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
"""
from parmed.amber.asciicrd import VELSCALE
global VELUNIT, FRCUNIT
if self.crds:
crds = state.getPositions().value_in_unit(u.angstrom)
elif self.vels: # crds/vels/frcs are exclusive, elif works
vels = state.getVelocities().value_in_unit(VELUNIT)
elif self.frcs:
frcs = state.getForces().value_in_unit(FRCUNIT)
if self._out is None:
# This must be the first frame, so set up the trajectory now
if self.crds:
self.atom = len(crds)
elif self.vels:
self.atom = len(vels)
elif self.frcs:
self.atom = len(frcs)
self.uses_pbc = simulation.topology.getUnitCellDimensions() is not None
self._out = AmberMdcrd(self.fname, self.atom, self.uses_pbc,
title="ParmEd-created trajectory using OpenMM", mode='w')
# Add the coordinates, velocities, and/or forces as needed
if self.crds:
flatcrd = [0 for i in range(self.atom*3)]
for i in range(self.atom):
i3 = i*3
flatcrd[i3], flatcrd[i3+1], flatcrd[i3+2] = crds[i]
self._out.add_coordinates(flatcrd)
if self.vels:
# Divide by the scaling factor (works if vels is a list of Vec3's)
# This is necessary since AmberMdcrd does not scale before writing
# (since it expects coordinates)
vels = [v / VELSCALE for v in vels]
flatvel = [0 for i in range(self.atom*3)]
for i in range(self.atom):
i3 = i*3
flatvel[i3], flatvel[i3+1], flatvel[i3+2] = vels[i]
self._out.add_coordinates(flatvel)
if self.frcs:
flatfrc = [0 for i in range(self.atom*3)]
for i in range(self.atom):
i3 = i*3
flatfrc[i3], flatfrc[i3+1], flatfrc[i3+2] = frcs[i]
self._out.add_coordinates(flatfrc)
# Now it's time to add the box lengths
if self.uses_pbc:
boxvecs = state.getPeriodicBoxVectors()
lengths, angles = box_vectors_to_lengths_and_angles(*boxvecs)
self._out.add_box(lengths.value_in_unit(u.angstroms))
class MdcrdReporter(object):
"""
MdcrdReporter prints a trajectory in ASCII Amber format. This reporter will
be significantly slower than binary file reporters (like DCDReporter or
NetCDFReporter).
Parameters
----------
file : str
Name of the file to write the trajectory to
reportInterval : int
Number of steps between writing trajectory frames
crds : bool=True
Write coordinates to this trajectory file?
vels : bool=False
Write velocities to this trajectory file?
frcs : bool=False
Write forces to this trajectory file?
Notes
-----
You can only write one of coordinates, forces, or velocities to a mdcrd
file.
"""
@needs_openmm
def __init__(self, file, reportInterval, crds=True, vels=False, frcs=False):
# ASCII mdcrds can have either coordinates, forces, or velocities
ntrue = 0
if crds: ntrue += 1
if vels: ntrue += 1
if frcs: ntrue += 1
if ntrue != 1:
raise ValueError('MdcrdReporter must print exactly one of either '
'coordinates, velocities, or forces.')
# Control flags
self.crds, self.vels, self.frcs = crds, vels, frcs
self._reportInterval = reportInterval
self._out = None # not written yet
self.fname = file
def describeNextReport(self, simulation):
"""
Get information about the next report this object will generate.
Parameters
----------
simulation : :class:`app.Simulation`
The Simulation to generate a report for
Returns
-------
nsteps, pos, vel, frc, ene : int, bool, bool, bool, bool
nsteps is the number of steps until the next report
pos, vel, frc, and ene are flags indicating whether positions,
velocities, forces, and/or energies are needed from the Context
"""
stepsleft = simulation.currentStep % self._reportInterval
steps = self._reportInterval - stepsleft
return (steps, self.crds, self.vels, self.frcs, False)
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
"""
from parmed.amber.asciicrd import VELSCALE
global VELUNIT, FRCUNIT
if self.crds:
crds = state.getPositions().value_in_unit(u.angstrom)
elif self.vels: # crds/vels/frcs are exclusive, elif works
vels = state.getVelocities().value_in_unit(VELUNIT)
elif self.frcs:
frcs = state.getForces().value_in_unit(FRCUNIT)
if self._out is None:
# This must be the first frame, so set up the trajectory now
if self.crds:
self.atom = len(crds)
elif self.vels:
self.atom = len(vels)
elif self.frcs:
self.atom = len(frcs)
self.uses_pbc = simulation.topology.getUnitCellDimensions() is not None
self._out = AmberMdcrd(self.fname, self.atom, self.uses_pbc,
title="ParmEd-created trajectory using OpenMM", mode='w')
# Add the coordinates, velocities, and/or forces as needed
if self.crds:
flatcrd = [0 for i in range(self.atom*3)]
for i in range(self.atom):
i3 = i*3
flatcrd[i3], flatcrd[i3+1], flatcrd[i3+2] = crds[i]
self._out.add_coordinates(flatcrd)
if self.vels:
# Divide by the scaling factor (works if vels is a list of Vec3's)
# This is necessary since AmberMdcrd does not scale before writing
# (since it expects coordinates)
vels = [v / VELSCALE for v in vels]
flatvel = [0 for i in range(self.atom*3)]
for i in range(self.atom):
i3 = i*3
flatvel[i3], flatvel[i3+1], flatvel[i3+2] = vels[i]
self._out.add_coordinates(flatvel)
if self.frcs:
flatfrc = [0 for i in range(self.atom*3)]
for i in range(self.atom):
i3 = i*3
flatfrc[i3], flatfrc[i3+1], flatfrc[i3+2] = frcs[i]
self._out.add_coordinates(flatfrc)
# Now it's time to add the box lengths
if self.uses_pbc:
boxvecs = state.getPeriodicBoxVectors()
lengths, angles = box_vectors_to_lengths_and_angles(*boxvecs)
self._out.add_box(lengths.value_in_unit(u.angstroms))
def __del__(self):
try:
if self._out is not None:
self._out.close()
except AttributeError:
pass
def finalize(self):
""" Closes any open file """
try:
if self._out is not None:
self._out.close()
except AttributeError: # pragma: no cover
pass # pragma: no cover
