def __call__(self, *args, **kwargs):
fail_reasons = []
for typespec in self._versions:
fargs, fkwargs_or_fail_reason = typespec.get_arg_list(*args, **kwargs)
if fargs is not None:
return typespec.func(*fargs, **fkwargs_or_fail_reason)
else:
fail_reasons.append(fkwargs_or_fail_reason or '<unknown reason for failed match>')
# Should we fall back on the original function's code here? If so, we should catch and reraise any type errors
raise TypeError("invalid function signature {0}.\n Available signatures are:\n{1}".format(
argtypespec.get_call_signature(self.__name__, *args, **kwargs),
indented('\n'.join(line + "\n" + indented("Not valid signature because: " + reason)
for line, reason in zip(self._build_allowed_string().splitlines(), fail_reasons)))
))
def parse_qchem_matrix(data):
ret_val = [[]]
def parse_line(cols, m):
row = int(m.group(1)) - 1
data = [float(f) for f in m.group(2).strip().split()]
while len(ret_val) < row + 1:
ret_val.append([])
while len(ret_val[row]) < cols[-1] + 1:
ret_val[row].append(None)
if len(cols) != len(data):
raise OutputParsingError("ragged matrix in output:\n{}".format(indented(data)))
for d, col in zip(data, cols):
ret_val[row][col] = d
def parse_group_of_lines(m):
columns = [int(s.strip()) - 1 for s in m.group(1).split()]
re.sub(r"(\d)((?:\s+-?\d+\.\d+)+)", partial(parse_line, columns), m.group(2))
re.sub(r"((?:\d+[ \t]*)+\n)[ \t]+((?:\d+(?:\s+-?\d+\.\d+)+\s+)+)", parse_group_of_lines, data)
if None in flattened(ret_val):
raise OutputParsingError("output matrix missing value:\n{}".format(indented(data)))
return Matrix(ret_val)
def __str__(self):
return "InternalRepresentation of {} with coordinates\n{}".format(
shortstr(self.molecule),
indented('\n'.join('[{}] {}: {}'.format(
i, shortstr(coord), str(coord.value_with_units)
) for i, coord in enumerate(self.coords)))
)
def assertOkayFdiffDerivative(self,
poly,
vars,
places=4,
robustness=2,
forward=False):
""" Assert almost equal with significant figures rather than digits after the decimal
"""
df = FiniteDifferenceDerivative(poly,
*tuple(vars),
robustness=robustness,
forward=forward).value
exp = poly.actual_derivative(*tuple(vars))
if abs(exp) > 0:
div = 10.0**float(math.ceil(math.log(abs(exp), 10.0)))
ract = round(df / div, places)
rexp = round(exp / div, places)
else:
ract = round(df, places)
rexp = round(exp, places)
tmp = self.longMessage
self.longMessage = True
try:
#("%"+str(places+1)+"f") % rexp, ("%"+str(places+1)+"f") % ract,
self.assertAlmostEqual(
ract,
rexp,
places,
msg="\nfor derivative {} with robustness {} of function:\n{}".
