Source code for psi4.driver.aliases

# 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 high-level functions calling wrappers and driver.

Place in this file quickly defined procedures such as
   - aliases for complex methods
   - simple modifications to existing methods


__all__ = [

import os
import re
import warnings
from typing import Any, Dict, List

CBSMetadata = List[Dict[str, Any]]

# Python procedures like these can be run directly from the input file or integrated
# with the energy(), etc. routines by means of lines like those at the end
# of this file.

def fake_file11(wfn: "psi4.core.Wavefunction", filename: str = 'fake_file11.dat', **kwargs):
    r"""Function to print a file *filename* of the old file11 format
    from molecule and gradient information in *wfn*.

    .. versionadded:: 0.6
       *wfn* parameter passed explicitly

    :returns: None

    :param filename: destination file name for file11 file

    :param wfn: set of molecule, gradient from which to generate file11


    >>> # [1] file11 for CISD calculation
    >>> G, wfn = gradient('cisd', return_wfn=True)
    >>> fake_file11(wfn, 'mycalc.11')

    molecule = wfn.molecule()
    gradient = wfn.gradient()

    with open(filename, 'w') as handle:
        handle.write('%d\n' % (molecule.natom()))

        for at in range(molecule.natom()):
            handle.write('%6s %16.8f %16.8f %16.8f\n' % (molecule.symbol(
                at), molecule.x(at), molecule.y(at), molecule.z(at)))

        for at in range(molecule.natom()):
            handle.write('%6s %16.8f %16.8f %16.8f\n' % (
                '', gradient.get(at, 0), gradient.get(at, 1), gradient.get(at, 2)))

