ChemWiki - User contributions [en]

Third Year TS and Reactivity Lab

2020-10-05T15:18:00Z

Jb6518: /* Assessment Information */

== Introduction ==

In this computational lab, you will model several pericyclic reactions by calculating and characterising Transition State (TS) structures.

In your first- and second-year computational labs you will have used Quantum Mechanical methods, through the programs Gaussian and PySCF, to calculate and analyse simple molecules. In this lab you will extend on these, using different Quantum Mechanical methods through Gaussian to model reaction pathways for familiar Diels-Alder reactions. You will learn how to calculate TS structures for a reaction and will gain understanding about how reactants, products and TS structures relate to a molecule’s potential energy surface. By analysing the geometry and MOs of the TS structures, you will gain insight into the reaction mechanism that cannot be gained from experimental organic labs alone. Different reaction paths and barrier heights will also be calculated which will give understanding to the thermodynamics/kinetics of the reactions.

The lab is split into two sections:

: 1) A [[Third_Year_TS_and_Reactivity_Lab:_Tutorial|tutorial section]] to work through frst. The tutorial will introduce you to the software, background and methods required to complete the lab.

: 2) An assessed [[Third_Year_TS_and_Reactivity_Lab:_Exercises|exercise section]] where you will apply what you have learnt during the tutorial to model different pericyclic reactions.

=== Computational Methods ===

The lab uses Quantum Mechanics to model reaction mechanisms. Gaussian is a compuational chemistry program that will be used to run Quantum Mechanical calculations. You will be using Gaussian to calculate the minimum and transition state structures for several reactions. Two differernt methods will be used for the calculations:

: '''PM6''' - A semi-empirical method. This means that the method is parameterised using experimental data which saves computational time and resources but does result in lower accuracy than ab initio methods. 
: '''B3LYP/6-31G(d)''' - Where '''B3LYP''' is a Density Functional Theory (DFT) method. B3LYP is reasonably fast compared to other DFT or ''ab inito'' methods and is capable of reproducing chemical data. '''6-31G(d)''' is a basis set, which generally are a set of functions that typically mimic atomic orbitals and when combined linearly generate molecular orbitals. In a way, they are the building blocks of molecular orbitals. The higher the basis set, the more blocks are available to construct a molecular orbital, at the cost of computational effort.

Both of the methods approximate the Schrodinger Equation in different ways to calculate the energy of a system.

== Assessment Information ==
=== Lab Objectives ===

The objectives of the lab are:
* Using Quantum Mechanical calculations (via Gaussian) to calculate and analyse structures and to develop understanding about the methods being used.
* Being able to explain what a Transition State and a Potential Energy Surface are.
* Being able to use chemical intuition to help locate stationary points on a potential energy surface (i.e. relate the energy balance of a reaction to its landscape).
* Being able to discuss the role of sterics and secondary orbital interactions in determining the kinetic and thermodynamic products of a reaction.

=== Mark Scheme ===

The break-down for the marks for this lab are as follows:
* '''Introduction''' 20%
* '''Exercises''' 60%
* '''Conclusions''' 20%
** Main discussion (10%)
** Further discussion (5%)
** Presentation and writing style (5%)

=== Write Up ===

Generally, try to use clear and concise writing style: short sentences that follow each other logically, with a simple writing style. Label all tables, diagrams, and figures with self-contained captions. Use the appropriate referencing style. Consider moving long lists of images to an SI section.

:'''Introduction''': This is where you should discuss the background theory and the computational methods that you have applied in this lab. You should include:
:* Potential Energy Surfaces and Transition States:
::* What is a potential energy surface (PES)?
::* What are the mathematical definitions of minima, maxima and saddle-points on a PES, and how can these features on the PES be related to chemical events/structures.
:* Computational methods:
::* A brief introduction to Quantum Mechanical methods
::* An introduction to the two methods being used including: what are the main approximations of the two methods? How are they different? Why we are using these two methods?

:'''Exercises''': Follow the guidelines for the 3 exercises to be completed in the [[Third_Year_TS_and_Reactivity_Lab:_Exercises|exercise section]].

:'''Conclusion''': The main part of the conclusions should summarise the key concepts of the lab and your results. You '''should''' include:
:* An evaluation of what your results mean and the chemistry of the reactions.
:* An evaluation of the computational methods used. 

:The further discussion element of the conclusion remains quite open and can be directed by what you found more interesting about the lab. You should consider justified suggestions for improvements or advancements on the systems studied or on the computational methods used in the lab.
Other points that you could consider include:
:* Were there any difficulties encountered etc. when locating TSs? In what situations would locating the TS become more difficult?
:* The accuracy of the methods, the results and the MOs.
:* What ways could you obtain better descriptions of the reactions you have studied?
:* Insight provided into the Diels-Alder reactions.
:* Can calculations help to understand how to run the reactions studied here in a lab (e.g. reaction conditions)?
:* Can calculations help to understand how to improve the reactions by modifying the reactants? (what functional groups would you add to modify the reactions?)

===Report Submission ===

The assigned lab hours are 10.00-17.00 Mon, Tue, Thu, Fri.

The '''report deadline is on Wednesday at 12.00 noon''', the week after starting the lab.

'''You must submit on Blackboard:'''
* A written report as a PDF.
* A zip file containing output (.log) files from '''all''' calculations which you use to answer the questions.

The lab time assigned is sufficient to be able to complete the tutorial, assessed exercises and write up within the lab time. In general, it is advised that:

* The tutorial should be completed before moving on to the assessed section. It is advised that you have started on the assessed exercises by Wednesday mornig at the latest.
* All calculations should be completed by the end of Friday.
* Write up as you go, it will help you keep track of results and answers.
* Submitted reports and output files will be checked for plagiarism
* Name your output files sensibly and use a unique name (e.g. your username or shortcode: hgr16_butadiene.log)
* ChemDraw is recommended to create MO diagrams and reaction coordinates

=== Demonstrator Sessions ===

The lab will start with an introduction at 10.00 am on Monday. There will be regular demonstrator sessions on Microsoft Teams lab channel () at:

:'''Monday 10.00 - 14.00''' 
:'''Tuesday 10.00 - 12.00''' 
:'''Thursday 10.00 - 12.00''' 
:'''Friday 10.00 - 12.00''' 

Outside of the above hours, please use the Year 3 Computational Labs forum, found on the 3rd Year Chemistry Laboratories and Coursework Blackboard page, to post any questions you have on the lab.

Additionally, there is a [[Mod:ts_troubleshooting|troubleshooting page]] for common errors.

File:Hunt runscripts G16.zip

2020-08-28T22:17:48Z

Jb6518: Jb6518 uploaded a new version of File:Hunt runscripts G16.zip

Mod:Hunt Research Group/new gf script

2020-08-28T22:14:21Z

Jb6518: /* How to set up for Gaussian16 */

==A new gf script==

This is a python script which does two jobs:

#Edits .com files so that
##.chk filename matches the .com file
##the ncps requested is correct
##the memory requested for gaussian is correct.
#Submits the job(s) (you can use wildcards in the command) using the standard runscripts ([https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/hpc[link]]) stored in a folder in your home directory.
Note: the first 3 lines of the .com file need to exist for the editing process to work. ie. You have 3 lines (with anything or nothing on, doesn't matter) BEFORE your method line. If your method line is in the first 3 lines it will get overwritten and the script won't work.

