def test_add_basis(tmp_path):
tmp_path = str(tmp_path) # Needed for python 3.5
for sf, refs in _source_data.items():
sf_path = os.path.join(auth_data_dir, sf)
name = sf.split('.')[0]
curate.add_basis(sf_path, tmp_path, 'test_subdir', 'test_' + name,
'test_basis_' + name, 'test_family', 'orbital',
'Test Basis Description: ' + name, '1',
'Test Basis Revision Description', 'Test Source',
refs)
md = api.get_metadata(tmp_path)
assert len(md) == len(_source_data)
# Re-read
for sf in _source_data.keys():
name = name = sf.split('.')[0]
name = 'test_basis_' + name
bse_dict = api.get_basis(name, data_dir=tmp_path)
assert bse_dict['family'] == 'test_family'
# Compare against the file we created from
sf_path = os.path.join(auth_data_dir, sf)
assert curate.compare_basis_against_file(name,
sf_path,
data_dir=tmp_path)
# Check that all the files exist and contain the right elements
for fpath, elements in _expected_files.items():
fpath = os.path.join(tmp_path, fpath)
assert os.path.isfile(fpath)
fdata = fileio.read_json_basis(fpath)
expect_elements = set(misc.expand_elements(elements, True))
assert set(fdata['elements'].keys()) == expect_elements
# Validate the new data dir
validator.validate_data_dir(tmp_path)
#!/usr/bin/env python3
from basis_set_exchange import curate
if False:
curate.add_basis(
bs_file='tzp-zora.gbs',
data_dir='/home/work/basis_set_exchange/basis_set_exchange/data',
subdir='jorge',
file_base='TZP-ZORA',
name='TZP-ZORA',
family='jorge',
role='orbital',
description=
'TZP-ZORA, all-electron triple-zeta basis for calculations with the ZORA approach',
version='1',
revision_description='Data from supporting information',
data_source='Data from supporting information',
refs='canalneto2021a',
file_fmt=None)
curate.add_basis(
bs_file='atzp-zora.gbs',
data_dir='/home/work/basis_set_exchange/basis_set_exchange/data',
subdir='jorge',
file_base='ATZP-ZORA',
name='ATZP-ZORA',
family='jorge',
role='orbital',
description=
'ATZP-ZORA, augmented all-electron triple-zeta basis for calculations with the ZORA approach',
version='1',
#!/usr/bin/env python3
from basis_set_exchange import curate
curate.add_basis(
bs_file='x2c-SVPall-s.tm.bz2',
data_dir=
'/home/ben/programming/bse_ng/basis_set_exchange/basis_set_exchange/data',
subdir='ahlrichs_x2c',
file_base='x2c-SVPall-s',
name='x2c-SVPall-s',
family='ahlrichs_x2c',
role='orbital',
description='All-electron relativistic split-valence for NMR shielding',
version='1',
revision_description='Data from Supporting info',
data_source='Supporting info of franzke2019a',
refs='franzke2019a',
file_fmt=None)
curate.add_basis(
bs_file='x2c-TZVPall-s.tm.bz2',
data_dir=
'/home/ben/programming/bse_ng/basis_set_exchange/basis_set_exchange/data',
subdir='ahlrichs_x2c',
file_base='x2c-TZVPall-s',
name='x2c-TZVPall-s',
family='ahlrichs_x2c',
role='orbital',
description='All-electron relativistic triple-zeta for NMR shielding',
version='1',
#!/usr/bin/env python3
from basis_set_exchange import curate
for basis in ['ano-r', 'ano-r0', 'ano-r1', 'ano-r2', 'ano-r3']:
print('Parsing {}'.format(basis))
curate.add_basis(
bs_file='{}.2.molcas'.format(basis),
data_dir='/home/work/basis_set_exchange/basis_set_exchange/data',
subdir='ano',
file_base=basis.upper(),
name=basis.upper(),
family='ano',
role='orbital',
description=basis.upper(),
version='2',
revision_description='Data from supporting information of erratum',
