#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 The Psi4 Developers.
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# The copyrights for code used from other parties are included in
# the corresponding files.
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# This file is part of Psi4.
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# 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.
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# Psi4 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 Lesser General Public License for more details.
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# with Psi4; if not, write to the Free Software Foundation, Inc.,
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# @END LICENSE
#
import re
import sys
import math
import numpy as np
from psi4 import core
from psi4.driver import qcdb
from psi4.driver import p4util
from psi4.driver import driver_util
from psi4.driver import psifiles as psif
from psi4.driver.p4util.exceptions import *
from psi4.driver.procrouting.interface_cfour import cfour_psivar_list
zeta_values = ['d', 't', 'q', '5', '6', '7', '8']
zeta_val2sym = {k + 2: v for k, v in zip(range(7), zeta_values)}
zeta_sym2val = {v: k for k, v in zeta_val2sym.items()}
def _expand_bracketed_basis(basisstring, molecule=None):
"""Function to transform and validate basis series specification for cbs().
Parameters
----------
basisstring : string
A string containing the basis sets to be expanded.
A basis set with no paired square brackets is passed through
with zeta level 0 (e.g., ``'6-31+G(d,p)'`` is returned as
``(["6-31+G(d,p)"], [0])``). A basis set with square brackets is checked
for sensible sequence and returned as separate basis sets
(e.g., ``'cc-pV[Q5]Z'` is returned as ``(["cc-pVQZ", "cc-pV5Z"], [4, 5])``).
Allows out-of-order zeta specification (e.g., ``[qtd]``) and numeral for
number (e.g., ``[23]``). Does not allow skipped zetas (e.g., ``[dq]``), zetas
outside the [2,8] range, non-Dunning, non-Ahlrichs, or non-Jensen sets,
or non-findable .gbs sets.
molecule : qcdb.molecule or psi4.core.Molecule
This function checks that the basis is valid by trying to build
the qcdb.BasisSet object for *molecule* or for H2 if None.
Returns
-------
tuple
Tuple in the ``([basis set names], [basis set zetas])`` format.
"""
BSET = []
ZSET = []
legit_compound_basis = re.compile(
r'^(?P<pre>.*cc-.*|def2-|.*pcs+eg-|.*)\[(?P<zeta>[dtq2345678,s1]*)\](?P<post>.*z.*|)$', re.IGNORECASE)
pc_basis = re.compile(r'.*pcs+eg-$', re.IGNORECASE)
def2_basis = re.compile(r'def2-', re.IGNORECASE)
zapa_basis = re.compile(r'.*zapa.*',re.IGNORECASE)
if legit_compound_basis.match(basisstring):
basisname = legit_compound_basis.match(basisstring)
# handle def2-svp* basis sets as double-zeta
if def2_basis.match(basisname.group('pre')):
bn_gz = basisname.group('zeta').replace("s", "d")
# handle pc-n basis set polarisation -> zeta conversion
elif pc_basis.match(basisname.group('pre')):
bn_gz = basisname.group('zeta').replace("4", "5").replace("3", "4").replace("2", "3").replace("1", "2")
else:
bn_gz = basisname.group('zeta')
# filter out commas and be forgiving of e.g., t5q or 3q
zetas = [z for z in zeta_values if (z in bn_gz or str(zeta_values.index(z) + 2) in bn_gz)]
for b in zetas:
if ZSET and (int(ZSET[len(ZSET) - 1]) - zeta_values.index(b)) != 1:
raise ValidationError("""Basis set '%s' has skipped zeta level '%s'.""" %
(basisstring, zeta_val2sym[zeta_sym2val[b] - 1]))
# reassemble def2-svp* properly instead of def2-dzvp*
if def2_basis.match(basisname.group('pre')) and b == "d":
BSET.append(basisname.group('pre') + "s" + basisname.group('post')[1:])
# reassemble pc-n basis sets properly
elif pc_basis.match(basisname.group('pre')):
BSET.append(basisname.group('pre') + "{0:d}".format(zeta_sym2val[b] - 1))
# assemble nZaPa basis sets
elif zapa_basis.match(basisname.group('post')):
bzapa = b.replace("d","2").replace("t","3").replace("q","4")
BSET.append(basisname.group('pre') + bzapa + basisname.group('post'))
else:
BSET.append(basisname.group('pre') + b + basisname.group('post'))
ZSET.append(zeta_values.index(b) + 2)
elif re.match(r'.*\[.*\].*$', basisstring, flags=re.IGNORECASE):
raise ValidationError(
"""Basis series '%s' invalid. Specify a basis series matching"""
""" '*cc-*[dtq2345678,]*z*'. or 'def2-[sdtq]zvp*' or '*pcs[s]eg-[1234]' or '[1234567]ZaPa' """ % (basisstring))
else:
BSET.append(basisstring)
ZSET.append(0)
if molecule is None:
molecule = """\nH\nH 1 1.00\n"""
elif isinstance(molecule, core.Molecule):
molecule = qcdb.Molecule(molecule.to_dict())
for basis in BSET:
try:
qcdb.BasisSet.pyconstruct(molecule, "BASIS", basis)
except qcdb.BasisSetNotFound:
e = sys.exc_info()[1]
raise ValidationError("""Basis set '%s' not available for molecule.""" % (basis))
return (BSET, ZSET)
def _contract_bracketed_basis(basisarray):
"""Function to reform a bracketed basis set string from a sequential series
of basis sets. Essentially the inverse of _expand_bracketed_basis(). Used to
print a nicely formatted basis set string in the results table.
Parameters
----------
basisarray : list
Basis set names, differing by zeta level, e.g. ``["cc-pvqz", "cc-pv5z"]``.
Returns
-------
string
A nicely formatted basis set string, e.g. ``"cc-pv[q5]z"`` for the above example.
"""
if len(basisarray) == 1:
return basisarray[0]
else:
zetaindx = [i for i in range(len(basisarray[0])) if basisarray[0][i] != basisarray[1][i]][0]
ZSET = [bas[zetaindx] for bas in basisarray]
pre = basisarray[1][:zetaindx]
post = basisarray[1][zetaindx + 1:]
basisstring = pre + '[' + ''.join(ZSET) + ']' + post
return basisstring
[docs]def xtpl_highest_1(functionname, zHI, valueHI, verbose=True, **kwargs):
r"""Scheme for total or correlation energies with a single basis or the highest
zeta-level among an array of bases. Used by :py:func:`~psi4.cbs`.
Parameters
----------
functionname : string
Name of the CBS component.
zHI : int
Zeta-level, only used for printing.
valueHI : float
Value of the CBS component.
Returns
-------
float
Returns :math:`E_{total}^{\infty}` which is equal to valueHI.
Notes
-----
.. math:: E_{total}^X = E_{total}^{\infty}
"""
if isinstance(valueHI, float):
if verbose:
# Output string with extrapolation parameters
cbsscheme = ''
cbsscheme += """\n ==> %s <==\n\n""" % (functionname.upper())
cbsscheme += """ HI-zeta (%s) Energy: % 16.12f\n""" % (str(zHI), valueHI)
core.print_out(cbsscheme)
return valueHI
elif isinstance(valueHI, (core.Matrix, core.Vector)):
if verbose > 2:
core.print_out(""" HI-zeta (%s) Total Energy:\n""" % (str(zHI)))
valueHI.print_out()
return valueHI
[docs]def scf_xtpl_helgaker_2(functionname, zLO, valueLO, zHI, valueHI, verbose=True, alpha=None):
r"""Extrapolation scheme using exponential form for reference energies with two adjacent
zeta-level bases. Used by :py:func:`~psi4.cbs`.
Parameters
----------
functionname : string
Name of the CBS component.
zLO : int
Lower zeta level.
valueLO : float
Lower value used for extrapolation.
zHI : int
Higher zeta level. Should be equal to zLO + 1.
valueHI : float
Higher value used for extrapolation.
alpha : float, optional
Overrides the default :math:`\alpha = 1.63`
Returns
-------
float
Returns :math:`E_{total}^{\infty}`, see below.
Notes
-----
The extrapolation is calculated according to [1]_:
:math:`E_{total}^X = E_{total}^{\infty} + \beta e^{-\alpha X}, \alpha = 1.63`
References
----------
.. [1] Halkier, Helgaker, Jorgensen, Klopper, & Olsen, Chem. Phys. Lett. 302 (1999) 437-446,
DOI: 10.1016/S0009-2614(99)00179-7
"""
if type(valueLO) != type(valueHI):
raise ValidationError(
"scf_xtpl_helgaker_2: Inputs must be of the same datatype! (%s, %s)" % (type(valueLO), type(valueHI)))
if alpha is None:
alpha = 1.63
beta_division = 1 / (math.exp(-1 * alpha * zLO) * (math.exp(-1 * alpha) - 1))
beta_mult = math.exp(-1 * alpha * zHI)
if isinstance(valueLO, float):
beta = (valueHI - valueLO) * beta_division
value = valueHI - beta * beta_mult
if verbose:
# Output string with extrapolation parameters
cbsscheme = ''
cbsscheme += """\n ==> Helgaker 2-point exponential SCF extrapolation for method: %s <==\n\n""" % (
functionname.upper())
cbsscheme += """ LO-zeta (%s) Energy: % 16.12f\n""" % (str(zLO), valueLO)
cbsscheme += """ HI-zeta (%s) Energy: % 16.12f\n""" % (str(zHI), valueHI)
cbsscheme += """ Alpha (exponent) Value: % 16.12f\n""" % (alpha)
cbsscheme += """ Beta (coefficient) Value: % 16.12f\n\n""" % (beta)
name_str = "%s/(%s,%s)" % (functionname.upper(), zeta_val2sym[zLO].upper(), zeta_val2sym[zHI].upper())
cbsscheme += """ @Extrapolated """
cbsscheme += name_str + ':'
cbsscheme += " " * (18 - len(name_str))
cbsscheme += """% 16.12f\n\n""" % value
core.print_out(cbsscheme)
return value
elif isinstance(valueLO, (core.Matrix, core.Vector)):
beta = valueHI.clone()
beta.name = 'Helgaker SCF (%s, %s) beta' % (zLO, zHI)
beta.subtract(valueLO)
beta.scale(beta_division)
beta.scale(beta_mult)
value = valueHI.clone()
value.subtract(beta)
value.name = 'Helgaker SCF (%s, %s) data' % (zLO, zHI)
if verbose > 2:
core.print_out("""\n ==> Helgaker 2-point exponential SCF extrapolation for method: %s <==\n\n""" %
(functionname.upper()))
core.print_out(""" LO-zeta (%s)""" % str(zLO))
core.print_out(""" LO-zeta Data""")
valueLO.print_out()
core.print_out(""" HI-zeta (%s)""" % str(zHI))
core.print_out(""" HI-zeta Data""")
valueHI.print_out()
core.print_out(""" Extrapolated Data:\n""")
value.print_out()
core.print_out(""" Alpha (exponent) Value: %16.8f\n""" % (alpha))
core.print_out(""" Beta Data:\n""")
beta.print_out()
return value
else:
raise ValidationError("scf_xtpl_helgaker_2: datatype is not recognized '%s'." % type(valueLO))
[docs]def scf_xtpl_truhlar_2(functionname, zLO, valueLO, zHI, valueHI, verbose=True, alpha=None):
r"""Extrapolation scheme using power form for reference energies with two adjacent
zeta-level bases. Used by :py:func:`~psi4.cbs`.
