Merge pull request #33 from CurtisColwell/33_slurm_submit

33 slurm submit

README.md

@@ -83,5 +83,12 @@ exactly or the script will not be able to translate the energy back to the base
 
 ## Using with SLURM
 
-These jobs can be submitted to a SLURM scheduler by creating an .srun file that runs the bash 
-script.
+These jobs can be submitted to a SLURM scheduler by running slurm.bash with the name of 
+the molecule to submit.
+```
+bash slurm.bash input/example-molecule
+```
+In slurm.bash, the partition defaults to short, but can be changed by editing the file. In 
+slurm_submit.srun, the number of processors defaults to 28, but can be changed by changing 
+the number in the header AND in the bash command. The level of theory can be changed in the 
+bash command as well.

slurm.bash

@@ -0,0 +1,8 @@
+#!bin/bash
+
+set -e
+
+inputname=$(basename -- "$1")
+inputname="${inputname%.*}"
+
+sbatch --job-name=$inputname --partition=short --output="output/"$inputname".txt" --account=$GROUP_NAME "slurm_submit.srun"

slurm_submit.srun

@@ -0,0 +1,7 @@
+#!/bin/bash
+#SBATCH -N 1
+#SBATCH -n 28
+
+set -e
+
+bash StrainViz.bash ${SLURM_JOB_NAME} 28 "M062X/6-31G(d)"