# -*- coding: utf-8 -*-
# Copyright (c) 2023, PyRETIS Development Team.
# Distributed under the LGPLv2.1+ License. See LICENSE for more info.
"""A GROMACS external MD integrator interface.
This module defines a class for using GROMACS as an external engine.
Important classes defined here
------------------------------
GromacsEngine (:py:class:`.GromacsEngine`)
A class responsible for interfacing GROMACS.
"""
import logging
import os
import shlex
from pyretis.core.box import box_matrix_to_list
from pyretis.engines.external import ExternalMDEngine
from pyretis.inout.settings import look_for_input_files
from pyretis.inout.formats.gromacs import (
read_gromos96_file,
read_gromacs_gro_file,
write_gromacs_gro_file,
write_gromos96_file,
read_xvg_file,
read_trr_frame,
)
logger = logging.getLogger(__name__) # pylint: disable=invalid-name
logger.addHandler(logging.NullHandler())
[docs]class GromacsEngine(ExternalMDEngine):
"""
A class for interfacing GROMACS.
This class defines the interface to GROMACS.
Attributes
----------
gmx : string
The command for executing GROMACS. Note that we are assuming
that we are using version 5 (or later) of GROMACS.
mdrun : string
The command for executing GROMACS mdrun. In some cases, this
executable can be different from ``gmx mdrun``.
mdrun_c : string
The command for executing GROMACS mdrun when continuing a
simulation. This is derived from the ``mdrun`` command.
input_path : string
The directory where the input files are stored.
subcycles : int,
The number of simulation steps of the external engine for each
PyRETIS step (e.g. interaction between the softwares frequency)
exe_path : string, optional
The absolute path at which the main PyRETIS simulation will be run.
maxwarn : integer
Setting for the GROMACS ``grompp -maxwarn`` option.
gmx_format : string
This string selects the output format for GROMACS.
write_vel : boolean, optional
True if we want to output the velocities.
write_force : boolean, optional
True if we want to output the forces.
domain_decomp: boolean, optional
Whether gromacs uses domain decomposition (DD) or not. This
does not set domain decomposition. The user should know whether
DD is executed or not.
"""
[docs] def __init__(self, gmx, mdrun, input_path, timestep, subcycles,
exe_path=os.path.abspath('.'),
maxwarn=0, gmx_format='gro',
write_vel=True,
write_force=False,
domain_decomp=False):
"""Set up the GROMACS engine.
Parameters
----------
gmx : string
The GROMACS executable.
mdrun : string
The GROMACS mdrun executable.
input_path : string
The absolute path to where the input files are stored.
timestep : float
The time step used in the GROMACS MD simulation.
subcycles : integer
The number of steps each GROMACS MD run is composed of.
exe_path : string, optional
The absolute path at which the main PyRETIS simulation will be run.
maxwarn : integer, optional
Setting for the GROMACS ``grompp -maxwarn`` option.
gmx_format : string, optional
The format used for GROMACS configurations.
write_vel : boolean, optional
Determines if GROMACS should write velocities or not.
write_force : boolean, optional
Determines if GROMACS should write forces or not.
domain_decomp: boolean, optional
Whether domain decomposition (DD) is executed by GROMACS or not.
User should know if this happens or not.
"""
super().__init__('GROMACS engine', timestep, subcycles)
self.ext = gmx_format
if self.ext not in ('g96', 'gro'):
msg = 'Unknown GROMACS format: "%s"'
logger.error(msg, self.ext)
raise ValueError(msg % self.ext)
# Define the GROMACS GMX command:
self.gmx = gmx
# Define GROMACS GMX MDRUN commands:
self.mdrun = mdrun + ' -s {} -deffnm {} -c {}'
# This is for continuation of a GROMACS simulation:
self.mdrun_c = mdrun + ' -s {} -cpi {} -append -deffnm {} -c {}'
# Whether DD is used or not:
self.domain_decomp = domain_decomp
self.ext_time = self.timestep * self.subcycles
self.maxwarn = maxwarn
# Define the energy terms, these are hard-coded, but
# here we open up for changing that:
self.energy_terms = self.select_energy_terms('path')
self.input_path = os.path.join(exe_path, input_path)
# Set the defaults input files:
default_files = {
'conf': f'conf.{self.ext}',
'input_o': 'grompp.mdp', # "o" = original input file.
