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Merge pull request #239 from OpenBioSim/backport_237
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Backport fix from PR #237
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@lohedges
lohedges authored Feb 8, 2024
2 parents 8dea6a8 + 37f52ed commit 4f140f7
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Showing 4 changed files with 299 additions and 83 deletions.
24 changes: 6 additions & 18 deletions python/BioSimSpace/FreeEnergy/_relative.py
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
######################################################################
# BioSimSpace: Making biomolecular simulation a breeze!
#
# Copyright: 2017-2023
# Copyright: 2017-2024
#
# Authors: Lester Hedges <[email protected]>
#
Expand Down Expand Up @@ -2060,9 +2060,7 @@ def _initialise_runner(self, system):
extra_lines=self._extra_lines,
property_map=self._property_map,
)
if self._setup_only:
del first_process
else:
if not self._setup_only:
processes.append(first_process)

# Loop over the rest of the lambda values.
Expand Down Expand Up @@ -2139,30 +2137,20 @@ def _initialise_runner(self, system):
f.write(line)

mdp = new_dir + "/gromacs.mdp"
mdp_out = new_dir + "/gromacs.out.mdp"
gro = new_dir + "/gromacs.gro"
top = new_dir + "/gromacs.top"
tpr = new_dir + "/gromacs.tpr"

# Use grompp to generate the portable binary run input file.
command = "%s grompp -f %s -po %s -c %s -p %s -r %s -o %s" % (
_gmx_exe,
_Process.Gromacs._generate_binary_run_file(
mdp,
mdp_out,
gro,
top,
gro,
tpr,
)

# Run the command. If this worked for the first lambda value,
# then it should work for all others.
proc = _subprocess.run(
_Utils.command_split(command),
shell=False,
text=True,
stdout=_subprocess.PIPE,
stderr=_subprocess.PIPE,
first_process._exe,
ignore_warnings=self._ignore_warnings,
show_errors=self._show_errors,
)

# Create a copy of the process and update the working
Expand Down
167 changes: 143 additions & 24 deletions python/BioSimSpace/Process/_gromacs.py
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
######################################################################
# BioSimSpace: Making biomolecular simulation a breeze!
#
# Copyright: 2017-2023
# Copyright: 2017-2024
#
# Authors: Lester Hedges <[email protected]>
#
Expand Down Expand Up @@ -421,40 +421,129 @@ def _generate_args(self):
if isinstance(self._protocol, (_Protocol.Metadynamics, _Protocol.Steering)):
self.setArg("-plumed", "plumed.dat")

def _generate_binary_run_file(self):
"""Use grommp to generate the binary run input file."""
@staticmethod
def _generate_binary_run_file(
mdp_file,
gro_file,
top_file,
ref_file,
tpr_file,
exe,
checkpoint_file=None,
ignore_warnings=False,
show_errors=True,
):
"""
Use grommp to generate the binary run input file.
Parameters
----------
mdp_file : str
The path to the input mdp file.
gro_file : str
The path to the input coordinate file.
top_file : str
The path to the input topology file.
ref_file : str
The path to the input reference coordinate file to be used for
position restraints.
tpr_file : str
The path to the output binary run file.
exe : str
The path to the GROMACS executable.
checkpoint_file : str
The path to a checkpoint file from a previous run. This can be used
to continue an existing simulation. Currently we only support the
use of checkpoint files for Equilibration protocols.
ignore_warnings : bool
Whether to ignore warnings when generating the binary run file
with 'gmx grompp'. By default, these warnings are elevated to
errors and will halt the program.
show_errors : bool
Whether to show warning/error messages when generating the binary
run file.
"""

if not isinstance(mdp_file, str):
raise ValueError("'mdp_file' must be of type 'str'.")
if not _os.path.isfile(mdp_file):
raise IOError(f"'mdp_file' doesn't exist: '{mdp_file}'")

if not isinstance(gro_file, str):
raise ValueError("'gro_file' must be of type 'str'.")
if not _os.path.isfile(gro_file):
raise IOError(f"'gro_file' doesn't exist: '{gro_file}'")

if not isinstance(top_file, str):
raise ValueError("'top_file' must be of type 'str'.")
if not _os.path.isfile(top_file):
raise IOError(f"'top_file' doesn't exist: '{top_file}'")

if not isinstance(ref_file, str):
raise ValueError("'ref_file' must be of type 'str'.")
if not _os.path.isfile(ref_file):
raise IOError(f"'ref_file' doesn't exist: '{ref_file}'")

if not isinstance(tpr_file, str):
raise ValueError("'tpr_file' must be of type 'str'.")

