read_gamess(file, scale_factor=1.0)[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 (n) 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. Please also check if the normal modes are mass-weighted.

Example usage:

>>> r, m, w, n = 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])
>>> n # 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]])
  • file (str) – path to the GAMESS output file

  • scale_factor (float) – empirical scale factor for correcting the vibrational frequencies


atomic coordinates, atomic masses, normal mode frequencies, normal modes

Return type

tuple[array, array, array, array]