'topology': 'topol.top'}
extra_files = {
'index': 'index.ndx',
}
# An user doesn't need to have problems with g96 and mdtraj.
file_g = os.path.join(self.input_path, 'conf.')
if self.ext == 'gro':
self.top, _, _, _ = read_gromacs_gro_file(file_g+self.ext)
elif self.ext == 'g96':
if not os.path.isfile(file_g+'gro'):
cmd = [self.gmx, 'editconf',
'-f', file_g+self.ext,
'-o', file_g+'gro']
self.execute_command(cmd, cwd=None)
self.top, _, _, _ = read_gromos96_file(file_g+self.ext)
self.top['VELOCITY'] = self.top['POSITION'].copy()
# Check the presence of the defaults input files or, if absent,
# try to find them by their expected extension.
self.input_files = look_for_input_files(self.input_path,
default_files,
extra_files)
logger.debug('Input files: %s', self.input_files)
# Check the input file and create a PyRETIS version with
# consistent settings:
settings = {
'dt': self.timestep,
'nstxout-compressed': 0,
'gen_vel': 'no'
}
for key in ('nsteps', 'nstxout', 'nstvout', 'nstfout', 'nstlog',
'nstcalcenergy', 'nstenergy'):
settings[key] = self.subcycles
if not write_vel:
settings['nstvout'] = 0
if not write_force:
settings['nstfout'] = 0
# PyRETIS construct its own mdp file
self.input_files['input'] = os.path.join(self.input_path,
'pyretis.mdp')
self._modify_input(self.input_files['input_o'],
self.input_files['input'], settings, delim='=')
logger.info(('Created GROMACS mdp input from %s. You might '
'want to check the input file: %s'),
self.input_files['input_o'], self.input_files['input'])
# Generate a tpr file using the input files:
logger.info('Creating ".tpr" for GROMACS in %s', self.input_path)
self.exe_dir = self.input_path
out_files = self._execute_grompp(self.input_files['input'],
self.input_files['conf'], 'topol')
# This will generate some noise, let's remove files we don't need:
mdout = os.path.join(self.input_path, out_files['mdout'])
self._removefile(mdout)
# We also remove GROMACS backup files after creating the tpr:
self._remove_gromacs_backup_files(self.input_path)
# Keep the tpr file.
self.input_files['tpr'] = os.path.join(self.input_path,
out_files['tpr'])
logger.info('GROMACS ".tpr" created: %s', self.input_files['tpr'])
[docs] @staticmethod
def select_energy_terms(terms):
"""Select energy terms to extract from GROMACS.
Parameters
----------
terms : string
This string will name the terms to extract. Currently
we only allow for two types of output, but this can be
customized in the future.
"""
allowed_terms = {
'full': ('\n'.join(('Potential', 'Kinetic-En.', 'Total-Energy',
'Temperature', 'Pressure'))).encode(),
'path': b'Potential\nKinetic-En.',
}
if terms not in allowed_terms:
return allowed_terms['path']
return allowed_terms[terms]
[docs] @staticmethod
def rename_energies(gmx_energy):
"""Rename GROMACS energy terms to PyRETIS convention."""
energy_map = {'potential': 'vpot',
'kinetic en.': 'ekin',
'temperature': 'temp',
'total energy': 'etot',
'pressure': 'press'}
energy = {}
for key, val in gmx_energy.items():
name = energy_map.get(key, key)
energy[name] = val[0]
return energy
[docs] def _execute_grompp(self, mdp_file, config, deffnm):
"""Execute the GROMACS preprocessor.
