Index

A

a (AbInt attribute), [1] AbInt (class in ichor.core.files) (class in ichor.core.files.aimall) (class in ichor.core.files.aimall.ab_int) active_dims (Kernel property), [1] acyclic_bond() (in module ichor.core.files.mol2) add() (Atoms method), [1] (FileTree method), [1] (Trajectory method), [1], [2] add_atom_names_to_database() (in module ichor.core.database.sql) (in module ichor.core.database.sql.add_to_database) add_command() (SubmissionScript method), [1] add_items_to_menu() (in module ichor.cli.console_menu) add_keyword() (GJF method), [1], [2] add_keywords() (GJF method), [1], [2] add_method_and_get_wfn_paths() (in module ichor.hpc.main.aimall) add_option() (SubmissionScript method), [1] add_point_to_database() (in module ichor.core.database.sql) (in module ichor.core.database.sql.add_to_database) advance() (Lexer method) Aim (class in ichor.core.files) (class in ichor.core.files.aimall) (class in ichor.core.files.aimall.aim) aimall_completed() (in module ichor.core.useful_functions) (in module ichor.core.useful_functions.check_aimall_completed) AIMAllCommand (class in ichor.hpc.submission_commands) (class in ichor.hpc.submission_commands.aimall_command) AimAtom (class in ichor.core.files.aimall.aim) Al (AtomType attribute) ALF (class in ichor.core.atoms) (class in ichor.core.atoms.alf) alf (Models property), [1] (ModelWithGradients attribute) alf() (Atom method), [1] (Atoms method), [1] (AtomView method), [1] (HasAtoms method) (ListOfAtoms method), [1] (PointsDirectory method), [1] (Trajectory method), [1], [2] alf_array() (Atom method), [1] alf_dict() (Atoms method), [1] (HasAtoms method) (PointsDirectory method), [1] (Trajectory method), [1], [2] alf_features_to_coordinates() (in module ichor.core.calculators) (in module ichor.core.calculators.alf_features_to_coordinates_calculator) alf_list() (Atoms method), [1] (HasAtoms method) All (ATIDSProps attribute) (SHMMax attribute) AllBonds (BondLengthConstraint attribute) Altered (SybylStatus attribute) Always (UseTwoe attribute) AmberCommand (class in ichor.hpc.submission_commands) (class in ichor.hpc.submission_commands.amber_command) AmberMDIn (class in ichor.core.molecular_dynamics.amber) AmberMenuFunctions (class in ichor.cli.main_menu_submenus.molecular_dynamics_menu.molecular_dynamics_submenus.amber_submenu) AmberMenuOptions (class in ichor.cli.main_menu_submenus.molecular_dynamics_menu.molecular_dynamics_submenus.amber_submenu) AmberThermostat (class in ichor.core.molecular_dynamics.amber) Amide (BondType attribute) Ampac (ChargeType attribute) AnalysisFunctions (class in ichor.cli.main_menu_submenus.analysis_menu.analysis_menu) Analyzed (SybylStatus attribute) Andersen (AmberThermostat attribute) Angle (class in ichor.core.common.units)

angle() (Atom method), [1] angle_names() (ConnectedAtoms method) (in module ichor.core.calculators) (in module ichor.core.calculators.geometry_calculator) angles (ConnectedAtoms property) angles() (in module ichor.core.calculators) (in module ichor.core.calculators.geometry_calculator) Angstroms (AtomicDistance attribute) AnnotatedDirectory (class in ichor.core.files.directory) append() (Atoms method), [1] arguments (AIMAllCommand property), [1] (CommandGroup property) (SubmissionCommand property) Aromatic (BondType attribute) arr() (SubmissionScript method), [1] array_index() (SubmissionScript method), [1] array_job() (BatchSystem class method) (LocalBatchSystem class method), [1] (SLURM class method), [1] (SunGridEngine class method), [1] as_dict() (Enum class method), [1] ask_user_for_mdcrd_paths() (in module ichor.cli.main_menu_submenus.molecular_dynamics_menu.molecular_dynamics_submenus.amber_submenu) ask_user_input_for_atom_name() (in module ichor.cli.main_menu_submenus.analysis_menu.analysis_menu) astar() (in module ichor.core.common.search) ASTNode (class in ichor.core.models.kernels.interpreter.ast) ATIDSProps (class in ichor.hpc.submission_commands.aimall_command) Atom (class in ichor.core.atoms) (class in ichor.core.atoms.atom) atom (Model property), [1] (ModelWithGradients property), [1] atom_id (Dataset attribute) atom_name (AtomView property), [1] (Int attribute), [1] (ModelWithGradients attribute) atom_names (Atoms property), [1] (AtomView property), [1] (HasAtoms property) (ListOfAtoms property), [1] (Models property), [1] (PointsDirectory property), [1] (Trajectory property), [1], [2] atom_names_parent (Dataset attribute) atom_num (Int property), [1], [2] (Model property), [1] (ModelWithGradients property), [1] atom_type (Mol2Atom property) atomic_contribution_to_molecular_dipole() (in module ichor.core.multipoles.dipole) atomic_contribution_to_molecular_quadrupole() (in module ichor.core.multipoles.quadrupole) AtomicDistance (class in ichor.core.common.units) AtomicMorfiOutput (class in ichor.core.files.pandora.mout) AtomNames (class in ichor.core.database.sql.database) AtomNotFound, [1] Atoms (class in ichor.core.atoms) (class in ichor.core.atoms.atoms) atoms (GaussianOutput attribute), [1] (PointDirectory property), [1] atoms_from_file() (PointDirectory method), [1] AtomsNotFoundError, [1] AtomType (class in ichor.core.files.mol2) AtomView (class in ichor.core.atoms) (class in ichor.core.atoms.list_of_atoms_atom_view) Auto (BasinIntegrationMethod attribute) (Boaq attribute) (Capture attribute) (MIR attribute) AutoGS2 (Boaq attribute) AutoGS4 (Boaq attribute)

B

b (AbInt attribute), [1] b_matrix_true_finite_differences() (in module ichor.core.models.gaussian_energy_derivative_wrt_features) Bar_func() (in module ichor.core.multipoles.octupole) bash_date (SubmissionScript property), [1] Basic (Capture attribute) (CPConn attribute) basin_integration_results (Int attribute), [1] BasinIntegrationMethod (class in ichor.hpc.submission_commands.aimall_command) basis_set (GJF attribute), [1] (OrcaInput attribute), [1] (RouteCard attribute) batched_array() (in module ichor.core.common.np) BatchSystem (class in ichor.hpc.batch_system.batch_system) bfs() (in module ichor.core.common.search) binary_contains() (in module ichor.core.common.search) BinOp (class in ichor.core.models.kernels.interpreter.ast) BioPolymer (MoleculeType attribute) block() (File method) Blocked (FileState attribute) Boaq (class in ichor.hpc.submission_commands.aimall_command) Bohr (AtomicDistance attribute) Bond (CriticalPointType attribute) bond_critical_points (AtomicMorfiOutput attribute) (Int property), [1], [2] (MOUT attribute)

bond_index_to_atom() (in module ichor.core.files.mol2) bond_lengths_differences_matrix() (Stability method), [1] bond_lengths_matrix (Stability property), [1] bond_names() (ConnectedAtoms method) (in module ichor.core.calculators) (in module ichor.core.calculators.geometry_calculator) BondCriticalPoint (class in ichor.core.files.pandora.mout) bonded_atoms() (Atom method), [1] bonded_atoms_i() (Atom method), [1] bonded_atoms_names() (Atom method), [1] BondLengthConstraint (class in ichor.core.molecular_dynamics.amber) bonds (ConnectedAtoms property) bonds() (in module ichor.core.calculators) (in module ichor.core.calculators.geometry_calculator) bonds_of_type() (in module ichor.core.files.mol2) BondType (class in ichor.core.files.mol2) bool_to_str() (in module ichor.cli.useful_functions) (in module ichor.cli.useful_functions.user_input) BoolToggle (class in ichor.core.common.types) (class in ichor.core.common.types.bool_toggle) Box_func() (in module ichor.core.multipoles.octupole) Br (AtomType attribute) buildermethod() (in module ichor.core.common.functools) (in module ichor.core.common.functools.functools)

C

C() (Atom method), [1] (AtomView method), [1] C1 (AtomType attribute) C2 (AtomType attribute) C3 (AtomType attribute) C_1() (in module ichor.core.models.fflux_derivative_helper_functions) C_2() (in module ichor.core.models.fflux_derivative_helper_functions) C_3() (in module ichor.core.models.fflux_derivative_helper_functions) C_matrix() (in module ichor.core.models.fflux_derivative_helper_functions) C_matrix_dict() (Atoms method), [1] (HasAtoms method) C_matrix_list() (Atoms method), [1] (HasAtoms method) Ca (AtomType attribute) cached_property (class in ichor.core.common.functools) (class in ichor.core.common.functools.functools) cached_property_ttl (in module ichor.core.common.functools.functools) cached_property_with_ntimes (class in ichor.core.common.functools.functools) cached_property_with_ttl (class in ichor.core.common.functools.functools) Cage (CriticalPointType attribute) cage_critical_points (AtomicMorfiOutput attribute) (Int property), [1], [2] (MOUT attribute) CageCriticalPoint (class in ichor.core.files.pandora.mout) calculate_alf_atom_sequence() (in module ichor.core.calculators) (in module ichor.core.calculators.alf.sequence_alf_calculator) calculate_alf_cahn_ingold_prelog() (in module ichor.core.calculators) (in module ichor.core.calculators.alf.cahn_ingold_prelog_alf_calculator) calculate_alf_features() (in module ichor.core.calculators) (in module ichor.core.calculators.features.alf_features_calculator) calculate_angle() (in module ichor.core.calculators) (in module ichor.core.calculators.geometry_calculator) calculate_angles() (in module ichor.core.calculators.geometry_calculator) calculate_bond() (in module ichor.core.calculators) (in module ichor.core.calculators.geometry_calculator) calculate_bonds() (in module ichor.core.calculators.geometry_calculator) calculate_c_matrix() (in module ichor.core.calculators) (in module ichor.core.calculators.c_matrix_calculator) calculate_compact_s_curves() (in module ichor.core.analysis.s_curves) (in module ichor.core.analysis.s_curves.compact_s_curves) calculate_compact_s_curves_from_files() (in module ichor.core.analysis.s_curves.compact_s_curves) calculate_compact_s_curves_from_true_predicted() (in module ichor.core.analysis.s_curves.compact_s_curves) calculate_dihedral() (in module ichor.core.calculators) (in module ichor.core.calculators.geometry_calculator) calculate_dihedrals() (in module ichor.core.calculators.geometry_calculator) calculate_internal_features() (in module ichor.core.calculators) (in module ichor.core.calculators.geometry_calculator) calculate_s_curves() (in module ichor.core.analysis.s_curves) (in module ichor.core.analysis.s_curves.s_curves) CannotParseJobID Capture (class in ichor.hpc.submission_commands.aimall_command) CAr (AtomType attribute) cat() (in module ichor.core.common.io) CCat (AtomType attribute) CCSD (PandoraCCSDmod attribute) CCSD_HF (PandoraCCSDmod attribute) CCSD_MULLER (PandoraCCSDmod attribute) ccsdmod (PandoraInput attribute), [1] Celsius (Temperature attribute) center_geometries_on_atom_and_write_xyz() (ListOfAtoms method), [1] center_geometry_on_atom_and_write_xyz() (HasAtoms method) centre() (Atoms method), [1] centroid (Atoms property), [1] change_atom_ordering() (Trajectory method), [1], [2] change_working_directory() (BatchSystem class method) (LocalBatchSystem class method), [1] (SLURM class method), [1] (SunGridEngine class method), [1] charge (GaussianOutput attribute), [1] (GJF attribute), [1] (OrcaInput attribute), [1] Charge (SHMMax attribute) charge() (in module ichor.core.files.mol2) ChargeType (class in ichor.core.files.mol2) check() (FileType class method), [1] check_bool() (in module ichor.core.common.bool) check_forces_less_than_value() (DlPolyIQAForces method), [1], [2] check_gaussian_and_aimall() (in module ichor.core.processing) (in module ichor.core.processing.check_functions) check_path() (AbInt class method), [1], [2] (Directory class method) (DlPolyFFLUX class method), [1], [2] (DlpolyHistory class method), [1], [2] (DlPolyIQAEnergies class method), [1], [2] (DlPolyIQAForces class method), [1], [2] (File class method) (Int class method), [1], [2] (IntDirectory class method), [1], [2] (Models class method), [1] (MorfiDirectory class method), [1], [2] (MorfiWFN class method) (PandoraDirectory class method), [1], [2] (PathObject class method) (PointDirectory class method), [1] (PointsDirectory class method), [1] (PointsDirectoryMenuOptions method) (PySCFDirectory class method), [1], [2] (ToolsMenuOptions method) check_selected_database_path() (SubmitCSVSMenuOptions method) check_selected_points_directory_path() (MainMenuMenuOptions method) (PointsDirectoryMenuOptions method) (ToolsMenuOptions method) check_selected_trajectory_path() (TrajectoryMenuOptions method) check_selected_xyz_path() (MolecularDynamicsMenuOptions method) check_supported_db_types() (in module ichor.core.database.query_database) children (AtomNames attribute) (Points attribute) chunker() (in module ichor.core.common.itertools) Cl (AtomType attribute) ClassDict (class in ichor.core.common.types) (class in ichor.core.common.types.class_dict)

