=====================================================
SLURM script file for Gaussian 16
=====================================================

.. code-block:: sh
    :caption: test
    :name: test333
    :emphasize-lines: 2
    :linenos:

    #!/bin/bash -l
    # Section for defining queueing system variables:
    # SLURM-section
    #SBATCH --job-name=watdim01    
    #SBATCH --output=watdim01.slurmout
    #SBATCH --partition=cluster8                
    #SBATCH --nodes=1
    #SBATCH --cpus-per-task=8
    #SBATCH --threads-per-core=1
    #SBATCH --mem-per-cpu=2000
    ######################################
    # Section for defining job variables and settings:
    g16root="/scr1/g16_a.03_sse4"
    g16dir="/scr1/g16_a.03_sse4/g16"
    LaunchDir=$PWD;
    LocalRunDir=/scr1/$USER/$SLURM_JOB_ID
    export GAUSS_SCRDIR=$LocalRunDir;
    mkdir -p $GAUSS_SCRDIR
    export GAUSS_EXEDIR=$g16dir
    export GAUSS_ARCHDIR=$g16dir
    cat >/$LocalRunDir/$SLURM_JOB_NAME.gjf <<EOF
    %chk=$GAUSS_SCRDIR/$SLURM_JOB_NAME.chk
    %CPU=0-7       
    %mem=16000MB
    #p b3lyp/6-31+G(d,p) opt=(Z-Matrix) iop(1/7=30) int=ultrafine  EmpiricalDispersion=GD3 

    watdim01 water dimer b3lyp-D3/6-31+G(d,p) opt tight Cs, int=ultrafine    

    0 1
    O1
    H2  1  r2
    H3  1  r3  2  a3
    X4  2  1.0  1  90.0  3  180.0
    O5  2  r5  4  a5  1  180.0
    H6  5  r6  2  a6  4  d6
    H7  5  r6  2  a6  4  -d6

    r2=0.9732       
    r3=0.9641      
    r5=1.9128    
    r6=0.9659   
    a3=105.9    
    a5=83.1         
    a6=112.1       
    d6=59.6         


    EOF
    $g16dir/g16 < $GAUSS_SCRDIR/$SLURM_JOB_NAME.gjf > $LaunchDir/$SLURM_JOB_NAME.log
    cp $GAUSS_SCRDIR/$SLURM_JOB_NAME.chk $LaunchDir/
    # The following line will clean up /scr1 after finishing the job
    rm -rf $LocalRunDir
    # If your job finishes normally, delete the empty .slurmout file
    slurmout_check=`cat $SLURM_JOB_NAME.slurmout`
    if [$slurmout_check = ""]; then
    rm -f $SLURM_JOB_NAME.slurmout
    fi

    exit 0




.. code-block:: sh
    :caption: test
    :name: test3333
    :emphasize-lines: 2
    :linenos:

    #!/bin/bash
    #SBATCH -J opt-CdSe33ZnS69LHis12
    #SBATCH -o %J.out
    #SBATCH -e %J.err
    #SBATCH -N 1
    #SBATCH -w node01
    #SBATCH -n 96
    #SBATCH -t 30-12:00:00
    #SBATCH -p hpc
    ###SBATCH --dependency=afterok:0
    #=======================
    export OMP_THREAD_LIMIT=256 # max cpu to 256 for gaussian version <=16 b01
    echo =======================
    echo Submit Time is [`date`].
    echo Working dir is [$SLURM_SUBMIT_DIR].
    cd $SLURM_SUBMIT_DIR
    NPROCS=$((SLURM_NTASKS))
    N_NODE=$((SLURM_JOB_NUM_NODES))
    echo This job has allocated [${N_NODE}] nodes with [${NPROCS}] processors.
    # echo Running on host [`hostname`].
    echo Running on host [$SLURM_JOB_NODELIST].
    echo This jobs runs on the following processors:
    echo =======================
    echo "**Start!!!"
    echo Job start Time is [`date`].
    echo This job name is [$SLURM_JOB_NAME] and job id is [$SLURM_JOB_ID]. >> $SLURM_JOB_ID.out
    #=======================
    unset PATH && \
    export PATH=/usr/local/bin:/usr/local/sbin:/usr/sbin:/usr/bin:/root/bin:$PATH && \
    unset LD_LIBRARY_PATH

    JOBNAME=opt-CdSe33ZnS69LHis12

    GAUSS_SCRDIR=/tmp/$SLURM_JOB_USER/$SLURM_JOB_ID

    if [ ! -a $GAUSS_SCRDIR ]; then
    echo "Scratch directory $GAUSS_SCRDIR created."
    mkdir -p $GAUSS_SCRDIR
    fi
    export GAUSS_SCRDIR
    echo "Using $GAUSS_SCRDIR for temporary Gaussian 16 files."
    ls -l $GAUSS_SCRDIR
    # for gaussian16 b01
    export g16root=/data1/apps/gaussian
    export PATH=$PATH:$g16root/g16
    export GAUSS_EXEDIR=$g16root/g16
    source $g16root/g16/bsd/g16.profile
    # for gaussian16 c01
    # export g16root=/data1/apps/gaussian-c
    # export PATH=$PATH:$g16root/g16
    # export GAUSS_EXEDIR=$g16root/g16
    # source $g16root/g16/bsd/g16.profile
    # cat $SLURM_JOB_NODELIST |uniq > $GAUSS_SCRDIR/working.nodes
    echo $SLURM_JOB_NODELIST > $GAUSS_SCRDIR/working.nodes # >> means append and > means replace
    echo "Gaussian16 nodes:"
    cat $GAUSS_SCRDIR/working.nodes
    export GAUSS_LFLAGS=" -mp 96 -vv -nodefile $GAUSS_SCRDIR/working.nodes"
    #=======================
    start_time=$(date +%s)
    #1
    task_start_time=$(date +%s)
    #Run a Gaussian command file
    echo "Starting Gaussian run at" `date`
    time g16 < $JOBNAME.gjf > $JOBNAME.out
    echo "Finished Gaussian run at" `date`
    echo "Removing GASUU_SCRDIR:"
    echo "$GAUSS_SCRDIR"
    rm -Rf $GAUSS_SCRDIR
    task_duration=$(( $(date +%s) - $task_start_time ))
    echo "Task 1 duration: $task_duration seconds." >> $SLURM_JOB_ID.out

    #2
    task_start_time=$(date +%s)
    #convert .chk to .fch
    # formchk ${JOBNAME}.chk
    formchk ${JOBNAME}.chk
    task_duration=$(( $(date +%s) - $task_start_time ))
    echo "Task 2 duration: $task_duration seconds." >> $SLURM_JOB_ID.out

    end_time=$(date +%s)
    duration=$(( $end_time - $start_time ))
    echo "Total duration: $duration seconds." >> $SLURM_JOB_ID.out

    echo Job finish Time is [`date`].
    echo "**Finished!!!"
    echo =======================
    echo "                       "