Index

A

Angle (class in mammoth.core.internal_coords) angle_list (mammoth.qm2ff.QM2FF attribute)

angles (mammoth.qm2ff.QM2FF attribute) as_dict() (mammoth.core.forcefield.ClassicalForceField method) (mammoth.core.internal_coords.Dihedral method)

B

Bond (class in mammoth.core.internal_coords) bond_list (mammoth.qm2ff.QM2FF attribute)

bond_orders (orca.OrcaOutfile attribute) bond_search (mammoth.qm2ff.QM2FF attribute) bonds (mammoth.qm2ff.QM2FF attribute)

C

charge (orca.OrcaOutfile attribute) ClassicalForceField (class in mammoth.core.forcefield) compute_periodicity() (mammoth.core.internal_coords.Dihedral method)

connectivity (mammoth.qm2ff.QM2FF attribute), [1] cubic_terms (orca.OrcaVPT2 attribute) cutoffb (mammoth.qm2ff.QM2FF attribute)

D

default_parameters() (mammoth.MammothControls class method) Dihedral (class in mammoth.core.internal_coords) dihedral_list (mammoth.qm2ff.QM2FF attribute) dihedral_type (mammoth.qm2ff.QM2FF attribute)

dihedrals (mammoth.qm2ff.QM2FF attribute) dipole (orca.OrcaOutfile attribute) dipole_derivative (orca.OrcaVPT2 attribute) dipole_moment (orca.OrcaOutfile attribute)

E

energy (orca.OrcaHessian attribute)

esp_charges (orca.OrcaOutfile attribute) export_lammps_data() (mammoth.core.forcefield.ClassicalForceField method)

F

filename (orca.OrcaHessian attribute) (orca.OrcaOutfile attribute) (orca.OrcaVPT2 attribute) final_energy (orca.OrcaOutfile attribute) final_structure (orca.OrcaOutfile attribute)

ForceField (class in mammoth.core.forcefield) frequencies (orca.OrcaHessian attribute) (orca.OrcaOutfile attribute) from_dict() (mammoth.core.internal_coords.Dihedral class method) from_file() (mammoth.MammothControls class method)

G

get_angle_list() (mammoth.qm2ff.QM2FF method) get_angles() (mammoth.qm2ff.QM2FF method) get_atoms_in_bond() (mammoth.core.molecule.Molecule method) get_bo_value() (mammoth.core.molecule.Molecule method) get_bonds() (mammoth.qm2ff.QM2FF method) get_dihedral_list() (mammoth.qm2ff.QM2FF method) get_dihedrals_harmonic() (mammoth.qm2ff.QM2FF method) get_dihedrals_parabolic() (mammoth.qm2ff.QM2FF method) get_forcefield() (mammoth.qm2ff.QM2FF method)

get_improper_list() (mammoth.qm2ff.QM2FF method) get_impropers() (mammoth.qm2ff.QM2FF method) get_md_params() (mammoth.MammothControls method) get_mol_ang() (orca.OrcaHessian method) (orca.OrcaVPT2 method) get_PDB_connectivity() (mammoth.qm2ff.QM2FF method) get_qm2ff_params() (mammoth.MammothControls method) get_string() (orca.OrcaInput method) gibbs_free_enthalpy (orca.OrcaOutfile attribute)

H

hessian (orca.OrcaHessian attribute) (orca.OrcaVPT2 attribute)

hirshfeld_charges (orca.OrcaOutfile attribute) hirshfeld_spin_pop (orca.OrcaOutfile attribute) homo (orca.OrcaOutfile attribute)

I

imag_th (mammoth.qm2ff.QM2FF attribute) Improper (class in mammoth.core.internal_coords) improper_list (mammoth.qm2ff.QM2FF attribute)

impropers (mammoth.qm2ff.QM2FF attribute) initial_structure (orca.OrcaOutfile attribute) is_spin (orca.OrcaOutfile attribute)

L

loe_charges (orca.OrcaOutfile attribute)

loe_spin_pop (orca.OrcaOutfile attribute) lumo (orca.OrcaOutfile attribute)

M

main() (mammoth.Mammoth method) Mammoth (class in mammoth) mammoth (module), [1] mammoth.core (module) mammoth.core.forcefield (module) mammoth.core.internal_coords (module) mammoth.core.molecule (module) mammoth.qm2ff (module) MammothControls (class in mammoth) mass (orca.OrcaOutfile attribute)

mo_dataframe (orca.OrcaOutfile attribute) mo_energies (orca.OrcaOutfile attribute) mo_matrix (orca.OrcaOutfile attribute) mo_occupations (orca.OrcaOutfile attribute) Molecule (class in mammoth.core.molecule) molecule (mammoth.qm2ff.QM2FF attribute) (orca.OrcaHessian attribute) (orca.OrcaInput attribute) (orca.OrcaVPT2 attribute) mul_charges (orca.OrcaOutfile attribute) mul_spin_pop (orca.OrcaOutfile attribute)

N

natom (mammoth.qm2ff.QM2FF attribute) normal_termination (orca.OrcaOutfile attribute)

nuclear_repulsion (orca.OrcaOutfile attribute) number_basis_functions (orca.OrcaOutfile attribute) number_electrons (orca.OrcaOutfile attribute)

O

optimization_converged (orca.OrcaOutfile attribute) orca (module) orca_input (orca.OrcaOutfile attribute)

OrcaHessian (class in orca) OrcaInput (class in orca) OrcaOutfile (class in orca) OrcaVPT2 (class in orca)

P

pressure (orca.OrcaOutfile attribute)

Q

QM2FF (class in mammoth.qm2ff)

S

semi_quartic_terms (orca.OrcaVPT2 attribute) set_PDB_connectivity() (mammoth.qm2ff.QM2FF method) settings (orca.OrcaVPT2 attribute) setup_molecule() (mammoth.Mammoth method)

spin_multiplicity (orca.OrcaOutfile attribute) structures (orca.OrcaOutfile attribute) symmetrize_hessian() (orca.OrcaHessian method) (orca.OrcaVPT2 method)

T

temperature (orca.OrcaOutfile attribute)

thermo_data (orca.OrcaOutfile attribute)

U

update() (mammoth.MammothControls method)