arkane.ess.QchemLog

class arkane.ess.QChemLog(path, check_for_errors=True, scratch_directory=None)

Represent an output file from QChem. The attribute path refers to the location on disk of the QChem output file of interest. Methods are provided to extract a variety of information into Arkane classes and/or NumPy arrays. QChemLog is an adapter for the abstract class ESSAdapter.

check_for_errors()

Checks for common errors in a QChem 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 QChem output 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 an output file created as the result of a QChem “Freq” calculation. As QChem’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 QChem output file will be adopted.

load_energy(zpe_scale_factor=1.0)

Load the energy in J/mol from a QChem log file. Prioritize the energy from a converged geometry optimization. If the file does not contain an optimization job or if the optimization hit the maximum cycles, return the next equivalent source, such as from a frequency job. The zero-point energy is not included in the returned value.

load_force_constant_matrix()

Return the force constant matrix (in Cartesian coordinates) from the QChem 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 QChem log file. If multiple such geometries are identified, only the last is returned.

load_negative_frequency()

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

load_scan_energies()

Extract the optimized energies in J/mol from a QChem log file, e.g. the result of a QChem “PES Scan” quantum chemistry calculation.

load_scan_frozen_atoms()

Not implemented for QChem

load_scan_pivot_atoms()

Not implemented for QChem

load_zero_point_energy()

Load the unscaled zero-point energy in J/mol from a QChem output file.