def finalize(self):
"""Finalizes the calculations (e.g. averaging the total term, output files creations ...).
"""
if self.architecture == 'monoprocessor':
t = self.trajectory
else:
# Load the whole trajectory set.
t = Trajectory(None, self.trajectoryFilename, 'r')
comsUniverse = t.universe.__copy__()
comsUniverse.removeObject(comsUniverse.objectList()[:])
orderedAtoms = sorted(t.universe.atomList(), key = operator.attrgetter('index'))
groups = [Collection([orderedAtoms[ind] for ind in g]) for g in self.group]
comp = 1
for g in groups:
comAtom = Atom('H', name = 'COM'+str(comp))
comAtom._mass = g.mass()
comsUniverse.addObject(comAtom)
comp += 1
# traj_new is the filtered trajectory
outputFile = Trajectory(comsUniverse, self.output, "w")
outputFile.jobinfo = self.information + '\nOutput file written on: %s\n\n' % asctime()
# Each time |snapshot| is called, the universe contents i flushed into the output file.
snapshot = SnapshotGenerator(comsUniverse,\
actions = [TrajectoryOutput(outputFile, ["configuration","time"], 0, None, 1)])
# Loop over the output frames.
for comp in range(self.nFrames):
frameIndex = self.frameIndexes[comp]
t.universe.setFromTrajectory(t, frameIndex)
comsUniverse.setCellParameters(t.universe.cellParameters())
aComp = 0
for at in comsUniverse.atomList():
at.setPosition(self.comsTrajectory[frameIndex][aComp])
aComp += 1
snapshot(data = {'time': self.times[comp]})
# The output COM trajectory is closed.
outputFile.close()
self.toPlot = None
def finalize(self):
"""Finalizes the calculations (e.g. averaging the total term, output files creations ...).
"""
if self.architecture == 'monoprocessor':
t = self.trajectory
else:
# Load the whole trajectory set.
t = Trajectory(None, self.trajectoryFilename, 'r')
orderedAtoms = sorted(t.universe.atomList(), key = operator.attrgetter('index'))
selectedAtoms = Collection([orderedAtoms[ind] for ind in self.subset])
targetAtoms = Collection([orderedAtoms[ind] for ind in self.target])
# traj_new is the filtered trajectory
outputFile = Trajectory(targetAtoms, self.output, "w")
outputFile.jobinfo = self.information + '\nOutput file written on: %s\n\n' % asctime()
# Create the snapshot generator
snapshot = SnapshotGenerator(t.universe, actions = [TrajectoryOutput(outputFile, ["configuration"], 0, None, 1)])
# Loop over the output frames.
for comp in range(self.nFrames):
frameIndex = self.frameIndexes[comp]
t.universe.setFromTrajectory(t, frameIndex)
for at in targetAtoms:
at.setPosition(Vector(self.filteredTrajectory[frameIndex][at.index]))
snapshot(data = {'time': self.times[comp]})
outputFile.close()
t.close()
self.toPlot = None
def finalize(self):
"""Finalizes the calculations (e.g. averaging the total term, output files creations ...).
"""
if self.architecture == 'monoprocessor':
t = self.trajectory
else:
# Load the whole trajectory set.
t = Trajectory(None, self.trajectoryFilename, 'r')
selectedAtoms = Collection()
orderedAtoms = sorted(t.universe.atomList(),
key=operator.attrgetter('index'))
groups = [[
selectedAtoms.addObject(orderedAtoms[index])
for index in atomIndexes
] for atomIndexes in self.group]
# Create trajectory
outputFile = Trajectory(selectedAtoms, self.output, 'w')
# Create the snapshot generator
snapshot = SnapshotGenerator(
t.universe,
actions=[
TrajectoryOutput(outputFile, ["configuration", "time"], 0,
None, 1)
])
# The output is written
for comp in range(self.nFrames):
frameIndex = self.frameIndexes[comp]
t.universe.setFromTrajectory(t, frameIndex)
for atom in selectedAtoms:
atom.setPosition(self.RBT['trajectory'][atom.index][comp, :])
snapshot(data={'time': self.times[comp]})
outputFile.close()
outputFile = NetCDFFile(self.output, 'a')
outputFile.title = self.__class__.__name__
outputFile.jobinfo = self.information + '\nOutput file written on: %s\n\n' % asctime(
)
outputFile.jobinfo += 'Input trajectory: %s\n\n' % self.trajectoryFilename
outputFile.createDimension('NFRAMES', self.nFrames)
outputFile.createDimension('NGROUPS', self.nGroups)
outputFile.createDimension('QUATERNIONLENGTH', 4)
# The NetCDF variable that stores the quaternions.
QUATERNIONS = outputFile.createVariable(
'quaternion', N.Float, ('NGROUPS', 'NFRAMES', 'QUATERNIONLENGTH'))
# The NetCDF variable that stores the centers of mass.
COM = outputFile.createVariable('com', N.Float,
('NGROUPS', 'NFRAMES', 'xyz'))
# The NetCDF variable that stores the rigid-body fit.
FIT = outputFile.createVariable('fit', N.Float, ('NGROUPS', 'NFRAMES'))
# Loop over the groups.
for comp in range(self.nGroups):
aIndexes = self.group[comp]
outputFile.jobinfo += 'Group %s: %s\n' % (
comp + 1, [index for index in aIndexes])
QUATERNIONS[comp, :, :] = self.RBT[comp]['quaternions'][:, :]
COM[comp, :, :] = self.RBT[comp]['com'][:, :]
FIT[comp, :] = self.RBT[comp]['fit'][:]
outputFile.close()
self.toPlot = None
