-
Notifications
You must be signed in to change notification settings - Fork 9
/
Copy pathsearchindex.js
1 lines (1 loc) · 118 KB
/
searchindex.js
1
Search.setIndex({"alltitles": {"Accessing a data group value": [[11, "accessing-a-data-group-value"]], "Additional information": [[18, "additional-information"], [18, null]], "Appendix": [[7, null]], "Backward-compatibility": [[17, "backward-compatibility"]], "Bug fixing": [[9, "bug-fixing"]], "Changelog": [[9, null]], "Common data objects": [[20, "common-data-objects"]], "Contributing": [[14, null]], "Contributing to turbomoleio": [[18, "contributing-to-turbomoleio"]], "Data and File Objects": [[20, "data-and-file-objects"]], "Define runner": [[13, null]], "Developer changes": [[9, "developer-changes"], [9, "id1"]], "Developer guide": [[18, null]], "Features added": [[9, "features-added"], [9, "id2"]], "File data objects": [[20, "file-data-objects"]], "Indices and tables": [[18, "indices-and-tables"]], "Integration tests": [[16, "integration-tests"], [16, "id1"]], "License": [[19, null]], "Modifying a data group value": [[11, "modifying-a-data-group-value"]], "Module contents": [[1, "module-turbomoleio"], [2, "module-turbomoleio.core"], [3, "module-turbomoleio.input"], [4, "module-turbomoleio.input.templates"], [5, "module-turbomoleio.output"], [6, "module-turbomoleio.testing"]], "Output logs parsing": [[15, null]], "Outputs parsing": [[20, null]], "Overall Structure": [[20, "overall-structure"]], "Parsing a new quantity": [[15, "parsing-a-new-quantity"]], "Parsing a new type of log": [[15, "parsing-a-new-type-of-log"]], "Periodic systems": [[10, "periodic-systems"]], "Quick Start": [[20, "quick-start"]], "Release 1.0.0 (Mar 11, 2021)": [[9, "release-1-0-0-mar-11-2021"]], "Release 1.1.0 (Sep 20, 2021)": [[9, "release-1-1-0-sep-20-2021"]], "Release 1.1.1 (Feb 15, 2022)": [[9, "release-1-1-1-feb-15-2022"]], "Release 1.2.0 (Feb 16, 2022)": [[9, "release-1-2-0-feb-16-2022"]], "Release 1.3.0 (Feb 24, 2022)": [[9, "release-1-3-0-feb-24-2022"]], "Release 1.4.0 (Mar 4, 2024)": [[9, "release-1-4-0-mar-4-2024"]], "Release 1.5.0 (Mar 27, 2024)": [[9, "release-1-5-0-mar-27-2024"]], "Release 1.6.0 (Sep 6, 2024)": [[9, "release-1-6-0-sep-6-2024"]], "Reporting bugs": [[8, null]], "Running define": [[12, null]], "Standard procedure": [[16, "standard-procedure"]], "Submodules": [[2, "submodules"], [3, "submodules"], [5, "submodules"]], "Subpackages": [[1, "subpackages"], [3, "subpackages"]], "Testing": [[16, null]], "Testing and development": [[9, "testing-and-development"]], "Tests": [[13, "tests"], [15, "tests"]], "Tests for output parsing": [[16, "tests-for-output-parsing"]], "The Control object": [[11, "the-control-object"]], "The DataGroups object": [[11, "the-datagroups-object"]], "The DefineRunner parameters": [[12, "the-definerunner-parameters"]], "The States object": [[20, "the-states-object"]], "The coord file": [[10, null]], "The data group files": [[11, null]], "The log files": [[20, "the-log-files"]], "The test suite": [[16, "the-test-suite"]], "Turbomole version change": [[16, "turbomole-version-change"]], "Unit tests": [[16, "unit-tests"]], "Unit-tests for output parsing": [[16, "unit-tests-for-output-parsing"]], "User guide": [[18, null]], "Validation": [[12, "validation"], [13, "validation"]], "Versioning": [[17, null]], "Writing new tests": [[16, "writing-new-tests"]], "turbomoleio": [[0, null], [18, null]], "turbomoleio package": [[1, null]], "turbomoleio.core package": [[2, null]], "turbomoleio.core.base module": [[2, "module-turbomoleio.core.base"]], "turbomoleio.core.control module": [[2, "module-turbomoleio.core.control"]], "turbomoleio.core.datagroups module": [[2, "module-turbomoleio.core.datagroups"]], "turbomoleio.core.molecule module": [[2, "module-turbomoleio.core.molecule"]], "turbomoleio.core.periodic module": [[2, "module-turbomoleio.core.periodic"]], "turbomoleio.core.symmetry module": [[2, "module-turbomoleio.core.symmetry"]], "turbomoleio.core.utils module": [[2, "module-turbomoleio.core.utils"]], "turbomoleio.input package": [[3, null]], "turbomoleio.input.define module": [[3, "module-turbomoleio.input.define"]], "turbomoleio.input.templates package": [[4, null]], "turbomoleio.input.utils module": [[3, "module-turbomoleio.input.utils"]], "turbomoleio.output package": [[5, null]], "turbomoleio.output.data module": [[5, "module-turbomoleio.output.data"]], "turbomoleio.output.files module": [[5, "module-turbomoleio.output.files"]], "turbomoleio.output.parser module": [[5, "module-turbomoleio.output.parser"]], "turbomoleio.output.states module": [[5, "module-turbomoleio.output.states"]], "turbomoleio.testing package": [[6, null]]}, "docnames": ["api/modules", "api/turbomoleio", "api/turbomoleio.core", "api/turbomoleio.input", "api/turbomoleio.input.templates", "api/turbomoleio.output", "api/turbomoleio.testing", "appendix", "bugs", "changelog", "coord", "datagroups", "definerunner", "developer/definerunner", "developer/introduction", "developer/parsing_logs", "developer/testing", "developer/versioning", "index", "license", "output_parsing"], "envversion": {"sphinx": 62, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.todo": 2, "sphinx.ext.viewcode": 1}, "filenames": ["api/modules.rst", "api/turbomoleio.rst", "api/turbomoleio.core.rst", "api/turbomoleio.input.rst", "api/turbomoleio.input.templates.rst", "api/turbomoleio.output.rst", "api/turbomoleio.testing.rst", "appendix.rst", "bugs.rst", "changelog.rst", "coord.rst", "datagroups.rst", "definerunner.rst", "developer/definerunner.rst", "developer/introduction.rst", "developer/parsing_logs.rst", "developer/testing.rst", "developer/versioning.rst", "index.rst", "license.rst", "output_parsing.rst"], "indexentries": {"add_bond_angle() (turbomoleio.core.molecule.moleculesystem method)": [[2, "turbomoleio.core.molecule.MoleculeSystem.add_bond_angle", false]], "add_cosmo() (turbomoleio.core.control.control method)": [[2, "turbomoleio.core.control.Control.add_cosmo", false]], "add_data_group() (turbomoleio.core.datagroups.datagroups method)": [[2, "turbomoleio.core.datagroups.DataGroups.add_data_group", false]], "add_dihedral() (turbomoleio.core.molecule.moleculesystem method)": [[2, "turbomoleio.core.molecule.MoleculeSystem.add_dihedral", false]], "add_distance() (turbomoleio.core.molecule.moleculesystem method)": [[2, "turbomoleio.core.molecule.MoleculeSystem.add_distance", false]], "adg() (in module turbomoleio.core.control)": [[2, "turbomoleio.core.control.adg", false]], "adg() (turbomoleio.core.datagroups.datagroups method)": [[2, "turbomoleio.core.datagroups.DataGroups.adg", false]], "all_done() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.all_done", false]], "aoforce_analysis() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.aoforce_analysis", false]], "aoforce_numerical_integration() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.aoforce_numerical_integration", false]], "aoforcenumericalintegrationdata (class in turbomoleio.output.data)": [[5, "turbomoleio.output.data.AoforceNumericalIntegrationData", false]], "aoforceoutput (class in turbomoleio.output.files)": [[5, "turbomoleio.output.files.AoforceOutput", false]], "aoforcerotationaldata (class in turbomoleio.output.data)": [[5, "turbomoleio.output.data.AoforceRotationalData", false]], "aoforcevibrationaldata (class in turbomoleio.output.data)": [[5, "turbomoleio.output.data.AoforceVibrationalData", false]], "as_dict() (turbomoleio.core.control.shells method)": [[2, "turbomoleio.core.control.Shells.as_dict", false]], "as_dict() (turbomoleio.core.datagroups.datagroups method)": [[2, "turbomoleio.core.datagroups.DataGroups.as_dict", false]], "as_dict() (turbomoleio.core.molecule.moleculesystem method)": [[2, "turbomoleio.core.molecule.MoleculeSystem.as_dict", false]], "as_dict() (turbomoleio.core.periodic.periodicsystem method)": [[2, "turbomoleio.core.periodic.PeriodicSystem.as_dict", false]], "as_dict() (turbomoleio.output.states.state method)": [[5, "turbomoleio.output.states.State.as_dict", false]], "as_dict() (turbomoleio.output.states.states method)": [[5, "turbomoleio.output.states.States.as_dict", false]], "assert_almost_equal() (in module turbomoleio.testing)": [[6, "turbomoleio.testing.assert_almost_equal", false]], "assert_msonable() (in module turbomoleio.testing)": [[6, "turbomoleio.testing.assert_MSONable", false]], "available_templates() (in module turbomoleio.input.templates)": [[4, "turbomoleio.input.templates.available_templates", false]], "basedata (class in turbomoleio.output.data)": [[5, "turbomoleio.output.data.BaseData", false]], "basesystem (class in turbomoleio.core.base)": [[2, "turbomoleio.core.base.BaseSystem", false]], "basis() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.basis", false]], "basisdata (class in turbomoleio.output.data)": [[5, "turbomoleio.output.data.BasisData", false]], "bondangle (class in turbomoleio.core.molecule)": [[2, "turbomoleio.core.molecule.BondAngle", false]], "cdg() (in module turbomoleio.core.control)": [[2, "turbomoleio.core.control.cdg", false]], "cdg() (turbomoleio.core.datagroups.datagroups method)": [[2, "turbomoleio.core.datagroups.DataGroups.cdg", false]], "centers() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.centers", false]], "change_data_group() (turbomoleio.core.datagroups.datagroups method)": [[2, "turbomoleio.core.datagroups.DataGroups.change_data_group", false]], "cleanup_string() (in module turbomoleio.core.datagroups)": [[2, "turbomoleio.core.datagroups.cleanup_string", false]], "collinearbendingangle (class in turbomoleio.core.molecule)": [[2, "turbomoleio.core.molecule.CollinearBendingAngle", false]], "compare() (turbomoleio.core.datagroups.datagroups method)": [[2, "turbomoleio.core.datagroups.DataGroups.compare", false]], "compare_datagroup_string() (in module turbomoleio.core.datagroups)": [[2, "turbomoleio.core.datagroups.compare_datagroup_string", false]], "compare_differences() (in module turbomoleio.testing)": [[6, "turbomoleio.testing.compare_differences", false]], "compare_states() (turbomoleio.output.states.eigeroutput method)": [[5, "turbomoleio.output.states.EigerOutput.compare_states", false]], "compute_value() (turbomoleio.core.molecule.bondangle method)": [[2, "turbomoleio.core.molecule.BondAngle.compute_value", false]], "compute_value() (turbomoleio.core.molecule.collinearbendingangle method)": [[2, "turbomoleio.core.molecule.CollinearBendingAngle.compute_value", false]], "compute_value() (turbomoleio.core.molecule.dihedralangle method)": [[2, "turbomoleio.core.molecule.DihedralAngle.compute_value", false]], "compute_value() (turbomoleio.core.molecule.distance method)": [[2, "turbomoleio.core.molecule.Distance.compute_value", false]], "compute_value() (turbomoleio.core.molecule.internaldefinition method)": [[2, "turbomoleio.core.molecule.InternalDefinition.compute_value", false]], "compute_value() (turbomoleio.core.molecule.inversedistance method)": [[2, "turbomoleio.core.molecule.InverseDistance.compute_value", false]], "compute_value() (turbomoleio.core.molecule.outofplaneangle method)": [[2, "turbomoleio.core.molecule.OutOfPlaneAngle.compute_value", false]], "compute_value() (turbomoleio.core.molecule.perpendicularbendingangle method)": [[2, "turbomoleio.core.molecule.PerpendicularBendingAngle.compute_value", false]], "control (class in turbomoleio.core.control)": [[2, "turbomoleio.core.control.Control", false]], "convert_float() (in module turbomoleio.output.parser)": [[5, "turbomoleio.output.parser.convert_float", false]], "convert_int() (in module turbomoleio.output.parser)": [[5, "turbomoleio.output.parser.convert_int", false]], "convert_time_string() (in module turbomoleio.output.parser)": [[5, "turbomoleio.output.parser.convert_time_string", false]], "coord_lines() (turbomoleio.core.base.basesystem method)": [[2, "turbomoleio.core.base.BaseSystem.coord_lines", false]], "coord_str (turbomoleio.core.molecule.bondangle attribute)": [[2, "turbomoleio.core.molecule.BondAngle.coord_str", false]], "coord_str (turbomoleio.core.molecule.collinearbendingangle attribute)": [[2, "turbomoleio.core.molecule.CollinearBendingAngle.coord_str", false]], "coord_str (turbomoleio.core.molecule.dihedralangle attribute)": [[2, "turbomoleio.core.molecule.DihedralAngle.coord_str", false]], "coord_str (turbomoleio.core.molecule.distance attribute)": [[2, "turbomoleio.core.molecule.Distance.coord_str", false]], "coord_str (turbomoleio.core.molecule.internaldefinition attribute)": [[2, "turbomoleio.core.molecule.InternalDefinition.coord_str", false]], "coord_str (turbomoleio.core.molecule.inversedistance attribute)": [[2, "turbomoleio.core.molecule.InverseDistance.coord_str", false]], "coord_str (turbomoleio.core.molecule.outofplaneangle attribute)": [[2, "turbomoleio.core.molecule.OutOfPlaneAngle.coord_str", false]], "coord_str (turbomoleio.core.molecule.perpendicularbendingangle attribute)": [[2, "turbomoleio.core.molecule.PerpendicularBendingAngle.coord_str", false]], "coord_type (turbomoleio.core.molecule.bondangle attribute)": [[2, "turbomoleio.core.molecule.BondAngle.coord_type", false]], "coord_type (turbomoleio.core.molecule.collinearbendingangle attribute)": [[2, "turbomoleio.core.molecule.CollinearBendingAngle.coord_type", false]], "coord_type (turbomoleio.core.molecule.dihedralangle attribute)": [[2, "turbomoleio.core.molecule.DihedralAngle.coord_type", false]], "coord_type (turbomoleio.core.molecule.distance attribute)": [[2, "turbomoleio.core.molecule.Distance.coord_type", false]], "coord_type (turbomoleio.core.molecule.internaldefinition attribute)": [[2, "turbomoleio.core.molecule.InternalDefinition.coord_type", false]], "coord_type (turbomoleio.core.molecule.inversedistance attribute)": [[2, "turbomoleio.core.molecule.InverseDistance.coord_type", false]], "coord_type (turbomoleio.core.molecule.outofplaneangle attribute)": [[2, "turbomoleio.core.molecule.OutOfPlaneAngle.coord_type", false]], "coord_type (turbomoleio.core.molecule.perpendicularbendingangle attribute)": [[2, "turbomoleio.core.molecule.PerpendicularBendingAngle.coord_type", false]], "coordinates() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.coordinates", false]], "cosmo_header() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.cosmo_header", false]], "cosmo_results() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.cosmo_results", false]], "cosmodata (class in turbomoleio.output.data)": [[5, "turbomoleio.output.data.CosmoData", false]], "cpc() (in module turbomoleio.core.control)": [[2, "turbomoleio.core.control.cpc", false]], "cpc() (turbomoleio.core.control.control