classproperty() (in module ichor.core.common.functools) (in module ichor.core.common.functools.functools) ClassPropertyDescriptor (class in ichor.core.common.functools.functools) cleanup_str() (in module ichor.core.common.str) clear_screen() (in module ichor.core.common.os) col2idx() (in module ichor.core.common.excel) col2num() (in module ichor.core.common.excel) command (AIMAllCommand attribute), [1] (AmberCommand property), [1] (CommandGroup property) (CP2KCommand property), [1] (DlpolyCommand property), [1] (GaussianCommand attribute), [1] (OrcaCommand attribute), [1] (PythonCommand attribute), [1] (SubmissionCommand attribute) (TycheCommand attribute), [1] CommandGroup (class in ichor.hpc.submission_script.command_group) Comparable (class in ichor.core.common.search) compile_strings_to_python_code() (in module ichor.hpc.useful_functions.submit_free_flow_python_on_compute) Complete (ForceEvaluation attribute) completer() (DoNothingCompleter method), [1] (PathCompleter method), [1] (TabCompleter method) Complex (CPConn attribute) CompositeKernel (class in ichor.core.models.kernels.kernel) compute_likelihood() (Model method), [1] compute_weights() (Model method), [1] ComputeNode (NodeType attribute), [1] conda_path (PythonEnvironmentPath property) ConnectedAtom (class in ichor.core.files.dl_poly.dl_poly_field) ConnectedAtoms (class in ichor.core.files.dl_poly.dl_poly_field) connectivity() (Atom method), [1] (Atoms method), [1] (AtomView method), [1] (HasAtoms method) (ListOfAtoms method), [1] (PointsDirectory method), [1] (Trajectory method), [1], [2] connectivity_calculator_distance() (in module ichor.core.calculators.connectivity.distance_connectivity_calculator) connectivity_calculator_valence() (in module ichor.core.calculators.connectivity.valence_connectivity_calculator) ConsoleMenu (class in ichor.cli.console_menu) ConstantEnergy (AmberThermostat attribute) ConstantKernel (class in ichor.core.models.kernels) (class in ichor.core.models.kernels.constant) ConstantMean (class in ichor.core.models.mean) (class in ichor.core.models.mean.constant) ConstantPressure (PeriodicBoundaryCondition attribute) ConstantTemperature (AmberThermostat attribute) ConstantVolume (PeriodicBoundaryCondition attribute) contents (AnnotatedDirectory attribute) (FFLUXDirectory attribute), [1], [2] (IntDirectory attribute), [1], [2] (MorfiDirectory attribute), [1], [2] (PandoraDirectory attribute), [1], [2] (PointDirectory attribute), [1] (PySCFDirectory attribute), [1], [2] convert_to_cartesian_forces() (in module ichor.core.models.gaussian_energy_derivative_wrt_features) convert_to_feature_forces() (in module ichor.core.models.gaussian_energy_derivative_wrt_features) convert_to_path() (in module ichor.core.common.io) CoOH (AtomType attribute) Coordinate (DlpolyTrajectoryKey attribute) coordinates (Atoms property), [1] (FFLUXDirectory property), [1], [2] (HasAtoms property) (ListOfAtoms property), [1] (PointsDirectory property), [1] (Trajectory property), [1], [2] Coordinates3D (class in ichor.core.common.types) (class in ichor.core.common.types.coordinates) coordinates_string (Atom property), [1] coordinates_to_xyz() (PointsDirectory method), [1] (Trajectory method), [1], [2] coordinates_to_xyz_with_errors() (PointsDirectory method), [1] CoordinateVelocity (DlpolyTrajectoryKey attribute) CoordinateVelocityForce (DlpolyTrajectoryKey attribute) copy() (Atoms method), [1] copyfile() (in module ichor.core.common.io) copytree() (in module ichor.core.common.io) count_digits() (in module ichor.core.common.int) cp() (in module ichor.core.common.io) CP2KCommand (class in ichor.hpc.submission_commands) (class in ichor.hpc.submission_commands.cp2k_command) CP2KInput (class in ichor.core.molecular_dynamics.cp2k) CP2KMenuFunctions (class in ichor.cli.main_menu_submenus.molecular_dynamics_menu.molecular_dynamics_submenus.cp2k_submenu) CP2KMenuOptions (class in ichor.cli.main_menu_submenus.molecular_dynamics_menu.molecular_dynamics_submenus.cp2k_submenu) CPConn (class in ichor.hpc.submission_commands.aimall_command) create_database() (in module ichor.core.database.sql) (in module ichor.core.database.sql.database) create_database_session() (in module ichor.core.database.sql) (in module ichor.core.database.sql.add_to_database) create_sqlite_db_connection() (in module ichor.core.database.sql.query_database) create_sqlite_db_engine() (in module ichor.core.database.sql.query_database) critical_points (Int attribute), [1] CriticalPoint (class in ichor.core.files.aimall.int) (class in ichor.core.files.pandora.mout) CriticalPointType (class in ichor.core.files.aimall.int) CSGTB (MagProps attribute) csv_file_with_specific_properties() (in module ichor.core.database.sql.query_database) Cubic (DlpolyPeriodicBoundary attribute) current_directory (Int attribute), [1] current_node() (BatchSystem static method) (LocalBatchSystem static method), [1] (SLURM static method), [1] (SunGridEngine static method), [1] current_user() (in module ichor.core.common.os) current_user_groups() (in module ichor.core.common.os) Custom (MIR attribute) cwd (Aim attribute), [1]

D

D (Orbitals attribute) data (AIMAllCommand property), [1] (AmberCommand property), [1] (CommandGroup property) (CP2KCommand property), [1] (DlpolyCommand property), [1] (GaussianCommand property), [1] (OrcaCommand property), [1] (PythonCommand property), [1] (SubmissionCommand property) (TycheCommand property), [1] data_names (HasData property) DATAFILE (SubmissionScript attribute), [1] Dataset (class in ichor.core.database.sql.database) date_added (Points attribute) dC1k_da() (in module ichor.core.models.fflux_derivative_helper_functions) dC2k_da() (in module ichor.core.models.fflux_derivative_helper_functions) dC3k_da() (in module ichor.core.models.fflux_derivative_helper_functions) dChi_da() (in module ichor.core.models.fflux_derivative_helper_functions) decode() (in module ichor.core.common.str) default_alf_calculator() (in module ichor.core.calculators) default_connectivity_calculator() (in module ichor.core.calculators) default_feature_calculator() (in module ichor.core.calculators) default_options (SubmissionScript property), [1] Degrees (Angle attribute) degrees_to_radians() (in module ichor.core.common.units) delete() (BatchSystem class method) (PathObject method) delete_job() (BatchSystem class method) delete_job_command (BatchSystem attribute) (LocalBatchSystem attribute), [1] (SLURM attribute), [1] (SunGridEngine attribute), [1] delete_jobs() (in module ichor.hpc.batch_system.utils) delete_sqlite_points_by_id() (in module ichor.core.database.sql.query_database) Deleting (JobStatus attribute), [1] DelRe (ChargeType attribute) delta_An() (in module ichor.core.models.fflux_derivative_helper_functions) delta_Ax() (in module ichor.core.models.fflux_derivative_helper_functions) delta_Axy() (in module ichor.core.models.fflux_derivative_helper_functions) delta_between_timesteps (DlPolyFFLUX property), [1], [2] delta_between_timesteps_kj_mol (DlPolyFFLUX property), [1], [2] delta_dirac() (TrajectoryAnalysis method), [1] dfs() (in module ichor.core.common.search) dft_model (Int attribute), [1] Dict (ChargeType attribute) dict_of_list_to_dict_of_array() (in module ichor.core.common.np) DictionaryMergeConflict DictList (class in ichor.core.common.types) (class in ichor.core.common.types.dict_list) dihedral_names() (ConnectedAtoms method) (in module ichor.core.calculators) (in module ichor.core.calculators.geometry_calculator) dihedrals (ConnectedAtoms property) dihedrals() (in module ichor.core.calculators) (in module ichor.core.calculators.geometry_calculator) DimensionError Dipole (SHMMax attribute) dipole_cartesian_to_spherical() (in module ichor.core.multipoles) (in module ichor.core.multipoles.dipole) dipole_mag (Int property), [1], [2]

dipole_one_term_general_expression() (in module ichor.core.multipoles.dipole) dipole_rotate_cartesian() (in module ichor.core.multipoles) (in module ichor.core.multipoles.dipole) dipole_spherical_to_cartesian() (in module ichor.core.multipoles) (in module ichor.core.multipoles.dipole) directories (AnnotatedDirectory property) Directory (class in ichor.core.files.directory) (FileType attribute), [1] dirname (MorfiDirectory attribute), [1], [2] (PandoraDirectory attribute), [1], [2] (PySCFDirectory attribute), [1], [2] dirpattern() (Models method), [1] dirtypes (AnnotatedDirectory attribute) displace_dipole_cartesian() (in module ichor.core.multipoles) (in module ichor.core.multipoles.dipole) displace_octupole_cartesian() (in module ichor.core.multipoles) (in module ichor.core.multipoles.octupole) displace_quadrupole_cartesian() (in module ichor.core.multipoles) (in module ichor.core.multipoles.quadrupole) display_status_of_running_jobs() (in module ichor.hpc.batch_system.utils) dist() (Atom method), [1] Distance (class in ichor.core.models.kernels.distance) Div (TokenType attribute) DlpolyCommand (class in ichor.hpc.submission_commands) (class in ichor.hpc.submission_commands.dlpoly_command) DlPolyConfig (class in ichor.core.files) (class in ichor.core.files.dl_poly) (class in ichor.core.files.dl_poly.dl_poly_config) DlPolyControl (class in ichor.core.files) (class in ichor.core.files.dl_poly) (class in ichor.core.files.dl_poly.dl_poly_control) DlPolyFFLUX (class in ichor.core.files) (class in ichor.core.files.dl_poly) (class in ichor.core.files.dl_poly.dl_poly_fflux) DlPolyField (class in ichor.core.files) (class in ichor.core.files.dl_poly) (class in ichor.core.files.dl_poly.dl_poly_field) DlpolyHistory (class in ichor.core.files) (class in ichor.core.files.dl_poly) (class in ichor.core.files.dl_poly.dl_poly_history) DlPolyIQAEnergies (class in ichor.core.files) (class in ichor.core.files.dl_poly) (class in ichor.core.files.dl_poly.dl_poly_iqa_energies) DlPolyIQAForces (class in ichor.core.files) (class in ichor.core.files.dl_poly) (class in ichor.core.files.dl_poly.dl_poly_iqa_forces) DlpolyPeriodicBoundary (class in ichor.core.files.dl_poly.dl_poly_history) DlpolyTimestep (class in ichor.core.files.dl_poly.dl_poly_history) DlpolyTimestepAtom (class in ichor.core.files.dl_poly.dl_poly_history) DlpolyTrajectoryKey (class in ichor.core.files.dl_poly.dl_poly_history) DoNothingCompleter (class in ichor.cli.completers) (class in ichor.cli.completers.tab_completer) Double (BondType attribute) dPhi_da() (in module ichor.core.models.fflux_derivative_helper_functions) dR_da() (in module ichor.core.models.fflux_derivative_helper_functions) dRaxdotRax_da() (in module ichor.core.models.fflux_derivative_helper_functions) dRaxdotRaxy_da() (in module ichor.core.models.fflux_derivative_helper_functions) dsigma_da() (in module ichor.core.models.fflux_derivative_helper_functions) dTheta_da() (in module ichor.core.models.fflux_derivative_helper_functions) Dummy (AtomType attribute) dyj_da() (in module ichor.core.models.fflux_derivative_helper_functions) dZj_da() (in module ichor.core.models.fflux_derivative_helper_functions)

E

e_inter (AbInt property), [1], [2] e_intra (Int property), [1], [2] eat() (Parser method) Ehren (class in ichor.hpc.submission_commands.aimall_command) electronegativity (Atom property), [1] electrostatic_energy (DlPolyFFLUX property), [1], [2] empty (PriorityQueue property) (Queue property) (Stack property) Encomp (class in ichor.hpc.submission_commands.aimall_command) ensure_array() (in module ichor.core.common.np) Enum (class in ichor.core.common.types) (class in ichor.core.common.types.enum) EnumStrList (class in ichor.core.common.types) (class in ichor.core.common.types.enum) Eof (TokenType attribute)

epilogue_description_text (MenuDescription attribute) EqC12() (in module ichor.core.models.fflux_derivative_helper_functions) Error (JobStatus attribute), [1] error() (Lexer method) (Parser method) error_directory() (BatchSystem class method) (LocalBatchSystem class method), [1] (SLURM class method), [1] (SunGridEngine class method), [1] Eta() (in module ichor.core.multipoles.octupole) euclidean_distance() (Distance static method) exists() (OptionalContentType method) (PathObject method) expr() (Parser method) Extended (Capture attribute) extout_path (Aim attribute), [1]

