[Feat]: New Job Script energy_dist.sh

.flake8

@@ -232,6 +232,7 @@ rst-substitutions =
     Lmod,
     rsync,
     Gromacs,
+    edr_file,
     gro_file,
     log_file,
     mdp_file,

analysis/lintf2_ether/mdt/energy_dist.sh

@@ -0,0 +1,160 @@
+#!/bin/bash
+
+#SBATCH --time=0-02:00:00
+#SBATCH --job-name="mdt_energy_dist"
+#SBATCH --output="mdt_energy_dist_slurm-%j.out"
+#SBATCH --nodes=1
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=2G
+# 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="energy_dist"
+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
+
+########################################################################
+# Decompress input file(s) if necessary                                #
+########################################################################
+
+echo -e "\n"
+echo "Decompressing input file(s) if necessary..."
+infile="${settings}_out_${system}.edr"
+decompressed=$(bash \
+    "${bash_dir}/decompress.sh" \
+    "${infile}" \
+    --keep \
+    --verbose)
+
+########################################################################
+# Start the Analysis                                                   #
+########################################################################
+
+echo -e "\n"
+echo "================================================================="
+${py_exe} -u \
+    "${mdt_path}/scripts/gmx/plot_energy_dist.py" \
+    -f "${infile}" \
+    --plot-out "${settings}_${system}_${analysis}_${begin}-${end}frame.pdf" \
+    --stats-out "${settings}_${system}_${analysis}_${begin}-${end}frame.txt" \
+    -b "${begin}" \
+    -e "${end}" \
+    --every "${every}" \
+    --observables \
+        "Potential" \
+        "Kinetic En." \
+        "Total Energy" \
+        "Temperature" \
+        "Pressure" \
+    --num-points 1000 ||
+    exit
+echo "================================================================="
+
+echo -e "\n"
+echo "================================================================="
+${py_exe} -u \
+    "${mdt_path}/scripts/gmx/plot_energy_dist.py" \
+    -f "${infile}" \
+    --plot-out "${settings}_${system}_${analysis}_diff_${begin}-${end}frame.pdf" \
+    --stats-out "${settings}_${system}_${analysis}_diff_${begin}-${end}frame.txt" \
+    -b "${begin}" \
+    -e "${end}" \
+    --every "${every}" \
+    --observables \
+        "Potential" \
+        "Kinetic En." \
+        "Total Energy" \
+        "Temperature" \
+        "Pressure" \
+    --diff \
+    --num-points 1000 ||
+    exit
+echo "================================================================="
+
+########################################################################
+# Cleanup                                                              #
+########################################################################
+
+if [[ ${decompressed} -eq 1 ]]; then
+    echo -e "\n"
+    echo "Removing decompressed input file(s)..."
+    rm -v "${infile}"
+fi
+
+save_dir="${analysis}_slurm-${SLURM_JOB_ID}"
+if [[ ! -d ${save_dir} ]]; then
+    echo -e "\n"
+    mkdir -v "${save_dir}" || exit
+    mv -v \
+        "${settings}_${system}_${analysis}_${begin}-${end}frame.pdf" \
+        "${settings}_${system}_${analysis}_${begin}-${end}frame.txt" \
+        "${settings}_${system}_${analysis}_diff_${begin}-${end}frame.pdf" \
+        "${settings}_${system}_${analysis}_diff_${begin}-${end}frame.txt" \
+        "${settings}_${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"

analysis/lintf2_ether/mdt/submit_mdt_analyses_lintf2_ether.py

@@ -33,6 +33,9 @@
     space-separated as one enquoted string.  To list all possible script
     names type
     :bash:`ls path/to/hpc_submit_scripts/analysis/lintf2_ether/mdt/`.
+    Note that scripts that take an |edr_file| as input are excluded from
+    the number options unless they are explicitily mentioned to be
+    included.
 
         :0:     All scripts.  Note that all lig_change_at_pos_change*
                 scripts are excluded.
@@ -45,7 +48,8 @@
                 excluded, because msd_layer_serial.py (and
                 msd_layer_parallel.py) must first be fixed for
                 simulations with periodc boundary conditions in the
-                discretized direction.
+                discretized direction (see MDTools Issue
+                `#98 <https://github.com/andthum/mdtools/issues/98>`_).
         :2:     All scripts analyzing a slab in xy plane.
 