method)": [[2, "turbomoleio.core.control.Control.cpc", false]], "datagroups (class in turbomoleio.core.datagroups)": [[2, "turbomoleio.core.datagroups.DataGroups", false]], "defaults (class in turbomoleio.core.control)": [[2, "turbomoleio.core.control.Defaults", false]], "define_quit() (in module turbomoleio.core.utils)": [[2, "turbomoleio.core.utils.define_quit", false]], "define_timeout (turbomoleio.testing.itestconfig attribute)": [[6, "turbomoleio.testing.ItestConfig.define_timeout", false]], "defineerror": [[3, "turbomoleio.input.define.DefineError", false]], "defineexpecterror": [[3, "turbomoleio.input.define.DefineExpectError", false]], "defineirederror": [[3, "turbomoleio.input.define.DefineIredError", false]], "defineparametererror": [[3, "turbomoleio.input.define.DefineParameterError", false]], "definerunner (class in turbomoleio.input.define)": [[3, "turbomoleio.input.define.DefineRunner", false]], "delete_tmp_dir (turbomoleio.testing.itestconfig attribute)": [[6, "turbomoleio.testing.ItestConfig.delete_tmp_dir", false]], "delta_e (turbomoleio.core.control.energy property)": [[2, "turbomoleio.core.control.Energy.delta_e", false]], "density_functional_data() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.density_functional_data", false]], "dftd() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.dftd", false]], "dftdata (class in turbomoleio.output.data)": [[5, "turbomoleio.output.data.DFTData", false]], "dihedralangle (class in turbomoleio.core.molecule)": [[2, "turbomoleio.core.molecule.DihedralAngle", false]], "dispersioncorrectiondata (class in turbomoleio.output.data)": [[5, "turbomoleio.output.data.DispersionCorrectionData", false]], "distance (class in turbomoleio.core.molecule)": [[2, "turbomoleio.core.molecule.Distance", false]], "dryrun (turbomoleio.testing.itestconfig attribute)": [[6, "turbomoleio.testing.ItestConfig.dryrun", false]], "dryrun_fpath (turbomoleio.testing.itestconfig attribute)": [[6, "turbomoleio.testing.ItestConfig.dryrun_fpath", false]], "dryrun_use_ref_control (turbomoleio.testing.itestconfig attribute)": [[6, "turbomoleio.testing.ItestConfig.dryrun_use_ref_control", false]], "dump_command_file() (turbomoleio.input.define.definerunner method)": [[3, "turbomoleio.input.define.DefineRunner.dump_command_file", false]], "egrad_excited_state() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.egrad_excited_state", false]], "egradoutput (class in turbomoleio.output.files)": [[5, "turbomoleio.output.files.EgradOutput", false]], "eigenvalues (turbomoleio.output.states.states property)": [[5, "turbomoleio.output.states.States.eigenvalues", false]], "eigeroutput (class in turbomoleio.output.states)": [[5, "turbomoleio.output.states.EigerOutput", false]], "eigerrunner (class in turbomoleio.output.states)": [[5, "turbomoleio.output.states.EigerRunner", false]], "electrostatic_moments() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.electrostatic_moments", false]], "electrostaticmomentsdata (class in turbomoleio.output.data)": [[5, "turbomoleio.output.data.ElectrostaticMomentsData", false]], "empty() (turbomoleio.core.datagroups.datagroups class method)": [[2, "turbomoleio.core.datagroups.DataGroups.empty", false]], "energy (class in turbomoleio.core.control)": [[2, "turbomoleio.core.control.Energy", false]], "energy (turbomoleio.core.control.control property)": [[2, "turbomoleio.core.control.Control.energy", false]], "escf_excitations() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.escf_excitations", false]], "escf_gs_total_en() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.escf_gs_total_en", false]], "escf_iterations() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.escf_iterations", false]], "escfdata (class in turbomoleio.output.data)": [[5, "turbomoleio.output.data.EscfData", false]], "escfiterationdata (class in turbomoleio.output.data)": [[5, "turbomoleio.output.data.EscfIterationData", false]], "escfonlyoutput (class in turbomoleio.output.files)": [[5, "turbomoleio.output.files.EscfOnlyOutput", false]], "escfoutput (class in turbomoleio.output.files)": [[5, "turbomoleio.output.files.EscfOutput", false]], "ex_setter() (in module turbomoleio.input.utils)": [[3, "turbomoleio.input.utils.ex_setter", false]], "fermi() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.fermi", false]], "filter_states() (turbomoleio.output.states.states method)": [[5, "turbomoleio.output.states.States.filter_states", false]], "from_dict() (turbomoleio.core.control.shells class method)": [[2, "turbomoleio.core.control.Shells.from_dict", false]], "from_dict() (turbomoleio.core.datagroups.datagroups class method)": [[2, "turbomoleio.core.datagroups.DataGroups.from_dict", false]], "from_dict() (turbomoleio.core.molecule.moleculesystem class method)": [[2, "turbomoleio.core.molecule.MoleculeSystem.from_dict", false]], "from_dict() (turbomoleio.core.periodic.periodicsystem class method)": [[2, "turbomoleio.core.periodic.PeriodicSystem.from_dict", false]], "from_dict() (turbomoleio.output.states.state class method)": [[5, "turbomoleio.output.states.State.from_dict", false]], "from_file() (turbomoleio.core.control.control class method)": [[2, "turbomoleio.core.control.Control.from_file", false]], "from_file() (turbomoleio.core.control.energy class method)": [[2, "turbomoleio.core.control.Energy.from_file", false]], "from_file() (turbomoleio.core.control.gradient class method)": [[2, "turbomoleio.core.control.Gradient.from_file", false]], "from_file() (turbomoleio.core.control.shells class method)": [[2, "turbomoleio.core.control.Shells.from_file", false]], "from_file() (turbomoleio.core.datagroups.datagroups class method)": [[2, "turbomoleio.core.datagroups.DataGroups.from_file", false]], "from_file() (turbomoleio.core.molecule.moleculesystem class method)": [[2, "turbomoleio.core.molecule.MoleculeSystem.from_file", false]], "from_file() (turbomoleio.core.periodic.periodicsystem class method)": [[2, "turbomoleio.core.periodic.PeriodicSystem.from_file", false]], "from_file() (turbomoleio.output.data.basedata class method)": [[5, "turbomoleio.output.data.BaseData.from_file", false]], "from_file() (turbomoleio.output.parser.parser class method)": [[5, "turbomoleio.output.parser.Parser.from_file", false]], "from_file() (turbomoleio.output.states.eigeroutput class method)": [[5, "turbomoleio.output.states.EigerOutput.from_file", false]], "from_file() (turbomoleio.output.states.states class method)": [[5, "turbomoleio.output.states.States.from_file", false]], "from_metric() (turbomoleio.core.control.control class method)": [[2, "turbomoleio.core.control.Control.from_metric", false]], "from_parser() (turbomoleio.output.data.aoforcenumericalintegrationdata class method)": [[5, "turbomoleio.output.data.AoforceNumericalIntegrationData.from_parser", false]], "from_parser() (turbomoleio.output.data.aoforcerotationaldata class method)": [[5, "turbomoleio.output.data.AoforceRotationalData.from_parser", false]], "from_parser() (turbomoleio.output.data.aoforcevibrationaldata class method)": [[5, "turbomoleio.output.data.AoforceVibrationalData.from_parser", false]], "from_parser() (turbomoleio.output.data.basedata class method)": [[5, "turbomoleio.output.data.BaseData.from_parser", false]], "from_parser() (turbomoleio.output.data.basisdata