F

F (AtomType attribute) (Orbitals attribute) F() (in module ichor.core.multipoles.octupole) F2W (class in ichor.hpc.submission_commands.aimall_command) F_prime() (in module ichor.core.multipoles.octupole) factor() (Parser method) features() (Atom method), [1] (Atoms method), [1] (AtomView method), [1] (HasAtoms method) (ListOfAtoms method), [1] (PointDirectory method), [1] features_dict() (Atoms method), [1] (HasAtoms method) features_file_to_trajectory() (Trajectory class method), [1], [2] features_to_csv() (ListOfAtoms method), [1] features_to_excel() (ListOfAtoms method), [1] features_with_properties_to_csv() (PointsDirectory method), [1] features_with_wfn_energy_and_dE_df_to_csv() (PointsDirectory method), [1] fflux_derivs() (in module ichor.core.models.calculate_fflux_derivatives) fflux_derivs_da_df_matrix() (in module ichor.core.models.calculate_fflux_derivatives) fflux_derivs_rbf_only() (in module ichor.core.models.calculate_fflux_derivatives) fflux_derivs_rbf_only_one_dimensional() (in module ichor.core.models.calculate_fflux_derivatives) fflux_gaussian_output_processing_function() (in module ichor.core.processing.callables) (in module ichor.core.processing.callables.gaussian_processing_callables) fflux_int_processing_function() (in module ichor.core.processing.callables) (in module ichor.core.processing.callables.int_processing_callables) fflux_ints_directory_processing_function() (in module ichor.core.processing.callables) (in module ichor.core.processing.callables.int_processing_callables) fflux_point_directory_processing() (in module ichor.core.processing) (in module ichor.core.processing.point_directory_processing) fflux_predict_value() (in module ichor.core.models.calculate_fflux_derivatives) fflux_predict_value_rbf_only() (in module ichor.core.models.calculate_fflux_derivatives) FFLUXDirectory (class in ichor.core.files) (class in ichor.core.files.dl_poly) (class in ichor.core.files.dl_poly.fflux_directory) File (class in ichor.core.files.file) (FileType attribute), [1]

file_structure (ScriptNames property) FileContentsType (class in ichor.core.files.file) FileNode (class in ichor.core.common.types) (class in ichor.core.common.types.file_tree) FileReadError files (AnnotatedDirectory property) FileState (class in ichor.core.files.file) FileTree (class in ichor.core.common.types) (class in ichor.core.common.types.file_tree) FileType (class in ichor.core.common.types) (class in ichor.core.common.types.file_tree) filetype (SubmissionScript attribute), [1] filetypes (AnnotatedDirectory attribute) FileWriteError find() (in module ichor.core.common.dict) find_in_inner_dicts() (in module ichor.core.common.dict) Fine (IASMesh attribute) first_index_where_delta_less_than() (DlPolyFFLUX method), [1], [2] force (DlpolyTimestepAtom property) force_x (Dataset attribute) force_y (Dataset attribute) force_z (Dataset attribute) ForceEvaluation (class in ichor.core.molecular_dynamics.amber) ForceNotDefined form_b_matrix() (in module ichor.core.models.gaussian_energy_derivative_wrt_features) form_g_inverse() (in module ichor.core.models.gaussian_energy_derivative_wrt_features) form_g_matrix() (in module ichor.core.models.gaussian_energy_derivative_wrt_features) format() (Mol2 method), [1] format_energy_plots() (in module ichor.core.analysis.dlpoly.plot_energy) format_number_with_comma() (in module ichor.core.common.formatting) formatter_check_function() (MenuOptions static method) formatter_menu_options() (MenuOptions static method) Four (Encomp attribute) FreeFlowPythonCommand (class in ichor.hpc.submission_commands.free_flow_python_command) from_atom() (Atom class method), [1] from_name() (Enum class method), [1] from_scientific_double() (in module ichor.core.common.float) from_trajectory() (PointsDirectory class method), [1] from_value() (Enum class method), [1]

G

Gasteiger (ChargeType attribute) gasteigger_charge() (in module ichor.core.files.mol2) GastHuck (ChargeType attribute) Gaussian (ChargeType attribute) GaussianCommand (class in ichor.hpc.submission_commands) (class in ichor.hpc.submission_commands.gaussian_command) GaussianOutput (class in ichor.core.files) (class in ichor.core.files.gaussian) (class in ichor.core.files.gaussian.gaussian_output) generate_str_for_reading_datafile() (SubmissionScript method), [1] get() (IntDirectory method), [1], [2] get_alf_from_first_db_geometry() (in module ichor.core.database) (in module ichor.core.database.query_database) get_atom_alf() (in module ichor.core.calculators) (in module ichor.core.calculators.alf) get_atom_bonds() (in module ichor.core.files.mol2) get_atom_name_and_alf_from_csv() (in module ichor.core.models.create_datasets) get_atom_type() (in module ichor.core.files.mol2) get_atoms_from_path() (in module ichor.core.useful_functions) (in module ichor.core.useful_functions.get_atoms) get_atoms_from_sqlite_point_id() (in module ichor.core.database.sql.query_database) get_bond_type() (in module ichor.core.files.mol2) get_bond_types() (in module ichor.core.files.mol2) get_bonded_atoms() (in module ichor.core.files.mol2) get_characters() (in module ichor.core.common.str) get_connected_atoms() (in module ichor.core.calculators.geometry_calculator) get_current_jobs() (in module ichor.hpc.batch_system.utils) get_current_python_environment_path() (in module ichor.hpc.useful_functions) (in module ichor.hpc.useful_functions.get_python_environment) get_data_for_point() (in module ichor.core.database.json) (in module ichor.core.database.json.add_to_database) get_database_info_from_db_type() (in module ichor.core.database) (in module ichor.core.database.query_database) get_digits() (in module ichor.core.common.str) get_dlpoly_energies() (in module ichor.core.analysis.dlpoly.dlpoly_analysis) get_features_dict() (Models method), [1] get_files_of_type() (in module ichor.core.common.io) get_filetype() (File class method) get_full_dataframe_for_all_atoms() (in module ichor.core.database.sql.query_database) get_functions_to_run() (in module ichor.core.common.functools) (in module ichor.core.common.functools.functools) get_gaussian_and_aimall_molecular_dipole() (in module ichor.core.multipoles) (in module ichor.core.multipoles.dipole) get_gaussian_and_aimall_molecular_octupole() (in module ichor.core.multipoles) (in module ichor.core.multipoles.octupole) get_gaussian_and_aimall_molecular_quadrupole() (in module ichor.core.multipoles) (in module ichor.core.multipoles.quadrupole) get_headings() (ListOfAtoms method), [1] get_int() (in module ichor.core.common.sorting) get_internal_feature_indices() (in module ichor.core.calculators) (in module ichor.core.calculators.geometry_calculator) get_json_db_info() (in module ichor.core.database.json) (in module ichor.core.database.json.query_database) get_list_of_atom_names_from_sqlite_db() (in module ichor.core.database.sql.query_database) get_list_of_point_ids_from_sqlite_db() (in module ichor.core.database.sql.query_database)

get_nbonds() (in module ichor.core.files.mol2) get_next_token() (Lexer method) get_one_json_dir_info() (in module ichor.core.database.json.query_database) get_param_from_config() (in module ichor.hpc.global_variables) get_plane() (in module ichor.core.common.linalg) get_predicted() (in module ichor.core.analysis.predictions) get_prologue_text() (ConsoleMenu method) get_queued_jobs() (BatchSystem class method) (SLURM class method), [1] (SunGridEngine class method), [1] get_random_geometries_from_fflux_simulation() (in module ichor.core.analysis.dlpoly.true_vs_predicted) get_ring() (in module ichor.core.files.mol2) get_sqlite_db_information() (in module ichor.core.database.sql) (in module ichor.core.database.sql.query_database) get_trajectory_from_path() (in module ichor.core.useful_functions) (in module ichor.core.useful_functions.get_atoms) get_true() (in module ichor.core.analysis.predictions) get_true_predicted() (in module ichor.core.analysis.predictions) get_uid() (in module ichor.hpc.uid) getch() (in module ichor.core.common.os) GIAO (MagProps attribute) give_xyz_file_and_center_trajectory_on_atom() (AnalysisFunctions static method) GJF (class in ichor.core.files) (class in ichor.core.files.gaussian) (class in ichor.core.files.gaussian.gjf) global_forces (GaussianOutput attribute), [1] global_multipole_moments (Int property), [1], [2] global_spherical_multipoles (Int attribute), [1] gradient (OrcaEngrad property), [1], [2] group (AmberCommand attribute), [1] (CP2KCommand attribute), [1] (GaussianCommand attribute), [1] (OrcaCommand attribute), [1] (SubmissionCommand attribute) (TycheCommand attribute), [1] grouped_commands (SubmissionScript property), [1] GS1 (Boaq attribute) GS10 (Boaq attribute) GS15 (Boaq attribute) GS2 (Boaq attribute) GS20 (Boaq attribute) GS25 (Boaq attribute) GS3 (Boaq attribute) GS30 (Boaq attribute) GS35 (Boaq attribute) GS4 (Boaq attribute) GS40 (Boaq attribute) GS45 (Boaq attribute) GS5 (Boaq attribute) GS50 (Boaq attribute) GS55 (Boaq attribute) GS6 (Boaq attribute) GS60 (Boaq attribute) GS7 (Boaq attribute) GS8 (Boaq attribute) GS9 (Boaq attribute)

H

H (AtomType attribute) HasAtoms (class in ichor.core.files.file_data) HasData (class in ichor.core.files.file_data) hash (Atoms property), [1] Hexadecapole (SHMMax attribute) hexadecapole_cartesian_to_spherical() (in module ichor.core.multipoles) (in module ichor.core.multipoles.hexadecapole) hexadecapole_rotate_cartesian() (in module ichor.core.multipoles) (in module ichor.core.multipoles.hexadecapole) hexadecapole_spherical_to_cartesian() (in module ichor.core.multipoles) (in module ichor.core.multipoles.hexadecapole) HexagonalPrism (DlpolyPeriodicBoundary attribute)

hold_job() (BatchSystem class method) (SLURM class method), [1] (SunGridEngine class method), [1] Holding (JobStatus attribute), [1] Host (BatchSystem attribute) (SLURM attribute), [1] (SunGridEngine attribute), [1] hr() (TrajectoryAnalysis method), [1] HSPC (AtomType attribute) HT3P (AtomType attribute) Huckel (ChargeType attribute) HydrogenBonds (BondLengthConstraint attribute)

I

i (Atom property), [1] I (AtomType attribute) i (Int property), [1], [2] (Model property), [1] (ModelWithGradients property), [1] ialf (Model property), [1] (Models property), [1] (ModelWithGradients property), [1] ialf_dict (Models property), [1] IASMesh (class in ichor.hpc.submission_commands.aimall_command) ichor.cli module ichor.cli.completers module ichor.cli.completers.tab_completer module ichor.cli.console_menu module ichor.cli.global_menu_variables module ichor.cli.main_menu module ichor.cli.main_menu_submenus module ichor.cli.main_menu_submenus.analysis_menu module ichor.cli.main_menu_submenus.analysis_menu.analysis_menu module ichor.cli.main_menu_submenus.database_menu module ichor.cli.main_menu_submenus.database_menu.submit_csvs_from_database module ichor.cli.main_menu_submenus.molecular_dynamics_menu module ichor.cli.main_menu_submenus.molecular_dynamics_menu.molecular_dynamics_menu module ichor.cli.main_menu_submenus.molecular_dynamics_menu.molecular_dynamics_submenus module ichor.cli.main_menu_submenus.molecular_dynamics_menu.molecular_dynamics_submenus.amber_submenu module ichor.cli.main_menu_submenus.molecular_dynamics_menu.molecular_dynamics_submenus.cp2k_submenu module ichor.cli.main_menu_submenus.points_directory_menu module ichor.cli.main_menu_submenus.points_directory_menu.points_directory_menu module ichor.cli.main_menu_submenus.points_directory_menu.points_directory_submenus module ichor.cli.main_menu_submenus.points_directory_menu.points_directory_submenus.submit_aimall_menu module ichor.cli.main_menu_submenus.points_directory_menu.points_directory_submenus.submit_database_menu module ichor.cli.main_menu_submenus.points_directory_menu.points_directory_submenus.submit_gaussian_menu module ichor.cli.main_menu_submenus.tools_menu module ichor.cli.main_menu_submenus.tools_menu.tools_menu module ichor.cli.main_menu_submenus.trajectory_menu module ichor.cli.main_menu_submenus.trajectory_menu.trajectory_menu module ichor.cli.menu_description module ichor.cli.menu_options module ichor.cli.useful_functions module ichor.cli.useful_functions.user_input module ichor.core module ichor.core.analysis module ichor.core.analysis.dlpoly module ichor.core.analysis.dlpoly.dlpoly_analysis module ichor.core.analysis.dlpoly.dlpoly_files module ichor.core.analysis.dlpoly.mae_forces module ichor.core.analysis.dlpoly.plot_energy module ichor.core.analysis.dlpoly.true_vs_predicted module ichor.core.analysis.predictions module ichor.core.analysis.s_curves module ichor.core.analysis.s_curves.compact_s_curves module ichor.core.analysis.s_curves.s_curves module ichor.core.analysis.trajectory_analysis module ichor.core.atoms module ichor.core.atoms.alf module ichor.core.atoms.atom module ichor.core.atoms.atoms module ichor.core.atoms.atoms_not_found_exception module ichor.core.atoms.list_of_atoms module ichor.core.atoms.list_of_atoms_atom_view module ichor.core.calculators module ichor.core.calculators.alf module ichor.core.calculators.alf.cahn_ingold_prelog_alf_calculator module ichor.core.calculators.alf.sequence_alf_calculator module ichor.core.calculators.alf_features_to_coordinates_calculator module ichor.core.calculators.c_matrix_calculator module ichor.core.calculators.connectivity module ichor.core.calculators.connectivity.distance_connectivity_calculator module ichor.core.calculators.connectivity.valence_connectivity_calculator module ichor.core.calculators.features module ichor.core.calculators.features.alf_features_calculator module ichor.core.calculators.geometry_calculator module ichor.core.calculators.spherical_to_cartesian_calculator module ichor.core.common module ichor.core.common.arith module ichor.core.common.bool module ichor.core.common.constants module ichor.core.common.conversion module ichor.core.common.dict module ichor.core.common.excel module ichor.core.common.float module ichor.core.common.formatting module ichor.core.common.functools module ichor.core.common.functools.functools module ichor.core.common.int module ichor.core.common.io module ichor.core.common.itertools module ichor.core.common.linalg module ichor.core.common.np module ichor.core.common.obj module ichor.core.common.os module ichor.core.common.pairwise module ichor.core.common.patterns module ichor.core.common.search module ichor.core.common.sorting module ichor.core.common.str module ichor.core.common.types module ichor.core.common.types.bool_toggle module ichor.core.common.types.class_dict module ichor.core.common.types.coordinates module ichor.core.common.types.dict_list module ichor.core.common.types.enum module ichor.core.common.types.file_tree module ichor.core.common.types.itypes module ichor.core.common.types.multipole_moments module ichor.core.common.types.mutable_value module ichor.core.common.types.no_str module ichor.core.common.types.range_dict module ichor.core.common.types.var_repr module ichor.core.common.types.version module ichor.core.common.units module ichor.core.database module ichor.core.database.json module ichor.core.database.json.add_to_database module ichor.core.database.json.query_database module ichor.core.database.query_database module ichor.core.database.sql module ichor.core.database.sql.add_to_database module ichor.core.database.sql.database module ichor.core.database.sql.query_database module ichor.core.files module ichor.core.files.aimall module ichor.core.files.aimall.ab_int module ichor.core.files.aimall.aim module ichor.core.files.aimall.int module ichor.core.files.aimall.ints module ichor.core.files.directory module ichor.core.files.dl_poly module ichor.core.files.dl_poly.dl_poly_config module ichor.core.files.dl_poly.dl_poly_control module ichor.core.files.dl_poly.dl_poly_fflux module ichor.core.files.dl_poly.dl_poly_field module ichor.core.files.dl_poly.dl_poly_history module ichor.core.files.dl_poly.dl_poly_iqa_energies module ichor.core.files.dl_poly.dl_poly_iqa_forces module ichor.core.files.dl_poly.fflux_directory module ichor.core.files.file module ichor.core.files.file_data module ichor.core.files.gaussian module ichor.core.files.gaussian.gaussian_output module ichor.core.files.gaussian.gjf module ichor.core.files.gaussian.wfn module

