#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, version 3.
#
# Psi4 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License along
# with Psi4; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
# @END LICENSE
#
import os
import re
import sys
import uuid
import warnings
import numpy as np
import qcelemental as qcel
from psi4 import core
from psi4.driver import qcdb
from . import optproc
from .exceptions import TestComparisonError, ValidationError
## Python basis helps
@staticmethod
def _pybuild_basis(mol,
key=None,
target=None,
fitrole='ORBITAL',
other=None,
puream=-1,
return_atomlist=False,
quiet=False):
if key == 'ORBITAL':
key = 'BASIS'
def _resolve_target(key, target):
"""Figure out exactly what basis set was intended by (key, target)
"""
horde = qcdb.libmintsbasisset.basishorde
if not target:
if not key:
key = 'BASIS'
target = core.get_global_option(key)
if target in horde:
return horde[target]
return target
# Figure out what exactly was meant by 'target'.
resolved_target = _resolve_target(key, target)
# resolved_target needs to be either a string or function for pyconstuct.
# if a string, they search for a gbs file with that name.
# if a function, it needs to apply a basis to each atom.
bs, basisdict = qcdb.BasisSet.pyconstruct(
mol.to_dict(), key, resolved_target, fitrole, other, return_dict=True, return_atomlist=return_atomlist)
if return_atomlist:
atom_basis_list = []
for atbs in basisdict:
atommol = core.Molecule.from_dict(atbs['molecule'])
lmbs = core.BasisSet.construct_from_pydict(atommol, atbs, puream)
atom_basis_list.append(lmbs)
return atom_basis_list
if isinstance(resolved_target, str):
basisdict['name'] = basisdict['name'].split('/')[-1].replace('.gbs', '')
if callable(resolved_target):
basisdict['name'] = resolved_target.__name__.replace('basisspec_psi4_yo__', '').upper()
if not quiet:
core.print_out(basisdict['message'])
if 'ECP' in basisdict['message']:
core.print_out(' !!! WARNING: ECP capability is in beta. Please check occupations closely. !!!\n\n')
if basisdict['key'] is None:
basisdict['key'] = 'BASIS'
psibasis = core.BasisSet.construct_from_pydict(mol, basisdict, puream)
return psibasis
core.BasisSet.build = _pybuild_basis
## Python wavefunction helps
@staticmethod
def _core_wavefunction_build(mol, basis=None):
if basis is None:
basis = core.BasisSet.build(mol)
elif isinstance(basis, str):
basis = core.BasisSet.build(mol, "ORBITAL", basis)
wfn = core.Wavefunction(mol, basis)
# Set basis for density-fitted calculations to the zero basis...
# ...until the user explicitly provides a DF basis.
wfn.set_basisset("DF_BASIS_SCF", core.BasisSet.zero_ao_basis_set())
return wfn
core.Wavefunction.build = _core_wavefunction_build
def _core_wavefunction_get_scratch_filename(self, filenumber):
""" Given a wavefunction and a scratch file number, canonicalizes the name
so that files can be consistently written and read """
fname = os.path.split(os.path.abspath(core.get_writer_file_prefix(self.molecule().name())))[1]
psi_scratch = core.IOManager.shared_object().get_default_path()
return os.path.join(psi_scratch, fname + '.' + str(filenumber))
core.Wavefunction.get_scratch_filename = _core_wavefunction_get_scratch_filename
@staticmethod
def _core_wavefunction_from_file(wfn_data):
"""Summary
Parameters
----------
wfn_data : str or dict
If a str reads a Wavefunction from a disk otherwise, assumes the data
is passed in.
