def test_manip_steep_augmentation(testdir):
full_testdir = os.path.join(steep_augmentation_test_data_dir, testdir)
basefile = testdir + '.nw.bz2'
base_data = readers.read_formatted_basis_file(
os.path.join(full_testdir, basefile))
for slevel, sprefix in [(0, ''), (1, 's'), (2, 'd')]:
# diffuse level 0 is augmented, 1 is doubly augmented
for dlevel, dprefix in [(0, ''), (1, 'd'), (2, 't')]:
if slevel == 0 and dlevel == 0:
continue
ref = testdir.replace('un-', 'un{}-'.format(sprefix)).replace(
'aug-', '{}aug-'.format(dprefix)) + '.nw.ref.bz2'
full_ref_path = os.path.join(full_testdir, ref)
ref_data = readers.read_formatted_basis_file(
full_ref_path, 'nwchem')
ref_data = manip.make_general(ref_data)
new_data = copy.deepcopy(base_data)
if slevel > 0:
new_data = manip.geometric_augmentation(new_data,
slevel,
steep=True)
if dlevel > 0:
new_data = manip.geometric_augmentation(new_data,
dlevel,
steep=False)
# The basis has to be sorted, since this also happens in the writers
new_data = sort.sort_basis(new_data)
new_data = manip.make_general(new_data)
assert curate.compare_basis(new_data, ref_data)
def test_reader_equivalent():
# Test the two dalton formats. These two files are the same basis in the two slightly-different
# format.
file1 = os.path.join(reader_test_data_dir, 'dalton', '6-31g.good.1.mol.bz2')
file2 = os.path.join(reader_test_data_dir, 'dalton', '6-31g.good.2.mol.bz2')
data1 = readers.read_formatted_basis_file(file1)
data2 = readers.read_formatted_basis_file(file2)
assert data1 == data2
def test_g94_scaling(tmp_path):
tmp_path = str(tmp_path) # Needed for python 3.5
filename1 = 'sbo4-dz-scaled.gbs.bz2'
filename2 = 'sbo4-dz-unscaled.gbs.bz2'
file1 = os.path.join(curate_test_data_dir, filename1)
file2 = os.path.join(curate_test_data_dir, filename2)
bs1 = readers.read_formatted_basis_file(file1)
bs2 = readers.read_formatted_basis_file(file2)
assert curate.compare_basis(bs1, bs2, rel_tol=1.0e-14)
def test_manip_dunningext(testdir):
full_testdir = os.path.join(dunningext_test_data_dir, testdir)
basefile = testdir + '.nw.bz2'
base_data = readers.read_formatted_basis_file(os.path.join(full_testdir, basefile))
for level, prefix in [(2, 'd-'), (3, 't-'), (4, 'q-')]:
ref = prefix + testdir + '.nw.ref.bz2'
full_ref_path = os.path.join(full_testdir, ref)
ref_data = readers.read_formatted_basis_file(full_ref_path, 'nwchem')
ref_data = manip.make_general(ref_data)
new_data = manip.extend_dunning_aug(base_data, level)
new_data = manip.make_general(new_data)
assert curate.compare_basis(new_data, ref_data)
def test_manip_remove_free(testdir):
full_testdir = os.path.join(rmfree_test_data_dir, testdir)
basefile = testdir + '.nw.bz2'
base_data = readers.read_formatted_basis_file(
os.path.join(full_testdir, basefile))
ref = 'min_' + testdir + '.nw.ref.bz2'
full_ref_path = os.path.join(full_testdir, ref)
ref_data = readers.read_formatted_basis_file(full_ref_path, 'nwchem')
ref_data = manip.make_general(ref_data)
new_data = manip.remove_free_primitives(base_data)
new_data = manip.make_general(new_data)
assert curate.compare_basis(new_data, ref_data)
def test_manip_diffuse_augmentation(testdir):
full_testdir = os.path.join(diffuse_augmentation_test_data_dir, testdir)
basefile = testdir + '.nw.bz2'
base_data = readers.read_formatted_basis_file(
os.path.join(full_testdir, basefile))
for level, prefix in [(1, 'd'), (2, 't'), (3, 'q')]:
ref = prefix + testdir + '.nw.ref.bz2'
full_ref_path = os.path.join(full_testdir, ref)
ref_data = readers.read_formatted_basis_file(full_ref_path, 'nwchem')
ref_data = manip.make_general(ref_data)
new_data = manip.geometric_augmentation(base_data, level, steep=False)
new_data = manip.make_general(new_data)
assert curate.compare_basis(new_data, ref_data)
def test_manip_truhlar(testdir):
full_testdir = os.path.join(truhlar_test_data_dir, testdir)
basefile = 'aug-' + testdir + '.nw.bz2'
base_data = readers.read_formatted_basis_file(os.path.join(full_testdir, basefile))
ref_files = os.listdir(full_testdir)
ref_files = [x for x in ref_files if x.endswith('.ref.bz2')]
# Made a mistake here once where reference files weren't being read
assert ref_files
for ref in ref_files:
month = ref.split('-')[0]
full_ref_path = os.path.join(full_testdir, ref)
ref_data = readers.read_formatted_basis_file(full_ref_path, 'nwchem')
ref_data = manip.make_general(ref_data)
new_data = manip.truhlar_calendarize(base_data, month, use_copy=True)
assert curate.compare_basis(new_data, ref_data)
def test_curate_roundtrip(tmp_path, basis, fmt):
tmp_path = str(tmp_path) # Needed for python 3.5
# Many formats have limitations on general contractions
if fmt == 'gaussian94':
uncontract_general = True
make_general = False
uncontract_spdf = 1
if fmt == 'turbomole':
uncontract_general = True
make_general = False
uncontract_spdf = 0
if fmt == 'nwchem':
uncontract_general = False
make_general = False
uncontract_spdf = 1
if fmt == 'cfour':
uncontract_general = False
make_general = True
uncontract_spdf = 0
bse_formatted = api.get_basis(basis, fmt=fmt)
bse_dict = api.get_basis(basis,
uncontract_general=uncontract_general,
make_general=make_general)
bse_dict = manip.uncontract_spdf(bse_dict, uncontract_spdf)
outfile_path = os.path.join(tmp_path, 'roundtrip.txt')
with open(outfile_path, 'w', encoding='utf-8') as outfile:
outfile.write(bse_formatted)
test_dict = readers.read_formatted_basis_file(outfile_path, fmt)
test_dict = sort.sort_basis(test_dict)
bse_dict = sort.sort_basis(bse_dict)
# Compare, ignoring metadata (not stored in most formats)
assert curate.compare_basis(bse_dict, test_dict, rel_tol=0.0)
def test_reader(file_rel_path):
file_path = os.path.join(reader_test_data_dir, file_rel_path)
is_bad = ".bad." in os.path.basename(file_path)
if is_bad:
# Read the first line of the file. This will contain the string
# that should match the exception
with bz2.open(file_path, 'rt', encoding='utf-8') as tf:
match = tf.readline()
# Get what we want to match as part of the exception
match = match[8:].strip()
with pytest.raises(Exception, match=match):
readers.read_formatted_basis_file(file_path)
else:
# Also validate the result (as both component and minimal)
readers.read_formatted_basis_file(file_path, validate=True, as_component=True)
readers.read_formatted_basis_file(file_path, validate=True, as_component=False)
def test_duplicate_fail(filename):
filepath = os.path.join(curate_test_data_dir, filename)
filedata = readers.read_formatted_basis_file(filepath, 'nwchem')
_test_duplicates(filedata, True)
