andthum · andthum · Jan 19, 2023 · Jan 18, 2023 · Jan 18, 2023 · Jan 19, 2023
diff --git a/.flake8 b/.flake8
@@ -236,6 +236,7 @@ rst-substitutions =
     gro_file,
     log_file,
     mdp_file,
+    trr_file,
     Python,
     PyPI,
     pip,

diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -4,35 +4,73 @@
     "autoDocstring.startOnNewLine": true,
     "black-formatter.importStrategy": "fromEnvironment",
     "cSpell.ignoreWords": [
+        "Andreas",
         "Bagheera",
+        "DTRJ",
+        "Gromacs",
         "Heuer",
         "Münster",
+        "PREC",
+        "Parrinello",
         "REAMDE",
+        "Rahman",
         "Slurm",
+        "TFSI",
+        "Thum",
+        "afterok",
+        "argparser",
+        "autocorr",
+        "autocorrelations",
         "autoupdate",
+        "barostat",
+        "binwidth",
         "builtins",
         "colorama",
+        "densmap",
+        "dimethyl",
+        "discretizations",
         "docstrings",
+        "enquoted",
+        "foss",
         "genindex",
         "hpcss",
+        "infile",
         "isort",
+        "jobname",
+        "lintf",
+        "lmod",
         "markdownlint",
         "mastertoc",
         "maxdepth",
+        "mdtools",
         "mksh",
         "modindex",
+        "nblocks",
+        "nojump",
         "noqa",
         "numpy",
+        "optdict",
+        "opthandler",
+        "polystat",
+        "posargs",
         "posix",
         "pymodules",
         "pyproject",
         "pytest",
         "sbatch",
         "shellcheck",
         "shfmt",
+        "slabwidth",
+        "strng",
+        "subproc",
+        "subvolume",
         "texlive",
         "titlesonly",
-        "toctree"
+        "toctree",
+        "topo",
+        "trjconv",
+        "zmax",
+        "zmin"
     ],
     "cSpell.language": "en",
     "cSpell.validateDirectives": true,
@@ -134,10 +172,13 @@
     "markdown.updateLinksOnFileMove.enabled": "prompt",
     "markdown.validate.enabled": true,
     "[python]": {
-        "editor.codeActionsOnSave": {
-            // Format import statements with isort.
-            "source.organizeImports": true,
-        },
+        // Somehow, the ms-python.isort removes blank lines before
+        // comments everywhere in the code.  Therefore, sorting imports
+        // on file save is disabled for now.
+        // "editor.codeActionsOnSave": {
+        //     // Format import statements with isort.
+        //     "source.organizeImports": true,
+        // },
         "editor.defaultFormatter": "ms-python.black-formatter",
     },
     "python.defaultInterpreterPath": "python3",

diff --git a/analysis/lintf2_ether/mdt/.cleanup_mdt_analyses.sh b/analysis/lintf2_ether/mdt/.cleanup_mdt_analyses.sh
@@ -17,10 +17,19 @@ gather() {
 }
 
 mv create_mda_universe_slurm-* create_mda_universe
+mv energy_dist_slurm-* energy_dist
+mv subvolume_charge_slurm-* subvolume_charge
 
 gather discrete-z
 gather lifetime_autocorr
 
+name=attribute_hist
+for cmp in Li NBT OBT OE NTf2 ether; do
+    gather "${name}"_"${cmp}"
+done
+mkdir "${name}" || exit
+mv "${name}"_* "${name}"/
+
 name=axial_hex_dist
 for cmp in 1nn 2nn; do
     gather "${name}"_"${cmp}"