class method)": [[5, "turbomoleio.output.data.BasisData.from_parser", false]], "from_parser() (turbomoleio.output.data.cosmodata class method)": [[5, "turbomoleio.output.data.CosmoData.from_parser", false]], "from_parser() (turbomoleio.output.data.dftdata class method)": [[5, "turbomoleio.output.data.DFTData.from_parser", false]], "from_parser() (turbomoleio.output.data.dispersioncorrectiondata class method)": [[5, "turbomoleio.output.data.DispersionCorrectionData.from_parser", false]], "from_parser() (turbomoleio.output.data.electrostaticmomentsdata class method)": [[5, "turbomoleio.output.data.ElectrostaticMomentsData.from_parser", false]], "from_parser() (turbomoleio.output.data.escfdata class method)": [[5, "turbomoleio.output.data.EscfData.from_parser", false]], "from_parser() (turbomoleio.output.data.escfiterationdata class method)": [[5, "turbomoleio.output.data.EscfIterationData.from_parser", false]], "from_parser() (turbomoleio.output.data.functionaldata class method)": [[5, "turbomoleio.output.data.FunctionalData.from_parser", false]], "from_parser() (turbomoleio.output.data.geometrydata class method)": [[5, "turbomoleio.output.data.GeometryData.from_parser", false]], "from_parser() (turbomoleio.output.data.integraldata class method)": [[5, "turbomoleio.output.data.IntegralData.from_parser", false]], "from_parser() (turbomoleio.output.data.mp2data class method)": [[5, "turbomoleio.output.data.MP2Data.from_parser", false]], "from_parser() (turbomoleio.output.data.mp2results class method)": [[5, "turbomoleio.output.data.MP2Results.from_parser", false]], "from_parser() (turbomoleio.output.data.periodicitydata class method)": [[5, "turbomoleio.output.data.PeriodicityData.from_parser", false]], "from_parser() (turbomoleio.output.data.relaxconvergencedata class method)": [[5, "turbomoleio.output.data.RelaxConvergenceData.from_parser", false]], "from_parser() (turbomoleio.output.data.relaxdata class method)": [[5, "turbomoleio.output.data.RelaxData.from_parser", false]], "from_parser() (turbomoleio.output.data.relaxgradientsdata class method)": [[5, "turbomoleio.output.data.RelaxGradientsData.from_parser", false]], "from_parser() (turbomoleio.output.data.ridata class method)": [[5, "turbomoleio.output.data.RiData.from_parser", false]], "from_parser() (turbomoleio.output.data.rundata class method)": [[5, "turbomoleio.output.data.RunData.from_parser", false]], "from_parser() (turbomoleio.output.data.scfdata class method)": [[5, "turbomoleio.output.data.ScfData.from_parser", false]], "from_parser() (turbomoleio.output.data.scfenergiesdata class method)": [[5, "turbomoleio.output.data.ScfEnergiesData.from_parser", false]], "from_parser() (turbomoleio.output.data.scfiterationdata class method)": [[5, "turbomoleio.output.data.ScfIterationData.from_parser", false]], "from_parser() (turbomoleio.output.data.smearingdata class method)": [[5, "turbomoleio.output.data.SmearingData.from_parser", false]], "from_parser() (turbomoleio.output.data.spindata class method)": [[5, "turbomoleio.output.data.SpinData.from_parser", false]], "from_parser() (turbomoleio.output.data.statptdata class method)": [[5, "turbomoleio.output.data.StatptData.from_parser", false]], "from_parser() (turbomoleio.output.data.symmetrydata class method)": [[5, "turbomoleio.output.data.SymmetryData.from_parser", false]], "from_parser() (turbomoleio.output.data.turbomoledata class method)": [[5, "turbomoleio.output.data.TurbomoleData.from_parser", false]], "from_parser() (turbomoleio.output.files.aoforceoutput class method)": [[5, "turbomoleio.output.files.AoforceOutput.from_parser", false]], "from_parser() (turbomoleio.output.files.egradoutput class method)": [[5, "turbomoleio.output.files.EgradOutput.from_parser", false]], "from_parser() (turbomoleio.output.files.escfonlyoutput class method)": [[5, "turbomoleio.output.files.EscfOnlyOutput.from_parser", false]], "from_parser() (turbomoleio.output.files.escfoutput class method)": [[5, "turbomoleio.output.files.EscfOutput.from_parser", false]], "from_parser() (turbomoleio.output.files.gradoutput class method)": [[5, "turbomoleio.output.files.GradOutput.from_parser", false]], "from_parser() (turbomoleio.output.files.jobexoutput class method)": [[5, "turbomoleio.output.files.JobexOutput.from_parser", false]], "from_parser() (turbomoleio.output.files.mp2output class method)": [[5, "turbomoleio.output.files.MP2Output.from_parser", false]], "from_parser() (turbomoleio.output.files.relaxoutput class method)": [[5, "turbomoleio.output.files.RelaxOutput.from_parser", false]], "from_parser() (turbomoleio.output.files.ricc2output class method)": [[5, "turbomoleio.output.files.Ricc2Output.from_parser", false]], "from_parser() (turbomoleio.output.files.scfoutput class method)": [[5, "turbomoleio.output.files.ScfOutput.from_parser", false]], "from_parser() (turbomoleio.output.files.statptoutput class method)": [[5, "turbomoleio.output.files.StatptOutput.from_parser", false]], "from_string() (turbomoleio.core.control.energy class method)": [[2, "turbomoleio.core.control.Energy.from_string", false]], "from_string() (turbomoleio.core.control.gradient class method)": [[2, "turbomoleio.core.control.Gradient.from_string", false]], "from_string() (turbomoleio.core.control.shells class method)": [[2, "turbomoleio.core.control.Shells.from_string", false]], "from_string() (turbomoleio.core.molecule.internaldefinition class method)": [[2, "turbomoleio.core.molecule.InternalDefinition.from_string", false]], "from_string() (turbomoleio.core.molecule.moleculesystem class method)": [[2, "turbomoleio.core.molecule.MoleculeSystem.from_string", false]], "from_string() (turbomoleio.core.periodic.periodicsystem class method)": [[2, "turbomoleio.core.periodic.PeriodicSystem.from_string", false]], "from_string() (turbomoleio.output.data.basedata class method)": [[5, "turbomoleio.output.data.BaseData.from_string", false]], "from_string() (turbomoleio.output.states.eigeroutput class method)": [[5, "turbomoleio.output.states.EigerOutput.from_string", false]], "functionaldata (class in turbomoleio.output.data)": [[5, "turbomoleio.output.data.FunctionalData", false]], "gap (turbomoleio.output.states.states property)": [[5, "turbomoleio.output.states.States.gap", false]], "generate_control_for_test() (in module turbomoleio.testing)": [[6, "turbomoleio.testing.generate_control_for_test", false]], "generate_lowest_filled_states() (turbomoleio.output.states.states method)": [[5, "turbomoleio.output.states.States.generate_lowest_filled_states", false]], "generate_ref (turbomoleio.testing.itestconfig attribute)": [[6, "turbomoleio.testing.ItestConfig.generate_ref", false]], "generate_reference_out_parser_files() (in module turbomoleio.testing)": [[6, "turbomoleio.testing.generate_reference_out_parser_files", false]], "generate_reference_output() (in module turbomoleio.testing)": [[6, "turbomoleio.testing.generate_reference_output", false]], "geometrydata (class in turbomoleio.output.data)": [[5, "turbomoleio.output.data.GeometryData", false]], "get_charge() (turbomoleio.core.control.control method)": [[2, "turbomoleio.core.control.Control.get_charge", false]], "get_control_integration() (in module