         :3:     discrete-z_Li and discrete-z_Li_state_lifetime_discrete.
@@ -297,6 +301,10 @@
     "topo_map_Li-OBT",
     "topo_map_Li-OE",
 )
+REQUIRE_EDR = (
+    # `${settings}_out_${system}.edr`
+    "energy_dist",
+)
 REQUIRE_XTC_WRAPPED = (
     # `${settings}_out_${system}_pbc_whole_mol.xtc`
     "axial_hex_dist_1nn_Li",
@@ -579,6 +587,7 @@ def _submit(sbatch_opts, job_script):
         required=True,
         help=(
             "The analysis script(s) to submit."
+            ""
             "  0 = All scripts.  Note that all lig_change_at_pos_change*"
             " scripts are excluded."
             "  1 = All scripts analyzing the bulk system (i.e. exclude scripts"
@@ -858,6 +867,7 @@ def _submit(sbatch_opts, job_script):
     gmx_infile_pattern = args["settings"] + "_" + args["system"]
     gmx_outfile_pattern = args["settings"] + "_out_" + args["system"]
     TPR_FILE = gmx_infile_pattern + ".tpr"
+    EDR_FILE = gmx_outfile_pattern + ".edr"
     GRO_FILE = gmx_outfile_pattern + ".gro"
     XTC_FILE_WRAPPED = gmx_outfile_pattern + "_pbc_whole_mol.xtc"
     XTC_FILE_UNWRAPPED = gmx_outfile_pattern + "_pbc_whole_mol_nojump.xtc"
@@ -937,6 +947,8 @@ def _submit(sbatch_opts, job_script):
     for script in args["scripts"].split():
         if script in REQUIRE_TPR:
             files.setdefault("run input", TPR_FILE)
+        if script in REQUIRE_EDR:
+            files.setdefault("energy", gmx.get_compressed_file(EDR_FILE))
         if script in REQUIRE_XTC_WRAPPED:
             files.setdefault("wrapped compressed trajectory", XTC_FILE_WRAPPED)
         if script in REQUIRE_XTC_UNWRAPPED:
@@ -1158,6 +1170,7 @@ def _submit(sbatch_opts, job_script):
         "discrete-z_Li_state_lifetime_discrete": (
             posargs_general + [posargs_trj[4]]
         ),
+        "energy_dist": posargs_general + posargs_trj[:3],
         "lifetime_autocorr_Li-ether": (
             posargs_general
             + posargs_trj
@@ -1356,6 +1369,9 @@ def _submit(sbatch_opts, job_script):
                 "renewal_events_Li-NTf2",
             ):
                 continue
+            if batch_script == "energy_dist":
+                # Exlcude all scripts that take an .edr file as input.
+                continue
             if "lig_change_at_pos_change" in batch_script:
                 # Exclude all lig_change_at_pos_change* scripts.
                 continue

docs/source/conf.py

@@ -165,6 +165,8 @@
     :raw-html:`<a href="https://rsync.samba.org/">rsync</a>`
 .. |Gromacs| replace::
     :raw-html:`<a href="https://manual.gromacs.org/">Gromacs</a>`
+.. |edr_file| replace::
+    :raw-html:`<a href="https://manual.gromacs.org/documentation/current/reference-manual/file-formats.html#edr">.edr file</a>`
 .. |gro_file| replace::
     :raw-html:`<a href="https://manual.gromacs.org/documentation/current/reference-manual/file-formats.html#gro">.gro file</a>`
 .. |log_file| replace::

python/gmx.py

@@ -37,7 +37,7 @@ def get_box_from_gro(fname):
 
 def get_compressed_file(fname):
     """
-    Check if the input file or a compressed version it exsists.
+    Check if the input file or a compressed version of it exsists.
 
     Check if the input file exsists.  If it does not exist, check
     whether a file with the same name but with one of the following

simulation/gmx/submit_gmx_mdrun.py

@@ -229,7 +229,9 @@
         " directory structure of this project".format(PYTHON_DIR)
     )
 sys.path.insert(1, PYTHON_DIR)
-# Third-party libraries
+
+
+# First-party libraries
 import gmx  # noqa: E402
 import opthandler  # noqa: E402
 import strng  # noqa: E402