Parameters
----------
mdp_file : string
The path to the mdp file.
config : string
The path to the GROMACS config file to use as input.
deffnm : string
A string used to name the GROMACS files.
Returns
-------
out_files : dict
This dict contains files that were created by the GROMACS
preprocessor.
"""
topol = self.input_files['topology']
tpr = f'{deffnm}.tpr'
cmd = [self.gmx, 'grompp', '-f', mdp_file, '-c', config,
'-p', topol, '-o', tpr]
if 'index' in self.input_files:
cmd.extend(['-n', self.input_files['index']])
if self.maxwarn > 0:
cmd.extend(['-maxwarn', str(self.maxwarn)])
self.execute_command(cmd, cwd=self.exe_dir)
out_files = {'tpr': tpr, 'mdout': 'mdout.mdp'}
return out_files
[docs] def _execute_mdrun(self, tprfile, deffnm):
"""
Execute GROMACS mdrun.
This method is intended as the initial ``gmx mdrun`` executed.
That is, we here assume that we do not continue a simulation.
Parameters
----------
tprfile : string
The .tpr file to use for executing GROMACS.
deffnm : string
To give the GROMACS simulation a name.
Returns
-------
out_files : dict
This dict contains the output files created by ``mdrun``.
Note that we here hard code the file names.
"""
confout = f'{deffnm}.{self.ext}'
cmd = shlex.split(self.mdrun.format(tprfile, deffnm, confout))
self.execute_command(cmd, cwd=self.exe_dir)
out_files = {'conf': confout,
'cpt_prev': f'{deffnm}_prev.cpt'}
for key in ('cpt', 'edr', 'log', 'trr'):
out_files[key] = f'{deffnm}.{key}'
self._remove_gromacs_backup_files(self.exe_dir)
return out_files
[docs] def _execute_grompp_and_mdrun(self, config, deffnm):
"""
Execute GROMACS ``grompp`` and ``mdrun``.
Here we use the input file given in the input directory.
Parameters
----------
config : string
The path to the GROMACS config file to use as input.
deffnm : string
A string used to name the GROMACS files.
Returns
-------
out_files : dict of strings
The files created by this command.
"""
out_files = {}
out_grompp = self._execute_grompp(self.input_files['input'],
config, deffnm)
tpr_file = out_grompp['tpr']
for key, value in out_grompp.items():
out_files[key] = value
out_mdrun = self._execute_mdrun(tpr_file,
deffnm)
for key, value in out_mdrun.items():
out_files[key] = value
return out_files
[docs] def _execute_mdrun_continue(self, tprfile, cptfile, deffnm):
"""
Continue the execution of GROMACS.
Here, we assume that we have already executed ``gmx mdrun`` and
that we are to append and continue a simulation.
Parameters
----------
tprfile : string
The .tpr file which defines the simulation.
cptfile : string
The last checkpoint file (.cpt) from the previous run.
deffnm : string
To give the GROMACS simulation a name.
Returns
-------
out_files : dict
The output files created/appended by GROMACS when we
continue the simulation.
"""
confout = f'{deffnm}.{self.ext}'.format(deffnm, self.ext)
self._removefile(confout)
cmd = shlex.split(self.mdrun_c.format(tprfile, cptfile,
deffnm, confout))
self.execute_command(cmd, cwd=self.exe_dir)
out_files = {'conf': confout}
for key in ('cpt', 'edr', 'log', 'trr'):
out_files[key] = f'{deffnm}.{key}'
self._remove_gromacs_backup_files(self.exe_dir)
return out_files
[docs] def _extend_gromacs(self, tprfile, time):
"""Extend a GROMACS simulation.
Parameters
----------
tprfile : string
The file to read for extending.
time : float
The time (in ps) to extend the simulation by.
Returns
-------
out_files : dict
The files created by GROMACS when we extend.
