def test_ensemble_potential_nompi(tpr_filename):
"""Test ensemble potential without an ensemble.
"""
print("Testing plugin potential with input file {}".format(os.path.abspath(tpr_filename)))
assert gmx.version.api_is_at_least(0, 0, 5)
md = from_tpr([tpr_filename], append_output=False)
# Create a WorkElement for the potential
params = {'sites': [1, 4],
'nbins': 10,
'binWidth': 0.1,
'min_dist': 0.,
'max_dist': 10.,
'experimental': [1.] * 10,
'nsamples': 1,
'sample_period': 0.001,
'nwindows': 4,
'k': 10000.,
'sigma': 1.}
potential = WorkElement(namespace="myplugin",
operation="ensemble_restraint",
params=params)
# Note that we could flexibly capture accessor methods as workflow elements, too. Maybe we can
# hide the extra Python bindings by letting myplugin.HarmonicRestraint automatically convert
# to a WorkElement when add_dependency is called on it.
potential.name = "ensemble_restraint"
md.add_dependency(potential)
context = ParallelArrayContext(md)
with context as session:
session.run()
def build_plugin(self):
"""Builds training phase plugin for BRER simulations.
Returns
-------
WorkElement
a gmxapi WorkElement to be added to the workflow graph
Raises
------
KeyError
if required parameters for building the plugin are missing.
"""
WorkElement = _get_workelement()
if self.get_missing_keys():
raise KeyError('Must define {}'.format(self.get_missing_keys()))
potential = WorkElement(namespace="brer",
operation="brer_restraint",
depends=[],
params=self.get_as_dictionary())
potential.name = '{}'.format(self.get('sites'))
return potential
def test_ensemble_potential_withmpi(tpr_filename):
import os
from mpi4py import MPI
rank = MPI.COMM_WORLD.Get_rank()
rank_dir = os.path.join(os.getcwd(), str(rank))
os.mkdir(rank_dir)
logger.info("Testing plugin potential with input file {}".format(os.path.abspath(tpr_filename)))
assert gmx_version.api_is_at_least(0, 0, 5)
md = from_tpr([tpr_filename, tpr_filename], append_output=False)
# Create a WorkElement for the potential
params = {'sites': [1, 4],
'nbins': 10,
'binWidth': 0.1,
'min_dist': 0.,
'max_dist': 10.,
'experimental': [0.5] * 10,
'nsamples': 1,
'sample_period': 0.001,
'nwindows': 4,
'k': 10000.,
'sigma': 1.}
potential = WorkElement(namespace="myplugin",
operation="ensemble_restraint",
params=params)
# Note that we could flexibly capture accessor methods as workflow elements, too. Maybe we can
# hide the extra Python bindings by letting myplugin.HarmonicRestraint automatically convert
# to a WorkElement when add_dependency is called on it.
potential.name = "ensemble_restraint"
md.add_dependency(potential)
context = ParallelArrayContext(md)
with context as session:
session.run()
def test_ensemble_potential_withmpi(spc_water_box):
tpr_filename = spc_water_box
logger.info("Testing plugin potential with input file {}".format(
os.path.abspath(tpr_filename)))
assert gmx_version.api_is_at_least(0, 0, 5)
# Note that *threads* argument causes errors for MPI-enabled GROMACS.
# Ref #3563 and #3573
md = from_tpr([tpr_filename, tpr_filename], append_output=False, threads=2)
# Create a WorkElement for the potential
params = {
'sites': [1, 4],
'nbins': 10,
'binWidth': 0.1,
'min_dist': 0.,
'max_dist': 10.,
'experimental': [0.5] * 10,
'nsamples': 1,
'sample_period': 0.001,
'nwindows': 4,
'k': 10000.,
'sigma': 1.
}
potential = WorkElement(namespace="myplugin",
operation="ensemble_restraint",
params=params)
# Note that we could flexibly capture accessor methods as workflow elements, too. Maybe we can
# hide the extra Python bindings by letting myplugin.HarmonicRestraint automatically convert
# to a WorkElement when add_dependency is called on it.
potential.name = "ensemble_restraint"
md.add_dependency(potential)
context = Context(md)
with context as session:
session.run()
def test_binding_protocol(spc_water_box, mdrun_kwargs):
"""Test that gmxapi successfully attaches MD plugins."""
import myplugin
if _MPI is not None:
_size = _MPI.COMM_WORLD.Get_size()
_rank = _MPI.COMM_WORLD.Get_rank()
else:
_size = 1
_rank = 0
tpr_filename = spc_water_box
logger.info("Testing plugin potential with input file {}".format(
os.path.abspath(tpr_filename)))
assert gmx.version.api_is_at_least(0, 2, 1)
md = from_tpr([tpr_filename] * _size, append_output=False, **mdrun_kwargs)
potential = WorkElement(namespace="myplugin",
operation="null_restraint",
params={'sites': [1, 4]})
potential.name = "null restraint"
md.add_dependency(potential)
context = Context(md)
with context as session:
session.run()
# See also #3038, #3145, #4079
assert isinstance(context.potentials, list)
assert len(context.potentials) > 0
for restraint in context.potentials:
if isinstance(restraint, myplugin.NullRestraint):
assert gmx.version.api_is_at_least(0, 2, 1)
assert restraint.count() > 1