format(vars, robustness, indented(str(poly))))
finally:
self.longMessage = tmp
def validate(self):
bmat = self.b_matrix
evals = np.linalg.eigvalsh(bmat * bmat.T)
nvalid = len([e for e in evals if abs(e) > InternalRepresentation.zero_eigenvalue])
if nvalid != self.molecule.ninternals:
raise RepresentationError("Have {} nonredundant internal coordinates, but need {}.\nCoordnates are:\n{}".format(
nvalid,
self.molecule.ninternals,
indented('\n'.join('[' + str(i) + '] ' + shortstr(c) for i, c in enumerate(self.coords)))
))
def __repr__(self):
return "FiniteDifferenceFormula({dord}, {rob}, [\n{terms}\n])".format(
dord=repr(self.orders),
rob=self.robustness,
terms=indented(
',\n'.join(repr((coeff, deltas)) for deltas, coeff in
sorted(self.coefficients.items(), key=lambda x: ' '.join(str(i) for i in x[0]))
if coeff != 0)
)
)
def __call__(self, *args, **kwargs):
fargs, fkwargs = self._typespec.get_arg_list(*args, **kwargs)
if fargs is not None:
return self._typespec.func(*fargs, **fkwargs)
else:
raise TypeError("invalid function signature {0}.\n Function call must have" \
" the form:\n{1}\n which is not a valid signature because: {2}".format(
argtypespec.get_call_signature(self.__name__, *args, **kwargs),
indented(self._typespec.signature),
fkwargs
))
def parse_line(cols, m):
row = int(m.group(1)) - 1
data = [float(f) for f in m.group(2).strip().split()]
while len(ret_val) < row + 1:
ret_val.append([])
while len(ret_val[row]) < cols[-1] + 1:
ret_val[row].append(None)
if len(cols) != len(data):
raise OutputParsingError("ragged matrix in output:\n{}".format(indented(data)))
for d, col in zip(data, cols):
ret_val[row][col] = d
def __call__(self, *args, **kwargs):
fail_reasons = []
for typespec in self._versions:
fargs, fkwargs_or_fail_reason = typespec.get_arg_list(
*args, **kwargs)
if fargs is not None:
return typespec.func(*fargs, **fkwargs_or_fail_reason)
else:
fail_reasons.append(fkwargs_or_fail_reason
or '<unknown reason for failed match>')
# Should we fall back on the original function's code here? If so, we should catch and reraise any type errors
raise TypeError(
"invalid function signature {0}.\n Available signatures are:\n{1}"
.format(
argtypespec.get_call_signature(self.__name__, *args, **kwargs),
indented('\n'.join(
line + "\n" +
indented("Not valid signature because: " + reason)
for line, reason in zip(
self._build_allowed_string().splitlines(),
fail_reasons)))))
def __repr__(self):
return "FiniteDifferenceFormula({dord}, {rob}, [\n{terms}\n])".format(
dord=repr(self.orders),
rob=self.robustness,
terms=indented(
",\n".join(
repr((coeff, deltas))
for deltas, coeff in sorted(self.coefficients.items(), key=lambda x: " ".join(str(i) for i in x[0]))
if coeff != 0
)
),
)
def validate(self):
bmat = self.b_matrix
evals = np.linalg.eigvalsh(bmat * bmat.T)
nvalid = len([
e for e in evals if abs(e) > InternalRepresentation.zero_eigenvalue
])
if nvalid != self.molecule.ninternals:
raise RepresentationError(
"Have {} nonredundant internal coordinates, but need {}.\nCoordnates are:\n{}"
.format(
nvalid, self.molecule.ninternals,
indented('\n'.join('[' + str(i) + '] ' + shortstr(c)
for i, c in enumerate(self.coords)))))
def assertOkayFdiffDerivative(self, poly, vars, places=4, robustness=2, forward=False):
""" Assert almost equal with significant figures rather than digits after the decimal
"""
df = FiniteDifferenceDerivative(poly, *tuple(vars), robustness=robustness, forward=forward).value
exp = poly.actual_derivative(*tuple(vars))
if abs(exp) > 0:
div = 10.0 ** float(math.ceil(math.log(abs(exp), 10.0)))
ract = round(df/div, places)
rexp = round(exp/div, places)
else:
ract = round(df, places)
rexp = round(exp, places)
tmp = self.longMessage
self.longMessage = True
try:
#("%"+str(places+1)+"f") % rexp, ("%"+str(places+1)+"f") % ract,
self.assertAlmostEqual(ract, rexp, places,
msg="\nfor derivative {} with robustness {} of function:\n{}".format(
vars, robustness, indented(str(poly)))
)
finally:
self.longMessage = tmp
def __str__(self):
return "InternalRepresentation of {} with coordinates\n{}".format(
shortstr(self.molecule),
indented('\n'.join('[{}] {}: {}'.format(
i, shortstr(coord), str(coord.value_with_units))
for i, coord in enumerate(self.coords))))
def __str__(self):
max_width = 80
indent_size = 4
function_name = "F"
disp_name = "h"
# ----------------------------------------#
def var(idx):
vars = "xyz" + str(reversed(string.ascii_lowercase[:-3]))
vars = vars.replace(disp_name, "")
vars = vars.replace(function_name, "")
try:
return vars[idx]
except IndexError:
return "x_" + idx
# ----------------------------------------#
flines = []
curr_line = "["
for dispnum, (disp, coeff) in enumerate(sorted(self.coefficients.items())):
if coeff == 0:
continue
if coeff.denominator == 1:
# Only print non-unit coefficients
if abs(coeff) != 1:
disp_f = str(abs(coeff))
else:
disp_f = ""
else:
disp_f = "(" + str(abs(coeff)) + ")"
disp_f += function_name + "("
for idx, d in enumerate(disp):
disp_f += var(idx)
if d == -1:
disp_f += " - " + disp_name + "_" + var(idx)
elif d == 1:
disp_f += " + " + disp_name + "_" + var(idx)
elif d < 0:
disp_f += " - " + str(abs(d)) + disp_name + "_" + var(idx)
elif d > 0:
disp_f += " + " + str(d) + disp_name + "_" + var(idx)
if d is not disp[-1]:
disp_f += ", "
disp_f += ")"
if dispnum != 0:
if coeff < 0:
disp_f = " - " + disp_f
else:
disp_f = " + " + disp_f
elif coeff < 0: # and dispnum == 0
disp_f = "-" + disp_f
if len(curr_line + disp_f) > (max_width if len(flines) == 0 else max_width - indent_size):
if curr_line != "":
flines.append(curr_line)
curr_line = disp_f
else:
