcolor="#CCCCCC">2 </td>
<tr valign="top">
<td>3 Ling doing Media Fellowship</td>
<td>4 Ling doing Media Fellowship</td>
<td>5 Ling doing Media Fellowship</td>
<td>6 Ling doing Media Fellowship</td>
<td>7 Ling doing Media Fellowship</td>
<td bgcolor="#CCCCCC">8 </td>
<td bgcolor="#CCCCCC">9 </td>
<tr valign="top">
<td>10 Ling doing Media Fellowship</td>
<td>11 Ling doing Media Fellowship</td>
<td>12 Ling doing Media Fellowship</td>
<td>13 Ling doing Media Fellowship </td>
<td>14 Ling doing Media Fellowship </td>
<td bgcolor="#CCCCCC">15 </td>
<td bgcolor="#CCCCCC">16 </td>

<tr valign="top">
<td>17 </td>
<td>18 </td>
<td>19 </td>
<td>20 </td>
<td>21 </td>
<td bgcolor="#CCCCCC">22 </td>
<td bgcolor="#CCCCCC">23 </td>

<tr valign="top">
<td>24 </td>
<td>25 </td>
<td>26 </td>
<td>27 </td>
<td>28 </td>
<td bgcolor="#954645">29 Autumn Term Starts </td>
<td bgcolor="#CCCCCC">30 </td>

<tr valign="top">
<td bgcolor="#4357CFF">October 1 </td>
<td>2 </td>
<td>3 </td>
<td>4 </td>
<td>5 </td>
<td bgcolor="#CCCCCC">6 </td>
<td bgcolor="#CCCCCC">7 </td>
<tr valign="top">
<td>8 </td>
<td>9 </td>
<td>10 </td>
<td>11 </td>
<td>12 </td>
<td bgcolor="#CCCCCC">13 </td>
<td bgcolor="#CCCCCC">14 </td>
<tr valign="top">
<td>15 </td>
<td>16 </td>
<td>17 </td>
<td>18 </td>
<td>19 </td>
<td bgcolor="#CCCCCC">20 </td>
<td bgcolor="#CCCCCC">21 </td>
<tr valign="top">
<td>22 </td>
<td>23 </td>
<td>24 </td>
<td>25 </td>
<td>26 </td>
<td bgcolor="#CCCCCC">27 </td>
<td bgcolor="#CCCCCC">28 </td>
<tr valign="top">
<td>29 </td>
<td>30 </td>
<td>31 </td>
<td bgcolor="#4357CFF">November 1 </td>
<td>2 </td>
<td bgcolor="#CCCCCC">3 </td>
<td bgcolor="#CCCCCC">4 </td>

</tr>
</table>

Mod:Hunt Research Group/calendar

2012-06-08T12:56:19Z

Lge:

== Calendar ==

*Tricia (not done)
*Abdihakim Hassan (not done)
*Bryan Ward (not done)
*Claire Ashworth (not done)
*Matthew Clough (not done)
*Dimitrios Katsikadakos (not done)
*Ling Ge (not done)
*Precious Ugbomah (not done)
*Richard Matthews (Done)
*Wendy Kuo (not done)
 
