sf.apps.qchem.read_gamess

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]