#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2023 The Psi4 Developers.
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# The copyrights for code used from other parties are included in
# the corresponding files.
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# This file is part of Psi4.
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# Psi4 is free software; you can redistribute it and/or modify
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# Psi4 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# with Psi4; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
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# @END LICENSE
#
"""
Module with PsiAPI helpers for PSIthon `{...}` syntax.
Also, many Python extensions to core classes:
- core (variable-related, gradient, python option),
- Wavefunction (variable-related, freq, Lagrangian, constructor, scratch file, serialization),
- Matrix (doublet, triplet),
- BasisSet (constructor)
- JK (constructor)
- VBase (grid)
- OEProp (avail prop)
- ERISieve (constructor)
"""
__all__ = [
"basis_helper",
"pcm_helper",
"plump_qcvar",
"set_options",
"set_module_options",
]
import math
import os
import re
import uuid
import warnings
from collections import Counter
from itertools import product
from pathlib import Path
from tempfile import NamedTemporaryFile
from typing import Any, Callable, Dict, List, Optional, Tuple, Union
import numpy as np
import qcelemental as qcel
from psi4 import core, extras
from .. import qcdb
from . import optproc
from .exceptions import TestComparisonError, UpgradeHelper, ValidationError
## Python basis helps
@staticmethod
def _pybuild_basis(
mol: core.Molecule,
key: Optional[str] = None,
target: Optional[Union[str, Callable]] = None,
fitrole: str = "ORBITAL",
other: Optional[Union[str, Callable]] = None,
puream: int = -1,
return_atomlist: bool = False,
*,
quiet: bool = False,
) -> Union[core.BasisSet, List[core.BasisSet]]:
"""Build a primary or auxiliary basis set.
Parameters
----------
mol
Molecule for which to build the basis set instance.
key
{'BASIS', 'ORBITAL', 'DF_BASIS_SCF', 'DF_BASIS_MP2', 'DF_BASIS_CC', 'BASIS_RELATIVISTIC', 'DF_BASIS_SAD'}
Label (effectively Psi4 keyword) to append the basis on the molecule.
The primary basis set is indicated by any of values None or
``"ORBITAL"`` or ``"BASIS"``.
target
Defines the basis set to be constructed. Can be a string (naming a
basis file) or a callable (providing shells or multiple basis files).
For auxiliary bases to be built entirely from primary default, can be
an empty string. If None, value taken from `key` in global options. If
a user-defined-basis callable is available at string `target`, `target`
value will be set to it. In practice, setting this argument to a
|PSIfour| keyword (e.g., ``core.get_option("SCF", "DF_BASIS_SCF")`` or
``core.get_global_option("BASIS")``) works to handle both simple and
user-defined bases.
fitrole
{'ORBITAL', 'JKFIT', 'RIFIT', 'DECON'}
Role for which to build basis. Only used when `key` indicates auxiliary
(i.e., *is not* ``"BASIS"``) and auxiliary spec from processing `target`
can't complete the `mol`. Then, primary spec from `other` can be used
to complete the auxiliary basis by looking up suitable default basis
according to `fitrole`.
other
Only used when building auxiliary basis sets. Defines the primary basis through a string or callable like `target`.
puream
Whether to override the native spherical/cartesian-ness of `target` for
returned basis? Value ``1`` forces spherical, value ``0`` forces
Cartesian, value ``-1`` (default) uses native puream. Note that
explicitly setting :term:`PUREAM <PUREAM (GLOBALS)>` trumps both native
puream and this `puream` argument.
return_atomlist
Build one-atom basis sets (e.g., for SAD) rather than one whole-`mol`
basis set.
quiet
When True, do not print to the output file.
Returns
-------
BasisSet or ~typing.List[BasisSet]
Single basis for `mol`, unless `return_atomlist` is True.
"""
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: core.Molecule,
basis: Union[None, str, core.BasisSet] = None,
*,
quiet: bool = False,
) -> core.Wavefunction:
"""Build a wavefunction from minimal inputs, molecule and basis set.
Parameters
----------
mol
Molecule for which to build the wavefunction instance.
basis
Basis set for which to build the wavefunction instance. If a
:class:`BasisSet`, taken as-is. If a string, taken as a name for the
primary basis. If None, name taken from :term:`BASIS <BASIS (MINTS)>`.
quiet
When True, do not print to the output file.
"""
if basis is None:
basis = core.BasisSet.build(mol, quiet=quiet)
elif isinstance(basis, str):
basis = core.BasisSet.build(mol, "ORBITAL", basis, quiet=quiet)
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: core.Wavefunction, filenumber: int) -> str:
"""Return canonical path to scratch file `filenumber` based on molecule on `self`.
Parameters
----------
self
Wavefunction instance.
filenumber
Scratch file number from :source:`psi4/include/psi4/psifiles.h`.
"""
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: Union[str, Dict, Path]) -> core.Wavefunction:
r"""Build Wavefunction from data laid out like
:meth:`~psi4.core.Wavefunction.to_file`.
Parameters
----------
wfn_data
If a dict, use data directly. Otherwise, path-like passed to
:py:func:`numpy.load` to read from disk.
