Index

_

__add__() (Molecule method) __array__() (Molecule method) __call__() (DCDTrajectoryFile method) (JobSettings.OnStatusChangeCallback method) (XYZTrajectoryFile method) __contains__() (JobAnalysis method) (KFFile method) (Results method) (Settings method) __delattr__() (JobAnalysis method) (Settings method) __delitem__() (JobAnalysis method) (Settings method) __dir__() (Settings method) __getattr__() (JobAnalysis method) (Settings method) __getitem__() (JobAnalysis method) (KFFile method) (Molecule method) (Results method) (Settings method) __getstate__() (Job method) (Molecule method) __iadd__() (Molecule method) __init__() (ADFFragmentJob method) (AMSAnalysisJob method) (AMSJob method) (AMSMSDJob method) (AMSNVESpawnerJob method) (AMSRDFJob method) (AMSVACFJob method) (AMSViscosityFromBinLogJob method) (Atom method) (Bond method) (ConfigSettings method) (ConformersJob method) (ConformersResults method) (Cp2kJob method) (CRSJob method) (DCDTrajectoryFile method) (DensfJob method) (DiracJob method) (FCFJob method) (GridRunner method) (Job method) (JobAnalysis method) (JobManager method) (JobManagerSettings method) (JobRunner method) (JobSettings method) (JobSettings.OnStatusChangeCallback method) (KFFile method) (KFHistory method) (KFReader method) (LogSettings method) (Molecule method) (MultiJob method) (NOCVBandFragmentJob method) (ORCAJob method) (PeriodicTable method) (RaspaJob method) (Results method) (RKFHistoryFile method) (RKFTrajectoryFile method) (RunScriptSettings method) (SafeRunSettings method) (Settings method) (SingleJob method) (Units method) (XYZHistoryFile method) (XYZTrajectoryFile method) __init_subclass__() (ApplyRestrict class method) __isub__() (Settings method) __iter__() (Atom method) (Bond method) (KFFile method) (KFReader method) (Molecule method) (MultiJob method) (Settings method) __len__() (Molecule method) __missing__() (Settings method) __new__() (_MetaRunner static method) (AMSCalculator static method) __repr__() (JobAnalysis method) (Molecule method) (Settings method) __round__() (Molecule method) __setattr__() (JobAnalysis method) (Settings method) __setitem__() (JobAnalysis method) (KFFile method) (Settings method)

__setstate__() (Molecule method) __str__() (Atom method) (Bond method) (ConformersResults method) (JobAnalysis method) (Molecule method) (Settings method) __sub__() (Settings method) __subclasshook__() (JobSettings.OnStatusChangeCallback method) __weakref__ (ApplyRestrict attribute) (JobSettings.OnStatusChangeCallback attribute) _atom_suffix() (AMSAnalysisJob static method) _autodetect() (GridRunner method) (KFReader method) _caller_name_and_arg() (in module scm.plams.core.results) _check_hash() (JobManager method) _check_initialized() (ConfigSettings method) _check_queue() (GridRunner method) _clean() (JobManager method) (Results method) _construct_array_dict() (CRSResults method) _copy_to() (Results method) _correct_chemical_system() (RKFHistoryFile method) _create_index() (KFReader method) _datablocks() (KFReader static method) _dict_to_df() (CRSResults static method) _execute() (Job method) (MultiJob method) (SingleJob method) _expand_analysis() (JobAnalysis method) _explicit_init (ConfigSettings property) _export_attribute() (Results method) _flatten_variable() (RKFTrajectoryFile method) _full_name() (Job method) _get_array_dict() (CRSResults method) _get_bond_id() (Molecule method) _get_data() (KFReader method) _get_property() (PeriodicTable class method) _get_ready() (Cp2kJob method) (DiracJob method) (Job method) (MultiJob method) (ORCAJob method) (RaspaJob method) (SingleJob method) _in_thread() (in module scm.plams.core.jobrunner) _limit() (in module scm.plams.core.jobrunner) _log_status() (Job method) _MetaRunner (class in scm.plams.core.jobrunner) _mol_from_rkf_section() (Molecule static method) _move_cursor_to_append_pos() (DCDTrajectoryFile method) (RKFTrajectoryFile method) (XYZTrajectoryFile method) _notify() (MultiJob method) _parse() (KFReader method) _privileged_access() (in module scm.plams.core.results) _process_file() (Results method) _read_block() (KFReader method) _register() (JobManager method) _remove_mol() (AMSAnalysisJob method) (DensfJob method) (FCFJob method) _replace_job_name() (Results static method) _result_type (ADFFragmentJob attribute) (BANDFragmentJob attribute) (ConformersJob attribute) (Cp2kJob attribute) (CRSJob attribute) (NOCVBandFragmentJob attribute) (ORCAJob attribute) (RaspaJob attribute) (VASPJob attribute) _rewrite_molecule() (RKFHistoryFile method) (RKFTrajectoryFile method) _run_job() (JobRunner method) _serialize_mol() (AMSAnalysisJob method) (DensfJob method) (FCFJob method) _set_energy() (RKFTrajectoryFile method) _set_fileobject() (DCDTrajectoryFile method) (RKFTrajectoryFile method) (XYZTrajectoryFile method) _set_mddata_items() (RKFTrajectoryFile method) _set_system_version_elements() (RKFHistoryFile method) _split() (KFFile static method) _store_historydata_for_step() (RKFTrajectoryFile method) _str() (KFFile static method) (Settings method) _update_celldata() (RKFTrajectoryFile method) _validate_atom() (Molecule method) _validate_bond() (Molecule method) _variable_type_equals() (KFFile method) _write_dictionary_to_history() (RKFTrajectoryFile method)