ichor.core.files.gaussian.wfx module ichor.core.files.mol2 module ichor.core.files.optional_content module ichor.core.files.orca module ichor.core.files.orca.orca_engrad module ichor.core.files.orca.orca_input module ichor.core.files.orca.orca_output module ichor.core.files.pandora module ichor.core.files.pandora.morfi_output module ichor.core.files.pandora.mout module ichor.core.files.pandora.pandora_directory module ichor.core.files.pandora.pandora_input module ichor.core.files.pandora.pyscf_output module ichor.core.files.path_object module ichor.core.files.point_directory module ichor.core.files.points_directory module ichor.core.files.points_directory_parent module ichor.core.files.qcp module ichor.core.files.xyz module ichor.core.files.xyz.trajectory module ichor.core.files.xyz.xyz module ichor.core.models module ichor.core.models.calculate_fflux_derivatives module ichor.core.models.create_datasets module ichor.core.models.fflux_derivative_helper_functions module ichor.core.models.gaussian_energy_derivative_wrt_features module ichor.core.models.kernels module ichor.core.models.kernels.constant module ichor.core.models.kernels.distance module ichor.core.models.kernels.interpreter module ichor.core.models.kernels.interpreter.ast module ichor.core.models.kernels.interpreter.interpreter module ichor.core.models.kernels.interpreter.lexer module ichor.core.models.kernels.interpreter.parser module ichor.core.models.kernels.interpreter.token module ichor.core.models.kernels.interpreter.token_type module ichor.core.models.kernels.kernel module ichor.core.models.kernels.mixed_kernel_with_derivatives module ichor.core.models.kernels.periodic_kernel module ichor.core.models.kernels.rbf module ichor.core.models.kernels.rbf_cyclic module ichor.core.models.mean module ichor.core.models.mean.constant module ichor.core.models.mean.linear module ichor.core.models.mean.mean module ichor.core.models.mean.quadratic module ichor.core.models.mean.zero module ichor.core.models.model module ichor.core.models.model_with_gradient module ichor.core.models.models module ichor.core.models.predict_forces_for_all_atoms module ichor.core.molecular_dynamics module ichor.core.molecular_dynamics.amber module ichor.core.molecular_dynamics.cp2k module ichor.core.multipoles module ichor.core.multipoles.dipole module ichor.core.multipoles.hexadecapole module ichor.core.multipoles.octupole module ichor.core.multipoles.quadrupole module ichor.core.processing module ichor.core.processing.callables module ichor.core.processing.callables.gaussian_processing_callables module ichor.core.processing.callables.int_processing_callables module ichor.core.processing.callables.no_processing_callables module ichor.core.processing.check_functions module ichor.core.processing.point_directory_processing module ichor.core.useful_functions module ichor.core.useful_functions.check_aimall_completed module ichor.core.useful_functions.check_points_dir_suffix module ichor.core.useful_functions.debugging module ichor.core.useful_functions.get_atoms module ichor.hpc module ichor.hpc.batch_system module ichor.hpc.batch_system.batch_system module ichor.hpc.batch_system.jobs module ichor.hpc.batch_system.local module ichor.hpc.batch_system.node module ichor.hpc.batch_system.parallel_environment module ichor.hpc.batch_system.sge module ichor.hpc.batch_system.slurm module ichor.hpc.batch_system.utils module ichor.hpc.global_variables module ichor.hpc.log module ichor.hpc.main module ichor.hpc.main.aimall module ichor.hpc.main.check_for_missing_files module ichor.hpc.main.database module ichor.hpc.main.gaussian module ichor.hpc.main.orca module ichor.hpc.main.trajectory module ichor.hpc.molecular_dynamics module ichor.hpc.molecular_dynamics.amber module ichor.hpc.molecular_dynamics.cp2k module ichor.hpc.submission_command module ichor.hpc.submission_commands module ichor.hpc.submission_commands.aimall_command module ichor.hpc.submission_commands.amber_command module ichor.hpc.submission_commands.cp2k_command module ichor.hpc.submission_commands.dlpoly_command module ichor.hpc.submission_commands.free_flow_python_command module ichor.hpc.submission_commands.gaussian_command module ichor.hpc.submission_commands.orca_command module ichor.hpc.submission_commands.python_command module ichor.hpc.submission_commands.tyche_command module ichor.hpc.submission_script module ichor.hpc.submission_script.command_group module ichor.hpc.submission_script.script_names module ichor.hpc.submission_script.submission_script module ichor.hpc.uid module ichor.hpc.useful_functions module ichor.hpc.useful_functions.get_machine module ichor.hpc.useful_functions.get_python_environment module ichor.hpc.useful_functions.submit_free_flow_python_on_compute module id (AtomNames attribute) (Dataset attribute) (Points attribute) Id (TokenType attribute) id() (Lexer method) idx2col() (in module ichor.core.common.excel) IGAIM (MagProps attribute) ignore_alpha() (in module ichor.core.common.sorting) in_sensitive() (in module ichor.core.common.str) index (Atom property), [1] init_batch_system() (in module ichor.hpc.batch_system) init_machine() (in module ichor.hpc.useful_functions) (in module ichor.hpc.useful_functions.get_machine) initialize_config() (in module ichor.hpc.global_variables) inp_file_path (Int attribute), [1] input() (Screen method) input_units (ModelWithGradients attribute) input_with_prefill() (in module ichor.core.common.os) Int (class in ichor.core.files) (class in ichor.core.files.aimall) (class in ichor.core.files.aimall.int) IntDirectory (class in ichor.core.files) (class in ichor.core.files.aimall) (class in ichor.core.files.aimall.ints) integration_error (Dataset attribute) (Int property), [1], [2] interaction_energy (AtomicMorfiOutput attribute) internal_feature_names() (in module ichor.core.calculators) (in module ichor.core.calculators.geometry_calculator) interpret() (KernelInterpreter method), [1] IntVeeAA (class in ichor.hpc.submission_commands.aimall_command) InvalidCharges (SybylStatus attribute) invR (Model property), [1] (ModelWithGradients property), [1] iqa (Dataset attribute) (Int property), [1], [2] iqa_diatomic_contributions (AbInt attribute), [1] iqa_energies (FFLUXDirectory property), [1], [2] iqa_energy_components (Int attribute), [1] iqa_forces (FFLUXDirectory property), [1], [2] is_atom_name_in_atom_names() (in module ichor.cli.main_menu_submenus.analysis_menu.analysis_menu) is_present() (BatchSystem static method) (SLURM static method), [1] (SunGridEngine static method), [1] items() (MOUT method), [1] iterdir() (Directory method)

J

Job (class in ichor.hpc.batch_system) (class in ichor.hpc.batch_system.jobs) JobID (BatchSystem attribute) (class in ichor.hpc.batch_system) (class in ichor.hpc.batch_system.jobs) (SLURM attribute), [1] (SunGridEngine attribute), [1]

JobStatus (class in ichor.hpc.batch_system.sge) (class in ichor.hpc.batch_system.slurm) join() (in module ichor.core.common.str)

K

K (AtomType attribute) k() (ConstantKernel method), [1] (Kernel method), [1] (KernelProd method) (KernelSum method) (MixedKernelWithDerivatives method), [1] (PeriodicKernel method), [1] (RBF method), [1] (RBFCyclic method), [1] kabsch() (Atoms method), [1] Kelvin (Temperature attribute) Kernel (class in ichor.core.models.kernels) (class in ichor.core.models.kernels.kernel)

kernel (ModelWithGradients attribute) KernelInterpreter (class in ichor.core.models.kernels.interpreter) (class in ichor.core.models.kernels.interpreter.interpreter) KernelProd (class in ichor.core.models.kernels.kernel) KernelSum (class in ichor.core.models.kernels.kernel) keywords (GJF attribute), [1] (RouteCard attribute) kill_pid() (in module ichor.core.common.os) kinetic_energy (DlPolyFFLUX property), [1], [2] kronecker() (in module ichor.core.models.fflux_derivative_helper_functions) kronecker_delta() (in module ichor.core.common.arith)

L

Langevin (AmberThermostat attribute) last_line() (in module ichor.core.common.io) last_modified() (in module ichor.core.common.io) Leb23 (Boaq attribute) Leb25 (Boaq attribute) Leb27 (Boaq attribute) Leb29 (Boaq attribute) Leb31 (Boaq attribute) Leb32 (Boaq attribute) lengthscale (MixedKernelWithDerivatives property), [1] lengthscales (MixedKernelWithDerivatives property), [1] (PeriodicKernel property), [1] (RBF property), [1] Lexer (class in ichor.core.models.kernels.interpreter.lexer) Li (AtomType attribute) license_check_succeeded (Aim attribute), [1]

linear_contains() (in module ichor.core.common.search) LinearMean (class in ichor.core.models.mean) (class in ichor.core.models.mean.linear) link0 (GJF attribute), [1] ListOfAtoms (class in ichor.core.atoms) (class in ichor.core.atoms.list_of_atoms) ln() (in module ichor.core.common.io) local_spherical_multipoles() (Int method), [1], [2] LocalBatchSystem (class in ichor.hpc.batch_system) (class in ichor.hpc.batch_system.local) logdet (Model property), [1] (ModelWithGradients property), [1] LoginNode (NodeType attribute), [1] LonePair (AtomType attribute) lower_cholesky (Model property), [1] (ModelWithGradients property), [1] LParen (TokenType attribute)