"""
tpxout = f'ext_{tprfile}'
self._removefile(tpxout)
cmd = [self.gmx, 'convert-tpr', '-s', tprfile,
'-extend', str(time), '-o', tpxout]
self.execute_command(cmd, cwd=self.exe_dir)
out_files = {'tpr': tpxout}
return out_files
[docs] def _extend_and_execute_mdrun(self, tpr_file, cpt_file, deffnm):
"""Extend GROMACS and execute mdrun.
Parameters
----------
tpr_file : string
The location of the "current" .tpr file.
cpt_file : string
The last checkpoint file (.cpt) from the previous run.
deffnm : string
To give the GROMACS simulation a name.
Returns
-------
out_files : dict
The files created by GROMACS when we extend.
"""
out_files = {}
out_grompp = self._extend_gromacs(tpr_file, self.ext_time)
ext_tpr_file = out_grompp['tpr']
for key, value in out_grompp.items():
out_files[key] = value
out_mdrun = self._execute_mdrun_continue(ext_tpr_file, cpt_file,
deffnm)
for key, value in out_mdrun.items():
out_files[key] = value
# Move extended tpr so that we can continue extending:
source = os.path.join(self.exe_dir, ext_tpr_file)
dest = os.path.join(self.exe_dir, tpr_file)
self._movefile(source, dest)
out_files['tpr'] = tpr_file
return out_files
[docs] def _remove_gromacs_backup_files(self, dirname):
"""Remove files GROMACS has backed up.
These are files starting with a '#'
Parameters
----------
dirname : string
The directory where we are to remove files.
"""
for entry in os.scandir(dirname):
if entry.name.startswith('#') and entry.is_file():
filename = os.path.join(dirname, entry.name)
self._removefile(filename)
[docs] def get_energies(self, energy_file, begin=None, end=None):
"""Return energies from a GROMACS run.
Parameters
----------
energy_file : string
The file to read energies from.
begin : float, optional
Select the time for the first frame to read.
end : float, optional
Select the time for the last frame to read.
Returns
-------
energy : dict fo numpy.arrays
The energies read from the produced GROMACS xvg file.
"""
cmd = [self.gmx, 'energy', '-f', energy_file]
if begin is not None:
begin = max(begin, 0)
cmd.extend(['-b', str(begin)])
if end is not None:
cmd.extend(['-e', str(end)])
self.execute_command(cmd, inputs=self.energy_terms,
cwd=self.exe_dir)
xvg_file = os.path.join(self.exe_dir, 'energy.xvg')
energy = read_xvg_file(xvg_file)
self._removefile(xvg_file)
return energy
[docs] def _propagate_from(self, name, path, ensemble, msg_file, reverse=False):
"""
Propagate with GROMACS from the current system configuration.
Here, we assume that this method is called after the propagate()
has been called in the parent. The parent is then responsible
for reversing the velocities and also for setting the initial
state of the system.
Parameters
----------
name : string
A name to use for the trajectory we are generating.
path : object like :py:class:`pyretis.core.path.PathBase`
This is the path we use to fill in phase-space points.
ensemble: dict
It contains:
* `system`: object like :py:class:`.System`
The system object gives the initial state for the
integration. The initial state is stored and the system is
reset to the initial state when the integration is done.
* `order_function`: object like :py:class:`.OrderParameter`
The object used for calculating the order parameter.
* `interfaces`: list of floats
These interfaces define the stopping criterion.
msg_file : object like :py:class:`.FileIO`
An object we use for writing out messages that are useful
for inspecting the status of the current propagation.
reverse : boolean, optional
If True, the system will be propagated backward in time.
Returns
-------
success : boolean
This is True if we generated an acceptable path.
status : string
A text description of the current status of the propagation.
