New Slurm Job Scripts densmap-z_*.sh to Run the MDTools Script densmap.py

analysis/lintf2_ether/gmx/.cleanup_gmx_analyses.sh

@@ -24,13 +24,51 @@ gather() {
     fi
 }
 
+gather_cmps() {
+    # Gather output of similar analyses scripts ordered by compounds
+    # into sub-directories.
+    local root="${1}"
+    local cmps="${2}"
+
+    # Create "root" directory.
+    if [[ -d ${root} ]]; then
+        echo "WARNING: Directory already exists: '${root}'"
+        return 0
+    else
+        mkdir "${root}/" || exit
+    fi
+
+    # Move all "compound" directories to the root directory.
+    for cmp in ${cmps}; do
+        if [[ -n $(find . -maxdepth 1 -type d -name "${root}_${cmp}*_slurm-[0-9]*" -print -quit) ]]; then
+            mv "${root}_${cmp}"*_slurm-[0-9]*/ "${root}/" || exit
+        fi
+    done
+
+    # Check if the root directory is empty.
+    if [[ -n $(find "${root}/" -prune -empty) ]]; then
+        echo "WARNING: No directory matching pattern '${root}_<compound>*_slurm-[0-9]*'"
+        rm -r "${root:?}/" || exit
+        return 0
+    fi
+
+    # Gather all compound analyses.
+    cd "${root}/" || exit
+    for cmp in ${cmps}; do
+        gather "${root}_${cmp}"
+    done
+    cd ../ || exit
+}
+
 gather "density-z"
-gather "densmap-z"
 gather "energy"
 gather "make_ndx"
 gather "msd"
 gather "polystat"
 gather "potential-z"
-gather "rdf_slab-z"
-gather "rdf"
 gather "trjconv"
+
+gather_cmps "densmap-z" "gra Li NBT OBT OE"
+
+gather_cmps "rdf_slab-z" "Li-com NTf2-com ether-com Li NBT OE"
+gather "rdf"

analysis/lintf2_ether/gmx/submit_gmx_analyses_lintf2_ether.py

@@ -281,7 +281,14 @@ def _assemble_submit_cmd(sbatch_opts, job_script):
     if "output" not in sbatch_opts and "o" not in sbatch_opts:
         sbatch_output = " --output " + gmx_infile_pattern + "_"
         submit += sbatch_output + job_script + "_slurm-%j.out"
-    submit += " " + job_script + ".sh " + posargs[job_script]
+    job_script_path = os.path.abspath(os.path.join(FILE_ROOT, job_script))
+    job_script_path += ".sh"
+    if not os.path.isfile(job_script_path):
+        raise FileNotFoundError(
+            "No such file: '{}'.  This might happen if you change the"
+            " directory structure of this project".format(job_script_path)
+        )
+    submit += " " + job_script_path + posargs[job_script]
     return submit
 
 
@@ -348,7 +355,14 @@ def _submit_discretized(sbatch_opts, job_script, bins):
         posargs_tmp = opthandler.posargs2str(
             posargs[job_script] + slab, prec=ARG_PREC
         )
-        submit += " " + job_script + ".sh " + posargs_tmp
+        job_script_path = os.path.abspath(os.path.join(FILE_ROOT, job_script))
+        job_script_path += ".sh "
+        if not os.path.isfile(job_script_path):
+            raise FileNotFoundError(
+                "No such file: '{}'.  This might happen if you change the"
+                " directory structure of this project".format(job_script_path)
+            )
+        submit += " " + job_script_path + posargs_tmp
         subproc.check_output(shlex.split(submit))
         n_jobs_submitted += 1
     return n_jobs_submitted

analysis/lintf2_ether/mdt/.cleanup_mdt_analyses.sh

@@ -70,6 +70,7 @@ gather "subvolume_charge"
 
 gather_cmps "attribute_hist" "Li NBT OBT OE NTf2 ether"
 gather_cmps "axial_hex_dist" "1nn 2nn"
+gather_cmps "densmap-z" "Li NBT OBT OE NTf2 ether"
 gather_cmps "renewal_events" "Li-ether Li-NTf2"
 gather_cmps "topo_map" "Li-OBT Li-OE"
 

analysis/lintf2_ether/mdt/densmap-z_Li.sh

@@ -0,0 +1,126 @@
+#!/bin/bash
+
+#SBATCH --time=0-02:00:00
+#SBATCH --job-name="mdt_densmap-z_Li"
+#SBATCH --output="mdt_densmap-z_Li_slurm-%j.out"
+#SBATCH --nodes=1
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=512M
+# 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_Li"
+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 Li" \
+    --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"

analysis/lintf2_ether/mdt/densmap-z_NBT.sh

@@ -0,0 +1,126 @@
+#!/bin/bash
+
+#SBATCH --time=0-02:00:00
+#SBATCH --job-name="mdt_densmap-z_NBT"
+#SBATCH --output="mdt_densmap-z_NBT_slurm-%j.out"
+#SBATCH --nodes=1
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=512M
+# 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_NBT"
+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 NBT" \
+    --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"