==How to set up for Gaussian16==

Go to /home/username/bin and type vi gf.py.
Press i and then copy and paste the following code in:

(instructions continue below the code - ignore the instructions in the code for now, they are just to help out if you are not looking at this page).

<pre>

import os
import glob
import sys

############
#HOW TO RUN#
############

# 0. Save this script in /rds/general/user/username/home as gf.py

# 1. Enter your username here:

username = "ab1234"

# 2. Save the runscripts from https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/new_gf_script in a directory called /rds/general/user/username/home/bin/runscripts

# 3. Go to the directory where your .com files are and type in:
# python /rds/general/user/username/home/bin/gf.py version queuname nprocs inputfiles

# For example:
# python /rds/general/user/username/home/bin/gf.py c01 pqph 20 "01.com" will submit job 01.com on 20 processors to the pqph queue to run on gaussian16 version c01.
# python /rds/general/user/username/home/bin/gf.py c01 pqph 40 "*.com" will submit all the .com files in the directory to run on 40 processors to the pqph queue to run on gaussian16 version c01.

#####################
#Setting the options#
#####################

#First variable sets which version of gaussian to use - use a01 usually.

version = sys.argv[1]
print("version = " + version)

#Second variable sets the queue - pqph

queue = sys.argv[2]
print("queue = " + queue)

#Third variable sets the number of processors:
#20, or 40

nprocs = sys.argv[3]
print("nprocs = " + nprocs)

#Last variable is the input files. You can use wildcards but you need to add "quotes" around the input

job_input = sys.argv[4]
print("job_input= " + job_input)
jobs = []
for job in glob.glob(job_input):
jobs.append(job)

print("list of jobs: ")
print(jobs)

#######################
#Finding the runscript#
#######################

runscript = "/rds/general/user/" + username + "/home/bin/runscripts/" + version + "_" + queue + "_" + nprocs
print(" ")
print("runscript = " + runscript)

########################
#Editing the input file#
########################

#Getting the correct nprocs and mem lines for the .com files:

gauss_nprocs_line = "undefined"
gauss_mem_line = "undefined"

if nprocs == "20":
gauss_nprocs_line = "%nprocs=20\n"
gauss_mem_line = "%mem=58000MB\n"
elif nprocs == "40":
gauss_nprocs_line = "%nprocs=40\n"
gauss_mem_line = "%mem=120000MB\n"
else:
print("Error: nprocs (argument 3) may only be 20, or 40.")

print("gauss_nprocs_line = " + gauss_nprocs_line)
print("gauss_mem_line = " + gauss_mem_line)

#Editing the files:

for job in jobs:

#Getting the chk line to overwrite the input file

name_list = job.split(".")
name = name_list[0]
chk_line = "%chk=" + name + ".chk\n"
print(name + " chk_line = " + chk_line)

#Overwriting the first 3 lines of the input file

with open(job, "r") as file:
file_lines = file.readlines()
#print file_lines
file_lines[0] = gauss_nprocs_line
file_lines[1] = gauss_mem_line
file_lines[2] = chk_line
#print file_lines
with open(job, "w") as file:
file.writelines(file_lines)

#####################
#Submitting the jobs#
#####################

#Getting the terminal to do this: "qsub -N jobname -v in=name runscript"

print("qsub -N " + name + " -v in=" + name + " " + runscript)
os.system("qsub -N " + name + " -v in=" + name + " " + runscript)

</pre>

Then change the username = at the top to your own username, and press :wq enter to save and quit.

Make a directory in /rds/general/user/username/home/bin/ called runscripts and put these scripts in it: [[:File:Hunt runscripts G16.zip|runscripts]]

==To use==

Go to the directory where your .com files are and type in:
python /rds/general/user/username/home/bin/gf.py version queuename nprocs inputfiles

For example:

<pre>python /rds/general/user/username/home/bin/gf.py a01 pqph 20 "01.com" </pre> will submit job 01.com on 20 processors to the pqph queue to run on gaussian16 version a01.
<pre>python /rds/general/user/username/home/bin/gf.py a01 pqph 40 "*.com" </pre> will submit all the .com files in the directory to run on 40 processors in the pqph queue to run on gaussian16 version a01.

==Possible options==

The version option may be a01.

The queue option may be pqph.

The nprocs options can be 20, or 40.

Depending on which of these you use a different runscript from the runscripts folder is called. The list of runscripts that that are included by default are:

a01_pqph_20
a01_pqph_40

This is every combination of the above options. If you want to use a different option to the ones provided simply make the runscript you want to use, and name it with the same convention. If you want a different nprocs option you must also edit the script slightly in the section headed: Editing the input file, in the subsection: Getting the correct nprocs and mem lines for the .com files. You will just need to copy and paste an elif block and change the nprocs and the memory requested to whatever you want. It should be easy to copy what I did for the other examples.

==How to set up for g09==

Go to /home/username/bin and type vi gf.py.
Press i and then copy and paste the following code in:

(instructions continue below the code - ignore the instructions in the code for now, they are just to help out if you are not looking at this page).

<pre>

import os
import glob
import sys

############
#HOW TO RUN#
############

# 0. Save this script in /rds/general/user/username/home as gf.py

# 1. Enter your username here:

username = "rr1210"

# 2. Save the runscripts from https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/new_gf_script in a directory called /rds/general/user/username/home/bin/runscripts

# 3. Go to the directory where your .com files are and type in:
# python /rds/general/user/username/home/bin/gf.py version queuname nprocs inputfiles

# For example:
# python /rds/general/user/username/home/bin/gf.py d01 pqph 12 "01.com" will submit job 01.com on 12 processors to the pqph queue to run on gaussian version d01.
# python /rds/general/user/username/home/bin/gf.py d01 pqchem 32 "*.com" will submit all the .com files in the directory to run on 32 processors in the pqchem queue to run on gaussian version d01.

#####################
#Setting the options#
#####################

#First variable sets which version of gaussian to use - use d01 usually or b01 for getting latest nbo.

version = sys.argv[1]
print "version = " + version

#Second variable sets the queue - pqph or pqchem

queue = sys.argv[2]
print "queue = " + queue

#Third variable sets the number of processors, as standard the options are the same as those defined by Tricia on the wiki:
#12, 24, 32, 40, 48

nprocs = sys.argv[3]
print "nprocs = " + nprocs

#Last variable is the input files. You can use wildcards but you need to add "quotes" around the input

job_input = sys.argv[4]
print "job_input= " + job_input
jobs = []
for job in glob.glob(job_input):
jobs.append(job)

print "list of jobs: "
print jobs

#######################
#Finding the runscript#
#######################

runscript = "/rds/general/user/" + username + "/home/bin/runscripts/" + version + "_" + queue + "_" + nprocs
print " "
print "runscript = " + runscript

########################
#Editing the input file#
########################

#Getting the correct nprocs and mem lines for the .com files:

gauss_nprocs_line = "undefined"
gauss_mem_line = "undefined"

if nprocs == "12":
gauss_nprocs_line = "%nprocs=12\n"
gauss_mem_line = "%mem=45000MB\n"
elif nprocs == "24":
gauss_nprocs_line = "%nprocs=24\n"
gauss_mem_line = "%mem=58000MB\n"
elif nprocs == "32":
gauss_nprocs_line = "%nprocs=32\n"
gauss_mem_line = "%mem=58000MB\n"
elif nprocs == "40":
gauss_nprocs_line = "%nprocs=40\n"
gauss_mem_line = "%mem=120000MB\n"
elif nprocs == "48":
gauss_nprocs_line = "%nprocs=48\n"
gauss_mem_line = "%mem=250000MB\n"
else:
print "Error: nprocs (argument 3) may only be 12, 24, 32, 40, 48."