Returns
-------
Wavefunction
A deserialized Wavefunction object
"""
# load the wavefunction from file
if isinstance(wfn_data, dict):
pass
elif isinstance(wfn_data, str):
if not wfn_data.endswith(".npy"):
wfn_data = wfn_data + ".npy"
wfn_data = np.load(wfn_data, allow_pickle=True).item()
else:
# Could be path-like or file-like, let `np.load` handle it
wfn_data = np.load(wfn_data, allow_pickle=True).item()
# variable type specific dictionaries to be passed into C++ constructor
wfn_matrix = wfn_data['matrix']
wfn_vector = wfn_data['vector']
wfn_dimension = wfn_data['dimension']
wfn_int = wfn_data['int']
wfn_string = wfn_data['string']
wfn_boolean = wfn_data['boolean']
wfn_float = wfn_data['float']
wfn_floatvar = wfn_data['floatvar']
wfn_matrixarr = wfn_data['matrixarr']
# reconstruct molecule from dictionary representation
wfn_molecule = wfn_data['molecule']
molecule = core.Molecule.from_dict(wfn_molecule)
# get basis set name and spherical harmonics boolean
basis_name = wfn_string['basisname']
if ".gbs" in basis_name:
basis_name = basis_name.split('/')[-1].replace('.gbs', '')
basis_puream = wfn_boolean['basispuream']
basisset = core.BasisSet.build(molecule, 'ORBITAL', basis_name, puream=basis_puream)
# change some variables to psi4 specific data types (Matrix, Vector, Dimension)
for label in wfn_matrix:
array = wfn_matrix[label]
wfn_matrix[label] = core.Matrix.from_array(array, name=label) if array is not None else None
for label in wfn_vector:
array = wfn_vector[label]
wfn_vector[label] = core.Vector.from_array(array, name=label) if array is not None else None
for label in wfn_dimension:
tup = wfn_dimension[label]
wfn_dimension[label] = core.Dimension.from_list(tup, name=label) if tup is not None else None
for label in wfn_matrixarr:
array = wfn_matrixarr[label]
wfn_matrixarr[label] = core.Matrix.from_array(array, name=label) if array is not None else None
# make the wavefunction
wfn = core.Wavefunction(molecule, basisset, wfn_matrix, wfn_vector, wfn_dimension, wfn_int, wfn_string,
wfn_boolean, wfn_float)
# some of the wavefunction's variables can be changed directly
for k, v in wfn_floatvar.items():
wfn.set_variable(k, v)
for k, v in wfn_matrixarr.items():
wfn.set_variable(k, v)
return wfn
core.Wavefunction.from_file = _core_wavefunction_from_file
def _core_wavefunction_to_file(wfn, filename=None):
"""Converts a Wavefunction object to a base class
Parameters
----------
wfn : Wavefunction
A Wavefunction or inherited class
filename : None, optional
An optional filename to write the data to
Returns
-------
dict
A dictionary and NumPy representation of the Wavefunction.
"""
# collect the wavefunction's variables in a dictionary indexed by varaible type
# some of the data types have to be made numpy-friendly first
if wfn.basisset().name().startswith("anonymous"):
raise ValidationError("Cannot serialize wavefunction with custom basissets.")
wfn_data = {
'molecule': wfn.molecule().to_dict(),
'matrix': {
'Ca': wfn.Ca().to_array() if wfn.Ca() else None,
'Cb': wfn.Cb().to_array() if wfn.Cb() else None,
'Da': wfn.Da().to_array() if wfn.Da() else None,
'Db': wfn.Db().to_array() if wfn.Db() else None,
'Fa': wfn.Fa().to_array() if wfn.Fa() else None,
'Fb': wfn.Fb().to_array() if wfn.Fb() else None,
'H': wfn.H().to_array() if wfn.H() else None,
'S': wfn.S().to_array() if wfn.S() else None,
'X': wfn.X().to_array() if wfn.X() else None,
'aotoso': wfn.aotoso().to_array() if wfn.aotoso() else None,
'gradient': wfn.gradient().to_array() if wfn.gradient() else None,
'hessian': wfn.hessian().to_array() if wfn.hessian() else None
},
'vector': {
'epsilon_a': wfn.epsilon_a().to_array() if wfn.epsilon_a() else None,