data_source='Data from supporting information of erratum',
refs=['zobel2020a', 'zobel2021a'],
file_fmt=None)
#!/usr/bin/env python3
from basis_set_exchange import curate
curate.add_basis(
bs_file='DFO-1.gbs',
data_dir=
'/home/ben/programming/bse_ng/basis_set_exchange/basis_set_exchange/data',
subdir='dfo',
file_base='DFO-1',
name='DFO-1',
family='dfo',
role='orbital',
description=
'Optimized gaussian basis set for Density-functional calculations',
version='1',
revision_description='Data from SI of paper',
data_source='Data from SI of paper',
refs='porezag1999a',
file_fmt=None)
curate.add_basis(
bs_file='DFO-2.gbs',
data_dir=
'/home/ben/programming/bse_ng/basis_set_exchange/basis_set_exchange/data',
subdir='dfo',
file_base='DFO-2',
name='DFO-2',
family='dfo',
role='orbital',
description=
#!/usr/bin/env python3
from basis_set_exchange import curate
if False:
curate.add_basis(
bs_file='minix.tm.bz2',
data_dir='/home/work/basis_set_exchange/basis_set_exchange/data',
subdir='grimme',
file_base='minix',
name='MINIX',
family='jensen',
role='orbital',
description='Small basis set used in HF-3c method',
version='1',
revision_description='Data from Stefan Grimme',
data_source='Data by email from Stefan Grimme',
refs='Sure2013a',
file_fmt=None)
curate.add_basis(
bs_file='def2-mTZVP.tm',
data_dir='/home/work/basis_set_exchange/basis_set_exchange/data',
subdir='grimme',
file_base='def2-mTZVP',
name='def2-mTZVP',
family='grimme',
role='orbital',
description='Small basis set used in B97-3c method',
version='1',
revision_description='Data from Sebastian Ehlert',
data_source='Data from Sebastian Ehlert',
#!/usr/bin/env python3
from basis_set_exchange import curate
curate.add_basis(
bs_file='SBO4-DZ(d)-3G.gbs',
data_dir=
'/home/ben/programming/bse_ng/basis_set_exchange/basis_set_exchange/data',
subdir='zorilla',
file_base='SBO4-DZ(d)-3G',
name='SBO4-DZ(d)-3G',
family='zorilla',
role='orbital',
description=
'SBO4-DZ(d)-3G Double-zeta expansion of simplified box orbitals',
version='1',
revision_description='Data from D. Zorilla',
data_source='Data from D. Zorilla',
refs='zorilla2019a',
file_fmt=None)
curate.add_basis(
bs_file='SBO4-SZ-3G.gbs',
data_dir=
'/home/ben/programming/bse_ng/basis_set_exchange/basis_set_exchange/data',
subdir='zorilla',
file_base='SBO4-SZ-3G',
name='SBO4-SZ-3G',
family='zorilla',
role='orbital',
description='SBO4-SZ-3G Single-zeta expansion of simplified box orbitals',
#!/usr/bin/env python3
from basis_set_exchange import curate
basis_list = [
'cc-pV5+dZ-X2C', 'cc-pV5Z-X2C', 'cc-pV6Z-X2C', 'cc-pVD+dZ-X2C',
'cc-pVDZ-X2C', 'cc-pVQ+dZ-X2C', 'cc-pVQZ-X2C', 'cc-pVT+dZ-X2C',
'cc-pVTZ-X2C'
]
for basis in basis_list:
curate.add_basis(
bs_file=basis + '.gbasis',
data_dir=
'/home/ben/programming/bse_ng/basis_set_exchange/basis_set_exchange/data',
subdir='dunning_x2c',
file_base='NEW_' + basis,
name='NEW_' + basis,
family='dunning_x2c',
role='orbital',
description=basis,
version=1,
revision_description='Data from ccRepo',
data_source='ccRepo/Grant Hill',
refs='peterson2018a',
file_fmt=None)
#!/usr/bin/env python3
from basis_set_exchange import curate
curate.add_basis(
bs_file='ANO-VT-QZ.2.genbas.bz2',
data_dir='/home/work/basis_set_exchange/basis_set_exchange/data',
subdir='ano_claudino',
file_base='ANO-VT-QZ',
name='ANO-VT-QZ',
family='ano_claudino',
role='orbital',
description=
'ANO-VT-QZ (Atomic Natural Orbital - Virial Theorem - Quadruple Zeta)',
