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# Psi4: an open-source quantum chemistry software package
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# Copyright (c) 2007-2018 The Psi4 Developers.
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# Psi4 is free software; you can redistribute it and/or modify
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#
"""Module with functions that call upon those in modules
:py:mod:`proc`, :py:mod:`driver`, and :py:mod:`wrappers`.
Place in this file quickly defined procedures such as
- aliases for complex methods
- simple modifications to existing methods
"""
from __future__ import print_function
from __future__ import absolute_import
import os
import re
import math
import warnings
from psi4.driver import driver_cbs
# 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, filename='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
:type filename: string
:param filename: destination file name for file11 file
:type wfn: :py:class:`~psi4.core.Wavefunction`
:param wfn: set of molecule, gradient from which to generate file11
:examples:
>>> # [1] file11 for CISD calculation
>>> G, wfn = gradient('cisd', return_wfn=True)
>>> fake_file11(wfn, 'mycalc.11')
"""
molecule = wfn.molecule()
molecule.update_geometry()
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(func, label, **kwargs):
r"""Function to call the quantum chemical method known as 'Gold Standard'
in the Sherrill group. Uses :py:func:`~driver_cbs.complete_basis_set` to evaluate
the following expression. Two-point extrapolation of the correlation energy
performed according to :py:func:`~driver_cbs.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')
"""
kwargs['scf_basis'] = kwargs.get('scf_basis', 'aug-cc-pVQZ')
kwargs['scf_scheme'] = kwargs.get('scf_scheme', driver_cbs.xtpl_highest_1)
kwargs['corl_wfn'] = kwargs.get('corl_wfn', 'mp2')
kwargs['corl_basis'] = kwargs.get('corl_basis', 'aug-cc-pV[TQ]Z')
kwargs['corl_scheme'] = kwargs.get('corl_scheme', driver_cbs.corl_xtpl_helgaker_2)
kwargs['delta_wfn'] = kwargs.get('delta_wfn', 'ccsd(t)')
kwargs['delta_wfn_lesser'] = kwargs.get('delta_wfn_lesser', 'mp2')
kwargs['delta_basis'] = kwargs.get('delta_basis', 'aug-cc-pVTZ')
kwargs['delta_scheme'] = kwargs.get('delta_scheme', driver_cbs.xtpl_highest_1)
if label == 'custom_function':
label = 'Sherrill Group Gold Standard'
return driver_cbs.cbs(func, label, **kwargs)
[docs]def allen_focal_point(func, label, **kwargs):
r"""Function to call Wes Allen-style Focal
Point Analysis. JCP 127 014306. Uses
:py:func:`~driver_cbs.complete_basis_set` to evaluate the following
expression. SCF employs a three-point extrapolation according
to :py:func:`~driver_cbs.scf_xtpl_helgaker_3`. MP2, CCSD, and
CCSD(T) employ two-point extrapolation performed according to
:py:func:`~driver_cbs.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] finite-difference geometry optimization embarrasingly parallel
>>> optimize('allen_focal_point', mode='sow')
"""
# SCF
kwargs['scf_basis'] = kwargs.get('scf_basis', 'cc-pV[Q56]Z')
kwargs['scf_scheme'] = kwargs.get('scf_scheme', driver_cbs.scf_xtpl_helgaker_3)
# delta MP2 - SCF
kwargs['corl_wfn'] = kwargs.get('corl_wfn', 'mp2')
kwargs['corl_basis'] = kwargs.get('corl_basis', 'cc-pV[56]Z')
kwargs['corl_scheme'] = kwargs.get('corl_scheme', driver_cbs.corl_xtpl_helgaker_2)
# delta CCSD - MP2
kwargs['delta_wfn'] = kwargs.get('delta_wfn', 'mrccsd')
kwargs['delta_wfn_lesser'] = kwargs.get('delta_wfn_lesser', 'mp2')
kwargs['delta_basis'] = kwargs.get('delta_basis', 'cc-pV[56]Z')
kwargs['delta_scheme'] = kwargs.get('delta_scheme', driver_cbs.corl_xtpl_helgaker_2)
# delta CCSD(T) - CCSD
kwargs['delta2_wfn'] = kwargs.get('delta2_wfn', 'mrccsd(t)')
kwargs['delta2_wfn_lesser'] = kwargs.get('delta2_wfn_lesser', 'mrccsd')
kwargs['delta2_basis'] = kwargs.get('delta2_basis', 'cc-pV[56]Z')
kwargs['delta2_scheme'] = kwargs.get('delta2_scheme', driver_cbs.corl_xtpl_helgaker_2)
# delta CCSDT - CCSD(T)
kwargs['delta3_wfn'] = kwargs.get('delta3_wfn', 'mrccsdt')
kwargs['delta3_wfn_lesser'] = kwargs.get('delta3_wfn_lesser', 'mrccsd(t)')
kwargs['delta3_basis'] = kwargs.get('delta3_basis', 'cc-pVTZ')
kwargs['delta3_scheme'] = kwargs.get('delta3_scheme', driver_cbs.xtpl_highest_1)
# delta CCSDT(Q) - CCSDT
kwargs['delta4_wfn'] = kwargs.get('delta4_wfn', 'mrccsdt(q)')
kwargs['delta4_wfn_lesser'] = kwargs.get('delta4_wfn_lesser', 'mrccsdt')
kwargs['delta4_basis'] = kwargs.get('delta4_basis', 'cc-pVDZ')
kwargs['delta4_scheme'] = kwargs.get('delta4_scheme', driver_cbs.xtpl_highest_1)
if label == 'custom_function':
label = 'Allen Focal Point'
return driver_cbs.cbs(func, label, **kwargs)