# one term per line is the best we can do, and we still overflow...yikes...
flines.append(disp_f)
else:
curr_line += disp_f
denom = "] / "
if len(self.orders) > 1:
denom += "("
for idx, exp in enumerate(self.orders):
denom += disp_name + "_" + var(idx)
if exp > 1:
denom += "^" + str(exp)
if len(self.orders) > 1:
denom += ")"
if len(curr_line + denom) > (max_width if len(flines) == 0 else max_width - indent_size):
if curr_line != "":
flines.append(curr_line)
curr_line = denom
else:
curr_line = denom
else:
curr_line += denom
flines.append(curr_line)
return (
"{cent} finite difference formula for df/{dvars},"
" correct to order {order} in displacement ({terms} terms):\n{formula}".format(
cent="Central" if self.direction == FiniteDifferenceFormula.CENTRAL else "Forward",
order=self.robustness,
dvars="".join(
"d" + var(idx) + ("^" + str(exp) if exp > 1 else "") for idx, exp in enumerate(self.orders)
),
formula=indented(("\n" + " " * indent_size).join(flines), indent_size),
terms=len([c for c in self.coefficients.values() if c != 0]),
)
)
def value_for_displacements(self, pairs):
# Type checking and sanity checking
if type_checking_enabled:
if not all(len(pair) == 2 and isinstance(pair[0], FiniteDifferenceVariable) and isinstance(pair[1], int) for pair in pairs):
raise TypeError
if sanity_checking_enabled:
for pair in pairs:
if not isinstance(pair[0], Coordinate):
raise ValueError(
"FiniteDifferenceVariable instances passed to"
" DisplacementManager.value_for_displacements"
" must be instances of Coordinate subclasses."
" (Got at least one that was a {0})".format(
type(pair[0]).__name__
))
#--------------------------------------------------------------------------------#
# prepare the increments
increments = [0]*len(self.representation)
for coord, ndeltas in pairs:
i = self.representation.coords.index(coord)
increments[i] = ndeltas
increments = tuple(increments)
#--------------------------------------------------------------------------------#
# get the displacement, and ask the displaced molecule for the property
try:
displacement = self.displacement_for(increments)
rv = displacement.displaced_molecule.get_property(
self.differentiable,
details=self.details
)
if rv is None:
raise ValueError("couldn't get displacement for increments {}".format(increments))
return rv
#--------------------------------------------------------------------------------#
# Old debugging code. Only applies to LegacyXMLResultGetter
except RuntimeError as e:
if all(isinstance(rg, LegacyXMLResultGetter)
for rg in self.displacements[increments].displaced_molecule.result_getters):
legacy_getters = [rg
for rg in self.base_molecule.result_getters
if isinstance(rg, LegacyXMLResultGetter)]
molecule = self.displacements[increments].displaced_molecule
smallest_dist = float('inf') * molecule.cartesian_units
smallest_dist_stub = None
best_rg = None
mol = copy(molecule); mol.convert_units(DistanceUnit.default)
for rg in legacy_getters:
for stub in rg.properties.keys():
st = copy(stub); st.convert_units(DistanceUnit.default)
ldiff = rg.properties.key_representation.value_for_molecule(stub)
ldiff -= rg.properties.key_representation.value_for_molecule(mol)
ldiff = abs(ldiff)
if max(ldiff) < smallest_dist:
best_rg = rg
smallest_dist = max(ldiff)
smallest_dist_stub = st
if smallest_dist_stub is not None:
# Print debugging information for legacy xml parser
print("Failed to find match. Smallest " \
"maximum geometric difference was {}".format(smallest_dist),
file=sys.stderr)
print(indented(
"Desired molecule representation " \
"was:\n{}".format(indented(str(molecule.internal_representation.copy_with_molecule(mol))))
), file=sys.stderr)
print(indented(
'-'*40 +
"\nClosest stub in the same representation:\n{}".format(
indented(str(molecule.internal_representation.copy_with_molecule(smallest_dist_stub))))
), file=sys.stderr)
print("Tree leaf: \n{}".format(
best_rg.properties._get_possibilities(mol)
), file=sys.stderr)
print("Chains: \nMolecule:\n{}\nStub:\n{}".format(
indented(str(best_rg.properties._key_chain_str(mol))),
indented(str(best_rg.properties._key_chain_str(smallest_dist_stub))),
), file=sys.stderr)
sys.stderr.flush()
raise RuntimeError("couldn't get {} for displacements {}".format(
self.differentiable.__name__,
increments
))
else:
raise
def __str__(self):
max_width=80
indent_size = 4
function_name = 'F'
disp_name = 'h'
#----------------------------------------#
def var(idx):
vars = 'xyz' + str(reversed(string.ascii_lowercase[:-3]))
vars = vars.replace(disp_name, '')
vars = vars.replace(function_name, '')
try:
return vars[idx]
except IndexError:
return 'x_' + idx
#----------------------------------------#
flines = []
curr_line = '['
for dispnum, (disp, coeff) in enumerate(sorted(self.coefficients.items())):
if coeff == 0:
continue
if coeff.denominator == 1:
# Only print non-unit coefficients
if abs(coeff) != 1:
disp_f = str(abs(coeff))
else:
disp_f = ''
else:
disp_f = '(' + str(abs(coeff)) + ')'
disp_f += function_name + '('
for idx, d in enumerate(disp):
disp_f += var(idx)
if d == -1:
disp_f += ' - ' + disp_name + '_' + var(idx)
elif d == 1:
disp_f += ' + ' + disp_name + '_' + var(idx)
elif d < 0:
disp_f += ' - ' + str(abs(d)) + disp_name + '_' + var(idx)
elif d > 0:
disp_f += ' + ' + str(d) + disp_name + '_' + var(idx)
if d is not disp[-1]:
disp_f += ', '
disp_f += ')'
if dispnum != 0:
if coeff < 0:
disp_f = ' - ' + disp_f
else:
disp_f = ' + ' + disp_f
elif coeff < 0: # and dispnum == 0
disp_f = '-' + disp_f
if len(curr_line + disp_f) > (max_width if len(flines) == 0 else max_width - indent_size):
if curr_line != '':
flines.append(curr_line)
curr_line = disp_f
else:
# one term per line is the best we can do, and we still overflow...yikes...
flines.append(disp_f)
else:
curr_line += disp_f
denom = '] / '
if len(self.orders) > 1:
denom += '('
for idx, exp in enumerate(self.orders):
denom += disp_name + '_' + var(idx)
if exp > 1:
denom += '^' + str(exp)
if len(self.orders) > 1:
denom += ')'
if len(curr_line + denom) > (max_width if len(flines) == 0 else max_width - indent_size):
if curr_line != '':
flines.append(curr_line)
curr_line = denom
else:
curr_line = denom
else:
curr_line += denom
flines.append(curr_line)
return '{cent} finite difference formula for df/{dvars},' \
' correct to order {order} in displacement ({terms} terms):\n{formula}'.format(
cent='Central' if self.direction == FiniteDifferenceFormula.CENTRAL else 'Forward',
order = self.robustness,
dvars=''.join('d' + var(idx) + ('^'+str(exp) if exp > 1 else '')
for idx, exp in enumerate(self.orders)),
formula=indented(('\n' + ' ' * indent_size).join(flines), indent_size),
terms=len([c for c in self.coefficients.values() if c != 0])
)