Source code for psi4.driver.molutil

# Psi4: an open-source quantum chemistry software package
# Copyright (c) 2007-2022 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
# 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.
"""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: 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": 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: 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)