Index

A

add_bond_angle() (turbomoleio.core.molecule.MoleculeSystem method) add_cosmo() (turbomoleio.core.control.Control method) add_data_group() (turbomoleio.core.datagroups.DataGroups method) add_dihedral() (turbomoleio.core.molecule.MoleculeSystem method) add_distance() (turbomoleio.core.molecule.MoleculeSystem method) adg() (in module turbomoleio.core.control) (turbomoleio.core.datagroups.DataGroups method) all_done() (turbomoleio.output.parser.Parser method) aoforce_analysis() (turbomoleio.output.parser.Parser method) aoforce_numerical_integration() (turbomoleio.output.parser.Parser method) AoforceNumericalIntegrationData (class in turbomoleio.output.data)

AoforceOutput (class in turbomoleio.output.files) AoforceRotationalData (class in turbomoleio.output.data) AoforceVibrationalData (class in turbomoleio.output.data) as_dict() (turbomoleio.core.control.Shells method) (turbomoleio.core.datagroups.DataGroups method) (turbomoleio.core.molecule.MoleculeSystem method) (turbomoleio.core.periodic.PeriodicSystem method) (turbomoleio.output.states.State method) (turbomoleio.output.states.States method) assert_almost_equal() (in module turbomoleio.testing) assert_MSONable() (in module turbomoleio.testing) available_templates() (in module turbomoleio.input.templates)

B

BaseData (class in turbomoleio.output.data) BaseSystem (class in turbomoleio.core.base)

basis() (turbomoleio.output.parser.Parser method) BasisData (class in turbomoleio.output.data) BondAngle (class in turbomoleio.core.molecule)

C

cdg() (in module turbomoleio.core.control) (turbomoleio.core.datagroups.DataGroups method) centers() (turbomoleio.output.parser.Parser method) change_data_group() (turbomoleio.core.datagroups.DataGroups method) cleanup_string() (in module turbomoleio.core.datagroups) CollinearBendingAngle (class in turbomoleio.core.molecule) compare() (turbomoleio.core.datagroups.DataGroups method) compare_datagroup_string() (in module turbomoleio.core.datagroups) compare_differences() (in module turbomoleio.testing) compare_states() (turbomoleio.output.states.EigerOutput method) compute_value() (turbomoleio.core.molecule.BondAngle method) (turbomoleio.core.molecule.CollinearBendingAngle method) (turbomoleio.core.molecule.DihedralAngle method) (turbomoleio.core.molecule.Distance method) (turbomoleio.core.molecule.InternalDefinition method) (turbomoleio.core.molecule.InverseDistance method) (turbomoleio.core.molecule.OutOfPlaneAngle method) (turbomoleio.core.molecule.PerpendicularBendingAngle method) Control (class in turbomoleio.core.control) convert_float() (in module turbomoleio.output.parser) convert_int() (in module turbomoleio.output.parser) convert_time_string() (in module turbomoleio.output.parser)

coord_lines() (turbomoleio.core.base.BaseSystem method) coord_str (turbomoleio.core.molecule.BondAngle attribute) (turbomoleio.core.molecule.CollinearBendingAngle attribute) (turbomoleio.core.molecule.DihedralAngle attribute) (turbomoleio.core.molecule.Distance attribute) (turbomoleio.core.molecule.InternalDefinition attribute) (turbomoleio.core.molecule.InverseDistance attribute) (turbomoleio.core.molecule.OutOfPlaneAngle attribute) (turbomoleio.core.molecule.PerpendicularBendingAngle attribute) coord_type (turbomoleio.core.molecule.BondAngle attribute) (turbomoleio.core.molecule.CollinearBendingAngle attribute) (turbomoleio.core.molecule.DihedralAngle attribute) (turbomoleio.core.molecule.Distance attribute) (turbomoleio.core.molecule.InternalDefinition attribute) (turbomoleio.core.molecule.InverseDistance attribute) (turbomoleio.core.molecule.OutOfPlaneAngle attribute) (turbomoleio.core.molecule.PerpendicularBendingAngle attribute) coordinates() (turbomoleio.output.parser.Parser method) cosmo_header() (turbomoleio.output.parser.Parser method) cosmo_results() (turbomoleio.output.parser.Parser method) CosmoData (class in turbomoleio.output.data) cpc() (in module turbomoleio.core.control) (turbomoleio.core.control.Control method)