version=2,
revision_description=
'Retranslated from ACES format; original Gaussian\'94 data had negative exponents',
data_source='Data from D. Claudino',
refs=['claudino2016a', 'claudino2016b'],
file_fmt='genbas')
#!/usr/bin/env python3
from basis_set_exchange import curate
curate.add_basis(bs_file='6-311xxG(d,p).gbs',
data_dir='/home/ben/programming/bse_ng/basis_set_exchange/basis_set_exchange/data',
subdir='zorilla',
file_base='6-311xxG(d,p)',
name='6-311xxG(d,p)',
family='zorilla',
role='orbital',
description='6-311xxG(d,p) basis set',
version='1',
revision_description='Data from D. Zorilla',
data_source='Data from D. Zorilla',
refs='sanchezmarquez2020a',
file_fmt=None
)
'ahgbs-9.gbs': 'AHGBS-9',
'ahgbsp1-9.gbs': 'AHGBSP1-9',
'ahgbsp2-9.gbs': 'AHGBSP2-9',
'ahgbsp3-9.gbs': 'AHGBSP3-9'
}
# Lehtola2020a
for basis_file, name in hgbs_sets.items():
curate.add_basis(
bs_file=basis_file,
data_dir=
'/home/ben/programming/bse_ng/basis_set_exchange/basis_set_exchange/data',
subdir='lehtola_hgbs',
file_base=name,
name=name,
family='lehtola_hgbs',
role='orbital',
description=name,
version=1,
revision_description='Data from S. Lehtola',
data_source='Direct from S. Lehtola',
refs='lehtola2020a',
file_fmt=None)
# Lehtola2020b
for basis_file, name in guess_sets.items():
curate.add_basis(
bs_file=basis_file,
data_dir=
'/home/ben/programming/bse_ng/basis_set_exchange/basis_set_exchange/data',
subdir='lehtola_sap',
# name = str(n) + 'ZaPa-NR-CV'
#
# print("Adding ", name)
# curate.add_basis(name.lower() + '.gbs.bz2',
# '/home/ben/programming/bse_ng/basis_set_exchange/basis_set_exchange/data',
# 'ranasinghe',
# name,
# name,
# 'ranasinghe',
# 'orbital',
# 'Ranasinghe-Petersson 2ZaPa-NR-CV basis set',
# '1',
# 'Data from Supplemental Information of publications',
# 'Data from Supplemental Information of publications',
# 'ranasinghe2015a'
# )
#
for n in range(2, 8):
name = str(n) + 'ZaPa-NR'
print("Adding ", name)
curate.add_basis(
name.lower() + '.gbs.bz2',
'/home/ben/programming/bse_ng/basis_set_exchange/basis_set_exchange/data',
'ranasinghe', name, name, 'ranasinghe', 'orbital',
'Ranasinghe-Petersson 2ZaPa-NR basis set', '1',
'Data from Supplemental Information of publications',
'Data from Supplemental Information of publications',
'ranasinghe2013a')
#!/usr/bin/env python3
from basis_set_exchange import curate
for b in [
'cc-pVDZ-F12_OPTRIplus', 'cc-pVTZ-F12_OPTRIplus',
'cc-pVQZ-F12_OPTRIplus'
]:
name = b.replace('_', '-').replace('plus', '+')
curate.add_basis(
bs_file='parsed/{}.gbasis'.format(b),
data_dir='/home/work/basis_set_exchange/basis_set_exchange/data',
subdir='dunning_fit',
file_base=name,
name=name,
family='dunning_fit',
role='optri',
description=name,
version=1,
revision_description="Data from Grant Hill's ccRepo",
data_source="Data from Grant Hill's ccRepo",
refs=['shaw2017a'])
#!/usr/bin/env python3
from basis_set_exchange import curate
for x in [2, 3, 4]:
curate.add_basis(
'acv{}z-J.c4bas.bz2'.format(x),
'/home/ben/programming/bse_ng/basis_set_exchange/basis_set_exchange/data',
'acvXz-J', 'acv{}z-J'.format(x), 'acv{}z-J'.format(x), 'acvXz-J',
'orbital',
'acv{}z-J basis for indirect nuclear spin-spin coupling'.format(x),
'1', 'Data from Supplemental Information of publications',
'Data from Supplemental Information of publications', 'rusakov2019a')
#!/usr/bin/env python3
from basis_set_exchange import curate