Parameters
----------
functionname : string
Name of the CBS component.
zLO : int
Lower zeta level.
valueLO : float
Lower value used for extrapolation.
zHI : int
Higher zeta level. Should be equal to zLO + 1.
valueHI : float
Higher value used for extrapolation.
alpha : float, optional
Overrides the default :math:`\alpha = 3.4`
Returns
-------
float
Returns :math:`E_{total}^{\infty}`, see below.
Notes
-----
The extrapolation is calculated according to [2]_:
:math:`E_{total}^X = E_{total}^{\infty} + \beta X^{-\alpha}, \alpha = 3.4`
References
----------
.. [2] Truhlar, Chem. Phys. Lett. 294 (1998) 45-48,
DOI: 10.1016/S0009-2614(98)00866-5
"""
if type(valueLO) != type(valueHI):
raise ValidationError(
"scf_xtpl_truhlar_2: Inputs must be of the same datatype! (%s, %s)" % (type(valueLO), type(valueHI)))
if alpha is None:
alpha = 3.40
beta_division = 1 / (zHI**(-1 * alpha) - zLO**(-1 * alpha))
beta_mult = zHI**(-1 * alpha)
if isinstance(valueLO, float):
beta = (valueHI - valueLO) * beta_division
value = valueHI - beta * beta_mult
if verbose:
# Output string with extrapolation parameters
cbsscheme = ''
cbsscheme += """\n ==> Truhlar 2-point power form SCF extrapolation for method: %s <==\n\n""" % (
functionname.upper())
cbsscheme += """ LO-zeta (%s) Energy: % 16.12f\n""" % (str(zLO), valueLO)
cbsscheme += """ HI-zeta (%s) Energy: % 16.12f\n""" % (str(zHI), valueHI)
cbsscheme += """ Alpha (exponent) Value: % 16.12f\n""" % (alpha)
cbsscheme += """ Beta (coefficient) Value: % 16.12f\n\n""" % (beta)
name_str = "%s/(%s,%s)" % (functionname.upper(), zeta_val2sym[zLO].upper(), zeta_val2sym[zHI].upper())
cbsscheme += """ @Extrapolated """
cbsscheme += name_str + ':'
cbsscheme += " " * (18 - len(name_str))
cbsscheme += """% 16.12f\n\n""" % value
core.print_out(cbsscheme)
return value
elif isinstance(valueLO, (core.Matrix, core.Vector)):
beta = valueHI.clone()
beta.name = 'Truhlar SCF (%s, %s) beta' % (zLO, zHI)
beta.subtract(valueLO)
beta.scale(beta_division)
beta.scale(beta_mult)
value = valueHI.clone()
value.subtract(beta)
value.name = 'Truhlar SCF (%s, %s) data' % (zLO, zHI)
if verbose > 2:
core.print_out("""\n ==> Truhlar 2-point power from SCF extrapolation for method: %s <==\n\n""" %
(functionname.upper()))
core.print_out(""" LO-zeta (%s)""" % str(zLO))
core.print_out(""" LO-zeta Data""")
valueLO.print_out()
core.print_out(""" HI-zeta (%s)""" % str(zHI))
core.print_out(""" HI-zeta Data""")
valueHI.print_out()
core.print_out(""" Extrapolated Data:\n""")
value.print_out()
core.print_out(""" Alpha (exponent) Value: %16.8f\n""" % (alpha))
core.print_out(""" Beta Data:\n""")
beta.print_out()
return value
else:
raise ValidationError("scf_xtpl_truhlar_2: datatype is not recognized '%s'." % type(valueLO))
[docs]def scf_xtpl_karton_2(functionname, zLO, valueLO, zHI, valueHI, verbose=True, alpha=None):
r"""Extrapolation scheme using root-power form for reference energies with two adjacent
zeta-level bases. Used by :py:func:`~psi4.cbs`.
Parameters
----------
functionname : str
Name of the CBS component.
zLO : int
Lower zeta level.
valueLO : float
Lower value used for extrapolation.
zHI : int
Higher zeta level. Should be equal to zLO + 1.
valueHI : float
Higher value used for extrapolation.
alpha : float, optional
Overrides the default :math:`\alpha = 6.3`
Returns
-------
float
Returns :math:`E_{total}^{\infty}`, see below.
Notes
-----
The extrapolation is calculated according to [3]_:
:math:`E_{total}^X = E_{total}^{\infty} + \beta e^{-\alpha\sqrt{X}}, \alpha = 6.3`
References
----------
.. [3] Karton, Martin, Theor. Chem. Acc. 115 (2006) 330-333,
DOI: 10.1007/s00214-005-0028-6
"""
if type(valueLO) != type(valueHI):
raise ValidationError(
"scf_xtpl_karton_2: Inputs must be of the same datatype! (%s, %s)" % (type(valueLO), type(valueHI)))
if alpha is None:
alpha = 6.30
beta_division = 1 / (math.exp(-1 * alpha) * (math.exp(math.sqrt(zHI)) - math.exp(math.sqrt(zLO))))
beta_mult = math.exp(-1 * alpha * math.sqrt(zHI))
if isinstance(valueLO, float):
beta = (valueHI - valueLO) * beta_division
value = valueHI - beta * beta_mult
if verbose:
# Output string with extrapolation parameters
cbsscheme = ''
cbsscheme += """\n ==> Karton 2-point power form SCF extrapolation for method: %s <==\n\n""" % (
functionname.upper())
cbsscheme += """ LO-zeta (%s) Energy: % 16.12f\n""" % (str(zLO), valueLO)
cbsscheme += """ HI-zeta (%s) Energy: % 16.12f\n""" % (str(zHI), valueHI)
cbsscheme += """ Alpha (exponent) Value: % 16.12f\n""" % (alpha)
cbsscheme += """ Beta (coefficient) Value: % 16.12f\n\n""" % (beta)
name_str = "%s/(%s,%s)" % (functionname.upper(), zeta_val2sym[zLO].upper(), zeta_val2sym[zHI].upper())
cbsscheme += """ @Extrapolated """
cbsscheme += name_str + ':'
cbsscheme += " " * (18 - len(name_str))
cbsscheme += """% 16.12f\n\n""" % value
core.print_out(cbsscheme)
return value
elif isinstance(valueLO, (core.Matrix, core.Vector)):
beta = valueHI.clone()
beta.name = 'Karton SCF (%s, %s) beta' % (zLO, zHI)
beta.subtract(valueLO)
beta.scale(beta_division)
beta.scale(beta_mult)
value = valueHI.clone()
value.subtract(beta)
value.name = 'Karton SCF (%s, %s) data' % (zLO, zHI)
if verbose > 2:
core.print_out("""\n ==> Karton 2-point power from SCF extrapolation for method: %s <==\n\n""" %
(functionname.upper()))
core.print_out(""" LO-zeta (%s)""" % str(zLO))
core.print_out(""" LO-zeta Data""")
valueLO.print_out()
core.print_out(""" HI-zeta (%s)""" % str(zHI))
core.print_out(""" HI-zeta Data""")
valueHI.print_out()
core.print_out(""" Extrapolated Data:\n""")
value.print_out()
core.print_out(""" Alpha (exponent) Value: %16.8f\n""" % (alpha))
core.print_out(""" Beta Data:\n""")
beta.print_out()
return value
else:
raise ValidationError("scf_xtpl_Karton_2: datatype is not recognized '%s'." % type(valueLO))
[docs]def scf_xtpl_helgaker_3(functionname, zLO, valueLO, zMD, valueMD, zHI, valueHI, verbose=True, alpha=None):
r"""Extrapolation scheme for reference energies with three adjacent zeta-level bases.
Used by :py:func:`~psi4.cbs`.
Parameters
----------
functionname : str
Name of the CBS component.
zLO : int
Lower zeta level.
valueLO : float
Lower value used for extrapolation.
zMD : int
Intermediate zeta level. Should be equal to zLO + 1.
valueMD : float
Intermediate value used for extrapolation.
zHI : int
Higher zeta level. Should be equal to zLO + 2.
valueHI : float
Higher value used for extrapolation.
alpha : float, optional
Not used.
Returns
-------
float
Returns :math:`E_{total}^{\infty}`, see below.
