def __init__(self, init, beads, nm, cell, fcomponents, ensemble=None, motion=None, prefix=""):
"""Initialises System class.
Args:
init: A class to deal with initializing the system.
beads: A beads object giving the atom positions.
cell: A cell object giving the system box.
fcomponents: A list of force components that are active for each
replica of the system.
bcomponents: A list of force components that are considered as bias, and act on each
replica of the system.
ensemble: An ensemble object giving the objects necessary for
producing the correct ensemble.
nm: A class dealing with path NM operations.
prefix: A string used to differentiate the output files of different
systems.
"""
info(" # Initializing system object ", verbosity.low)
self.prefix = prefix
self.init = init
self.ensemble = ensemble
self.motion = motion
self.beads = beads
self.cell = cell
self.nm = nm
self.fcomp = fcomponents
self.forces = Forces()
self.properties = Properties()
self.trajs = Trajectories()
def __init__(self, eens=0.0, econs=0.0, temp=None, pext=None, stressext=None, bcomponents=None, bweights=None, hweights=None, time=0.0):
"""Initialises Ensemble.
Args:
temp: The temperature.
fixcom: An optional boolean which decides whether the centre of mass
motion will be constrained or not. Defaults to False.
"""
dself = dd(self)
dself.temp = depend_value(name='temp')
if temp is not None:
self.temp = temp
else:
self.temp = -1.0
dself.stressext = depend_array(name='stressext',
value=np.zeros((3, 3), float))
if stressext is not None:
self.stressext = np.reshape(np.asarray(stressext), (3, 3))
else:
self.stressext = -1.0
dself.pext = depend_value(name='pext')
if pext is not None:
self.pext = pext
else:
self.pext = -1.0
dself.eens = depend_value(name='eens')
if eens is not None:
self.eens = eens
else:
self.eens = 0.0
# the bias force contains two bits: explicit biases (that are meant to represent non-physical external biasing potentials)
# and hamiltonian weights (that will act by scaling different physical components of the force). Both are bound as components
# of the "bias force" evaluator, but their meaning (and the wiring further down in bind()) differ.
# these are the additional bias components
if bcomponents is None:
bcomponents = []
self.bcomp = bcomponents
self.bias = Forces()
# and their weights
if bweights is None or len(bweights) == 0:
bweights = np.ones(len(self.bcomp))
dself.bweights = depend_array(name="bweights", value=np.asarray(bweights))
# weights of the Hamiltonian scaling
if hweights is None:
hweights = np.ones(0)
self.hweights = np.asarray(hweights)
# Internal time counter
dd(self).time = depend_value(name='time')
self.time = time
def __init__(self,
beads,
cell,
forces,
ensemble,
prng,
outputs,
nm,
init,
step=0,
tsteps=1000,
ttime=0):
"""Initialises Simulation class.
Args:
beads: A beads object giving the atom positions.
cell: A cell object giving the system box.
forces: A forcefield object giving the force calculator for each
replica of the system.
ensemble: An ensemble object giving the objects necessary for
producing the correct ensemble.
prng: A random number object.
outputs: A list of output objects.
nm: A class dealing with path NM operations.
init: A class to deal with initializing the simulation object.
step: An optional integer giving the current simulation time step.
Defaults to 0.
tsteps: An optional integer giving the total number of steps. Defaults
to 1000.
ttime: The simulation running time. Used on restart, to keep a
cumulative total.
"""
info(" # Initializing simulation object ", verbosity.low)
self.prng = prng
self.ensemble = ensemble
self.beads = beads
self.cell = cell
self.nm = nm
# initialize the configuration of the system
self.init = init
init.init_stage1(self)
self.flist = forces
self.forces = Forces()
self.outputs = outputs
dset(self, "step", depend_value(name="step", value=step))
self.tsteps = tsteps
self.ttime = ttime
self.properties = Properties()
self.trajs = Trajectories()
self.chk = None
self.rollback = True