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: core.Wavefunction, filename: str = None) -> Dict[str, Dict[str, Any]]:
"""Serialize a Wavefunction object. Opposite of
:meth:`~psi4.core.Wavefunction.from_file`.
Parameters
----------
wfn
Wavefunction or inherited class instance.
filename
An optional filename to which to write the data.
Returns
-------
~typing.Dict[str, ~typing.Dict[str, ~typing.Any]]
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.lagrangian().to_array() if wfn.lagrangian() 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(),
'module': wfn.module(),
'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(),
'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, allow_pickle=True)
return wfn_data
core.Wavefunction.to_file = _core_wavefunction_to_file
## Python JK helps
@staticmethod
def _core_jk_build(
orbital_basis: core.BasisSet,
aux: Optional[core.BasisSet] = None,
jk_type: Optional[str] = None,
do_wK: Optional[bool] = None,
memory: Optional[int] = None,
) -> core.JK:
"""
Constructs a Psi4 JK object from an input basis.
Parameters
----------
orbital_basis
Orbital basis to use in the JK object.
aux
Optional auxiliary basis set for density-fitted tensors. Defaults
to the :term:`DF_BASIS_SCF <DF_BASIS_SCF (SCF)>` if set, otherwise the corresponding JKFIT basis
to the passed in `orbital_basis`.
jk_type
Type of JK object to build (DF, Direct, PK, etc). Defaults to the
current :term:`SCF_TYPE <SCF_TYPE (GLOBALS)>` option.
do_wK
Set up JK to do omega K tasks. Set `do_wK` and `memory` together to
activate either.
memory
Memory in doubles to use for JK. Set `do_wK` and `memory` together to
activate either.
Returns
-------
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(self: core.VBase) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]:
"""
Returns the x, y, z, and weights of a grid as a tuple of NumPy array objects.
Parameters
----------
self
VBase instance.
"""
x_list = []
y_list = []
z_list = []
w_list = []
# Loop over every block in the potenital
for b in range(self.nblocks()):
# Obtain the block
block = self.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: Dict[str, Any], verbose: int = 1):
"""Sets Psi4 options from an input dictionary.
Parameters
----------
options_dict
Dictionary where keys are case insensitive and values are the option value.
- For global options, keys are ``"<option_name>"``.
- For option local to "<module_name>", keys are ``"<module_name>__<option_name>"``
(double underscore separation).
- For contents that would be in ``pcm = {...}``, use ``"PCM__INPUT"`` key.
verbose
Control print volume.
Returns
-------
None
Examples
--------
>>> psi4.set_options({
"basis": "cc-pvtz",
"df_basis_scf": "cc-pvtz-jkfit",
"scf__reference": "uhf",
"print": 2})
"""
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.strip())
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')]) and ((module, option) not in [('PCM', 'INPUT')]):
# 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)
if (module, option) == ("PCM", "INPUT"):
pcm_helper(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: str, options_dict: Dict[str, Any]) -> None:
"""
Sets Psi4 module options from a module specification and input dictionary.
.. deprecated:: 1.5
Use :py:func:`psi4.driver.p4util.set_options` instead.
"""
warnings.warn(
"Using `psi4.set_module_options(<module>, {<key>: <val>})` instead of `psi4.set_options({<module>__<key>: <val>})` is deprecated, and as soon as 1.5 it will stop working\n",
category=FutureWarning,
stacklevel=2)
for k, v, in options_dict.items():
core.set_local_option(module.upper(), k.upper(), v)
## OEProp helpers
[docs]
def pcm_helper(block: str):
"""Helper to specify the multiline PCMSolver syntax for PCM.
Prefer to use :py:func:`set_options` with key ``"PCM__INPUT"``.
Parameters
----------
block
Text that goes in a PSIthon ``pcm = {...}`` block.
"""
import pcmsolver
# delete=True works for Unix but not for Windows
with NamedTemporaryFile(mode="w+t", delete=False) as fl:
fl.write(block)
fl.flush()
parsed_pcm = pcmsolver.parse_pcm_input(fl.name)
extras.register_scratch_file(fl.name)
with NamedTemporaryFile(mode="w+t", delete=False) as fl:
fl.write(parsed_pcm)
core.set_local_option("PCM", "PCMSOLVER_PARSED_FNAME", fl.name)
extras.register_scratch_file(fl.name) # retain with -m (messy) option
def _basname(name: str) -> str:
"""Imitates :py:meth:`core.BasisSet.make_filename` without the gbs extension."""
return name.lower().replace('+', 'p').replace('*', 's').replace('(', '_').replace(')', '_').replace(',', '_')
[docs]
def basis_helper(block: str, name: str = '', key: str = 'BASIS', set_option: bool = True):
"""Helper to specify a custom basis set in PsiAPI mode.
This function 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 :srcsample:`mints2`, :srcsample:`mints9`, and
:srcsample:`cc54` test cases.
Parameters
----------
block
Text that goes in a PSIthon ``basis {...}`` block.
name
Name label to associated with basis specified by `block`.
key
Basis keyword specified by `block`.
set_option
When True, execute the equivalent of ``set key name`` or ``set_option({key: name})``. When False, skip execution.