A

add_atom() (Molecule method) add_bond() (Molecule method) add_field() (JobAnalysis method) add_hatoms() (Molecule method) add_Hs() (in module scm.plams.interfaces.molecule.rdkit) add_job() (JobAnalysis method) add_molecule() (Molecule method) add_rkf_field() (JobAnalysis method) add_settings_field() (JobAnalysis method) add_settings_fields() (JobAnalysis method) add_settings_input_fields() (JobAnalysis method) add_standard_field() (JobAnalysis method) add_standard_fields() (JobAnalysis method) add_to_instance() (in module scm.plams.core.functions) ADFCOSMORSCompoundJob (class in scm.plams.recipes.adfcosmorscompound) ADFCOSMORSCompoundResults (class in scm.plams.recipes.adfcosmorscompound) ADFCOSMORSConfFilter (class in scm.plams.recipes.adfcosmorsconformers) ADFCOSMORSConfJob (class in scm.plams.recipes.adfcosmorsconformers) ADFCOSMORSConfResults (class in scm.plams.recipes.adfcosmorsconformers) ADFFragmentJob (class in scm.plams.recipes.adffragment) ADFFragmentResults (class in scm.plams.recipes.adffragment) align2mol() (Molecule method) align_lattice() (Molecule method) AMSAnalysisJob (class in scm.plams.interfaces.adfsuite.amsanalysis) AMSCalculator (class in scm.plams.interfaces.adfsuite.ase_calculator) AMSJob (class in scm.plams.interfaces.adfsuite.ams) AMSMDJob (class in scm.plams.recipes.md.amsmdjob) AMSMDScanDensityJob (class in scm.plams.recipes.md.scandensity) AMSMSDJob (class in scm.plams.recipes.md.trajectoryanalysis) AMSMSDResults (class in scm.plams.recipes.md.trajectoryanalysis) AMSNPTJob (class in scm.plams.recipes.md.amsmdjob) AMSNPTResults (class in scm.plams.recipes.md.amsmdjob)

AMSNVEJob (class in scm.plams.recipes.md.amsmdjob) AMSNVESpawnerJob (class in scm.plams.recipes.md.nvespawner) AMSNVTJob (class in scm.plams.recipes.md.amsmdjob) AMSRDFJob (class in scm.plams.recipes.md.trajectoryanalysis) AMSRDFResults (class in scm.plams.recipes.md.trajectoryanalysis) AMSResults (class in scm.plams.interfaces.adfsuite.ams) AMSVACFJob (class in scm.plams.recipes.md.trajectoryanalysis) AMSVACFResults (class in scm.plams.recipes.md.trajectoryanalysis) AMSViscosityFromBinLogJob (class in scm.plams.recipes.md.trajectoryanalysis) AMSViscosityFromBinLogResults (class in scm.plams.recipes.md.trajectoryanalysis) AMSWorker (class in scm.plams.interfaces.adfsuite.amsworker) AMSWorkerPool (class in scm.plams.interfaces.adfsuite.amsworker) AMSWorkerResults (class in scm.plams.interfaces.adfsuite.amsworker) angle() (Atom method) (in module scm.plams.tools.geometry) apply_reaction_smarts() (in module scm.plams.interfaces.molecule.rdkit) apply_strain() (Molecule method) apply_template() (in module scm.plams.interfaces.molecule.rdkit) apply_to_children() (MultiJob class method) ApplyRestrict (class in scm.plams.core.results) are_orbitals_fractionally_occupied() (AMSResults method) as_array (Molecule property) as_dict() (Molecule method) (Settings method) as_vector() (Bond method) ascii2unicode() (Units class method) assign_chirality() (Molecule method) atexit_timeout (ConfigSettings property) Atom (class in scm.plams.mol.atom) awk_file() (Results method) awk_output() (Results method) axis_rotation_matrix() (in module scm.plams.tools.geometry)

