def transform_forcefield(self, ff, to_representation):
self.freeze()
to_representation.freeze()
if sanity_checking_enabled and ff.representation is not self:
raise ValueError(
"int_rep.transform_forcefield must be given a force field whose"
" representation is int_rep")
rv = ForceField(to_representation, ff.max_order, ff.molecular_property,
ff.property_units)
if isinstance(to_representation, CartesianRepresentation):
B = self.b_tensor(cartesian_representation=to_representation)
rv.for_order(1)[...] = self.transform_tensor(
ff.for_order(1), to_representation)
for o in xrange(1, ff.max_order + 1):
B.for_order(o).fill()
if ff.max_order >= 2:
# Do this by hand to speed things up...
rv['i1,i2'] = ff['p1'] * B['p1,i1,i2'] + ff['p1,p2'] * B[
'p1,i1'] * B['p2,i2']
# TODO Permutational symmetry?
#if ff.max_order >= 3:
# # Do this by hand also to speed things up...
# # The three middle terms could be done more efficiently by first summing
# # over them and then doing the contraction, but this is not yet implemented
# # for einstein summation
# rv['i1,i2,i3'] = ff['p1']*B['p1,i1,i2,i3'] + ff['p1,p2,p3']*B['p1,i1']*B['p2,i2']*B['p3,i3']
# for s in I_lubar(3, 2, ('i1','i2','i3')):
# rv['i1,i2,i3'] += ff['p1,p2']*B[('p1',)+s[0]]*B[('p2',) + s[1]]
if ff.max_order >= 3:
def idxstrs(letter, num):
return tuple(
map(lambda x: letter + str(x), xrange(num)))
for order in xrange(3, ff.max_order + 1):
iidxs = idxstrs('i', order)
for k in xrange(1, order + 1):
for cartsets in I_lubar(order, k, iidxs):
rv[iidxs] += ff[idxstrs('p', k)] * prod(
B[('p' + str(m), ) + cartsets[m]]
for m in xrange(k))
return rv
elif isinstance(to_representation, InternalRepresentation):
# use an intermediary
intermed = self.molecule.cartesian_representation
return ff.in_representation(intermed).in_representation(
to_representation)
elif isinstance(to_representation, NormalRepresentation):
# use an intermediary
intermed = self.molecule.cartesian_representation
return ff.in_representation(intermed).in_representation(
to_representation)
else:
raise NotImplementedError
def transform_forcefield(self, ff, to_representation):
self.freeze()
to_representation.freeze()
if sanity_checking_enabled and ff.representation is not self:
raise ValueError("int_rep.transform_forcefield must be given a force field whose"
" representation is int_rep")
rv = ForceField(to_representation, ff.max_order, ff.molecular_property, ff.property_units)
if isinstance(to_representation, CartesianRepresentation):
B = self.b_tensor(cartesian_representation=to_representation)
rv.for_order(1)[...] = self.transform_tensor(ff.for_order(1), to_representation)
for o in xrange(1, ff.max_order+1):
B.for_order(o).fill()
if ff.max_order >= 2:
# Do this by hand to speed things up...
rv['i1,i2'] = ff['p1']*B['p1,i1,i2'] + ff['p1,p2']*B['p1,i1']*B['p2,i2']
# TODO Permutational symmetry?
#if ff.max_order >= 3:
