class CVInternalCoordinate(CollectiveVariable):
'''
An InternalCoordinate disguised as a CollectiveVariable so that it can
be used together with a BiasPotential.
This is less efficient than using the InternalCoordinate with a
ValenceTerm, so the latter is preferred if it is possible.
'''
def __init__(self, system, ic, comlist=None):
raise NotImplementedError
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 get_conversion(self):
return self.ic.get_conversion()
def compute(self, gpos=None, vtens=None):
if self.comlist is not None:
self.comlist.forward()
self.dlist.forward()
self.iclist.forward()
self.value = self.iclist.ictab[0]['value']
if gpos is not None: gpos[:] = 0.0
if vtens is not None: vtens[:] = 0.0
if not ((gpos is None) and (vtens is None)):
self.iclist.ictab[0]['grad'] = 1.0
self.iclist.back()
if self.comlist is None:
self.dlist.back(gpos, vtens)
else:
self.comlist.gpos[:] = 0.0
self.dlist.back(self.comlist.gpos, vtens)
self.comlist.back(gpos)
return self.value
class CVLinCombIC(CollectiveVariable):
'''
A linear combination of InternalCoordinates:
cv = w0*ic0 + w1*ic1 + ...
'''
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 get_conversion(self):
# Units depend on the particular linear combination of internal
# coordinates
return 1.0
def compute(self, gpos=None, vtens=None):
if self.comlist is not None:
self.comlist.forward()
self.dlist.forward()
self.iclist.forward()
self.value = 0.0
for iic in range(len(self.ics)):
self.value += self.weights[iic] * self.iclist.ictab[iic]['value']
if gpos is not None: gpos[:] = 0.0
if vtens is not None: vtens[:] = 0.0
if not ((gpos is None) and (vtens is None)):
for iic in range(len(self.ics)):
# Derivative of the linear combination to this particular
# internal coordinate
self.iclist.ictab[iic]['grad'] = self.weights[iic]
self.iclist.back()
if self.comlist is None:
self.dlist.back(gpos, vtens)
else:
self.comlist.gpos[:] = 0.0
self.dlist.back(self.comlist.gpos, vtens)
self.comlist.back(gpos)
return self.value
