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[submit_gmx_analyses_lintf2_ether.py]: Replace --every Option by Gromacs-Specific --skip and --dt Options #126

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Merged
andthum merged 2 commits into from
Jun 22, 2023
Merged

[submit_gmx_analyses_lintf2_ether.py]: Replace --every Option by Gromacs-Specific --skip and --dt Options #126

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22e573e
[submit_gmx_analyses_lintf2_ether.py]: Replace `--every` by `--skip` …
andthum Jun 22, 2023
7ad3ba4
[energy.sh]: Add `-skip` Option to the Call of `gmx energy`
andthum Jun 22, 2023
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5 changes: 4 additions & 1 deletion analysis/lintf2_ether/gmx/energy.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,7 @@ system=${4} # The name of the system to analyze
settings=${5} # The used simulation settings
begin=${6} # First frame to read from trajectory in ps
end=${7} # Last frame to read from trajectory in ps
skip=${8} # Skip every n-th frame

echo -e "\n"
echo "Parsed arguments:"
Expand All @@ -42,6 +43,7 @@ echo "system = ${system}"
echo "settings = ${settings}"
echo "begin = ${begin}"
echo "end = ${end}"
echo "skip = ${skip}"

if [[ ! -d ${bash_dir} ]]; then
echo
Expand Down Expand Up @@ -98,7 +100,8 @@ echo -e \
-s "${settings}_${system}.tpr" \
-o "${outfile}" \
-b "${begin}" \
-e "${end}" ||
-e "${end}" \
-skip "${skip}" ||
exit
echo "================================================================="

Expand Down
92 changes: 55 additions & 37 deletions analysis/lintf2_ether/gmx/submit_gmx_analyses_lintf2_ether.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,13 +56,16 @@
Last frame (in ps) to read from trajectory. Default: Last frame in
:file:`${settings}_out_${system}.log`. Reading from |log_file|\s
compressed with gzip, bzip2, XZ or LZMA is supported.
--every
Read every n-th frame from the trajectory. The value given here is
passed to the -skip option of the submitted Gromacs tools that
support this option. If the -skip option is not supported, the
value of \--every is passed to the -dt option. For Gromacs tools
that do not support either of the two options, \--every has no
effect. Default: ``1``.
--skip
Read every n-th frame from the trajectory. Takes precedence over
`--dt` for Gromacs tools that support the `-skip` option. Has no
effect for Gromacs tools that do not support the `-skip` option.
Default: ``1``.
--dt
Only read frames when ``t_frame % dt == t0`` (all times in ps). If
you want all frames to be read, set --dt to the time step between
two trajectory frames. Has no effect for Gromacs tools that do not
support the `-dt` option. Default: ``1``.

