ocal package

Subpackages

• ocal.utils package
  • Submodules
  • ocal.utils.cif_reader module
    • CifReader
      • CifReader.parent_dir
      • CifReader.ELEMENT_PROP
      • CifReader.ATOMIC_WEIGHTS
      • CifReader.COVALENT_RADII
      • CifReader.calc_cen_of_weight()
      • CifReader.convert_cart_to_frac()
      • CifReader.convert_frac_to_cart()
      • CifReader.expand_mols()
      • CifReader.export_unit_cell_file()
      • CifReader.remove_duplicates()
    • ElementPropertiesIsNotDefinedError
    • SymmetryIsNotDefinedError
    • ZValueIsNotMatchError
    • FileIO
      • FileIO.add_adjacency_mat()
      • FileIO.add_coordinates()
      • FileIO.add_symbols()
      • FileIO.export_mol_file()
      • FileIO.export_xyz_file()
  • ocal.utils.cube_reader module
    • load_element_tables()
    • read_cubefile()
    • calc_distance_matrix()
    • calc_otf()
  • ocal.utils.gaus_log_reader module
    • check_normal_termination()
    • FileReader
      • FileReader.close()
      • FileReader.reversed_readline()
  • ocal.utils.gjf_maker module
    • GjfMaker
      • GjfMaker.parent_dir
      • GjfMaker.ELEMENT_PROP
      • GjfMaker.ELEMENTS_NUM
      • GjfMaker.add_link()
      • GjfMaker.add_root()
      • GjfMaker.create_chk_file()
      • GjfMaker.create_rwf_file()
      • GjfMaker.export_gjf()
      • GjfMaker.opt()
      • GjfMaker.output_detail()
      • GjfMaker.reset_variable()
      • GjfMaker.set_charge_spin()
      • GjfMaker.set_coordinates()
      • GjfMaker.set_function()
      • GjfMaker.set_resource()
      • GjfMaker.set_symbols()
      • GjfMaker.set_title()
  • ocal.utils.structure_reader module
    • read_gjf()
    • read_xyz()
    • read_mol()
    • read_mol2()
    • read_cif()
    • read_structure()
  • Module contents

Submodules

ocal.ocal module

ocal: single-molecule orbital tail fraction (OTF) calculator.

Assumes a neutral closed-shell molecule (charge/spin fixed to 0 1). Input charge/spin information in structure files is ignored. Gaussian functional/basis is fixed to B3LYP/6-31G(d,p) for comparability with previous OTF results; only Ocal._create_gjf(method=...) may override.

ocal.ocal.main()

Run the ocal CLI: compute OTF for one molecule from a structure, fchk, or cube.

Return type:

None

ocal.ocal.parse_args()

Parse command-line arguments.

Returns:

The parser (for parser.error) and parsed arguments.

Return type:

tuple[argparse.ArgumentParser, argparse.Namespace]

class ocal.ocal.Ocal(file, cpu=4, mem=10)

Bases: object

Calculate orbital tail fraction (OTF) for a single molecule.

Charge and spin multiplicity are fixed to 0 1 (neutral singlet). Structure-file inputs always run Opt=Tight at B3LYP/6-31G(d,p).

Parameters:

• file (str)

• cpu (int)

• mem (int)

static check_normal_termination(log_file)

Check whether a Gaussian log ended with normal termination.

Parameters:

log_file (str) – Path to the Gaussian log file.

Returns:

True if the calculation terminated normally.

Return type:

bool

static print_timestamp()

Print timestamp.

Return type:

None

create_gjf()

Read the structure file and write a Gaussian input (.gjf).

Return type:

None

run_gaussian(gau_com='g16')

Run Gaussian on the generated gjf.

The subprocess runs with cwd set to the work directory and a relative gjf filename so Windows Gaussian does not concatenate an absolute path onto the current directory.

Parameters:

gau_com (str) – Gaussian executable name (default g16). Stored on the instance as gau_com for future CLI extension (e.g. g09).

Raises:

RuntimeError – If the subprocess fails, no .log/.out is found, or the log does not show normal termination.

Return type:

None

create_fchk()

Convert the checkpoint file to a formatted checkpoint via formchk.

Raises:

RuntimeError – If formchk fails.

Return type:

None

create_cube()

Generate NHOMO/HOMO/LUMO/NLUMO cube files with cubegen.

MO indices are derived from the number of alpha electrons na in the fchk: NHOMO=na-1, HOMO=na, LUMO=na+1, NLUMO=na+2.

Raises:

RuntimeError – If cubegen fails for any orbital.

Return type:

None

calc_otf()

Compute OTF and density_sum for the target cube file(s).

Returns:

Mapping of orbital label (or cube stem) to (otf, density_sum).

Return type:

dict[str, tuple[float, float]]

Module contents

ocal: program for the calculation of orbital tail fraction (OTF).