'''
Conversion from the Basis Set Exchange format to PySCF format
17 Nov 2021 Susi Lehtola
'''
try:
import basis_set_exchange
from basis_set_exchange import lut, manip, sort
except ImportError:
basis_set_exchange = None
def _orbital_basis(basis, make_general=False):
'''Extracts the orbital basis from the BSE format in PySCF format'''
r = {}
if make_general:
basis = manip.make_general(basis, False, use_copy=True)
basis = sort.sort_basis(basis, use_copy=False)
else:
basis = sort.sort_basis(basis, use_copy=True)
# Elements for which we have electron basis
electron_elements = [k for k, v in basis['elements'].items() if 'electron_shells' in v]
# List of references in the used basis
reference_list = []
# Electron Basis
if electron_elements:
for z in electron_elements:
data = basis['elements'][z]
sym = lut.element_sym_from_Z(z, True)
# List of shells
atom_shells = []
for shell in data['electron_shells']:
exponents = shell['exponents']
coefficients = shell['coefficients']
ncontr = len(coefficients)
nprim = len(exponents)
am = shell['angular_momentum']
if len(am) == len(coefficients): # SP basis
for l, c in zip(am, coefficients):
shell_data = [l]
for iprim in range(nprim):
row = [float(exponents[iprim]), float(c[iprim])]
shell_data.append(row)
atom_shells.append(shell_data)
else:
assert len(am) == 1
shell_data = [am[0]]
for iprim in range(nprim):
row = [float(coefficients[ic][iprim]) for ic in range(ncontr)]
row.insert(0, float(exponents[iprim]))
shell_data.append(row)
atom_shells.append(shell_data)
r[sym] = atom_shells
# Collect the literature references
if 'references' in data:
for ref in data['references']:
for key in ref['reference_keys']:
if key not in reference_list:
reference_list.append(key)
return r, reference_list
def _ecp_basis(basis):
'''Extracts the ECP from the BSE format in PySCF format'''
r = {}
basis = manip.make_general(basis, False, True)
basis = sort.sort_basis(basis, False)
# Elements for which we have ECP
ecp_elements = [k for k, v in basis['elements'].items() if 'ecp_potentials' in v]
# Electron Basis
if ecp_elements:
for z in ecp_elements:
data = basis['elements'][z]
sym = lut.element_sym_from_Z(z, True)
# Sort lowest->highest
ecp_list = sorted(data['ecp_potentials'], key=lambda x: x['angular_momentum'])
# List of ECP
atom_ecp = [data['ecp_electrons'], []]
for ir, pot in enumerate(ecp_list):
rexponents = pot['r_exponents']
gexponents = pot['gaussian_exponents']
coefficients = pot['coefficients']
am = pot['angular_momentum']
nprim = len(rexponents)
shell_data = [am[0], []]
# PySCF wants the data in order of rexp=0, 1, 2, ..
for rexpval in range(max(rexponents) + 1):
rcontr = []
for i in range(nprim):
if rexponents[i] == rexpval:
rcontr.append([float(gexponents[i]), float(coefficients[0][i])])
shell_data[1].append(rcontr)
atom_ecp[1].append(shell_data)
r[sym] = atom_ecp
return r
def _print_basis_information(basis):
name = basis['name']
version = basis['version']
revision_description = basis['revision_description']
revision_date = basis['revision_date']
print('{} basis set, version {}'.format(name, version))
print('Last revised on {}'.format(revision_date))
print('Revision description: {}'.format(revision_description))
[docs]
def get_basis(name, elements):
'''
Obtain a basis set
Args:
name : str
Name of the basis set, case insensitive.
elements : str, int or list
Returns:
A dict of basis set in PySCF internal basis format.
'''
basis = basis_set_exchange.api.get_basis(name, elements)
return _orbital_basis(basis)[0]
[docs]
def autoaux(name, elements):
'''
Create an auxiliary basis set for the given orbital basis set using
the Auto-Aux algorithm.
See also: G. L. Stoychev, A. A. Auer, and F. Neese
Automatic Generation of Auxiliary Basis Sets
J. Chem. Theory Comput. 13, 554 (2017)
http://doi.org/10.1021/acs.jctc.6b01041
'''
obs = basis_set_exchange.api.get_basis(name, elements)
auxbs = manip.autoaux_basis(obs)
return _orbital_basis(auxbs)[0]
[docs]
def autoabs(name, elements):
'''
Create a Coulomb fitting basis set for the given orbital basis set.
See also:
R. Yang, A. P. Rendell, and M. J. Frisch
Automatically generated Coulomb fitting basis sets: Design and accuracy for systems containing H to Kr
J. Chem. Phys. 127, 074102 (2007)
http://doi.org/10.1063/1.2752807
'''
obs = basis_set_exchange.api.get_basis(name, elements)
auxbs = manip.autoabs_basis(obs)
return _orbital_basis(auxbs)[0]
if __name__ == '__main__':
from basis_set_exchange import api, references
# Get reference data
reference_data = api.get_reference_data()
#print(references)
o631gbas = api.get_basis('6-31g', elements='O')
#print('O 6-31G basis, BSE format\n{}'.format(o631gbas))
_print_basis_information(o631gbas)
o631gorb, o631gref = _orbital_basis(o631gbas)
print('O 6-31G orbital basis, PySCF format\n{}'.format(o631gorb))
print('Literature references')
for ref in o631gref:
print(references.reference_text(ref, reference_data[ref]))
print('')
nalanl2dzbas = api.get_basis('lanl2dz', elements='Na')
#print('Na LANL2DZ basis, BSE format\n{}'.format(nalanl2dzbas))
_print_basis_information(nalanl2dzbas)
nalanl2dzorb, nalanl2dzref = _orbital_basis(nalanl2dzbas)
print('Na LANL2DZ orbital basis, PySCF format\n{}'.format(nalanl2dzorb))
nalanl2dzecp = _ecp_basis(nalanl2dzbas)
print('Na LANL2DZ ECP basis, PySCF format\n{}'.format(nalanl2dzecp))
print('Literature references')
for ref in nalanl2dzref:
print(references.reference_text(ref, reference_data[ref]))
print('')