print "gauss_nprocs_line = " + gauss_nprocs_line
print "gauss_mem_line = " + gauss_mem_line

#Editing the files:

for job in jobs:

#Getting the chk line to overwrite the input file

name_list = job.split(".")
name = name_list[0]
chk_line = "%chk=" + name + ".chk\n"
print name + " chk_line = " + chk_line

#Overwriting the first 3 lines of the input file

with open(job, "r") as file:
file_lines = file.readlines()
#print file_lines
file_lines[0] = gauss_nprocs_line
file_lines[1] = gauss_mem_line
file_lines[2] = chk_line
#print file_lines
with open(job, "w") as file:
file.writelines(file_lines)

#####################
#Submitting the jobs#
#####################

#Getting the terminal to do this: "qsub -N jobname -v in=name runscript"

print "qsub -N " + name + " -v in=" + name + " " + runscript
os.system("qsub -N " + name + " -v in=" + name + " " + runscript)

</pre>

Then change the username = at the top to your own username, and press :wq enter to save and quit.

Make a directory in /rds/general/user/username/home/bin/ called runscripts and put these scripts in it: [runscripts[https://wiki.ch.ic.ac.uk/wiki/images/a/aa/Phunt_new_gf_script_runscripts.zip]]

==To use==

Go to the directory where your .com files are and type in:
python /rds/general/user/username/home/bin/gf.py version queuename nprocs inputfiles

For example:

<pre>python /rds/general/user/username/home/bin/gf.py d01 pqph 12 "01.com" </pre> will submit job 01.com on 12 processors to the pqph queue to run on gaussian version d01.
<pre>python /rds/general/user/username/home/bin/gf.py d01 pqchem 32 "*.com" </pre> will submit all the .com files in the directory to run on 32 processors in the pqchem queue to run on gaussian version d01.

==Possible options==

The version option may be eith d01 or b01.

The queue option may be either pqph or pqchem.

The nprocs options can be 12, 24, 32, 40 or 48.

Depending on which of these you use a different runscript from the runscripts folder is called. The list of runscripts that that are included by default are:

b01_pqchem_12
b01_pqchem_24
b01_pqchem_32
b01_pqchem_40
b01_pqchem_48
b01_pqph_12
b01_pqph_24
b01_pqph_32
b01_pqph_40
b01_pqph_48
d01_pqchem_12
d01_pqchem_24
d01_pqchem_32
d01_pqchem_40
d01_pqchem_48
d01_pqph_12
d01_pqph_24
d01_pqph_32
d01_pqph_40
d01_pqph_48

This is every combination of the above options. If you want to use a different option to the ones provided simply make the runscript you want to use, and name it with the same convention. If you want a different nprocs option you must also edit the script slightly in the section headed: Editing the input file, in the subsection: Getting the correct nprocs and mem lines for the .com files. You will just need to copy and paste an elif block and change the nprocs and the memory requested to whatever you want. It should be easy to copy what I did for the other examples.

Mod:Hunt Research Group/new gf script

2020-08-28T22:01:41Z

Jb6518: /* How to set up for Gaussian16 */

==A new gf script==

This is a python script which does two jobs:

#Edits .com files so that
##.chk filename matches the .com file
##the ncps requested is correct
##the memory requested for gaussian is correct.
#Submits the job(s) (you can use wildcards in the command) using the standard runscripts ([https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/hpc[link]]) stored in a folder in your home directory.
Note: the first 3 lines of the .com file need to exist for the editing process to work. ie. You have 3 lines (with anything or nothing on, doesn't matter) BEFORE your method line. If your method line is in the first 3 lines it will get overwritten and the script won't work.

==How to set up for Gaussian16==

Go to /home/username/bin and type vi gf.py.
Press i and then copy and paste the following code in:

(instructions continue below the code - ignore the instructions in the code for now, they are just to help out if you are not looking at this page).

<pre>

import os
import glob
import sys

############
#HOW TO RUN#
############

# 0. Save this script in /rds/general/user/username/home as gf.py

# 1. Enter your username here:

username = "ab1234"

# 2. Save the runscripts from https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/new_gf_script in a directory called /rds/general/user/username/home/bin/runscripts

# 3. Go to the directory where your .com files are and type in:
# python /rds/general/user/username/home/bin/gf.py version queuname nprocs inputfiles

# For example:
# python /rds/general/user/username/home/bin/gf.py a01 pqph 20 "01.com" will submit job 01.com on 20 processors to the pqph queue to run on gaussian16 version a01.
# python /rds/general/user/username/home/bin/gf.py a01 pqph 40 "*.com" will submit all the .com files in the directory to run on 40 processors to the pqph queue to run on gaussian16 version a01.

#####################
#Setting the options#
#####################

#First variable sets which version of gaussian to use - use a01 usually.

version = sys.argv[1]
print("version = " + version)

#Second variable sets the queue - pqph

queue = sys.argv[2]
print("queue = " + queue)

#Third variable sets the number of processors:
#20, or 40

nprocs = sys.argv[3]
print("nprocs = " + nprocs)

#Last variable is the input files. You can use wildcards but you need to add "quotes" around the input

job_input = sys.argv[4]
print("job_input= " + job_input)
jobs = []
for job in glob.glob(job_input):
jobs.append(job)

print("list of jobs: ")
print(jobs)

#######################
#Finding the runscript#
#######################

runscript = "/rds/general/user/" + username + "/home/bin/runscripts/" + version + "_" + queue + "_" + nprocs
print(" ")
print("runscript = " + runscript)

########################
#Editing the input file#
########################

#Getting the correct nprocs and mem lines for the .com files:

gauss_nprocs_line = "undefined"
gauss_mem_line = "undefined"

if nprocs == "20":
gauss_nprocs_line = "%nprocs=20\n"
gauss_mem_line = "%mem=58000MB\n"
elif nprocs == "40":
gauss_nprocs_line = "%nprocs=40\n"
gauss_mem_line = "%mem=120000MB\n"
else:
print("Error: nprocs (argument 3) may only be 20, or 40.")

print("gauss_nprocs_line = " + gauss_nprocs_line)
print("gauss_mem_line = " + gauss_mem_line)

#Editing the files:

for job in jobs:

#Getting the chk line to overwrite the input file

name_list = job.split(".")
name = name_list[0]
chk_line = "%chk=" + name + ".chk\n"
print(name + " chk_line = " + chk_line)

#Overwriting the first 3 lines of the input file

with open(job, "r") as file:
file_lines = file.readlines()
#print file_lines
file_lines[0] = gauss_nprocs_line
file_lines[1] = gauss_mem_line
file_lines[2] = chk_line
#print file_lines
with open(job, "w") as file:
file.writelines(file_lines)

#####################
#Submitting the jobs#
#####################

#Getting the terminal to do this: "qsub -N jobname -v in=name runscript"

print("qsub -N " + name + " -v in=" + name + " " + runscript)
os.system("qsub -N " + name + " -v in=" + name + " " + runscript)

</pre>

Then change the username = at the top to your own username, and press :wq enter to save and quit.