turbomoleio.testing)": [[6, "turbomoleio.testing.get_control_integration", false]], "get_coord_lines() (in module turbomoleio.core.base)": [[2, "turbomoleio.core.base.get_coord_lines", false]], "get_define_template() (in module turbomoleio.input.utils)": [[3, "turbomoleio.input.utils.get_define_template", false]], "get_eiger_output() (turbomoleio.output.states.eigerrunner method)": [[5, "turbomoleio.output.states.EigerRunner.get_eiger_output", false]], "get_freqs_df() (turbomoleio.output.data.aoforcevibrationaldata method)": [[5, "turbomoleio.output.data.AoforceVibrationalData.get_freqs_df", false]], "get_int_def_inconsistencies() (turbomoleio.core.molecule.moleculesystem method)": [[2, "turbomoleio.core.molecule.MoleculeSystem.get_int_def_inconsistencies", false]], "get_mol_and_indices_frozen() (in module turbomoleio.core.base)": [[2, "turbomoleio.core.base.get_mol_and_indices_frozen", false]], "get_mos_energies() (in module turbomoleio.output.states)": [[5, "turbomoleio.output.states.get_mos_energies", false]], "get_shells() (turbomoleio.core.control.control method)": [[2, "turbomoleio.core.control.Control.get_shells", false]], "get_shells() (turbomoleio.output.states.states method)": [[5, "turbomoleio.output.states.States.get_shells", false]], "get_sp() (in module turbomoleio.testing)": [[6, "turbomoleio.testing.get_sp", false]], "get_split_jobex_parsers() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.get_split_jobex_parsers", false]], "get_subclass_from_str() (turbomoleio.core.molecule.internaldefinition static method)": [[2, "turbomoleio.core.molecule.InternalDefinition.get_subclass_from_str", false]], "get_subfiles_list() (turbomoleio.core.control.control method)": [[2, "turbomoleio.core.control.Control.get_subfiles_list", false]], "get_test_data_dir() (in module turbomoleio.testing)": [[6, "turbomoleio.testing.get_test_data_dir", false]], "get_tests_configs_tm_versions() (in module turbomoleio.testing)": [[6, "turbomoleio.testing.get_tests_configs_tm_versions", false]], "get_tfp() (in module turbomoleio.testing)": [[6, "turbomoleio.testing.get_tfp", false]], "get_tm_version() (in module turbomoleio.core.utils)": [[2, "turbomoleio.core.utils.get_tm_version", false]], "get_value() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.get_value", false]], "gisnan() (in module turbomoleio.testing)": [[6, "turbomoleio.testing.gisnan", false]], "gradient (class in turbomoleio.core.control)": [[2, "turbomoleio.core.control.Gradient", false]], "gradient (turbomoleio.core.control.control property)": [[2, "turbomoleio.core.control.Control.gradient", false]], "gradient() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.gradient", false]], "gradoutput (class in turbomoleio.output.files)": [[5, "turbomoleio.output.files.GradOutput", false]], "grep_line() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.grep_line", false]], "has_fractional_occ (turbomoleio.output.states.state property)": [[5, "turbomoleio.output.states.State.has_fractional_occ", false]], "has_fractional_occ (turbomoleio.output.states.states property)": [[5, "turbomoleio.output.states.States.has_fractional_occ", false]], "has_hole (turbomoleio.output.states.states property)": [[5, "turbomoleio.output.states.States.has_hole", false]], "has_inconsistencies() (turbomoleio.core.molecule.moleculesystem method)": [[2, "turbomoleio.core.molecule.MoleculeSystem.has_inconsistencies", false]], "has_matplotlib() (in module turbomoleio.testing)": [[6, "turbomoleio.testing.has_matplotlib", false]], "header() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.header", false]], "homo (turbomoleio.output.states.states property)": [[5, "turbomoleio.output.states.States.homo", false]], "homo_index (turbomoleio.output.states.states property)": [[5, "turbomoleio.output.states.States.homo_index", false]], "insert() (turbomoleio.output.states.states method)": [[5, "turbomoleio.output.states.States.insert", false]], "integral() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.integral", false]], "integraldata (class in turbomoleio.output.data)": [[5, "turbomoleio.output.data.IntegralData", false]], "internaldefinition (class in turbomoleio.core.molecule)": [[2, "turbomoleio.core.molecule.InternalDefinition", false]], "inversedistance (class in turbomoleio.core.molecule)": [[2, "turbomoleio.core.molecule.InverseDistance", false]], "irrep_indices (turbomoleio.output.states.states property)": [[5, "turbomoleio.output.states.States.irrep_indices", false]], "irreps (turbomoleio.core.control.shells property)": [[2, "turbomoleio.core.control.Shells.irreps", false]], "irreps (turbomoleio.output.states.states property)": [[5, "turbomoleio.output.states.States.irreps", false]], "is_uhf (turbomoleio.core.control.control property)": [[2, "turbomoleio.core.control.Control.is_uhf", false]], "is_uhf (turbomoleio.output.states.states property)": [[5, "turbomoleio.output.states.States.is_uhf", false]], "is_uhf() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.is_uhf", false]], "is_valid() (turbomoleio.core.molecule.internaldefinition method)": [[2, "turbomoleio.core.molecule.InternalDefinition.is_valid", false]], "itestconfig (class in turbomoleio.testing)": [[6, "turbomoleio.testing.ItestConfig", false]], "itesterror": [[6, "turbomoleio.testing.ItestError", false]], "jobexoutput (class in turbomoleio.output.files)": [[5, "turbomoleio.output.files.JobexOutput", false]], "kdg() (in module turbomoleio.core.control)": [[2, "turbomoleio.core.control.kdg", false]], "kdg() (turbomoleio.core.datagroups.datagroups method)": [[2, "turbomoleio.core.datagroups.DataGroups.kdg", false]], "kill_data_group() (turbomoleio.core.datagroups.datagroups method)": [[2, "turbomoleio.core.datagroups.DataGroups.kill_data_group", false]], "last_grad_max (turbomoleio.core.control.gradient property)": [[2, "turbomoleio.core.control.Gradient.last_grad_max", false]], "last_grad_norm (turbomoleio.core.control.gradient property)": [[2, "turbomoleio.core.control.Gradient.last_grad_norm", false]], "lumo (turbomoleio.output.states.states property)": [[5, "turbomoleio.output.states.States.lumo", false]], "lumo_index (turbomoleio.output.states.states property)": [[5, "turbomoleio.output.states.States.lumo_index", false]], "max_gradients (turbomoleio.core.control.gradient property)": [[2, "turbomoleio.core.control.Gradient.max_gradients", false]], "max_occupation (turbomoleio.output.states.state property)": [[5, "turbomoleio.output.states.State.max_occupation", false]], "mdgo() (in module turbomoleio.core.control)": [[2, "turbomoleio.core.control.mdgo", false]], "mdgo() (turbomoleio.core.datagroups.datagroups method)": [[2, "turbomoleio.core.datagroups.DataGroups.mdgo", false]], "metric (turbomoleio.core.control.defaults attribute)": [[2, "turbomoleio.core.control.Defaults.METRIC", false]], "modify_data_group_options() (turbomoleio.core.datagroups.datagroups