'epsilon_b': wfn.epsilon_b().to_array() if wfn.epsilon_b() else None,
'frequencies': wfn.frequencies().to_array() if wfn.frequencies() else None
},
'dimension': {
'doccpi': wfn.doccpi().to_tuple(),
'frzcpi': wfn.frzcpi().to_tuple(),
'frzvpi': wfn.frzvpi().to_tuple(),
'nalphapi': wfn.nalphapi().to_tuple(),
'nbetapi': wfn.nbetapi().to_tuple(),
'nmopi': wfn.nmopi().to_tuple(),
'nsopi': wfn.nsopi().to_tuple(),
'soccpi': wfn.soccpi().to_tuple()
},
'int': {
'nalpha': wfn.nalpha(),
'nbeta': wfn.nbeta(),
'nfrzc': wfn.nfrzc(),
'nirrep': wfn.nirrep(),
'nmo': wfn.nmo(),
'nso': wfn.nso(),
'print': wfn.get_print(),
},
'string': {
'name': wfn.name(),
'basisname': wfn.basisset().name()
},
'boolean': {
'PCM_enabled': wfn.PCM_enabled(),
'same_a_b_dens': wfn.same_a_b_dens(),
'same_a_b_orbs': wfn.same_a_b_orbs(),
'density_fitted': wfn.density_fitted(),
'basispuream': wfn.basisset().has_puream()
},
'float': {
'energy': wfn.energy(),
'efzc': wfn.efzc(),
'dipole_field_x': wfn.get_dipole_field_strength()[0],
'dipole_field_y': wfn.get_dipole_field_strength()[1],
'dipole_field_z': wfn.get_dipole_field_strength()[2]
},
'floatvar': wfn.scalar_variables(),
'matrixarr': {k: v.to_array() for k, v in wfn.array_variables().items()}
} # yapf: disable
if filename is not None:
if not filename.endswith('.npy'): filename += '.npy'
np.save(filename, wfn_data)
return wfn_data
core.Wavefunction.to_file = _core_wavefunction_to_file
## Python JK helps
@staticmethod
def _core_jk_build(orbital_basis, aux=None, jk_type=None, do_wK=None, memory=None):
"""
Constructs a Psi4 JK object from an input basis.
Parameters
----------
orbital_basis : :py:class:`~psi4.core.BasisSet`
Orbital basis to use in the JK object.
aux : :py:class:`~psi4.core.BasisSet`, optional
Optional auxiliary basis set for density-fitted tensors. Defaults
to the DF_BASIS_SCF if set, otherwise the correspond JKFIT basis
to the passed in `orbital_basis`.
jk_type : str, optional
Type of JK object to build (DF, Direct, PK, etc). Defaults to the
current global SCF_TYPE option.
Returns
-------
:py:class:`~psi4.core.JK`
Uninitialized JK object.
Example
-------
jk = psi4.core.JK.build(bas)
jk.set_memory(int(5e8)) # 4GB of memory
jk.initialize()
...
jk.C_left_add(matirx)
jk.compute()
jk.C_clear()
...
"""
optstash = optproc.OptionsState(["SCF_TYPE"])
if jk_type is not None:
core.set_global_option("SCF_TYPE", jk_type)
if aux is None:
if core.get_global_option("SCF_TYPE") == "DF":
aux = core.BasisSet.build(orbital_basis.molecule(), "DF_BASIS_SCF", core.get_option("SCF", "DF_BASIS_SCF"),
"JKFIT", orbital_basis.name(), orbital_basis.has_puream())
else:
aux = core.BasisSet.zero_ao_basis_set()
if (do_wK is None) or (memory is None):
jk = core.JK.build_JK(orbital_basis, aux)
else:
jk = core.JK.build_JK(orbital_basis, aux, bool(do_wK), int(memory))
optstash.restore()
return jk
core.JK.build = _core_jk_build
## Grid Helpers
def _core_vbase_get_np_xyzw(Vpot):
"""
Returns the x, y, z, and weights of a grid as a tuple of NumPy array objects.
"""
x_list = []
y_list = []
z_list = []
w_list = []
# Loop over every block in the potenital
for b in range(Vpot.nblocks()):
# Obtain the block
block = Vpot.get_block(b)
# Obtain the x, y, and z coordinates along with the weight
x_list.append(block.x())
y_list.append(block.y())
z_list.append(block.z())
w_list.append(block.w())
x = np.hstack(x_list)
y = np.hstack(y_list)
z = np.hstack(z_list)
w = np.hstack(w_list)
return (x, y, z, w)
core.VBase.get_np_xyzw = _core_vbase_get_np_xyzw
## Python other helps
[docs]def set_options(options_dict, verbose=1):
"""Sets Psi4 options from an input dictionary.
