#!/bin/tcsh
#  Sample Batch Script for a MVAPICH2-Intel job on NCSA forge
#
#  Submit this script using the command: qsub <script_name>
#
#  Use the "qstat" command to check the status of a job.
#
# The following are embedded QSUB options. The syntax is #PBS (the # does
# _not_  denote that the lines are commented out so do not remove).
#
# walltime : maximum wall clock time (hh:mm:ss)
#PBS -l walltime=01:00:00
#
# nodes: number of 16-core nodes
# ppn: how many cores per node to use (1 through 16)
#       (you are always charged for the entire node)
#PBS -l nodes=1:ppn=16
#

# export all my environment variables to the job
#PBS -V
#PBS -q normal
# job name (default = name of script file)
#PBS -N yank
#
#
# filename for standard output (default = <job_name>.o<job_id>)
# at end of job, it is in directory from which qsub was executed
# remove extra ## from the line below if you want to name your own file
###PBS -o testjob.out
#
# filename for standard error (default = <job_name>.e<job_id>)
# at end of job, it is in directory from which qsub was executed
# remove extra ## from the line below if you want to name your own file
###PBS -e testjob.err
#
# End of embedded QSUB options
#
# set echo               # echo commands before execution; use for debugging
#

#cd ${HOME}/code/yank/proof-of-concept/alchemical-repex-volume

setenv NP `wc -l ${PBS_NODEFILE} | cut -d'/' -f1`

##setenv MV2_SRQ_SIZE 4000

### setenv any other vars you might need

### run mpi: This will place ranks in the order in which nodes appear in
### the host file; the default, $PBS_NODEFILE, lists hosts in "packed"
### order, i.e.,
### host1
### host1
### ...
### host2
### host2
#mpirun_rsh -ssh -np ${NP} -hostfile ${PBS_NODEFILE} python alchemical-repex-volume.py

cd $YANKHOME/src

# DEBUG
#setenv SYSTEM 1-methylpyrrole
#setenv JOBDIR "${HOME}/code/yank/test-systems/T4-lysozyme-L99A/amber-gbsa/amber-gbsa/$SYSTEM/"

# DEBUG
#setenv JOBDIR "examples/benzene-toluene"
setenv JOBDIR "examples/p-xylene"

rm -f ${JOBDIR}/*.nc

# Flat-bottom restraints, specifying AMBER .crd.
mpirun -np ${NP} -hostfile ${PBS_NODEFILE} python yank.py --complex_prmtop $JOBDIR/complex.prmtop  --receptor_prmtop $JOBDIR/receptor.prmtop --ligand_prmtop $JOBDIR/ligand.prmtop --complex_crd $JOBDIR/complex.crd --output $JOBDIR --mpi --restraints flat-bottom --verbose --iterations 10

# Flat-bottom restraints, specifying PDB.
#mpirun_rsh -ssh -np ${NP} -hostfile ${PBS_NODEFILE} python yank.py --complex_prmtop $JOBDIR/complex.prmtop  --receptor_prmtop $JOBDIR/receptor.prmtop --ligand_prmtop $JOBDIR/ligand.prmtop --complex_pdb $JOBDIR/complex.pdb --output $JOBDIR --mpi --restraints flat-bottom --verbose

# Harmonic restraints
#mpirun_rsh -ssh -np ${NP} -hostfile ${PBS_NODEFILE} python yank.py --complex_prmtop $JOBDIR/complex.prmtop --receptor_prmtop $JOBDIR/receptor.prmtop --ligand_prmtop $JOBDIR/ligand.prmtop --complex_crd $JOBDIR/complex.crd --output $JOBDIR --mpi --randomize_ligand --verbose