D

DataGroups (class in turbomoleio.core.datagroups) Defaults (class in turbomoleio.core.control) define_quit() (in module turbomoleio.core.utils) define_timeout (turbomoleio.testing.ItestConfig attribute) DefineError DefineExpectError DefineIredError DefineParameterError DefineRunner (class in turbomoleio.input.define) delete_tmp_dir (turbomoleio.testing.ItestConfig attribute)

delta_e (turbomoleio.core.control.Energy property) density_functional_data() (turbomoleio.output.parser.Parser method) dftd() (turbomoleio.output.parser.Parser method) DFTData (class in turbomoleio.output.data) DihedralAngle (class in turbomoleio.core.molecule) DispersionCorrectionData (class in turbomoleio.output.data) Distance (class in turbomoleio.core.molecule) dryrun (turbomoleio.testing.ItestConfig attribute) dryrun_fpath (turbomoleio.testing.ItestConfig attribute) dryrun_use_ref_control (turbomoleio.testing.ItestConfig attribute) dump_command_file() (turbomoleio.input.define.DefineRunner method)

E

egrad_excited_state() (turbomoleio.output.parser.Parser method) EgradOutput (class in turbomoleio.output.files) eigenvalues (turbomoleio.output.states.States property) EigerOutput (class in turbomoleio.output.states) EigerRunner (class in turbomoleio.output.states) electrostatic_moments() (turbomoleio.output.parser.Parser method) ElectrostaticMomentsData (class in turbomoleio.output.data) empty() (turbomoleio.core.datagroups.DataGroups class method) Energy (class in turbomoleio.core.control)

energy (turbomoleio.core.control.Control property) escf_excitations() (turbomoleio.output.parser.Parser method) escf_gs_total_en() (turbomoleio.output.parser.Parser method) escf_iterations() (turbomoleio.output.parser.Parser method) EscfData (class in turbomoleio.output.data) EscfIterationData (class in turbomoleio.output.data) EscfOnlyOutput (class in turbomoleio.output.files) EscfOutput (class in turbomoleio.output.files) ex_setter() (in module turbomoleio.input.utils)

F

fermi() (turbomoleio.output.parser.Parser method) filter_states() (turbomoleio.output.states.States method) from_dict() (turbomoleio.core.control.Shells class method) (turbomoleio.core.datagroups.DataGroups class method) (turbomoleio.core.molecule.MoleculeSystem class method) (turbomoleio.core.periodic.PeriodicSystem class method) (turbomoleio.output.states.State class method) from_file() (turbomoleio.core.control.Control class method) (turbomoleio.core.control.Energy class method) (turbomoleio.core.control.Gradient class method) (turbomoleio.core.control.Shells class method) (turbomoleio.core.datagroups.DataGroups class method) (turbomoleio.core.molecule.MoleculeSystem class method) (turbomoleio.core.periodic.PeriodicSystem class method) (turbomoleio.output.data.BaseData class method) (turbomoleio.output.parser.Parser class method) (turbomoleio.output.states.EigerOutput class method) (turbomoleio.output.states.States class method) from_metric() (turbomoleio.core.control.Control class method) from_parser() (turbomoleio.output.data.AoforceNumericalIntegrationData class method) (turbomoleio.output.data.AoforceRotationalData class method) (turbomoleio.output.data.AoforceVibrationalData class method) (turbomoleio.output.data.BaseData class method) (turbomoleio.output.data.BasisData class method) (turbomoleio.output.data.CosmoData class method) (turbomoleio.output.data.DFTData class method) (turbomoleio.output.data.DispersionCorrectionData class method) (turbomoleio.output.data.ElectrostaticMomentsData class method) (turbomoleio.output.data.EscfData class method) (turbomoleio.output.data.EscfIterationData class method) (turbomoleio.output.data.FunctionalData class method) (turbomoleio.output.data.GeometryData class method) (turbomoleio.output.data.IntegralData class method) (turbomoleio.output.data.MP2Data class method) (turbomoleio.output.data.MP2Results class method) (turbomoleio.output.data.PeriodicityData class method) (turbomoleio.output.data.RelaxConvergenceData class method) (turbomoleio.output.data.RelaxData class method) (turbomoleio.output.data.RelaxGradientsData class method) (turbomoleio.output.data.RiData class method) (turbomoleio.output.data.RunData class method) (turbomoleio.output.data.ScfData class method) (turbomoleio.output.data.ScfEnergiesData class method) (turbomoleio.output.data.ScfIterationData class method) (turbomoleio.output.data.SmearingData class method) (turbomoleio.output.data.SpinData class method) (turbomoleio.output.data.StatptData class method) (turbomoleio.output.data.SymmetryData class method) (turbomoleio.output.data.TurbomoleData class method) (turbomoleio.output.files.AoforceOutput class method) (turbomoleio.output.files.EgradOutput class method) (turbomoleio.output.files.EscfOnlyOutput class method) (turbomoleio.output.files.EscfOutput class method) (turbomoleio.output.files.GradOutput class method) (turbomoleio.output.files.JobexOutput class method) (turbomoleio.output.files.MP2Output class method) (turbomoleio.output.files.RelaxOutput class method) (turbomoleio.output.files.Ricc2Output class method) (turbomoleio.output.files.ScfOutput class method) (turbomoleio.output.files.StatptOutput class method)