"""
status = f'propagating with GROMACS (reverse = {reverse})'
logger.debug(status)
success = False
interfaces = ensemble['interfaces']
left, _, right = interfaces
# Dumping of the initial config were done by the parent, here
# we will just use it:
initial_conf = ensemble['system'].particles.get_pos()[0]
# Get the current order parameter:
order = self.calculate_order(ensemble)
msg_file.write(
f'# Initial order parameter: {" ".join([str(i) for i in order])}'
)
# In some cases, we don't really have to perform a step as the
# initial config might be left/right of the interface in
# question. Here, we will perform a step anyway. This is to be
# sure that we obtain energies and also a trajectory segment.
# Note that all the energies are obtained after we are done
# with the integration from the .edr file of the trajectory.
msg_file.write('# Running grompp and mdrun (initial step).')
out_files = self._execute_grompp_and_mdrun(initial_conf, name)
# Define name of some files:
tpr_file = out_files['tpr']
cpt_file = out_files['cpt']
traj_file = os.path.join(self.exe_dir, out_files['trr'])
msg_file.write(f'# Trajectory file is: {traj_file}')
conf_abs = os.path.join(self.exe_dir, out_files['conf'])
# Note: The order parameter is calculated AT THE END of each iteration.
msg_file.write('# Starting GROMACS.')
msg_file.write('# Step order parameter cv1 cv2 ...')
for i in range(path.maxlen):
msg_file.write(
f'{i} {" ".join([str(j) for j in order])}'
)
# We first add the previous phase point, and then we propagate.
snapshot = {'order': order,
'config': (traj_file, i),
'vel_rev': reverse}
phase_point = self.snapshot_to_system(ensemble['system'],
snapshot)
status, success, stop, _ = self.add_to_path(path, phase_point,
left, right)
if stop:
logger.debug('GROMACS propagation ended at %i. Reason: %s',
i, status)
break
if i == 0:
# This step was performed before entering the main loop.
pass
elif i > 0:
out_extnd = self._extend_and_execute_mdrun(tpr_file, cpt_file,
name)
out_files.update(out_extnd)
# Calculate the order parameter using the current system:
ensemble['system'].particles.set_vel(reverse)
ensemble['system'].particles.set_pos((conf_abs, None))
order = self.calculate_order(ensemble)
# We now have the order parameter, for GROMACS just remove the
# config file to avoid the GROMACS #conf_abs# backup clutter:
self._removefile(conf_abs)
msg_file.flush()
logger.debug('GROMACS propagation done, obtaining energies')
msg_file.write('# Propagation done.')
msg_file.write(f'# Reading energies from: {out_files["edr"]}')
msg_file.flush()
energy = self.get_energies(out_files['edr'])
path.update_energies(energy['kinetic en.'], energy['potential'])
logger.debug('Removing GROMACS output after propagate.')
remove = [val for key, val in out_files.items()
if key not in ('trr', 'gro', 'g96')]
self._remove_files(self.exe_dir, remove)
self._remove_gromacs_backup_files(self.exe_dir)
return success, status
[docs] def step(self, system, name):
"""Perform a single step with GROMACS.
Parameters
----------
system : object like :py:class:`.System`
The system we are integrating.
name : string
To name the output files from the GROMACS step.
Returns
-------
out : string
The name of the output configuration, obtained after
completing the step.
"""
initial_conf = self.dump_frame(system)
# Save as a single snapshot file:
system.particles.set_pos((initial_conf, None))
system.particles.set_vel(False)
out_grompp = self._execute_grompp(self.input_files['input'],
initial_conf,
name)
out_mdrun = self._execute_mdrun(out_grompp['tpr'], name)
conf_abs = os.path.join(self.exe_dir, out_mdrun['conf'])
logger.debug('Obtaining GROMACS energies after single step.')
energy = self.get_energies(out_mdrun['edr'])
system.particles.set_pos((conf_abs, None))
system.particles.set_vel(False)
system.particles.vpot = energy['potential'][-1]
system.particles.ekin = energy['kinetic en.'][-1]
logger.debug('Removing GROMACS output after single step.')
remove = [val for _, val in out_grompp.items()]
remove += [val for key, val in out_mdrun.items() if key != 'conf']
self._remove_files(self.exe_dir, remove)
return out_mdrun['conf']
[docs] def _prepare_shooting_point(self, input_file):
"""
Create the initial configuration for a shooting move.