Options for MSD Calculation
^^^^^^^^^^^^^^^^^^^^^^^^^^^
Expand Down Expand Up @@ -458,12 +461,25 @@ def _submit(sbatch_opts, job_script):
),
)
parser_trj_reading.add_argument(
"--every",
"--skip",
type=int,
required=False,
default=1,
help=(
"Read every n-th frame from the trajectory. Default: %(default)s."
"Read every n-th frame from the trajectory. Takes precedence over"
" --dt for Gromacs tools that support the -skip option. Default:"
" %(default)s."
),
)
parser_trj_reading.add_argument(
"--dt",
type=float,
required=False,
default=1,
help=(
"Only read frames when ``t_frame % dt == t0`` (all times in ps)."
" Has no effect for Gromacs tools that do not support the -dt"
" option. Default: %(default)s."
),
)
parser_msd = parser.add_argument_group(title="Options for MSD Calculation")
Expand Down Expand Up @@ -771,56 +787,58 @@ def _submit(sbatch_opts, job_script):
args["system"],
args["settings"],
]
posargs_trj = [args["begin"], args["end"], args["every"]]
posargs_trj = [args["begin"], args["end"]]
posargs_trj_skip = posargs_trj + [args["skip"]]
posargs_trj_dt = posargs_trj + [args["dt"]]
posargs_msd = [args["beginfit"], args["endfit"], args["restart"]]
posargs_dist = [args["binwidth"]]
posargs_slab = [args["zmin"], args["zmax"]]
# Position arguments must be in the right order for each job script.
posargs = {
"density-z_charge": posargs_general + posargs_trj + [nbins],
"density-z_mass": posargs_general + posargs_trj + [nbins],
"density-z_number": posargs_general + posargs_trj + [nbins],
"density-z_charge": posargs_general + posargs_trj_dt + [nbins],
"density-z_mass": posargs_general + posargs_trj_dt + [nbins],
"density-z_number": posargs_general + posargs_trj_dt + [nbins],
"densmap-z_gra": (
posargs_general + posargs_trj + posargs_dist + posargs_slab
posargs_general + posargs_trj_dt + posargs_dist + posargs_slab
),
"densmap-z_Li": (
posargs_general + posargs_trj + posargs_dist + posargs_slab
posargs_general + posargs_trj_dt + posargs_dist + posargs_slab
),
"densmap-z_NBT": (
posargs_general + posargs_trj + posargs_dist + posargs_slab
posargs_general + posargs_trj_dt + posargs_dist + posargs_slab
),
"densmap-z_OBT": (
posargs_general + posargs_trj + posargs_dist + posargs_slab
posargs_general + posargs_trj_dt + posargs_dist + posargs_slab
),
"densmap-z_OE": (
posargs_general + posargs_trj + posargs_dist + posargs_slab
posargs_general + posargs_trj_dt + posargs_dist + posargs_slab
),
"energy": posargs_general + posargs_trj[:2],
"energy": posargs_general + posargs_trj_skip,
"make_ndx": posargs_general,
"msd": posargs_general + posargs_trj[:2] + posargs_msd,
"msd_electrodes": posargs_general + posargs_trj[:2] + posargs_msd,
"msd_lateral-z": posargs_general + posargs_trj[:2] + posargs_msd,
"msd_parallel-z": posargs_general + posargs_trj[:2] + posargs_msd,
"msd_tensor": posargs_general + posargs_trj[:2] + posargs_msd,
"polystat": posargs_general + posargs_trj,
"potential-z": posargs_general + posargs_trj + [nbins],
"rdf_ether-com": posargs_general + posargs_trj + posargs_dist,
"rdf_Li": posargs_general + posargs_trj + posargs_dist,
"rdf_Li-com": posargs_general + posargs_trj + posargs_dist,
"rdf_NBT": posargs_general + posargs_trj + posargs_dist,
"rdf_NTf2-com": posargs_general + posargs_trj + posargs_dist,
"rdf_OE": posargs_general + posargs_trj + posargs_dist,
"msd": posargs_general + posargs_trj + posargs_msd,
"msd_electrodes": posargs_general + posargs_trj + posargs_msd,
"msd_lateral-z": posargs_general + posargs_trj + posargs_msd,
"msd_parallel-z": posargs_general + posargs_trj + posargs_msd,
"msd_tensor": posargs_general + posargs_trj + posargs_msd,
"polystat": posargs_general + posargs_trj_dt,
"potential-z": posargs_general + posargs_trj_dt + [nbins],
"rdf_ether-com": posargs_general + posargs_trj_dt + posargs_dist,
"rdf_Li": posargs_general + posargs_trj_dt + posargs_dist,
"rdf_Li-com": posargs_general + posargs_trj_dt + posargs_dist,
"rdf_NBT": posargs_general + posargs_trj_dt + posargs_dist,
"rdf_NTf2-com": posargs_general + posargs_trj_dt + posargs_dist,
"rdf_OE": posargs_general + posargs_trj_dt + posargs_dist,
"rdf_slab-z_Li": (
posargs_general + posargs_trj + posargs_dist + posargs_slab
posargs_general + posargs_trj_dt + posargs_dist + posargs_slab
),
"rdf_slab-z_NBT": (
posargs_general + posargs_trj + posargs_dist + posargs_slab
posargs_general + posargs_trj_dt + posargs_dist + posargs_slab
),
"rdf_slab-z_OE": (
posargs_general + posargs_trj + posargs_dist + posargs_slab
posargs_general + posargs_trj_dt + posargs_dist + posargs_slab
),
"trjconv_nojump": posargs_general + posargs_trj,
"trjconv_whole": posargs_general + posargs_trj,
"trjconv_nojump": posargs_general + posargs_trj_skip,
"trjconv_whole": posargs_general + posargs_trj_skip,
}
posargs = {
k: opthandler.posargs2str(v, prec=ARG_PREC) for k, v in posargs.items()
Expand Down