Source code for aliases

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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 re
import os
import math
import warnings
import driver_cbs
#from wrappers import *
#from gaussian_n import *  # CU
#from wrappers_cfour import *  # CU
#from qmmm import *  # CU

# 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.


[docs]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: :ref:`Wavefunction<sec:psimod_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)