arkane.ess.GaussianLog¶
- class arkane.ess.GaussianLog(path, check_for_errors=True)¶
Represent a log file from Gaussian. The attribute path refers to the location on disk of the Gaussian log file of interest. Methods are provided to extract a variety of information into Arkane classes and/or NumPy arrays. GaussianLog is an adapter for the abstract class ESSAdapter.
- check_for_errors()¶
Checks for common errors in a Gaussian log file. If any are found, this method will raise an error and crash.
- get_D1_diagnostic()¶
Returns the D1 diagnostic from output log. If multiple occurrences exist, returns the last occurrence. Should be implemented by the relevant subclass.
- get_T1_diagnostic()¶
Returns the T1 diagnostic from output log. If multiple occurrences exist, returns the last occurrence. Should be implemented by the relevant subclass.
- get_number_of_atoms()¶
Return the number of atoms in the molecular configuration used in the Gaussian log file.
- get_software()¶
Return the name of the software. Should correspond to the class name without ‘Log’.
- get_symmetry_properties()¶
This method uses the symmetry package from RMG’s QM module and returns a tuple where the first element is the number of optical isomers, the second element is the symmetry number, and the third element is the point group identified.
- load_conformer(symmetry=None, spin_multiplicity=0, optical_isomers=None, label='')¶
Load the molecular degree of freedom data from a log file created as the result of a Gaussian “Freq” quantum chemistry calculation. As Gaussian’s guess of the external symmetry number is not always correct, you can use the symmetry parameter to substitute your own value; if not provided, the value in the Gaussian log file will be adopted. In a log file with multiple Thermochemistry sections, only the last one will be kept.
- load_energy(zpe_scale_factor=1.0)¶
Load the energy in J/mol from a Gaussian log file. The file is checked for a complete basis set extrapolation; if found, that value is returned. Only the last energy in the file is returned. The zero-point energy is not included in the returned value; it is removed from the CBS-QB3 value.
- load_force_constant_matrix()¶
Return the force constant matrix from the Gaussian log file. The job that generated the log file must have the option
iop(7/33=1)
in order for the proper force constant matrix (in Cartesian coordinates) to be printed in the log file. If multiple such matrices are identified, only the last is returned. The units of the returned force constants are J/m^2. If no force constant matrix can be found in the log file,None
is returned.
- load_geometry()¶
Return the optimum geometry of the molecular configuration from the Gaussian log file. If multiple such geometries are identified, only the last is returned.
- load_negative_frequency()¶
Return the negative frequency from a transition state frequency calculation in cm^-1.
- load_scan_energies()¶
Extract the optimized energies in J/mol from a log file, e.g. the result of a Gaussian “Scan” quantum chemistry calculation.
- load_scan_frozen_atoms()¶
Extract the atom numbers which were frozen during the scan Return a list of list of atom numbers starting with the first atom as 1 Each element of the outer lists represents a frozen bond Inner lists with length 2 represent frozen bond lengths Inner lists with length 3 represent frozen bond angles Inner lists with length 4 represent frozen dihedral angles
- load_scan_pivot_atoms()¶
Extract the atom numbers which the rotor scan pivots around Return a list of atom numbers starting with the first atom as 1
- load_zero_point_energy()¶
Load the unscaled zero-point energy in J/mol from a Gaussian log file.