B

balance() (in module scm.plams.tools.reaction) balance_equation() (in module scm.plams.tools.reaction_energies) BANDFragmentJob (class in scm.plams.recipes.bandfragment) BANDFragmentResults (class in scm.plams.recipes.bandfragment)

bend() (in module scm.plams.mol.identify) block_keys() (Settings method) Bond (class in scm.plams.mol.bond) bond_matrix() (Molecule method) broaden_results() (in module scm.plams.tools.postprocess_results)

C

calculate() (AMSCalculator method) call() (GridRunner method) (JobRunner method) canonicalize_mol() (in module scm.plams.interfaces.molecule.rdkit) cell_angles() (Molecule method) cell_lengths() (Molecule method) cell_shape() (in module scm.plams.tools.geometry) cellvectors_from_shape() (in module scm.plams.tools.geometry) check() (ADFFragmentResults method) (AMSAnalysisJob method) (AMSJob method) (ConformersJob method) (Cp2kJob method) (CrystalJob method) (DensfJob method) (DFTBPlusJob method) (DiracJob method) (Job method) (MultiJob method) (ORCAJob method) (ORCAResults method) (RaspaJob method) (SingleJob method) (VASPJob method) check_go() (Cp2kResults method) check_go_conv() (ORCAResults method) check_nocv_eigenvalues() (ADFFragmentResults method) check_scf() (Cp2kResults method) check_scf_conv() (ORCAResults method) clean_exit() (AMSCalculator method) clear() (in module scm.plams.mol.identify) close() (DCDTrajectoryFile method) (RKFTrajectoryFile method) (XYZTrajectoryFile method)

closest_atom() (Molecule method) collapse_field() (JobAnalysis method) collect() (AMSResults method) (ConformersResults method) (DiracResults method) (RaspaResults method) (Results method) compare() (Settings method) ConfigSettings (class in scm.plams.core.settings) ConformersJob (class in scm.conformers) ConformersResults (class in scm.conformers) connection_table (DCDTrajectoryFile property) (XYZTrajectoryFile property) contains_nested() (Settings method) conversion_ratio() (Units class method) convert() (Units class method) convert_to_coskf() (ADFCOSMORSCompoundJob static method) copy() (JobAnalysis method) (Molecule method) (Settings method) cos_to_coskf() (CRSJob static method) coskfpath() (ADFCOSMORSCompoundResults method) counter_len (JobManagerSettings property) Cp2kJob (class in scm.plams.interfaces.thirdparty.cp2k) Cp2kResults (class in scm.plams.interfaces.thirdparty.cp2k) Cp2kSettings2Mol() (in module scm.plams.interfaces.thirdparty.cp2k) CRSJob (class in scm.plams.interfaces.adfsuite.crs) CRSResults (class in scm.plams.interfaces.adfsuite.crs) CrystalJob (class in scm.plams.interfaces.thirdparty.crystal) csv (LogSettings property) current_dir_for_jobs (JobManager property)

D

daemon_threads (ConfigSettings property) date (LogSettings property) DCDTrajectoryFile (class in scm.plams.trajectories.dcdfile) default_jobmanager (ConfigSettings property) default_jobrunner (ConfigSettings property) delay (SafeRunSettings property) delete_all_bonds() (Molecule method) delete_atom() (Molecule method) delete_atoms() (Molecule method) delete_bond() (Molecule method) delete_section() (KFFile method) DensfJob (class in scm.plams.interfaces.adfsuite.densf)

DFTBPlusJob (class in scm.plams.interfaces.thirdparty.dftbplus) DFTBPlusResults (class in scm.plams.interfaces.thirdparty.dftbplus) difference() (Settings method) dihedral() (in module scm.plams.tools.geometry) DiracJob (class in scm.plams.interfaces.thirdparty.dirac) DiracResults (class in scm.plams.interfaces.thirdparty.dirac) display_table() (JobAnalysis method) display_timeline() (JobAnalysis method) distance_array() (in module scm.plams.tools.geometry) distance_to() (Atom method) distance_to_mol() (Molecule method) distance_to_point() (Molecule method)

E

engine_names() (AMSResults method) ensure_property() (AMSCalculator method)

erase_workdir (ConfigSettings property) expand_field() (JobAnalysis method)