Make a directory in /rds/general/user/username/home/bin/ called runscripts and put these scripts in it: [[:File:Hunt runscripts G16.zip|runscripts]]

==To use==

Go to the directory where your .com files are and type in:
python /rds/general/user/username/home/bin/gf.py version queuename nprocs inputfiles

For example:

<pre>python /rds/general/user/username/home/bin/gf.py a01 pqph 20 "01.com" </pre> will submit job 01.com on 20 processors to the pqph queue to run on gaussian16 version a01.
<pre>python /rds/general/user/username/home/bin/gf.py a01 pqph 40 "*.com" </pre> will submit all the .com files in the directory to run on 40 processors in the pqph queue to run on gaussian16 version a01.

==Possible options==

The version option may be a01.

The queue option may be pqph.

The nprocs options can be 20, or 40.

Depending on which of these you use a different runscript from the runscripts folder is called. The list of runscripts that that are included by default are:

a01_pqph_20
a01_pqph_40

This is every combination of the above options. If you want to use a different option to the ones provided simply make the runscript you want to use, and name it with the same convention. If you want a different nprocs option you must also edit the script slightly in the section headed: Editing the input file, in the subsection: Getting the correct nprocs and mem lines for the .com files. You will just need to copy and paste an elif block and change the nprocs and the memory requested to whatever you want. It should be easy to copy what I did for the other examples.

==How to set up for g09==

Go to /home/username/bin and type vi gf.py.
Press i and then copy and paste the following code in:

(instructions continue below the code - ignore the instructions in the code for now, they are just to help out if you are not looking at this page).

<pre>

import os
import glob
import sys

############
#HOW TO RUN#
############

# 0. Save this script in /rds/general/user/username/home as gf.py

# 1. Enter your username here:

username = "rr1210"

# 2. Save the runscripts from https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/new_gf_script in a directory called /rds/general/user/username/home/bin/runscripts

# 3. Go to the directory where your .com files are and type in:
# python /rds/general/user/username/home/bin/gf.py version queuname nprocs inputfiles

# For example:
# python /rds/general/user/username/home/bin/gf.py d01 pqph 12 "01.com" will submit job 01.com on 12 processors to the pqph queue to run on gaussian version d01.
# python /rds/general/user/username/home/bin/gf.py d01 pqchem 32 "*.com" will submit all the .com files in the directory to run on 32 processors in the pqchem queue to run on gaussian version d01.

#####################
#Setting the options#
#####################

#First variable sets which version of gaussian to use - use d01 usually or b01 for getting latest nbo.

version = sys.argv[1]
print "version = " + version

#Second variable sets the queue - pqph or pqchem

queue = sys.argv[2]
print "queue = " + queue

#Third variable sets the number of processors, as standard the options are the same as those defined by Tricia on the wiki:
#12, 24, 32, 40, 48

nprocs = sys.argv[3]
print "nprocs = " + nprocs

#Last variable is the input files. You can use wildcards but you need to add "quotes" around the input

job_input = sys.argv[4]
print "job_input= " + job_input
jobs = []
for job in glob.glob(job_input):
jobs.append(job)

print "list of jobs: "
print jobs

#######################
#Finding the runscript#
#######################

runscript = "/rds/general/user/" + username + "/home/bin/runscripts/" + version + "_" + queue + "_" + nprocs
print " "
print "runscript = " + runscript

########################
#Editing the input file#
########################

#Getting the correct nprocs and mem lines for the .com files:

gauss_nprocs_line = "undefined"
gauss_mem_line = "undefined"

if nprocs == "12":
gauss_nprocs_line = "%nprocs=12\n"
gauss_mem_line = "%mem=45000MB\n"
elif nprocs == "24":
gauss_nprocs_line = "%nprocs=24\n"
gauss_mem_line = "%mem=58000MB\n"
elif nprocs == "32":
gauss_nprocs_line = "%nprocs=32\n"
gauss_mem_line = "%mem=58000MB\n"
elif nprocs == "40":
gauss_nprocs_line = "%nprocs=40\n"
gauss_mem_line = "%mem=120000MB\n"
elif nprocs == "48":
gauss_nprocs_line = "%nprocs=48\n"
gauss_mem_line = "%mem=250000MB\n"
else:
print "Error: nprocs (argument 3) may only be 12, 24, 32, 40, 48."

print "gauss_nprocs_line = " + gauss_nprocs_line
print "gauss_mem_line = " + gauss_mem_line

#Editing the files:

for job in jobs:

#Getting the chk line to overwrite the input file

name_list = job.split(".")
name = name_list[0]
chk_line = "%chk=" + name + ".chk\n"
print name + " chk_line = " + chk_line

#Overwriting the first 3 lines of the input file

with open(job, "r") as file:
file_lines = file.readlines()
#print file_lines
file_lines[0] = gauss_nprocs_line
file_lines[1] = gauss_mem_line
file_lines[2] = chk_line
#print file_lines
with open(job, "w") as file:
file.writelines(file_lines)

#####################
#Submitting the jobs#
#####################

#Getting the terminal to do this: "qsub -N jobname -v in=name runscript"

print "qsub -N " + name + " -v in=" + name + " " + runscript
os.system("qsub -N " + name + " -v in=" + name + " " + runscript)

</pre>

Then change the username = at the top to your own username, and press :wq enter to save and quit.

Make a directory in /rds/general/user/username/home/bin/ called runscripts and put these scripts in it: [runscripts[https://wiki.ch.ic.ac.uk/wiki/images/a/aa/Phunt_new_gf_script_runscripts.zip]]

==To use==

Go to the directory where your .com files are and type in:
python /rds/general/user/username/home/bin/gf.py version queuename nprocs inputfiles

For example:

<pre>python /rds/general/user/username/home/bin/gf.py d01 pqph 12 "01.com" </pre> will submit job 01.com on 12 processors to the pqph queue to run on gaussian version d01.
<pre>python /rds/general/user/username/home/bin/gf.py d01 pqchem 32 "*.com" </pre> will submit all the .com files in the directory to run on 32 processors in the pqchem queue to run on gaussian version d01.

==Possible options==

The version option may be eith d01 or b01.

The queue option may be either pqph or pqchem.

The nprocs options can be 12, 24, 32, 40 or 48.

Depending on which of these you use a different runscript from the runscripts folder is called. The list of runscripts that that are included by default are:

b01_pqchem_12
b01_pqchem_24
b01_pqchem_32
b01_pqchem_40
b01_pqchem_48
b01_pqph_12
b01_pqph_24
b01_pqph_32
b01_pqph_40
b01_pqph_48
d01_pqchem_12
d01_pqchem_24
d01_pqchem_32
d01_pqchem_40
d01_pqchem_48
d01_pqph_12
d01_pqph_24
d01_pqph_32
d01_pqph_40
d01_pqph_48

This is every combination of the above options. If you want to use a different option to the ones provided simply make the runscript you want to use, and name it with the same convention. If you want a different nprocs option you must also edit the script slightly in the section headed: Editing the input file, in the subsection: Getting the correct nprocs and mem lines for the .com files. You will just need to copy and paste an elif block and change the nprocs and the memory requested to whatever you want. It should be easy to copy what I did for the other examples.

