arkane.ess.ESSAdapter

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

An abstract ESS Adapter class

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.

abstract load_conformer(symmetry=None, spin_multiplicity=0, optical_isomers=None, label='')

Return the optimum geometry of the molecular configuration.

abstract load_energy(zpe_scale_factor=1.0)

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.

abstract load_force_constant_matrix()

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.

abstract load_geometry()

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

abstract load_negative_frequency()

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

abstract load_scan_energies()

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

abstract 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.

abstract 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.

abstract load_zero_point_energy()

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