F

FCFJob (class in scm.plams.interfaces.adfsuite.fcf) field_keys (JobAnalysis property) file (LogSettings property) file_to_traj() (in module scm.plams.tools.converters) filter_fields() (JobAnalysis method) filter_jobs() (JobAnalysis method) find_bond() (Molecule method) find_case() (Settings method) find_permutation() (Molecule method) finish() (in module scm.plams.core.functions) flatten() (Settings method) forcefield_params_from_rkf() (Molecule method)

format_field() (JobAnalysis method) from_array() (Molecule method) from_dict() (Molecule class method) from_elements() (Molecule class method) from_input() (AMSJob class method) from_inputfile() (AMSJob class method) from_rdmol() (in module scm.plams.interfaces.molecule.rdkit) from_sequence() (in module scm.plams.interfaces.molecule.rdkit) from_smarts() (in module scm.plams.interfaces.molecule.rdkit) from_smiles() (in module scm.plams.interfaces.molecule.rdkit) fromASE() (in module scm.plams.interfaces.molecule.ase) full_runscript() (SingleJob method)

G

gaussian_output_to_ams() (in module scm.plams.tools.converters) GeometryOptimization() (AMSWorker method) GeometryOptimizations() (AMSWorkerPool method) get() (Settings method) get_activity_coefficient() (CRSResults method) get_analysis() (JobAnalysis method) get_atom_types() (AMSResults method) get_atomic_charges() (DFTBPlusResults method) (ORCAResults method) get_atomic_number() (PeriodicTable class method) get_atomic_temperatures_at_step() (AMSResults method) get_backbone_atoms() (in module scm.plams.interfaces.molecule.rdkit) get_band_structure() (AMSResults method) get_block_value() (RaspaResults method) get_boltzmann_distribution() (ConformersResults method) get_ccsd_energy_correction() (SerenityResults method) get_center_of_mass() (Molecule method) get_charges() (AMSResults method) (AMSWorkerResults method) get_chirality() (Molecule method) get_complete_molecules_within_threshold() (Molecule method) get_conformations() (in module scm.plams.interfaces.molecule.rdkit) get_conformers() (ConformersResults method) get_connection_table() (Molecule method) get_connectors() (PeriodicTable class method) get_density() (Molecule method) get_density_along_axis() (AMSResults method) get_diffusion_coefficient() (AMSMSDResults method) get_diffusion_coefficient_from_velocity_acf() (AMSResults method) get_dipole() (ORCAResults method) get_dipole_derivatives_acf() (AMSResults method) get_dipole_vector() (ADFFragmentResults method) (ORCAResults method) get_dipolegradients() (AMSResults method) (AMSWorkerResults method) get_dipolemoment() (AMSResults method) (AMSWorkerResults method) get_dispersion() (Cp2kResults method) (ORCAResults method) get_dispersion_energy() (VASPResults method) get_double_exponential_fit() (AMSViscosityFromBinLogResults method) get_elastictensor() (AMSResults method) (AMSWorkerResults method) get_electron_affinity() (PeriodicTable class method) get_electronegative() (PeriodicTable class method) get_electrons() (ORCAResults method) get_elements() (DCDTrajectoryFile method) (XYZTrajectoryFile method) get_energies() (ConformersResults method) get_energy() (ADFFragmentResults method) (AMSResults method) (AMSWorkerResults method) (Cp2kResults method) (CRSResults method) (DFTBPlusResults method) (ORCAResults method) (SerenityResults method) (VASPResults method) get_energy_decomposition() (ADFFragmentResults method) (BANDFragmentResults method) get_energy_landscape() (AMSResults method) get_energy_uncertainty() (AMSResults method) get_engine_properties() (AMSResults method) get_engine_results() (AMSResults method) get_enthalpy() (ORCAResults method) get_entropy() (ORCAResults method) get_equilibrated_molecule() (AMSNPTResults method) get_errormsg() (AMSJob method) (AMSResults method) (AMSWorkerResults method) (Job method) get_exit_condition_message() (AMSResults method) get_file_chunk() (Results method) get_force_constants() (AMSResults method) get_forcefield_params() (AMSResults method) get_forces() (Cp2kResults method) get_formula() (Molecule method) get_fragment() (Molecule method) get_frequencies() (AMSResults method) get_frequency_spectrum() (AMSResults method) get_from_all_files() (RaspaResults method) get_gibbs_free_energy() (ORCAResults method) get_gradients() (AMSResults method) (AMSWorkerResults method) (ORCAResults method) get_gradients_magnitude_uncertainty() (AMSResults method) get_gradients_uncertainty() (AMSResults method) get_green_kubo_viscosity() (AMSResults method) get_gyration_radius() (Molecule method) get_hessian() (AMSResults method) (AMSWorkerResults method) get_hirshfeld() (ORCAResults method) get_hirshfeld_charges() (Cp2kResults method) get_history_length() (AMSResults method) get_history_molecule() (AMSResults method) get_history_property() (AMSResults method) get_history_variables() (AMSResults method) get_homo_energies() (AMSResults method) get_inertia_matrix() (Molecule method) get_inner_energy() (ORCAResults method) get_input() (AMSJob method) (AMSMSDJob method) (AMSRDFJob method) (AMSVACFJob method) (AMSViscosityFromBinLogJob method) (ConformersJob method) (Cp2kJob method) (CrystalJob method) (DFTBPlusJob method) (DiracJob method) (ORCAJob method) (RaspaJob method) (SerenityJob method) (SingleJob method) (VASPJob method) get_input_molecule() (ADFCOSMORSCompoundResults method) (ADFFragmentResults method) (AMSResults method) (AMSWorkerResults method) get_input_molecules() (AMSResults method) get_input_system() (AMSResults method)