Mod:Hunt Research Group/new gf script

2020-08-28T21:30:52Z

Jb6518:

==A new gf script==

This is a python script which does two jobs:

#Edits .com files so that
##.chk filename matches the .com file
##the ncps requested is correct
##the memory requested for gaussian is correct.
#Submits the job(s) (you can use wildcards in the command) using the standard runscripts ([https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/hpc[link]]) stored in a folder in your home directory.
Note: the first 3 lines of the .com file need to exist for the editing process to work. ie. You have 3 lines (with anything or nothing on, doesn't matter) BEFORE your method line. If your method line is in the first 3 lines it will get overwritten and the script won't work.

==How to set up for Gaussian16==

Go to /home/username/bin and type vi gf.py.
Press i and then copy and paste the following code in:

(instructions continue below the code - ignore the instructions in the code for now, they are just to help out if you are not looking at this page).

<pre>

import os
import glob
import sys

############
#HOW TO RUN#
############

# 0. Save this script in /rds/general/user/username/home as gf.py

# 1. Enter your username here:

username = "ab1234"

# 2. Save the runscripts from https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/new_gf_script in a directory called /rds/general/user/username/home/bin/runscripts

# 3. Go to the directory where your .com files are and type in:
# python /rds/general/user/username/home/bin/gf.py version queuname nprocs inputfiles

# For example:
# python /rds/general/user/username/home/bin/gf.py a01 pqph 20 "01.com" will submit job 01.com on 20 processors to the pqph queue to run on gaussian16 version a01.
# python /rds/general/user/username/home/bin/gf.py a01 pqph 40 "*.com" will submit all the .com files in the directory to run on 40 processors to the pqph queue to run on gaussian16 version a01.

#####################
#Setting the options#
#####################

#First variable sets which version of gaussian to use - use a01 usually.

version = sys.argv[1]
print "version = " + version

#Second variable sets the queue - pqph

queue = sys.argv[2]
print "queue = " + queue

#Third variable sets the number of processors:
#20, or 40

nprocs = sys.argv[3]
print "nprocs = " + nprocs

#Last variable is the input files. You can use wildcards but you need to add "quotes" around the input

job_input = sys.argv[4]
print "job_input= " + job_input
jobs = []
for job in glob.glob(job_input):
jobs.append(job)

print "list of jobs: "
print jobs

#######################
#Finding the runscript#
#######################

runscript = "/rds/general/user/" + username + "/home/bin/runscripts/" + version + "_" + queue + "_" + nprocs
print " "
print "runscript = " + runscript

########################
#Editing the input file#
########################

#Getting the correct nprocs and mem lines for the .com files:

gauss_nprocs_line = "undefined"
gauss_mem_line = "undefined"

if nprocs == "20":
gauss_nprocs_line = "%nprocs=20\n"
gauss_mem_line = "%mem=58000MB\n"
elif nprocs == "40":
gauss_nprocs_line = "%nprocs=40\n"
gauss_mem_line = "%mem=120000MB\n"
else:
print "Error: nprocs (argument 3) may only be 20, or 40."

print "gauss_nprocs_line = " + gauss_nprocs_line
print "gauss_mem_line = " + gauss_mem_line

#Editing the files:

for job in jobs:

#Getting the chk line to overwrite the input file

name_list = job.split(".")
name = name_list[0]
chk_line = "%chk=" + name + ".chk\n"
print name + " chk_line = " + chk_line

#Overwriting the first 3 lines of the input file

with open(job, "r") as file:
file_lines = file.readlines()
#print file_lines
file_lines[0] = gauss_nprocs_line
file_lines[1] = gauss_mem_line
file_lines[2] = chk_line
#print file_lines
with open(job, "w") as file:
file.writelines(file_lines)

#####################
#Submitting the jobs#
#####################

#Getting the terminal to do this: "qsub -N jobname -v in=name runscript"

print "qsub -N " + name + " -v in=" + name + " " + runscript
os.system("qsub -N " + name + " -v in=" + name + " " + runscript)

</pre>

Then change the username = at the top to your own username, and press :wq enter to save and quit.

Make a directory in /rds/general/user/username/home/bin/ called runscripts and put these scripts in it: [[:File:Hunt runscripts G16.zip|runscripts]]

==To use==

Go to the directory where your .com files are and type in:
python /rds/general/user/username/home/bin/gf.py version queuename nprocs inputfiles

For example:

<pre>python /rds/general/user/username/home/bin/gf.py a01 pqph 20 "01.com" </pre> will submit job 01.com on 20 processors to the pqph queue to run on gaussian16 version a01.
<pre>python /rds/general/user/username/home/bin/gf.py a01 pqph 40 "*.com" </pre> will submit all the .com files in the directory to run on 40 processors in the pqph queue to run on gaussian16 version a01.

==Possible options==

The version option may be a01.

The queue option may be pqph.

The nprocs options can be 20, or 40.

Depending on which of these you use a different runscript from the runscripts folder is called. The list of runscripts that that are included by default are:

a01_pqph_20
a01_pqph_40

This is every combination of the above options. If you want to use a different option to the ones provided simply make the runscript you want to use, and name it with the same convention. If you want a different nprocs option you must also edit the script slightly in the section headed: Editing the input file, in the subsection: Getting the correct nprocs and mem lines for the .com files. You will just need to copy and paste an elif block and change the nprocs and the memory requested to whatever you want. It should be easy to copy what I did for the other examples.

==How to set up for g09==

Go to /home/username/bin and type vi gf.py.
Press i and then copy and paste the following code in:

(instructions continue below the code - ignore the instructions in the code for now, they are just to help out if you are not looking at this page).

<pre>

import os
import glob
import sys

############
#HOW TO RUN#
############

# 0. Save this script in /rds/general/user/username/home as gf.py

# 1. Enter your username here:

username = "rr1210"

# 2. Save the runscripts from https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/new_gf_script in a directory called /rds/general/user/username/home/bin/runscripts

# 3. Go to the directory where your .com files are and type in:
# python /rds/general/user/username/home/bin/gf.py version queuname nprocs inputfiles

# For example:
# python /rds/general/user/username/home/bin/gf.py d01 pqph 12 "01.com" will submit job 01.com on 12 processors to the pqph queue to run on gaussian version d01.
# python /rds/general/user/username/home/bin/gf.py d01 pqchem 32 "*.com" will submit all the .com files in the directory to run on 32 processors in the pqchem queue to run on gaussian version d01.

#####################
#Setting the options#
#####################

#First variable sets which version of gaussian to use - use d01 usually or b01 for getting latest nbo.

version = sys.argv[1]
print "version = " + version

#Second variable sets the queue - pqph or pqchem

queue = sys.argv[2]
print "queue = " + queue

#Third variable sets the number of processors, as standard the options are the same as those defined by Tricia on the wiki:
#12, 24, 32, 40, 48

nprocs = sys.argv[3]
print "nprocs = " + nprocs

#Last variable is the input files. You can use wildcards but you need to add "quotes" around the input

job_input = sys.argv[4]
print "job_input= " + job_input
jobs = []
for job in glob.glob(job_input):
jobs.append(job)

print "list of jobs: "
print jobs

#######################
#Finding the runscript#
#######################

runscript = "/rds/general/user/" + username + "/home/bin/runscripts/" + version + "_" + queue + "_" + nprocs
print " "
print "runscript = " + runscript