"""
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',
'MBIS_CHARGES','MBIS_VOLUME_RATIOS', '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
_qcvar_transitions = {
# old: (replacement, release after next)
"SCSN-MP2 CORRELATION ENERGY": ("SCS(N)-MP2 CORRELATION ENERGY", 1.5),
"SCSN-MP2 TOTAL ENERGY": ("SCS(N)-MP2 TOTAL ENERGY", 1.5),
"MAYER_INDICES": ("MAYER INDICES", 1.5),
"WIBERG_LOWDIN_INDICES": ("WIBERG LOWDIN INDICES", 1.5),
"LOWDIN_CHARGES": ("LOWDIN CHARGES", 1.5),
"MULLIKEN_CHARGES": ("MULLIKEN CHARGES", 1.5),
"(AT) CORRECTION ENERGY": ("A-(T) CORRECTION ENERGY", 1.5),
"CCSD(AT) TOTAL ENERGY": ("A-CCSD(T) TOTAL ENERGY", 1.5),
"CCSD(AT) CORRELATION ENERGY": ("A-CCSD(T) CORRELATION ENERGY", 1.5),
"CP-CORRECTED 2-BODY INTERACTION ENERGY": ("CP-CORRECTED INTERACTION ENERGY THROUGH 2-BODY", 1.7),
"CP-CORRECTED 3-BODY INTERACTION ENERGY": ("CP-CORRECTED INTERACTION ENERGY THROUGH 3-BODY", 1.7),
"CP-CORRECTED 4-BODY INTERACTION ENERGY": ("CP-CORRECTED INTERACTION ENERGY THROUGH 4-BODY", 1.7),
"CP-CORRECTED 5-BODY INTERACTION ENERGY": ("CP-CORRECTED INTERACTION ENERGY THROUGH 5-BODY", 1.7),
"NOCP-CORRECTED 2-BODY INTERACTION ENERGY": ("NOCP-CORRECTED INTERACTION ENERGY THROUGH 2-BODY", 1.7),
"NOCP-CORRECTED 3-BODY INTERACTION ENERGY": ("NOCP-CORRECTED INTERACTION ENERGY THROUGH 3-BODY", 1.7),
"NOCP-CORRECTED 4-BODY INTERACTION ENERGY": ("NOCP-CORRECTED INTERACTION ENERGY THROUGH 4-BODY", 1.7),
"NOCP-CORRECTED 5-BODY INTERACTION ENERGY": ("NOCP-CORRECTED INTERACTION ENERGY THROUGH 5-BODY", 1.7),
"VMFC-CORRECTED 2-BODY INTERACTION ENERGY": ("VMFC-CORRECTED INTERACTION ENERGY THROUGH 2-BODY", 1.7),
"VMFC-CORRECTED 3-BODY INTERACTION ENERGY": ("VMFC-CORRECTED INTERACTION ENERGY THROUGH 3-BODY", 1.7),
"VMFC-CORRECTED 4-BODY INTERACTION ENERGY": ("VMFC-CORRECTED INTERACTION ENERGY THROUGH 4-BODY", 1.7),
"VMFC-CORRECTED 5-BODY INTERACTION ENERGY": ("VMFC-CORRECTED INTERACTION ENERGY THROUGH 5-BODY", 1.7),
"COUNTERPOISE CORRECTED TOTAL ENERGY": ("CP-CORRECTED TOTAL ENERGY", 1.7),
"COUNTERPOISE CORRECTED INTERACTION ENERGY": ("CP-CORRECTED INTERACTION ENERGY", 1.7),
"NON-COUNTERPOISE CORRECTED TOTAL ENERGY": ("NOCP-CORRECTED TOTAL ENERGY", 1.7),
"NON-COUNTERPOISE CORRECTED INTERACTION ENERGY": ("NOCP-CORRECTED INTERACTION ENERGY", 1.7),
"VALIRON-MAYER FUNCTION COUTERPOISE TOTAL ENERGY": ("VALIRON-MAYER FUNCTION COUNTERPOISE TOTAL ENERGY", 1.7), # note misspelling
"VALIRON-MAYER FUNCTION COUTERPOISE INTERACTION ENERGY": ("VMFC-CORRECTED INTERACTION ENERGY", 1.7), # note misspelling
}
_qcvar_cancellations = {
"SCSN-MP2 SAME-SPIN CORRELATION ENERGY": ["MP2 SAME-SPIN CORRELATION ENERGY"],
"SCSN-MP2 OPPOSITE-SPIN CORRELATION ENERGY": ["MP2 OPPOSITE-SPIN CORRELATION ENERGY"],
"SCS-CCSD SAME-SPIN CORRELATION ENERGY": ["CCSD SAME-SPIN CORRELATION ENERGY"],
"SCS-CCSD OPPOSITE-SPIN CORRELATION ENERGY": ["CCSD OPPOSITE-SPIN CORRELATION ENERGY"],
"SCS-MP2 SAME-SPIN CORRELATION ENERGY": ["MP2 SAME-SPIN CORRELATION ENERGY"],
"SCS-MP2 OPPOSITE-SPIN CORRELATION ENERGY": ["MP2 OPPOSITE-SPIN CORRELATION ENERGY"],
"SCS(N)-OMP2 CORRELATION ENERGY": ["OMP2 SAME-SPIN CORRELATION ENERGY", "OMP2 OPPOSITE-SPIN CORRELATION ENERGY"],
"SCS(N)-OMP2 TOTAL ENERGY": ["OMP2 SAME-SPIN CORRELATION ENERGY", "OMP2 OPPOSITE-SPIN CORRELATION ENERGY"],
"SCSN-OMP2 CORRELATION ENERGY": ["OMP2 SAME-SPIN CORRELATION ENERGY", "OMP2 OPPOSITE-SPIN CORRELATION ENERGY"],
"SCSN-OMP2 TOTAL ENERGY": ["OMP2 SAME-SPIN CORRELATION ENERGY", "OMP2 OPPOSITE-SPIN CORRELATION ENERGY"],
}
def _qcvar_warnings(key: str) -> str:
"""Intercept QCVariable keys to issue warnings or upgrade hints. Otherwise,
pass through.