M

mae_forces() (in module ichor.core.analysis.dlpoly.mae_forces) mag() (in module ichor.core.common.linalg) MagProps (class in ichor.hpc.submission_commands.aimall_command) main_input (OrcaInput attribute), [1] MainMenuMenuOptions (class in ichor.cli.main_menu) MainMenuOptions (class in ichor.cli.main_menu) major (Version attribute), [1] make_chart_settings() (in module ichor.core.analysis.s_curves.compact_s_curves) (in module ichor.core.analysis.s_curves.s_curves) make_csvs_from_database() (SubmitCSVSFunctions static method) mask (RBFCyclic attribute), [1] mass (Atom property), [1] masses (Atoms property), [1] max_running_tasks() (BatchSystem class method) (SLURM class method), [1] (SunGridEngine class method), [1] maxsect (AtomicMorfiOutput attribute) mdcrd_to_xyz() (in module ichor.core.molecular_dynamics.amber) Mean (class in ichor.core.models.mean) (class in ichor.core.models.mean.mean) mean (ModelWithGradients attribute) Medium (IASMesh attribute) MenuDescription (class in ichor.cli.menu_description) MenuOptions (class in ichor.cli.menu_options) merge() (in module ichor.core.common.dict) merge_mutable() (in module ichor.core.common.dict) method (GJF attribute), [1] (OrcaInput attribute), [1] (RouteCard attribute) mgp_path (Aim attribute), [1] mgpviz_path (Aim attribute), [1] minor (Version attribute), [1] Minus (TokenType attribute) MIR (class in ichor.hpc.submission_commands.aimall_command) mirror_point() (in module ichor.core.common.linalg) MissingIchorConfig MixedKernelWithDerivatives (class in ichor.core.models.kernels) (class in ichor.core.models.kernels.mixed_kernel_with_derivatives) mkdir() (Directory method) (in module ichor.core.common.io) MMFF94 (ChargeType attribute) Model (class in ichor.core.models) (class in ichor.core.models.model) Models (class in ichor.core.models) (class in ichor.core.models.models) ModelsView (class in ichor.core.models.models) ModelWithGradients (class in ichor.core.models) (class in ichor.core.models.model_with_gradient) Moderate (CPConn attribute) module ichor.cli ichor.cli.completers ichor.cli.completers.tab_completer ichor.cli.console_menu ichor.cli.global_menu_variables ichor.cli.main_menu ichor.cli.main_menu_submenus ichor.cli.main_menu_submenus.analysis_menu ichor.cli.main_menu_submenus.analysis_menu.analysis_menu ichor.cli.main_menu_submenus.database_menu ichor.cli.main_menu_submenus.database_menu.submit_csvs_from_database ichor.cli.main_menu_submenus.molecular_dynamics_menu ichor.cli.main_menu_submenus.molecular_dynamics_menu.molecular_dynamics_menu ichor.cli.main_menu_submenus.molecular_dynamics_menu.molecular_dynamics_submenus ichor.cli.main_menu_submenus.molecular_dynamics_menu.molecular_dynamics_submenus.amber_submenu ichor.cli.main_menu_submenus.molecular_dynamics_menu.molecular_dynamics_submenus.cp2k_submenu ichor.cli.main_menu_submenus.points_directory_menu ichor.cli.main_menu_submenus.points_directory_menu.points_directory_menu ichor.cli.main_menu_submenus.points_directory_menu.points_directory_submenus ichor.cli.main_menu_submenus.points_directory_menu.points_directory_submenus.submit_aimall_menu ichor.cli.main_menu_submenus.points_directory_menu.points_directory_submenus.submit_database_menu ichor.cli.main_menu_submenus.points_directory_menu.points_directory_submenus.submit_gaussian_menu ichor.cli.main_menu_submenus.tools_menu ichor.cli.main_menu_submenus.tools_menu.tools_menu ichor.cli.main_menu_submenus.trajectory_menu ichor.cli.main_menu_submenus.trajectory_menu.trajectory_menu ichor.cli.menu_description ichor.cli.menu_options ichor.cli.useful_functions ichor.cli.useful_functions.user_input ichor.core ichor.core.analysis ichor.core.analysis.dlpoly ichor.core.analysis.dlpoly.dlpoly_analysis ichor.core.analysis.dlpoly.dlpoly_files ichor.core.analysis.dlpoly.mae_forces ichor.core.analysis.dlpoly.plot_energy ichor.core.analysis.dlpoly.true_vs_predicted ichor.core.analysis.predictions ichor.core.analysis.s_curves ichor.core.analysis.s_curves.compact_s_curves ichor.core.analysis.s_curves.s_curves ichor.core.analysis.trajectory_analysis ichor.core.atoms ichor.core.atoms.alf ichor.core.atoms.atom ichor.core.atoms.atoms ichor.core.atoms.atoms_not_found_exception ichor.core.atoms.list_of_atoms ichor.core.atoms.list_of_atoms_atom_view ichor.core.calculators ichor.core.calculators.alf ichor.core.calculators.alf.cahn_ingold_prelog_alf_calculator ichor.core.calculators.alf.sequence_alf_calculator ichor.core.calculators.alf_features_to_coordinates_calculator ichor.core.calculators.c_matrix_calculator ichor.core.calculators.connectivity ichor.core.calculators.connectivity.distance_connectivity_calculator ichor.core.calculators.connectivity.valence_connectivity_calculator ichor.core.calculators.features ichor.core.calculators.features.alf_features_calculator ichor.core.calculators.geometry_calculator ichor.core.calculators.spherical_to_cartesian_calculator ichor.core.common ichor.core.common.arith ichor.core.common.bool ichor.core.common.constants ichor.core.common.conversion ichor.core.common.dict ichor.core.common.excel ichor.core.common.float ichor.core.common.formatting ichor.core.common.functools ichor.core.common.functools.functools ichor.core.common.int ichor.core.common.io ichor.core.common.itertools ichor.core.common.linalg ichor.core.common.np ichor.core.common.obj ichor.core.common.os ichor.core.common.pairwise ichor.core.common.patterns ichor.core.common.search ichor.core.common.sorting ichor.core.common.str ichor.core.common.types ichor.core.common.types.bool_toggle ichor.core.common.types.class_dict ichor.core.common.types.coordinates ichor.core.common.types.dict_list ichor.core.common.types.enum ichor.core.common.types.file_tree ichor.core.common.types.itypes ichor.core.common.types.multipole_moments ichor.core.common.types.mutable_value ichor.core.common.types.no_str ichor.core.common.types.range_dict ichor.core.common.types.var_repr ichor.core.common.types.version ichor.core.common.units ichor.core.database ichor.core.database.json ichor.core.database.json.add_to_database ichor.core.database.json.query_database ichor.core.database.query_database ichor.core.database.sql ichor.core.database.sql.add_to_database ichor.core.database.sql.database ichor.core.database.sql.query_database ichor.core.files ichor.core.files.aimall ichor.core.files.aimall.ab_int ichor.core.files.aimall.aim ichor.core.files.aimall.int ichor.core.files.aimall.ints ichor.core.files.directory ichor.core.files.dl_poly ichor.core.files.dl_poly.dl_poly_config ichor.core.files.dl_poly.dl_poly_control ichor.core.files.dl_poly.dl_poly_fflux ichor.core.files.dl_poly.dl_poly_field ichor.core.files.dl_poly.dl_poly_history ichor.core.files.dl_poly.dl_poly_iqa_energies ichor.core.files.dl_poly.dl_poly_iqa_forces ichor.core.files.dl_poly.fflux_directory ichor.core.files.file ichor.core.files.file_data ichor.core.files.gaussian ichor.core.files.gaussian.gaussian_output ichor.core.files.gaussian.gjf ichor.core.files.gaussian.wfn ichor.core.files.gaussian.wfx ichor.core.files.mol2 ichor.core.files.optional_content ichor.core.files.orca ichor.core.files.orca.orca_engrad ichor.core.files.orca.orca_input ichor.core.files.orca.orca_output ichor.core.files.pandora ichor.core.files.pandora.morfi_output ichor.core.files.pandora.mout ichor.core.files.pandora.pandora_directory ichor.core.files.pandora.pandora_input ichor.core.files.pandora.pyscf_output ichor.core.files.path_object ichor.core.files.point_directory ichor.core.files.points_directory ichor.core.files.points_directory_parent ichor.core.files.qcp ichor.core.files.xyz ichor.core.files.xyz.trajectory ichor.core.files.xyz.xyz ichor.core.models ichor.core.models.calculate_fflux_derivatives ichor.core.models.create_datasets ichor.core.models.fflux_derivative_helper_functions ichor.core.models.gaussian_energy_derivative_wrt_features ichor.core.models.kernels ichor.core.models.kernels.constant ichor.core.models.kernels.distance ichor.core.models.kernels.interpreter ichor.core.models.kernels.interpreter.ast ichor.core.models.kernels.interpreter.interpreter ichor.core.models.kernels.interpreter.lexer ichor.core.models.kernels.interpreter.parser ichor.core.models.kernels.interpreter.token ichor.core.models.kernels.interpreter.token_type ichor.core.models.kernels.kernel ichor.core.models.kernels.mixed_kernel_with_derivatives ichor.core.models.kernels.periodic_kernel ichor.core.models.kernels.rbf ichor.core.models.kernels.rbf_cyclic ichor.core.models.mean ichor.core.models.mean.constant ichor.core.models.mean.linear ichor.core.models.mean.mean ichor.core.models.mean.quadratic ichor.core.models.mean.zero ichor.core.models.model ichor.core.models.model_with_gradient ichor.core.models.models ichor.core.models.predict_forces_for_all_atoms ichor.core.molecular_dynamics ichor.core.molecular_dynamics.amber ichor.core.molecular_dynamics.cp2k ichor.core.multipoles ichor.core.multipoles.dipole ichor.core.multipoles.hexadecapole ichor.core.multipoles.octupole ichor.core.multipoles.quadrupole ichor.core.processing ichor.core.processing.callables ichor.core.processing.callables.gaussian_processing_callables ichor.core.processing.callables.int_processing_callables ichor.core.processing.callables.no_processing_callables ichor.core.processing.check_functions ichor.core.processing.point_directory_processing ichor.core.useful_functions ichor.core.useful_functions.check_aimall_completed ichor.core.useful_functions.check_points_dir_suffix ichor.core.useful_functions.debugging ichor.core.useful_functions.get_atoms ichor.hpc ichor.hpc.batch_system ichor.hpc.batch_system.batch_system ichor.hpc.batch_system.jobs ichor.hpc.batch_system.local ichor.hpc.batch_system.node ichor.hpc.batch_system.parallel_environment ichor.hpc.batch_system.sge ichor.hpc.batch_system.slurm ichor.hpc.batch_system.utils ichor.hpc.global_variables ichor.hpc.log ichor.hpc.main ichor.hpc.main.aimall ichor.hpc.main.check_for_missing_files ichor.hpc.main.database ichor.hpc.main.gaussian ichor.hpc.main.orca ichor.hpc.main.trajectory ichor.hpc.molecular_dynamics ichor.hpc.molecular_dynamics.amber ichor.hpc.molecular_dynamics.cp2k ichor.hpc.submission_command ichor.hpc.submission_commands ichor.hpc.submission_commands.aimall_command ichor.hpc.submission_commands.amber_command ichor.hpc.submission_commands.cp2k_command ichor.hpc.submission_commands.dlpoly_command ichor.hpc.submission_commands.free_flow_python_command ichor.hpc.submission_commands.gaussian_command ichor.hpc.submission_commands.orca_command ichor.hpc.submission_commands.python_command ichor.hpc.submission_commands.tyche_command ichor.hpc.submission_script ichor.hpc.submission_script.command_group ichor.hpc.submission_script.script_names ichor.hpc.submission_script.submission_script ichor.hpc.uid ichor.hpc.useful_functions ichor.hpc.useful_functions.get_machine ichor.hpc.useful_functions.get_python_environment ichor.hpc.useful_functions.submit_free_flow_python_on_compute

modules (AIMAllCommand attribute), [1] (AmberCommand attribute), [1] (CommandGroup property) (CP2KCommand attribute), [1] (DlpolyCommand attribute), [1] (GaussianCommand attribute), [1] (OrcaCommand attribute), [1] (PythonCommand attribute), [1] (SubmissionCommand attribute) (SubmissionScript property), [1] (TycheCommand attribute), [1] Mol2 (class in ichor.core.files) (class in ichor.core.files.mol2) Mol2Atom (class in ichor.core.files.mol2) molecular_dipole (GaussianOutput attribute), [1] molecular_hexadecapole (GaussianOutput attribute), [1] molecular_octupole (GaussianOutput attribute), [1] molecular_quadrupole (GaussianOutput attribute), [1] MolecularDipole (class in ichor.core.common.types.multipole_moments) MolecularDynamicsMenuFunctions (class in ichor.cli.main_menu_submenus.molecular_dynamics_menu.molecular_dynamics_menu) MolecularDynamicsMenuOptions (class in ichor.cli.main_menu_submenus.molecular_dynamics_menu.molecular_dynamics_menu) MolecularHexadecapole (class in ichor.core.common.types.multipole_moments) MolecularOctupole (class in ichor.core.common.types.multipole_moments) MolecularOrbital (class in ichor.core.files.gaussian.wfn) (class in ichor.core.files.gaussian.wfx) MolecularQuadrupole (class in ichor.core.common.types.multipole_moments) MoleculeType (class in ichor.core.files.mol2) morfi_grid_angular (PandoraInput attribute), [1] morfi_grid_angular_h (PandoraInput attribute), [1] morfi_grid_radial (PandoraInput attribute), [1] morfi_grid_radial_h (PandoraInput attribute), [1] MorfiDirectory (class in ichor.core.files) (class in ichor.core.files.pandora) (class in ichor.core.files.pandora.morfi_output) MorfiWFN (class in ichor.core.files.pandora.pyscf_output) MOUT (class in ichor.core.files.pandora) (class in ichor.core.files.pandora.mout) move() (Directory method) (File method) (in module ichor.core.common.io) (PathObject method) mpl_get_true_vals_dict() (in module ichor.core.analysis.s_curves.compact_s_curves) Mul (TokenType attribute) Mulliken (ChargeType attribute) multiplicity (GaussianOutput attribute), [1] MutableValue (class in ichor.core.common.types) (class in ichor.core.common.types.mutable_value)

N

N1 (AtomType attribute) N2 (AtomType attribute) N3 (AtomType attribute) N4 (AtomType attribute) n_bonds_of_type() (in module ichor.core.files.mol2) Na (AtomType attribute) nacps (Aim attribute), [1] NAm (AtomType attribute) name (Atom property), [1] (AtomNames attribute) (Directory property) (KernelProd property) (KernelSum property) (Points attribute) name_without_suffix (Directory property) names (Atoms property), [1] (Enum attribute), [1] names() (ConnectedAtoms method) NAr (AtomType attribute) natoms (Atoms property), [1] (AtomView property), [1] (FFLUXDirectory property), [1], [2] (HasAtoms property) (ListOfAtoms property), [1] (ModelWithGradients attribute) (PointsDirectory property), [1] (Trajectory property), [1], [2] nbcp (MOUT attribute) nbcps (Aim attribute), [1] nccp (MOUT attribute) nccps (Aim attribute), [1] ncores (TycheCommand attribute), [1] NCriticalPoint (class in ichor.core.files.pandora.mout) ndata (SubmissionCommand property) ndims (MixedKernelWithDerivatives property), [1] net_charge (Int attribute), [1] New (IntVeeAA attribute) nfeats (ModelWithGradients attribute) nkernel (CompositeKernel property) (Kernel property), [1] nnacps (Aim attribute), [1] nnuc (MOUT attribute) No (ATIDSProps attribute) (Ehren attribute) (SCP attribute) (UseTwoe attribute) (VerifyW attribute)

no_processing_function() (in module ichor.core.processing.callables) (in module ichor.core.processing.callables.no_processing_callables) NoBoundary (DlpolyPeriodicBoundary attribute) NoCharges (ChargeType attribute) NoConstraint (BondLengthConstraint attribute) Node (class in ichor.core.common.search) node_options() (BatchSystem class method) (SLURM class method), [1] (SunGridEngine class method), [1] node_to_path() (in module ichor.core.common.search) NodeType (class in ichor.hpc.batch_system) (class in ichor.hpc.batch_system.node) NONE (MagProps attribute) (SHMMax attribute) (SybylStatus attribute) nonmet() (in module ichor.core.files.mol2) NoPeriodicBoundary (PeriodicBoundaryCondition attribute) Normal (PrintLevel attribute) NoStr (class in ichor.core.common.types) (class in ichor.core.common.types.no_str) notes (ModelWithGradients attribute) NP13 (AtomType attribute) np_array_to_trajectory() (Trajectory class method), [1], [2] nproc (Aim attribute), [1] nrcp (MOUT attribute) nrcps (Aim attribute), [1] ntimes_cached_property (in module ichor.core.common.functools) (in module ichor.core.common.functools.functools) ntimesteps (DlPolyFFLUX property), [1], [2] ntrain (Models property), [1] (ModelWithGradients attribute) ntypes (CommandGroup property) nuclear_charge (Atom property), [1] nuclear_charge_sum (Atoms property), [1] NucleicAcid (MoleculeType attribute) Num (class in ichor.core.models.kernels.interpreter.ast) num2col() (in module ichor.core.common.excel) Number (TokenType attribute) number() (Lexer method) NumProcs (BatchSystem attribute) (SLURM attribute), [1] (SunGridEngine attribute), [1]

