def report(self, topology, state, currentStep, stepsize):
if self._dcd is None:
self._dcd = DCDFile(
self._out, topology, stepsize,
currentStep, self._reportInterval, self._append
)
self._dcd.writeModel(state.getPositions(), periodicBoxVectors=state.getPeriodicBoxVectors())
def report_ns(self, topology, pos, boxvec, currentStep, stepsize):
if self._dcd is None:
self._dcd = DCDFile(
self._out, topology, stepsize,
currentStep, self._reportInterval, self._append
)
self._dcd.writeModel(pos, boxvec)
def report(self, simulation, state):
"""Generate a report.
Parameters
----------
simulation : Simulation
The Simulation to generate a report for
state : State
The current state of the simulation
"""
state = simulation.context.getState(getPositions=True, enforcePeriodicBox=self._enforcePeriodicBox)
if self._dcd is None:
self._dcd = DCDFile(self._out, simulation.topology, simulation.integrator.getStepSize(), 0, self._reportInterval)
self._dcd.writeModel(state.getPositions(), periodicBoxVectors=state.getPeriodicBoxVectors())
def report(self, simulation, state):
"""Generate a report.
Parameters
----------
simulation : Simulation
The Simulation to generate a report for
state : State
The current state of the simulation
"""
if self._dcd is None:
self._dcd = DCDFile(self._out, simulation.topology, simulation.integrator.getStepSize(), 0, self._reportInterval)
a,b,c = state.getPeriodicBoxVectors()
self._dcd.writeModel(state.getPositions(), mm.Vec3(a[0].value_in_unit(nanometer), b[1].value_in_unit(nanometer), c[2].value_in_unit(nanometer))*nanometer)
def report(self, simulation, state):
"""Generate a report.
Parameters
----------
simulation : Simulation
The Simulation to generate a report for
state : State
The current state of the simulation
"""
if self._dcd is None:
self._dcd = DCDFile(self._out, simulation.topology,
simulation.integrator.getStepSize(),
simulation.currentStep, self._reportInterval,
self._append)
self._dcd.writeModel(state.getPositions(),
periodicBoxVectors=state.getPeriodicBoxVectors())
def report(self, simulation, state):
"""Generate a report.
Parameters
----------
simulation : Simulation
The Simulation to generate a report for
state : State
The current state of the simulation
"""
if self._tempDCD is None:
# Create DCDFile object
self._tempDCD = DCDFile(self._tempOut, simulation.topology,
simulation.integrator.getStepSize(),
simulation.currentStep,
self._reportInterval, False)
# Save molecules and masses
for molecule in simulation.context.getMolecules():
self._reportedMolecules.append(np.array(molecule))
self._reportedMoleculesMass.append(
self._getMoleculeMass(simulation.system, molecule))
# Create temporary pdb file
PDBFile.writeFile(simulation.topology, state.getPositions(),
open(self._tempPDBFileName, 'w'))
# Get time and step from simulation
self._times.append(state.getTime().value_in_unit(unit.picosecond))
if self._step:
self._steps.append(simulation.currentStep)
# Write to dcd file
self._tempDCD.writeModel(
state.getPositions(),
periodicBoxVectors=state.getPeriodicBoxVectors())