get_ionization_energy() (PeriodicTable class method) get_ir_intensities() (AMSResults method) get_ir_spectrum() (AMSResults method) get_ir_spectrum_md() (AMSResults method) get_irc_results() (AMSResults method) get_isotherm() (RaspaResults method) get_length() (DCDTrajectoryFile method) (RKFTrajectoryFile method) (XYZTrajectoryFile method) get_linear_fit() (AMSMSDResults method) get_lowest_conformer() (ConformersResults method) get_lowest_energy() (ConformersResults method) get_lumo_energies() (AMSResults method) get_main_ase_atoms() (AMSResults method) (AMSWorkerResults method) get_main_engine_name() (AMSResults method) get_main_molecule() (ADFCOSMORSCompoundResults method) (ADFFragmentResults method) (AMSResults method) (AMSWorkerResults method) get_main_system() (AMSResults method) get_mass() (Molecule method) (PeriodicTable class method) get_masses() (Molecule method) get_md_cell_volumes() (Cp2kResults method) get_md_infos() (Cp2kResults method) get_md_pressure() (Cp2kResults method) get_metallic() (PeriodicTable class method) get_molecule() (AMSResults method) (DFTBPlusResults method) get_molecule_indices() (Molecule method) get_moments_of_inertia() (Molecule method) get_msd() (AMSMSDResults method) get_mulliken_charges() (Cp2kResults method) get_multigrid_info() (Cp2kResults method) get_multispecies_dist() (CRSResults method) get_n_spin() (AMSResults method) get_neb_results() (AMSResults method) get_nested() (Settings method) get_nocv_eigenvalues() (ADFFragmentResults method) get_nocv_orbital_interaction() (ADFFragmentResults method) get_normal_modes() (AMSResults method) get_orbital_energies() (AMSResults method) (ORCAResults method) get_orbital_occupations() (AMSResults method) get_output_chunk() (Results method) get_pesscan_results() (AMSResults method) get_phonons_band_structure() (AMSResults method) get_phonons_dos() (AMSResults method) get_phonons_thermodynamic_properties() (AMSResults method) get_plamsmol() (DCDTrajectoryFile method) (RKFHistoryFile method) (RKFTrajectoryFile method) (XYZTrajectoryFile method) get_polarizability() (AMSResults method) get_power_spectrum() (AMSResults method) (AMSVACFResults method) get_prop_names() (CRSResults method) get_properties() (ADFFragmentResults method) get_property_at_step() (AMSResults method) get_pvdos() (AMSResults method) get_radius() (PeriodicTable class method) get_raman_intensities() (AMSResults method) get_raman_spectrum() (AMSResults method) get_rdf() (AMSRDFResults method) get_reaction_image() (in module scm.plams.interfaces.molecule.rdkit) get_reduced_masses() (AMSResults method) get_relative_energies() (ConformersResults method) get_results() (CRSResults method) get_rkf_field_key() (JobAnalysis static method) get_rkf_skeleton() (AMSResults method) get_runscript() (AMSJob method) (ConformersJob method) (Cp2kJob method) (CrystalJob method) (DFTBPlusJob method) (DiracJob method) (ORCAJob method) (RaspaJob method) (SerenityJob method) (SingleJob method) (VASPJob method) get_runtime() (Cp2kResults method) (ORCAResults method) get_scf_iterations() (ORCAResults method) get_settings_field_key() (JobAnalysis static method) get_sigma_potential() (CRSResults method) get_sigma_profile() (ADFCOSMORSCompoundResults method) (CRSResults method) get_skeleton() (KFFile method) get_smallest_homo_lumo_gap() (AMSResults method) get_stresstensor() (AMSResults method) (AMSWorkerResults method) get_structure_energy() (CRSResults method) get_substructure() (in module scm.plams.interfaces.molecule.rdkit) get_symbol() (PeriodicTable class method) get_system() (AMSResults method) get_system_version() (AMSResults method) get_task() (AMSJob method) get_time_step() (AMSResults method) get_timeline() (JobAnalysis method) get_timings() (AMSResults method) (Cp2kResults method) (ORCAResults method) get_unique_angles() (Molecule method) get_unique_bonds() (Molecule method) get_vacf() (AMSVACFResults method) get_value() (RaspaResults method) get_vcd_rotational_strength() (AMSResults method) get_vcd_spectrum() (AMSResults method) get_velocities_from() (AMSMDJob method) get_velocity_acf() (AMSResults method) get_viscosity_integral() (AMSViscosityFromBinLogResults method) get_work_function_results() (AMSResults method) get_zero_point_energy() (AMSResults method) get_zpe() (ORCAResults method) grep_file() (Results method) grep_output() (Results method) GridRunner (class in scm.plams.core.jobrunner) guess_atomic_charges() (Molecule method) guess_bonds() (Molecule method) guess_system_charge() (Molecule method)