Notes
-----
The extrapolation is calculated according to [4]_:
:math:`E_{total}^X = E_{total}^{\infty} + \beta e^{-\alpha X}, \alpha = 3.0`
References
----------
.. [4] Halkier, Helgaker, Jorgensen, Klopper, & Olsen, Chem. Phys. Lett. 302 (1999) 437-446,
DOI: 10.1016/S0009-2614(99)00179-7
"""
if (type(valueLO) != type(valueMD)) or (type(valueMD) != type(valueHI)):
raise ValidationError("scf_xtpl_helgaker_3: Inputs must be of the same datatype! (%s, %s, %s)" %
(type(valueLO), type(valueMD), type(valueHI)))
if isinstance(valueLO, float):
ratio = (valueHI - valueMD) / (valueMD - valueLO)
alpha = -1 * math.log(ratio)
beta = (valueHI - valueMD) / (math.exp(-1 * alpha * zMD) * (ratio - 1))
value = valueHI - beta * math.exp(-1 * alpha * zHI)
if verbose:
# Output string with extrapolation parameters
cbsscheme = ''
cbsscheme += """\n ==> Helgaker 3-point SCF extrapolation for method: %s <==\n\n""" % (
functionname.upper())
cbsscheme += """ LO-zeta (%s) Energy: % 16.12f\n""" % (str(zLO), valueLO)
cbsscheme += """ MD-zeta (%s) Energy: % 16.12f\n""" % (str(zMD), valueMD)
cbsscheme += """ HI-zeta (%s) Energy: % 16.12f\n""" % (str(zHI), valueHI)
cbsscheme += """ Alpha (exponent) Value: % 16.12f\n""" % (alpha)
cbsscheme += """ Beta (coefficient) Value: % 16.12f\n\n""" % (beta)
name_str = "%s/(%s,%s,%s)" % (functionname.upper(), zeta_val2sym[zLO].upper(), zeta_val2sym[zMD].upper(),
zeta_val2sym[zHI].upper())
cbsscheme += """ @Extrapolated """
cbsscheme += name_str + ':'
cbsscheme += " " * (18 - len(name_str))
cbsscheme += """% 16.12f\n\n""" % value
core.print_out(cbsscheme)
return value
elif isinstance(valueLO, (core.Matrix, core.Vector)):
valueLO = np.array(valueLO)
valueMD = np.array(valueMD)
valueHI = np.array(valueHI)
nonzero_mask = np.abs(valueHI) > 1.e-14
top = (valueHI - valueMD)[nonzero_mask]
bot = (valueMD - valueLO)[nonzero_mask]
ratio = top / bot
alpha = -1 * np.log(np.abs(ratio))
beta = top / (np.exp(-1 * alpha * zMD) * (ratio - 1))
np_value = valueHI.copy()
np_value[nonzero_mask] -= beta * np.exp(-1 * alpha * zHI)
np_value[~nonzero_mask] = 0.0
# Build and set from numpy routines
value = core.Matrix(*valueHI.shape)
value_view = np.asarray(value)
value_view[:] = np_value
return value
else:
raise ValidationError("scf_xtpl_helgaker_3: datatype is not recognized '%s'." % type(valueLO))
#def corl_xtpl_helgaker_2(functionname, valueSCF, zLO, valueLO, zHI, valueHI, verbose=True):
[docs]def corl_xtpl_helgaker_2(functionname, zLO, valueLO, zHI, valueHI, verbose=True, alpha=None):
r"""Extrapolation scheme for correlation energies with two adjacent zeta-level bases.
Used by :py:func:`~psi4.cbs`.
Parameters
----------
functionname : str
Name of the CBS component.
zLO : int
Lower zeta level.
valueLO : float
Lower value used for extrapolation.
zHI : int
Higher zeta level. Should be equal to zLO + 1.
valueHI : float
Higher value used for extrapolation.
alpha : float, optional
Overrides the default :math:`\alpha = 3.0`
Returns
-------
float
Returns :math:`E_{total}^{\infty}`, see below.
Notes
-----
The extrapolation is calculated according to [5]_:
:math:`E_{corl}^X = E_{corl}^{\infty} + \beta X^{-alpha}`
References
----------
.. [5] Halkier, Helgaker, Jorgensen, Klopper, Koch, Olsen, & Wilson,
Chem. Phys. Lett. 286 (1998) 243-252,
DOI: 10.1016/S0009-2614(99)00179-7
"""
if type(valueLO) != type(valueHI):
raise ValidationError(
"corl_xtpl_helgaker_2: Inputs must be of the same datatype! (%s, %s)" % (type(valueLO), type(valueHI)))
if alpha is None:
alpha = 3.0
if isinstance(valueLO, float):
value = (valueHI * zHI**alpha - valueLO * zLO**alpha) / (zHI**alpha - zLO**alpha)
beta = (valueHI - valueLO) / (zHI**(-alpha) - zLO**(-alpha))
# final = valueSCF + value
final = value
if verbose:
# Output string with extrapolation parameters
cbsscheme = """\n\n ==> Helgaker 2-point correlated extrapolation for method: %s <==\n\n""" % (
functionname.upper())
# cbsscheme += """ HI-zeta (%1s) SCF Energy: % 16.12f\n""" % (str(zHI), valueSCF)
cbsscheme += """ LO-zeta (%s) Energy: % 16.12f\n""" % (str(zLO), valueLO)
cbsscheme += """ HI-zeta (%s) Energy: % 16.12f\n""" % (str(zHI), valueHI)
cbsscheme += """ Alpha (exponent) Value: % 16.12f\n""" % alpha
cbsscheme += """ Extrapolated Energy: % 16.12f\n\n""" % value
#cbsscheme += """ LO-zeta (%s) Correlation Energy: % 16.12f\n""" % (str(zLO), valueLO)
#cbsscheme += """ HI-zeta (%s) Correlation Energy: % 16.12f\n""" % (str(zHI), valueHI)
#cbsscheme += """ Beta (coefficient) Value: % 16.12f\n""" % beta
#cbsscheme += """ Extrapolated Correlation Energy: % 16.12f\n\n""" % value
name_str = "%s/(%s,%s)" % (functionname.upper(), zeta_val2sym[zLO].upper(), zeta_val2sym[zHI].upper())
cbsscheme += """ @Extrapolated """
cbsscheme += name_str + ':'
cbsscheme += " " * (19 - len(name_str))
cbsscheme += """% 16.12f\n\n""" % final
core.print_out(cbsscheme)
return final
elif isinstance(valueLO, (core.Matrix, core.Vector)):
beta = valueHI.clone()
beta.subtract(valueLO)
beta.scale(1 / (zHI**(-alpha) - zLO**(-alpha)))
beta.name = 'Helgaker Corl (%s, %s) beta' % (zLO, zHI)
value = valueHI.clone()
value.scale(zHI**alpha)
tmp = valueLO.clone()
tmp.scale(zLO**alpha)
value.subtract(tmp)
value.scale(1 / (zHI**alpha - zLO**alpha))
value.name = 'Helgaker Corr (%s, %s) data' % (zLO, zHI)
if verbose > 2:
core.print_out("""\n ==> Helgaker 2-point correlated extrapolation for """
"""method: %s <==\n\n""" % (functionname.upper()))
core.print_out(""" LO-zeta (%s) Data\n""" % (str(zLO)))
valueLO.print_out()
core.print_out(""" HI-zeta (%s) Data\n""" % (str(zHI)))
valueHI.print_out()
core.print_out(""" Extrapolated Data:\n""")
value.print_out()
core.print_out(""" Alpha (exponent) Value: %16.8f\n""" % alpha)
core.print_out(""" Beta Data:\n""")
beta.print_out()
# value.add(valueSCF)
return value
else:
raise ValidationError("corl_xtpl_helgaker_2: datatype is not recognized '%s'." % type(valueLO))
def return_energy_components():
# yapf: disable
VARH = {}
VARH['scf'] = {
'scf': 'SCF TOTAL ENERGY'}
VARH['hf'] = {
'hf': 'HF TOTAL ENERGY'}
VARH['mp2'] = {
'hf': 'HF TOTAL ENERGY',
'mp2': 'MP2 TOTAL ENERGY'}
VARH['mp2.5'] = {
'hf': 'HF TOTAL ENERGY',
'mp2': 'MP2 TOTAL ENERGY',
'mp2.5': 'MP2.5 TOTAL ENERGY',
'mp3': 'MP3 TOTAL ENERGY'}
VARH['mp3'] = {
'hf': 'HF TOTAL ENERGY',
'mp2': 'MP2 TOTAL ENERGY',
'mp2.5': 'MP2.5 TOTAL ENERGY',
'mp3': 'MP3 TOTAL ENERGY'}
VARH['mp4(sdq)'] = {
'hf': 'HF TOTAL ENERGY',
'mp2': 'MP2 TOTAL ENERGY',
'mp2.5': 'MP2.5 TOTAL ENERGY',
'mp3': 'MP3 TOTAL ENERGY',
'mp4(sdq)': 'MP4(SDQ) TOTAL ENERGY'}
VARH['mp4'] = {
'hf': 'HF TOTAL ENERGY',
'mp2': 'MP2 TOTAL ENERGY',
'mp2.5': 'MP2.5 TOTAL ENERGY',
'mp3': 'MP3 TOTAL ENERGY',
'mp4(sdq)': 'MP4(SDQ) TOTAL ENERGY',
'mp4': 'MP4 TOTAL ENERGY'}
VARH['omp2'] = {
'hf': 'HF TOTAL ENERGY',
'mp2': 'MP2 TOTAL ENERGY',
'omp2': 'OMP2 TOTAL ENERGY'}
VARH['omp2.5'] = {
'hf': 'HF TOTAL ENERGY',
'mp2': 'MP2 TOTAL ENERGY',
'mp2.5': 'MP2.5 TOTAL ENERGY',
'omp2.5': 'OMP2.5 TOTAL ENERGY'}
VARH['omp3'] = {
'hf': 'HF TOTAL ENERGY',
'mp2': 'MP2 TOTAL ENERGY',
'mp3': 'MP3 TOTAL ENERGY',
'omp3': 'OMP3 TOTAL ENERGY'}
VARH['olccd'] = {
'hf': 'HF TOTAL ENERGY',
'mp2': 'MP2 TOTAL ENERGY',
'olccd': 'OLCCD TOTAL ENERGY'}