"""
if any([key.upper().endswith(" DIPOLE " + cart) for cart in ["X", "Y", "Z"]]):
raise UpgradeHelper(key.upper(), key.upper()[:-2], 1.6, " Note the Debye -> a.u. units change.")
if any([key.upper().endswith(" QUADRUPOLE " + cart) for cart in ["XX", "YY", "ZZ", "XY", "XZ", "YZ"]]):
raise UpgradeHelper(key.upper(), key.upper()[:-3], 1.6, " Note the Debye -> a.u. units change.")
if key.upper() in _qcvar_transitions:
replacement, version = _qcvar_transitions[key.upper()]
warnings.warn(
f"Using QCVariable `{key.upper()}` instead of `{replacement}` is deprecated, and as soon as {version} it will stop working\n",
category=FutureWarning,
stacklevel=3)
return replacement
if key.upper() in _qcvar_cancellations:
raise UpgradeHelper(key.upper(), "no direct replacement", 1.4, " Consult QCVariables " + ", ".join(_qcvar_cancellations[key.upper()]) + " to recompose the quantity.")
return key
[docs]
def plump_qcvar(
key: str,
val: Union[float, str, List]) -> Union[float, np.ndarray]:
"""Prepare serialized QCVariables for QCSchema AtomicResult.extras["qcvars"] by
converting flat arrays into numpy, shaped ones and floating strings.
Unlike _qcvar_reshape_get/set, multipoles aren't compressed or plumped, only reshaped.
Parameters
----------
key
Shape clue (usually QCVariable key) that includes (case insensitive) an identifier like
'gradient' as a clue to the array's natural dimensions.
val
flat (?, ) list or scalar or string, probably from JSON storage.
Returns
-------
float or numpy.ndarray
Reshaped array of `val` with natural dimensions of `key`.
"""
if isinstance(val, (np.ndarray, core.Matrix)):
raise TypeError
elif isinstance(val, list):
tgt = np.asarray(val)
else:
# presumably scalar. may be string
return float(val)
if key.upper().startswith("MBIS"):
if key.upper().endswith("CHARGES"):
reshaper = (-1, )
elif key.upper().endswith("DIPOLES"):
reshaper = (-1, 3)
elif key.upper().endswith("QUADRUPOLES"):
reshaper = (-1, 3, 3)
elif key.upper().endswith("OCTUPOLES"):
reshaper = (-1, 3, 3, 3)
elif key.upper().endswith("DIPOLE") or "DIPOLE -" in key.upper():
reshaper = (3, )
elif "QUADRUPOLE POLARIZABILITY TENSOR" in key.upper():
reshaper = (3, 3, 3)
elif any((key.upper().endswith(p) or f"{p} -" in key.upper()) for p in _multipole_order):
p = [p for p in _multipole_order if (key.upper().endswith(p) or f"{p} -" in key.upper())]
reshaper = tuple([3] * _multipole_order.index(p[0]))
elif key.upper() in ["MULLIKEN_CHARGES", "LOWDIN_CHARGES", "MULLIKEN CHARGES", "LOWDIN CHARGES"]:
reshaper = (-1, )
elif "GRADIENT" in key.upper():
reshaper = (-1, 3)
elif "HESSIAN" in key.upper():
ndof = int(math.sqrt(len(tgt)))
reshaper = (ndof, ndof)
else:
raise ValidationError(f'Uncertain how to reshape array: {key}')
return tgt.reshape(reshaper)
_multipole_order = ["dummy", "dummy", "QUADRUPOLE", "OCTUPOLE", "HEXADECAPOLE"]
for order in range(5, 10):
_multipole_order.append(f"{int(2**order)}-POLE")
def _qcvar_reshape_set(key: str, val: np.ndarray) -> np.ndarray:
"""Reverse :py:func:`_qcvar_reshape_get` for internal
:py:class:`psi4.core.Matrix` storage.
