#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2024 The Psi4 Developers.
#
# 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
# it under the terms of the GNU Lesser General Public License as published by
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# Psi4 is distributed in the hope that it will be useful,
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# GNU Lesser General Public License for more details.
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# @END LICENSE
#
"""Module with utility functions that act on molecule objects."""
from typing import Dict, Tuple, Union
import numpy as np
import qcelemental as qcel
from psi4 import core
from . import qcdb
from .constants import constants
from .p4util.exceptions import *
[docs]
def molecule_set_attr(self, name, value):
"""Function to redefine __setattr__ method of molecule class."""
fxn = object.__getattribute__(self, "is_variable")
isvar = fxn(name)
if isvar:
fxn = object.__getattribute__(self, "set_variable")
fxn(name, value)
return
object.__setattr__(self, name, value)
[docs]
def molecule_get_attr(self, name):
"""Function to redefine __getattr__ method of molecule class."""
fxn = object.__getattribute__(self, "is_variable")
isvar = fxn(name)
if isvar:
fxn = object.__getattribute__(self, "get_variable")
return fxn(name)
return object.__getattribute__(self, name)
@classmethod
def _molecule_from_string(cls,
molstr,
dtype=None,
name=None,
fix_com=None,
fix_orientation=None,
fix_symmetry=None,
return_dict=False,
enable_qm=True,
enable_efp=True,
missing_enabled_return_qm='none',
missing_enabled_return_efp='none',
verbose=1):
molrec = qcel.molparse.from_string(
molstr=molstr,
dtype=dtype,
name=name,
fix_com=fix_com,
fix_orientation=fix_orientation,
fix_symmetry=fix_symmetry,
return_processed=False,
enable_qm=enable_qm,
enable_efp=enable_efp,
missing_enabled_return_qm=missing_enabled_return_qm,
missing_enabled_return_efp=missing_enabled_return_efp,
verbose=verbose)
if return_dict:
return core.Molecule.from_dict(molrec['qm']), molrec
else:
return core.Molecule.from_dict(molrec['qm'])
@classmethod
def _molecule_from_arrays(cls,
geom=None,
elea=None,
elez=None,
elem=None,
mass=None,
real=None,
elbl=None,
name=None,
units='Angstrom',
input_units_to_au=None,
fix_com=None,
fix_orientation=None,
fix_symmetry=None,
fragment_separators=None,
fragment_charges=None,
fragment_multiplicities=None,
molecular_charge=None,
molecular_multiplicity=None,
comment=None,
provenance=None,
connectivity=None,
missing_enabled_return='error',
tooclose=0.1,
zero_ghost_fragments=False,
nonphysical=False,
mtol=1.e-3,
verbose=1,
return_dict=False):
"""Construct Molecule from unvalidated arrays and variables.
Light wrapper around :py:func:`~qcelemental.molparse.from_arrays`
that is a full-featured constructor to dictionary representa-
tion of Molecule. This follows one step further to return
Molecule instance.
Parameters
----------
See :py:func:`~qcelemental.molparse.from_arrays`.
Returns
-------
:py:class:`psi4.core.Molecule`
"""
molrec = qcel.molparse.from_arrays(
geom=geom,
elea=elea,
elez=elez,
elem=elem,
mass=mass,
real=real,
elbl=elbl,
name=name,
units=units,
input_units_to_au=input_units_to_au,
fix_com=fix_com,
fix_orientation=fix_orientation,
fix_symmetry=fix_symmetry,
fragment_separators=fragment_separators,
fragment_charges=fragment_charges,
fragment_multiplicities=fragment_multiplicities,
molecular_charge=molecular_charge,
molecular_multiplicity=molecular_multiplicity,
comment=comment,
provenance=provenance,
connectivity=connectivity,
domain='qm',
missing_enabled_return=missing_enabled_return,
tooclose=tooclose,
zero_ghost_fragments=zero_ghost_fragments,
nonphysical=nonphysical,
mtol=mtol,
verbose=verbose)
qmol = core.Molecule.from_dict(molrec)
geom = np.array(molrec["geom"]).reshape((-1, 3))
qmol._initial_cartesian = core.Matrix.from_array(geom)
if return_dict:
return qmol, molrec
else:
return qmol
@classmethod
def _molecule_from_schema(cls, molschema: Dict, return_dict: bool = False, nonphysical: bool = False, verbose: int = 1) -> Union[core.Molecule, Tuple[core.Molecule, Dict]]:
"""Construct Molecule from non-Psi4 schema.
