def create_dict_CGFs(path_hdf5: dict,
basis_name: str,
mol: List,
package_name='cp2k',
package_config: Dict = None):
"""
Try to read the basis from the HDF5 otherwise read it from a file and store
it in the HDF5 file. Finally, it reads the basis Set from HDF5 and
calculate the CGF for each atom.
:param path_hdf5: Path to the HDF5 file that contains the
numerical results.
type path_hdf5: String
:param basisname: Name of the Gaussian basis set.
:type basisname: String
:param xyz: List of Atoms.
:type xyz: [nac.common.AtomXYZ]
"""
functions = {'cp2k': cp2k2hdf5, 'turbomole': turbomole2hdf5}
basis_location = join(package_name, 'basis')
with h5py.File(path_hdf5) as f5:
if basis_location not in f5:
# Search Path to the file containing the basis set
pathBasis = package_config["basis"]
keyBasis = InputKey("basis", [pathBasis])
# Store the basis sets
functions[package_name](f5, [keyBasis])
# CGFs in Cartesian coordinates
cgfs = create_normalized_CGFs(f5, basis_name, package_name, mol)
return cgfs
def create_dict_CGFs(f5, packageHDF5, pathBasis, basisname, packageName, xyz):
"""
If the Cp2k Basis are already stored in the hdf5 file continue,
otherwise read and store them in the hdf5 file
"""
keyBasis = InputKey("basis", [pathBasis])
packageHDF5(f5, [keyBasis]) # Store the basis sets
return create_normalized_CGFs(f5, basisname, packageName, xyz)
def saveBasis(f5, path_basis, softName):
keyBasis = InputKey("basis", [path_basis])
if softName == 'cp2k':
cp2k2hdf5(f5, [keyBasis])
elif softName == 'turbomole':
turbomole2hdf5(f5, [keyBasis])
def test_store_basisSet():
"""
Check if the turbomole basis set are read
and store in HDF5 format.
"""
keyBasis = InputKey("basis", [path_basis])
with h5py.File(path_hdf5) as f5:
turbomole2hdf5(f5, [keyBasis])
if not f5["turbomole/basis"]:
assert False
def save_basis_to_hdf5(config: dict, package_name: str = "cp2k") -> None:
"""
Store the specification of the basis set in the HDF5 to compute the integrals
"""
basis_location = join(package_name, 'basis')
with h5py.File(config["path_hdf5"]) as f5:
if basis_location not in f5:
# Search Path to the file containing the basis set
path_basis = pkg_resources.resource_filename(
"nac", "basis/BASIS_MOLOPT")
keyBasis = InputKey("basis", [path_basis])
cp2k2hdf5(f5, [keyBasis])
def dump_MOs_coeff(handle_hdf5, packageHDF5, path_MO, pathEs, pathCs,
nOrbitals):
"""
MO coefficients are stored in row-major order, they must be transposed
to get the standard MO matrix.
:param files: Files to calculate the MO coefficients
:type files: Namedtuple (fileXYZ,fileInput,fileOutput)
:param job: Output File
:type job: String
"""
key = InputKey('orbitals', [path_MO, nOrbitals, pathEs, pathCs])
packageHDF5(handle_hdf5, [key])
return pathEs, pathCs
def dump_MOs_coeff(handle_hdf5, path_es, path_css, number_of_orbs,
number_of_orb_funs):
"""
MO coefficients are stored in row-major order, they must be transposed
to get the standard MO matrix.
:param files: Files to calculate the MO coefficients
:type files: Namedtuple (fileXYZ,fileInput,fileOutput)
:param job: Output File
:type job: String
"""
key = InputKey(
'orbitals',
[path_MO, number_of_orbs, number_of_orb_funs, path_es, path_css])
turbomole2hdf5(handle_hdf5, [key])
return path_es, path_css