VARH['lccd'] = {
'hf': 'HF TOTAL ENERGY',
'mp2': 'MP2 TOTAL ENERGY',
'lccd': 'LCCD TOTAL ENERGY'}
VARH['lccsd'] = {
'hf': 'HF TOTAL ENERGY',
'mp2': 'MP2 TOTAL ENERGY',
'lccsd': 'LCCSD TOTAL ENERGY'}
VARH['cepa(0)'] = {
'hf': 'HF TOTAL ENERGY',
'mp2': 'MP2 TOTAL ENERGY',
'cepa(0)': 'CEPA(0) TOTAL ENERGY'}
VARH['cepa(1)'] = {
'hf': 'HF TOTAL ENERGY',
'mp2': 'MP2 TOTAL ENERGY',
'cepa(1)': 'CEPA(1) TOTAL ENERGY'}
VARH['cepa(3)'] = {
'hf': 'HF TOTAL ENERGY',
'mp2': 'MP2 TOTAL ENERGY',
'cepa(3)': 'CEPA(3) TOTAL ENERGY'}
VARH['acpf'] = {
'hf': 'HF TOTAL ENERGY',
'mp2': 'MP2 TOTAL ENERGY',
'acpf': 'ACPF TOTAL ENERGY'}
VARH['aqcc'] = {
'hf': 'HF TOTAL ENERGY',
'mp2': 'MP2 TOTAL ENERGY',
'aqcc': 'AQCC TOTAL ENERGY'}
VARH['qcisd'] = {
'hf': 'HF TOTAL ENERGY',
'mp2': 'MP2 TOTAL ENERGY',
'mp2.5': 'MP2.5 TOTAL ENERGY',
'mp3': 'MP3 TOTAL ENERGY',
'mp4(sdq)': 'MP4(SDQ) TOTAL ENERGY',
'qcisd': 'QCISD TOTAL ENERGY'}
VARH['cc2'] = {
'hf': 'HF TOTAL ENERGY',
'mp2': 'MP2 TOTAL ENERGY',
'cc2': 'CC2 TOTAL ENERGY'}
VARH['ccsd'] = {
'hf': 'HF TOTAL ENERGY',
'mp2': 'MP2 TOTAL ENERGY',
'ccsd': 'CCSD TOTAL ENERGY'}
VARH['bccd'] = {
'hf': 'HF TOTAL ENERGY',
'mp2': 'MP2 TOTAL ENERGY',
'bccd': 'CCSD TOTAL ENERGY'}
VARH['cc3'] = {
'hf': 'HF TOTAL ENERGY',
'mp2': 'MP2 TOTAL ENERGY',
'cc3': 'CC3 TOTAL ENERGY'}
VARH['fno-ccsd'] = {
'hf': 'HF TOTAL ENERGY',
'mp2': 'MP2 TOTAL ENERGY',
'fno-ccsd': 'CCSD TOTAL ENERGY'}
VARH['fno-ccsd(t)'] = {
'hf': 'HF TOTAL ENERGY',
'mp2': 'MP2 TOTAL ENERGY',
'fno-ccsd': 'CCSD TOTAL ENERGY',
'fno-ccsd(t)': 'CCSD(T) TOTAL ENERGY'}
VARH['qcisd(t)'] = {
'hf': 'HF TOTAL ENERGY',
'mp2': 'MP2 TOTAL ENERGY',
'mp2.5': 'MP2.5 TOTAL ENERGY',
'mp3': 'MP3 TOTAL ENERGY',
'mp4(sdq)': 'MP4(SDQ) TOTAL ENERGY',
'qcisd': 'QCISD TOTAL ENERGY',
'qcisd(t)': 'QCISD(T) TOTAL ENERGY'}
VARH['ccsd(t)'] = {
'hf': 'HF TOTAL ENERGY',
'mp2': 'MP2 TOTAL ENERGY',
'ccsd': 'CCSD TOTAL ENERGY',
'ccsd(t)': 'CCSD(T) TOTAL ENERGY'}
VARH['bccd(t)'] = {
'hf': 'HF TOTAL ENERGY',
'mp2': 'MP2 TOTAL ENERGY',
'ccsd': 'CCSD TOTAL ENERGY',
'bccd(t)': 'CCSD(T) TOTAL ENERGY'}
VARH['cisd'] = {
'hf': 'HF TOTAL ENERGY',
'cisd': 'CISD TOTAL ENERGY'}
VARH['cisdt'] = {
'hf': 'HF TOTAL ENERGY',
'cisdt': 'CISDT TOTAL ENERGY'}
VARH['cisdtq'] = {
'hf': 'HF TOTAL ENERGY',
'cisdtq': 'CISDTQ TOTAL ENERGY'}
VARH['fci'] = {
'hf': 'HF TOTAL ENERGY',
'fci': 'FCI TOTAL ENERGY'}
VARH['mrccsd'] = {
'hf': 'HF TOTAL ENERGY',
'mp2': 'MP2 TOTAL ENERGY',
'mrccsd': 'CCSD TOTAL ENERGY'}
VARH['mrccsd(t)'] = {
'hf': 'HF TOTAL ENERGY',
'mp2': 'MP2 TOTAL ENERGY',
'mrccsd': 'CCSD TOTAL ENERGY',
'mrccsd(t)': 'CCSD(T) TOTAL ENERGY'}
VARH['mrccsdt'] = {
'hf': 'HF TOTAL ENERGY',
'mp2': 'MP2 TOTAL ENERGY',
'mrccsdt': 'CCSDT TOTAL ENERGY'}
VARH['mrccsdt(q)'] = {
'hf': 'HF TOTAL ENERGY',
'mp2': 'MP2 TOTAL ENERGY',
'mrccsdt': 'CCSDT TOTAL ENERGY',
'mrccsdt(q)': 'CCSDT(Q) TOTAL ENERGY'}
for cilevel in range(2, 99):
VARH['ci%s' % (str(cilevel))] = {
'hf': 'HF TOTAL ENERGY',
'ci%s' % (str(cilevel)): 'CI TOTAL ENERGY'}
for mplevel in range(5, 99):
VARH['mp%s' % (str(mplevel))] = {
'hf': 'HF TOTAL ENERGY',
'mp%s' % (str(mplevel)): 'MP%s TOTAL ENERGY' % (str(mplevel))}
for mplevel2 in range(2, mplevel):
VARH['mp%s' % (str(mplevel))]['mp%s' % (str(mplevel2))] = \
'MP%s TOTAL ENERGY' % (str(mplevel2))
# Integrate CFOUR methods
VARH.update(cfour_psivar_list())
return VARH
# yapf: enable
VARH = return_energy_components()
[docs]def _get_default_xtpl(nbasis, xtpl_type):
""" A helper function to determine default extrapolation type.
Parameters
----------
nbasis : int
Number of basis sets
xtpl_type : {'scf', 'corl'}
Extrapolation type: 'scf' for the total energy, 'corl' for just the
correlation component.
Returns
-------
function
Extrapolation function to be used.
"""
if nbasis == 1 and xtpl_type in ["scf", "corl"]:
return xtpl_highest_1
elif xtpl_type == "scf":
if nbasis == 2:
return scf_xtpl_helgaker_2
elif nbasis == 3:
return scf_xtpl_helgaker_3
else:
raise ValidationError("Wrong number of basis sets supplied to scf_xtpl: %d" % nbasis)
elif xtpl_type == "corl":
if nbasis == 2:
return corl_xtpl_helgaker_2
else:
raise ValidationError("Wrong number of basis sets supplied to corl_xtpl: %d" % nbasis)
else:
raise ValidationError("Stage treatment must be 'corl' or 'scf', not '%s'" % xtpl_type)
def _validate_cbs_inputs(cbs_metadata, molecule):
""" A helper function which validates the ``cbs_metadata`` format,
expands basis sets, and provides sensible defaults for optional arguments.
Parameters
----------
cbs_metadata : list
List of dicts containing CBS stage keywords.
molecule : qcdb.molecule or psi4.core.Molecule
Molecule to be passed to _expand_bracketed_basis()
Returns
-------
list
Validated list of dictionaries, with each item consisting of an extrapolation
stage. All validation takes place here.
"""
metadata = []
for item in cbs_metadata:
# 1a) all items must have wfn
if "wfn" not in item:
raise ValidationError("Stage {:d} doesn't have defined level of theory!".format(cbs_metadata.index(item)))
# 1b) all items must have basis set
if "basis" not in item:
raise ValidationError("Stage {:d} doesn't have defined basis sets!".format(cbs_metadata.index(item)))
# 2a) process required stage parameters and assign defaults
stage = {}
stage["wfn"] = item["wfn"].lower()
stage["basis"] = _expand_bracketed_basis(item["basis"].lower(), molecule)
# 2b) if first item is not HF, generate it
if len(metadata) == 0 and stage["wfn"] not in ["hf", "c4-hf", "scf", "c4-scf"]:
scf = {}
if stage["wfn"].startswith("c4"):
scf["wfn"] = "c4-hf"
else:
scf["wfn"] = "hf"
scf["basis"] = ([stage["basis"][0][-1]], [stage["basis"][1][-1]])
scf["treatment"] = "scf"
scf["stage"] = "scf"
scf["scheme"] = _get_default_xtpl(len(scf["basis"][1]), scf["treatment"])
scf["alpha"] = None
scf["options"] = False
metadata.append(scf)
# 2c) keep processing current stage
stage["treatment"] = item.get("treatment", "scf" if len(metadata) == 0 else "corl")
stage["stage"] = item.get("stage", False)
if not stage["stage"]:
if len(metadata) == 0:
stage["stage"] = "scf"
elif len(metadata) == 1:
stage["stage"] = "corl"
else:
stage["stage"] = "delta{0:d}".format(len(metadata) - 1)
stage["scheme"] = item.get("scheme", _get_default_xtpl(len(stage["basis"][1]), stage["treatment"]))
if len(metadata) > 0:
stage["wfn_lo"] = item.get("wfn_lo", metadata[-1].get("wfn")).lower()
stage["basis_lo"] = _expand_bracketed_basis(item.get("basis_lo", item["basis"]).lower(), molecule)
if len(stage["basis"][0]) != len(stage["basis_lo"][0]):
raise ValidationError("""Number of basis sets inconsistent
between high ({0:d}) and low ({1:d}) levels.""".format(
len(stage["basis"][0]), len(stage["basis_lo"][0])))
stage["alpha"] = item.get("alpha", None)
stage["options"] = item.get("options", False)
metadata.append(stage)
return (metadata)
def _process_cbs_kwargs(kwargs):
""" A helper function which translates supplied kwargs into the
``cbs_metadata`` format and passes it for validation.
Parameters
----------
kwargs : dict
kwargs containing the CBS function specification.
Returns
-------
list
List of dictionaries, with each item consisting of an extrapolation
stage. All validation takes place here.
