def report(self, sim, state):
"""Generate a report.
Parameters
----------
sim : :class:`app.Simulation`
The Simulation to generate a report for
state : :class:`mm.State`
The current state of the simulation
"""
global VELUNIT
crds = state.getPositions().value_in_unit(u.angstrom)
if self.rst7 is None:
self.uses_pbc = sim.topology.getUnitCellDimensions() is not None
self.atom = len(crds)
# First time written
self.rst7 = Rst7(
natom=self.atom,
title='Restart file written by ParmEd with OpenMM')
self.rst7.time = state.getTime().value_in_unit(u.picosecond)
flatcrd = [0.0 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.rst7.coordinates = flatcrd
if self.write_velocities:
vels = state.getVelocities().value_in_unit(VELUNIT)
flatvel = [0.0 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.rst7.vels = flatvel
if self.uses_pbc:
boxvecs = state.getPeriodicBoxVectors()
lengths, angles = box_vectors_to_lengths_and_angles(*boxvecs)
lengths = lengths.value_in_unit(u.angstrom)
angles = angles.value_in_unit(u.degree)
self.rst7.box = [
lengths[0], lengths[1], lengths[2], angles[0], angles[1],
angles[2]
]
if self.write_multiple:
fname = self.fname + '.%d' % sim.currentStep
else:
fname = self.fname
self.rst7.write(fname, self.netcdf)
