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:

The instructions here assume you use bash
To find out which shell you use open a terminal and type
```
echo $0
```
The default is often bash. If it is not, then type "bash" (followed by pressing the "Enter" key).
The program is available as /vol/cursus/QuantumChemistry/bin/nwchem
To run the program without using the full pathname add the directory to your path:
```
if [ -d /vol/cursus/QuantumChemistry/bin ]; then
  export PATH="$PATH:/vol/cursus/QuantumChemistry/bin"
fi
```
Or just copy this from /vol/cursus/QuantumChemistry/setup/.bashrc
(if you to this and want to use all aliases set in here, also copy as follows: cp -rp /vol/cursus/QuantumChemistry/setup/.bash_functions ~/,
alternatively you can unalias: unalias cd , etc.)
To execute this command automatically each time you start bash put it in $HOME/.bashrc
For this purpose you may use an editor like gedit

If it does not work add this to $HOME/.profile

if [ $SHELL == /bin/bash ]; then
  test -s ~/.bashrc && . ~/.bashrc || true
fi

The program NWChem creates large (temporary) files during the computation. Putting these files on a network disk ($HOME) slows the computations down. For this purpose create a directory in /tmp
```
mkdir -p /tmp/$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
To copy an entire directory with all its subdirectories you use, e.g.
```
cd     # without argument this brings you to $HOME
rsync -avz /tmp/$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 may make things a little faster on a slow network, but it 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.
When using the command line it is useful to know your currect directory. Use
```
pwd
```
for this purpose.
There are many tricks to make working with the command line easier. To use some of my favorite tricks:
```
cd								# to go to $HOME
cp -rp /vol/cursus/QuantumChemistry/setup/.bash_functions .
touch .bashrc							# creates an empty file if .bashrc does not yet exist
cat /vol/cursus/QuantumChemistry/setup/.bashrc >> .bashrc	# this appends the file
```
The tricks will work after opening a new window, or after "sourcing" the file:
```
. ~/.bashrc			# the "." means "source" the file
```
The current directory should now appear in the prompt. 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 tmp
```
cd /tmp/$USER
mkdir job1
cd job1
```

Create an input file (e.g., using gedit) 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 338 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

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)

C2V symmetry

To impose C2v point group symmetry, change the geometry block into:

 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: 26-Nov-2019.