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 chemistry.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 xrange(self.atom*3)]
for i in xrange(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 xrange(self.atom*3)]
for i in xrange(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 xrange(self.atom*3)]
for i in xrange(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 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 chemistry.amber.mdcrd import VELSCALE
global RADDEG, VELUNIT, FRCUNIT
if self._out is None:
# This must be the first frame, so set up the trajectory now
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:
crds = state.getPositions().value_in_unit(u.angstrom)
flatcrd = [0 for i in range(self.atom * 3)]
for i in range(self.atom):
flatcrd[3 * i], flatcrd[3 * i + 1], flatcrd[3 * i + 2] = crds[i]
self._out.add_coordinates(flatcrd)
if self.vels:
vels = state.getVelocities().value_in_unit(VELUNIT)
# 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):
flatvel[3 * i], flatvel[3 * i + 1], flatvel[3 * i + 2] = vels[i]
self._out.add_coordinates(flatvel)
if self.frcs:
frcs = state.getForces().value_in_unit(FRCUNIT)
flatfrc = [0 for i in range(self.atom * 3)]
for i in range(self.atom):
flatfrc[3 * i], flatfrc[3 * i + 1], flatfrc[3 * i + 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 = _process_box_vectors(*boxvecs)
self._out.add_box(lengths)
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 chemistry.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 xrange(self.atom * 3)]
for i in xrange(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 xrange(self.atom * 3)]
for i in xrange(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 xrange(self.atom * 3)]
for i in xrange(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 chemistry.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 xrange(self.atom * 3)]
for i in xrange(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 xrange(self.atom * 3)]
for i in xrange(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 xrange(self.atom * 3)]
for i in xrange(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 NameError:
pass
def finalize(self):
""" Closes any open file """
try:
if self._out is not None:
self._out.close()
except NameError:
pass
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).
"""
@needs_openmm
def __init__(self, file, reportInterval, atom, uses_pbc, crds=True, vels=False, frcs=False):
"""
Create a MdcrdReporter instance.
Parameters:
- file (string): file name to write
- reportInterval (int): time step interval b/w frame writes
- atom (int): number of atoms in the system
- uses_pbc (bool): uses periodic boundary conditions
- crds (bool): Print coordinates?
- vels (bool): Print velocities?
- frcs (bool): Print forces?
"""
# 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.uses_pbc, self.atom = uses_pbc, atom
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 (Simulation) The Simulation to generate a report for
Returns:
A five element tuple. The first element is the number of steps
until the next report. The remaining elements specify whether that
report will require positions, velocities, forces, and energies
respectively.
"""
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 chemistry.amber.mdcrd import VELSCALE
global RADDEG, VELUNIT, FRCUNIT
if self._out is None:
# This must be the first frame, so set up the trajectory now
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:
crds = state.getPositions().value_in_unit(u.angstrom)
flatcrd = [0 for i in range(self.atom * 3)]
for i in range(self.atom):
flatcrd[3 * i], flatcrd[3 * i + 1], flatcrd[3 * i + 2] = crds[i]
self._out.add_coordinates(flatcrd)
if self.vels:
vels = state.getVelocities().value_in_unit(VELUNIT)
# 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):
flatvel[3 * i], flatvel[3 * i + 1], flatvel[3 * i + 2] = vels[i]
self._out.add_coordinates(flatvel)
if self.frcs:
frcs = state.getForces().value_in_unit(FRCUNIT)
flatfrc = [0 for i in range(self.atom * 3)]
for i in range(self.atom):
flatfrc[3 * i], flatfrc[3 * i + 1], flatfrc[3 * i + 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 = _process_box_vectors(*boxvecs)
self._out.add_box(lengths)
def __del__(self):
if self._out is not None:
self._out.close()
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 chemistry.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 xrange(self.atom*3)]
for i in xrange(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 xrange(self.atom*3)]
for i in xrange(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 xrange(self.atom*3)]
for i in xrange(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 NameError:
pass
def finalize(self):
""" Closes any open file """
try:
if self._out is not None:
self._out.close()
except NameError:
pass