O

O2 (AtomType attribute) O3 (AtomType attribute) object_get_properties() (in module ichor.core.common.obj) object_get_properties_and_values() (in module ichor.core.common.obj) object_getattribute() (in module ichor.core.common.obj) object_getdict() (in module ichor.core.common.obj) object_hasattr() (in module ichor.core.common.obj) object_setattr() (in module ichor.core.common.obj) OCO2 (AtomType attribute) Octupole (SHMMax attribute) octupole_cartesian_to_spherical() (in module ichor.core.multipoles) (in module ichor.core.multipoles.octupole) octupole_element_conversion() (in module ichor.core.multipoles.octupole) octupole_nontraceless_to_traceless() (in module ichor.core.multipoles.octupole) octupole_one_term_general_expression() (in module ichor.core.multipoles.octupole) octupole_rotate_cartesian() (in module ichor.core.multipoles) (in module ichor.core.multipoles.octupole) octupole_spherical_to_cartesian() (in module ichor.core.multipoles) (in module ichor.core.multipoles.octupole) Old (IntVeeAA attribute) Omega_prime() (in module ichor.core.multipoles.octupole) OmitAll (ForceEvaluation attribute) OmitAngle (ForceEvaluation attribute) OmitBonds (ForceEvaluation attribute) OmitDihedral (ForceEvaluation attribute) OmitHAngle (ForceEvaluation attribute) OmitHBonds (ForceEvaluation attribute) OmitHDihedral (ForceEvaluation attribute) One (Encomp attribute) OneElectronGradient (Ehren attribute) Only (VerifyW attribute) OptimisedIsokineticNoseHoover (AmberThermostat attribute) OptionalContentType (class in ichor.core.files.optional_content) OptionCmd (BatchSystem attribute) (LocalBatchSystem property), [1] (SLURM attribute), [1] (SunGridEngine attribute), [1]

options (CommandGroup property) (SubmissionCommand property) (SubmissionScript property), [1] Orbital (class in ichor.core.common.constants) Orbitals (class in ichor.core.common.constants) OrcaCommand (class in ichor.hpc.submission_commands) (class in ichor.hpc.submission_commands.orca_command) OrcaEngrad (class in ichor.core.files) (class in ichor.core.files.orca) (class in ichor.core.files.orca.orca_engrad) OrcaInput (class in ichor.core.files) (class in ichor.core.files.orca) (class in ichor.core.files.orca.orca_input) OrcaOutput (class in ichor.core.files) (class in ichor.core.files.orca) (class in ichor.core.files.orca.orca_output) order_of_magnitude() (in module ichor.core.common.arith) origin_idx (ALF attribute), [1] Orthorhombic (DlpolyPeriodicBoundary attribute) OSPC (AtomType attribute) OT3P (AtomType attribute) other_atom() (in module ichor.core.files.mol2) other_atom_bonds() (in module ichor.core.files.mol2) other_bonded_atoms() (in module ichor.core.files.mol2) out_file_path (Int attribute), [1] output_directory() (BatchSystem class method) (LocalBatchSystem class method), [1] (SLURM class method), [1] (SunGridEngine class method), [1] output_file (Aim attribute), [1] output_unit (ModelWithGradients attribute) output_wfn() (GJF method), [1], [2]

P

P (Orbitals attribute) P3 (AtomType attribute) pack_cartesian_dipole() (in module ichor.core.multipoles) (in module ichor.core.multipoles.dipole) pack_cartesian_hexadecapole() (in module ichor.core.multipoles) (in module ichor.core.multipoles.hexadecapole) pack_cartesian_octupole() (in module ichor.core.multipoles) (in module ichor.core.multipoles.octupole) pack_cartesian_quadrupole() (in module ichor.core.multipoles) (in module ichor.core.multipoles.quadrupole) pairwise() (in module ichor.core.common.pairwise) PandoraCCSDmod (class in ichor.core.files.pandora.pandora_input) PandoraDirectory (class in ichor.core.files) (class in ichor.core.files.pandora) (class in ichor.core.files.pandora.pandora_directory) PandoraInput (class in ichor.core.files) (class in ichor.core.files.pandora) (class in ichor.core.files.pandora.pandora_input) parallel_environment() (BatchSystem class method) (LocalBatchSystem class method), [1] (SLURM class method), [1] (SunGridEngine class method), [1] ParallelEnvironment (class in ichor.hpc.batch_system) (class in ichor.hpc.batch_system.parallel_environment) Parallelepiped (DlpolyPeriodicBoundary attribute) params (CompositeKernel property) (ConstantKernel property), [1] (KernelProd property) (MixedKernelWithDerivatives property), [1] (PeriodicKernel property), [1] (RBF property), [1] (RBFCyclic property), [1] params() (Kernel method), [1] parent (Atom property), [1] parent_menu_options (ConsoleMenu property) parse() (Parser method) parse_from_string() (Version method), [1] parse_from_version() (Version method), [1] parse_job_id() (BatchSystem class method) (LocalBatchSystem class method), [1] (SLURM class method), [1] (SunGridEngine class method), [1] parse_route_card() (GJF class method), [1], [2] Parser (class in ichor.core.models.kernels.interpreter.parser) patch (Version attribute), [1] path (AbInt attribute), [1], [2] (Aim attribute), [1], [2] (AmberMDIn attribute) (AnnotatedDirectory attribute) (CP2KInput attribute) (Directory attribute) (DlPolyConfig attribute), [1], [2] (DlPolyControl attribute), [1], [2] (DlPolyFFLUX attribute), [1], [2] (DlPolyField attribute), [1], [2] (DlpolyHistory attribute), [1], [2] (DlPolyIQAEnergies attribute), [1], [2] (DlPolyIQAForces attribute), [1], [2] (FFLUXDirectory attribute), [1], [2] (File attribute) (FileNode property), [1] (GaussianOutput attribute), [1], [2] (GJF attribute), [1], [2] (Int attribute), [1], [2] (IntDirectory attribute), [1], [2] (Model attribute), [1] (Models attribute), [1] (ModelsView attribute) (ModelWithGradients attribute), [1] (Mol2 attribute), [1] (MorfiDirectory attribute), [1], [2] (MorfiWFN attribute) (MOUT attribute), [1] (OrcaEngrad attribute), [1], [2] (OrcaInput attribute), [1], [2] (OrcaOutput attribute), [1], [2] (PandoraDirectory attribute), [1], [2] (PandoraInput attribute), [1], [2] (PathObject attribute) (PointDirectory attribute), [1] (PointsDirectory attribute), [1] (PointsDirectoryParent attribute), [1] (PySCFDirectory attribute), [1], [2] (ReadFile attribute) (Stability attribute), [1] (Trajectory attribute), [1], [2] (TrajectoryAnalysis attribute), [1] (WFN attribute), [1], [2] (WFX attribute), [1], [2] (WriteFile attribute) (XYZ attribute), [1], [2]

path_objects (AnnotatedDirectory property) PathCompleter (class in ichor.cli.completers) (class in ichor.cli.completers.tab_completer) PathObject (class in ichor.core.files.path_object) pathtypes (AnnotatedDirectory attribute) Pending (JobStatus attribute), [1] percentile() (in module ichor.core.analysis.s_curves.compact_s_curves) (in module ichor.core.analysis.s_curves.s_curves) periodic_lengthscales (MixedKernelWithDerivatives property), [1] PeriodicBoundaryCondition (class in ichor.core.molecular_dynamics.amber) PeriodicKernel (class in ichor.core.models.kernels) (class in ichor.core.models.kernels.periodic_kernel) permissions() (in module ichor.core.common.os) phi (Quadrature attribute) pid_exists() (in module ichor.core.common.os) plot_abs_differences() (DlPolyFFLUX method), [1], [2] plot_differences() (in module ichor.core.analysis.dlpoly.plot_energy) plot_hr() (TrajectoryAnalysis method), [1] plot_total_energy() (in module ichor.core.analysis.dlpoly.plot_energy) plot_total_energy_from_array() (in module ichor.core.analysis.dlpoly.plot_energy) plot_true_vs_predicted_from_arrays() (in module ichor.core.analysis.dlpoly.true_vs_predicted) plot_true_vs_predicted_from_arrays_one_system() (in module ichor.core.analysis.dlpoly.true_vs_predicted) plot_with_matplotlib() (in module ichor.core.analysis.s_curves.compact_s_curves) plot_with_matplotlib_simple() (in module ichor.core.analysis.s_curves.compact_s_curves) Plus (TokenType attribute) point_id (Dataset attribute) PointDirectory (class in ichor.core.files) (class in ichor.core.files.point_directory) Points (class in ichor.core.database.sql.database) points_directory_to_aimall_on_compute() (SubmitAIMALLFunctions static method) points_directory_to_database() (SubmitDatabaseFunctions static method) points_directory_to_gaussian_on_compute() (SubmitGaussianFunctions static method) points_parent (Dataset attribute) PointsDirectory (class in ichor.core.files) (class in ichor.core.files.points_directory) PointsDirectoryFunctions (class in ichor.cli.main_menu_submenus.points_directory_menu.points_directory_menu) PointsDirectoryMenuOptions (class in ichor.cli.main_menu_submenus.points_directory_menu.points_directory_menu) PointsDirectoryParent (class in ichor.core.files) (class in ichor.core.files.points_directory_parent) pop() (PriorityQueue method) (Queue method) (Stack method) predict() (Model method), [1] (Models method), [1] (ModelWithGradients method), [1] predict_fflux_forces_for_all_atoms() (in module ichor.core.models.predict_forces_for_all_atoms) predict_fflux_forces_for_all_atoms_dict() (in module ichor.core.models.predict_forces_for_all_atoms) predict_fflux_forces_for_all_atoms_one_dimensional() (in module ichor.core.models.predict_forces_for_all_atoms) print_level (RouteCard attribute) PrintLevel (class in ichor.core.files.gaussian.gjf) printq() (in module ichor.core.useful_functions.debugging) PriorityQueue (class in ichor.core.common.search) ProAIM (BasinIntegrationMethod attribute) processed_data() (HasData method) (PointsDirectory method), [1] (PointsDirectoryParent method), [1] program (ModelWithGradients attribute) program_version (ModelWithGradients attribute) prologue_description_text (MenuDescription attribute) ProMega (BasinIntegrationMethod attribute) ProMega1 (BasinIntegrationMethod attribute) ProMega5 (BasinIntegrationMethod attribute) prop (ModelWithGradients attribute) properties (MOUT property), [1] (WFX property), [1], [2] properties() (IntDirectory method), [1], [2] (PointsDirectory method), [1] Protein (MoleculeType attribute) Pullman (ChargeType attribute) push() (PriorityQueue method) (Queue method) (Stack method) pushd() (in module ichor.core.common.io) PySCFDirectory (class in ichor.core.files) (class in ichor.core.files.pandora) (class in ichor.core.files.pandora.pyscf_output) PythonCommand (class in ichor.hpc.submission_commands) (class in ichor.hpc.submission_commands.python_command) PythonEnvironmentNotFound PythonEnvironmentPath (class in ichor.hpc.useful_functions.get_python_environment)

Q

q (Int property), [1], [2] q00 (Dataset attribute) (Int property), [1], [2] q10 (Dataset attribute) q10_prime() (in module ichor.core.multipoles.dipole) q11c (Dataset attribute) q11c_prime() (in module ichor.core.multipoles.dipole) q11s (Dataset attribute) q11s_prime() (in module ichor.core.multipoles.dipole) q20 (Dataset attribute) q20_prime() (in module ichor.core.multipoles.quadrupole) q21c (Dataset attribute) q21c_prime() (in module ichor.core.multipoles.quadrupole) q21s (Dataset attribute) q21s_prime() (in module ichor.core.multipoles.quadrupole) q22c (Dataset attribute) q22c_prime() (in module ichor.core.multipoles.quadrupole) q22s (Dataset attribute) q22s_prime() (in module ichor.core.multipoles.quadrupole) q30 (Dataset attribute) q31c (Dataset attribute) q31s (Dataset attribute) q32c (Dataset attribute) q32s (Dataset attribute) q33c (Dataset attribute) q33s (Dataset attribute) q40 (Dataset attribute) q41c (Dataset attribute) q41s (Dataset attribute) q42c (Dataset attribute) q42s (Dataset attribute)

q43c (Dataset attribute) q43s (Dataset attribute) q44c (Dataset attribute) q44s (Dataset attribute) q50 (Dataset attribute) q51c (Dataset attribute) q51s (Dataset attribute) q52c (Dataset attribute) q52s (Dataset attribute) q53c (Dataset attribute) q53s (Dataset attribute) q54c (Dataset attribute) q54s (Dataset attribute) q55c (Dataset attribute) q55s (Dataset attribute) quadin (AtomicMorfiOutput attribute) quadout (AtomicMorfiOutput attribute) QuadraticMean (class in ichor.core.models.mean) (class in ichor.core.models.mean.quadratic) Quadrature (class in ichor.core.files.pandora.mout) Quadrupole (SHMMax attribute) quadrupole_cartesian_to_spherical() (in module ichor.core.multipoles) (in module ichor.core.multipoles.quadrupole) quadrupole_element_conversion() (in module ichor.core.multipoles.quadrupole) quadrupole_nontraceless_to_traceless() (in module ichor.core.multipoles.quadrupole) quadrupole_one_term_general_expression() (in module ichor.core.multipoles.quadrupole) quadrupole_rotate_cartesian() (in module ichor.core.multipoles) (in module ichor.core.multipoles.quadrupole) quadrupole_spherical_to_cartesian() (in module ichor.core.multipoles) (in module ichor.core.multipoles.quadrupole) QuantumChemistryProgramInput (class in ichor.core.files.qcp) Queue (class in ichor.core.common.search)