H

hash() (Job method) (MultiJob method) (SingleJob method) hash_input() (AMSJob method) (SingleJob method)

hash_runscript() (SingleJob method) hashing (JobManagerSettings property) hybrid_committee_engine_settings() (in module scm.plams.interfaces.adfsuite.ams) hydrogen_to_deuterium() (Molecule method)

I

ignore_failure (ConfigSettings property) implemented_properties (AMSCalculator property) in_ring() (Molecule method) index() (Molecule method) init (ConfigSettings property) init() (in module scm.plams.core.functions)

initialize() (in module scm.plams.mol.identify) is_aromatic() (Bond method) is_valid_stepnumber() (AMSResults method) iter() (KFHistory method) iter_optional() (KFHistory method) iterate() (in module scm.plams.mol.identify)

J

Job (class in scm.plams.core.basejob) job (ConfigSettings property) job_logger (JobManager property) JobAnalysis (class in scm.plams.tools.job_analysis) JobManager (class in scm.plams.core.jobmanager)

jobmanager (ConfigSettings property) JobManagerSettings (class in scm.plams.core.settings) JobRunner (class in scm.plams.core.jobrunner) jobs (JobAnalysis property) JobSettings (class in scm.plams.core.settings) JobSettings.OnStatusChangeCallback (class in scm.plams.core.settings)

K

keep (JobSettings property) keys() (KFFile method) KFFile (class in scm.plams.tools.kftools)

KFHistory (class in scm.plams.tools.kftools) KFReader (class in scm.plams.tools.kftools) knock() (in module scm.plams.mol.identify)

L

label() (Molecule method) label_atoms() (in module scm.plams.mol.identify) length() (Bond method) link_files (JobSettings property) load() (in module scm.plams.core.functions) (SingleJob class method) load_all() (in module scm.plams.core.functions) load_external() (ADFFragmentJob class method) (AMSJob class method) (BANDFragmentJob class method) (ConformersJob class method) (NOCVBandFragmentJob class method) (SingleJob class method)

load_job() (JobAnalysis method) (JobManager method) locate_rings() (Molecule method) locate_rings_acm() (Molecule method) locate_rings_networkx() (Molecule method) log (ConfigSettings property) log() (in module scm.plams.core.functions) LogSettings (class in scm.plams.core.settings)

M

map_atoms_to_bonds() (Molecule method) map_to_central_cell() (Molecule method) maxjobs (JobRunner property) maxthreads (JobRunner property) merge() (Settings method) modify_atom() (in module scm.plams.interfaces.molecule.rdkit) module scm.plams.interfaces.molecule.ase scm.plams.interfaces.molecule.rdkit scm.plams.recipes.adfcosmorscompound scm.plams.recipes.adfcosmorsconformers scm.plams.tools.converters scm.plams.tools.geometry scm.plams.tools.plot scm.plams.tools.postprocess_results scm.plams.tools.reaction_energies

mol2CrystalConf() (in module scm.plams.interfaces.thirdparty.crystal) Molecule (class in scm.plams.mol.molecule) molecule (DCDTrajectoryFile property) (XYZTrajectoryFile property) molecule_name() (in module scm.plams.mol.identify) move_to() (Atom method) MultiJob (class in scm.plams.core.basejob)

N

name (AMSResults property) (AMSWorkerResults property) neighbors() (Atom method) (Molecule method) nested_keys() (Settings method)

new_children() (BANDFragmentJob method) (MultiJob method) (NOCVBandFragmentJob method) new_name() (in module scm.plams.mol.identify) NOCVBandFragmentJob (class in scm.plams.recipes.bandfragment) numbers (Molecule property)

O

ok() (AMSResults method) (AMSWorkerResults method) (Job method) on_status_change (JobSettings property)

ORCAJob (class in scm.plams.interfaces.thirdparty.orca) ORCAResults (class in scm.plams.interfaces.thirdparty.orca) order_ring() (Molecule method) other_end() (Bond method) other_jobs() (MultiJob method)

