abstract check_for_errors()

Checks the log file for common errors. Optionally runs when the class is initialized to catch errors before parsing relevant information.

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.

abstract get_number_of_atoms()

Return the number of atoms in the molecular configuration.

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.

Return the optimum geometry of the molecular configuration.

Load the energy in J/mol from a log file. Only the last energy in the file is returned. The zero-point energy is not included in the returned value.

Return the force constant matrix (in Cartesian coordinates). 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.

Return the optimum geometry of the molecular configuration. If multiple such geometries are identified, only the last is returned.

Return the imaginary frequency from a transition state frequency calculation in cm^-1.

Extract the optimized energies in J/mol from a torsional scan log file.

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.

Extract the atom numbers which the rotor scan pivots around. Return a list of atom numbers starting with the first atom as 1.