<table border="1" cellpadding="5">
<tr bgcolor="#66CCFF">
<th width="90px">Mon</th>
<th width="90px">Tues</th>
<th width="90px">Wed</th>
<th width="90px">Thur</th>
<th width="90px">Fri</th>
<th width="90px" bgcolor="#CCCCCC">Sat</th>
<th width="90px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td bgcolor="#4357CFF">June 4 </td>
<td>5 </td>
<td>6 </td>
<td>7 </td>
<td>8 </td>
<td bgcolor="#CCCCCC">9 </td>
<td bgcolor="#CCCCCC">10 </td>
</tr>
<tr valign="top">
<td>11 </td>
<td>12 </td>
<td>13 Richard Workshop (Afternoon) </td>
<td>14 </td>
<td>15 Ling working from Home</td>
<td bgcolor="#CCCCCC">16 </td>
<td bgcolor="#CCCCCC">17 </td>
</tr>
<tr valign="top">
<td>18 Bryan Summer School </td>
<td>19 Bryan Summer School </td>
<td>20 Bryan Summer School </td>
<td>21 Bryan Summer School Richard Workshop </td>
<td>22 Bryan Summer School </td>
<td bgcolor="#CCCCCC">23 </td>
<td bgcolor="#CCCCCC">24 Richard CMS2012 </td>
</tr>
<tr valign="top">
<td>25 Richard CMS2012 </td>
<td>26 Richard CMS2012 </td>
<td>27 Richard CMS2012 </td>
<td>28 </td>
<td bgcolor="#954645">29 Summer Term Ends </td>
<td bgcolor="#CCCCCC">30 </td>
<td bgcolor="#4357CFF">July 1 </td>
</tr>
<tr valign="top">
<td>2 </td>
<td>3 </td>
<td>4 </td>
<td>5 </td>
<td>6 </td>
<td bgcolor="#CCCCCC">7 </td>
<td bgcolor="#CCCCCC">8 </td>
</tr>
<tr valign="top">
<td>9 </td>
<td>10 </td>
<td>11 </td>
<td>12 </td>
<td>13 </td>
<td bgcolor="#CCCCCC">14 </td>
<td bgcolor="#CCCCCC">15 </td>
</tr>
<tr valign="top">
<td>16 </td>
<td>17 Richard Away </td>
<td>18 Richard Away </td>
<td>19 Richard Away </td>
<td>20 Richard Away </td>
<td bgcolor="#CCCCCC">21 Richard Away </td>
<td bgcolor="#CCCCCC">22 Richard Away </td>
</tr>
<tr valign="top">
<td>23 Richard Away </td>
<td>24 Richard Away </td>
<td>25 </td>
<td>26 </td>
<td bgcolor="#2E8B57">27 Olympics </td>
<td bgcolor="#2E8B57">28 Olympics </td>
<td bgcolor="#2E8B57">29 Olympics </td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">30 Olympics </td>
<td bgcolor="#2E8B57">31 Olympics </td>
<td bgcolor="#2E8B57">August 1 Olympics </td>
<td bgcolor="#2E8B57">2 Olympics </td>
<td bgcolor="#2E8B57">3 Olympics </td>
<td bgcolor="#2E8B57">4 Olympics </td>
<td bgcolor="#2E8B57">5 Olympics </td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">6 Olympics </td>
<td bgcolor="#2E8B57">7 Olympics </td>
<td bgcolor="#2E8B57">8 Olympics </td>
<td bgcolor="#2E8B57">9 Olympics </td>
<td bgcolor="#2E8B57">10 Olympics </td>
<td bgcolor="#2E8B57">11 Olympics </td>
<td bgcolor="#2E8B57">12 Olympics </td>
<tr valign="top">
<td>13 </td>
<td>14 </td>
<td>15 </td>
<td>16 </td>
<td>17 </td>
<td bgcolor="#CCCCCC">18 </td>
<td bgcolor="#CCCCCC">19 </td>
<tr valign="top">
<td>20 </td>
<td>21 </td>
<td>22 </td>
<td>23 </td>
<td>24 </td>
<td bgcolor="#CCCCCC">25 </td>
<td bgcolor="#CCCCCC">26 </td>
<tr valign="top">
<td>27 </td>
<td>28 </td>
<td>29 </td>
<td>30 </td>
<td>31 </td>
<td bgcolor="#4357CFF">September 1 </td>
<td bgcolor="#CCCCCC">2 </td>
<tr valign="top">
<td>3 </td>
<td>4 </td>
<td>5 </td>
<td>6 </td>
<td>7 </td>
<td bgcolor="#CCCCCC">8 </td>
<td bgcolor="#CCCCCC">9 </td>
<tr valign="top">
<td>10 </td>
<td>11 </td>
<td>12 </td>
<td>13 </td>
<td>14 </td>
<td bgcolor="#CCCCCC">15 </td>
<td bgcolor="#CCCCCC">16 </td>

<tr valign="top">
<td>17 </td>
<td>18 </td>
<td>19 </td>
<td>20 </td>
<td>21 </td>
<td bgcolor="#CCCCCC">22 </td>
<td bgcolor="#CCCCCC">23 </td>

<tr valign="top">
<td>24 </td>
<td>25 </td>
<td>26 </td>
<td>27 </td>
<td>28 </td>
<td bgcolor="#954645">29 Autumn Term Starts </td>
<td bgcolor="#CCCCCC">30 </td>