P

packmol() (in module scm.plams.interfaces.molecule.packmol) packmol_around() (in module scm.plams.interfaces.molecule.packmol) packmol_in_void() (in module scm.plams.interfaces.molecule.packmol) packmol_microsolvation() (in module scm.plams.interfaces.molecule.packmol) packmol_on_slab() (in module scm.plams.interfaces.molecule.packmol) parallel (JobRunner property) ParseInput() (AMSWorker method) partition_protein() (in module scm.plams.interfaces.molecule.rdkit) PeriodicTable (class in scm.plams.tools.periodic_table) perturb_atoms() (Molecule method) perturb_lattice() (Molecule method) pickle (JobSettings property) pickle() (Job method) pickle_protocol (JobSettings property) plot() (CRSResults method) plot_band_structure() (in module scm.plams.tools.plot) plot_conformers() (in module scm.conformers.plams.plot)

plot_correlation() (in module scm.plams.tools.plot) plot_grid_molecules() (in module scm.plams.tools.plot) plot_molecule() (in module scm.plams.tools.plot) plot_msd() (in module scm.plams.tools.plot) plot_phonons_band_structure() (in module scm.plams.tools.plot) plot_phonons_dos() (in module scm.plams.tools.plot) plot_phonons_thermodynamic_properties() (in module scm.plams.tools.plot) plot_work_function() (in module scm.plams.tools.plot) pop() (Settings method) pop_nested() (Settings method) popitem() (Settings method) postrun() (Job method) preoptimize() (in module scm.plams.interfaces.adfsuite.quickjobs) prerun() (ADFFragmentJob method) (BANDFragmentJob method) (Job method) preview (ConfigSettings property) print_molecule() (ORCAJob method)

Q

qe_output_to_ams() (in module scm.plams.tools.converters)

R

RaspaJob (class in scm.plams.interfaces.thirdparty.raspa) RaspaResults (class in scm.plams.interfaces.thirdparty.raspa) reaction_energy() (in module scm.plams.tools.reaction_energies) read() (KFFile method) (KFReader method) (Molecule method) read_all() (KFHistory method) read_all_molecules_in_xyz_file() (in module scm.plams.core.functions) read_file() (Results method) read_frame() (DCDTrajectoryFile method) (RKFTrajectoryFile method) (XYZTrajectoryFile method) read_hybrid_term_rkf() (AMSResults method) read_int() (KFFile method) read_ints() (KFFile method) read_last_frame() (DCDTrajectoryFile method) (RKFTrajectoryFile method) (XYZTrajectoryFile method) read_logical() (KFFile method) read_logicals() (KFFile method) read_molecules() (in module scm.plams.core.functions) read_next() (DCDTrajectoryFile method) (RKFTrajectoryFile method) (XYZTrajectoryFile method) read_real() (KFFile method) read_reals() (KFFile method) read_rkf_section() (AMSResults method) read_section() (KFFile method) read_string() (KFFile method) readase() (Molecule method) readin() (Molecule method) readpdb() (in module scm.plams.interfaces.molecule.rdkit) (Molecule method) readrkf() (AMSResults method) readxyz() (Molecule method) recreate_molecule() (AMSResults method) (Results method) recreate_settings() (AMSResults method) (Cp2kResults method) (Results method) refine_density() (in module scm.plams.interfaces.adfsuite.quickjobs) refine_lattice() (in module scm.plams.interfaces.adfsuite.quickjobs) refresh() (AMSResults method) (Results method)

regex_file() (Results method) remove() (Settings method) remove_child() (MultiJob method) remove_empty_directories (JobManagerSettings property) remove_empty_fields() (JobAnalysis method) remove_field() (JobAnalysis method) remove_fields() (JobAnalysis method) remove_job() (JobAnalysis method) (JobManager method) remove_settings_fields() (JobAnalysis method) remove_uniform_fields() (JobAnalysis method) rename() (Job method) (Results method) rename_field() (JobAnalysis method) rename_job() (JobManager method) reorder_fields() (JobAnalysis method) repeat (SafeRunSettings property) resize() (Bond method) resize_bond() (Molecule method) restart_from() (AMSMDJob class method) Results (class in scm.plams.core.results) rewind() (DCDTrajectoryFile method) (RKFTrajectoryFile method) (XYZTrajectoryFile method) rkf_to_ase_atoms() (in module scm.plams.tools.converters) rkf_to_ase_traj() (in module scm.plams.tools.converters) RKFHistoryFile (class in scm.plams.trajectories.rkfhistoryfile) rkfpath() (AMSResults method) (ConformersResults method) RKFTrajectoryFile (class in scm.plams.trajectories.rkffile) rmsd() (Molecule static method) rotate() (Atom method) (Bond method) (Molecule method) rotate_bond() (Molecule method) rotate_lattice() (Molecule method) rotation_matrix() (in module scm.plams.tools.geometry) round_coords() (Molecule method) run() (AMSJob method) (Job method) run_analysis() (Trajectory method) runscript (JobSettings property) RunScriptSettings (class in scm.plams.core.settings)