curate.add_basis(
bs_file='ANO-R.molcas',
data_dir=
'/home/ben/programming/bse_ng/basis_set_exchange/basis_set_exchange/data',
subdir='ano',
file_base='ANO-R',
name='ANO-R',
family='ano',
role='orbital',
description='ANO-R',
version='1',
revision_description='Data from Supporting Information',
data_source='Data from Supporting Information',
refs='zobel2019a',
file_fmt=None)
#!/usr/bin/env python3
from basis_set_exchange import curate
curate.add_basis(
bs_file='',
data_dir=
'/home/ben/programming/bse_ng/basis_set_exchange/basis_set_exchange/data',
subdir='',
file_base='',
name='',
family='',
role='',
description='',
version='',
revision_description='',
data_source='',
refs='',
file_fmt=None)
#!/usr/bin/env python3
from basis_set_exchange import curate
for aug in ["", "aug-"]:
for cv in ["", "wC"]:
for v in ['D', 'T', 'Q', '5']:
basis = '{}seg-cc-p{}V{}Z-PP'.format(aug, cv, v)
print('Processing {}'.format(basis))
curate.add_basis(
bs_file='{}.nw'.format(basis.lower()),
data_dir=
'/home/work/basis_set_exchange/basis_set_exchange/data',
subdir='dunning',
file_base=basis,
name=basis,
family='dunning',
role='orbital',
description=basis,
version=1,
revision_description='Data from George Schoendorff',
data_source='Data from George Schoendorff',
refs='schoendorff2022a',
file_fmt=None)
polarization_name = ['', 'p1', 'p2', 'p3']
augmentation_type = ['', ', with more diffuse functions']
aug_name = ['', 'a']
for tol in [5, 7]:
for pol in range(len(polarization_type)):
for aug in [False, True]:
name = '{}hgbs{}-{}'.format(aug_name[aug], polarization_name[pol],
tol)
basis_file = '{}.gbs'.format(name)
description = 'Hydrogenic Gaussian basis set formed at tolerance 10^{{-{}}} {}{}'.format(
tol, polarization_type[pol], augmentation_type[aug])
print(f'{name=}')
print(f'{basis_file=}')
print(f'{description=}')
curate.add_basis(
bs_file=basis_file,
data_dir=
'/home/work/basis_set_exchange/basis_set_exchange/data',
subdir='lehtola_hgbs',
file_base=name.upper(),
name=name.upper(),
family='lehtola_hgbs',
role='orbital',
description=description,
version=1,
revision_description='Data from S. Lehtola',
data_source='Direct from S. Lehtola',
refs='lehtola2020a',
file_fmt=None)
#!/usr/bin/env python3
from basis_set_exchange import curate
if False:
for basis in ['pob-DZVP-rev2', 'pob-TZVP-rev2']:
print('Adding {}'.format(basis))
curate.add_basis(bs_file='{}.crystal.bz2'.format(basis),
data_dir='/home/work/basis_set_exchange/basis_set_exchange/data',
subdir='pob',
file_base=basis,
name=basis,
family='pob',
role='orbital',
description=basis,
version=1,
revision_description='Data from Bredow\'s web site',
data_source='Data from Bredow\'s web site',
refs='Oliveira2019b',
file_fmt=None
)
curate.add_basis(bs_file='pob-TZVP.crystal.bz2',
data_dir='/home/work/basis_set_exchange/basis_set_exchange/data',
subdir='pob',
file_base='pob-TZVP',
name='pob-TZVP',
family='pob',
role='orbital',
description='pob-TZVP',
version=1,
for aug in [False, True]:
# for nval in range(2,6):
for nval in range(5, 6):
# Input file name
infile = 'ccX{:02d}'.format(nval - 1)
# Basis set name is
basname = 'ccX-{}Z'.format(valence[nval - 2])
if aug:
infile = 'a' + infile
basname = 'aug-' + basname
# Description
description = '{} set for calculation of core excitations by the correlated wave function linear response and equation-of-motion methods'.format(
'Augmented basis' if aug else 'Basis')