"""
molecule = kwargs.get('molecule', core.get_active_molecule())
if "cbs_metadata" in kwargs:
# if we passed in a dict, validate it right away
cbs_metadata = kwargs["cbs_metadata"]
else:
# if we passed in options, check for consecutive correlations first
if "delta_wfn" in kwargs and "corl_wfn" not in kwargs:
raise ValidationError("Delta function supplied without corl_wfn defined.")
if "delta2_wfn" in kwargs and "delta_wfn" not in kwargs:
raise ValidationError("Second delta function supplied without delta_wfn defined.")
cbs_metadata = []
possible_stages = ["scf", "corl"]
while len(possible_stages) > 0:
sn = possible_stages.pop(0)
# either both *_wfn and *_basis have to be specified
if "{:s}_wfn".format(sn) in kwargs and "{:s}_basis".format(sn) in kwargs:
stage = {"wfn": kwargs["{:s}_wfn".format(sn)], "basis": kwargs["{:s}_basis".format(sn)]}
# or we're at a scf stage which can be implied with a provided scf_basis
elif sn == "scf" and "{:s}_basis".format(sn) in kwargs:
stage = {"wfn": "hf", "basis": kwargs["{:s}_basis".format(sn)]}
# otherwise go to the next possible stage
else:
continue
# if we made it here, stage exists - parse other keywords
if "{:s}_scheme".format(sn) in kwargs:
stage["scheme"] = kwargs["{:s}_scheme".format(sn)]
if "{:s}_wfn_lesser".format(sn) in kwargs:
stage["wfn_lo"] = kwargs["{:s}_wfn_lesser".format(sn)]
if "cbs_{:s}_alpha".format(sn) in kwargs:
stage["alpha"] = kwargs["cbs_{:s}_alpha".format(sn)]
elif "{:s}_alpha".format(sn) in kwargs:
stage["alpha"] = kwargs["{:s}_alpha".format(sn)]
cbs_metadata.append(stage)
if sn == "corl":
possible_stages.append("delta")
elif sn == "delta":
possible_stages.append("delta2")
return _validate_cbs_inputs(cbs_metadata, molecule)
###################################
## Start of Complete Basis Set ##
###################################
[docs]def cbs(func, label, **kwargs):
r"""Function to define a multistage energy method from combinations of
basis set extrapolations and delta corrections and condense the
components into a minimum number of calculations.
:aliases: complete_basis_set()
:returns: (*float*) -- Total electronic energy in Hartrees
:PSI variables:
.. hlist::
:columns: 1
* :psivar:`CBS TOTAL ENERGY <CBSTOTALENERGY>`
* :psivar:`CBS REFERENCE ENERGY <CBSREFERENCEENERGY>`
* :psivar:`CBS CORRELATION ENERGY <CBSCORRELATIONENERGY>`
* :psivar:`CURRENT ENERGY <CURRENTENERGY>`
* :psivar:`CURRENT REFERENCE ENERGY <CURRENTREFERENCEENERGY>`
* :psivar:`CURRENT CORRELATION ENERGY <CURRENTCORRELATIONENERGY>`
.. caution:: Some features are not yet implemented. Buy a developer a coffee.
- No way to tell function to boost fitting basis size for all calculations.
- Need to add more extrapolation schemes
As represented in the equation below, a CBS energy method is defined in several
sequential stages (scf, corl, delta1, delta2, ... ) covering treatment
of the reference total energy, the correlation energy, a delta correction to the
correlation energy, and a second delta correction, etc.. Each is activated by its
stage_wfn keyword, or as a field in the ```cbs_metadata``` list, and is only
allowed if all preceding stages are active.
.. include:: ../cbs_eqn.rst
* Energy Methods
The presence of a stage_wfn keyword is the indicator to incorporate
(and check for stage_basis and stage_scheme keywords) and compute
that stage in defining the CBS energy.
The cbs() function requires, at a minimum, ``name='scf'`` and ``scf_basis``
keywords to be specified for reference-step only jobs and ``name`` and
``corl_basis`` keywords for correlated jobs.
The following energy methods have been set up for cbs().
.. hlist::
:columns: 5
* scf
* hf
* mp2
* mp2.5
* mp3
* mp4(sdq)
* mp4
* mp\ *n*
* omp2
* omp2.5
* omp3
* olccd
* lccd
* lccsd
* cepa(0)
* cepa(1)
* cepa(3)
* acpf
* aqcc
* qcisd
* cc2
* ccsd
* fno-ccsd
* bccd
* cc3
* qcisd(t)
* ccsd(t)
* fno-ccsd(t)
* bccd(t)
* cisd
* cisdt
* cisdtq
* ci\ *n*
* fci
* mrccsd
* mrccsd(t)
* mrccsdt
* mrccsdt(q)
:type name: str
:param name: ``'scf'`` || ``'ccsd'`` || etc.
First argument, usually unlabeled. Indicates the computational method
for the correlation energy, unless only reference step to be performed,
in which case should be ``'scf'``. Overruled if stage_wfn keywords supplied.
:type scf_wfn: str
:param scf_wfn: |dl| ``'scf'`` |dr| || ``'c4-scf'`` || etc.
Indicates the energy method for which the reference energy is to be
obtained. Generally unnecessary, as 'scf' is *the* scf in |PSIfour| but
can be used to direct lone scf components to run in |PSIfour| or Cfour
in a mixed-program composite method.
:type corl_wfn: str
:param corl_wfn: ``'mp2'`` || ``'ccsd(t)'`` || etc.
Indicates the energy method for which the correlation energy is to be
obtained. Can also be specified with ``name`` or as the unlabeled
first argument to the function.
:type delta_wfn: str
:param delta_wfn: ``'ccsd'`` || ``'ccsd(t)'`` || etc.
Indicates the (superior) energy method for which a delta correction
to the correlation energy is to be obtained.
:type delta_wfn_lesser: str
:param delta_wfn_lesser: |dl| ``corl_wfn`` |dr| || ``'mp2'`` || etc.
Indicates the inferior energy method for which a delta correction
to the correlation energy is to be obtained.
:type delta2_wfn: str
:param delta2_wfn: ``'ccsd'`` || ``'ccsd(t)'`` || etc.
Indicates the (superior) energy method for which a second delta correction
to the correlation energy is to be obtained.
:type delta2_wfn_lesser: str
:param delta2_wfn_lesser: |dl| ``delta_wfn`` |dr| || ``'ccsd(t)'`` || etc.
Indicates the inferior energy method for which a second delta correction
to the correlation energy is to be obtained.
* Basis Sets
Currently, the basis set set through ``set`` commands have no influence
on a cbs calculation.
:type scf_basis: :ref:`basis string <apdx:basisElement>`
:param scf_basis: |dl| ``corl_basis`` |dr| || ``'cc-pV[TQ]Z'`` || ``'jun-cc-pv[tq5]z'`` || ``'6-31G*'`` || etc.
Indicates the sequence of basis sets employed for the reference energy.
If any correlation method is specified, ``scf_basis`` can default
to ``corl_basis``.
:type corl_basis: :ref:`basis string <apdx:basisElement>`
:param corl_basis: ``'cc-pV[TQ]Z'`` || ``'jun-cc-pv[tq5]z'`` || ``'6-31G*'`` || etc.
Indicates the sequence of basis sets employed for the correlation energy.
:type delta_basis: :ref:`basis string <apdx:basisElement>`
:param delta_basis: ``'cc-pV[TQ]Z'`` || ``'jun-cc-pv[tq5]z'`` || ``'6-31G*'`` || etc.
Indicates the sequence of basis sets employed for the delta correction
to the correlation energy.
:type delta2_basis: :ref:`basis string <apdx:basisElement>`
:param delta2_basis: ``'cc-pV[TQ]Z'`` || ``'jun-cc-pv[tq5]z'`` || ``'6-31G*'`` || etc.
Indicates the sequence of basis sets employed for the second delta correction
to the correlation energy.
* Schemes
Transformations of the energy through basis set extrapolation for each
stage of the CBS definition. A complaint is generated if number of basis
sets in stage_basis does not exactly satisfy requirements of stage_scheme.
An exception is the default, ``'xtpl_highest_1'``, which uses the best basis
set available. See :ref:`sec:cbs_xtpl` for all available schemes.
:type scf_scheme: function
:param scf_scheme: |dl| ``xtpl_highest_1`` |dr| || ``scf_xtpl_helgaker_3`` || etc.
Indicates the basis set extrapolation scheme to be applied to the reference energy.
Defaults to :py:func:`~scf_xtpl_helgaker_3` if three valid basis sets
present in ``scf_basis``, :py:func:`~scf_xtpl_helgaker_2` if two valid basis
sets present in ``scf_basis``, and :py:func:`~xtpl_highest_1` otherwise.
.. hlist::
:columns: 1
* xtpl_highest_1
* scf_xtpl_helgaker_3
* scf_xtpl_helgaker_2
* scf_xtpl_truhlar_2
* scf_xtpl_karton_2
:type corl_scheme: function
:param corl_scheme: |dl| ``xtpl_highest_1`` |dr| || ``corl_xtpl_helgaker_2`` || etc.
Indicates the basis set extrapolation scheme to be applied to the correlation energy.
Defaults to :py:func:`~corl_xtpl_helgaker_2` if two valid basis sets
present in ``corl_basis`` and :py:func:`~xtpl_highest_1` otherwise.
.. hlist::
:columns: 1
* xtpl_highest_1
* corl_xtpl_helgaker_2
:type delta_scheme: function
:param delta_scheme: |dl| ``xtpl_highest_1`` |dr| || ``corl_xtpl_helgaker_2`` || etc.
Indicates the basis set extrapolation scheme to be applied to the delta correction
to the correlation energy.
Defaults to :py:func:`~corl_xtpl_helgaker_2` if two valid basis sets
present in ``delta_basis`` and :py:func:`~xtpl_highest_1` otherwise.
.. hlist::
:columns: 1
* xtpl_highest_1
* corl_xtpl_helgaker_2
:type delta2_scheme: function
:param delta2_scheme: |dl| ``xtpl_highest_1`` |dr| || ``corl_xtpl_helgaker_2`` || etc.
Indicates the basis set extrapolation scheme to be applied to the second delta correction
to the correlation energy.
Defaults to :py:func:`~corl_xtpl_helgaker_2` if two valid basis sets
present in ``delta2_basis`` and :py:func:`~xtpl_highest_1` otherwise.
.. hlist::
:columns: 1
* xtpl_highest_1
* corl_xtpl_helgaker_2
:type scf_alpha: float
Overrides the default \alpha parameter used in the listed SCF extrapolation procedures.
Has no effect on others, including :py:func:`~xtpl_highest_1` and :py:func:`~scf_xtpl_helgaker_3`.