diff --git a/analysis/lintf2_ether/mdt/attribute_hist_Li.sh b/analysis/lintf2_ether/mdt/attribute_hist_Li.sh
@@ -0,0 +1,127 @@
+#!/bin/bash
+
+#SBATCH --time=7-00:00:00
+#SBATCH --job-name="mdt_attribute_hist_Li"
+#SBATCH --output="mdt_attribute_hist_Li_slurm-%j.out"
+#SBATCH --nodes=1
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=4G
+# The above options are only default values that can be overwritten by
+# command-line arguments
+
+# MIT License
+# Copyright (c) 2021, 2022  All authors listed in the file AUTHORS.rst
+
+# This script is meant to be submitted by
+# submit_mdt_analyses_lintf2_ether.py
+
+analysis="attribute_hist_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
+
+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}"
+
+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                                                   #
+########################################################################
+
+attributes="velocities forces positions"
+components="x y z xyz norm"
+for attr in ${attributes}; do
+    echo -e "\n"
+    echo "Attribute: ${attr}"
+    echo "============================================================="
+    ${py_exe} -u \
+        "${mdt_path}/scripts/other/attribute_hist.py" \
+        -f "${settings}_out_${system}.trr" \
+        -s "${settings}_${system}.tpr" \
+        -o "${settings}_${system}_${analysis}_${attr}" \
+        -b "${begin}" \
+        -e "${end}" \
+        --every "${every}" \
+        --sel "type Li" \
+        --attribute "${attr}" ||
+        exit
+    echo "============================================================="
+    echo -e "\n"
+    for comp in ${components}; do
+        gzip --best --verbose \
+            "${settings}_${system}_${analysis}_${attr}_${comp}.txt"
+    done
+done
+
+########################################################################
+# Cleanup                                                              #
+########################################################################
+
+save_dir="${analysis}_slurm-${SLURM_JOB_ID}"
+if [[ ! -d ${save_dir} ]]; then
+    echo -e "\n"
+    mkdir -v "${save_dir}" || exit
+    for attr in ${attributes}; do
+        for comp in ${components}; do
+            f="${settings}_${system}_${analysis}_${attr}_${comp}.txt.gz"
+            mv -v "${f}" "${save_dir}"
+        done
+    done
+    mv -v \
+        "${settings}_${system}_${analysis}_slurm-${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"
diff --git a/analysis/lintf2_ether/mdt/attribute_hist_NBT.sh b/analysis/lintf2_ether/mdt/attribute_hist_NBT.sh
@@ -0,0 +1,127 @@
+#!/bin/bash
+
+#SBATCH --time=7-00:00:00
+#SBATCH --job-name="mdt_attribute_hist_NBT"
+#SBATCH --output="mdt_attribute_hist_NBT_slurm-%j.out"
+#SBATCH --nodes=1
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=4G
+# The above options are only default values that can be overwritten by
+# command-line arguments
+
+# MIT License
+# Copyright (c) 2021, 2022  All authors listed in the file AUTHORS.rst
+
+# This script is meant to be submitted by
+# submit_mdt_analyses_lintf2_ether.py
+
+analysis="attribute_hist_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
+
+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}"
+
+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                                                   #
+########################################################################
+
+attributes="velocities forces positions"
+components="x y z xyz norm"
+for attr in ${attributes}; do
+    echo -e "\n"
+    echo "Attribute: ${attr}"
+    echo "============================================================="
+    ${py_exe} -u \
+        "${mdt_path}/scripts/other/attribute_hist.py" \
+        -f "${settings}_out_${system}.trr" \
+        -s "${settings}_${system}.tpr" \
+        -o "${settings}_${system}_${analysis}_${attr}" \
+        -b "${begin}" \
+        -e "${end}" \
+        --every "${every}" \
+        --sel "type NBT" \
+        --attribute "${attr}" ||
+        exit
+    echo "============================================================="
+    echo -e "\n"
+    for comp in ${components}; do
+        gzip --best --verbose \
+            "${settings}_${system}_${analysis}_${attr}_${comp}.txt"
+    done
+done
+
+########################################################################
+# Cleanup                                                              #
+########################################################################
+
+save_dir="${analysis}_slurm-${SLURM_JOB_ID}"
+if [[ ! -d ${save_dir} ]]; then
+    echo -e "\n"
+    mkdir -v "${save_dir}" || exit
+    for attr in ${attributes}; do
+        for comp in ${components}; do
+            f="${settings}_${system}_${analysis}_${attr}_${comp}.txt.gz"
+            mv -v "${f}" "${save_dir}"
+        done
+    done
+    mv -v \
+        "${settings}_${system}_${analysis}_slurm-${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"