########################
#Editing the input file#
########################

#Getting the correct nprocs and mem lines for the .com files:

gauss_nprocs_line = "undefined"
gauss_mem_line = "undefined"

if nprocs == "12":
gauss_nprocs_line = "%nprocs=12\n"
gauss_mem_line = "%mem=45000MB\n"
elif nprocs == "24":
gauss_nprocs_line = "%nprocs=24\n"
gauss_mem_line = "%mem=58000MB\n"
elif nprocs == "32":
gauss_nprocs_line = "%nprocs=32\n"
gauss_mem_line = "%mem=58000MB\n"
elif nprocs == "40":
gauss_nprocs_line = "%nprocs=40\n"
gauss_mem_line = "%mem=120000MB\n"
elif nprocs == "48":
gauss_nprocs_line = "%nprocs=48\n"
gauss_mem_line = "%mem=250000MB\n"
else:
print "Error: nprocs (argument 3) may only be 12, 24, 32, 40, 48."

print "gauss_nprocs_line = " + gauss_nprocs_line
print "gauss_mem_line = " + gauss_mem_line

#Editing the files:

for job in jobs:

#Getting the chk line to overwrite the input file

name_list = job.split(".")
name = name_list[0]
chk_line = "%chk=" + name + ".chk\n"
print name + " chk_line = " + chk_line

#Overwriting the first 3 lines of the input file

with open(job, "r") as file:
file_lines = file.readlines()
#print file_lines
file_lines[0] = gauss_nprocs_line
file_lines[1] = gauss_mem_line
file_lines[2] = chk_line
#print file_lines
with open(job, "w") as file:
file.writelines(file_lines)

#####################
#Submitting the jobs#
#####################

#Getting the terminal to do this: "qsub -N jobname -v in=name runscript"

print "qsub -N " + name + " -v in=" + name + " " + runscript
os.system("qsub -N " + name + " -v in=" + name + " " + runscript)

</pre>

Then change the username = at the top to your own username, and press :wq enter to save and quit.

Make a directory in /rds/general/user/username/home/bin/ called runscripts and put these scripts in it: [runscripts[https://wiki.ch.ic.ac.uk/wiki/images/a/aa/Phunt_new_gf_script_runscripts.zip]]

==To use==

Go to the directory where your .com files are and type in:
python /rds/general/user/username/home/bin/gf.py version queuename nprocs inputfiles

For example:

<pre>python /rds/general/user/username/home/bin/gf.py d01 pqph 12 "01.com" </pre> will submit job 01.com on 12 processors to the pqph queue to run on gaussian version d01.
<pre>python /rds/general/user/username/home/bin/gf.py d01 pqchem 32 "*.com" </pre> will submit all the .com files in the directory to run on 32 processors in the pqchem queue to run on gaussian version d01.

==Possible options==

The version option may be eith d01 or b01.

The queue option may be either pqph or pqchem.

The nprocs options can be 12, 24, 32, 40 or 48.

Depending on which of these you use a different runscript from the runscripts folder is called. The list of runscripts that that are included by default are:

b01_pqchem_12
b01_pqchem_24
b01_pqchem_32
b01_pqchem_40
b01_pqchem_48
b01_pqph_12
b01_pqph_24
b01_pqph_32
b01_pqph_40
b01_pqph_48
d01_pqchem_12
d01_pqchem_24
d01_pqchem_32
d01_pqchem_40
d01_pqchem_48
d01_pqph_12
d01_pqph_24
d01_pqph_32
d01_pqph_40
d01_pqph_48

This is every combination of the above options. If you want to use a different option to the ones provided simply make the runscript you want to use, and name it with the same convention. If you want a different nprocs option you must also edit the script slightly in the section headed: Editing the input file, in the subsection: Getting the correct nprocs and mem lines for the .com files. You will just need to copy and paste an elif block and change the nprocs and the memory requested to whatever you want. It should be easy to copy what I did for the other examples.

Mod:Hunt Research Group/new gf script

2020-08-28T21:27:27Z

Jb6518:

==A new gf script==

This is a python script which does two jobs:

#Edits .com files so that
##.chk filename matches the .com file
##the ncps requested is correct
##the memory requested for gaussian is correct.
#Submits the job(s) (you can use wildcards in the command) using the standard runscripts ([https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/hpc[link]]) stored in a folder in your home directory.
Note: the first 3 lines of the .com file need to exist for the editing process to work. ie. You have 3 lines (with anything or nothing on, doesn't matter) BEFORE your method line. If your method line is in the first 3 lines it will get overwritten and the script won't work.

==How to set up for Gaussian16==

Go to /home/username/bin and type vi gf.py.
Press i and then copy and paste the following code in:

(instructions continue below the code - ignore the instructions in the code for now, they are just to help out if you are not looking at this page).

<pre>

import os
import glob
import sys

############
#HOW TO RUN#
############

# 0. Save this script in /rds/general/user/username/home as gf.py

# 1. Enter your username here:

username = "ab1234"

# 2. Save the runscripts from https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/new_gf_script in a directory called /rds/general/user/username/home/bin/runscripts

# 3. Go to the directory where your .com files are and type in:
# python /rds/general/user/username/home/bin/gf.py version queuname nprocs inputfiles

# For example:
# python /rds/general/user/username/home/bin/gf.py a01 pqph 20 "01.com" will submit job 01.com on 20 processors to the pqph queue to run on gaussian16 version a01.
# python /rds/general/user/username/home/bin/gf.py a01 pqph 40 "*.com" will submit all the .com files in the directory to run on 40 processors to the pqph queue to run on gaussian16 version a01.

#####################
#Setting the options#
#####################

#First variable sets which version of gaussian to use - use a01 usually.

version = sys.argv[1]
print "version = " + version

#Second variable sets the queue - pqph

queue = sys.argv[2]
print "queue = " + queue

#Third variable sets the number of processors:
#20, or 40

nprocs = sys.argv[3]
print "nprocs = " + nprocs

#Last variable is the input files. You can use wildcards but you need to add "quotes" around the input

job_input = sys.argv[4]
print "job_input= " + job_input
jobs = []
for job in glob.glob(job_input):
jobs.append(job)

print "list of jobs: "
print jobs

#######################
#Finding the runscript#
#######################

runscript = "/rds/general/user/" + username + "/home/bin/runscripts/" + version + "_" + queue + "_" + nprocs
print " "
print "runscript = " + runscript

########################
#Editing the input file#
########################

#Getting the correct nprocs and mem lines for the .com files:

gauss_nprocs_line = "undefined"
gauss_mem_line = "undefined"

if nprocs == "20":
gauss_nprocs_line = "%nprocs=20\n"
gauss_mem_line = "%mem=58000MB\n"
elif nprocs == "40":
gauss_nprocs_line = "%nprocs=40\n"
gauss_mem_line = "%mem=120000MB\n"
else:
print "Error: nprocs (argument 3) may only be 20, or 40."

print "gauss_nprocs_line = " + gauss_nprocs_line
print "gauss_mem_line = " + gauss_mem_line

#Editing the files:

for job in jobs:

#Getting the chk line to overwrite the input file

name_list = job.split(".")
name = name_list[0]
chk_line = "%chk=" + name + ".chk\n"
print name + " chk_line = " + chk_line

#Overwriting the first 3 lines of the input file

with open(job, "r") as file:
file_lines = file.readlines()
#print file_lines
file_lines[0] = gauss_nprocs_line
file_lines[1] = gauss_mem_line
file_lines[2] = chk_line
#print file_lines
with open(job, "w") as file:
file.writelines(file_lines)

#####################
#Submitting the jobs#
#####################

#Getting the terminal to do this: "qsub -N jobname -v in=name runscript"

print "qsub -N " + name + " -v in=" + name + " " + runscript
os.system("qsub -N " + name + " -v in=" + name + " " + runscript)

</pre>

Then change the username = at the top to your own username, and press :wq enter to save and quit.

