Merge pull request #61 from uit-no/radovan/gaussian-doc

Refactor Gaussian documentation

applications/chemistry/Gaussian/GaussView.rst

@@ -1,25 +1,21 @@
 
-======================
-GaussView for Gaussian
-======================
+=========
+GaussView
+=========
 
 Gaussview is a visualization program that can be used to open Gaussian output
 files and checkpoint files (.chk) to display structures, molecular orbitals,
 normal modes, etc. You can also set up jobs and submit them directly.
 
+Official documentation: https://gaussian.com/gaussview6/
 
-GaussView on Stallo
---------------------
-
-The GaussView version for Gaussian 09 is release 5.0.8 To load and run
-GaussView on Stallo, you first have to load the relevant gaussian module, and
-then call gaussview::
 
-   $ module load Gaussian/09.d01
-   $ gview
+GaussView on Stallo
+-------------------
 
-More information about GaussView
---------------------------------
+To load and run GaussView on Stallo, load the relevant Gaussian module, and
+then call GaussView::
 
-* General info about the program: http://www.gaussian.com/g_prod/gv5.htm
-* Online reference: http://www.gaussian.com/g_tech/gv5ref/gv5ref_toc.htm
+  $ module avail Gaussian
+  $ module load Gaussian/g16_B.01
+  $ gview

applications/chemistry/Gaussian/example.com

@@ -0,0 +1,21 @@
+%chk=example
+%mem=500MB
+#p b3lyp/cc-pVDZ opt
+
+benzene molecule example
+
+0 1
+C        0.00000        1.40272        0.00000
+C        0.00000       -1.40272        0.00000
+C        1.21479        0.70136        0.00000
+C        1.21479       -0.70136        0.00000
+C       -1.21479        0.70136        0.00000
+C       -1.21479       -0.70136        0.00000
+H        0.00000        2.49029        0.00000
+H        0.00000       -2.49029        0.00000
+H        2.15666        1.24515        0.00000
+H        2.15666       -1.24515        0.00000
+H       -2.15666        1.24515        0.00000
+H       -2.15666       -1.24515        0.00000
+
+

applications/chemistry/Gaussian/gaussian-runscript.sh

@@ -0,0 +1,61 @@
+#!/bin/bash -l
+
+#SBATCH --account=nn....k
+
+#SBATCH --job-name=example
+#SBATCH --output=example.log
+
+# Stallo nodes have either 16 or 20 cores: 80 is a multiple of both
+#SBATCH --ntasks=80
+
+# make sure no other job runs on the same node
+#SBATCH --exclusive
+
+# syntax is    DD-HH:MM:SS
+#SBATCH --time=00-00:30:00
+
+# allocating 30 GB on a node and leaving a bit over 2 GB for the system
+#SBATCH --mem-per-cpu=1500MB
+
+################################################################################
+# no bash commands above this line
+# all sbatch directives need to be placed before the first bash command
+
+# name of the input file without the .com extention
+input=example
+
+# flush the environment for unwanted settings
+module --quiet purge
+# load default program system settings
+module load Gaussian/g16_B.01
+
+# set the heap size for the job to 20 GB
+export GAUSS_LFLAGS2="--LindaOptions -s 20000000"
+
+# split large temporary files into smaller parts
+lfs setstripe –c 8 .
+
+# create scratch space for the job
+export GAUSS_SCRDIR=/global/work/${USER}/${SLURM_JOB_ID}
+tempdir=${GAUSS_SCRDIR}
+mkdir -p ${tempdir}
+
+# copy input and checkpoint file to scratch directory
+cp ${SLURM_SUBMIT_DIR}/${input}.com ${tempdir}
+if [ -f "${SLURM_SUBMIT_DIR}/${input}.chk" ]; then
+    cp ${SLURM_SUBMIT_DIR}/${input}.chk ${tempdir}
+fi
+
+# run the code
+cd ${tempdir}
+time g16.ib ${input}.com > ${input}.out
+
+# copy output and checkpoint file back
+cp ${input}.out ${SLURM_SUBMIT_DIR}
+cp ${input}.chk ${SLURM_SUBMIT_DIR}
+
+# remove the scratch directory after the job is done
+# cd ${SLURM_SUBMIT_DIR}
+# rm -rf /global/work/${USER}/${SLURM_JOB_ID}
+
+exit 0