#
# @BEGIN LICENSE
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# Psi4: an open-source quantum chemistry software package
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# Copyright (c) 2007-2022 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,
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"""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 psi4.driver.p4util import temp_circular_import_blocker
from psi4.driver import qcdb
from psi4.driver.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)
if return_dict:
return core.Molecule.from_dict(molrec), molrec
else:
return core.Molecule.from_dict(molrec)
@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, name="default"):
"""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":
geom = geom / qcel.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):
"""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)