.. hlist::
:columns: 1
* :py:func:`scf_xtpl_helgaker_2`
* :py:func:`scf_xtpl_truhlar_2`
* :py:func:`scf_xtpl_karton_2`
:type corl_alpha: float
Overrides the default \alpha parameter used in the listed :py:func:`corl_xtpl_helgaker_2` correlation
extrapolation to the corl stage. The supplied \alpha does not impact delta or any further stages.
.. hlist::
:columns: 1
* :py:func:`corl_xtpl_helgaker_2`
:type delta_alpha: float
Overrides the default \alpha parameter used in the listed
:py:func:`corl_xtpl_helgaker_2` correlation extrapolation for the delta correction. Useful when
delta correction is performed using smaller basis sets for which a different \alpha might
be more appropriate.
.. hlist::
:columns: 1
* :py:func:`corl_xtpl_helgaker_2`
* Combined interface
:type cbs_metadata: list of dicts
This is the interface to which all of the above calls are internally translated. The first item in
the array is always defining the SCF contribution to the total energy. The required items in the
dictionary are:
* ```wfn```: typically ```HF```, which is subsumed in correlated methods anyway.
* ```basis```: basis set, can be in a bracketed form (eg. ```cc-pv[tq]z```)
Other supported arguments for the first dictionary are:
* ```scheme```: scf extrapolation scheme function, by default it is worked out from the number of
basis sets (1 - 3) supplied as ```basis```.
* ```alpha```: alpha for the above scheme, if the default is to be overriden
* ```options```: if special options are required for a step, they should be entered as a dict here.
This is helpful for calculating all electron corrections in otherwise frozen core calculations, or
relativistic (DKH) Hamiltionian corrections for otherwise 2-component Hamiltonians.
* ```treatment```: treat extrapolation stage as ```scf``` or ```corl```, by default only the first
stage is ```scf``` and every later one is ```corl```.
* ```stage```: tag for the stage used in tables.
The next items in the ```cbs_metadata``` array extrapolate correlation. All of the above parameters
are available, with only the ```wfn``` and ```basis``` keywords required. Other supported parameters
are:
* ```wfn_lo```: the lower method from which the delta correction is to be calculated. By default, it
is set to ```wfn``` from the previous field in the ```cbs_metadata``` array.
* ```basis_lo```: basis set to be used for the delta correction. By default, it is the same as the
```basis``` specified above.
* Others
:type molecule: :ref:`molecule <op_py_molecule>`
:param molecule: ``h2o`` || etc.
The target molecule, if not the last molecule defined.
:examples:
>>> # [1] replicates with cbs() the simple model chemistry scf/cc-pVDZ: set basis cc-pVDZ energy('scf')
>>> energy(cbs, scf_wfn='scf', scf_basis='cc-pVDZ')
>>> # [2] replicates with cbs() the simple model chemistry mp2/jun-cc-pVDZ: set basis jun-cc-pVDZ energy('mp2')
>>> energy(cbs, corl_wfn='mp2', corl_basis='jun-cc-pVDZ')
>>> # [3] DTQ-zeta extrapolated scf reference energy
>>> energy(cbs, scf_wfn='scf', scf_basis='cc-pV[DTQ]Z', scf_scheme=scf_xtpl_helgaker_3)
>>> # [4] DT-zeta extrapolated mp2 correlation energy atop a T-zeta reference
>>> energy(cbs, corl_wfn='mp2', corl_basis='cc-pv[dt]z', corl_scheme=corl_xtpl_helgaker_2)
>>> # [5] a DT-zeta extrapolated coupled-cluster correction atop a TQ-zeta extrapolated mp2 correlation energy atop a Q-zeta reference (both equivalent)
>>> energy(cbs, corl_wfn='mp2', corl_basis='aug-cc-pv[tq]z', delta_wfn='ccsd(t)', delta_basis='aug-cc-pv[dt]z')
>>> energy(cbs, corl_wfn='mp2', corl_basis='aug-cc-pv[tq]z', corl_scheme=corl_xtpl_helgaker_2, delta_wfn='ccsd(t)', delta_basis='aug-cc-pv[dt]z', delta_scheme=corl_xtpl_helgaker_2)
>>> # [6] a D-zeta ccsd(t) correction atop a DT-zeta extrapolated ccsd cluster correction atop a TQ-zeta extrapolated mp2 correlation energy atop a Q-zeta reference
>>> energy(cbs, corl_wfn='mp2', corl_basis='aug-cc-pv[tq]z', corl_scheme=corl_xtpl_helgaker_2, delta_wfn='ccsd', delta_basis='aug-cc-pv[dt]z', delta_scheme=corl_xtpl_helgaker_2, delta2_wfn='ccsd(t)', delta2_wfn_lesser='ccsd', delta2_basis='aug-cc-pvdz')
>>> # [7] a Q5-zeta MP2 calculation, corrected by CCSD(T) at the TQ-zeta extrapolated level, and all-electron CCSD(T) correlation at T-zeta level
>>> energy(cbs, cbs_metadata=[{"wfn": "hf", "basis": "cc-pv5z"}, {"wfn": "mp2", "basis": "cc-pv[q5]z"}, {"wfn": "ccsd(t)", "basis": "cc-pv[tq]z"}, {"wfn": "ccsd(t)", "basis": "cc-pvtz", "options": {"freeze_core": "False"}}])
>>> # [8] cbs() coupled with database()
>>> TODO database('mp2', 'BASIC', subset=['h2o','nh3'], symm='on', func=cbs, corl_basis='cc-pV[tq]z', corl_scheme=corl_xtpl_helgaker_2, delta_wfn='ccsd(t)', delta_basis='sto-3g')
>>> # [9] cbs() coupled with optimize()
>>> TODO optimize('mp2', corl_basis='cc-pV[DT]Z', corl_scheme=corl_xtpl_helgaker_2, func=cbs)
"""
kwargs = p4util.kwargs_lower(kwargs)
metadata = _process_cbs_kwargs(kwargs)
return_wfn = kwargs.pop('return_wfn', False)
verbose = kwargs.pop('verbose', 0)
ptype = kwargs.pop('ptype')
if ptype not in ['energy', 'gradient', 'hessian']:
raise ValidationError("""Wrapper complete_basis_set is unhappy to be calling
function '%s' instead of 'energy', 'gradient' or 'hessian'.""" % ptype)
optstash = p4util.OptionsState(['BASIS'], ['WFN'], ['WRITER_FILE_LABEL'])
# Define some quantum chemical knowledge, namely what methods are subsumed in others
user_writer_file_label = core.get_global_option('WRITER_FILE_LABEL')
# Make sure the molecule the user provided is the active one
molecule = kwargs.pop('molecule', core.get_active_molecule())
molecule.update_geometry()
natom = molecule.natom()
if metadata[0]["wfn"] not in VARH.keys():
raise ValidationError(
"""Requested SCF method '%s' is not recognized. Add it to VARH in wrapper.py to proceed.""" %
(metadata[0]["wfn"]))
if len(metadata) > 1:
for delta in metadata[1:]:
if delta["wfn"] not in VARH.keys():
raise ValidationError(
"""Requested higher %s method '%s' is not recognized. Add it to VARH in wrapper.py to proceed.""" %
(delta["treatment"], delta["wfn"]))
if delta["wfn_lo"] not in VARH.keys():
raise ValidationError(
"""Requested lesser %s method '%s' is not recognized. Add it to VARH in wrapper.py to proceed.""" %
(delta["treatment"], delta["wfn_lo"]))
# Build string of title banner
cbsbanners = ''
cbsbanners += """core.print_out('\\n')\n"""
cbsbanners += """p4util.banner(' CBS Setup: %s ' % label)\n"""
cbsbanners += """core.print_out('\\n')\n\n"""
exec(cbsbanners)
# Call schemes for each portion of total energy to 'place orders' for calculations needed
d_fields = [
'd_stage', 'd_scheme', 'd_basis', 'd_wfn', 'd_need', 'd_coef', 'd_energy', 'd_gradient', 'd_hessian', 'd_alpha'
]
f_fields = ['f_wfn', 'f_basis', 'f_zeta', 'f_energy', 'f_gradient', 'f_hessian', 'f_options']
GRAND_NEED = []
MODELCHEM = []
NEED = _expand_scheme_orders(metadata[0]["scheme"], metadata[0]["basis"][0], metadata[0]["basis"][1],
metadata[0]["wfn"], metadata[0]["options"], natom)
GRAND_NEED.append(
dict(
zip(d_fields, [
'scf', metadata[0]["scheme"],
_contract_bracketed_basis(metadata[0]["basis"][0]), metadata[0]["wfn"], NEED, +1, 0.0, None, None,
metadata[0]["alpha"]
])))
if len(metadata) > 1:
for delta in metadata[1:]:
NEED = _expand_scheme_orders(delta["scheme"], delta["basis"][0], delta["basis"][1], delta["wfn"],
delta["options"], natom)
GRAND_NEED.append(
dict(
zip(d_fields, [
delta["stage"], delta["scheme"],
_contract_bracketed_basis(delta["basis"][0]), delta["wfn"], NEED, +1, 0.0, None, None,
delta["alpha"]
])))
NEED = _expand_scheme_orders(delta["scheme"], delta["basis_lo"][0], delta["basis_lo"][1], delta["wfn_lo"],
False, natom)
GRAND_NEED.append(
dict(
zip(d_fields, [
delta["stage"], delta["scheme"],
_contract_bracketed_basis(delta["basis_lo"][0]), delta["wfn_lo"], NEED, -1, 0.0, None, None,
delta["alpha"]
])))
for stage in GRAND_NEED:
for lvl in stage['d_need'].items():
MODELCHEM.append(lvl[1])
# Apply chemical reasoning to choose the minimum computations to run
JOBS = MODELCHEM[:]
addlremark = {'energy': '', 'gradient': ', GRADIENT', 'hessian': ', HESSIAN'}
instructions = ''
instructions += """ Naive listing of computations required.\n"""
for mc in JOBS:
instructions += """ %12s / %-24s for %s%s\n""" % \
(mc['f_wfn'], mc['f_basis'] + " + options"*bool(mc['f_options']),
VARH[mc['f_wfn']][mc['f_wfn']], addlremark[ptype])
# Remove duplicate modelchem portion listings
for mc in MODELCHEM:
dups = -1
for indx_job, job in enumerate(JOBS):
if (job['f_wfn'] == mc['f_wfn']) and (job['f_basis'] == mc['f_basis']) and \
(job['f_options'] == mc['f_options']) and (job['f_options'] != False):
dups += 1
if dups >= 1:
del JOBS[indx_job]
# Remove chemically subsumed modelchem portion listings
if ptype == 'energy':
for mc in MODELCHEM:
for wfn in VARH[mc['f_wfn']]:
for indx_job, job in enumerate(JOBS):
if (VARH[mc['f_wfn']][wfn] == VARH[job['f_wfn']][job['f_wfn']]) and \
(mc['f_basis'] == job['f_basis']) and not \
(mc['f_wfn'] == job['f_wfn']) and \
(mc['f_options'] == False):
del JOBS[indx_job]
