#
#@BEGIN LICENSE
#
# PSI4: an ab initio quantum chemistry software package
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
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# You should have received a copy of the GNU General Public License along
# with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
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#@END LICENSE
#
"""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
"""
import re
import os
import math
import warnings
import psi4
import p4util
from driver import *
from wrappers import *
#from extend_Molecule import *
from molutil import *
# 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 sherrill_gold_standard(name='mp2', **kwargs):
r"""Function to call the quantum chemical method known as 'Gold Standard'
in the Sherrill group. Uses :py:func:`~wrappers.complete_basis_set` to evaluate
the following expression. Two-point extrapolation of the correlation energy
performed according to :py:func:`~wrappers.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')
"""
lowername = name.lower()
kwargs = p4util.kwargs_lower(kwargs)
if not ('func_cbs' in kwargs):
kwargs['func_cbs'] = energy
if not ('scf_basis' in kwargs):
kwargs['scf_basis'] = 'aug-cc-pVQZ'
if not ('scf_scheme' in kwargs):
kwargs['scf_scheme'] = highest_1
if not ('corl_wfn' in kwargs):
kwargs['corl_wfn'] = 'mp2'
name = 'mp2'
if not ('corl_basis' in kwargs):
kwargs['corl_basis'] = 'aug-cc-pV[TQ]Z'
if not ('corl_scheme' in kwargs):
kwargs['corl_scheme'] = corl_xtpl_helgaker_2
if not ('delta_wfn' in kwargs):
kwargs['delta_wfn'] = 'ccsd(t)'
if not ('delta_wfn_lesser' in kwargs):
kwargs['delta_wfn_lesser'] = 'mp2'
if not ('delta_basis' in kwargs):
kwargs['delta_basis'] = 'aug-cc-pVTZ'
if not ('delta_scheme' in kwargs):
kwargs['delta_scheme'] = highest_1
return cbs(name, **kwargs)
[docs]def allen_focal_point(name='mp2', **kwargs):
r"""Function to call Wes Allen-style Focal
Point Analysis. JCP 127 014306. Uses
:py:func:`~wrappers.complete_basis_set` to evaluate the following
expression. SCF employs a three-point extrapolation according
to :py:func:`~wrappers.scf_xtpl_helgaker_3`. MP2, CCSD, and
CCSD(T) employ two-point extrapolation performed according to
:py:func:`~wrappers.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')
"""
lowername = name.lower()
kwargs = p4util.kwargs_lower(kwargs)
if not ('func_cbs' in kwargs):
kwargs['func_cbs'] = energy
# SCF
if not ('scf_basis' in kwargs):
kwargs['scf_basis'] = 'cc-pV[Q56]Z'
if not ('scf_scheme' in kwargs):
kwargs['scf_scheme'] = scf_xtpl_helgaker_3
# delta MP2 - SCF
if not ('corl_wfn' in kwargs):
kwargs['corl_wfn'] = 'mp2'
name = 'mp2'
if not ('corl_basis' in kwargs):
kwargs['corl_basis'] = 'cc-pV[56]Z'
if not ('corl_scheme' in kwargs):
kwargs['corl_scheme'] = corl_xtpl_helgaker_2
# delta CCSD - MP2
if not ('delta_wfn' in kwargs):
kwargs['delta_wfn'] = 'mrccsd'
if not ('delta_wfn_lesser' in kwargs):
kwargs['delta_wfn_lesser'] = 'mp2'
if not ('delta_basis' in kwargs):
kwargs['delta_basis'] = 'cc-pV[56]Z'
if not ('delta_scheme' in kwargs):
kwargs['delta_scheme'] = corl_xtpl_helgaker_2
# delta CCSD(T) - CCSD
if not ('delta2_wfn' in kwargs):
kwargs['delta2_wfn'] = 'mrccsd(t)'
if not ('delta2_wfn_lesser' in kwargs):
kwargs['delta2_wfn_lesser'] = 'mrccsd'
if not ('delta2_basis' in kwargs):
kwargs['delta2_basis'] = 'cc-pV[56]Z'
if not ('delta2_scheme' in kwargs):
kwargs['delta2_scheme'] = corl_xtpl_helgaker_2
# delta CCSDT - CCSD(T)
if not ('delta3_wfn' in kwargs):
kwargs['delta3_wfn'] = 'mrccsdt'
if not ('delta3_wfn_lesser' in kwargs):
kwargs['delta3_wfn_lesser'] = 'mrccsd(t)'
if not ('delta3_basis' in kwargs):
kwargs['delta3_basis'] = 'cc-pVTZ'
if not ('delta3_scheme' in kwargs):
kwargs['delta3_scheme'] = highest_1
# delta CCSDT(Q) - CCSDT
if not ('delta4_wfn' in kwargs):
kwargs['delta4_wfn'] = 'mrccsdt(q)'
if not ('delta4_wfn_lesser' in kwargs):
kwargs['delta4_wfn_lesser'] = 'mrccsdt'
if not ('delta4_basis' in kwargs):
kwargs['delta4_basis'] = 'cc-pVDZ'
if not ('delta4_scheme' in kwargs):
kwargs['delta4_scheme'] = highest_1
return cbs(name, **kwargs)
#def run_mp2_5(name, **kwargs):