[docs]def sherrill_gold_standard(**kwargs) -> CBSMetadata: r"""Function to call the quantum chemical method known as 'Gold Standard' in the Sherrill group. Uses the composite wrapper to evaluate the following expression. Two-point extrapolation of the correlation energy performed according to :py:func:`~psi4.driver.driver_cbs_helper.corl_xtpl_helgaker_2`. .. math:: E_{total}^{\text{Au\_std}} = E_{total,\; \text{SCF}}^{\text{aug-cc-pVQZ}} \; + E_{corl,\; \text{MP2}}^{\text{aug-cc-pV[TQ]Z}} \; + \delta_{\text{MP2}}^{\text{CCSD(T)}}\big\vert_{\text{aug-cc-pVTZ}} >>> # [1] single-point energy by this composite method >>> energy('sherrill_gold_standard') >>> # [2] finite-difference geometry optimization >>> optimize('sherrill_gold_standard') >>> # [3] finite-difference geometry optimization, overwriting some pre-defined sherrill_gold_standard options >>> optimize('sherrill_gold_standard', corl_basis='cc-pV[DT]Z', delta_basis='3-21g') """ scf = { 'wfn': 'hf', 'basis': kwargs.pop('scf_basis', 'aug-cc-pVQZ'), 'scheme': kwargs.pop('scf_scheme', 'xtpl_highest_1') } corl = { 'wfn': kwargs.pop('corl_wfn', 'mp2'), 'basis': kwargs.pop('corl_basis', 'aug-cc-pV[TQ]Z'), 'scheme': kwargs.pop('corl_scheme', 'corl_xtpl_helgaker_2') } delta = { 'wfn': kwargs.pop('delta_wfn', 'ccsd(t)'), 'wfn_lesser': kwargs.pop('delta_wfn_lesser', 'mp2'), 'basis': kwargs.pop('delta_basis', 'aug-cc-pVTZ'), 'scheme': kwargs.pop('delta_scheme', 'xtpl_highest_1') } return [scf, corl, delta]
[docs]def allen_focal_point(**kwargs) -> CBSMetadata: r"""Function to call Wes Allen-style Focal Point Analysis. JCP 127 014306, . Uses the composite wrapper to evaluate the following expression. SCF employs a three-point extrapolation according to :py:func:`~psi4.driver.driver_cbs_helper.scf_xtpl_helgaker_3`. MP2, CCSD, and CCSD(T) employ two-point extrapolation performed according to :py:func:`~psi4.driver.driver_cbs_helper.corl_xtpl_helgaker_2`. CCSDT and CCSDT(Q) are plain deltas. This wrapper requires :ref:`Kallay's MRCC code <sec:mrcc>`. .. math:: E_{total}^{\text{FPA}} = E_{total,\; \text{SCF}}^{\text{cc-pV[Q56]Z}} \; + E_{corl,\; \text{MP2}}^{\text{cc-pV[56]Z}} \; + \delta_{\text{MP2}}^{\text{CCSD}}\big\vert_{\text{cc-pV[56]Z}} \; + \delta_{\text{CCSD}}^{\text{CCSD(T)}}\big\vert_{\text{cc-pV[56]Z}} \; + \delta_{\text{CCSD(T)}}^{\text{CCSDT}}\big\vert_{\text{cc-pVTZ}} \; + \delta_{\text{CCSDT}}^{\text{CCSDT(Q)}}\big\vert_{\text{cc-pVDZ}} >>> # [1] single-point energy by this composite method >>> energy('allen_focal_point') >>> # [2] single-point energy reducing the Hartree-Fock basis sets size >>> energy('allen_focal_point', scf_basis='cc-pV[TQ5]Z') """ import psi4 if not psi4.addons("mrcc"): raise ImportError("Install MRCC (executable 'dmrcc') to use the allen_focal_point function.") # Note: HF and MP2 steps (which don't need MRCC and indeed can't be # run directly in MRCC through the Psi4 interface) nevertheless have # qc_module=mrcc set here so that options sets (below, `"options"` # and `"options_lo"`) are the same and the cbs() driver knows it's # safe (that is, consistent) to use the "free" values (e.g., # HF from CCSD) resulting from # MRCC CCSD calcs. This logic can be made smarter if needed. scf = { # HF 'wfn': 'hf', 'basis': kwargs.pop('scf_basis', 'cc-pV[Q56]Z'), 'scheme': kwargs.pop('scf_scheme', 'scf_xtpl_helgaker_3'), 'options': {"qc_module": "mrcc"}, } corl = { # MP2 - HF 'wfn': kwargs.pop('corl_wfn', 'mp2'), 'basis': kwargs.pop('corl_basis', 'cc-pV[56]Z'), 'scheme': kwargs.pop('corl_scheme', 'corl_xtpl_helgaker_2'), 'options': {"qc_module": "mrcc"}, 'options_lo': {"qc_module": "mrcc"}, } delta = { # CCSD - MP2 'wfn': kwargs.pop('delta_wfn', 'ccsd'), 'wfn_lesser': kwargs.pop('delta_wfn_lesser', 'mp2'), 'basis': kwargs.pop('delta_basis', 'cc-pV[56]Z'), 'scheme': kwargs.pop('delta_scheme', 'corl_xtpl_helgaker_2'), 'options': {"qc_module": "mrcc"}, 'options_lo': {"qc_module": "mrcc"}, } delta2 = { # CCSD(T) - CCSD 'wfn': kwargs.pop('delta2_wfn', 'ccsd(t)'), 'wfn_lesser': kwargs.pop('delta2_wfn_lesser', 'ccsd'), 'basis': kwargs.pop('delta2_basis', 'cc-pV[56]Z'), 'scheme': kwargs.pop('delta2_scheme', 'corl_xtpl_helgaker_2'), 'options': {"qc_module": "mrcc"}, 'options_lo': {"qc_module": "mrcc"}, } delta3 = { # CCSDT - CCSD(T) 'wfn': kwargs.pop('delta3_wfn', 'ccsdt'), 'wfn_lesser': kwargs.pop('delta3_wfn_lesser', 'ccsd(t)'), 'basis': kwargs.pop('delta3_basis', 'cc-pVTZ'), 'scheme': kwargs.pop('delta3_scheme', 'xtpl_highest_1'), 'options': {"qc_module": "mrcc"}, 'options_lo': {"qc_module": "mrcc"}, } delta4 = { # CCSDT(Q) - CCSDT 'wfn': kwargs.pop('delta4_wfn', 'ccsdt(q)'), 'wfn_lesser': kwargs.pop('delta4_wfn_lesser', 'ccsdt'), 'basis': kwargs.pop('delta4_basis', 'cc-pVDZ'), 'scheme': kwargs.pop('delta4_scheme', 'xtpl_highest_1'), 'options': {"qc_module": "mrcc"}, 'options_lo': {"qc_module": "mrcc"}, } return [scf, corl, delta, delta2, delta3, delta4]