NWChem computer exercise

Quantumchemistry, NWI-MOL406, Computer exercises, week 4

The NWChem quantum chemistry program package is being developed by Environmental Molecular Science Laboratory (EMSL) located at the Pacific Northwest National Laboratory (PNNL). The code is open-source and available under the Educational Community License version 2.0 (ECL 2.0).

Linux preliminaries:

For help with the following, you could consult e.g. a linux primer.
The instructions here assume you use bash.
To find out which shell you use open a terminal and type
```
echo $0
```
he default is often bash. If it is not, then type "bash" (followed by pressing the "Enter" key).
The program is available as /vol/cursus/QuantumChemistry/bin/nwchem
To run the program without using the full pathname add the directory to your path:
```
if [ -d /vol/cursus/QuantumChemistry/bin ]; then
  export PATH="/vol/cursus/QuantumChemistry/bin:$PATH"
fi
```
It is easiest to add these lines to $HOME/.profile. In your login directory just edit .profile (probably does not yet exist) and add these lines, e.g. using "nano".
This is the minumum setup. It is sufficient to run nwchem.

Alternatively you can do the following:
```
cp /vol/cursus/QuantumChemistry/setup/.bashrc ~/.
cp -rp /vol/cursus/QuantumChemistry/setup/.bash_functions ~/.
```
and put the following lines in $HOME/.profile
```
if [ $SHELL == /bin/bash ]; then
  test -s ~/.bashrc && . ~/.bashrc || true
fi
```
This gives you a lot of extra nice commands and extra safety all made by Gerrit Groenenboom.

To check that you have the correct version of nwchem, type:
```
which nwchem
```
This should give you the executable with the full path:
```
/vol/cursus/QuantumChemistry/bin/nwchem
```
If you have the wrong version, you will see:
```
/usr/bin/nwchem
```
That is not good.
The program NWChem creates large (temporary) files during the computation. Putting these files on a network disk ($HOME) slows the computations down. And for some calculations your disk space might be insuffient. For this purpose create a directory in /tmp
```
mkdir -p /tmp/$USER
```
Because of the -p the command will not give an error message if the directory also exists. To check use
```
ls -l /tmp
```
Of course you may put the mkdir command in your $HOME/.bashrc.

To run NWChem create a subdirectory on the tmp file system, and work there:
```
cd /tmp/$USER
mkdir -p job1
cd job1
# now create the input file here, etc (see below)
```
(Everything after the "#" is just a comment that is ignored by bash)
Be aware that there is no backup of the /tmp filesystem, so copy important files to $HOME (or better $HOME/QuantumChemistry)
To copy an entire directory with all its subdirectories you use, e.g.
```
cd     # without argument this brings you to $HOME
cd QuantumChemistry
mkdir -p job1
cd job1
rsync -avz /tmp/$USER/job1 .
```
Note: the "-a" flag means "archive", the "v" is for "verbose" (i.e., you'll get some information on what rsync is doing), and the "z" means compress the data during the copy. The latter is not essential.
Usually, you may not need a backup of large binary files, so just making a backup of input and output files may be sufficient.
NOTE: running NMChem from /tmp will only be needed for larger jobs in the last 2 weeks. Avoid running on /tmp as much as possible: /tmp is local to the cluster node that you are using. If the connection is broken, and you log on to jupyterhub again, you might end up on another cluster node, where /tmp is another file system that does not have your job's data.
There are many tricks to make working with the command line easier. Some goodies:
```
pwd                                                             # show path to current directory
cd								# to go to $HOME
touch .bashrc							# creates an empty file if .bashrc does not yet exist
cat /vol/cursus/QuantumChemistry/setup/.bashrc >> .bashrc	# this appends the file
```
If you opted for the elaborate alternative above (copying .bashrc, etc.) the following might also work. Your prompt should display your current working directory. After changing to a new directory you may go to the previous by type
```
b			# b = go back
```
and go forward with
```
f			# f = forward, i.e., undo "b"
```
To see your file sorted with most recent first use
```
l			# alias for "ls -lt"
```
The rm is changed by an alias such that
```
rm some_file
```
will move some_file to $HOME/waste, rather than deleting it. To actually remove a file use
```
\rm some_file		# you will get /bin/rm and not the alias
```

Single point Hartree-Fock/SCF calculation for water

First do a small test run:

Go to $HOME/QuantumChemistry and make a directory for your calculation
```
cd
cd QuantumChemistry
mkdir jobH2O
cd jobH2O
```

Create an input file (e.g., using nano) with the name job1.nw with the following

START
title "Single point SCF energy calculation for H2O in 3-21G basis"
geometry
  zmatrix
    O
    H1 1 ROH
    H2 1 ROH 2 AHOH
    variables
    ROH 1.0
    AHOH 109
  end
end
basis
  * library 3-21G
end
task scf

Run the calculation:
```
nwchem job1.nw > job1.out
```
Read the output file job1.out, try to understand the information of the basis set.
For now simply ignore the parts you do not understand. At line 346 of the output file you should find the
Total SCF energy = -75.583831691188
This is the energy in atomic units (Hartree).
Look at the files that are created by NWChem:
```
ls -l job1.*
```
The information from the input file and results are stored in the database file job1.db

NWChem documentation

This is the NWChem website
Have a quick look at the Science section, to get an overview of the capabilities of the program
Go to the Documentation section (alternatively, you can go the most recent version on github) and read the Getting started section.

Geometry optimization

We continue with the water molecule.

Create a new input file:
```
cp job1.nw job2.nw
```
Now modify the last line of the file into
```
task scf optimize
```
This instructs NWChem to optimize the geometry.
Anwer these questions:
- What is the optimized bond length and bond angle?
- How much lower in energy is this geometry than the structure of job1.nw? Give the answer in Hartree, eV, and kcal/mol
  (1 Hartree = 27.2113834 eV = 627.50956 kcal/mol)

To impose C2v point group symmetry, change the geometry block into and repeat the optimization run:

 geometry units au
   symmetry C2v
   O      0.00000000    0.00000000    0.00000000
   H      0.00000000    1.43042809   -1.10715266
   H      0.00000000   -1.43042809   -1.10715266
 end

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Last updated: 22-Nov-2022.