# r"""Function that computes MP2.5 energy from results of a FNOCC
# MP3 calculation.
#
# .. math:: E_{total}^{\text{MP2.5}} = E_{total,\; \text{SCF}} \; + E_{corl,\; \text{MP2}} + E_{corl, \; \text{MP3}}
#
# :PSI variables:
#
# .. hlist::
# :columns: 1
#
# * :psivar:`MP2.5 TOTAL ENERGY <MP2.5TOTALENERGY>`
# * :psivar:`MP2.5 CORRELATION ENERGY <MP2.5CORRELATIONENERGY>`
#
# >>> energy('mp2.5')
#
# """
# lowername = name.lower()
# kwargs = kwargs_lower(kwargs)
#
# # Run detci calculation and collect conventional quantities
# energy('mp3', **kwargs)
# e_scf = psi4.get_variable('SCF TOTAL ENERGY')
# ce_mp2 = psi4.get_variable('MP2 CORRELATION ENERGY')
# ce_mp3 = psi4.get_variable('MP3 CORRELATION ENERGY')
# e_mp2 = e_scf + ce_mp2
# e_mp3 = e_scf + ce_mp3
#
# # Compute quantities particular to MP2.5
# ce_mp25 = 0.5 * (ce_mp2 + ce_mp3)
# e_mp25 = e_scf + ce_mp25
# psi4.set_variable('MP2.5 CORRELATION ENERGY', ce_mp25)
# psi4.set_variable('MP2.5 TOTAL ENERGY', e_mp25)
# psi4.set_variable('CURRENT CORRELATION ENERGY', ce_mp25)
# psi4.set_variable('CURRENT ENERGY', e_mp25)
#
# # build string of title banner and print results
# banners = ''
# banners += """psi4.print_out('\\n')\n"""
# banners += """banner(' MP2.5 ')\n"""
# banners += """psi4.print_out('\\n')\n\n"""
# exec(banners)
#
# tables = ''
# tables += """ SCF total energy: %16.8f\n""" % (e_scf)
# tables += """ MP2 total energy: %16.8f\n""" % (e_mp2)
# tables += """ MP2.5 total energy: %16.8f\n""" % (e_mp25)
# tables += """ MP3 total energy: %16.8f\n\n""" % (e_mp3)
# tables += """ MP2 correlation energy: %16.8f\n""" % (ce_mp2)
# tables += """ MP2.5 correlation energy: %16.8f\n""" % (ce_mp25)
# tables += """ MP3 correlation energy: %16.8f\n""" % (ce_mp3)
# psi4.print_out(tables)
#
# return e_mp25
# A direct translation of a plugin input file into a function call. Function calls are the only
# way to call plugins in sow/reap mode for db(), opt(), etc. This isn't best practices
# but is an example of what to do for a more complicated procedure where different options
# are set for different qc steps.
#def run_plugin_omega(name, **kwargs):
# r"""Function encoding sequence of PSI module and plugin calls, as well
# as typical options, to access Rob Parrish's omega plugin.
#
# >>> energy('plugin_omega')
#
# """
# lowername = name.lower()
# kwargs = p4util.kwargs_lower(kwargs)
#
# plugfile = psi4.Process.environment["PSIDATADIR"] + "/../tests/plugin_omega/plugin_omega.so"
# psi4.plugin_load("%s" % (plugfile))
#
# psi4.set_global_option('BASIS', 'AUG-CC-PVDZ')
# psi4.set_global_option('DF_BASIS_SCF', 'AUG-CC-PVDZ-RI')
# psi4.set_global_option('REFERENCE', 'UHF')
# psi4.set_global_option('SCF_TYPE', 'DF')
# energy('scf', **kwargs)
#
# psi4.set_global_option('dft_functional', 'wB97')
# psi4.set_global_option('dft_order_spherical', 25)
# psi4.set_global_option('dft_num_radial', 35)
# psi4.set_global_option('omega_procedure', 'ip')
# psi4.set_global_option('maxiter', 50)
# psi4.set_global_option('d_convergence', 5)
# psi4.set_global_option('e_convergence', 7)
# psi4.plugin("plugin_omega.so")
#
# return psi4.get_variable('SCF TOTAL ENERGY')
# Integration with driver routines
#procedures['energy']['mp2.5'] = run_mp2_5
procedures['energy']['sherrill_gold_standard'] = sherrill_gold_standard
procedures['energy']['allen_focal_point'] = allen_focal_point
#procedures['energy']['plugin_omega'] = run_plugin_omega