def _init_gle_matrices(self, simulator):
a_matrix, c_matrix = load_gle_matrices(self.gle_file)
if a_matrix is None:
raise ThermostatError('Error reading GLE matrices '
'from {:s}'.format(self.gle_file))
if a_matrix.shape[0] != self.n_replicas:
raise ThermostatError('Expected {:d} beads but '
'found {:d}.'.format(self.n_replicas,
a_matrix.shape[0]))
if not type(simulator.integrator) is RingPolymer:
raise ThermostatError('PIGLET thermostat should only be used with '
'RPMD.')
all_c1 = []
all_c2 = []
# Generate main matrices
for b in range(self.n_replicas):
c1, c2 = self._init_single_gle_matrix(a_matrix[b],
(c_matrix[b],
None)[c_matrix is None],
simulator)
# Add extra dimension for use with torch.cat, correspond to normal
# modes of ring polymer
all_c1.append(c1[None, ...])
all_c2.append(c2[None, ...])
# Bring to correct shape for later matmul broadcasting
c1 = torch.cat(all_c1)[:, None, None, :, :]
c2 = torch.cat(all_c2)[:, None, None, :, :]
return c1, c2
def _init_gle_matrices(self, simulator):
a_matrix, c_matrix = load_gle_matrices(self.gle_file)
if a_matrix is None:
raise ThermostatError('Error reading GLE matrices from {:s}'.format(self.gle_file))
elif a_matrix.shape[0] > 1:
raise ThermostatError('More than one A matrix found. Could be PIGLET input.')
else:
# Remove leading dimension (for normal modes)
a_matrix = a_matrix.squeeze()
c1, c2 = self._init_single_gle_matrix(a_matrix, c_matrix, simulator)
return c1, c2