def _initialize_findif(mol,
freq_irrep_only,
mode,
initialize_string,
verbose=0):
"""Perform initialization tasks needed by all primary functions.
Parameters
----------
mol : qcdb.molecule or psi4.core.Molecule
The molecule to displace
freq_irrep_only : int
The Cotton ordered irrep to get frequencies for. Choose -1 for all
irreps.
mode : {"1_0", "2_0", "2_1"}
The first number specifies the derivative level determined from
displacements, and the second number is the level determined at.
initialize_string : function
A function that returns the string to print to show the caller was entered.
The string is both caller-specific and dependent on values determined
in this function.
verbose : int
Set to 0 to silence extra print information, regardless of the print level.
Used so the information is printed only during geometry generation, and not
during the derivative computation as well.
:returns: *dict*
Miscellaneous information required by callers.
"""
core.print_out(
"\n ----------------------------------------------------------\n"
)
core.print_out(" FINDIF\n")
core.print_out(" R. A. King and Jonathon Misiewicz\n")
core.print_out(
" ---------------------------------------------------------\n\n"
)
print_lvl = core.get_option("FINDIF", "PRINT")
num_pts = core.get_option("FINDIF", "POINTS")
disp_size = core.get_option("FINDIF", "DISP_SIZE")
data = {"print_lvl": print_lvl, "num_pts": num_pts, "disp_size": disp_size}
if print_lvl:
core.print_out(initialize_string(data))
# Get settings for CdSalcList, then get the CdSalcList.
method_allowed_irreps = 0x1 if mode == "1_0" else 0xFF
t_project = not core.get_global_option("EXTERN") and (
not core.get_global_option("PERTURB_H"))
# core.get_option returns an int, but CdSalcList expect a bool, so re-cast
r_project = t_project and bool(core.get_option("FINDIF", "FD_PROJECT"))
salc_list = core.CdSalcList(mol, method_allowed_irreps, t_project,
r_project)
n_atom = mol.natom()
n_irrep = salc_list.nirrep()
n_salc = salc_list.ncd()
if print_lvl and verbose:
core.print_out(" Number of atoms is {:d}.\n".format(n_atom))
if method_allowed_irreps != 0x1:
core.print_out(" Number of irreps is {:d}.\n".format(n_irrep))
core.print_out(" Number of {!s}SALCs is {:d}.\n".format(
"" if method_allowed_irreps != 0x1 else "symmetric ", n_salc))
core.print_out(
" Translations projected? {:d}. Rotations projected? {:d}.\n".
format(t_project, r_project))
# TODO: Replace with a generator from a stencil to a set of points.
# Diagonal displacements differ between the totally symmetric irrep, compared to all others.
# Off-diagonal displacements are the same for both.
pts_dict = {
3: {
"sym_irr": ((-1, ), (1, )),
"asym_irr": ((-1, ), ),
"off": ((1, 1), (-1, -1))
},
5: {
"sym_irr": ((-2, ), (-1, ), (1, ), (2, )),
"asym_irr": ((-2, ), (-1, )),
"off": ((-1, -2), (-2, -1), (-1, -1), (1, -1), (-1, 1), (1, 1),
(2, 1), (1, 2))
}
}
if num_pts not in pts_dict:
raise ValidationError("FINDIF: Invalid number of points!")
# Convention: x_pi means x_per_irrep. The ith element is x for irrep i, with Cotton ordering.
salc_indices_pi = [[] for h in range(n_irrep)]
# Validate that we have an irrep matching the user-specified irrep, if any.
try:
salc_indices_pi[freq_irrep_only]
except (TypeError, IndexError):
if freq_irrep_only != -1:
raise ValidationError("FINDIF: Irrep value not in valid range.")