This creates a new initial configuration with random velocities.
Here, the random velocities are obtained by running a zero-step
GROMACS simulation.
Parameters
----------
input_file : string
The input configuration to generate velocities for.
Returns
-------
output_file : string
The name of the file created.
energy : dict
The energy terms read from the GROMACS .edr file.
"""
gen_mdp = os.path.join(self.exe_dir, 'genvel.mdp')
if os.path.isfile(gen_mdp):
logger.debug('%s found. Re-using it!', gen_mdp)
else:
# Create output file to generate velocities:
settings = {'gen_vel': 'yes', 'gen_seed': -1, 'nsteps': 0,
'continuation': 'no'}
self._modify_input(self.input_files['input'], gen_mdp, settings,
delim='=')
# Run GROMACS grompp for this input file:
out_grompp = self._execute_grompp(gen_mdp, input_file, 'genvel')
remove = [val for _, val in out_grompp.items()]
# Run GROMACS mdrun for this tpr file:
out_mdrun = self._execute_mdrun(out_grompp['tpr'], 'genvel')
remove += [val for key, val in out_mdrun.items() if key != 'conf']
confout = os.path.join(self.exe_dir, out_mdrun['conf'])
energy = self.get_energies(out_mdrun['edr'])
# Remove run-files:
logger.debug('Removing GROMACS output after velocity generation.')
self._remove_files(self.exe_dir, remove)
return confout, energy
[docs] def _read_configuration(self, filename):
"""Read output from GROMACS .g96/gro files.
Parameters
----------
filename : string
The file to read the configuration from.
Returns
-------
box : numpy.array
The box dimensions.
xyz : numpy.array
The positions.
vel : numpy.array
The velocities.
"""
box = None
if self.ext == 'g96':
_, xyz, vel, box = read_gromos96_file(filename)
elif self.ext == 'gro':
_, xyz, vel, box = read_gromacs_gro_file(filename)
else:
msg = 'GROMACS engine does not support reading "%s"'
logger.error(msg, self.ext)
raise ValueError(msg % self.ext)
return box, xyz, vel
[docs] def _reverse_velocities(self, filename, outfile):
"""Reverse velocity in a given snapshot.
Parameters
----------
filename : string
The configuration to reverse velocities in.
outfile : string
The output file for storing the configuration with
reversed velocities.
"""
if self.ext == 'g96':
txt, xyz, vel, _ = read_gromos96_file(filename)
write_gromos96_file(outfile, txt, xyz, -1 * vel)
elif self.ext == 'gro':
txt, xyz, vel, _ = read_gromacs_gro_file(filename)
write_gromacs_gro_file(outfile, txt, xyz, -1 * vel)
else:
msg = 'GROMACS engine does not support writing "%s"'
logger.error(msg, self.ext)
raise ValueError(msg % self.ext)
[docs] def modify_velocities(self, ensemble, vel_settings):
"""Modify the velocities of the current state.
This method will modify the velocities of a time slice.
Parameters
----------
ensemble : dict
It contains:
* `system`: object like :py:class:`.System`
This is the system that contains the particles we are
investigating.
vel_settings: dict
It contains:
* `sigma_v`: numpy.array, optional
These values can be used to set a standard deviation (one
for each particle) for the generated velocities.
* `aimless`: boolean, optional
Determines if we should do aimless shooting or not.
* `momentum`: boolean, optional
If True, we reset the linear momentum to zero after
generating.