# # Do this by hand also to speed things up...
# # The three middle terms could be done more efficiently by first summing
# # over them and then doing the contraction, but this is not yet implemented
# # for einstein summation
# rv['i1,i2,i3'] = ff['p1']*B['p1,i1,i2,i3'] + ff['p1,p2,p3']*B['p1,i1']*B['p2,i2']*B['p3,i3']
# for s in I_lubar(3, 2, ('i1','i2','i3')):
# rv['i1,i2,i3'] += ff['p1,p2']*B[('p1',)+s[0]]*B[('p2',) + s[1]]
if ff.max_order >= 3:
def idxstrs(letter, num): return tuple(map(lambda x: letter + str(x), xrange(num)))
for order in xrange(3, ff.max_order + 1):
iidxs = idxstrs('i', order)
for k in xrange(1, order+1):
for cartsets in I_lubar(order, k, iidxs):
rv[iidxs] += ff[idxstrs('p', k)] * prod(
B[('p'+str(m),) + cartsets[m]] for m in xrange(k)
)
return rv
elif isinstance(to_representation, InternalRepresentation):
# use an intermediary
intermed = self.molecule.cartesian_representation
return ff.in_representation(intermed).in_representation(to_representation)
elif isinstance(to_representation, NormalRepresentation):
# use an intermediary
intermed = self.molecule.cartesian_representation
return ff.in_representation(intermed).in_representation(to_representation)
else:
raise NotImplementedError
def transform_forcefield(self, ff, to_representation):
self.freeze()
to_representation.freeze()
if sanity_checking_enabled and ff.representation is not self:
raise ValueError(
"cart_rep.transform_forcefield must be given a force field whose"
" representation is cart_rep")
rv = ForceField(to_representation, ff.max_order, ff.molecular_property,
ff.property_units)
if isinstance(to_representation, CartesianRepresentation):
for order in xrange(1, ff.max_order + 1):
rv[...] = self.transform_tensor(ff.for_order(order),
to_representation)
return rv
elif isinstance(to_representation, NormalRepresentation):
for order in xrange(1, ff.max_order + 1):
rv[...] = self.transform_tensor(ff.for_order(order),
to_representation)
return rv
elif isinstance(to_representation, InternalRepresentation):
# Units should take care of themselves here. This is because
# the B tensor should have units (to-representation units)/(cart-representation units)**order
# TODO write a test that checks the fact that units take care of themselves
A = DerivativeCollection(
representation=self,
first_dimension_different=True,
secondary_representation=to_representation,
uncomputed=False)
A.for_order(1)[...] = to_representation.a_matrix
B = to_representation.b_tensor(cartesian_representation=self)
rv.for_order(1)[...] = A.for_order(1).view(
Matrix).T * ff.for_order(1).view(Vector)
if ff.max_order >= 2:
C = DerivativeCollection(representation=to_representation,
uncomputed=False)
C['q,p1,p2'] = B['q,i1,i2'] * A['i1,p1'] * A['i2,p2']
rv['p1,p2'] = ff['i1,i2'] * A['i1,p1'] * A['i2,p2'] - rv[
'q'] * C['q,p1,p2']
#--------------------------------------------------------------------------------#
if ff.max_order >= 3:
# Do third order by hand...
C['q,p1,p2,p3'] = B['q,i1,i2,i3'] * A['i1,p1'] * A[
'i2,p2'] * A['i3,p3']
rv['p1,p2,p3'] = ff['i1,i2,i3'] * A['i1,p1'] * A[
'i2,p2'] * A['i3,p3']
rv['p1,p2,p3'] -= rv['q,p1'] * C['q,p2,p3']
rv['p1,p2,p3'] -= rv['q,p2'] * C['q,p1,p3']
rv['p1,p2,p3'] -= rv['q,p3'] * C['q,p1,p2']
rv['p1,p2,p3'] -= rv['q'] * C['q,p1,p2,p3']
if ff.max_order >= 4:
def idxstrs(letter, num):
return tuple(
map(lambda x: letter + str(x), xrange(num)))
for order in xrange(4, ff.max_order + 1):
p_s = idxstrs('p', order)
i_s = idxstrs('i', order)
C[('q', ) + p_s] = B[('q', ) + i_s] * prod(
A[i, p] for i, p in zip(i_s, p_s))
rv[p_s] = ff[i_s] * prod(A[i, p]
for i, p in zip(i_s, p_s))
rv[p_s] -= rv['q'] * C[('q', ) + p_s]
for k in xrange(2, order):