R

R (Model property), [1] (ModelWithGradients property), [1] R() (ConstantKernel method), [1] r() (ConstantKernel method), [1] R() (Kernel method), [1] r() (Kernel method), [1] R() (KernelProd method) r() (KernelProd method) R() (KernelSum method) r() (KernelSum method) (Model method), [1] (ModelWithGradients method), [1] R() (PeriodicKernel method), [1] r() (PeriodicKernel method), [1] (TrajectoryAnalysis method), [1] r2_score() (in module ichor.core.analysis.dlpoly.true_vs_predicted) rad (Quadrature attribute) Radians (Angle attribute) radians_to_degrees() (in module ichor.core.common.units) radius (Atom property), [1] RangeDict (class in ichor.core.common.types) (class in ichor.core.common.types.range_dict) raw_data (AbInt property), [1], [2] (GaussianOutput property), [1], [2] (HasData property) (Int property), [1], [2] (IntDirectory property), [1], [2] (OrcaEngrad property), [1], [2] (OrcaOutput property), [1], [2] (PointDirectory property), [1] (PointsDirectory property), [1] (PointsDirectoryParent property), [1] (WFN property), [1], [2] raw_one_atom_data_to_df_sqlite() (in module ichor.core.database.sql.query_database) RBF (class in ichor.core.models.kernels) (class in ichor.core.models.kernels.rbf) rbf_lengthscales (MixedKernelWithDerivatives property), [1] RBFCyclic (class in ichor.core.models.kernels) (class in ichor.core.models.kernels.rbf_cyclic) Read (FileState attribute) read() (ReadFile method) read_bcp() (in module ichor.core.files.pandora.mout) read_ccp() (in module ichor.core.files.pandora.mout) read_cp() (in module ichor.core.files.pandora.mout) read_cp_and_ncp() (in module ichor.core.files.pandora.mout) read_fflux() (in module ichor.core.analysis.dlpoly.dlpoly_analysis) read_jid() (in module ichor.hpc.batch_system.utils) read_ncp() (in module ichor.core.files.pandora.mout) read_rcp() (in module ichor.core.files.pandora.mout) read_wfn_energy() (in module ichor.core.analysis.dlpoly.dlpoly_analysis) ReadFile (class in ichor.core.files.file) Reading (FileState attribute) recover_molecular_dipole() (in module ichor.core.multipoles) (in module ichor.core.multipoles.dipole) recover_molecular_octupole() (in module ichor.core.multipoles) (in module ichor.core.multipoles.octupole) recover_molecular_quadrupole() (in module ichor.core.multipoles) (in module ichor.core.multipoles.quadrupole)

recursive_move() (in module ichor.core.common.io) RefAngle (SybylStatus attribute) relpath() (in module ichor.core.common.io) remove() (in module ichor.core.common.io) (PathObject method) remove_completer() (DoNothingCompleter method), [1] (TabCompleter method) remove_items() (in module ichor.core.common.dict) remove_with_suffix() (in module ichor.core.common.io) repr() (AIMAllCommand method), [1] (AmberCommand method), [1] (CommandGroup method) (CP2KCommand method), [1] (DlpolyCommand method), [1] (FreeFlowPythonCommand method) (GaussianCommand method), [1] (OrcaCommand method), [1] (PythonCommand method), [1] (SubmissionCommand method) (TycheCommand method), [1] Resubmit (JobStatus attribute), [1] revision (Version attribute), [1] rho (AtomicMorfiOutput attribute) RhombicDodecahedral (DlpolyPeriodicBoundary attribute) Ring (CriticalPointType attribute) ring_critical_points (AtomicMorfiOutput attribute) (Int property), [1], [2] (MOUT attribute) RingCriticalPoint (class in ichor.core.files.pandora.mout) rmsd() (Atoms method), [1] (Trajectory method), [1], [2] rotate() (Atoms method), [1] rotate_dipole() (in module ichor.core.multipoles) (in module ichor.core.multipoles.dipole) rotate_hexadecapole() (in module ichor.core.multipoles) (in module ichor.core.multipoles.hexadecapole) rotate_multipole_moments() (in module ichor.core.database.query_database) rotate_octupole() (in module ichor.core.multipoles) (in module ichor.core.multipoles.octupole) rotate_quadrupole() (in module ichor.core.multipoles) (in module ichor.core.multipoles.quadrupole) rotated_forces() (GaussianOutput method), [1], [2] round_base_10() (in module ichor.core.analysis.dlpoly.plot_energy) RouteCard (class in ichor.core.files.gaussian.gjf) RParen (TokenType attribute) run_check_functions() (MenuOptions method) run_cmd() (in module ichor.core.common.os) run_function() (in module ichor.core.common.functools) (in module ichor.core.common.functools.functools) run_main_menu() (in module ichor.cli.main_menu) run_once() (in module ichor.core.common.functools) (in module ichor.core.common.functools.functools) Running (JobStatus attribute), [1] RuOH (AtomType attribute) Rx() (in module ichor.core.common.linalg) Ry() (in module ichor.core.common.linalg) Rz() (in module ichor.core.common.linalg)

S

S (Orbitals attribute) S2 (AtomType attribute) S3 (AtomType attribute) Saccharide (MoleculeType attribute) SCP (class in ichor.hpc.submission_commands.aimall_command) Screen (class in ichor.cli.console_menu) ScriptNames (class in ichor.hpc.submission_script.script_names) select_basis_set() (CP2KMenuFunctions static method) (SubmitGaussianFunctions static method) select_calculate_feature_forces() (SubmitCSVSFunctions static method) select_database() (SubmitDatabaseFunctions static method) select_database_format() (SubmitCSVSFunctions static method) select_database_path() (SubmitCSVSFunctions static method) select_difference_IQA_and_WFN_threshold() (SubmitCSVSFunctions static method) select_dt() (AmberMenuFunctions static method) select_encomp() (SubmitAIMALLFunctions static method) select_filter_by_energy() (SubmitCSVSFunctions static method) select_filter_by_integration_error() (SubmitCSVSFunctions static method) select_force_calculate_wfns() (SubmitGaussianFunctions static method) select_integration_error_threshold() (SubmitCSVSFunctions static method) select_ln_gamma() (AmberMenuFunctions static method) select_method() (CP2KMenuFunctions static method) (SubmitAIMALLFunctions static method) (SubmitGaussianFunctions static method) select_molecular_charge() (CP2KMenuFunctions static method) select_naat() (SubmitAIMALLFunctions static method) select_number_of_cores() (SubmitAIMALLFunctions static method) (SubmitCSVSFunctions static method) (SubmitGaussianFunctions static method) select_number_of_timesteps() (AmberMenuFunctions static method) (CP2KMenuFunctions static method) select_numer_of_cores() (CP2KMenuFunctions static method) select_overwrite_existing_gjfs() (SubmitGaussianFunctions static method) select_points_directory() (PointsDirectoryFunctions static method) (ToolsMenuFunctions static method) select_rotate_multipole_moments() (SubmitCSVSFunctions static method) select_spin_multiplicity() (CP2KMenuFunctions static method) select_submit_on_compute() (SubmitCSVSFunctions static method) (SubmitDatabaseFunctions static method) select_temperature() (AmberMenuFunctions static method) (CP2KMenuFunctions static method) select_trajectory() (TrajectoryFunctions static method) select_write_every_nth_timestep() (AmberMenuFunctions static method) select_xyz() (MolecularDynamicsMenuFunctions static method) selected_basis_set (CP2KMenuOptions attribute) (SubmitGaussianMenuOptions attribute) selected_calculate_feature_forces (SubmitCSVSMenuOptions attribute) selected_database_format (SubmitCSVSMenuOptions attribute) (SubmitDatabaseMenuOptions attribute) selected_database_path (SubmitCSVSMenuOptions attribute) selected_difference_iqa_and_wfn_kj_per_mol (SubmitCSVSMenuOptions attribute) selected_dt (AmberMenuOptions attribute) selected_encomp (SubmitAIMALLMenuOptions attribute) selected_filter_by_energy (SubmitCSVSMenuOptions attribute) selected_filter_by_integration_error (SubmitCSVSMenuOptions attribute) selected_force_calculate_wfn (SubmitGaussianMenuOptions attribute) selected_ichor_config_file (MainMenuMenuOptions attribute) selected_integration_error (SubmitCSVSMenuOptions attribute) selected_ln_gamma (AmberMenuOptions attribute) selected_method (CP2KMenuOptions attribute) (SubmitAIMALLMenuOptions attribute) (SubmitGaussianMenuOptions attribute) selected_molecular_charge (CP2KMenuOptions attribute) selected_naat (SubmitAIMALLMenuOptions attribute) selected_number_of_cores (CP2KMenuOptions attribute) (SubmitAIMALLMenuOptions attribute) (SubmitCSVSMenuOptions attribute) (SubmitGaussianMenuOptions attribute) selected_number_of_timesteps (AmberMenuOptions attribute) (CP2KMenuOptions attribute) selected_overwrite_existing_gjfs (SubmitGaussianMenuOptions attribute) selected_points_directory_path (PointsDirectoryMenuOptions attribute) (ToolsMenuOptions attribute) selected_rotate_multipole_moments (SubmitCSVSMenuOptions attribute) selected_spin_multiplicity (CP2KMenuOptions attribute) selected_submit_on_compute (SubmitCSVSMenuOptions attribute) (SubmitDatabaseMenuOptions attribute), [1] selected_temperature (AmberMenuOptions attribute) (CP2KMenuOptions attribute) selected_trajectory_path (TrajectoryMenuOptions attribute) selected_write_coordinates_every_nth_timestep (AmberMenuOptions attribute) selected_xyz_path (MolecularDynamicsMenuOptions attribute) SEPARATOR (SubmissionScript attribute), [1] set_angle() (ConnectedAtom method) set_bond() (ConnectedAtom method) set_dihedral() (ConnectedAtom method) set_mem() (GJF method), [1], [2] set_nproc() (GJF method), [1], [2] set_permission() (in module ichor.core.common.os) setter() (ClassPropertyDescriptor method) setup_completer() (DoNothingCompleter method), [1] (TabCompleter method) setup_datafile() (SubmissionScript method), [1] setup_logger() (in module ichor.hpc.log) SHMMax (class in ichor.hpc.submission_commands.aimall_command)

show_exit_option (MenuDescription attribute) Si (AtomType attribute) sigma_fflux() (in module ichor.core.models.fflux_derivative_helper_functions) sign_j() (in module ichor.core.models.fflux_derivative_helper_functions) Simple (CPConn attribute) simplified_write_to_excel() (in module ichor.core.analysis.s_curves.compact_s_curves) Single (BondType attribute) single_or_many_points_directories() (in module ichor.core.useful_functions) (in module ichor.core.useful_functions.check_points_dir_suffix) skip_whitespace() (Lexer method) SLURM (class in ichor.hpc.batch_system) (class in ichor.hpc.batch_system.slurm) Small (MoleculeType attribute) SO (AtomType attribute) SO2 (AtomType attribute) Some (ATIDSProps attribute) (SCP attribute) Sparse (IASMesh attribute) spherical_to_cartesian() (in module ichor.core.calculators) (in module ichor.core.calculators.spherical_to_cartesian_calculator) spin_multiplicity (GJF attribute), [1] (OrcaInput attribute), [1] split_by() (in module ichor.core.common.str) split_every() (in module ichor.core.common.str) split_packmol_trajectory() (Trajectory method), [1], [2] split_traj() (Trajectory method), [1], [2] split_trajectory_into_many_points_directories() (TrajectoryFunctions static method) split_trajectory_into_points_directory() (TrajectoryFunctions static method) squared_euclidean_distance() (Distance static method) Stability (class in ichor.core.analysis) (class in ichor.core.analysis.trajectory_analysis) stable_trajectory() (Stability method), [1] Stack (class in ichor.core.common.search) status() (BatchSystem static method) (LocalBatchSystem static method), [1] (SLURM static method), [1] (SunGridEngine static method), [1] stem (PathObject property) StochasticIsokineticNoseHoover (AmberThermostat attribute) StressDivergence (Ehren attribute) SubmissionCommand (class in ichor.hpc.submission_command) SubmissionScript (class in ichor.hpc.submission_script) (class in ichor.hpc.submission_script.submission_script) submit() (SubmissionScript method), [1] submit_amber() (in module ichor.hpc.molecular_dynamics) (in module ichor.hpc.molecular_dynamics.amber) submit_amber_to_compute() (AmberMenuFunctions static method) submit_center_trajectory_on_atom() (in module ichor.hpc.main.trajectory) submit_check_gaussian_and_aimall() (ToolsMenuFunctions static method) submit_check_points_directory_for_missing_files() (in module ichor.hpc.main) (in module ichor.hpc.main.check_for_missing_files) submit_cp2k() (in module ichor.hpc.molecular_dynamics) (in module ichor.hpc.molecular_dynamics.cp2k) submit_cp2k_to_compute() (CP2KMenuFunctions static method) submit_free_flow_python_command_on_compute() (in module ichor.hpc.useful_functions.submit_free_flow_python_on_compute) submit_gjfs() (in module ichor.hpc.main) (in module ichor.hpc.main.gaussian) submit_make_csvs_from_database() (in module ichor.hpc.main) (in module ichor.hpc.main.database) submit_make_database() (in module ichor.hpc.main.database) submit_orca_to_compute() (in module ichor.hpc.main.orca) submit_points_directory_to_aimall() (in module ichor.hpc.main) (in module ichor.hpc.main.aimall) submit_points_directory_to_gaussian() (in module ichor.hpc.main) (in module ichor.hpc.main.gaussian) submit_points_directory_to_orca() (in module ichor.hpc.main) (in module ichor.hpc.main.orca) submit_script() (BatchSystem class method) submit_script_command (BatchSystem attribute) (LocalBatchSystem attribute), [1] (SLURM attribute), [1] (SunGridEngine attribute), [1] submit_wfns() (in module ichor.hpc.main.aimall) SubmitAIMALLFunctions (class in ichor.cli.main_menu_submenus.points_directory_menu.points_directory_submenus.submit_aimall_menu) SubmitAIMALLMenuOptions (class in ichor.cli.main_menu_submenus.points_directory_menu.points_directory_submenus.submit_aimall_menu) SubmitCSVSFunctions (class in ichor.cli.main_menu_submenus.database_menu.submit_csvs_from_database) SubmitCSVSMenuOptions (class in ichor.cli.main_menu_submenus.database_menu.submit_csvs_from_database) SubmitDatabaseFunctions (class in ichor.cli.main_menu_submenus.points_directory_menu.points_directory_submenus.submit_database_menu) SubmitDatabaseMenuOptions (class in ichor.cli.main_menu_submenus.analysis_menu.analysis_menu) (class in ichor.cli.main_menu_submenus.points_directory_menu.points_directory_submenus.submit_database_menu) SubmitGaussianFunctions (class in ichor.cli.main_menu_submenus.points_directory_menu.points_directory_submenus.submit_gaussian_menu) SubmitGaussianMenuOptions (class in ichor.cli.main_menu_submenus.points_directory_menu.points_directory_submenus.submit_gaussian_menu) Substituted (SybylStatus attribute) subtitle (MenuDescription attribute) sum_iqa_energy (DlPolyFFLUX property), [1], [2] sum_path (Aim attribute), [1] sumviz_path (Aim attribute), [1] SunGridEngine (class in ichor.hpc.batch_system) (class in ichor.hpc.batch_system.sge) SuperFine (IASMesh attribute) Suspended (JobStatus attribute), [1] SybylStatus (class in ichor.core.files.mol2) symlink() (in module ichor.core.common.io) system (Models property), [1] System (SybylStatus attribute) system_name (ModelWithGradients attribute)