"""
reshaper = None
if key.upper().startswith("MBIS"):
if key.upper().endswith("CHARGES"):
return val
elif key.upper().endswith("DIPOLES"):
reshaper = (-1, 3)
return val.reshape(reshaper)
elif key.upper().endswith("QUADRUPOLES"):
val = val.reshape(-1, 3, 3)
val = np.array([_multipole_compressor(val[iat], 2) for iat in range(len(val))])
return val
elif key.upper().endswith("OCTUPOLES"):
val = val.reshape(-1, 3, 3, 3)
val = np.array([_multipole_compressor(val[iat], 3) for iat in range(len(val))])
return val
elif key.upper().endswith("DIPOLE") or "DIPOLE -" in key.upper():
reshaper = (1, 3)
elif "QUADRUPOLE POLARIZABILITY TENSOR" in key.upper():
reshaper = (3, 3, 3)
elif any((key.upper().endswith(p) or f"{p} -" in key.upper()) for p in _multipole_order):
p = [p for p in _multipole_order if (key.upper().endswith(p) or f"{p} -" in key.upper())]
val = _multipole_compressor(val, _multipole_order.index(p[0]))
reshaper = (1, -1)
elif key.upper() in ["MULLIKEN_CHARGES", "LOWDIN_CHARGES", "MULLIKEN CHARGES", "LOWDIN CHARGES"]:
reshaper = (1, -1)
if reshaper:
return val.reshape(reshaper)
else:
return val
def _qcvar_reshape_get(key: str, val: core.Matrix) -> Union[core.Matrix, np.ndarray]:
"""For QCVariables where the 2D :py:class:`psi4.core.Matrix` shape is
unnatural, convert to natural shape in :class:`numpy.ndarray`.
"""
reshaper = None
if key.upper().startswith("MBIS"):
if key.upper().endswith("CHARGES"):
return val.np
elif key.upper().endswith("DIPOLES"):
reshaper = (-1, 3)
return val.np.reshape(reshaper)
elif key.upper().endswith("QUADRUPOLES"):
val = val.np.reshape(-1, 6)
val = np.array([_multipole_plumper(val[iat], 2) for iat in range(len(val))])
return val
elif key.upper().endswith("OCTUPOLES"):
val = val.np.reshape(-1, 10)
val = np.array([_multipole_plumper(val[iat], 3) for iat in range(len(val))])
return val
elif key.upper().endswith("DIPOLE") or "DIPOLE -" in key.upper():
reshaper = (3, )
elif "QUADRUPOLE POLARIZABILITY TENSOR" in key.upper():
reshaper = (3, 3, 3)
elif any((key.upper().endswith(p) or f"{p} -" in key.upper()) for p in _multipole_order):
p = [p for p in _multipole_order if (key.upper().endswith(p) or f"{p} -" in key.upper())]
return _multipole_plumper(val.np.reshape((-1, )), _multipole_order.index(p[0]))
elif key.upper() in ["MULLIKEN_CHARGES", "LOWDIN_CHARGES", "MULLIKEN CHARGES", "LOWDIN CHARGES"]:
reshaper = (-1, )
if reshaper:
return val.np.reshape(reshaper)
else:
return val
def _multipole_compressor(complete: np.ndarray, order: int) -> np.ndarray:
"""Form flat unique components multipole array from complete Cartesian array.
Parameters
----------
order
Multipole order. e.g., 1 for dipole, 4 for hexadecapole.
complete
Multipole array, order-dimensional Cartesian array expanded to complete components.
Returns
-------
compressed : numpy.ndarray
Multipole array, length (order + 1) * (order + 2) / 2 compressed to unique components.
"""
compressed = []
for ii in range(order + 1):
lx = order - ii
for lz in range(ii + 1):
ly = ii - lz
np_index = []
for xval in range(lx):
np_index.append(0)
for yval in range(ly):
np_index.append(1)
for zval in range(lz):
np_index.append(2)
compressed.append(complete[tuple(np_index)])
assert len(compressed) == ((order + 1) * (order + 2) / 2)
return np.array(compressed)
def _multipole_plumper(compressed: np.ndarray, order: int) -> np.ndarray:
"""Form multidimensional multipole array from unique components array.
Parameters
----------
order
Multipole order. e.g., 1 for dipole, 4 for hexadecapole.
compressed
Multipole array, length (order + 1) * (order + 2) / 2 compressed to unique components.
Returns
-------
complete : numpy.ndarray
Multipole array, order-dimensional Cartesian array expanded to complete components.
"""
shape = tuple([3] * order)
complete = np.zeros(shape)
def compound_index(counter):
# thanks, https://www.pamoc.it/tpc_cart_mom.html Eqn 2.2!
# jn = nz + (ny + nz)(ny + nz + 1) / 2
return int(
counter.get("2", 0) + (counter.get("1", 0) + counter.get("2", 0)) *
(counter.get("1", 0) + counter.get("2", 0) + 1) / 2)
for idx in product("012", repeat=order):
xyz_counts = Counter(idx) # "010" --> {"0": 2, "1": 1}
np_index = tuple(int(x) for x in idx) # ('0', '1') --> (0, 1)
complete[np_index] = compressed[compound_index(xyz_counts)]
return complete
def _core_has_variable(key: str) -> bool:
"""Whether scalar or array :ref:`QCVariable <sec:appendices:qcvars>` *key*
has been set in global memory.
