def test_get_references_1(basis_name, fmt):
""" Tests getting references for all basis sets
Also test getting references for a random selection of elements
"""
this_metadata = bs_metadata[basis_name]
for ver in this_metadata['versions'].keys():
bse.get_references(basis_name, fmt=fmt, version=ver)
avail_elements = this_metadata['versions'][ver]['elements']
nelements = random.randint(1, len(avail_elements))
selected_elements = random.sample(avail_elements, nelements)
bse.get_references(basis_name, elements=selected_elements, fmt=fmt, version=ver)
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 writebs(md, bas_name, summary_file, get_aux=0):
md_bas_name = bas_name.lower()
md_bas_name = md_bas_name.replace("*", "_st_")
md_bas_name = md_bas_name.replace("/", "_sl_")
print(' md_bas_name ' + md_bas_name + "\n")
print(' bas_name ' + bas_name + "\n")
version_bs = md[md_bas_name]['latest_version']
elements_list = md[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(" ", "_")
#replace forward slash with underscore
file_name = file_name.replace("/", "_")
#lowercase
file_name = file_name.lower()
if get_aux == 1:
file_name = file_name + "-autoaux"
print(' file name is ' + file_name + "\n")
output_file = open(file_name, 'w')
output_file.write('# BSE Version ' + bse.version() + '\n')
output_file.write('# Data downloaded on ' + today + '\n')
if get_aux == 0:
output_file.write('# ' + bas_name + ' version number ' + version_bs +
'\n')
output_file.write('# Description: ' + md[md_bas_name]['description'] +
'\n')
output_file.write('# Role: ' + md[md_bas_name]['role'] + '\n')
output_file.write(
'# ' +
bse.get_references(bas_name, fmt='txt').replace('\n', '\n# '))
output_file.write('# \n')
elif get_aux == 1:
output_file.write('# ' + bas_name + ' version number ' + version_bs +
' AutoAux \n')
output_file.write('# Role: JK Fitting \n')
output_file.write(
'# Stoychev GL, Auer AA, Neese F. \n# Automatic Generation of Auxiliary Basis Sets.\n# J Chem Theory Comput. 2017 Feb 14;13(2):554-562.\n# doi: 10.1021/acs.jctc.6b01041.\n'
)
output_file.write('# \n')
n_elements = 0
for element in elements_list:
n_elements = n_elements + 1
if get_aux == 1:
summary_file.write('Basis set \"' + bas_name +
'-autoaux\" (number of atoms ' + str(n_elements) +
')\n')
else:
summary_file.write('Basis set \"' + bas_name + '\" (number of atoms ' +
str(n_elements) + ')\n')
for element in elements_list:
#element='h'
try:
bs_str = bse.get_basis(bas_name,
header=False,
elements=element,
fmt='nwchem',
optimize_general=True,
uncontract_general=True,
get_aux=get_aux)
except:
# print("failed for"+element)
pass
else:
bs_str = bs_str.replace("BASIS", "basis")
bs_str = bs_str.replace("END", "end")
bs_str = bs_str.replace("PRINT", "")
element_str = bse.misc.compact_elements([element])
if get_aux == 1:
bs_str = bs_str.replace(
"ao basis", element_str + "_" + bas_name + "-autoaux")
else:
bs_str = bs_str.replace("ao basis",
element_str + "_" + bas_name)
#ECP
bs_str = bs_str.replace(
"ECP", "ecp \"" + element_str + "_" + bas_name + "\"")
output_file.write(bs_str)
#
print(bas_name + " " + element_str)
return
#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")
output_file = open(file_name, 'w')
output_file.write('# BSE Version ' + bse.version() + '\n')
output_file.write('# Data downloaded at ' + today + '\n')
output_file.write('# ' + bas_name + ' version number ' + version_bs + '\n')
output_file.write('# Description: ' + md[bas_name]['description'] + '\n')
output_file.write('# Role: ' + md[bas_name]['role'] + '\n')
output_file.write(
'# ' + bse.get_references(bas_name, fmt='txt').replace('\n', '\n# '))
output_file.write('# \n')
for element in elements_list:
#element='h'
try:
bs_str = bse.get_basis(bas_name,
header=False,
elements=element,
fmt='nwchem',
optimize_general=True)
except:
# print("failed for"+element)
pass
else:
bs_str = bs_str.replace("BASIS", "basis")
bs_str = bs_str.replace("END", "end")
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(" ","_")
#replace forward slash with underscore
file_name = file_name.replace("/","_")
print(' file name is '+file_name+"\n")
output_file = open(file_name,'w')
output_file.write('# BSE Version '+bse.version()+'\n')
output_file.write('# Data downloaded at '+today+'\n')
output_file.write('# '+bas_name+' version number '+version_bs+'\n')
output_file.write('# Description: '+md[bas_name]['description']+'\n')
output_file.write('# Role: '+md[bas_name]['role']+'\n')
output_file.write('# '+bse.get_references(bas_name,fmt='txt').replace('\n','\n# '))
output_file.write('# \n')
for element in elements_list:
#element='h'
try:
bs_str=bse.get_basis(bas_name, header=False, elements=element, fmt='nwchem', optimize_general=True, uncontract_general=True)
except:
# print("failed for"+element)
pass
else:
bs_str=bs_str.replace("BASIS","basis")
bs_str=bs_str.replace("END","end")
bs_str=bs_str.replace("PRINT","")
element_str=bse.misc.compact_elements([element])
bs_str=bs_str.replace("ao basis",element_str+"_"+bas_name)
#ECP