method)": [[2, "turbomoleio.core.datagroups.DataGroups.modify_data_group_options", false]], "module": [[1, "module-turbomoleio", false], [2, "module-turbomoleio.core", false], [2, "module-turbomoleio.core.base", false], [2, "module-turbomoleio.core.control", false], [2, "module-turbomoleio.core.datagroups", false], [2, "module-turbomoleio.core.molecule", false], [2, "module-turbomoleio.core.periodic", false], [2, "module-turbomoleio.core.symmetry", false], [2, "module-turbomoleio.core.utils", false], [3, "module-turbomoleio.input", false], [3, "module-turbomoleio.input.define", false], [3, "module-turbomoleio.input.utils", false], [4, "module-turbomoleio.input.templates", false], [5, "module-turbomoleio.output", false], [5, "module-turbomoleio.output.data", false], [5, "module-turbomoleio.output.files", false], [5, "module-turbomoleio.output.parser", false], [5, "module-turbomoleio.output.states", false], [6, "module-turbomoleio.testing", false]], "molecule (turbomoleio.core.molecule.moleculesystem property)": [[2, "turbomoleio.core.molecule.MoleculeSystem.molecule", false]], "moleculesystem (class in turbomoleio.core.molecule)": [[2, "turbomoleio.core.molecule.MoleculeSystem", false]], "mp2_data() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.mp2_data", false]], "mp2_results() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.mp2_results", false]], "mp2data (class in turbomoleio.output.data)": [[5, "turbomoleio.output.data.MP2Data", false]], "mp2output (class in turbomoleio.output.files)": [[5, "turbomoleio.output.files.MP2Output", false]], "mp2results (class in turbomoleio.output.data)": [[5, "turbomoleio.output.data.MP2Results", false]], "n_atoms (turbomoleio.core.molecule.bondangle attribute)": [[2, "turbomoleio.core.molecule.BondAngle.n_atoms", false]], "n_atoms (turbomoleio.core.molecule.collinearbendingangle attribute)": [[2, "turbomoleio.core.molecule.CollinearBendingAngle.n_atoms", false]], "n_atoms (turbomoleio.core.molecule.dihedralangle attribute)": [[2, "turbomoleio.core.molecule.DihedralAngle.n_atoms", false]], "n_atoms (turbomoleio.core.molecule.distance attribute)": [[2, "turbomoleio.core.molecule.Distance.n_atoms", false]], "n_atoms (turbomoleio.core.molecule.internaldefinition attribute)": [[2, "turbomoleio.core.molecule.InternalDefinition.n_atoms", false]], "n_atoms (turbomoleio.core.molecule.inversedistance attribute)": [[2, "turbomoleio.core.molecule.InverseDistance.n_atoms", false]], "n_atoms (turbomoleio.core.molecule.outofplaneangle attribute)": [[2, "turbomoleio.core.molecule.OutOfPlaneAngle.n_atoms", false]], "n_atoms (turbomoleio.core.molecule.perpendicularbendingangle attribute)": [[2, "turbomoleio.core.molecule.PerpendicularBendingAngle.n_atoms", false]], "n_negative_freqs() (turbomoleio.output.data.aoforcevibrationaldata method)": [[5, "turbomoleio.output.data.AoforceVibrationalData.n_negative_freqs", false]], "n_positive_freqs() (turbomoleio.output.data.aoforcevibrationaldata method)": [[5, "turbomoleio.output.data.AoforceVibrationalData.n_positive_freqs", false]], "n_states (turbomoleio.output.states.states property)": [[5, "turbomoleio.output.states.States.n_states", false]], "n_steps (turbomoleio.core.control.energy property)": [[2, "turbomoleio.core.control.Energy.n_steps", false]], "n_steps (turbomoleio.core.control.gradient property)": [[2, "turbomoleio.core.control.Gradient.n_steps", false]], "n_zero_freqs() (turbomoleio.output.data.aoforcevibrationaldata method)": [[5, "turbomoleio.output.data.AoforceVibrationalData.n_zero_freqs", false]], "ndg (turbomoleio.core.datagroups.datagroups property)": [[2, "turbomoleio.core.datagroups.DataGroups.ndg", false]], "norms (turbomoleio.core.control.gradient property)": [[2, "turbomoleio.core.control.Gradient.norms", false]], "number_of_data_groups (turbomoleio.core.datagroups.datagroups property)": [[2, "turbomoleio.core.datagroups.DataGroups.number_of_data_groups", false]], "occupations (turbomoleio.output.states.states property)": [[5, "turbomoleio.output.states.States.occupations", false]], "outofplaneangle (class in turbomoleio.core.molecule)": [[2, "turbomoleio.core.molecule.OutOfPlaneAngle", false]], "parametersvalidationerror": [[3, "turbomoleio.input.utils.ParametersValidationError", false]], "parser (class in turbomoleio.output.parser)": [[5, "turbomoleio.output.parser.Parser", false]], "periodicity_data() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.periodicity_data", false]], "periodicitydata (class in turbomoleio.output.data)": [[5, "turbomoleio.output.data.PeriodicityData", false]], "periodicsystem (class in turbomoleio.core.periodic)": [[2, "turbomoleio.core.periodic.PeriodicSystem", false]], "perpendicularbendingangle (class in turbomoleio.core.molecule)": [[2, "turbomoleio.core.molecule.PerpendicularBendingAngle", false]], "plot() (turbomoleio.core.control.energy method)": [[2, "turbomoleio.core.control.Energy.plot", false]], "plot() (turbomoleio.core.control.gradient method)": [[2, "turbomoleio.core.control.Gradient.plot", false]], "plot_energies() (turbomoleio.output.data.scfiterationdata method)": [[5, "turbomoleio.output.data.ScfIterationData.plot_energies", false]], "pre_escf_run() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.pre_escf_run", false]], "pre_scf_run() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.pre_scf_run", false]], "rdgrad_memory() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.rdgrad_memory", false]], "relax_conv_info() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.relax_conv_info", false]], "relax_gradient_values() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.relax_gradient_values", false]], "relax_info() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.relax_info", false]], "relaxconvergencedata (class in turbomoleio.output.data)": [[5, "turbomoleio.output.data.RelaxConvergenceData", false]], "relaxdata (class in turbomoleio.output.data)": [[5, "turbomoleio.output.data.RelaxData", false]], "relaxgradientsdata (class in turbomoleio.output.data)": [[5, "turbomoleio.output.data.RelaxGradientsData", false]], "relaxoutput (class in turbomoleio.output.files)": [[5, "turbomoleio.output.files.RelaxOutput", false]], "remove_comments() (in module turbomoleio.core.datagroups)": [[2, "turbomoleio.core.datagroups.remove_comments", false]], "remove_dg_from_list() (in module turbomoleio.core.datagroups)": [[2, "turbomoleio.core.datagroups.remove_dg_from_list", false]], "remove_last_energy() (turbomoleio.core.control.control method)": [[2, "turbomoleio.core.control.Control.remove_last_energy", false]], "remove_last_gradient() (turbomoleio.core.control.control method)": [[2, "turbomoleio.core.control.Control.remove_last_gradient", false]], "ricc2output (class in turbomoleio.output.files)": [[5, "turbomoleio.output.files.Ricc2Output", false]], "ridata (class in turbomoleio.output.data)": [[5, "turbomoleio.output.data.RiData", false]], "rij_info() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.rij_info", false]], "riper_scf_energies() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.riper_scf_energies", false]], "run() (turbomoleio.output.states.eigerrunner method)": [[5, "turbomoleio.output.states.EigerRunner.run", false]], "run_full() (turbomoleio.input.define.definerunner method)": [[3, "turbomoleio.input.define.DefineRunner.run_full", false]], "run_generate_mo_files() (turbomoleio.input.define.definerunner method)": [[3, "turbomoleio.input.define.DefineRunner.run_generate_mo_files", false]], "run_itest() (in module turbomoleio.testing)": [[6, "turbomoleio.testing.run_itest", false]], "run_update_internal_coords() (turbomoleio.input.define.definerunner