<tr valign="top">
<td bgcolor="#4357CFF">October 1 </td>
<td>2 </td>
<td>3 </td>
<td>4 </td>
<td>5 </td>
<td bgcolor="#CCCCCC">6 </td>
<td bgcolor="#CCCCCC">7 </td>
<tr valign="top">
<td>8 </td>
<td>9 </td>
<td>10 </td>
<td>11 </td>
<td>12 </td>
<td bgcolor="#CCCCCC">13 </td>
<td bgcolor="#CCCCCC">14 </td>
<tr valign="top">
<td>15 </td>
<td>16 </td>
<td>17 </td>
<td>18 </td>
<td>19 </td>
<td bgcolor="#CCCCCC">20 </td>
<td bgcolor="#CCCCCC">21 </td>
<tr valign="top">
<td>22 </td>
<td>23 </td>
<td>24 </td>
<td>25 </td>
<td>26 </td>
<td bgcolor="#CCCCCC">27 </td>
<td bgcolor="#CCCCCC">28 </td>
<tr valign="top">
<td>29 </td>
<td>30 </td>
<td>31 </td>
<td bgcolor="#4357CFF">November 1 </td>
<td>2 </td>
<td bgcolor="#CCCCCC">3 </td>
<td bgcolor="#CCCCCC">4 </td>

</tr>
</table>

Mod:Hunt Research Group/calendar

2012-03-30T13:03:23Z

Lge:

== Calendar ==

*Tricia (done)
*Abdihakim Hassan (done)
*Bryan Ward (done)
*Claire Ashworth (done)
*Matthew Clough (done)
*Dimitrios Katsikadakos (not done)
*Ling Ge (done)
*Precious Ugbomah ( done)
*Richard Matthews (done)
*Wendy Kuo (done)
 