T

TabCompleter (class in ichor.cli.completers.tab_completer) tail() (in module ichor.core.common.io) task_noises (ModelWithGradients attribute) TaskID (BatchSystem attribute) (SLURM attribute), [1] (SunGridEngine attribute), [1] TaskLast (BatchSystem attribute) (SLURM attribute), [1] (SunGridEngine attribute), [1] Temperature (class in ichor.core.common.units) temperature_formatter() (in module ichor.core.common.formatting) term() (Parser method) Terse (PrintLevel attribute) test_array_not_null() (SubmissionScript method), [1] theta (Quadrature attribute) Theta_prime() (in module ichor.core.multipoles.octupole) (in module ichor.core.multipoles.quadrupole) threaded_cached_property (class in ichor.core.common.functools) (class in ichor.core.common.functools.functools) threaded_cached_property_ttl (in module ichor.core.common.functools.functools) threaded_cached_property_with_ttl (class in ichor.core.common.functools.functools) Three (Encomp attribute) timed_cached_property (in module ichor.core.common.functools) (in module ichor.core.common.functools.functools) timed_threaded_cached_property (in module ichor.core.common.functools) (in module ichor.core.common.functools.functools) timer() (in module ichor.core.useful_functions.debugging) title (Int attribute), [1] (MenuDescription attribute) to_angstroms() (Atom method), [1] (Atoms method), [1] to_bohr() (Atom method), [1] (Atoms method), [1] to_dir() (Trajectory method), [1], [2] to_dirs() (Trajectory method), [1], [2] to_multiple_parent_dirs() (Trajectory method), [1], [2] Token (class in ichor.core.models.kernels.interpreter.token) TokenType (class in ichor.core.models.kernels.interpreter.token_type) ToolsMenuFunctions (class in ichor.cli.main_menu_submenus.tools_menu.tools_menu) ToolsMenuOptions (class in ichor.cli.main_menu_submenus.tools_menu.tools_menu) total_energy (DlPolyFFLUX property), [1], [2] (PointsDirectory property), [1]

total_energy_kj_mol (DlPolyFFLUX property), [1], [2] total_iqa_energies (FFLUXDirectory property), [1], [2] total_time (AbInt attribute), [1] (Int attribute), [1] traceless_molecular_quadrupole (GaussianOutput attribute), [1] TracelessMolecularQuadrupole (class in ichor.core.common.types.multipole_moments) Trajectory (class in ichor.core.files) (class in ichor.core.files.xyz) (class in ichor.core.files.xyz.trajectory) trajectory_from_sqlite_database() (in module ichor.core.database.sql.query_database) TrajectoryAnalysis (class in ichor.core.analysis) (class in ichor.core.analysis.trajectory_analysis) TrajectoryFunctions (class in ichor.cli.main_menu_submenus.trajectory_menu.trajectory_menu) TrajectoryMenuOptions (class in ichor.cli.main_menu_submenus.trajectory_menu.trajectory_menu) Transferring (JobStatus attribute), [1] translate() (Atoms method), [1] Triple (BondType attribute) true_lengthscales (Kernel property), [1] truncate() (in module ichor.core.common.int) TruncatedOctahedral (DlpolyPeriodicBoundary attribute) try_convert() (in module ichor.core.common.conversion) try_float() (in module ichor.core.common.conversion) try_int() (in module ichor.core.common.conversion) Two (Encomp attribute) TycheCommand (class in ichor.hpc.submission_commands) (class in ichor.hpc.submission_commands.tyche_command) type (AtomView property), [1] (Model property), [1] (ModelWithGradients property), [1] type_to_contents (AnnotatedDirectory property) types (Atoms property), [1] (ListOfAtoms property), [1] (Models property), [1] (PointsDirectory property), [1] (Trajectory property), [1], [2] types_extended (Atoms property), [1] (HasAtoms property) (ListOfAtoms property), [1] (PointsDirectory property), [1] (Trajectory property), [1], [2]

U

UnaryOp (class in ichor.core.models.kernels.interpreter.ast) unblock() (File method) unpack_cartesian_dipole() (in module ichor.core.multipoles) (in module ichor.core.multipoles.dipole) unpack_cartesian_hexadecapole() (in module ichor.core.multipoles) (in module ichor.core.multipoles.hexadecapole) unpack_cartesian_octupole() (in module ichor.core.multipoles) (in module ichor.core.multipoles.octupole) unpack_cartesian_quadrupole() (in module ichor.core.multipoles) (in module ichor.core.multipoles.quadrupole) unpaired_electrons (Mol2Atom property) Unread (FileState attribute) Unspecified (BondType attribute) unwrap_item() (in module ichor.core.common.dict) unwrap_single_entry() (in module ichor.core.common.dict) unwrap_single_item() (in module ichor.core.common.dict)

User (ChargeType attribute) user_input_bool() (in module ichor.cli.useful_functions) (in module ichor.cli.useful_functions.user_input) user_input_float() (in module ichor.cli.useful_functions) (in module ichor.cli.useful_functions.user_input) user_input_free_flow() (in module ichor.cli.useful_functions) (in module ichor.cli.useful_functions.user_input) user_input_int() (in module ichor.cli.useful_functions) (in module ichor.cli.useful_functions.user_input) user_input_path() (in module ichor.cli.useful_functions) (in module ichor.cli.useful_functions.user_input) user_input_restricted() (in module ichor.cli.useful_functions) (in module ichor.cli.useful_functions.user_input) uses_conda (PythonEnvironmentPath property) uses_venv (PythonEnvironmentPath property) UseTwoe (class in ichor.hpc.submission_commands.aimall_command)

V

valence (Atom property), [1] (Mol2Atom property) value() (ConstantMean method), [1] (LinearMean method), [1] (Mean method), [1] (QuadraticMean method), [1] (ZeroMean method), [1] values (Enum attribute), [1] Var (class in ichor.core.models.kernels.interpreter.ast) var() (SubmissionScript method), [1] variable() (Parser method) variance() (Model method), [1] (Models method), [1] (ModelWithGradients method), [1] VarReprMixin (class in ichor.core.common.types) (class in ichor.core.common.types.var_repr) vdw_energy (DlPolyFFLUX property), [1], [2]

vdwr (Atom property), [1] vec_to() (Atom method), [1] Vee_aa (UseTwoe attribute) velocity (DlpolyTimestepAtom property) VelocityNotDefined venv_path (PythonEnvironmentPath property) Verbose (PrintLevel attribute) VerifyW (class in ichor.hpc.submission_commands.aimall_command) version (Aim attribute), [1] Version (class in ichor.core.common.types) (class in ichor.core.common.types.version) VeryFine (IASMesh attribute) visit() (ASTNode method) (BinOp method) (Num method) (UnaryOp method) (Var method)

W

WFN (class in ichor.core.files) (class in ichor.core.files.gaussian) (class in ichor.core.files.gaussian.wfn) (F2W attribute) wfn_energy (Points attribute) (PointsDirectory property), [1] wfn_file_path (Int attribute), [1] wfn_path (Aim attribute), [1] WFX (class in ichor.core.files) (class in ichor.core.files.gaussian) (class in ichor.core.files.gaussian.wfx) (F2W attribute) worker() (in module ichor.core.database.query_database) worker_init() (in module ichor.core.database.query_database) write() (JobID method), [1] (PandoraDirectory method), [1], [2] (SubmissionScript method), [1] (WriteFile method) write_cp2k_input() (in module ichor.core.molecular_dynamics.cp2k) write_csvs_intersection() (in module ichor.core.models.create_datasets) write_datafile() (SubmissionScript method), [1] write_final_geometry_to_xyz() (DlpolyHistory method), [1], [2] write_gjfs() (in module ichor.hpc.main.gaussian) write_mdin() (in module ichor.core.molecular_dynamics.amber) write_multiple_train_sets_and_one_test_set() (in module ichor.core.models.create_datasets) write_orca_inputs() (in module ichor.hpc.main.orca)

write_processed_data_for_atoms() (in module ichor.core.database.query_database) write_processed_data_for_atoms_parallel() (in module ichor.core.database) (in module ichor.core.database.query_database) write_processed_one_atom_data_to_csv() (in module ichor.core.database.query_database) write_random_train_test_sets() (in module ichor.core.models.create_datasets) write_raw_one_atom_data_to_csv_sqlite() (in module ichor.core.database.sql.query_database) write_str() (CompositeKernel method) (ConstantKernel method), [1] (ConstantMean method), [1] (Kernel method), [1] (LinearMean method), [1] (Mean method), [1] (MixedKernelWithDerivatives method), [1] (PeriodicKernel method), [1] (QuadraticMean method), [1] (RBF method), [1] (RBFCyclic method), [1] (ZeroMean method), [1] write_to_excel() (in module ichor.core.analysis.s_curves.compact_s_curves) (in module ichor.core.analysis.s_curves.s_curves) write_to_json_database() (PointsDirectory method), [1] (PointsDirectoryParent method), [1] write_to_sqlite3_database() (PointsDirectory method), [1] (PointsDirectoryParent method), [1] write_to_trajectory() (DlpolyHistory method), [1], [2] WriteFile (class in ichor.core.files.file) WrongFileType, [1]

X

x (Coordinates3D property), [1] (Dataset attribute) (ModelWithGradients attribute) (MolecularDipole attribute) x_axis_idx (ALF attribute), [1] x_to_features() (in module ichor.core.models.models) xx (MolecularQuadrupole attribute) (TracelessMolecularQuadrupole attribute) xxx (MolecularOctupole attribute) xxxx (MolecularHexadecapole attribute) xxxy (MolecularHexadecapole attribute) xxxz (MolecularHexadecapole attribute) xxy (MolecularOctupole attribute) xxyy (MolecularHexadecapole attribute) xxyz (MolecularHexadecapole attribute) xxz (MolecularOctupole attribute)

xxzz (MolecularHexadecapole attribute) xy (MolecularQuadrupole attribute) (TracelessMolecularQuadrupole attribute) xy_plane_idx (ALF attribute), [1] XYParallelogram (DlpolyPeriodicBoundary attribute) xyy (MolecularOctupole attribute) XYZ (class in ichor.core.files) (class in ichor.core.files.xyz) (class in ichor.core.files.xyz.xyz) xyz (MolecularOctupole attribute) xyz_from_mdcrd() (AmberMenuFunctions static method) xyz_string (Atom property), [1] (Atoms property), [1] xz (MolecularQuadrupole attribute) (TracelessMolecularQuadrupole attribute) xzz (MolecularOctupole attribute)

Y

y (Coordinates3D property), [1] (Dataset attribute) (ModelWithGradients attribute) (MolecularDipole attribute) y_vec() (in module ichor.core.models.fflux_derivative_helper_functions) Yes (SCP attribute) (VerifyW attribute) yy (MolecularQuadrupole attribute) (TracelessMolecularQuadrupole attribute)

yyxz (MolecularHexadecapole attribute) yyy (MolecularOctupole attribute) yyyx (MolecularHexadecapole attribute) yyyy (MolecularHexadecapole attribute) yyyz (MolecularHexadecapole attribute) yyz (MolecularOctupole attribute) yyzz (MolecularHexadecapole attribute) yz (MolecularQuadrupole attribute) (TracelessMolecularQuadrupole attribute) yzz (MolecularOctupole attribute)

Z

z (Coordinates3D property), [1] (Dataset attribute) (MolecularDipole attribute) Zero (Encomp attribute) ZeroMean (class in ichor.core.models.mean) (class in ichor.core.models.mean.zero)

zz (MolecularQuadrupole attribute) (TracelessMolecularQuadrupole attribute) zzxy (MolecularHexadecapole attribute) zzz (MolecularOctupole attribute) zzzx (MolecularHexadecapole attribute) zzzy (MolecularHexadecapole attribute) zzzz (MolecularHexadecapole attribute)