method)": [[3, "turbomoleio.input.define.DefineRunner.run_update_internal_coords", false]], "rundata (class in turbomoleio.output.data)": [[5, "turbomoleio.output.data.RunData", false]], "s2() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.s2", false]], "scf_energies() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.scf_energies", false]], "scf_iterations() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.scf_iterations", false]], "scfdata (class in turbomoleio.output.data)": [[5, "turbomoleio.output.data.ScfData", false]], "scfenergiesdata (class in turbomoleio.output.data)": [[5, "turbomoleio.output.data.ScfEnergiesData", false]], "scfiterationdata (class in turbomoleio.output.data)": [[5, "turbomoleio.output.data.ScfIterationData", false]], "scfoutput (class in turbomoleio.output.files)": [[5, "turbomoleio.output.files.ScfOutput", false]], "schema_define_params (in module turbomoleio.input.utils)": [[3, "turbomoleio.input.utils.schema_define_params", false]], "sdg() (in module turbomoleio.core.control)": [[2, "turbomoleio.core.control.sdg", false]], "sdg() (turbomoleio.core.datagroups.datagroups method)": [[2, "turbomoleio.core.datagroups.DataGroups.sdg", false]], "sdgo() (in module turbomoleio.core.control)": [[2, "turbomoleio.core.control.sdgo", false]], "sdgo() (turbomoleio.core.datagroups.datagroups method)": [[2, "turbomoleio.core.datagroups.DataGroups.sdgo", false]], "set_disp() (turbomoleio.core.control.control method)": [[2, "turbomoleio.core.control.Control.set_disp", false]], "shells (class in turbomoleio.core.control)": [[2, "turbomoleio.core.control.Shells", false]], "show_data_group() (turbomoleio.core.datagroups.datagroups method)": [[2, "turbomoleio.core.datagroups.DataGroups.show_data_group", false]], "show_data_group_option() (turbomoleio.core.datagroups.datagroups method)": [[2, "turbomoleio.core.datagroups.DataGroups.show_data_group_option", false]], "show_subfile_fname() (turbomoleio.core.datagroups.datagroups method)": [[2, "turbomoleio.core.datagroups.DataGroups.show_subfile_fname", false]], "singleexcitation (class in turbomoleio.output.data)": [[5, "turbomoleio.output.data.SingleExcitation", false]], "smearingdata (class in turbomoleio.output.data)": [[5, "turbomoleio.output.data.SmearingData", false]], "spindata (class in turbomoleio.output.data)": [[5, "turbomoleio.output.data.SpinData", false]], "spins (turbomoleio.output.states.states property)": [[5, "turbomoleio.output.states.States.spins", false]], "split_string_to_dg_list() (in module turbomoleio.core.datagroups)": [[2, "turbomoleio.core.datagroups.split_string_to_dg_list", false]], "state (class in turbomoleio.output.states)": [[5, "turbomoleio.output.states.State", false]], "states (class in turbomoleio.output.states)": [[5, "turbomoleio.output.states.States", false]], "statpt_info() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.statpt_info", false]], "statptdata (class in turbomoleio.output.data)": [[5, "turbomoleio.output.data.StatptData", false]], "statptoutput (class in turbomoleio.output.files)": [[5, "turbomoleio.output.files.StatptOutput", false]], "string (turbomoleio.output.parser.parser property)": [[5, "turbomoleio.output.parser.Parser.string", false]], "structure (turbomoleio.core.periodic.periodicsystem property)": [[2, "turbomoleio.core.periodic.PeriodicSystem.structure", false]], "symmetry() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.symmetry", false]], "symmetrydata (class in turbomoleio.output.data)": [[5, "turbomoleio.output.data.SymmetryData", false]], "temp_dir() (in module turbomoleio.testing)": [[6, "turbomoleio.testing.temp_dir", false]], "timings() (turbomoleio.output.parser.parser method)": [[5, "turbomoleio.output.parser.Parser.timings", false]], "to_coord_file() (turbomoleio.core.base.basesystem method)": [[2, "turbomoleio.core.base.BaseSystem.to_coord_file", false]], "to_coord_string() (turbomoleio.core.base.basesystem method)": [[2, "turbomoleio.core.base.BaseSystem.to_coord_string", false]], "to_coord_string() (turbomoleio.core.molecule.moleculesystem method)": [[2, "turbomoleio.core.molecule.MoleculeSystem.to_coord_string", false]], "to_coord_string() (turbomoleio.core.periodic.periodicsystem method)": [[2, "turbomoleio.core.periodic.PeriodicSystem.to_coord_string", false]], "to_datagroup() (turbomoleio.core.control.shells method)": [[2, "turbomoleio.core.control.Shells.to_datagroup", false]], "to_file() (turbomoleio.core.base.basesystem method)": [[2, "turbomoleio.core.base.BaseSystem.to_file", false]], "to_file() (turbomoleio.core.control.control method)": [[2, "turbomoleio.core.control.Control.to_file", false]], "to_file() (turbomoleio.core.datagroups.datagroups method)": [[2, "turbomoleio.core.datagroups.DataGroups.to_file", false]], "to_file() (turbomoleio.output.states.eigerrunner method)": [[5, "turbomoleio.output.states.EigerRunner.to_file", false]], "to_string() (turbomoleio.core.molecule.internaldefinition method)": [[2, "turbomoleio.core.molecule.InternalDefinition.to_string", false]], "tol (turbomoleio.testing.itestconfig attribute)": [[6, "turbomoleio.testing.ItestConfig.tol", false]], "total_electrons (turbomoleio.core.control.shells property)": [[2, "turbomoleio.core.control.Shells.total_electrons", false]], "total_electrons (turbomoleio.output.states.states property)": [[5, "turbomoleio.output.states.States.total_electrons", false]], "touch_file() (in module turbomoleio.testing)": [[6, "turbomoleio.testing.touch_file", false]], "turbomoledata (class in turbomoleio.output.data)": [[5, "turbomoleio.output.data.TurbomoleData", false]], "turbomoleio": [[1, "module-turbomoleio", false]], "turbomoleio.core": [[2, "module-turbomoleio.core", false]], "turbomoleio.core.base": [[2, "module-turbomoleio.core.base", false]], "turbomoleio.core.control": [[2, "module-turbomoleio.core.control", false]], "turbomoleio.core.datagroups": [[2, "module-turbomoleio.core.datagroups", false]], "turbomoleio.core.molecule": [[2, "module-turbomoleio.core.molecule", false]], "turbomoleio.core.periodic": [[2, "module-turbomoleio.core.periodic", false]], "turbomoleio.core.symmetry": [[2, "module-turbomoleio.core.symmetry", false]], "turbomoleio.core.utils": [[2, "module-turbomoleio.core.utils", false]], "turbomoleio.input": [[3, "module-turbomoleio.input", false]], "turbomoleio.input.define": [[3, "module-turbomoleio.input.define", false]], "turbomoleio.input.templates": [[4, "module-turbomoleio.input.templates", false]], "turbomoleio.input.utils": [[3, "module-turbomoleio.input.utils", false]], "turbomoleio.output": [[5, "module-turbomoleio.output", false]], "turbomoleio.output.data": [[5, "module-turbomoleio.output.data", false]], "turbomoleio.output.files": [[5, "module-turbomoleio.output.files", false]], "turbomoleio.output.parser": [[5, "module-turbomoleio.output.parser", false]], "turbomoleio.output.states": [[5, "module-turbomoleio.output.states", false]], "turbomoleio.testing": [[6, "module-turbomoleio.testing", false]], "unsupporteddefinestateerror": [[3, "turbomoleio.input.define.UnsupportedDefineStateError", false]], "validate_parameters() (in module turbomoleio.input.utils)": [[3, "turbomoleio.input.utils.validate_parameters", false]]}, "objects": {"": [[1, 0, 0, "-", "turbomoleio"]], "turbomoleio": [[2, 0, 0, "-", "core"], [3, 0, 0, "-", "input"], [5, 