<table border="1" cellpadding="5">
<tr bgcolor="#66CCFF">
<th width="90px">Mon</th>
<th width="90px">Tues</th>
<th width="90px">Wed</th>
<th width="90px">Thur</th>
<th width="90px">Fri</th>
<th width="90px" bgcolor="#CCCCCC">Sat</th>
<th width="90px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td bgcolor="#275">Feb 27 </td>
<td>28 </td>
<td>29 </td>
<td bgcolor="#275">March 1 </td>
<td>2 </td>
<td bgcolor="#CCCCCC">3 </td>
<td bgcolor="#CCCCCC">4 </td>
</tr>
<tr valign="top">
<td>5 </td>
<td>6 </td>
<td>7 </td>
<td>8 </td>
<td>9 </td>
<td bgcolor="#CCCCCC">10 </td>
<td bgcolor="#CCCCCC">11 </td>
</tr>
<tr valign="top">
<td>12 </td>
<td>13 </td>
<td>14 </td>
<td>15 </td>
<td>16 </td>
<td bgcolor="#CCCCCC">17 </td>
<td bgcolor="#CCCCCC">18 </td>
</tr>
<tr valign="top">
<td>19 </td>
<td>20 </td>
<td>21 </td>
<td bgcolor="#FFCCFF">22 Tricia away</td>
<td bgcolor="#ERHRTHW">23 Spring Term Ends Tricia away</td>
<td bgcolor="#CCCCCC">24 Tricia away</td>
<td bgcolor="#CCCCCC">25 Tricia away</td>
</tr>
<tr valign="top">
<td bgcolor="#FFCCFF">26 Wendy away Tricia away</td>
<td bgcolor="#FFCCFF">27 Tricia away precious away Ling away </td>
<td bgcolor="#FFCCFF">28 Tricia away precious away Ling away </td>
<td bgcolor="#FFCCFF">29 Tricia away</td>
<td bgcolor="#FFCCFF">30 Tricia away</td>
<td bgcolor="#CCCCCC">31 Tricia away</td>
<td bgcolor="#275">April 1 Tricia away</td>
</tr>
<tr valign="top">
<td bgcolor="#FFCCFF">2 Bryan away Tricia away</td>
<td bgcolor="#FFCCFF">3 Bryan away precious away </td>
<td bgcolor="#FFCCFF">4 Bryan away Claire away Tricia away precious away</td>
<td bgcolor="#6699CC">5 College closed Bryan away Claire away Ling away Wendy away Matthew away Tricia away precious away Hakim away Richard away</td>
<td bgcolor="#6699CC">6 College closed - Good Friday Bryan away Claire away Wendy away Matthew away Tricia away precious away Hakim away Richard away</td>
<td bgcolor="#6699CC">7 College closed Bryan away Claire away Wendy away Matthew away Tricia away precious away Hakim away Richard away</td>
<td bgcolor="#6699CC">8 College closed Bryan away Claire away Wendy away Matthew away Tricia away precious away Hakim away Richard away</td>
</tr>
<tr valign="top">
<td bgcolor="#6699CC">9 College closed - Easter Monday Bryan away Claire away Wendy away Matthew away Tricia away precious away Hakim away Richard away</td>
<td bgcolor="#6699CC">10 College closed Bryan away Claire away Wendy away Matthew away Tricia away precious away Hakim away Richard away Ling away</td>
<td bgcolor="#FFCCFF">11 Claire away Wendy away Tricia away precious away</td>
<td>12 Wendy away </td>
<td>13 Wendy away </td>
<td bgcolor="#CCCCCC">14 Wendy away </td>
<td bgcolor="#CCCCCC">15 Wendy away </td>
</tr>
<tr valign="top">
<td>16 Wendy away </td>
<td>17 Wendy away Richard at Gaussian workshop </td>
<td>18 Wendy away Richard at Gaussian workshop </td>
<td>19 </td>
<td>20 </td>
<td bgcolor="#CCCCCC">21 </td>
<td bgcolor="#CCCCCC">22 </td>
</tr>
<tr valign="top">
<td>23 </td>
<td>24 </td>
<td>25 </td>
<td>26 </td>
<td>27 </td>
<td bgcolor="#ERHRTHW">28 Summer Term Starts </td>
<td bgcolor="#CCCCCC">29 </td>
</tr>
<tr valign="top">
<td>30 </td>
<td bgcolor="#275">May 1 </td>
<td>2 </td>
<td>3 </td>
<td>4 </td>
<td bgcolor="#CCCCCC">5 </td>
<td bgcolor="#CCCCCC">6 </td>
<tr valign="top">
<td>7 </td>
<td>8 </td>
<td bgcolor="#FFCCFF">9 tricia away</td>
<td>10 </td>
<td>11 </td>
<td bgcolor="#CCCCCC">12 </td>
<td bgcolor="#CCCCCC">13 </td>
<tr valign="top">
<td>14 </td>
<td>15 </td>
<td>16 </td>
<td>17 </td>
<td>18 </td>
<td bgcolor="#CCCCCC">19 </td>
<td bgcolor="#CCCCCC">20 </td>
<tr valign="top">
<td>21 </td>
<td>22 </td>
<td>23 </td>
<td>24 </td>
<td>25 </td>
<td bgcolor="#CCCCCC">26 </td>
<td bgcolor="#CCCCCC">27 </td>
<tr valign="top">
<td>28 </td>
<td>29 </td>
<td>30 </td>
<td>31 </td>
<td bgcolor="#275">June 1 </td>
<td bgcolor="#CCCCCC">2 </td>
<td bgcolor="#CCCCCC">3 </td>
<tr valign="top">
<td>4 </td>
<td>5 </td>
<td>6 </td>
<td>7 </td>
<td>8 </td>
<td bgcolor="#CCCCCC">9 </td>
<td bgcolor="#CCCCCC">10 </td>

</tr>
</table>

Mod:Hunt Research Group/calendar

2012-03-26T10:27:03Z

Lge:

== Calendar ==

*Tricia (done)
*Abdihakim Hassan (done)
*Bryan Ward (done)
*Claire Ashworth (done)
*Matthew Clough (done)
*Dimitrios Katsikadakos (not done)
*Ling Ge (done)
*Precious Ugbomah ( done)
*Richard Matthews (done)
*Wendy Kuo (done)
 