instructions += """\n Enlightened listing of computations required.\n"""
for mc in JOBS:
instructions += """ %12s / %-24s for %s%s\n""" % \
(mc['f_wfn'], mc['f_basis'] + " + options"*bool(mc['f_options']),
VARH[mc['f_wfn']][mc['f_wfn']], addlremark[ptype])
# Expand listings to all that will be obtained
JOBS_EXT = []
for job in JOBS:
for wfn in VARH[job['f_wfn']]:
JOBS_EXT.append(
dict(
zip(f_fields, [
wfn, job['f_basis'], job['f_zeta'], 0.0,
core.Matrix(natom, 3),
core.Matrix(3 * natom, 3 * natom), job['f_options']
])))
instructions += """\n Full listing of computations to be obtained (required and bonus).\n"""
for mc in JOBS_EXT:
instructions += """ %12s / %-24s for %s%s\n""" % \
(mc['f_wfn'], mc['f_basis'] + " + options"*bool(mc['f_options']),
VARH[mc['f_wfn']][mc['f_wfn']], addlremark[ptype])
core.print_out(instructions)
psioh = core.IOManager.shared_object()
psioh.set_specific_retention(psif.PSIF_SCF_MOS, True)
# projection across point groups not allowed and cbs() usually a mix of symm-enabled and symm-tol calls
# needs to be communicated to optimize() so reset by that optstash
core.set_local_option('SCF', 'GUESS_PERSIST', True)
Njobs = 0
# Run necessary computations
for mc in JOBS:
kwargs['name'] = mc['f_wfn']
# Build string of title banner
cbsbanners = ''
cbsbanners += """core.print_out('\\n')\n"""
cbsbanners += """p4util.banner(' CBS Computation: %s / %s%s ')\n""" % \
(mc['f_wfn'].upper(), mc['f_basis'].upper() + " + opts."*bool(mc['f_options']), addlremark[ptype])
cbsbanners += """core.print_out('\\n')\n\n"""
exec(cbsbanners)
# Build string of molecule and commands that are dependent on the database
commands = '\n'
commands += """\ncore.set_global_option('BASIS', '%s')\n""" % (mc['f_basis'])
commands += """core.set_global_option('WRITER_FILE_LABEL', '%s')\n""" % \
(user_writer_file_label + ('' if user_writer_file_label == '' else '-') + mc['f_wfn'].lower() + '-' + mc['f_basis'].lower().replace('*', 's'))
exec(commands)
# Stash and set options if any
if mc["f_options"]:
optionstash = p4util.OptionsState(*[[opt] for opt in list(mc["f_options"])])
for k, v, in mc["f_options"].items():
core.set_global_option(k.upper(), v)
else:
optionstash = False
# Make energy(), etc. call
response = func(molecule=molecule, **kwargs)
if ptype == 'energy':
mc['f_energy'] = response
elif ptype == 'gradient':
mc['f_gradient'] = response
mc['f_energy'] = core.variable('CURRENT ENERGY')
if verbose > 1:
mc['f_gradient'].print_out()
elif ptype == 'hessian':
mc['f_hessian'] = response
mc['f_energy'] = core.variable('CURRENT ENERGY')
if verbose > 1:
mc['f_hessian'].print_out()
Njobs += 1
if verbose > 1:
core.print_out("\nCURRENT ENERGY: %14.16f\n" % mc['f_energy'])
# Restore modified options
if optionstash:
optionstash.restore()
# Fill in energies for subsumed methods
if ptype == 'energy':
for wfn in VARH[mc['f_wfn']]:
for job in JOBS_EXT:
if (wfn == job['f_wfn']) and (mc['f_basis'] == job['f_basis']) and \
(mc['f_options'] == job['f_options']):
job['f_energy'] = core.variable(VARH[wfn][wfn])
if verbose > 1:
core.print_variables()
core.clean_variables()
core.clean()
# Copy data from 'run' to 'obtained' table
for mce in JOBS_EXT:
if (mc['f_wfn'] == mce['f_wfn']) and (mc['f_basis'] == mce['f_basis']) and \
(mc['f_options'] == mce['f_options']):
mce['f_energy'] = mc['f_energy']
mce['f_gradient'] = mc['f_gradient']
mce['f_hessian'] = mc['f_hessian']
psioh.set_specific_retention(psif.PSIF_SCF_MOS, False)
# Build string of title banner
cbsbanners = ''
cbsbanners += """core.print_out('\\n')\n"""
cbsbanners += """p4util.banner(' CBS Results: %s ' % label)\n"""
cbsbanners += """core.print_out('\\n')\n\n"""
exec(cbsbanners)
# Insert obtained energies into the array that stores the cbs stages
for stage in GRAND_NEED:
for lvl in stage['d_need'].items():
MODELCHEM.append(lvl[1])
for job in JOBS_EXT:
# Dont ask
if (((lvl[1]['f_wfn'] == job['f_wfn']) or
((lvl[1]['f_wfn'][3:] == job['f_wfn']) and lvl[1]['f_wfn'].startswith('c4-')) or
((lvl[1]['f_wfn'] == job['f_wfn'][3:]) and job['f_wfn'].startswith('c4-')) or
(('c4-' + lvl[1]['f_wfn']) == job['f_wfn']) or (lvl[1]['f_wfn'] == ('c4-' + job['f_wfn'])))
and (lvl[1]['f_basis'] == job['f_basis']) and (lvl[1]['f_options'] == job['f_options'])):
lvl[1]['f_energy'] = job['f_energy']
lvl[1]['f_gradient'] = job['f_gradient']
lvl[1]['f_hessian'] = job['f_hessian']
# Make xtpl() call
finalenergy = 0.0
finalgradient = core.Matrix(natom, 3)
finalhessian = core.Matrix(3 * natom, 3 * natom)
for stage in GRAND_NEED:
hiloargs = {'alpha': stage['d_alpha']}
hiloargs.update(_contract_scheme_orders(stage['d_need'], 'f_energy'))
stage['d_energy'] = stage['d_scheme'](**hiloargs)
finalenergy += stage['d_energy'] * stage['d_coef']
if ptype == 'gradient':
hiloargs.update(_contract_scheme_orders(stage['d_need'], 'f_gradient'))
stage['d_gradient'] = stage['d_scheme'](**hiloargs)
work = stage['d_gradient'].clone()
work.scale(stage['d_coef'])
finalgradient.add(work)
elif ptype == 'hessian':
hiloargs.update(_contract_scheme_orders(stage['d_need'], 'f_hessian'))
stage['d_hessian'] = stage['d_scheme'](**hiloargs)
work = stage['d_hessian'].clone()
work.scale(stage['d_coef'])
finalhessian.add(work)
# Build string of results table
table_delimit = ' ' + '-' * 105 + '\n'
tables = ''
tables += """\n ==> %s <==\n\n""" % ('Components')
tables += table_delimit
tables += """ %6s %20s %1s %-26s %3s %16s %-s\n""" % ('', 'Method', '/', 'Basis', 'Rqd', 'Energy [Eh]',
'Variable')
tables += table_delimit
for job in JOBS_EXT:
star = ''
for mc in MODELCHEM:
if (job['f_wfn'] == mc['f_wfn']) and (job['f_basis'] == mc['f_basis']):
star = '*'
tables += """ %6s %20s %1s %-27s %2s %16.8f %-s\n""" % (
'', job['f_wfn'], '/', job['f_basis'] + " + options" * bool(job['f_options']), star, job['f_energy'],
VARH[job['f_wfn']][job['f_wfn']])
tables += table_delimit
tables += """\n ==> %s <==\n\n""" % ('Stages')
tables += table_delimit
tables += """ %6s %20s %1s %-27s %2s %16s %-s\n""" % ('Stage', 'Method', '/', 'Basis', 'Wt', 'Energy [Eh]',
'Scheme')
tables += table_delimit
for stage in GRAND_NEED:
tables += """ %6s %20s %1s %-27s %2d %16.8f %-s\n""" % (stage['d_stage'], stage['d_wfn'], '/',
stage['d_basis'], stage['d_coef'],
stage['d_energy'], stage['d_scheme'].__name__)
tables += table_delimit
tables += """\n ==> %s <==\n\n""" % ('CBS')
tables += table_delimit
tables += """ %6s %20s %1s %-27s %2s %16s %-s\n""" % ('Stage', 'Method', '/', 'Basis', '', 'Energy [Eh]',
'Scheme')
tables += table_delimit
tables += """ %6s %20s %1s %-27s %2s %16.8f %-s\n""" % (
GRAND_NEED[0]['d_stage'], GRAND_NEED[0]['d_wfn'], '/', GRAND_NEED[0]['d_basis'], '', GRAND_NEED[0]['d_energy'],
GRAND_NEED[0]['d_scheme'].__name__)
if len(metadata) > 1:
tables += """ %6s %20s %1s %-27s %2s %16.8f %-s\n""" % (
GRAND_NEED[1]['d_stage'], GRAND_NEED[1]['d_wfn'], '/', GRAND_NEED[1]['d_basis'], '',
GRAND_NEED[1]['d_energy'] - GRAND_NEED[2]['d_energy'], GRAND_NEED[1]['d_scheme'].__name__)
if len(metadata) > 2:
dc = 3
for delta in metadata[2:]:
tables += """ %6s %20s %1s %-27s %2s %16.8f %-s\n""" % (
GRAND_NEED[dc]['d_stage'], GRAND_NEED[dc]['d_wfn'] + ' - ' + GRAND_NEED[dc + 1]['d_wfn'], '/',
GRAND_NEED[dc]['d_basis'], '', GRAND_NEED[dc]['d_energy'] - GRAND_NEED[dc + 1]['d_energy'],
GRAND_NEED[dc]['d_scheme'].__name__)
dc += 2
tables += """ %6s %20s %1s %-27s %2s %16.8f %-s\n""" % ('total', 'CBS', '', '', '', finalenergy, '')
tables += table_delimit
core.print_out(tables)
core.set_variable('CBS REFERENCE ENERGY', GRAND_NEED[0]['d_energy'])
core.set_variable('CBS CORRELATION ENERGY', finalenergy - GRAND_NEED[0]['d_energy'])
core.set_variable('CBS TOTAL ENERGY', finalenergy)
core.set_variable('CURRENT REFERENCE ENERGY', GRAND_NEED[0]['d_energy'])
core.set_variable('CURRENT CORRELATION ENERGY', finalenergy - GRAND_NEED[0]['d_energy'])
core.set_variable('CURRENT ENERGY', finalenergy)
core.set_variable('CBS NUMBER', Njobs)
# new skeleton wavefunction w/mol, highest-SCF basis (just to choose one), & not energy
basis = core.BasisSet.build(molecule, "ORBITAL", 'def2-svp')
wfn = core.Wavefunction(molecule, basis)
optstash.restore()
if ptype == 'energy':
finalquantity = finalenergy
elif ptype == 'gradient':
finalquantity = finalgradient
wfn.set_gradient(finalquantity)
if finalquantity.rows(0) < 20:
core.print_out('CURRENT GRADIENT')
finalquantity.print_out()
elif ptype == 'hessian':
finalquantity = finalhessian
wfn.set_gradient(finalgradient)
wfn.set_hessian(finalquantity)
if finalquantity.rows(0) < 20:
core.print_out('CURRENT HESSIAN')
finalquantity.print_out()
if return_wfn:
return (finalquantity, wfn)
else:
return finalquantity
_lmh_labels = {
1: ['HI'],
2: ['LO', 'HI'],
3: ['LO', 'MD', 'HI'],
4: ['LO', 'MD', 'M2', 'HI'],
5: ['LO', 'MD', 'M2', 'M3', 'HI']
}
def _expand_scheme_orders(scheme, basisname, basiszeta, wfnname, options, natom):
"""Check that the length of *basiszeta* array matches the implied degree of
extrapolation in *scheme* name. Return a dictionary of same length as
basiszeta, with *basisname* and *basiszeta* distributed therein.