if not isinstance(exe, str):
raise ValueError("'exe' must be of type 'str'.")
if not _os.path.isfile(exe):
raise IOError(f"'exe' doesn't exist: '{exe}'")

if checkpoint_file is not None:
if not isinstance(checkpoint_file, str):
raise ValueError("'checkpoint_file' must be of type 'str'.")
if not _os.path.isfile(checkpoint_file):
raise IOError(f"'checkpoint_file' doesn't exist: '{checkpoint_file}'")

if not isinstance(ignore_warnings, bool):
raise ValueError("'ignore_warnings' must be of type 'bool'")

if not isinstance(show_errors, bool):
raise ValueError("'show_errors' must be of type 'bool'")

# Create the name of the output mdp file.
mdp_out = (
_os.path.dirname(self._config_file)
+ "/%s.out.mdp" % _os.path.basename(self._config_file).split(".")[0]
_os.path.dirname(mdp_file)
+ "/%s.out.mdp" % _os.path.basename(mdp_file).split(".")[0]
)

# Use grompp to generate the portable binary run input file.
if self._checkpoint_file is not None:
if checkpoint_file is not None:
command = "%s grompp -f %s -po %s -c %s -p %s -r %s -t %s -o %s" % (
self._exe,
self._config_file,
exe,
mdp_file,
mdp_out,
self._gro_file,
self._top_file,
self._gro_file,
self._checkpoint_file,
self._tpr_file,
gro_file,
top_file,
ref_file,
checkpoint_file,
tpr_file,
)
else:
command = "%s grompp -f %s -po %s -c %s -p %s -r %s -o %s" % (
self._exe,
self._config_file,
exe,
mdp_file,
mdp_out,
self._gro_file,
self._top_file,
self._gro_file,
self._tpr_file,
gro_file,
top_file,
ref_file,
tpr_file,
)

# Warnings don't trigger an error.
if self._ignore_warnings:
if ignore_warnings:
command += " --maxwarn 9999"

# Run the command.
Expand All @@ -469,7 +558,7 @@ def _generate_binary_run_file(self):
# Check that grompp ran successfully.
if proc.returncode != 0:
# Handle errors and warnings.
if self._show_errors:
if show_errors:
# Capture errors and warnings from the grompp output.
errors = []
warnings = []
Expand Down Expand Up @@ -531,14 +620,34 @@ def addToConfig(self, config):
super().addToConfig(config)

# Use grompp to generate the portable binary run input file.
self._generate_binary_run_file()
self._generate_binary_run_file(
self._config_file,
self._gro_file,
self._top_file,
self._gro_file,
self._tpr_file,
self._exe,
self._checkpoint_file,
self._ignore_warnings,
self._show_errors,
)

def resetConfig(self):
"""Reset the configuration parameters."""
self._generate_config()

# Use grompp to generate the portable binary run input file.
self._generate_binary_run_file()
self._generate_binary_run_file(
self._config_file,
self._gro_file,
self._top_file,
self._gro_file,
self._tpr_file,
self._exe,
self._checkpoint_file,
self._ignore_warnings,
self._show_errors,
)

def setConfig(self, config):
"""
Expand All @@ -556,7 +665,17 @@ def setConfig(self, config):
super().setConfig(config)

# Use grompp to generate the portable binary run input file.
self._generate_binary_run_file()
self._generate_binary_run_file(
self._config_file,
self._gro_file,
self._top_file,
self._gro_file,
self._tpr_file,
self._exe,
self._checkpoint_file,
self._ignore_warnings,
self._show_errors,
)

def start(self):
"""
Expand Down
22 changes: 6 additions & 16 deletions python/BioSimSpace/Sandpit/Exscientia/FreeEnergy/_alchemical_free_energy.py
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
######################################################################
# BioSimSpace: Making biomolecular simulation a breeze!
#
# Copyright: 2017-2023
# Copyright: 2017-2024
#
# Authors: Lester Hedges <[email protected]>
#
Expand Down Expand Up @@ -1373,7 +1373,7 @@ def _initialise_runner(self, system):
extra_lines=self._extra_lines,
)

if self._setup_only:
if self._setup_only and not self._engine == "GROMACS":
del first_process
else:
processes.append(first_process)
Expand Down Expand Up @@ -1462,30 +1462,20 @@ def _initialise_runner(self, system):
f.write(line)

mdp = new_dir + "/gromacs.mdp"
mdp_out = new_dir + "/gromacs.out.mdp"
gro = new_dir + "/gromacs.gro"
top = new_dir + "/gromacs.top"
tpr = new_dir + "/gromacs.tpr"

# Use grompp to generate the portable binary run input file.
command = "%s grompp -f %s -po %s -c %s -p %s -r %s -o %s" % (
self._exe,
_Process.Gromacs._generate_binary_run_file(
mdp,
mdp_out,
gro,
top,
gro,
tpr,
)

# Run the command. If this worked for the first lambda value,
# then it should work for all others.
proc = _subprocess.run(
_Utils.command_split(command),
shell=False,
text=True,
stdout=_subprocess.PIPE,
stderr=_subprocess.PIPE,
first_process._exe,
ignore_warnings=self._ignore_warnings,
show_errors=self._show_errors,
)

# Create a copy of the process and update the working
Expand Down
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