<table border="1" cellpadding="5">
<tr bgcolor="#66CCFF">
<th width="90px">Mon</th>
<th width="90px">Tues</th>
<th width="90px">Wed</th>
<th width="90px">Thur</th>
<th width="90px">Fri</th>
<th width="90px" bgcolor="#CCCCCC">Sat</th>
<th width="90px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td bgcolor="#275">Feb 27 </td>
<td>28 </td>
<td>29 </td>
<td bgcolor="#275">March 1 </td>
<td>2 </td>
<td bgcolor="#CCCCCC">3 </td>
<td bgcolor="#CCCCCC">4 </td>
</tr>
<tr valign="top">
<td>5 </td>
<td>6 </td>
<td>7 </td>
<td>8 </td>
<td>9 </td>
<td bgcolor="#CCCCCC">10 </td>
<td bgcolor="#CCCCCC">11 </td>
</tr>
<tr valign="top">
<td>12 </td>
<td>13 </td>
<td>14 </td>
<td>15 </td>
<td>16 </td>
<td bgcolor="#CCCCCC">17 </td>
<td bgcolor="#CCCCCC">18 </td>
</tr>
<tr valign="top">
<td>19 </td>
<td>20 </td>
<td>21 </td>
<td bgcolor="#FFCCFF">22 Tricia away</td>
<td bgcolor="#ERHRTHW">23 Spring Term Ends Tricia away</td>
<td bgcolor="#CCCCCC">24 Tricia away</td>
<td bgcolor="#CCCCCC">25 Tricia away</td>
</tr>
<tr valign="top">
<td bgcolor="#FFCCFF">26 Wendy away Tricia away</td>
<td bgcolor="#FFCCFF">27 Tricia away precious away Ling away </td>
<td bgcolor="#FFCCFF">28 Tricia away precious away Ling away </td>
<td bgcolor="#FFCCFF">29 Tricia away</td>
<td bgcolor="#FFCCFF">30 Tricia away</td>
<td bgcolor="#CCCCCC">31 Tricia away</td>
<td bgcolor="#275">April 1 Tricia away</td>
</tr>
<tr valign="top">
<td bgcolor="#FFCCFF">2 Bryan away Tricia away</td>
<td bgcolor="#FFCCFF">3 Bryan away precious away </td>
<td bgcolor="#FFCCFF">4 Bryan away Claire away Tricia away precious away</td>
<td bgcolor="#6699CC">5 College closed Bryan away Claire away Ling away Wendy away Matthew away Tricia away precious away Hakim away Richard away</td>
<td bgcolor="#6699CC">6 College closed - Good Friday Bryan away Claire away Wendy away Matthew away Tricia away precious away Hakim away Richard away</td>
<td bgcolor="#6699CC">7 College closed Bryan away Claire away Wendy away Matthew away Tricia away precious away Hakim away Richard away</td>
<td bgcolor="#6699CC">8 College closed Bryan away Claire away Wendy away Matthew away Tricia away precious away Hakim away Richard away</td>
</tr>
<tr valign="top">
<td bgcolor="#6699CC">9 College closed - Easter Monday Bryan away Claire away Wendy away Matthew away Tricia away precious away Hakim away Richard away</td>
<td bgcolor="#6699CC">10 College closed Bryan away Claire away Wendy away Matthew away Tricia away precious away Hakim away Richard away</td>
<td bgcolor="#FFCCFF">11 Claire away Wendy away Tricia away precious away</td>
<td>12 Wendy away </td>
<td>13 Wendy away </td>
<td bgcolor="#CCCCCC">14 Wendy away </td>
<td bgcolor="#CCCCCC">15 Wendy away </td>
</tr>
<tr valign="top">
<td>16 Wendy away </td>
<td>17 Wendy away Richard at Gaussian workshop </td>
<td>18 Wendy away Richard at Gaussian workshop </td>
<td>19 </td>
<td>20 </td>
<td bgcolor="#CCCCCC">21 </td>
<td bgcolor="#CCCCCC">22 </td>
</tr>
<tr valign="top">
<td>23 </td>
<td>24 </td>
<td>25 </td>
<td>26 </td>
<td>27 </td>
<td bgcolor="#ERHRTHW">28 Summer Term Starts </td>
<td bgcolor="#CCCCCC">29 </td>
</tr>
<tr valign="top">
<td>30 </td>
<td bgcolor="#275">May 1 </td>
<td>2 </td>
<td>3 </td>
<td>4 </td>
<td bgcolor="#CCCCCC">5 </td>
<td bgcolor="#CCCCCC">6 </td>
<tr valign="top">
<td>7 </td>
<td>8 </td>
<td bgcolor="#FFCCFF">9 tricia away</td>
<td>10 </td>
<td>11 </td>
<td bgcolor="#CCCCCC">12 </td>
<td bgcolor="#CCCCCC">13 </td>
<tr valign="top">
<td>14 </td>
<td>15 </td>
<td>16 </td>
<td>17 </td>
<td>18 </td>
<td bgcolor="#CCCCCC">19 </td>
<td bgcolor="#CCCCCC">20 </td>
<tr valign="top">
<td>21 </td>
<td>22 </td>
<td>23 </td>
<td>24 </td>
<td>25 </td>
<td bgcolor="#CCCCCC">26 </td>
<td bgcolor="#CCCCCC">27 </td>
<tr valign="top">
<td>28 </td>
<td>29 </td>
<td>30 </td>
<td>31 </td>
<td bgcolor="#275">June 1 </td>
<td bgcolor="#CCCCCC">2 </td>
<td bgcolor="#CCCCCC">3 </td>
<tr valign="top">
<td>4 </td>
<td>5 </td>
<td>6 </td>
<td>7 </td>
<td>8 </td>
<td bgcolor="#CCCCCC">9 </td>
<td bgcolor="#CCCCCC">10 </td>