* `rescale or rescale_energy`: float, optional
In some NVE simulations, we may wish to re-scale the
energy to a fixed value. If `rescale` is a float > 0,
we will re-scale the energy (after modification of
the velocities) to match the given float.
Returns
-------
dek : float
The change in the kinetic energy.
kin_new : float
The new kinetic energy.
"""
dek = None
kin_old = None
kin_new = None
system = ensemble['system']
rescale = vel_settings.get('rescale_energy',
vel_settings.get('rescale'))
if rescale is not None and rescale is not False and rescale > 0:
msgtxt = 'GROMACS engine does not support energy re-scale.'
logger.error(msgtxt)
raise NotImplementedError(msgtxt)
kin_old = system.particles.ekin
if vel_settings.get('aimless', False):
pos = self.dump_frame(system)
posvel, energy = self._prepare_shooting_point(pos)
kin_new = energy['kinetic en.'][-1]
system.particles.set_pos((posvel, None))
system.particles.set_vel(False)
system.particles.ekin = kin_new
system.particles.vpot = energy['potential'][-1]
else: # Soft velocity change, from a Gaussian distribution:
msgtxt = 'GROMACS engine only support aimless shooting!'
logger.error(msgtxt)
raise NotImplementedError(msgtxt)
if vel_settings.get('momentum', False):
pass
if kin_old is None or kin_new is None:
dek = float('inf')
logger.debug(('Kinetic energy not found for previous point.'
'\n(This happens when the initial configuration '
'does not contain energies.)'))
else:
dek = kin_new - kin_old
return dek, kin_new
[docs] def integrate(self, ensemble, steps, thermo='full'):
"""
Perform several integration steps.
This method will perform several integration steps using
GROMACS. It will also calculate order parameter(s) and energy
terms if requested.
Parameters
----------
ensemble: dict
It contains:
* `system`: object like :py:class:`.System`
The system object gives the initial state for the
integration. The initial state is stored and the system is
reset to the initial state when the integration is done.
* `order_function`: object like :py:class:`.OrderParameter`
The object used for calculating the order parameter.
steps : integer
The number of steps we are going to perform. Note that we
do not integrate on the first step (e.g. step 0) but we do
obtain the other properties. This is to output the starting
configuration.
thermo : string, optional
Select the thermodynamic properties we are to calculate.
Yields
------
results : dict
The results from a MD step. This contains the state of the system
and order parameter(s) and energies (if calculated).
"""
logger.debug('Integrating with GROMACS')
# Dump the initial config:
system = ensemble['system']
order_function = ensemble.get('order_function')
initial_file = self.dump_frame(system)
out_files = {}
conf_abs = None
self.energy_terms = self.select_energy_terms(thermo)
# For step zero, obtain the order parameter:
if order_function:
order = self.calculate_order(ensemble)
else:
order = None
for i in range(steps):
if i == 0:
out_files = self._execute_grompp_and_mdrun(
initial_file,
'pyretis-gmx'
)
conf_abs = os.path.join(self.exe_dir, out_files['conf'])
elif 0 < i < steps - 1:
out_extnd = self._extend_and_execute_mdrun(
out_files['tpr'],
out_files['cpt'],
'pyretis-gmx'
)
out_files.update(out_extnd)
else:
pass
# Update with results from previous step:
results = {}
if order:
results['order'] = order
# Update for order parameter:
if order_function:
system.particles.set_pos((conf_abs, None, None))
order = self.calculate_order(ensemble)
# Obtain latest energies:
time1 = i * self.timestep * self.subcycles
time2 = (i + 1) * self.timestep * self.subcycles
# time1 and time2 should be correct now, but we are victims
# of floating points. Subtract/add something small so that
# we round to correct time.
time1 -= self.timestep * 0.1
time2 += self.timestep * 0.1
energy = self.get_energies(out_files['edr'], begin=time1,
end=time2)
# Rename energies into the PyRETIS convention:
results['thermo'] = self.rename_energies(energy)
yield results