epsman.elecStructure.util module

ePSman electronic structure utility functions

Utility functions for use with ePSman.

24/01/24 v1

See also ../_util.py for general utility functions

epsman.elecStructure.util.readMoldenGeoms(fileName, keyWord='[Atoms]', skiprowsOffset=0, nrowType='auto', widths=[2, 7, 7, 20, 20, 20], names=['Ind', 'Species', 'Atomic Num.', 'x', 'y', 'z'], verbose=0)[source]

Read geometry/ies in Molden format.

Parameters:

  • fileName (str or Path object) – File to read.

  • keyWord (str, default = '[Atoms]') – Keyword to search for in file. Default case flags Molden geometry sections. If multiple sections are found they will all be read in.

  • skiprowsOffset (int, default = 0) – Additional header rows to skip. Default case

  • nrowType (str or int, default = 'auto') – If ‘auto’ tries to read all lines until next section. If an int, read this number of lines after keyWord.

  • widths (list, default = [2,7,7,20,20,20]) – Column widths, passed to pd.read_fwf() for reading sections. Default case for normal Molden format.

  • names (list, default = ['Ind','Species','Atomic Num.','x','y','z']) – Columns names. Default case matches epsman.elecStructure.gamess.getAtoms()

Returns:

Contains geometries keyed by integer, as Pandas DataFrames. Also key ‘details’ for metadata.

Return type:

dict

Notes