S

saferun (ConfigSettings property) SafeRunSettings (class in scm.plams.core.settings) save (JobSettings property) save() (KFFile method) scm.plams.interfaces.molecule.ase module scm.plams.interfaces.molecule.rdkit module scm.plams.recipes.adfcosmorscompound module scm.plams.recipes.adfcosmorsconformers module scm.plams.tools.converters module scm.plams.tools.geometry module scm.plams.tools.plot module scm.plams.tools.postprocess_results module scm.plams.tools.reaction_energies module sections() (KFFile method) separate() (Molecule method) SerenityJob (class in scm.plams.interfaces.thirdparty.serenity) SerenityResults (class in scm.plams.interfaces.thirdparty.serenity) set_atoms_id() (Molecule method) set_byteorder() (DCDTrajectoryFile method) set_connectors() (PeriodicTable class method) set_density() (Molecule method) set_elements() (DCDTrajectoryFile method) (XYZTrajectoryFile method) set_field() (JobAnalysis method) set_integer_bonds() (Molecule method)

set_local_labels() (Molecule method) set_mass() (PeriodicTable class method) set_name() (XYZTrajectoryFile method) set_nested() (Settings method) set_radius() (PeriodicTable class method) setdefault() (Settings method) Settings (class in scm.plams.core.settings) settings_to_mol() (AMSJob static method) shakemd() (in module scm.plams.interfaces.adfsuite.quickjobs) shebang (RunScriptSettings property) shortest_path_dijkstra() (Molecule method) SingleJob (class in scm.plams.core.basejob) SinglePoint() (AMSWorker method) SinglePoints() (AMSWorkerPool method) sleepstep (ConfigSettings property) soft_update() (Settings method) sort_fields() (JobAnalysis method) sort_jobs() (JobAnalysis method) status (Job property) status_log (Job property) stdout (LogSettings property) stdout_redirect (RunScriptSettings property) stop() (AMSWorker method) (AMSWorkerPool method) stop_worker() (AMSCalculator method) store_historydata() (RKFTrajectoryFile method) (XYZTrajectoryFile method) store_mddata() (RKFTrajectoryFile method) str() (Atom method) (Molecule method) style (XYZTrajectoryFile property) substitute() (Molecule method) supercell() (Molecule method) suppress_missing() (Settings class method) symbols (Molecule property)

T

time (LogSettings property) to_csv_file() (JobAnalysis method) to_dataframe() (JobAnalysis method) to_image() (in module scm.plams.interfaces.molecule.rdkit) to_rdmol() (in module scm.plams.interfaces.molecule.rdkit) to_smiles() (in module scm.plams.interfaces.molecule.rdkit)

to_table() (JobAnalysis method) toASE() (in module scm.plams.interfaces.molecule.ase) traj_to_rkf() (in module scm.plams.tools.converters) Trajectory (class in scm.plams.trajectories.trajectory) translate() (Atom method) (Molecule method) twist() (in module scm.plams.mol.identify)

U

unflatten() (Settings method) unique_atoms() (in module scm.plams.mol.identify) unit_cell_volume() (Molecule method)

Units (class in scm.plams.tools.units) unset_atoms_id() (Molecule method) update() (Settings method) update_hbc_to_coskf() (ADFCOSMORSCompoundJob static method)

V

validate() (ViewConfig method) variable_type() (KFReader method) vasp_output_to_ams() (in module scm.plams.tools.converters) VASPJob (class in scm.plams.interfaces.thirdparty.vasp)

VASPResults (class in scm.plams.interfaces.thirdparty.vasp) vector_to() (Atom method) view() (in module scm.plams.tools.view) ViewConfig (class in scm.plams.tools.view)

W

wait() (Results method) workdir (JobManager property) wrap() (Molecule method) write() (KFFile method) (Molecule method) write_next() (DCDTrajectoryFile method) (RKFHistoryFile method) (RKFTrajectoryFile method) (XYZHistoryFile method) (XYZTrajectoryFile method)

writease() (Molecule method) writein() (Molecule method) writepdb() (in module scm.plams.interfaces.molecule.rdkit) (Molecule method) writexyz() (Molecule method)

X

XYZHistoryFile (class in scm.plams.trajectories.xyzhistoryfile)

XYZTrajectoryFile (class in scm.plams.trajectories.xyzfile)

Y

yield_coords() (in module scm.plams.interfaces.molecule.rdkit)