Light wrapper around :py:func:`~psi4.core.Molecule.from_arrays`.
Parameters
----------
molschema
Dictionary form of Molecule following known schema.
return_dict
Additionally return Molecule dictionary intermediate.
nonphysical
Do allow masses outside an element's natural range to pass validation?
verbose
Amount of printing.
Returns
-------
mol : :py:class:`psi4.core.Molecule`
molrec : dict
Dictionary representation of instance.
Only provided if `return_dict` is True.
"""
molrec = qcel.molparse.from_schema(molschema, nonphysical=nonphysical, verbose=verbose)
qmol = core.Molecule.from_dict(molrec)
geom = np.array(molrec["geom"]).reshape((-1, 3))
qmol._initial_cartesian = core.Matrix.from_array(geom)
if return_dict:
return qmol, molrec
else:
return qmol
[docs]
def dynamic_variable_bind(cls):
"""Function to dynamically add extra members to
the core.Molecule class.
"""
cls.__setattr__ = molecule_set_attr
cls.__getattr__ = molecule_get_attr
cls.to_arrays = qcdb.Molecule.to_arrays
cls.to_dict = qcdb.Molecule.to_dict
cls.BFS = qcdb.Molecule.BFS
cls.B787 = qcdb.Molecule.B787
cls.scramble = qcdb.Molecule.scramble
cls.from_arrays = _molecule_from_arrays
cls.from_string = _molecule_from_string
cls.to_string = qcdb.Molecule.to_string
cls.from_schema = _molecule_from_schema
cls.to_schema = qcdb.Molecule.to_schema
cls.run_dftd3 = qcdb.Molecule.run_dftd3
cls.run_dftd4 = qcdb.Molecule.run_dftd4
cls.run_gcp = qcdb.Molecule.run_gcp
cls.format_molecule_for_mol = qcdb.Molecule.format_molecule_for_mol
dynamic_variable_bind(core.Molecule) # pass class type, not class instance
#
# Define geometry to be used by PSI4.
# The molecule created by this will be set in options.
#
# geometry("
# O 1.0 0.0 0.0
# H 0.0 1.0 0.0
# H 0.0 0.0 0.0
#
[docs]
def geometry(geom: str, name: str = "default") -> core.Molecule:
"""Function to create a molecule object of name *name* from the
geometry in string *geom*. Permitted for user use but deprecated
in driver in favor of explicit molecule-passing. Comments within
the string are filtered.
"""
molrec = qcel.molparse.from_string(
geom, enable_qm=True, missing_enabled_return_qm='minimal', enable_efp=True, missing_enabled_return_efp='none')
molecule = core.Molecule.from_dict(molrec['qm'])
if "geom" in molrec["qm"]:
geom = np.array(molrec["qm"]["geom"]).reshape((-1, 3))
if molrec["qm"]["units"] == "Angstrom":
# beware if qcel and psi4 choose different sets of constants
geom = geom / constants.bohr2angstroms
molecule._initial_cartesian = core.Matrix.from_array(geom)
molecule.set_name(name)
if 'efp' in molrec:
try:
import pylibefp
except ImportError as e: # py36 ModuleNotFoundError
raise ImportError("""Install pylibefp to use EFP functionality. `conda install pylibefp -c psi4` Or build with `-DENABLE_libefp=ON`""") from e
#print('Using pylibefp: {} (version {})'.format(pylibefp.__file__, pylibefp.__version__))
efpobj = pylibefp.from_dict(molrec['efp'])
# pylibefp.core.efp rides along on molecule
molecule.EFP = efpobj
# Attempt to go ahead and construct the molecule
try:
molecule.update_geometry()
except Exception:
core.print_out("Molecule: geometry: Molecule is not complete, please use 'update_geometry'\n"
" once all variables are set.\n")
activate(molecule)
return molecule
[docs]
def activate(mol: core.Molecule):
"""Function to set molecule object *mol* as the current active molecule.
Permitted for user use but deprecated in driver in favor of explicit
molecule-passing.
"""
core.set_active_molecule(mol)