Parameters
----------
options_dict : dict
Dictionary where keys are "option_name" for global options or
"module_name__option_name" (double underscore separation) for
option local to "module_name". Values are the option value. All
are case insensitive.
verbose : int, optional
Control print volume.
Returns
-------
None
"""
optionre = re.compile(r'\A(?P<module>\w+__)?(?P<option>\w+)\Z', re.IGNORECASE)
rejected = {}
for k, v, in options_dict.items():
mobj = optionre.match(k)
module = mobj.group('module').upper()[:-2] if mobj.group('module') else None
option = mobj.group('option').upper()
if module:
if (module, option, v) not in [('SCF', 'GUESS', 'READ')]:
# TODO guess/read exception is for distributed driver. should be handled differently.
try:
core.set_local_option(module, option, v)
except RuntimeError as err:
rejected[k] = (v, err)
if verbose > 1:
print('Setting: core.set_local_option', module, option, v)
else:
try:
core.set_global_option(option, v)
except RuntimeError as err:
rejected[k] = (v, err)
if verbose > 1:
print('Setting: core.set_global_option', option, v)
if rejected:
raise ValidationError(f'Error setting options: {rejected}')
# TODO could subclass ValidationError and append rejected so that run_json could handle remanants.
[docs]def set_module_options(module, options_dict):
"""
Sets Psi4 module options from a module specification and input dictionary.
"""
for k, v, in options_dict.items():
core.set_local_option(module.upper(), k.upper(), v)
## OEProp helpers
[docs]def pcm_helper(block):
"""
Passes multiline string *block* to PCMSolver parser.
Parameters
----------
block: multiline string with PCM input in PCMSolver syntax.
"""
suffix = str(os.getpid()) + '.' + str(uuid.uuid4())[:8]
pcmsolver_fname = 'pcmsolver.' + suffix + '.inp'
with open(pcmsolver_fname, 'w') as handle:
handle.write(block)
import pcmsolver
parsed_pcm = pcmsolver.parse_pcm_input(pcmsolver_fname)
os.remove(pcmsolver_fname)
pcmsolver_parsed_fname = '@pcmsolver.' + suffix
with open(pcmsolver_parsed_fname, 'w') as tmp:
tmp.write(parsed_pcm)
core.set_local_option('PCM', 'PCMSOLVER_PARSED_FNAME', '{}'.format(pcmsolver_parsed_fname))
def basname(name):
"""Imitates BasisSet.make_filename() without the gbs extension"""
return name.lower().replace('+', 'p').replace('*', 's').replace('(', '_').replace(')', '_').replace(',', '_')
[docs]def temp_circular_import_blocker():
pass
[docs]def basis_helper(block, name='', key='BASIS', set_option=True):
"""For PsiAPI mode, forms a basis specification function from *block*
and associates it with keyword *key* under handle *name*. Registers
the basis spec with Psi4 so that it can be applied again to future
molecules. For usage, see mints2, mints9, and cc54 test cases. Unless
*set_option* is False, *name* will be set as current active *key*,
equivalent to `set key name` or `set_option({key: name})`.
