#!/bin/bash

#SBATCH --time=1-00:00:00
#SBATCH --ntasks-per-node=1
#SBATCH --mem=16GB
#SBATCH --partition=cpu
#SBATCH --qos=cpu
#SBATCH --job-name=run_caver
#SBATCH --output=%x.o%j
#SBATCH --error=%x.e%j

echo "JOB NAME    : $SLURM_JOB_NAME"
echo "PARTITION   : $SLURM_JOB_PARTITION"
echo "MEMORY      : $SLURM_MEM_PER_NODE MB"
echo "HOSTNAME    : $HOSTNAME"

module load caver

# MAX_HEAP_MEM: specification of maximum Java heap size (DON'T CHANGE)
MAX_HEAP_MEM="$(($SLURM_MEM_PER_NODE*90/100))m" #calculated as 90% of slurm memory requested

#----------------EDIT BELOW-------------------------------------------------------------------------------------
# PDB_DIR: directory of pdb files (input files)
PDB_DIR="$CAVER_DIR/examples/QUICK_START/md_snapshots"
# OUT_DIR: directory of output files
OUT_DIR="$HOME/out2"
# CONFIG_EXAMPLE: path to the CAVER configuration file (config.txt). This parameter is optional—if not specified
# Path_to_caver_home/config.txt will be used
CONFIG_EXAMPLE="$CAVER_DIR/examples/QUICK_START/inputs/config.txt"
#--------------------------------------------------------------------------------------------------------------

mkdir -p "$OUT_DIR"

java -Xmx${MAX_HEAP_MEM} -cp "$CAVER_DIR/caver/lib" -jar "$CAVER_DIR/caver/caver.jar" -home "$CAVER_DIR/caver" \
-pdb "$PDB_DIR" -conf "$CONFIG_EXAMPLE" -out "$OUT_DIR"