sf.apps.qchem.read_gamess¶
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read_gamess
(file)[source]¶ Reads molecular data from the output file generated by the GAMESS quantum chemistry package [12].
This function extracts the atomic coordinates (r), atomic masses (m), vibrational frequencies (w), and normal modes (l) of a molecule from the output file of a vibrational frequency calculation performed with the GAMESS quantum chemistry package. The output file must contain the results of a RUNTYP=HESSIAN calculation performed with GAMESS. We recommend checking the output of this function with the GAMESS results to assure that the GAMESS output file is parsed correctly.
Example usage:
>>> r, m, w, l = read_gamess('../BH_data.out') >>> r # atomic coordinates array([[0.0000000, 0.0000000, 0.0000000], [1.2536039, 0.0000000, 0.0000000]]) >>> m # atomic masses array([11.00931, 1.00782]) >>> w # vibrational frequencies array([19.74, 19.73, 0.00, 0.00, 0.00, 2320.32]) >>> l # normal modes array([[-0.0000000e+00, -7.5322000e-04, -8.7276210e-02, 0.0000000e+00, 8.2280900e-03, 9.5339055e-01], [-0.0000000e+00, -8.7276210e-02, 7.5322000e-04, 0.0000000e+00, 9.5339055e-01, -8.2280900e-03], [ 2.8846925e-01, -2.0000000e-08, 2.0000000e-08, 2.8846925e-01, -2.0000000e-08, 2.0000000e-08], [ 2.0000000e-08, 2.8846925e-01, -2.0000000e-08, 2.0000000e-08, 2.8846925e-01, -2.0000000e-08], [-2.0000000e-08, 2.0000000e-08, 2.8846925e-01, -2.0000000e-08, 2.0000000e-08, 2.8846925e-01], [-8.7279460e-02, 0.0000000e+00, 0.0000000e+00, 9.5342606e-01, -0.0000000e+00, -0.0000000e+00]])
- Parameters
file (str) – path to the GAMESS output file
- Returns
atomic coordinates, atomic masses, normal mode frequencies, normal modes
- Return type
tuple[array, array, array, array]