"""
key = key.upper()
name = ('anonymous' + str(uuid.uuid4())[:8]) if name == '' else name
cleanbas = basname(name).replace('-', '') # further remove hyphens so can be function name
block = qcel.util.filter_comments(block)
command_lines = re.split('\n', block)
symbol_re = re.compile(r'^\s*assign\s+(?P<symbol>[A-Z]{1,3})\s+(?P<basis>[-+*\(\)\w]+)\s*$', re.IGNORECASE)
label_re = re.compile(
r'^\s*assign\s+(?P<label>(?P<symbol>[A-Z]{1,3})(?:(_\w+)|(\d+))?)\s+(?P<basis>[-+*\(\)\w]+)\s*$',
re.IGNORECASE)
all_re = re.compile(r'^\s*assign\s+(?P<basis>[-+*\(\)\w]+)\s*$', re.IGNORECASE)
basislabel = re.compile(r'\s*\[\s*([-*\(\)\w]+)\s*\]\s*')
def anon(mol, role):
basstrings = {}
# Start by looking for assign lines, and remove them
leftover_lines = []
assignments = False
for line in command_lines:
if symbol_re.match(line):
m = symbol_re.match(line)
mol.set_basis_by_symbol(m.group('symbol'), m.group('basis'), role=role)
assignments = True
elif label_re.match(line):
m = label_re.match(line)
mol.set_basis_by_label(m.group('label'), m.group('basis'), role=role)
assignments = True
elif all_re.match(line):
m = all_re.match(line)
mol.set_basis_all_atoms(m.group('basis'), role=role)
assignments = True
else:
# Ignore blank lines and accumulate remainder
if line and not line.isspace():
leftover_lines.append(line.strip())
# Now look for regular basis set definitions
basblock = list(filter(None, basislabel.split('\n'.join(leftover_lines))))
if len(basblock) == 1:
if not assignments:
# case with no [basname] markers where whole block is contents of gbs file
mol.set_basis_all_atoms(name, role=role)
basstrings[basname(name)] = basblock[0]
else:
message = (
"Conflicting basis set specification: assign lines present but shells have no [basname] label."
"")
raise TestComparisonError(message)
else:
# case with specs separated by [basname] markers
for idx in range(0, len(basblock), 2):
basstrings[basname(basblock[idx])] = basblock[idx + 1]
return basstrings
anon.__name__ = 'basisspec_psi4_yo__' + cleanbas
qcdb.libmintsbasisset.basishorde[name.upper()] = anon
if set_option:
core.set_global_option(key, name)
core.OEProp.valid_methods = [
'DIPOLE', 'QUADRUPOLE', 'MULLIKEN_CHARGES', 'LOWDIN_CHARGES', 'WIBERG_LOWDIN_INDICES', 'MAYER_INDICES',
'MAYER_INDICES', 'MO_EXTENTS', 'GRID_FIELD', 'GRID_ESP', 'ESP_AT_NUCLEI', 'NO_OCCUPATIONS'
]
## Option helpers
def _core_set_global_option_python(key, EXTERN):
"""
This is a fairly hacky way to get around EXTERN issues. Effectively we are routing this option Python side through attributes until the general Options overhaul.
"""
if (key != "EXTERN"):
raise ValidationError("Options: set_global_option_python does not recognize keyword %s" % key)
if EXTERN is None:
core.EXTERN = None
core.set_global_option("EXTERN", False)
elif isinstance(EXTERN, core.ExternalPotential):
# Well this is probably the worst hack I have done, thats saying something
core.EXTERN = EXTERN
core.set_global_option("EXTERN", True)
else:
raise ValidationError("Options: set_global_option_python can either be a NULL or External Potential object")
core.set_global_option_python = _core_set_global_option_python
## QCvar helps
def _core_has_variable(key):
return core.has_scalar_variable(key) or core.has_array_variable(key)
def _core_wavefunction_has_variable(cls, key):
return cls.has_scalar_variable(key) or cls.has_array_variable(key)
def _core_variable(key):
if core.has_scalar_variable(key):
return core.scalar_variable(key)
elif core.has_array_variable(key):
return core.array_variable(key)
else:
raise KeyError("psi4.core.variable: Requested variable " + key + " was not set!\n")
def _core_wavefunction_variable(cls, key):
if cls.has_scalar_variable(key):
return cls.scalar_variable(key)
elif cls.has_array_variable(key):
return cls.array_variable(key)
else:
raise KeyError("psi4.core.Wavefunction.variable: Requested variable " + key + " was not set!\n")
def _core_set_variable(key, val):
if isinstance(val, core.Matrix):
if core.has_scalar_variable(key):
raise ValidationError("psi4.core.set_variable: Target variable " + key + " already a scalar variable!")
else:
core.set_array_variable(key, val)
elif isinstance(val, np.ndarray):
if core.has_scalar_variable(key):
raise ValidationError("psi4.core.set_variable: Target variable " + key + " already a scalar variable!")
