def step(self, step=None):
""" Does one simulation time step.
Attributes:
qtime : The time taken in updating the real positions.
tr : current trust radius
"""
self.qtime = -time.time()
info("\nMD STEP %d" % step, verbosity.debug)
if step == 0:
info(" @GEOP: Initializing BFGSTRM", verbosity.debug)
self.old_x[:] = self.beads.q
self.old_u[:] = self.forces.pot
self.old_f[:] = self.forces.f
if len(self.fixatoms) > 0:
for dqb in self.old_f:
dqb[self.fixatoms * 3] = 0.0
dqb[self.fixatoms * 3 + 1] = 0.0
dqb[self.fixatoms * 3 + 2] = 0.0
# Reduce dimensionality
masked_old_x = self.old_x[:, self.gm.fixatoms_mask]
masked_hessian = self.hessian[np.ix_(self.gm.fixatoms_mask,
self.gm.fixatoms_mask)]
# Do one iteration of BFGSTRM.
# The Hessian is updated inside. Everything is passed inside BFGSTRM() in masked form, including the Hessian
BFGSTRM(masked_old_x, self.old_u,
self.old_f[:, self.gm.fixatoms_mask], masked_hessian,
self.tr, self.gm, self.big_step)
# Restore dimensionality of the hessian
self.hessian[np.ix_(self.gm.fixatoms_mask,
self.gm.fixatoms_mask)] = masked_hessian
else:
# Make one step. ( A step is finished when a movement is accepted)
BFGSTRM(self.old_x, self.old_u, self.old_f, self.hessian, self.tr,
self.gm, self.big_step)
info(" Number of force calls: %d" % (self.gm.fcount))
self.gm.fcount = 0
# Update positions and forces
self.beads.q = self.gm.dbeads.q
self.forces.transfer_forces(
self.gm.dforces) # This forces the update of the forces
# Exit simulation step
d_x_max = np.amax(np.absolute(np.subtract(self.beads.q, self.old_x)))
self.exitstep(self.forces.pot, self.old_u, d_x_max)
def step(self, step=None):
""" Does one simulation time step.
Attributes:
qtime : The time taken in updating the real positions.
tr : current trust radius
"""
self.qtime = -time.time()
info("\nMD STEP %d" % step, verbosity.debug)
if step == 0:
info(" @GEOP: Initializing BFGSTRM", verbosity.debug)
self.old_x[:] = self.beads.q
self.old_u[:] = self.forces.pot
self.old_f[:] = self.forces.f
if len(self.fixatoms) > 0:
for dqb in self.old_f:
dqb[self.fixatoms * 3] = 0.0
dqb[self.fixatoms * 3 + 1] = 0.0
dqb[self.fixatoms * 3 + 2] = 0.0
# Make one step. ( A step is finished when a movement is accepted)
BFGSTRM(self.old_x, self.old_u, self.old_f, self.hessian, self.tr,
self.gm, self.big_step)
info(" Number of force calls: %d" % (self.gm.fcount))
self.gm.fcount = 0
# Update positions and forces
self.beads.q = self.gm.dbeads.q
self.forces.transfer_forces(
self.gm.dforces) # This forces the update of the forces
# Exit simulation step
d_x_max = np.amax(np.absolute(np.subtract(self.beads.q, self.old_x)))
self.exitstep(self.forces.pot, self.old_u, d_x_max)