def __init__(self, system, ics, weights, comlist=None):
'''
**Arguments:**
system
An instance of the ``System`` class.
ics
A list of InternalCoordinate instances.
weights
A list defining the weight of each InternalCoordinate that is
used when computing the linear combination.
**Optional arguments:**
comlist
An instance COMList; if provided, this is used instead of the
normal DeltaList to compute the InternalCoordinates
'''
raise NotImplementedError
assert len(weights) == len(ics)
self.system = system
self.ics = ics
self.comlist = comlist
self.dlist = DeltaList(system if comlist is None else comlist)
self.iclist = InternalCoordinateList(self.dlist)
for ic in self.ics:
self.iclist.add_ic(ic)
self.weights = weights
def __init__(self, system, rules=None, cases=None):
self.system = system
self.cases = cases
# Compile the rules if they are present
if cases is None:
if rules is None:
rules = ['!0'] * self.natom
compiled_rules = []
for rule in rules:
if isinstance(rule, str):
rule = atsel_compile(rule)
compiled_rules.append(rule)
self.rules = compiled_rules
self.cases = list(self._iter_cases())
elif rules is not None:
raise ValueError(
'Either rules are cases must be provided, not both.')
# Construct a fake system, a dlist and an iclist for just one ic
self.fake_system = System(numbers=np.zeros(self.natom, int),
pos=np.zeros((self.natom, 3), float),
rvecs=self.system.cell.rvecs)
self.dlist = DeltaList(self.fake_system)
self.iclist = InternalCoordinateList(self.dlist)
self.tangent = np.zeros((self.natom, 3), float)
def __init__(self, system, ic, comlist=None):
self.system = system
self.ic = ic
self.comlist = comlist
self.dlist = DeltaList(system if comlist is None else comlist)
self.iclist = InternalCoordinateList(self.dlist)
self.iclist.add_ic(ic)
def __init__(self, comsystem, scaling=None):
ForcePart.__init__(self, 'valence_com', comsystem)
#ForcePartValence.__init__(self, system)
self.comlist = comsystem.comlist
self.gpos = np.zeros((comsystem.gpos_dim, 3), float)
self.dlist = DeltaList(self.comlist)
self.iclist = InternalCoordinateList(self.dlist)
self.vlist = ValenceList(self.iclist)
self.scaling = scaling
if log.do_medium:
with log.section('FPINIT'):
log('Force part: %s' % self.name)
log.hline()
self.term = None # volume term
def __init__(self, system):
'''
**Arguments:**
system
An instance of the ``System`` class.
'''
ForcePart.__init__(self, 'valence', system)
self.dlist = DeltaList(system)
self.iclist = InternalCoordinateList(self.dlist)
self.vlist = ValenceList(self.iclist)
if log.do_medium:
with log.section('FPINIT'):
log('Force part: %s' % self.name)
log.hline()
def __init__(self, system):
'''
Parameters
----------
system
An instance of the ``System`` class.
'''
ForcePart.__init__(self, 'valence', system)
# override self.gpos to the correct size!
# natom of COMSystem object will return number of beads
# but gpos has to have the size (n_atoms, 3), to be consisten
# with the other parts of the force field
self.dlist = DeltaList(system)
self.iclist = InternalCoordinateList(self.dlist)
self.vlist = ValenceList(self.iclist)
if log.do_medium:
with log.section('FPINIT'):
log('Force part: %s' % self.name)
log.hline()
def __init__(self, system, comlist=None):
'''
Parameters
----------
system
An instance of the ``System`` class.
comlist
An optional layer to derive centers of mass from the atomic positions.
These centers of mass are used as input for the first layer, the relative
vectors.
'''
ForcePart.__init__(self, 'valence', system)
self.comlist = comlist
self.dlist = DeltaList(system if comlist is None else comlist)
self.iclist = InternalCoordinateList(self.dlist)
self.vlist = ValenceList(self.iclist)
if log.do_medium:
with log.section('FPINIT'):
log('Force part: %s' % self.name)
log.hline()