# Populate salc_indices_pi for all irreps.
for i, salc in enumerate(salc_list):
salc_indices_pi[salc.irrep_index()].append(i)
# If the method allows more than one irrep, print how the irreps partition the SALCS.
if print_lvl and method_allowed_irreps != 0x1 and verbose:
core.print_out(" Index of SALCs per irrep:\n")
for h in range(n_irrep):
if print_lvl > 1 or freq_irrep_only in {h, -1}:
tmp = (" {:d} " *
len(salc_indices_pi[h])).format(*salc_indices_pi[h])
core.print_out(" {:d} : ".format(h + 1) + tmp + "\n")
core.print_out(" Number of SALCs per irrep:\n")
for h in range(n_irrep):
if print_lvl > 1 or freq_irrep_only in {h, -1}:
core.print_out(" Irrep {:d}: {:d}\n".format(
h + 1, len(salc_indices_pi[h])))
# Now that we've printed the SALCs, clear any that are not of user-specified symmetry.
if freq_irrep_only != -1:
for h in range(n_irrep):
if h != freq_irrep_only:
salc_indices_pi[h].clear()
n_disp_pi = []
disps = pts_dict[num_pts] # We previously validated num_pts in pts_dict.
for irrep, indices in enumerate(salc_indices_pi):
n_disp = len(indices) * len(
disps["asym_irr" if irrep != 0 else "sym_irr"])
if mode == "2_0":
# Either len(indices) or len(indices)-1 is even, so dividing by two is safe.
n_disp += len(indices) * (len(indices) - 1) // 2 * len(
disps["off"])
n_disp_pi.append(n_disp)
# Let's print out the number of geometries, the displacement multiplicity, and the CdSALCs!
if print_lvl and verbose:
core.print_out(
" Number of geometries (including reference) is {:d}.\n".format(
sum(n_disp_pi) + 1))
if method_allowed_irreps != 0x1:
core.print_out(" Number of displacements per irrep:\n")
for i, ndisp in enumerate(n_disp_pi, start=1):
core.print_out(" Irrep {:d}: {:d}\n".format(i, ndisp))
if print_lvl > 1 and verbose:
for salc in salc_list:
salc.print_out()
data.update({
"n_disp_pi": n_disp_pi,
"n_irrep": n_irrep,
"n_salc": n_salc,
"n_atom": n_atom,
"salc_list": salc_list,
"salc_indices_pi": salc_indices_pi,
"disps": disps
})
return data
def _initialize_findif(mol: Union["qcdb.Molecule", core.Molecule],
freq_irrep_only: int,
mode: str,
stencil_size: int,
step_size: float,
initialize_string: Callable,
t_project: bool,
r_project: bool,
initialize: bool,
verbose: int = 0) -> Dict:
"""Perform initialization tasks needed by all primary functions.
Parameters
----------
mol
The molecule to displace
freq_irrep_only
The Cotton ordered irrep to get frequencies for. Choose -1 for all
irreps.
mode : {"1_0", "2_0", "2_1"}
The first number specifies the derivative level determined from
displacements, and the second number is the level determined at.
stencil_size : {3, 5}
Number of points to evaluate for each displacement basis vector inclusive of central reference geometry.
step_size
[a0]
initialize_string
A function that returns the string to print to show the caller was entered.
The string is both caller-specific and dependent on values determined
in this function.
initialize
For printing, whether call is from generator or assembly stages.
verbose
Set to 0 to silence extra print information, regardless of the print level.
Used so the information is printed only during geometry generation, and not
during the derivative computation as well.
Returns
-------
data
Miscellaneous information required by callers.
"""
info = """
----------------------------------------------------------
FINDIF
R. A. King and Jonathon Misiewicz
----------------------------------------------------------
"""
if initialize:
core.print_out(info)
logger.info(info)
print_lvl = core.get_option("FINDIF", "PRINT")
data = {
"print_lvl": print_lvl,
"stencil_size": stencil_size,
"step_size": step_size
}
if print_lvl:
info = initialize_string(data)
core.print_out(info)
logger.info(info)
# Get settings for CdSalcList, then get the CdSalcList.
method_allowed_irreps = 0x1 if mode == "1_0" else 0xFF
# core.get_option returns an int, but CdSalcList expect a bool, so re-cast
salc_list = core.CdSalcList(mol, method_allowed_irreps, t_project,
r_project)
n_atom = mol.natom()
n_irrep = salc_list.nirrep()
n_salc = salc_list.ncd()
if print_lvl and verbose:
info = f" Number of atoms is {n_atom}.\n"
if method_allowed_irreps != 0x1:
info += f" Number of irreps is {n_irrep}.\n"
info += " Number of {!s}SALCs is {:d}.\n".format(
"" if method_allowed_irreps != 0x1 else "symmetric ", n_salc)
info += f" Translations projected? {t_project:d}. Rotations projected? {r_project:d}.\n"
core.print_out(info)
logger.info(info)