"""
Nxtpl = len(basiszeta)
if int(scheme.__name__.split('_')[-1]) != Nxtpl:
raise ValidationError("""Call to '%s' not valid with '%s' basis sets.""" % (scheme.__name__, len(basiszeta)))
f_fields = ['f_wfn', 'f_basis', 'f_zeta', 'f_energy', 'f_gradient', 'f_hessian', 'f_options']
NEED = {}
for idx in range(Nxtpl):
NEED[_lmh_labels[Nxtpl][idx]] = dict(
zip(f_fields, [
wfnname, basisname[idx], basiszeta[idx], 0.0,
core.Matrix(natom, 3),
core.Matrix(3 * natom, 3 * natom), options
]))
return NEED
def _contract_scheme_orders(needdict, datakey='f_energy'):
"""Prepared named arguments for extrapolation functions by
extracting zetas and values (which one determined by *datakey*) out
of *needdict* and returning a dictionary whose keys are constructed
from _lmh_labels.
"""
largs = {}
largs['functionname'] = needdict['HI']['f_wfn']
Nxtpl = len(needdict)
zlabels = _lmh_labels[Nxtpl] # e.g., ['LO', 'HI']
for zeta in range(Nxtpl):
zlab = zlabels[zeta] # e.g., LO
largs['z' + zlab] = needdict[zlab]['f_zeta']
largs['value' + zlab] = needdict[zlab][datakey]
return largs
## Aliases ##
complete_basis_set = cbs
def _cbs_wrapper_methods(**kwargs):
""" A helper function for the driver to enumerate methods used in the
cbs calculation.
Parameters
----------
kwargs : dict
kwargs containing cbs specification either in the ``cbs_metadata``
format, or in separate keywords (``scf_wfn``, ``corl_wfn`` etc.).
Returns
-------
list
List containing method names.
"""
cbs_methods = []
if "cbs_metadata" in kwargs:
for item in kwargs["cbs_metadata"]:
cbs_methods.append(item.get("wfn"))
else:
cbs_method_kwargs = ['scf_wfn', 'corl_wfn', 'delta_wfn']
cbs_method_kwargs += ['delta%d_wfn' % x for x in range(2, 6)]
for method in cbs_method_kwargs:
if method in kwargs:
cbs_methods.append(kwargs[method])
return cbs_methods
def _parse_cbs_gufunc_string(method_name):
""" A helper function that parses a ``"method/basis"`` input string
into separate method and basis components. Also handles delta corrections.
Parameters
----------
method_name : str
A ``"method/basis"`` style string defining the calculation.
Returns
-------
tuple
Tuple in the ``(method_list, basis_list)`` format, where ``method_list``
is the list of the component methods, and ``basis_list`` is the list of
basis sets forming the extrapolation for each specified method.
E.g. ``"mp2/cc-pv[tq]z+D:ccsd(t)/cc-pvtz"`` would return:
``(["mp2", "ccsd(t)"], ["cc-pv[tq]z", "cc-pvtz"])``.
"""
method_name_list = re.split("""\+(?=\s*[Dd]:)""", method_name)
if len(method_name_list) > 2:
raise ValidationError(
"CBS gufunc: Text parsing is only valid for a single delta, please use the CBS wrapper directly")
method_list = []
basis_list = []
for num, method_str in enumerate(method_name_list):
if (method_str.count("[") > 1) or (method_str.count("]") > 1):
raise ValidationError("""CBS gufunc: Too many brackets given! %s """ % method_str)
if method_str.count('/') != 1:
raise ValidationError("""CBS gufunc: All methods must specify a basis with '/'. %s""" % method_str)
if num > 0:
method_str = method_str.strip()
if method_str[:2].lower() != 'd:':
raise ValidationError("""CBS gufunc: Delta method must start with 'D:'.""")
else:
method_str = method_str[2:]
method, basis = method_str.split('/')
method_list.append(method)
basis_list.append(basis)
return method_list, basis_list
def _cbs_gufunc(func, total_method_name, **kwargs):
"""
A text based wrapper of the CBS function. Provided to handle "method/basis"
specification of the requested calculations. Also handles "simple" (i.e.
one-method and one-basis) calls.
Parameters
----------
func : function
Function to be called (energy, gradient, frequency or cbs).
total_method_name : str
String in a ``"method/basis"`` syntax. Simple calls (e.g. ``"blyp/sto-3g"``) are
bounced out of CBS. More complex calls (e.g. ``"mp2/cc-pv[tq]z"`` or
``"mp2/cc-pv[tq]z+D:ccsd(t)/cc-pvtz"``) are expanded by `_parse_cbs_gufunc_string()`
and pushed through :py:func:`~psi4.cbs`.
Returns
-------
tuple or float
Float, or if ``return_wfn`` is specified, a tuple of ``(value, wavefunction)``.
"""
# Catch kwarg issues for all methods
kwargs = p4util.kwargs_lower(kwargs)
return_wfn = kwargs.pop('return_wfn', False)
core.clean_variables()
ptype = kwargs.pop('ptype', None)
# Make sure the molecule the user provided is the active one
molecule = kwargs.pop('molecule', core.get_active_molecule())
molecule.update_geometry()
# Sanitize total_method_name
label = total_method_name
total_method_name = total_method_name.lower()
total_method_name = total_method_name.replace(' ', '')
# Split into components
method_list, basis_list = _parse_cbs_gufunc_string(total_method_name)
# Single energy call?
single_call = len(method_list) == 1
single_call &= '[' not in basis_list[0]
single_call &= ']' not in basis_list[0]
if single_call:
method_name = method_list[0]
basis = basis_list[0]
# Save some global variables so we can reset them later
optstash = p4util.OptionsState(['BASIS'])
core.set_global_option('BASIS', basis)
ptype_value, wfn = func(method_name, return_wfn=True, molecule=molecule, **kwargs)
core.clean()
optstash.restore()
if return_wfn:
return (ptype_value, wfn)
else:
return ptype_value
# Drop out for unsupported calls
if ptype not in ["energy", "gradient", "hessian"]:
raise ValidationError("%s: Cannot extrapolate or delta correct %s yet." % (ptype.title(), ptype))
# Catch kwarg issues for CBS methods only
user_dertype = kwargs.pop('dertype', None)
cbs_verbose = kwargs.pop('cbs_verbose', False)
# If we are not a single call, let CBS wrapper handle it!
cbs_kwargs = {}
cbs_kwargs['ptype'] = ptype
cbs_kwargs['return_wfn'] = True
cbs_kwargs['molecule'] = molecule
cbs_kwargs['verbose'] = cbs_verbose
if user_dertype != None:
cbs_kwargs['dertype'] = user_dertype
# Find method and basis
metadata = []
if method_list[0] in ['scf', 'hf', 'c4-scf', 'c4-hf']:
stage = {}
stage['wfn'] = method_list[0]
stage['basis'] = basis_list[0]
if 'scf_scheme' in kwargs:
stage['scheme'] = kwargs.pop('scf_scheme')
stage['stage'] = "scf"
stage['treatment'] = "scf"
else:
# _validate_cbs_inputs will produce scf stage automatically
stage = {}
stage['wfn'] = method_list[0]
stage['basis'] = basis_list[0]
if 'corl_scheme' in kwargs:
stage['scheme'] = kwargs.pop('corl_scheme')
stage['stage'] = "corl"
stage['treatment'] = "corl"
metadata.append(stage)
# "method/basis" syntax only allows for one delta correction
# via "method/basis+D:delta/basis". Maximum length of method_list is 2.
if len(method_list) == 2:
stage = {}
stage['wfn'] = method_list[1]
stage['basis'] = basis_list[1]
if 'delta_scheme' in kwargs:
stage['scheme'] = kwargs.pop('delta_scheme')
stage['stage'] = "delta1"
stage['treatment'] = "corl"
metadata.append(stage)
cbs_kwargs["cbs_metadata"] = metadata
ptype_value, wfn = cbs(func, label, **cbs_kwargs)
if return_wfn:
return (ptype_value, wfn)
else:
return ptype_value