Make a directory in /rds/general/user/username/home/bin/ called runscripts and put these scripts in it: [runscripts[Hunt runscripts G16.zip]]

==To use==

Go to the directory where your .com files are and type in:
python /rds/general/user/username/home/bin/gf.py version queuename nprocs inputfiles

For example:

<pre>python /rds/general/user/username/home/bin/gf.py a01 pqph 20 "01.com" </pre> will submit job 01.com on 20 processors to the pqph queue to run on gaussian16 version a01.
<pre>python /rds/general/user/username/home/bin/gf.py a01 pqph 40 "*.com" </pre> will submit all the .com files in the directory to run on 40 processors in the pqph queue to run on gaussian16 version a01.

==Possible options==

The version option may be a01.

The queue option may be pqph.

The nprocs options can be 20, or 40.

Depending on which of these you use a different runscript from the runscripts folder is called. The list of runscripts that that are included by default are:

a01_pqph_20
a01_pqph_40

This is every combination of the above options. If you want to use a different option to the ones provided simply make the runscript you want to use, and name it with the same convention. If you want a different nprocs option you must also edit the script slightly in the section headed: Editing the input file, in the subsection: Getting the correct nprocs and mem lines for the .com files. You will just need to copy and paste an elif block and change the nprocs and the memory requested to whatever you want. It should be easy to copy what I did for the other examples.

==How to set up for g09==

Go to /home/username/bin and type vi gf.py.
Press i and then copy and paste the following code in:

(instructions continue below the code - ignore the instructions in the code for now, they are just to help out if you are not looking at this page).

<pre>

import os
import glob
import sys

############
#HOW TO RUN#
############

# 0. Save this script in /rds/general/user/username/home as gf.py

# 1. Enter your username here:

username = "rr1210"

# 2. Save the runscripts from https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/new_gf_script in a directory called /rds/general/user/username/home/bin/runscripts

# 3. Go to the directory where your .com files are and type in:
# python /rds/general/user/username/home/bin/gf.py version queuname nprocs inputfiles

# For example:
# python /rds/general/user/username/home/bin/gf.py d01 pqph 12 "01.com" will submit job 01.com on 12 processors to the pqph queue to run on gaussian version d01.
# python /rds/general/user/username/home/bin/gf.py d01 pqchem 32 "*.com" will submit all the .com files in the directory to run on 32 processors in the pqchem queue to run on gaussian version d01.

#####################
#Setting the options#
#####################

#First variable sets which version of gaussian to use - use d01 usually or b01 for getting latest nbo.

version = sys.argv[1]
print "version = " + version

#Second variable sets the queue - pqph or pqchem

queue = sys.argv[2]
print "queue = " + queue

#Third variable sets the number of processors, as standard the options are the same as those defined by Tricia on the wiki:
#12, 24, 32, 40, 48

nprocs = sys.argv[3]
print "nprocs = " + nprocs

#Last variable is the input files. You can use wildcards but you need to add "quotes" around the input

job_input = sys.argv[4]
print "job_input= " + job_input
jobs = []
for job in glob.glob(job_input):
jobs.append(job)

print "list of jobs: "
print jobs

#######################
#Finding the runscript#
#######################

runscript = "/rds/general/user/" + username + "/home/bin/runscripts/" + version + "_" + queue + "_" + nprocs
print " "
print "runscript = " + runscript

########################
#Editing the input file#
########################

#Getting the correct nprocs and mem lines for the .com files:

gauss_nprocs_line = "undefined"
gauss_mem_line = "undefined"

if nprocs == "12":
gauss_nprocs_line = "%nprocs=12\n"
gauss_mem_line = "%mem=45000MB\n"
elif nprocs == "24":
gauss_nprocs_line = "%nprocs=24\n"
gauss_mem_line = "%mem=58000MB\n"
elif nprocs == "32":
gauss_nprocs_line = "%nprocs=32\n"
gauss_mem_line = "%mem=58000MB\n"
elif nprocs == "40":
gauss_nprocs_line = "%nprocs=40\n"
gauss_mem_line = "%mem=120000MB\n"
elif nprocs == "48":
gauss_nprocs_line = "%nprocs=48\n"
gauss_mem_line = "%mem=250000MB\n"
else:
print "Error: nprocs (argument 3) may only be 12, 24, 32, 40, 48."

print "gauss_nprocs_line = " + gauss_nprocs_line
print "gauss_mem_line = " + gauss_mem_line

#Editing the files:

for job in jobs:

#Getting the chk line to overwrite the input file

name_list = job.split(".")
name = name_list[0]
chk_line = "%chk=" + name + ".chk\n"
print name + " chk_line = " + chk_line

#Overwriting the first 3 lines of the input file

with open(job, "r") as file:
file_lines = file.readlines()
#print file_lines
file_lines[0] = gauss_nprocs_line
file_lines[1] = gauss_mem_line
file_lines[2] = chk_line
#print file_lines
with open(job, "w") as file:
file.writelines(file_lines)

#####################
#Submitting the jobs#
#####################

#Getting the terminal to do this: "qsub -N jobname -v in=name runscript"

print "qsub -N " + name + " -v in=" + name + " " + runscript
os.system("qsub -N " + name + " -v in=" + name + " " + runscript)

</pre>

Then change the username = at the top to your own username, and press :wq enter to save and quit.

Make a directory in /rds/general/user/username/home/bin/ called runscripts and put these scripts in it: [runscripts[https://wiki.ch.ic.ac.uk/wiki/images/a/aa/Phunt_new_gf_script_runscripts.zip]]

==To use==

Go to the directory where your .com files are and type in:
python /rds/general/user/username/home/bin/gf.py version queuename nprocs inputfiles

For example:

<pre>python /rds/general/user/username/home/bin/gf.py d01 pqph 12 "01.com" </pre> will submit job 01.com on 12 processors to the pqph queue to run on gaussian version d01.
<pre>python /rds/general/user/username/home/bin/gf.py d01 pqchem 32 "*.com" </pre> will submit all the .com files in the directory to run on 32 processors in the pqchem queue to run on gaussian version d01.

==Possible options==

The version option may be eith d01 or b01.

The queue option may be either pqph or pqchem.

The nprocs options can be 12, 24, 32, 40 or 48.

Depending on which of these you use a different runscript from the runscripts folder is called. The list of runscripts that that are included by default are:

b01_pqchem_12
b01_pqchem_24
b01_pqchem_32
b01_pqchem_40
b01_pqchem_48
b01_pqph_12
b01_pqph_24
b01_pqph_32
b01_pqph_40
b01_pqph_48
d01_pqchem_12
d01_pqchem_24
d01_pqchem_32
d01_pqchem_40
d01_pqchem_48
d01_pqph_12
d01_pqph_24
d01_pqph_32
d01_pqph_40
d01_pqph_48

This is every combination of the above options. If you want to use a different option to the ones provided simply make the runscript you want to use, and name it with the same convention. If you want a different nprocs option you must also edit the script slightly in the section headed: Editing the input file, in the subsection: Getting the correct nprocs and mem lines for the .com files. You will just need to copy and paste an elif block and change the nprocs and the memory requested to whatever you want. It should be easy to copy what I did for the other examples.