from_string() (turbomoleio.core.control.Energy class method) (turbomoleio.core.control.Gradient class method) (turbomoleio.core.control.Shells class method) (turbomoleio.core.molecule.InternalDefinition class method) (turbomoleio.core.molecule.MoleculeSystem class method) (turbomoleio.core.periodic.PeriodicSystem class method) (turbomoleio.output.data.BaseData class method) (turbomoleio.output.states.EigerOutput class method) FunctionalData (class in turbomoleio.output.data)

G

gap (turbomoleio.output.states.States property) generate_control_for_test() (in module turbomoleio.testing) generate_lowest_filled_states() (turbomoleio.output.states.States method) generate_ref (turbomoleio.testing.ItestConfig attribute) generate_reference_out_parser_files() (in module turbomoleio.testing) generate_reference_output() (in module turbomoleio.testing) GeometryData (class in turbomoleio.output.data) get_charge() (turbomoleio.core.control.Control method) get_control_integration() (in module turbomoleio.testing) get_coord_lines() (in module turbomoleio.core.base) get_define_template() (in module turbomoleio.input.utils) get_eiger_output() (turbomoleio.output.states.EigerRunner method) get_freqs_df() (turbomoleio.output.data.AoforceVibrationalData method) get_int_def_inconsistencies() (turbomoleio.core.molecule.MoleculeSystem method) get_mol_and_indices_frozen() (in module turbomoleio.core.base) get_mos_energies() (in module turbomoleio.output.states)

get_shells() (turbomoleio.core.control.Control method) (turbomoleio.output.states.States method) get_sp() (in module turbomoleio.testing) get_split_jobex_parsers() (turbomoleio.output.parser.Parser method) get_subclass_from_str() (turbomoleio.core.molecule.InternalDefinition static method) get_subfiles_list() (turbomoleio.core.control.Control method) get_test_data_dir() (in module turbomoleio.testing) get_tests_configs_tm_versions() (in module turbomoleio.testing) get_tfp() (in module turbomoleio.testing) get_tm_version() (in module turbomoleio.core.utils) get_value() (turbomoleio.output.parser.Parser method) gisnan() (in module turbomoleio.testing) Gradient (class in turbomoleio.core.control) gradient (turbomoleio.core.control.Control property) gradient() (turbomoleio.output.parser.Parser method) GradOutput (class in turbomoleio.output.files) grep_line() (turbomoleio.output.parser.Parser method)

H

has_fractional_occ (turbomoleio.output.states.State property) (turbomoleio.output.states.States property) has_hole (turbomoleio.output.states.States property) has_inconsistencies() (turbomoleio.core.molecule.MoleculeSystem method)

has_matplotlib() (in module turbomoleio.testing) header() (turbomoleio.output.parser.Parser method) homo (turbomoleio.output.states.States property) homo_index (turbomoleio.output.states.States property)