Parameters
----------
key
Case-insensitive key to global double or :py:class:`~psi4.core.Matrix`
storage maps.
"""
return core.has_scalar_variable(key) or core.has_array_variable(key)
def _core_wavefunction_has_variable(self: core.Wavefunction, key: str) -> bool:
"""Whether scalar or array :ref:`QCVariable <sec:appendices:qcvars>` *key*
has been set on *self*.
Parameters
----------
self
Wavefunction instance.
key
Case-insensitive key to instance's double or
:py:class:`~psi4.core.Matrix` storage maps.
"""
return self.has_scalar_variable(key) or self.has_array_variable(key)
def _core_variable(key: str) -> Union[float, core.Matrix, np.ndarray]:
"""Return copy of scalar or array :ref:`QCVariable <sec:appendices:qcvars>`
*key* from global memory.
Parameters
----------
key
Case-insensitive key to global double or :py:class:`~psi4.core.Matrix`
storage maps.
Returns
-------
float or ~numpy.ndarray or Matrix
Requested QCVariable from global memory.
- Scalar variables are returned as floats.
- Array variables not naturally 2D (like multipoles or per-atom charges)
are returned as :class:`~numpy.ndarray` of natural dimensionality.
- Other array variables are returned as :py:class:`~psi4.core.Matrix` and
may have an extra dimension with symmetry information.
Raises
------
KeyError
If `key` not set on `self`.
Example
-------
>>> psi4.gradient("hf/cc-pvdz")
>>> psi4.variable("CURRENT ENERGY")
-100.00985995185668
>>> psi4.variable("CURRENT DIPOLE")
array([ 0. , 0. , -0.83217802])
>>> psi4.variable("CURRENT GRADIENT")
<psi4.core.Matrix object at 0x12d884fc0>
>>> psi4.variable("CURRENT GRADIENT").np
array([[ 6.16297582e-33, 6.16297582e-33, -9.41037138e-02],
[-6.16297582e-33, -6.16297582e-33, 9.41037138e-02]])
"""
key = _qcvar_warnings(key)
if core.has_scalar_variable(key):
return core.scalar_variable(key)
elif core.has_array_variable(key):
return _qcvar_reshape_get(key, core.array_variable(key))
else:
raise KeyError(f"psi4.core.variable: Requested variable '{key}' was not set!\n")
def _core_wavefunction_variable(self: core.Wavefunction, key: str) -> Union[float, core.Matrix, np.ndarray]:
"""Return copy of scalar or array :ref:`QCVariable <sec:appendices:qcvars>`
*key* from *self*.
Parameters
----------
self
Wavefunction instance.
key
Case-insensitive key to instance's double or :py:class:`~psi4.core.Matrix`
storage maps.
Returns
-------
float or ~numpy.ndarray or Matrix
Requested QCVariable from `self`.
- Scalar variables are returned as floats.
- Array variables not naturally 2D (like multipoles or per-atom charges)
are returned as :class:`~numpy.ndarray` of natural dimensionality.
- Other array variables are returned as :py:class:`~psi4.core.Matrix` and
may have an extra dimension with symmetry information.
Raises
------
KeyError
If `key` not set on `self`.
Example
-------
>>> g, wfn = psi4.gradient("hf/cc-pvdz", return_wfn=True)
>>> wfn.variable("CURRENT ENERGY")
-100.00985995185668
>>> wfn.variable("CURRENT DIPOLE")
array([ 0. , 0. , -0.83217802])
>>> wfn.variable("CURRENT GRADIENT")
<psi4.core.Matrix object at 0x12d884fc0>
>>> wfn.variable("CURRENT GRADIENT").np
array([[ 6.16297582e-33, 6.16297582e-33, -9.41037138e-02],
[-6.16297582e-33, -6.16297582e-33, 9.41037138e-02]])
"""
key = _qcvar_warnings(key)
if self.has_scalar_variable(key):
return self.scalar_variable(key)
elif self.has_array_variable(key):
return _qcvar_reshape_get(key, self.array_variable(key))
else:
raise KeyError(f"psi4.core.Wavefunction.variable: Requested variable '{key}' was not set!\n")
def _core_set_variable(key: str, val: Union[core.Matrix, np.ndarray, float]) -> None:
"""Sets scalar or array :ref:`QCVariable <sec:appendices:qcvars>` *key* to
*val* in global memory.
Parameters
----------
key
Case-insensitive key to global double or :py:class:`~psi4.core.Matrix`
storage maps.
val
Scalar or array to be stored in `key`. If :class:`~numpy.ndarray` and
data `key` does not naturally fit in 2D Matrix (often charge and
multipole QCVariables), it will be reshaped, as all
:class:`~numpy.ndarray` are stored as :class:`~psi4.core.Matrix`.
Raises
------
ValidationError
If `val` is a scalar but `key` already exists as an array variable. Or
if `val` is an array but `key` already exists as a scalar variable.