2020-06-19T09:20:53Z

2020-06-18T11:54:20Z

Jb6518:

Mod:Hunt Research Group

2020-06-03T12:32:46Z

Jb6518:

==Hunt Group Wiki==

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Mod:Hunt Research Group/SAPT

2020-06-03T12:30:06Z

Jb6518:

==Run SAPT calculations using Psi4==

===Installing Psi4 on the HPC===

Psi4 comes as a pyhton module, thus we can use conda to create personal versions of Psi4 on the HPC.

'''1. Create your personal conda'''

Have a look at the [https://www.imperial.ac.uk/admin-services/ict/self-service/research-support/rcs/support/applications/conda/ HPC webpage].

The command to install your personal conda is:

''anaconda-setup''

'''2. Create a Psi4 environment'''

Load conda via:

''module load anaconda3/personal''

Create a Psi4 environment of the latest stable Psi4 release which will be called p4env via:

''conda create -n p4env psi4 -c psi4''

'''3. Check the installation'''

Load the environment you just created:

''conda activate p4env''

Check the version you installed:

''psi4 --version''

===PBS submission script===

Copy the submission script below into a file called p4run.sh

<pre>
#!/bin/bash
#PBS -N psi4job
#PBS -q pqph
#PBS -l walltime=5:00:00
#PBS -l select=1:ncpus=20:mem=5gb
#PBS -j oe
# Load relevant modules
module load anaconda3/personal
source activate p4env
#export MYSCRATCH=/scratch/user/psi4.$PBS_JOBID
#foreach i (`sort $PBS_NODEFILE | uniq`)
# echo "Creating scratch directory " ${MYSCRATCH} " on " $i
# ssh $i rm -rf ${MYSCRATCH}
# ssh $i mkdir -p ${MYSCRATCH}
#end
#unsetenv PSIDATADIR
# Change directory and set scratch directory
cd $PBS_O_WORKDIR
export PSI_SCRATCH=$TMPDIR
#if ! ( $?PSIPATH ) setenv PSIPATH ""
#setenv PSIPATH /path/to/external/modules:${PSIPATH}
# Execute psi4 job
psi4 -i ${in}.in -o ${in}.out -n 20
#foreach i (`sort $PBS_NODEFILE | uniq`)
# echo "Removing scratch directory " ${MYSCRATCH} " on " $i
# ssh $i rm -rf ${MYSCRATCH}
#end
</pre>

'''IMPORTANT:''' You need to specify the memory and number of CPUs as usual in the submission script (#PBS -l select=1:ncpus=20:mem=30gb). You still need to take care that these numbers match the number of CPUs you give in the fifth row from the bottom (psi4 -i ${in}.in -o ${in}.out -n '''20''') and the memory specified in the actual input file. If you have mismatching parameters the job still might start running but not with the full capacity of the recourses you requested. For example if you request 20 cores and 30 GB of memory in the submission script but you only submit the job with 4 cores and 5 GB, you will have 16 cores and 20 GB which are not used during the computation.

===Example Input===

Here is an examplpe input file for the SAPT(2) calculation of the H3N-HCl dimer. Copy the content into a file called NH4Cl.in

<pre>
memory 16 GB

molecule mol {
0 1
N 1.876377 0.000001 -0.000006
H 2.237648 0.661745 -0.680615
H 2.237486 0.258575 0.913443
H 2.237570 -0.920339 -0.232740
--
0 1
Cl -1.177795 0.000000 -0.000001
H 0.175168 0.000012 -0.000026

units angstrom
symmetry c1
no_reorient
}

set basis 6-311+G(d,p)

energy('sapt2')
</pre>

Assuming that both the PBS script and the input file are located in the same directory, submit the job via:

''qsub -N SAPT2 -v in=NH4Cl p4run.sh''

The results of the SAPT(2) calculation is a .out file. At the end of the NH4Cl.out file you will find the results of the SAPT(2) analysis which should be similar to this (slight differences might occur depending on the version of Psi4 you used):

<pre>
SAPT Results
--------------------------------------------------------------------------------------------------------
Electrostatics -36.32899016 [mEh] -22.79678645 [kcal/mol] -95.38176366 [kJ/mol]
Elst10,r -36.63905676 [mEh] -22.99135619 [kcal/mol] -96.19584351 [kJ/mol]
Elst12,r 0.31006660 [mEh] 0.19456974 [kcal/mol] 0.81407985 [kJ/mol]

Exchange 51.13218109 [mEh] 32.08592939 [kcal/mol] 134.24754146 [kJ/mol]
Exch10 48.11718409 [mEh] 30.19399013 [kcal/mol] 126.33166682 [kJ/mol]
Exch10(S^2) 46.43751367 [mEh] 29.13998098 [kcal/mol] 121.92169213 [kJ/mol]
Exch11(S^2) 0.99070562 [mEh] 0.62167719 [kcal/mol] 2.60109761 [kJ/mol]
Exch12(S^2) 2.02429139 [mEh] 1.27026208 [kcal/mol] 5.31477704 [kJ/mol]

Induction -22.98775238 [mEh] -14.42503300 [kcal/mol] -60.35434386 [kJ/mol]
Ind20,r -25.00378267 [mEh] -15.69011116 [kcal/mol] -65.64743140 [kJ/mol]
Ind22 -1.93327324 [mEh] -1.21314732 [kcal/mol] -5.07580888 [kJ/mol]
Exch-Ind20,r 14.66201899 [mEh] 9.20055621 [kcal/mol] 38.49513087 [kJ/mol]
Exch-Ind22 1.13365603 [mEh] 0.71137993 [kcal/mol] 2.97641390 [kJ/mol]
delta HF,r (2) -11.84637149 [mEh] -7.43371065 [kcal/mol] -31.10264835 [kJ/mol]

Dispersion -7.02240313 [mEh] -4.40662468 [kcal/mol] -18.43731942 [kJ/mol]
Disp20 -9.19384826 [mEh] -5.76922712 [kcal/mol] -24.13844860 [kJ/mol]
Exch-Disp20 2.17144513 [mEh] 1.36260245 [kcal/mol] 5.70112918 [kJ/mol]

Total HF -10.71000784 [mEh] -6.72063166 [kcal/mol] -28.11912557 [kJ/mol]
Total SAPT0 -17.73241096 [mEh] -11.12725634 [kcal/mol] -46.55644499 [kJ/mol]
Total SAPT2 -15.20696457 [mEh] -9.54251473 [kcal/mol] -39.92588548 [kJ/mol]

Special recipe for scaled SAPT0 (see Manual):
Electrostatics sSAPT0 -36.63905676 [mEh] -22.99135619 [kcal/mol] -96.19584351 [kJ/mol]
Exchange sSAPT0 48.11718409 [mEh] 30.19399013 [kcal/mol] 126.33166682 [kJ/mol]
Induction sSAPT0 -20.53889410 [mEh] -12.88835117 [kcal/mol] -53.92486646 [kJ/mol]
Dispersion sSAPT0 -6.77815052 [mEh] -4.25335384 [kcal/mol] -17.79603418 [kJ/mol]
Total sSAPT0 -15.83891729 [mEh] -9.93907107 [kcal/mol] -41.58507733 [kJ/mol]
--------------------------------------------------------------------------------------------------------
</pre>

Mod:Hunt Research Group/SAPT

2020-06-03T12:29:09Z

Jb6518: /* Example Input */