[densmap-z_NBT.sh]: Create

Create a Slurm job script that runs the MDTools script
`scripts/structure/densmap.py` for nitrogen atoms of PEO chains.

Author: andthum

analysis/lintf2_ether/mdt/densmap-z_ether.sh

@@ -0,0 +1,128 @@
+#!/bin/bash
+
+#SBATCH --time=1-00:00:00
+#SBATCH --job-name="mdt_densmap-z_ether"
+#SBATCH --output="mdt_densmap-z_ether_slurm-%j.out"
+#SBATCH --nodes=1
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=8G
+# The above options are only default values that can be overwritten by
+# command-line arguments
+
+# MIT License
+# Copyright (c) 2021-2023  All authors listed in the file AUTHORS.rst
+
+# This script is meant to be submitted by
+# submit_mdt_analyses_lintf2_ether.py
+
+analysis="densmap-z_ether"
+thisfile=$(basename "${BASH_SOURCE[0]}")
+echo "${thisfile}"
+start_time=$(date --rfc-3339=seconds || exit)
+echo "Start time = ${start_time}"
+
+########################################################################
+# Argument Parsing                                                     #
+########################################################################
+
+bash_dir=${1}   # Directory containing bash scripts used by this script
+py_lmod=${2}    # File containing the modules to load Python
+py_exe=${3}     # Name of the Python executable
+mdt_path=${4}   # Path to the MDTools installation
+system=${5}     # The name of the system to analyze
+settings=${6}   # The used simulation settings
+begin=${7}      # First frame to read.  Frame numbering starts at 0
+end=${8}        # Last frame to read (exclusive)
+every=${9}      # Read every n-th frame
+bin_width=${10} # Grid size in the investigated plane in Angstrom
+zmin=${11}      # Only atoms in a slab in the xy-plane between zmin
+zmax=${12}      # and zmax are considered (in Angstrom)
+
+echo -e "\n"
+echo "Parsed arguments:"
+echo "bash_dir  = ${bash_dir}"
+echo "py_lmod   = ${py_lmod}"
+echo "py_exe    = ${py_exe}"
+echo "mdt_path  = ${mdt_path}"
+echo "system    = ${system}"
+echo "settings  = ${settings}"
+echo "begin     = ${begin}"
+echo "end       = ${end}"
+echo "every     = ${every}"
+echo "bin_width = ${bin_width}"
+echo "zmin      = ${zmin}"
+echo "zmax      = ${zmax}"
+
+if [[ ! -d ${bash_dir} ]]; then
+    echo
+    echo "ERROR: No such directory: '${bash_dir}'"
+    exit 1
+fi
+
+echo -e "\n"
+bash "${bash_dir}/echo_slurm_output_environment_variables.sh"
+
+########################################################################
+# Load required executable(s)                                          #
+########################################################################
+
+# shellcheck source=/dev/null
+source "${bash_dir}/load_python.sh" "${py_lmod}" "${py_exe}" || exit
+
+########################################################################
+# Start the Analysis                                                   #
+########################################################################
+
+echo -e "\n"
+echo "================================================================="
+${py_exe} -u \
+    "${mdt_path}/scripts/structure/densmap.py" \
+    -f "${settings}_out_${system}_pbc_whole_mol.xtc" \
+    -s "${settings}_${system}.tpr" \
+    -o "${settings}_${system}_${analysis}_${zmin}-${zmax}A.txt.gz" \
+    -b "${begin}" \
+    -e "${end}" \
+    --every "${every}" \
+    --sel "type ether" \
+    --cmp "residues" \
+    --center "com" \
+    --direction "z" \
+    --min "${zmin}" \
+    --max "${zmax}" \
+    --grid-spacing "${bin_width}" ||
+    exit
+echo "================================================================="
+
+########################################################################
+# Cleanup                                                              #
+########################################################################
+
+echo -e "\n"
+mv -v \
+    "${settings}_${system}_${analysis}_slurm-${SLURM_JOB_ID}.out" \
+    "${settings}_${system}_${analysis}_${zmin}-${zmax}A_slurm-${SLURM_JOB_ID}.out"
+
+save_dir="${analysis}_${zmin}-${zmax}A_slurm-${SLURM_JOB_ID}"
+if [[ ! -d ${save_dir} ]]; then
+    echo -e "\n"
+    mkdir -v "${save_dir}" || exit
+    mv -v \
+        "${settings}_${system}_${analysis}_${zmin}-${zmax}A.txt.gz" \
+        "${settings}_${system}_${analysis}_${zmin}-${zmax}A_slurm-${SLURM_JOB_ID}.out" \
+        "${save_dir}"
+    bash "${bash_dir}/cleanup_analysis.sh" \
+        "${system}" \
+        "${settings}" \
+        "${save_dir}" \
+        "mdt"
+fi
+
+end_time=$(date --rfc-3339=seconds)
+elapsed_time=$(bash \
+    "${bash_dir}/date_time_diff.sh" \
+    -s "${start_time}" \
+    -e "${end_time}")
+echo -e "\n"
+echo "End time     = ${end_time}"
+echo "Elapsed time = ${elapsed_time}"
+echo "${thisfile} done"