print('Parsing {} -> {}'.format(infile, basname))
curate.add_basis(
bs_file=infile,
data_dir='/home/work/basis_set_exchange/basis_set_exchange/data',
subdir='jensen',
file_base=basname,
name=basname,
family='jensen',
role='orbital',
description=description,
version='1',
revision_description='Data from Frank Jensen',
data_source='Data directly from Frank Jensen',
refs='ambroise2021a',
file_fmt='gaussian94')
#!/usr/bin/env python3
from basis_set_exchange import curate
for basis in [
'cc-pVDZ-F12rev2', 'cc-pVTZ-F12rev2', 'cc-pVQZ-F12rev2',
'cc-pV5Z-F12rev2'
]:
print(basis)
curate.add_basis(
bs_file=basis + '.nw.bz2',
data_dir=
'/home/ben/programming/bse_ng/basis_set_exchange/basis_set_exchange/data',
subdir='dunning_f12',
file_base=basis,
name=basis,
family='dunning_f12',
role='orbital',
description=basis,
version='1',
revision_description='Data from K. Peterson',
data_source='K. Peterson Website',
refs='peterson2015a',
file_fmt=None)
#!/usr/bin/env python3
from basis_set_exchange import curate
for val in ['D', 'T', 'Q', '5']:
for aug in ['', 'saug-', 'aug-']:
basis = '{}ano-pV{}Z'.format(aug, val)
print('Parsing {}'.format(basis))
curate.add_basis(
bs_file='{}.bas'.format(basis),
data_dir='/home/work/basis_set_exchange/basis_set_exchange/data',
subdir='ano',
file_base=basis,
name=basis,
family='ano',
role='orbital',
description=basis,
version='1',
revision_description='Data from supporting information',
data_source='Data from supporting information',
refs=['neese2011a'],
file_fmt='gamess_us')
description += ' for one-component calculations'
else:
description += ' for two-component calculations'
if nmr:
basname += '-s'
description += ' of NMR shielding'
curate.add_basis(
bs_file='{}.tm.bz2'.format(basname),
data_dir=
'/home/work/basis_set_exchange/basis_set_exchange/data',
subdir='ahlrichs_x2c',
file_base=basname,
name=basname,
family='ahlrichs_x2c',
role='orbital',
description=description,
version='1',
revision_description='Data from Supporting info',
data_source='Supporting info of franzke2020a',
refs='franzke2020a',
file_fmt=None)
curate.add_basis(
bs_file='x2c-JFIT.tm.bz2',
data_dir='/home/work/basis_set_exchange/basis_set_exchange/data',
subdir='ahlrichs_x2c',
file_base='x2c-JFIT',
name='x2c-JFIT',
family='ahlrichs_fit',
from basis_set_exchange import curate
print(curate)
flist = {
'aug-pcH-1': 'aug-pcH-1',
'aug-pcH-2': 'aug-pcH-2',
'aug-pcH-3': 'aug-pcH-3',
'aug-pcH-4': 'aug-pcH-4',
'pcH-1': 'pcH-1',
'pcH-2': 'pcH-2',
'pcH-3': 'pcH-3',
'pcH-4': 'pcH-4',
}
for k, v in flist.items():
curate.add_basis(
bs_file=k,
data_dir=
'/home/ben/programming/bse_ng/basis_set_exchange/basis_set_exchange/data',
subdir='jensen',
file_base=k,
name=k,
family='jensen',
role='orbital',
description=v,
version='1',
revision_description='Data from Frank Jensen',
data_source='Data from Frank Jensen',
refs='jakobsen2019a',
file_fmt='dalton')
#!/usr/bin/env python3
from basis_set_exchange import curate
for val in ['1', '2']:
basis='pecJ-{}'.format(val)
print('Parsing {}'.format(basis))
curate.add_basis(bs_file='{}.1.cfour'.format(basis),
data_dir='/home/work/basis_set_exchange/basis_set_exchange/data',
subdir='pec',
file_base=basis,
name=basis,
family='pec',
role='orbital',
description=basis,
version='1',
revision_description='Data from supporting information',
data_source='Data from supporting information',
refs=['rusakov2021a'],
file_fmt='genbas'
)
