def _run_test_bundles(tmp_path, fmt, reffmt, ext, data_dir):
'''Test functionality related to creating archive of basis set'''
tmp_path = str(tmp_path) # Needed for python 3.5
bs_ext = bse.writers.get_format_extension(fmt)
ref_ext = bse.refconverters.get_format_extension(reffmt)
filename = "bundletest_" + fmt + "_" + reffmt + ext
filepath = os.path.join(tmp_path, filename)
bse.create_bundle(filepath, fmt, reffmt, None, data_dir)
extract_dir = "extract_" + filename
extract_path = os.path.join(tmp_path, extract_dir)
_extract_all(filepath, extract_path)
# Keep track of all the basis sets we have found
# Start with all found in the data dir, and remove
# each time we process one
all_bs = []
for k, v in bse.get_metadata(data_dir).items():
for ver in v['versions'].keys():
all_bs.append((k, ver))
all_ref = all_bs.copy()
for root, dirs, files in os.walk(extract_path):
for basename in files:
if basename == 'README.txt':
continue
fpath = os.path.join(root, basename)
name, ver = basename.split('.')[:2]
tr_name = bse.misc.basis_name_from_filename(name)
if basename.endswith('.ref' + ref_ext):
compare_data = bse.get_references(tr_name,
fmt=reffmt,
version=ver,
data_dir=data_dir)
all_ref.remove((name, ver))
elif basename.endswith(bs_ext):
compare_data = bse.get_basis(name,
fmt=fmt,
version=ver,
data_dir=data_dir)
all_bs.remove((name, ver))
elif basename.endswith('.family_notes'):
compare_data = bse.get_family_notes(name, data_dir)
elif basename.endswith('.notes'):
compare_data = bse.get_basis_notes(name, data_dir)
else:
raise RuntimeError("Unknown file found: " + fpath)
with open(fpath, 'r', encoding='utf-8') as ftmp:
assert compare_data == ftmp.read()
assert len(all_bs) == 0
assert len(all_ref) == 0
def main():
d = {}
for basisset_name, meta in basis_set_exchange.get_metadata().items():
basisset = {}
elements = basis_set_exchange.get_basis(
basisset_name)['basis_set_elements']
try:
for Z in meta['versions'][meta['latest_version']]['elements']:
element = basis_set_exchange.lut.element_data_from_Z(
Z)[0].capitalize()
shells = elements[Z].get('element_electron_shells')
if shells is None:
raise ValueError('no shells: {}/{}'.format(
basisset_name, element))
basisset[element] = number_of_functions(shells)
except ValueError as e:
print(e, file=sys.stderr)
else:
d[basisset_name] = basisset
json.dump(d, sys.stdout)
'''
Some data common to all tests
'''
import os
import basis_set_exchange as bse
# The directory containing this file
_my_dir = os.path.dirname(os.path.abspath(__file__))
# Use random for getting sets of elements
rand_seed = 39466 # from random.org
# Load all the metadata once
data_dir = bse.api._default_data_dir
bs_metadata = bse.get_metadata()
bs_names = list(bs_metadata.keys())
bs_read_formats = list(bse.get_reader_formats().keys())
bs_write_formats = list(bse.get_writer_formats()) + [None]
bs_write_formats_ecp = list(bse.get_writer_formats(['scalar_ecp'
]).keys()) + [None]
bs_write_formats_noecp = list(
set(bs_write_formats) - set(bs_write_formats_ecp))
ref_formats = list(bse.get_reference_formats().keys()) + [None]
all_families = bse.get_families()
all_roles = bse.get_roles()
true_false = [True, False]
# All basis names/versions combinations
bs_names_vers = []
for k, v in bs_metadata.items():
def list_basis_sets() -> Tuple[str, str]:
return sorted((v['display_name'], v['display_name']) for k, v in bse.get_metadata().items())
#!/usr/bin/env python3
# This script determines what basis sets are missing authoritative sources
# that should be placed in this directory
import os
from basis_set_exchange import get_metadata, misc
my_dir = os.path.dirname(os.path.abspath(__file__))
auth_sources = [x for x in os.listdir(my_dir) if x.endswith('.bz2')]
md = get_metadata()
found_ver = {}
# Start with everything in the metadata, removing what we find
# in this directory
missing = {k: list(v['versions'].keys()) for k, v in md.items()}
for s in auth_sources:
bsname, ver, _, _ = s.split('.')
if not bsname in missing:
raise RuntimeError(
"Source {} does not correspond to a basis set in the library".
format(bsname))
if not ver in missing[bsname]:
raise RuntimeError(
"Source {} version {} does not correspond to a basis set version in the library"
.format(bsname, ver))
# to use, set the env. variable NWCHEM_BASIS_LIBRARY=$NWCHEM_TOP/src/basis/libraries.bse/
# Requires the installation of the python env. from
# https://github.com/MolSSI-BSE/basis_set_exchange
# See https://molssi-bse.github.io/basis_set_exchange/
#
# names changed
# def2-universal-jfit was weigend_coulomb_fitting
# dgauss-a1-dftjfit was dgauss_a1_dft_coulomb_fitting
# dgauss-a2-dftjfit was dgauss_a2_dft_coulomb_fitting
#
import basis_set_exchange as bse
from datetime import datetime
today = datetime.now().isoformat(timespec='minutes')
print(today)
all_bs = bse.get_all_basis_names()
md = bse.get_metadata()
for bas_name in all_bs:
#get version and list of elements
version_bs = md[bas_name]['latest_version']
elements_list = md[bas_name]['versions'][version_bs]['elements']
#open file
# get rid of asterisks
file_name = bas_name.replace("*", "s")
#get rid of parenthesis
file_name = file_name.replace("(", "")
file_name = file_name.replace(")", "")
#replace commas with underscore
file_name = file_name.replace(",", "_")
#replace whitespace with underscore
file_name = file_name.replace(" ", "_")
print(' file name is ' + file_name + "\n")
