Source code for aliases

"""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 PsiMod
import re
import os
import input
import math
import warnings
from driver import *
from wrappers import *
from molutil import *
from text import *
from procutil 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 sherrillgroup_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 evaluateo 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}} >>> energy('sherrillgroup_gold_standard') """ lowername = name.lower() kwargs = 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' 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 run_mp2_5(name, **kwargs): r"""Function that computes MP2.5 energy from results of a DETCI 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 = PsiMod.get_variable('SCF TOTAL ENERGY') ce_mp2 = PsiMod.get_variable('MP2 CORRELATION ENERGY') ce_mp3 = PsiMod.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 PsiMod.set_variable('MP2.5 CORRELATION ENERGY', ce_mp25) PsiMod.set_variable('MP2.5 TOTAL ENERGY', e_mp25) PsiMod.set_variable('CURRENT CORRELATION ENERGY', ce_mp25) PsiMod.set_variable('CURRENT ENERGY', e_mp25) # build string of title banner and print results banners = '' banners += """PsiMod.print_out('\\n')\n""" banners += """banner(' MP2.5 ')\n""" banners += """PsiMod.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) PsiMod.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.
[docs]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 = kwargs_lower(kwargs) plugfile = PsiMod.Process.environment["PSIDATADIR"] + "/../tests/plugin_omega/" PsiMod.plugin_load("%s" % (plugfile)) PsiMod.set_global_option('BASIS', 'AUG-CC-PVDZ') PsiMod.set_global_option('DF_BASIS_SCF', 'AUG-CC-PVDZ-RI') PsiMod.set_global_option('REFERENCE', 'UHF') PsiMod.set_global_option('SCF_TYPE', 'DF') energy('scf', **kwargs) PsiMod.set_global_option('dft_functional', 'wB97') PsiMod.set_global_option('dft_order_spherical', 25) PsiMod.set_global_option('dft_num_radial', 35) PsiMod.set_global_option('omega_procedure', 'ip') PsiMod.set_global_option('maxiter', 50) PsiMod.set_global_option('d_convergence', 5) PsiMod.set_global_option('e_convergence', 7) PsiMod.plugin("") return PsiMod.get_variable('SCF TOTAL ENERGY') # Integration with driver routines
procedures['energy']['mp2.5'] = run_mp2_5 procedures['energy']['sherrillgroup_gold_standard'] = sherrillgroup_gold_standard procedures['energy']['plugin_omega'] = run_plugin_omega