q_s = idxstrs('q', k)
for s in I_lubar(order, k, p_s):
if any(len(seg) == 1 for seg in s):
continue
rv[p_s] -= rv[q_s] * prod(
C[(q_s[m], ) + s[m]]
for m in xrange(k))
q_s = idxstrs('q', k - 1)
for part1len in xrange(1, order - 2 * (k - 1) +
1):
part2len = order - part1len
for p1idxs, p2idxs in m_way_ordered_combinations(
order, [part1len, part2len]):
p1s = tuple(p_s[pidx]
for pidx in p1idxs)
p2s = tuple(p_s[pidx]
for pidx in p2idxs)
print(p1s, p2s, k)
for s in I_lubar(part2len, k - 1, p2s):
rv[p_s] -= rv[q_s + p1s] * prod(
C[(alpha, ) + betas]
for alpha, betas in zip(
q_s, s))
return rv
else:
raise NotImplementedError
def transform_forcefield(self, ff, to_representation):
self.freeze()
to_representation.freeze()
if sanity_checking_enabled and ff.representation is not self:
raise ValueError(
"cart_rep.transform_forcefield must be given a force field whose" " representation is cart_rep"
)
rv = ForceField(to_representation, ff.max_order, ff.molecular_property, ff.property_units)
if isinstance(to_representation, CartesianRepresentation):
for order in xrange(1, ff.max_order + 1):
rv[...] = self.transform_tensor(ff.for_order(order), to_representation)
return rv
elif isinstance(to_representation, NormalRepresentation):
for order in xrange(1, ff.max_order + 1):
rv[...] = self.transform_tensor(ff.for_order(order), to_representation)
return rv
elif isinstance(to_representation, InternalRepresentation):
# Units should take care of themselves here. This is because
# the B tensor should have units (to-representation units)/(cart-representation units)**order
# TODO write a test that checks the fact that units take care of themselves
A = DerivativeCollection(
representation=self,
first_dimension_different=True,
secondary_representation=to_representation,
uncomputed=False,
)
A.for_order(1)[...] = to_representation.a_matrix
B = to_representation.b_tensor(cartesian_representation=self)
rv.for_order(1)[...] = A.for_order(1).view(Matrix).T * ff.for_order(1).view(Vector)
if ff.max_order >= 2:
C = DerivativeCollection(representation=to_representation, uncomputed=False)
C["q,p1,p2"] = B["q,i1,i2"] * A["i1,p1"] * A["i2,p2"]
rv["p1,p2"] = ff["i1,i2"] * A["i1,p1"] * A["i2,p2"] - rv["q"] * C["q,p1,p2"]
# --------------------------------------------------------------------------------#
if ff.max_order >= 3:
# Do third order by hand...
C["q,p1,p2,p3"] = B["q,i1,i2,i3"] * A["i1,p1"] * A["i2,p2"] * A["i3,p3"]
rv["p1,p2,p3"] = ff["i1,i2,i3"] * A["i1,p1"] * A["i2,p2"] * A["i3,p3"]
rv["p1,p2,p3"] -= rv["q,p1"] * C["q,p2,p3"]
rv["p1,p2,p3"] -= rv["q,p2"] * C["q,p1,p3"]
rv["p1,p2,p3"] -= rv["q,p3"] * C["q,p1,p2"]
rv["p1,p2,p3"] -= rv["q"] * C["q,p1,p2,p3"]
if ff.max_order >= 4:
def idxstrs(letter, num):
return tuple(map(lambda x: letter + str(x), xrange(num)))
for order in xrange(4, ff.max_order + 1):
p_s = idxstrs("p", order)
i_s = idxstrs("i", order)
C[("q",) + p_s] = B[("q",) + i_s] * prod(A[i, p] for i, p in zip(i_s, p_s))
rv[p_s] = ff[i_s] * prod(A[i, p] for i, p in zip(i_s, p_s))
rv[p_s] -= rv["q"] * C[("q",) + p_s]
for k in xrange(2, order):
q_s = idxstrs("q", k)
for s in I_lubar(order, k, p_s):
if any(len(seg) == 1 for seg in s):
continue
rv[p_s] -= rv[q_s] * prod(C[(q_s[m],) + s[m]] for m in xrange(k))
q_s = idxstrs("q", k - 1)
for part1len in xrange(1, order - 2 * (k - 1) + 1):
part2len = order - part1len
for p1idxs, p2idxs in m_way_ordered_combinations(order, [part1len, part2len]):
p1s = tuple(p_s[pidx] for pidx in p1idxs)
p2s = tuple(p_s[pidx] for pidx in p2idxs)
print(p1s, p2s, k)
for s in I_lubar(part2len, k - 1, p2s):
rv[p_s] -= rv[q_s + p1s] * prod(
C[(alpha,) + betas] for alpha, betas in zip(q_s, s)
)
return rv
else:
raise NotImplementedError
