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()
