def qcstep(self):
"""Propagates the centroid position and momentum and the volume."""
v = self.p / self.m[0]
expq, expp = (matrix_exp(v * self.dt), matrix_exp(-v * self.dt))
m = dstrip(self.beads.m)
saveq = self.nm.qnm[0].copy()
savep = self.nm.pnm[0].copy()
for i in range(self.beads.natoms):
self.nm.qnm[0, 3 * i:3 * (i + 1)] = np.dot(
expq, self.nm.qnm[0, 3 * i:3 * (i + 1)])
self.nm.qnm[0, 3 * i:3 * (i + 1)] += np.dot(
np.dot(invert_ut3x3(v), (expq - expp) / (2.0)),
dstrip(self.nm.pnm)[0, 3 * i:3 * (i + 1)] / m[i])
self.nm.pnm[0, 3 * i:3 * (i + 1)] = np.dot(
expp, self.nm.pnm[0, 3 * i:3 * (i + 1)])
#self.cell.h[:2, :2] = np.dot(expq[:2, :2], self.cell.h[:2, :2])
#self.cell.h[2, :2] = 0.
#self.cell.h[:2, 2] = 0.
# Only expand and contract cell parallel to x-y axes; do not shear or change z
self.cell.h = np.array([[expq[0, 0] * self.cell.h[0, 0], 0., 0.],
[0., expq[1, 1] * self.cell.h[1, 1], 0.],
[0., 0., self.cell.h[2, 2]]])
def qcstep(self):
"""Propagates the centroid position and momentum and the volume."""
v = self.p/self.m[0]
expq, expp = (matrix_exp(v*self.dt), matrix_exp(-v*self.dt))
m = depstrip(self.beads.m)
saveq=self.nm.qnm[0].copy()
savep=self.nm.pnm[0].copy()
for i in range(self.beads.natoms):
self.nm.qnm[0,3*i:3*(i+1)] = np.dot(expq, self.nm.qnm[0,3*i:3*(i+1)])
self.nm.qnm[0,3*i:3*(i+1)] += np.dot(np.dot(invert_ut3x3(v),(expq-expp)/(2.0)),depstrip(self.nm.pnm)[0,3*i:3*(i+1)]/m[i])
self.nm.pnm[0,3*i:3*(i+1)] = np.dot(expp, self.nm.pnm[0,3*i:3*(i+1)])
self.cell.h = np.dot(expq,self.cell.h)
def qcstep(self):
"""Propagates the centroid position and momentum and the volume."""
v = self.p / self.m[0]
halfdt = self.qdt
expq, expp = (matrix_exp(v * halfdt), matrix_exp(-v * halfdt))
m = dstrip(self.beads.m)
sinh = np.dot(invert_ut3x3(v), (expq - expp) / (2.0))
for i in range(self.beads.natoms):
self.nm.qnm[0, 3 * i:3 * (i + 1)] = np.dot(expq, self.nm.qnm[0, 3 * i:3 * (i + 1)])
self.nm.qnm[0, 3 * i:3 * (i + 1)] += np.dot(sinh, dstrip(self.nm.pnm)[0, 3 * i:3 * (i + 1)] / m[i])
self.nm.pnm[0, 3 * i:3 * (i + 1)] = np.dot(expp, self.nm.pnm[0, 3 * i:3 * (i + 1)])
self.cell.h = np.dot(expq, self.cell.h)
def qcstep(self):
"""Propagates the centroid position and momentum and the volume."""
v = self.p / self.m[0]
halfdt = self.qdt
expq, expp = (matrix_exp(v * halfdt), matrix_exp(-v * halfdt))
m = dstrip(self.beads.m)
sinh = np.dot(invert_ut3x3(v), (expq - expp) / (2.0))
for i in range(self.beads.natoms):
self.nm.qnm[0, 3 * i:3 * (i + 1)] = np.dot(
expq, self.nm.qnm[0, 3 * i:3 * (i + 1)])
self.nm.qnm[0, 3 * i:3 * (i + 1)] += np.dot(
sinh,
dstrip(self.nm.pnm)[0, 3 * i:3 * (i + 1)] / m[i])
self.nm.pnm[0, 3 * i:3 * (i + 1)] = np.dot(
expp, self.nm.pnm[0, 3 * i:3 * (i + 1)])
self.cell.h = np.dot(expq, self.cell.h)
def qcstep(self):
"""Propagates the centroid position and momentum and the volume."""
v = self.p / self.m[0]
halfdt = self.qdt
expq, expp = (matrix_exp(v * halfdt), matrix_exp(-v * halfdt))
sinh = np.dot(invert_ut3x3(v), (expq - expp) / (2.0))
q = dstrip(self.nm.qnm)[0].copy().reshape((self.beads.natoms, 3))
p = dstrip(self.nm.pnm)[0].copy()
q = np.dot(q, expq.T)
q += np.dot((p / self.beads.m3[0]).reshape((self.beads.natoms, 3)),
sinh.T)
p = np.dot(p.reshape((self.beads.natoms, 3)), expp.T)
self.nm.qnm[0] = q.reshape((self.beads.natoms * 3))
self.nm.pnm[0] = p.reshape((self.beads.natoms * 3))
self.cell.h = np.dot(expq, self.cell.h)
def qcstep(self):
"""Propagates the centroid position and momentum and the volume."""
v = self.p / self.m[0]
halfdt = self.qdt
# compute in one go dt sinh v/v to handle zero-velocity cases
# check eigen vector exists
if np.count_nonzero(v.diagonal()) == 0:
# compute sinhv/v by directly taylor, if eigen vector not exists
sinh = mat_taylor(v * halfdt, function="sinhx/x")
else:
eigvals, eigvecs = np.linalg.eig(v)
ieigvecs = np.linalg.inv(eigvecs)
sinh = halfdt * np.dot(
eigvecs, np.dot(np.diag(sinch(halfdt * eigvals)), ieigvecs))
expq, expp = (matrix_exp(v * halfdt), matrix_exp(-v * halfdt))
# oldsinh = np.dot(invert_ut3x3(v), (expq - expp) / (2.0))
q = dstrip(self.nm.qnm)[0].copy().reshape((self.beads.natoms, 3))
p = dstrip(self.nm.pnm)[0].copy()
q = np.dot(q, expq.T)
q += np.dot((p / self.beads.m3[0]).reshape((self.beads.natoms, 3)),
sinh.T)
p = np.dot(p.reshape((self.beads.natoms, 3)), expp.T)
# now apply the mask (and accumulate the associated change in conserved quantity)
# we use the thermostat conserved quantity accumulator, so we don't need to create a new one
self.thermostat.ethermo += self.kin
self.p *= self.hmask
self.thermostat.ethermo -= self.kin
self.nm.qnm[0] = q.reshape((self.beads.natoms * 3))
self.nm.pnm[0] = p.reshape((self.beads.natoms * 3))
self.cell.h = np.dot(expq, self.cell.h)
def get_T(self):
"""Calculates the matrix for the overall drift of the velocities."""
return matrix_exp(-self.dt * self.A)
def get_T(self):
"""Calculates the matrix for the overall drift of the velocities."""
return matrix_exp(-0.5*self.dt*self.A)