else:
core.set_array_variable(key, core.Matrix.from_array(val))
else:
if core.has_array_variable(key):
raise ValidationError("psi4.core.set_variable: Target variable " + key + " already an array variable!")
else:
core.set_scalar_variable(key, val)
def _core_wavefunction_set_variable(cls, key, val):
if isinstance(val, core.Matrix):
if cls.has_scalar_variable(key):
raise ValidationError("psi4.core.Wavefunction.set_variable: Target variable " + key +
" already a scalar variable!")
else:
cls.set_array_variable(key, val)
elif isinstance(val, np.ndarray):
if cls.has_scalar_variable(key):
raise ValidationError("psi4.core.Wavefunction.set_variable: Target variable " + key +
" already a scalar variable!")
else:
cls.set_array_variable(key, core.Matrix.from_array(val))
else:
if cls.has_array_variable(key):
raise ValidationError("psi4.core.Wavefunction.set_variable: Target variable " + key +
" already an array variable!")
else:
cls.set_scalar_variable(key, val)
def _core_del_variable(key):
if core.has_scalar_variable(key):
core.del_scalar_variable(key)
elif core.has_array_variable(key):
core.del_array_variable(key)
def _core_wavefunction_del_variable(cls, key):
if cls.has_scalar_variable(key):
cls.del_scalar_variable(key)
elif cls.has_array_variable(key):
cls.del_array_variable(key)
def _core_variables():
return {**core.scalar_variables(), **core.array_variables()}
def _core_wavefunction_variables(cls):
return {**cls.scalar_variables(), **cls.array_variables()}
core.has_variable = _core_has_variable
core.variable = _core_variable
core.set_variable = _core_set_variable
core.del_variable = _core_del_variable
core.variables = _core_variables
core.Wavefunction.has_variable = _core_wavefunction_has_variable
core.Wavefunction.variable = _core_wavefunction_variable
core.Wavefunction.set_variable = _core_wavefunction_set_variable
core.Wavefunction.del_variable = _core_wavefunction_del_variable
core.Wavefunction.variables = _core_wavefunction_variables
## Psi4 v1.4 Export Deprecations
def _core_get_variable(key):
warnings.warn(
"Using `psi4.core.get_variable` instead of `psi4.core.variable` (or `psi4.core.scalar_variable` for scalar variables only) is deprecated, and in 1.4 it will stop working\n",
category=FutureWarning,
stacklevel=2)
return core.scalar_variable(key)
def _core_get_variables():
warnings.warn(
"Using `psi4.core.get_variables` instead of `psi4.core.variables` (or `psi4.core.scalar_variables` for scalar variables only) is deprecated, and in 1.4 it will stop working\n",
category=FutureWarning,
stacklevel=2)
return core.scalar_variables()
def _core_get_array_variable(key):
warnings.warn(
"Using `psi4.core.get_array_variable` instead of `psi4.core.variable` (or `psi4.core.array_variable` for array variables only) is deprecated, and in 1.4 it will stop working\n",
category=FutureWarning,
stacklevel=2)
return core.array_variable(key)
def _core_get_array_variables():
warnings.warn(
"Using `psi4.core.get_array_variables` instead of `psi4.core.variables` (or `psi4.core.array_variables` for array variables only) is deprecated, and in 1.4 it will stop working\n",
category=FutureWarning,
stacklevel=2)
return core.array_variables()
core.get_variable = _core_get_variable
core.get_variables = _core_get_variables
core.get_array_variable = _core_get_array_variable
core.get_array_variables = _core_get_array_variables
def _core_wavefunction_get_variable(cls, key):
warnings.warn(
"Using `psi4.core.Wavefunction.get_variable` instead of `psi4.core.Wavefunction.variable` (or `psi4.core.Wavefunction.scalar_variable` for scalar variables only) is deprecated, and in 1.4 it will stop working\n",
category=FutureWarning,
stacklevel=2)
return cls.scalar_variable(key)
