====NWChem====

NWChem is a scalable computational tool for large scale molecular simulations. Along with computational chemistry the package also inculdes quantum chemical and molecular dynamics functionality. It was developed at the [[https://en.wikipedia.org/wiki/Pacific_Northwest_National_Laboratory|Pacific Northwest National Labratory]]. More documentation is avaliable at the [[http://www.nwchem-sw.org/index.php/Main_Page|NWChem main page]].

====Enviornment Setup====

First add these modules to your ''.bashrc'' file to satisfy the dependencies for and load NWChem itself. 

<code>
module load intel/12.1.5 
module load mvapich2/1.8 
module load mkl/12.1.5 
module load nwchem
</code>

Also two environmental variables are needed to adjust the behavior of MVAPICH2 library. Add these two lines to your $HOME/.bashrc file.

<code>
export MV2_ENABLE_AFFINITY=0
export IPATH_NO_CPUAFFINITY=1
</code>

Additionally, NWChem looks for a $HOME/.nwchemrc file which specifies the location of the basis library and force field parameters. To use the preconfigured default nchemrc file run:

<code>
razor-l1:jokinsey:~$ ln -s /share/apps/NWChem/nwchem-6.1.1/data/default.nwchemrc ~/.nwchemrc
</code>  

This links the default nchemrc file to your ''$HOME'' directory so NWChem knows where to find the file

====Example Job====

Create a directory ''NWCHEM-JOBS'' to store the output from the example. A set of example input files is located in ''/share/apps/NWChem/nwchem-6.1.1/examples'' directory. We'll use the ''benzene.nw'' example. Copy the input file to your ''$HOME/NWHCEM-JOBS'' directory. This example uses a separate file to store geometry of the molecule ''benzene.pdb'' which also needs to be copied.

<code>
razor-l1:jokinsey:~$ mkdir NWCHEM-JOBS
razor-l1:jokinsey:~$ cp /share/apps/NWChem/nwchem-6.1.1/examples/md/benzene/benzene.* ~/NWCHEM-JOBS
</code>

Edit the ''benzene.nw'' file to specify the scratch directory.

<code>
start benzene

scratch_dir /scratch/YourUserNameHere

prepare
 system benzene_em
 new_top new_seq
 solvate
end

task prepare

md
 system benzene_em
 sd 100
end

task md optimize

task shell "cp benzene_em.qrs benzene_md.rst"

md
 system benzene_md
 data 100
 isotherm
 isobar
 print step 10 stat 100
end

task md dynamics
</code>

In the directory contianing the benzene.nw input file, create a ''PBS'' script and name it nwchem.pbs.

<code>
#!/bin/bash
#PBS -N nwchem
#PBS -q tiny12core
#PBS -j oe
#PBS -o nwchem.$PBS_JOBID
#PBS -l nodes=1:ppn=12
#PBS -l walltime=1:00:00

cd $PBS_O_WORKDIR
cp benzene.* /scratch/$PBS_JOBID
cd /scratch/$PBS_JOBID

NP=$(wc -l < $PBS_NODEFILE)

mpirun -np $NP -machinefile $PBS_NODEFILE nwchem benzene.nw > benzene.out
mv benzene* bnz*  $PBS_O_WORKDIR
</code>

This ''PBS'' script moves the test files to the ''/scratch/$PBS_JOBID'' directory where we will run the job then moves the output files back to the ''$PBS_O_WORKDIR'' where we submitted the job from.

Then submit the job to be run in the queue ''tiny12core'' which we specified in the PBS file.

<code>
razor-l1:jokinsey:~/NWCHEM-JOBS$ qsub nwchem.pbs
</code>

The job will produce several files . benzene.out as specified in the PBS input script will contain the most relevant output.