I

insert() (turbomoleio.output.states.States method) integral() (turbomoleio.output.parser.Parser method) IntegralData (class in turbomoleio.output.data) InternalDefinition (class in turbomoleio.core.molecule) InverseDistance (class in turbomoleio.core.molecule) irrep_indices (turbomoleio.output.states.States property) irreps (turbomoleio.core.control.Shells property) (turbomoleio.output.states.States property)

is_uhf (turbomoleio.core.control.Control property) (turbomoleio.output.states.States property) is_uhf() (turbomoleio.output.parser.Parser method) is_valid() (turbomoleio.core.molecule.InternalDefinition method) ItestConfig (class in turbomoleio.testing) ItestError

J

JobexOutput (class in turbomoleio.output.files)

K

kdg() (in module turbomoleio.core.control) (turbomoleio.core.datagroups.DataGroups method)

kill_data_group() (turbomoleio.core.datagroups.DataGroups method)

L

last_grad_max (turbomoleio.core.control.Gradient property) last_grad_norm (turbomoleio.core.control.Gradient property)

lumo (turbomoleio.output.states.States property) lumo_index (turbomoleio.output.states.States property)

M

max_gradients (turbomoleio.core.control.Gradient property) max_occupation (turbomoleio.output.states.State property) mdgo() (in module turbomoleio.core.control) (turbomoleio.core.datagroups.DataGroups method) METRIC (turbomoleio.core.control.Defaults attribute) modify_data_group_options() (turbomoleio.core.datagroups.DataGroups method) module turbomoleio turbomoleio.core turbomoleio.core.base turbomoleio.core.control turbomoleio.core.datagroups turbomoleio.core.molecule turbomoleio.core.periodic turbomoleio.core.symmetry turbomoleio.core.utils turbomoleio.input turbomoleio.input.define turbomoleio.input.templates turbomoleio.input.utils turbomoleio.output turbomoleio.output.data turbomoleio.output.files turbomoleio.output.parser turbomoleio.output.states turbomoleio.testing

molecule (turbomoleio.core.molecule.MoleculeSystem property) MoleculeSystem (class in turbomoleio.core.molecule) mp2_data() (turbomoleio.output.parser.Parser method) mp2_results() (turbomoleio.output.parser.Parser method) MP2Data (class in turbomoleio.output.data) MP2Output (class in turbomoleio.output.files) MP2Results (class in turbomoleio.output.data)

N

n_atoms (turbomoleio.core.molecule.BondAngle attribute) (turbomoleio.core.molecule.CollinearBendingAngle attribute) (turbomoleio.core.molecule.DihedralAngle attribute) (turbomoleio.core.molecule.Distance attribute) (turbomoleio.core.molecule.InternalDefinition attribute) (turbomoleio.core.molecule.InverseDistance attribute) (turbomoleio.core.molecule.OutOfPlaneAngle attribute) (turbomoleio.core.molecule.PerpendicularBendingAngle attribute)

n_negative_freqs() (turbomoleio.output.data.AoforceVibrationalData method) n_positive_freqs() (turbomoleio.output.data.AoforceVibrationalData method) n_states (turbomoleio.output.states.States property) n_steps (turbomoleio.core.control.Energy property) (turbomoleio.core.control.Gradient property) n_zero_freqs() (turbomoleio.output.data.AoforceVibrationalData method) ndg (turbomoleio.core.datagroups.DataGroups property) norms (turbomoleio.core.control.Gradient property) number_of_data_groups (turbomoleio.core.datagroups.DataGroups property)

O

occupations (turbomoleio.output.states.States property)

OutOfPlaneAngle (class in turbomoleio.core.molecule)

P

ParametersValidationError Parser (class in turbomoleio.output.parser) periodicity_data() (turbomoleio.output.parser.Parser method) PeriodicityData (class in turbomoleio.output.data) PeriodicSystem (class in turbomoleio.core.periodic)

PerpendicularBendingAngle (class in turbomoleio.core.molecule) plot() (turbomoleio.core.control.Energy method) (turbomoleio.core.control.Gradient method) plot_energies() (turbomoleio.output.data.ScfIterationData method) pre_escf_run() (turbomoleio.output.parser.Parser method) pre_scf_run() (turbomoleio.output.parser.Parser method)

