Columbus Parser

class pyopencap.analysis.colparser(molden_file, tranls)[source]

A class that parses COLUMBUS electronic structure package generated files to generate state density and transition density matrices for projected-CAP calculation on MR-CI level.

__init__(molden_file, tranls)[source]

Initializes the colparser class

Parameters

  • molden_file (str) – molden MO filename (generated in MOLDEN/ folder in COLUMBUS calculation Directory)

  • tranls (str) – Path to tranls file generated by Columbus in WORK directory

get_H0(correction_type='eci+pople', filename='ciudgsm')[source]

Parses energies from a Columbus ciudgsm file.

Parameters

  • correction_type (str, optional) – One of {‘eci+pople’, ‘eci’, ‘eci+dv1’, ‘eci+dv2’, ‘eci+dv3’ }. Default is ‘eci+pople’

  • filename (str, optional) – Path to Columbus ciudgsm file located in WORK directory. If unspecified, assumed to be ‘./ciudgsm’.

Notes

See https://aip.scitation.org/doi/pdf/10.1063/1.5144267 for discussion of corrections.

Returns

H0_mat – Diagonal hamiltonian with CI energies.

Return type

np.ndarray

mo_summary()[source]

Prints information about active space and symmetries of MOs.

Returns

Total number of basis functions (nbft) Number of basis functions in each symmetry block (NBPSY). Number of orbitals in each of the symmetry blocks.(NMPSY<= NBSPSY) Number of frozen orbitals in each of the symmetry blocks (NFCSY ). Character labels for the symmetry blocks (SLABEL).

Return type

str

sdm_ao(i, DRTn=1, data_dir='.', filename=None)[source]

Returns state density matrix in atomic orbital basis by parsing a Columbus cid1trfl.iwfmt file.

Parameters

  • i (int) – State index

  • DRTn (int, optional) – DRT index

  • data_dir (str, optional) – Directory to search for .iwfmt file. Should not be used in conjunction with filename kwarg

  • filename (str, optional) – Path to file to parse. If not specified, the filename is assumed to be cid1trfl.FROMdrt{drtFrom}.state{i}TOdrt{drtTo}.state{i}.iwfmt in the current directory.

Returns

sdm – State density matrix in AO basis

Return type

np.ndarray

sdm_ao_cid1fl(i, DRTn)[source]

Read CI state densities from state density cid1fl*.iwfmt files.

Currently NYI.

Parameters

  • i (int) – State index

  • DRTn (int) – DRT index

Raises

NotImplementedError –

Returns

State density matrix in AO basis

Return type

np.ndarray

tdm_ao(iFROM, iTO, drtFrom=1, drtTo=1, data_dir='.', filename=None)[source]

Returns transition density matrix in atomic orbital basis by parsing a Columbus cid1trfl.iwfmt file.

Parameters

  • iFROM (int) – Initial state index and final state indices respectively.

  • iTO (int) – Initial state index and final state indices respectively.

  • drtFrom (int, optional) – DRT indices

  • drtTo (int, optional) – DRT indices

  • data_dir (str, optional) – Directory to search for .iwfmt file. Should not be used in conjunction with filename kwarg

  • filename (str, optional) – Path to file to parse. If not specified, the filename is assumed to be cid1trfl.FROMdrt{drtFrom}.state{iFrom}TOdrt{drtTo}.state{iTO}.iwfmt in the current directory.

Returns

tdm – Transition density matrix in AO basis

Return type

np.ndarray