"""
if isinstance(val, core.Matrix):
if core.has_scalar_variable(key):
raise ValidationError(f"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(f"psi4.core.set_variable: Target variable '{key}' already a scalar variable!")
else:
core.set_array_variable(key, core.Matrix.from_array(_qcvar_reshape_set(key, val)))
else:
if core.has_array_variable(key):
raise ValidationError(f"psi4.core.set_variable: Target variable '{key}' already an array variable!")
else:
core.set_scalar_variable(key, val)
# TODO _qcvar_warnings(key)
def _core_wavefunction_set_variable(self: core.Wavefunction, key: str, val: Union[core.Matrix, np.ndarray, float]) -> None:
"""Sets scalar or array :ref:`QCVariable <sec:appendices:qcvars>` *key* to
*val* on *self*.
Parameters
----------
self
Wavefunction instance.
key
Case-insensitive key to instance's double or :class:`~psi4.core.Matrix`
storage maps.
- If ``CURRENT ENERGY``, syncs with ``self.energy_``.
- If ``CURRENT GRADIENT``, syncs with ``gradient_``.
- If ``CURRENT HESSIAN``, syncs with ``self.hessian_``.
val
Scalar or array to be stored in `key`. If :class:`~numpy.ndarray` and
data `key` does not naturally fit in 2D Matrix (often charge and
multipole QCVariables), it will be reshaped, as all
:class:`~numpy.ndarray` are stored as :class:`~psi4.core.Matrix`.
Raises
------
~psi4.driver.ValidationError
If `val` is a scalar but `key` already exists as an array variable. Or
if `val` is an array but `key` already exists as a scalar variable.
"""
if isinstance(val, core.Matrix):
if self.has_scalar_variable(key):
raise ValidationError("psi4.core.Wavefunction.set_variable: Target variable '{key}' already a scalar variable!")
else:
self.set_array_variable(key, val)
elif isinstance(val, np.ndarray):
if self.has_scalar_variable(key):
raise ValidationError("psi4.core.Wavefunction.set_variable: Target variable '{key}' already a scalar variable!")
else:
self.set_array_variable(key, core.Matrix.from_array(_qcvar_reshape_set(key, val)))
else:
if self.has_array_variable(key):
raise ValidationError("psi4.core.Wavefunction.set_variable: Target variable '{key}' already an array variable!")
else:
self.set_scalar_variable(key, val)
# TODO _qcvar_warnings(key)
def _core_del_variable(key: str) -> None:
"""Removes scalar or array :ref:`QCVariable <sec:appendices:qcvars>` *key*
from global memory if present.
Parameters
----------
key
Case-insensitive key to global double or :py:class:`~psi4.core.Matrix`
storage maps.
"""
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(self: core.Wavefunction, key: str) -> None:
"""Removes scalar or array :ref:`QCVariable <sec:appendices:qcvars>` *key*
from *self* if present.
Parameters
----------
self
Wavefunction instance.
key
Case-insensitive key to instance's double or
:py:class:`~psi4.core.Matrix` storage maps.
"""
if self.has_scalar_variable(key):
self.del_scalar_variable(key)
elif self.has_array_variable(key):
self.del_array_variable(key)
def _core_variables(include_deprecated_keys: bool = False) -> Dict[str, Union[float, core.Matrix, np.ndarray]]:
"""Return all scalar or array :ref:`QCVariables <sec:appendices:qcvars>`
from global memory.
Parameters
----------
include_deprecated_keys
Also return duplicate entries with keys that have been deprecated.
Returns
-------
~typing.Dict[str, ~typing.Union[float, ~numpy.ndarray, Matrix]
Map of all QCVariables that have been set.
- Scalar variables are returned as floats.
- Array variables not naturally 2D (like multipoles or per-atom charges)
are returned as :class:`~numpy.ndarray` of natural dimensionality.
- Other array variables are returned as :py:class:`~psi4.core.Matrix` and
may have an extra dimension with symmetry information.
"""
dicary = {**core.scalar_variables(), **{k: _qcvar_reshape_get(k, v) for k, v in core.array_variables().items()}}
if include_deprecated_keys:
for old_key, (current_key, version) in _qcvar_transitions.items():
if current_key in dicary:
dicary[old_key] = dicary[current_key]
return dicary
def _core_wavefunction_variables(self, include_deprecated_keys: bool = False) -> Dict[str, Union[float, core.Matrix, np.ndarray]]:
"""Return all scalar or array :ref:`QCVariables <sec:appendices:qcvars>`
from *self*.
Parameters
----------
self
Wavefunction instance.
include_deprecated_keys
Also return duplicate entries with keys that have been deprecated.
Returns
-------
~typing.Dict[str, ~typing.Union[float, ~numpy.ndarray, Matrix]
Map of all QCVariables that have been set on `self`.
- Scalar variables are returned as floats.
- Array variables not naturally 2D (like multipoles or per-atom charges)
are returned as :class:`~numpy.ndarray` of natural dimensionality.
- Other array variables are returned as :py:class:`~psi4.core.Matrix` and
may have an extra dimension with symmetry information.
