def take_snapshot(wrapped_context):
#
context = wrapped_context.context.context # extra indirection for OpenMM
context_view = wrapped_context.view
#
positions = asarray(dlext.positions(context_view))
forces = asarray(dlext.forces(context_view))
ids = asarray(dlext.atom_ids(context_view))
#
velocities = asarray(dlext.velocities(context_view))
if is_on_gpu(context_view):
vel_mass = velocities
else:
inverse_masses = asarray(dlext.inverse_masses(context_view))
vel_mass = (velocities, inverse_masses.reshape((-1, 1)))
#
box_vectors = context.getSystem().getDefaultPeriodicBoxVectors()
a = box_vectors[0].value_in_unit(unit.nanometer)
b = box_vectors[1].value_in_unit(unit.nanometer)
c = box_vectors[2].value_in_unit(unit.nanometer)
H = ((a[0], b[0], c[0]), (a[1], b[1], c[1]), (a[2], b[2], c[2]))
origin = (0.0, 0.0, 0.0)
dt = context.getIntegrator().getStepSize() / unit.picosecond
# OpenMM doesn't have images
return Snapshot(positions, vel_mass, forces, ids, None, Box(H, origin), dt)
def update_snapshot(snapshot, sysview, location=default_location()):
#
positions = asarray(positions_types(sysview, location, AccessMode.Read))
vel_mass = asarray(velocities_masses(sysview, location, AccessMode.Read))
forces = asarray(net_forces(sysview, location, AccessMode.ReadWrite))
ids = asarray(rtags(sysview, location, AccessMode.Read))
imgs = asarray(images(sysview, location, AccessMode.Read))
#
return Snapshot(positions, vel_mass, forces, ids, imgs, snapshot.box,
snapshot.dt)
def python_update(positions, vel_mass, rtags, imgs, forces):
positions = asarray(positions)
vel_mass = asarray(vel_mass)
ids = asarray(rtags)
images = asarray(imgs)
forces = asarray(forces)
snap = Snapshot(positions=positions,
vel_mass=vel_mass,
forces=forces,
ids=ids,
images=images,
box=self.pybox,
dt=self.dt)
self.state = update(snap, self.state)
self.bias(snap, self.state)
if self.callback:
self.callback(snap, self.state, 0)
def take_snapshot(wrapped_context, location=default_location()):
#
context = wrapped_context.context
sysview = wrapped_context.view
#
positions = asarray(positions_types(sysview, location, AccessMode.Read))
vel_mass = asarray(velocities_masses(sysview, location, AccessMode.Read))
forces = asarray(net_forces(sysview, location, AccessMode.ReadWrite))
ids = asarray(rtags(sysview, location, AccessMode.Read))
imgs = asarray(images(sysview, location, AccessMode.Read))
#
box = sysview.particle_data().getGlobalBox()
L = box.getL()
xy = box.getTiltFactorXY()
xz = box.getTiltFactorXZ()
yz = box.getTiltFactorYZ()
lo = box.getLo()
H = ((L.x, xy * L.y, xz * L.z), (0.0, L.y, yz * L.z), (0.0, 0.0, L.z))
origin = (lo.x, lo.y, lo.z)
dt = context.integrator.dt
#
return Snapshot(positions, vel_mass, forces, ids, imgs, Box(H, origin), dt)