R

rdgrad_memory() (turbomoleio.output.parser.Parser method) relax_conv_info() (turbomoleio.output.parser.Parser method) relax_gradient_values() (turbomoleio.output.parser.Parser method) relax_info() (turbomoleio.output.parser.Parser method) RelaxConvergenceData (class in turbomoleio.output.data) RelaxData (class in turbomoleio.output.data) RelaxGradientsData (class in turbomoleio.output.data) RelaxOutput (class in turbomoleio.output.files) remove_comments() (in module turbomoleio.core.datagroups) remove_dg_from_list() (in module turbomoleio.core.datagroups) remove_last_energy() (turbomoleio.core.control.Control method)

remove_last_gradient() (turbomoleio.core.control.Control method) Ricc2Output (class in turbomoleio.output.files) RiData (class in turbomoleio.output.data) rij_info() (turbomoleio.output.parser.Parser method) riper_scf_energies() (turbomoleio.output.parser.Parser method) run() (turbomoleio.output.states.EigerRunner method) run_full() (turbomoleio.input.define.DefineRunner method) run_generate_mo_files() (turbomoleio.input.define.DefineRunner method) run_itest() (in module turbomoleio.testing) run_update_internal_coords() (turbomoleio.input.define.DefineRunner method) RunData (class in turbomoleio.output.data)

S

s2() (turbomoleio.output.parser.Parser method) scf_energies() (turbomoleio.output.parser.Parser method) scf_iterations() (turbomoleio.output.parser.Parser method) ScfData (class in turbomoleio.output.data) ScfEnergiesData (class in turbomoleio.output.data) ScfIterationData (class in turbomoleio.output.data) ScfOutput (class in turbomoleio.output.files) schema_define_params (in module turbomoleio.input.utils) sdg() (in module turbomoleio.core.control) (turbomoleio.core.datagroups.DataGroups method) sdgo() (in module turbomoleio.core.control) (turbomoleio.core.datagroups.DataGroups method) set_disp() (turbomoleio.core.control.Control method) Shells (class in turbomoleio.core.control) show_data_group() (turbomoleio.core.datagroups.DataGroups method)

show_data_group_option() (turbomoleio.core.datagroups.DataGroups method) show_subfile_fname() (turbomoleio.core.datagroups.DataGroups method) SingleExcitation (class in turbomoleio.output.data) SmearingData (class in turbomoleio.output.data) SpinData (class in turbomoleio.output.data) spins (turbomoleio.output.states.States property) split_string_to_dg_list() (in module turbomoleio.core.datagroups) State (class in turbomoleio.output.states) States (class in turbomoleio.output.states) statpt_info() (turbomoleio.output.parser.Parser method) StatptData (class in turbomoleio.output.data) StatptOutput (class in turbomoleio.output.files) string (turbomoleio.output.parser.Parser property) structure (turbomoleio.core.periodic.PeriodicSystem property) symmetry() (turbomoleio.output.parser.Parser method) SymmetryData (class in turbomoleio.output.data)

T

temp_dir() (in module turbomoleio.testing) timings() (turbomoleio.output.parser.Parser method) to_coord_file() (turbomoleio.core.base.BaseSystem method) to_coord_string() (turbomoleio.core.base.BaseSystem method) (turbomoleio.core.molecule.MoleculeSystem method) (turbomoleio.core.periodic.PeriodicSystem method) to_datagroup() (turbomoleio.core.control.Shells method) to_file() (turbomoleio.core.base.BaseSystem method) (turbomoleio.core.control.Control method) (turbomoleio.core.datagroups.DataGroups method) (turbomoleio.output.states.EigerRunner method) to_string() (turbomoleio.core.molecule.InternalDefinition method) tol (turbomoleio.testing.ItestConfig attribute) total_electrons (turbomoleio.core.control.Shells property) (turbomoleio.output.states.States property) touch_file() (in module turbomoleio.testing) TurbomoleData (class in turbomoleio.output.data) turbomoleio module turbomoleio.core module turbomoleio.core.base module turbomoleio.core.control module turbomoleio.core.datagroups module

turbomoleio.core.molecule module turbomoleio.core.periodic module turbomoleio.core.symmetry module turbomoleio.core.utils module turbomoleio.input module turbomoleio.input.define module turbomoleio.input.templates module turbomoleio.input.utils module turbomoleio.output module turbomoleio.output.data module turbomoleio.output.files module turbomoleio.output.parser module turbomoleio.output.states module turbomoleio.testing module

U

UnsupportedDefineStateError

V

validate_parameters() (in module turbomoleio.input.utils)