def _core_wavefunction_get_array(cls, key):
warnings.warn(
"Using `psi4.core.Wavefunction.get_array` instead of `psi4.core.Wavefunction.variable` (or `psi4.core.Wavefunction.array_variable` for array variables only) is deprecated, and in 1.4 it will stop working\n",
category=FutureWarning,
stacklevel=2)
return cls.array_variable(key)
def _core_wavefunction_set_array(cls, key, val):
warnings.warn(
"Using `psi4.core.Wavefunction.set_array` instead of `psi4.core.Wavefunction.set_variable` (or `psi4.core.Wavefunction.set_array_variable` for array variables only) is deprecated, and in 1.4 it will stop working\n",
category=FutureWarning,
stacklevel=2)
return cls.set_array_variable(key, val)
def _core_wavefunction_arrays(cls):
warnings.warn(
"Using `psi4.core.Wavefunction.arrays` instead of `psi4.core.Wavefunction.variables` (or `psi4.core.Wavefunction.array_variables` for array variables only) is deprecated, and in 1.4 it will stop working\n",
category=FutureWarning,
stacklevel=2)
return cls.array_variables()
core.Wavefunction.get_variable = _core_wavefunction_get_variable
core.Wavefunction.get_array = _core_wavefunction_get_array
core.Wavefunction.set_array = _core_wavefunction_set_array
core.Wavefunction.arrays = _core_wavefunction_arrays
def _core_wavefunction_frequencies(cls):
if not hasattr(cls, 'frequency_analysis'):
return None
vibinfo = cls.frequency_analysis
vibonly = qcdb.vib.filter_nonvib(vibinfo)
return core.Vector.from_array(qcdb.vib.filter_omega_to_real(vibonly['omega'].data))
def _core_wavefunction_legacy_frequencies(cls):
warnings.warn(
"Using `psi4.core.Wavefunction.legacy_frequencies` (accessing c-side member data) is deprecated, and in 1.4 it will stop working\n",
category=FutureWarning,
stacklevel=2)
return cls.legacy_frequencies()
def _core_wavefunction_set_frequencies(cls, val):
warnings.warn(
"Using `psi4.core.Wavefunction.set_frequencies` (accessing c-side member data) instead of `psi4.core.Wavefunction.frequency_analysis` (py-side member data) is deprecated, and in 1.4 it will stop working\n",
category=FutureWarning,
stacklevel=2)
return cls.set_legacy_frequencies(val)
core.Wavefunction.frequencies = _core_wavefunction_frequencies
core.Wavefunction.legacy_frequencies = _core_wavefunction_legacy_frequencies
core.Wavefunction.set_frequencies = _core_wavefunction_set_frequencies
## Psi4 v1.3 Export Deprecations
def _core_get_gradient():
warnings.warn(
"Using `psi4.core.get_gradient` (only used internally for C++ optking; deprecated silently in 1.2) is deprecated, and in 1.4 (or whenever Py optking is adopted) it will stop working\n",
category=FutureWarning,
stacklevel=2)
return core.get_legacy_gradient()
def _core_set_gradient(val):
warnings.warn(
"Using `psi4.core.set_gradient` (only used internally for C++ optking; deprecated silently in 1.2) is deprecated, and in 1.4 (or whenever Py optking is adopted) it will stop working\n",
category=FutureWarning,
stacklevel=2)
return core.set_legacy_gradient(val)
core.get_gradient = _core_get_gradient
core.set_gradient = _core_set_gradient
def _core_doublet(A, B, transA, transB):
warnings.warn(
"Using `psi4.core.Matrix.doublet` instead of `psi4.core.doublet` is deprecated, and in 1.4 it will stop working\n",
category=FutureWarning,
stacklevel=2)
return core.doublet(A, B, transA, transB)
def _core_triplet(A, B, C, transA, transB, transC):
warnings.warn(
"Using `psi4.core.Matrix.triplet` instead of `psi4.core.triplet` is deprecated, and in 1.4 it will stop working\n",
category=FutureWarning,
stacklevel=2)
return core.triplet(A, B, C, transA, transB, transC)
core.Matrix.doublet = staticmethod(_core_doublet)
core.Matrix.triplet = staticmethod(_core_triplet)