# TODO: Replace with a generator from a stencil to a set of points.
# Diagonal displacements differ between the totally symmetric irrep, compared to all others.
# Off-diagonal displacements are the same for both.
pts_dict = {
3: {
"sym_irr": ((-1, ), (1, )),
"asym_irr": ((-1, ), ),
"off": ((1, 1), (-1, -1))
},
5: {
"sym_irr": ((-2, ), (-1, ), (1, ), (2, )),
"asym_irr": ((-2, ), (-1, )),
"off": ((-1, -2), (-2, -1), (-1, -1), (1, -1), (-1, 1), (1, 1),
(2, 1), (1, 2))
}
}
try:
disps = pts_dict[stencil_size]
except KeyError:
raise ValidationError(
f"FINDIF: Number of points ({stencil_size}) not among {pts_dict.keys()}!"
)
# Convention: x_pi means x_per_irrep. The ith element is x for irrep i, with Cotton ordering.
salc_indices_pi = [[] for h in range(n_irrep)]
# Validate that we have an irrep matching the user-specified irrep, if any.
try:
salc_indices_pi[freq_irrep_only]
except (TypeError, IndexError):
if freq_irrep_only != -1:
raise ValidationError(
f"FINDIF: 0-indexed Irrep value ({freq_irrep_only}) not in valid range: <{len(salc_indices_pi)}."
)
# Populate salc_indices_pi for all irreps.
# * Python error if iterate through `salc_list`
for i in range(len(salc_list)):
salc_indices_pi[salc_list[i].irrep_index()].append(i)
# If the method allows more than one irrep, print how the irreps partition the SALCS.
if print_lvl and method_allowed_irreps != 0x1 and verbose:
info = " Index of SALCs per irrep:\n"
for h in range(n_irrep):
if print_lvl > 1 or freq_irrep_only in {h, -1}:
tmp = (" {:d} " *
len(salc_indices_pi[h])).format(*salc_indices_pi[h])
info += " {:d} : ".format(h + 1) + tmp + "\n"
info += " Number of SALCs per irrep:\n"
for h in range(n_irrep):
if print_lvl > 1 or freq_irrep_only in {h, -1}:
info += " Irrep {:d}: {:d}\n".format(
h + 1, len(salc_indices_pi[h]))
core.print_out(info)
logger.info(info)
# Now that we've printed the SALCs, clear any that are not of user-specified symmetry.
if freq_irrep_only != -1:
for h in range(n_irrep):
if h != freq_irrep_only:
salc_indices_pi[h].clear()
n_disp_pi = []
for irrep, indices in enumerate(salc_indices_pi):
n_disp = len(indices) * len(
disps["asym_irr" if irrep != 0 else "sym_irr"])
if mode == "2_0":
# Either len(indices) or len(indices)-1 is even, so dividing by two is safe.
n_disp += len(indices) * (len(indices) - 1) // 2 * len(
disps["off"])
n_disp_pi.append(n_disp)
# Let's print out the number of geometries, the displacement multiplicity, and the CdSALCs!
if print_lvl and verbose:
info = f" Number of geometries (including reference) is {sum(n_disp_pi) + 1}.\n"
if method_allowed_irreps != 0x1:
info += " Number of displacements per irrep:\n"
for i, ndisp in enumerate(n_disp_pi, start=1):
info += f" Irrep {i}: {ndisp}\n"
core.print_out(info)
logger.info(info)
if print_lvl > 1 and verbose:
for i in range(len(salc_list)):
salc_list[i].print_out()
data.update({
"n_disp_pi": n_disp_pi,
"n_irrep": n_irrep,
"n_salc": n_salc,
"n_atom": n_atom,
"salc_list": salc_list,
"salc_indices_pi": salc_indices_pi,
"disps": disps,
"project_translations": t_project,
"project_rotations": r_project
})
return data