"""
dicary = {**self.scalar_variables(), **{k: _qcvar_reshape_get(k, v) for k, v in self.array_variables().items()}}
if include_deprecated_keys:
for old_key, (current_key, version) in _qcvar_transitions.items():
if current_key in dicary:
dicary[old_key] = dicary[current_key]
return dicary
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):
"""
.. deprecated:: 1.4
Use :py:func:`psi4.core.variable` instead.
"""
warnings.warn(
"Using `psi4.core.get_variable` instead of `psi4.core.variable` (or `psi4.core.scalar_variable` for scalar variables only) is deprecated, and as soon as 1.4 it will stop working\n",
category=FutureWarning,
stacklevel=2)
return core.scalar_variable(key)
def _core_get_variables():
"""
.. deprecated:: 1.4
Use :py:func:`psi4.core.variables` instead.
"""
warnings.warn(
"Using `psi4.core.get_variables` instead of `psi4.core.variables` (or `psi4.core.scalar_variables` for scalar variables only) is deprecated, and as soon as 1.4 it will stop working\n",
category=FutureWarning,
stacklevel=2)
return core.scalar_variables()
def _core_get_array_variable(key):
"""
.. deprecated:: 1.4
Use :py:func:`psi4.core.variable` instead.
"""
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 as soon as 1.4 it will stop working\n",
category=FutureWarning,
stacklevel=2)
return core.array_variable(key)
def _core_get_array_variables():
"""
.. deprecated:: 1.4
Use :py:func:`psi4.core.variables` instead.
"""
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 as soon as 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):
"""
.. deprecated:: 1.4
Use :py:func:`psi4.core.Wavefunction.variable` instead.
"""
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 as soon as 1.4 it will stop working\n",
category=FutureWarning,
stacklevel=2)
return cls.scalar_variable(key)
def _core_wavefunction_get_array(cls, key):
"""
.. deprecated:: 1.4
Use :py:func:`psi4.core.Wavefunction.variable` instead.
"""
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 as soon as 1.4 it will stop working\n",
category=FutureWarning,
stacklevel=2)
return cls.array_variable(key)
def _core_wavefunction_set_array(cls, key, val):
"""
.. deprecated:: 1.4
Use :py:func:`psi4.core.Wavefunction.set_variable` instead.
"""
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 as soon as 1.4 it will stop working\n",
category=FutureWarning,
stacklevel=2)
return cls.set_array_variable(key, val)
def _core_wavefunction_arrays(cls):
"""
.. deprecated:: 1.4
Use :py:func:`psi4.core.Wavefunction.variables` instead.
"""
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 as soon as 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(self):
"""Returns the results of a frequency analysis.
Parameters
----------
self
Wavefunction instance.
Returns
-------
~typing.Optional[~typing.Dict[str, ~numpy.ndarray]]
A dictionary of vibrational information. See :py:func:`psi4.driver.qcdb.vib.harmonic_analysis`
"""
if not hasattr(self, 'frequency_analysis'):
return None
vibinfo = self.frequency_analysis
vibonly = qcdb.vib.filter_nonvib(vibinfo)
return core.Vector.from_array(qcdb.vib.filter_omega_to_real(vibonly['omega'].data))
core.Wavefunction.frequencies = _core_wavefunction_frequencies
def _core_doublet(A, B, transA, transB):
"""Multiply two matrices together.
.. deprecated:: 1.4
Use :py:func:`psi4.core.doublet` instead.
"""
warnings.warn(
"Using `psi4.core.Matrix.doublet` instead of `psi4.core.doublet` is deprecated, and as soon as 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):
"""Multiply three matrices together.
.. deprecated:: 1.4
Use :py:func:`psi4.core.triplet` instead.
"""
warnings.warn(
"Using `psi4.core.Matrix.triplet` instead of `psi4.core.triplet` is deprecated, and as soon as 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)
@staticmethod
def _core_erisieve_build(
orbital_basis: core.BasisSet,
cutoff: float = 0.0,
do_csam: bool = False
) -> core.ERISieve:
"""
This function previously constructed a Psi4 ERISieve object from an input basis set, with an optional cutoff threshold for
ERI screening and an optional input to enable CSAM screening (over Schwarz screening).
However, as the ERISieve class was removed from Psi4 in v1.9, the function now throws with an UpgradeHelper
exception, and lets the user know to use TwoBodyAOInt instead.
Parameters
----------
orbital_basis
Basis set to use in the ERISieve object.
cutoff
Integral cutoff threshold to use for Schwarz/CSAM screening. Defaults to 0.0, disabling screening entirely.
do_csam
Use CSAM screening? If True, CSAM screening is used; else, Schwarz screening is used. By default,
Schwarz screening is utilized.
Returns
-------
ERISieve
Initialized ERISieve object.
Example
-------
>>> sieve = psi4.core.ERISieve.build(bas, cutoff, csam)
"""
raise UpgradeHelper("ERISieve", "TwoBodyAOInt", 1.8, " The ERISieve class has been removed and replaced with the TwoBodyAOInt class. ERISieve.build(orbital_basis, cutoff, do_csam) can be replaced with the command sequence factory = psi4.core.IntegralFactory(basis); factory.eri(0).")
core.ERISieve.build = _core_erisieve_build