</tr>
</table>

Mod:Hunt Research Group/calendar

2012-03-05T14:07:51Z

Lge:

== Calendar ==

*Tricia (not done)
*Abdihakin Hassan (not done)
*Bryan Ward (not done)
*Claire Ashworth (done)
*Matthew Clough (not done)
*Dimitrios Katsikadakos (not done)
*Ling Ge (done)
*Precious Ugbomah (not done)
*Richard Matthews (not Done)
*Wendy Kuo (not done)
 
<table border="1" cellpadding="5">
<tr bgcolor="#66CCFF">
<th width="90px">Mon</th>
<th width="90px">Tues</th>
<th width="90px">Wed</th>
<th width="90px">Thur</th>
<th width="90px">Fri</th>
<th width="90px" bgcolor="#CCCCCC">Sat</th>
<th width="90px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td bgcolor="#275">Feb 27 </td>
<td>28 </td>
<td>29 </td>
<td bgcolor="#275">March 1 </td>
<td>2 </td>
<td bgcolor="#CCCCCC">3 </td>
<td bgcolor="#CCCCCC">4 </td>
</tr>
<tr valign="top">
<td>5 </td>
<td>6 </td>
<td>7 </td>
<td>8 </td>
<td>9 </td>
<td bgcolor="#CCCCCC">10 </td>
<td bgcolor="#CCCCCC">11 </td>
</tr>
<tr valign="top">
<td>12 </td>
<td>13 </td>
<td>14 </td>
<td>15 </td>
<td>16 </td>
<td bgcolor="#CCCCCC">17 </td>
<td bgcolor="#CCCCCC">18 </td>
</tr>
<tr valign="top">
<td>19 </td>
<td>20 </td>
<td>21 </td>
<td>22 </td>
<td bgcolor="#ERHRTHW">23 Spring Term Ends </td>
<td bgcolor="#CCCCCC">24 </td>
<td bgcolor="#CCCCCC">25 </td>
</tr>
<tr valign="top">
<td>26 </td>
<td>27 </td>
<td>28 </td>
<td>29 </td>
<td>30 </td>
<td bgcolor="#CCCCCC">31</td>
<td bgcolor="#275">April 1</td>
</tr>
<tr valign="top">
<td>2 </td>
<td>3 </td>
<td>4 Claire away</td>
<td bgcolor="#395476">5 College closed Claire away Ling away </td>
<td bgcolor="#395476">6 College closed - Good Friday Claire away </td>
<td bgcolor="#395476">7 College closed Claire away </td>
<td bgcolor="#395476">8 College closed Claire away </td>
</tr>
<tr valign="top">
<td bgcolor="#395476">9 College closed - Easter Monday Claire away </td>
<td bgcolor="#395476">10 College closed Claire away </td>
<td>11 Claire away </td>
<td>12 </td>
<td>13 </td>
<td bgcolor="#CCCCCC">14 </td>
<td bgcolor="#CCCCCC">15 </td>
</tr>
<tr valign="top">
<td>16 </td>
<td>17 </td>
<td>18 </td>
<td>19 </td>
<td>20 </td>
<td bgcolor="#CCCCCC">21 </td>
<td bgcolor="#CCCCCC">22 </td>
</tr>
<tr valign="top">
<td>23 </td>
<td>24 </td>
<td>25 </td>
<td>26 </td>
<td>27 </td>
<td bgcolor="#ERHRTHW">28 Summer Term Starts </td>
<td bgcolor="#CCCCCC">29 </td>
</tr>
<tr valign="top">
<td>30 </td>
<td bgcolor="#275">May 1 </td>
<td>2 </td>
<td>3 </td>
<td>4 </td>
<td bgcolor="#CCCCCC">5 </td>
<td bgcolor="#CCCCCC">6 </td>
<tr valign="top">
<td>7 </td>
<td>8 </td>
<td>8 </td>
<td>10 </td>
<td>11 </td>
<td bgcolor="#CCCCCC">12 </td>
<td bgcolor="#CCCCCC">13 </td>
<tr valign="top">
<td>14 </td>
<td>15 </td>
<td>16 </td>
<td>17 </td>
<td>18 </td>
<td bgcolor="#CCCCCC">19 </td>
<td bgcolor="#CCCCCC">20 </td>
<tr valign="top">
<td>21 </td>
<td>22 </td>
<td>23 </td>
<td>24 </td>
<td>25 </td>
<td bgcolor="#CCCCCC">26 </td>
<td bgcolor="#CCCCCC">27 </td>
<tr valign="top">
<td>28 </td>
<td>29 </td>
<td>30 </td>
<td>31 </td>
<td bgcolor="#275">June 1 </td>
<td bgcolor="#CCCCCC">2 </td>
<td bgcolor="#CCCCCC">3 </td>
<tr valign="top">
<td>4 </td>
<td>5 </td>
<td>6 </td>
<td>7 </td>
<td>8 </td>
<td bgcolor="#CCCCCC">9 </td>
<td bgcolor="#CCCCCC">10 </td>

</tr>
</table>

Mod:Hunt Research Group

2012-02-22T17:02:17Z

Lge: /* Installing packages */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===Resources===

#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link] (notes by Tricia)

===Gaussian General===
#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] (notes by Everyone!)
#Instructions for visualizing electrostatic potentials [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link] (notes by Flo)
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#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] (notes by Heiko)
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9] (notes by Richard)

===Unix and HPC===
#Setting up a connection to HPC if you have a PC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link] (notes by Hieu)
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link] (notes by Heiko)
#HPC servers and run scripts [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link] (notes by Tricia and Ling)]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link] (notes by Heiko)
#How to set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link] (notes by Heiko)
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link] (notes by Heiko)
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link] (notes by Heiko)
#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] (notes by Rachael and Weihong)
#How to set up cx2 [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cx2 link] (notes by Ling)

===Installing packages===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link] (notes by Ling)
#VMD: a molecular dynamics visualisation package [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link] (notes by Ling)
#DLPOLY a MD simmulation package, Installation on an IMac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link] (notes by Ling)
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link] (notes by Tricia)
#How to install Geomview [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/geomview link] (notes by Tricia)
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/] (Ling)

===Research Notes===
#Voids in ILs[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids link] (notes by Ling)
#How to equilibrate an MD run[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/equilibration link] (notes by Tricia and Ling)]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link] (notes by Ling)]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link] (notes by Ling and Tricia)]
#Cl- in water[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link] (notes by Ling)]
#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] (notes by Yannis)
#Functional for ILs using CPMD[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/IL_cpmd_functional link] (notes by Ling)
#[bmim]Cl using CPMD[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cpmd link] (notes by Ling)
#[bmim]Cl using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cp2k link] (notes by Ling)
#mman using CPMD and Gaussian [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/mman link] (notes by Ling)
#[emim]SCN using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emimscn link] (notes by Ling)
#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] (notes by Ling)

===Teaching Stuff===
#Tutorial group A [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Tutorial_A notes]
#Tutorial group B [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Tutorial_B notes]

===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] (notes by Tricia)
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link] (notes by Tricia)
#[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/calendar Calendar] (notes by Tricia)
#Demonstrating in the 3rd year computational chemistry lab [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/compchemlab Timetable] (notes by Tricia)
#computational chemistry lab [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/comp_chem_results results] (notes by Yannis)
#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] notes by Tricia