0, 0, "-", "output"], [6, 0, 0, "-", "testing"]], "turbomoleio.core": [[2, 0, 0, "-", "base"], [2, 0, 0, "-", "control"], [2, 0, 0, "-", "datagroups"], [2, 0, 0, "-", "molecule"], [2, 0, 0, "-", "periodic"], [2, 0, 0, "-", "symmetry"], [2, 0, 0, "-", "utils"]], "turbomoleio.core.base": [[2, 1, 1, "", "BaseSystem"], [2, 3, 1, "", "get_coord_lines"], [2, 3, 1, "", "get_mol_and_indices_frozen"]], "turbomoleio.core.base.BaseSystem": [[2, 2, 1, "", "coord_lines"], [2, 2, 1, "", "to_coord_file"], [2, 2, 1, "", "to_coord_string"], [2, 2, 1, "", "to_file"]], "turbomoleio.core.control": [[2, 1, 1, "", "Control"], [2, 1, 1, "", "Defaults"], [2, 1, 1, "", "Energy"], [2, 1, 1, "", "Gradient"], [2, 1, 1, "", "Shells"], [2, 3, 1, "", "adg"], [2, 3, 1, "", "cdg"], [2, 3, 1, "", "cpc"], [2, 3, 1, "", "kdg"], [2, 3, 1, "", "mdgo"], [2, 3, 1, "", "sdg"], [2, 3, 1, "", "sdgo"]], "turbomoleio.core.control.Control": [[2, 2, 1, "", "add_cosmo"], [2, 2, 1, "", "cpc"], [2, 4, 1, "", "energy"], [2, 2, 1, "", "from_file"], [2, 2, 1, "", "from_metric"], [2, 2, 1, "", "get_charge"], [2, 2, 1, "", "get_shells"], [2, 2, 1, "", "get_subfiles_list"], [2, 4, 1, "", "gradient"], [2, 4, 1, "", "is_uhf"], [2, 2, 1, "", "remove_last_energy"], [2, 2, 1, "", "remove_last_gradient"], [2, 2, 1, "", "set_disp"], [2, 2, 1, "", "to_file"]], "turbomoleio.core.control.Defaults": [[2, 5, 1, "", "METRIC"]], "turbomoleio.core.control.Energy": [[2, 4, 1, "", "delta_e"], [2, 2, 1, "", "from_file"], [2, 2, 1, "", "from_string"], [2, 4, 1, "", "n_steps"], [2, 2, 1, "", "plot"]], "turbomoleio.core.control.Gradient": [[2, 2, 1, "", "from_file"], [2, 2, 1, "", "from_string"], [2, 4, 1, "", "last_grad_max"], [2, 4, 1, "", "last_grad_norm"], [2, 4, 1, "", "max_gradients"], [2, 4, 1, "", "n_steps"], [2, 4, 1, "", "norms"], [2, 2, 1, "", "plot"]], "turbomoleio.core.control.Shells": [[2, 2, 1, "", "as_dict"], [2, 2, 1, "", "from_dict"], [2, 2, 1, "", "from_file"], [2, 2, 1, "", "from_string"], [2, 4, 1, "", "irreps"], [2, 2, 1, "", "to_datagroup"], [2, 4, 1, "", "total_electrons"]], "turbomoleio.core.datagroups": [[2, 1, 1, "", "DataGroups"], [2, 3, 1, "", "cleanup_string"], [2, 3, 1, "", "compare_datagroup_string"], [2, 3, 1, "", "remove_comments"], [2, 3, 1, "", "remove_dg_from_list"], [2, 3, 1, "", "split_string_to_dg_list"]], "turbomoleio.core.datagroups.DataGroups": [[2, 2, 1, "", "add_data_group"], [2, 2, 1, "", "adg"], [2, 2, 1, "", "as_dict"], [2, 2, 1, "", "cdg"], [2, 2, 1, "", "change_data_group"], [2, 2, 1, "", "compare"], [2, 2, 1, "", "empty"], [2, 2, 1, "", "from_dict"], [2, 2, 1, "", "from_file"], [2, 2, 1, "", "kdg"], [2, 2, 1, "", "kill_data_group"], [2, 2, 1, "", "mdgo"], [2, 2, 1, "", "modify_data_group_options"], [2, 4, 1, "", "ndg"], [2, 4, 1, "", "number_of_data_groups"], [2, 2, 1, "", "sdg"], [2, 2, 1, "", "sdgo"], [2, 2, 1, "", "show_data_group"], [2, 2, 1, "", "show_data_group_option"], [2, 2, 1, "", "show_subfile_fname"], [2, 2, 1, "", "to_file"]], "turbomoleio.core.molecule": [[2, 1, 1, "", "BondAngle"], [2, 1, 1, "", "CollinearBendingAngle"], [2, 1, 1, "", "DihedralAngle"], [2, 1, 1, "", "Distance"], [2, 1, 1, "", "InternalDefinition"], [2, 1, 1, "", "InverseDistance"], [2, 1, 1, "", "MoleculeSystem"], [2, 1, 1, "", "OutOfPlaneAngle"], [2, 1, 1, "", "PerpendicularBendingAngle"]], "turbomoleio.core.molecule.BondAngle": [[2, 2, 1, "", "compute_value"], [2, 5, 1, "", "coord_str"], [2, 5, 1, "", "coord_type"], [2, 5, 1, "", "n_atoms"]], "turbomoleio.core.molecule.CollinearBendingAngle": [[2, 2, 1, "", "compute_value"], [2, 5, 1, "", "coord_str"], [2, 5, 1, "", "coord_type"], [2, 5, 1, "", "n_atoms"]], "turbomoleio.core.molecule.DihedralAngle": [[2, 2, 1, "", "compute_value"], [2, 5, 1, "", "coord_str"], [2, 5, 1, "", "coord_type"], [2, 5, 1, "", "n_atoms"]], "turbomoleio.core.molecule.Distance": [[2, 2, 1, "", "compute_value"], [2, 5, 1, "", "coord_str"], [2, 5, 1, "", "coord_type"], [2, 5, 1, "", "n_atoms"]], "turbomoleio.core.molecule.InternalDefinition": [[2, 2, 1, "", "compute_value"], [2, 5, 1, "", "coord_str"], [2, 5, 1, "", "coord_type"], [2, 2, 1, "", "from_string"], [2, 2, 1, "", "get_subclass_from_str"], [2, 2, 1, "", "is_valid"], [2, 5, 1, "", "n_atoms"], [2, 2, 1, "", "to_string"]], "turbomoleio.core.molecule.InverseDistance": [[2, 2, 1, "", "compute_value"], [2, 5, 1, "", "coord_str"], [2, 5, 1, "", "coord_type"], [2, 5, 1, "", "n_atoms"]], "turbomoleio.core.molecule.MoleculeSystem": [[2, 2, 1, "", "add_bond_angle"], [2, 2, 1, "", "add_dihedral"], [2, 2, 1, "", "add_distance"], [2, 2, 1, "", "as_dict"], [2, 2, 1, "", "from_dict"], [2, 2, 1, "", "from_file"], [2, 2, 1, "", "from_string"], [2, 2, 1, "", "get_int_def_inconsistencies"], [2, 2, 1, "", "has_inconsistencies"], [2, 4, 1, "", "molecule"], [2, 2, 1, "", "to_coord_string"]], "turbomoleio.core.molecule.OutOfPlaneAngle": [[2, 2, 1, "", "compute_value"], [2, 5, 1, "", "coord_str"], [2, 5, 1, "", "coord_type"], [2, 5, 1, "", "n_atoms"]], "turbomoleio.core.molecule.PerpendicularBendingAngle": [[2, 2, 1, "", "compute_value"], [2, 5, 1, "", "coord_str"], [2, 5, 1, "", "coord_type"], [2, 5, 1, "", "n_atoms"]], "turbomoleio.core.periodic": [[2, 1, 1, "", "PeriodicSystem"]], "turbomoleio.core.periodic.PeriodicSystem": [[2, 2, 1, "", "as_dict"], [2, 2, 1, "", "from_dict"], [2, 2, 1, "", "from_file"], [2, 2, 1, "", "from_string"], [2, 4, 1, "", "structure"], [2, 2, 1, "", "to_coord_string"]], "turbomoleio.core.utils": [[2, 3, 1, "", "define_quit"], [2, 3, 1, "", "get_tm_version"]], "turbomoleio.input": [[3, 0, 0, "-", "define"], [4, 0, 0, "-", "templates"], [3, 0, 0, "-", "utils"]], "turbomoleio.input.define": [[3, 6, 1, "", "DefineError"], [3, 6, 1, "", "DefineExpectError"], [3, 6, 1, "", "DefineIredError"], [3, 6, 1, "", "DefineParameterError"], [3, 1, 1, "", "DefineRunner"], [3, 6, 1, "", "UnsupportedDefineStateError"]], "turbomoleio.input.define.DefineRunner": [[3, 2, 1, "", "dump_command_file"], [3, 2, 1, "", "run_full"], [3, 2, 1, "", "run_generate_mo_files"], [3, 2, 1, "", "run_update_internal_coords"]], "turbomoleio.input.templates": [[4, 3, 1, "", "available_templates"]], "turbomoleio.input.utils": [[3, 6, 1, "", "ParametersValidationError"], [3, 3, 1, "", "ex_setter"], [3, 3, 1, "", "get_define_template"], [3, 7, 1, "", "schema_define_params"], [3, 3, 1, "", "validate_parameters"]], "turbomoleio.output": [[5, 0, 0, "-", "data"], [5, 0, 0, "-", "files"], [5, 0, 0, "-", "parser"], [5, 0, 0, "-", "states"]], "turbomoleio.output.data": [[5, 1, 1, "", "AoforceNumericalIntegrationData"], [5, 1, 1, "", "AoforceRotationalData"], [5, 1, 1, "", "AoforceVibrationalData"], [5, 1, 1, "", "BaseData"], [5, 1, 1, "", "BasisData"], [5, 1, 1, "", "CosmoData"], [5, 1, 1, "", "DFTData"], [5, 1, 1, "", "DispersionCorrectionData"], [5, 1, 1, "", "ElectrostaticMomentsData"], [5, 1, 1, "", "EscfData"], [5, 1, 1, "", "EscfIterationData"], [5, 1, 1, "", "FunctionalData"], [5, 1, 1, "", "GeometryData"], [5, 1, 1, "", "IntegralData"], [5, 1, 1, "", "MP2Data"], [5, 1, 1, "", "MP2Results"], [5, 1, 1, "", "PeriodicityData"], [5, 1, 1, "", "RelaxConvergenceData"], [5, 1, 1, "", "RelaxData"], [5, 1, 1, "", "RelaxGradientsData"], [5, 1, 1, "", "RiData"], [5, 1, 1, "", "RunData"], [5, 1, 1, "", "ScfData"], [5, 1, 1, "", "ScfEnergiesData"], [5, 1, 1, "", "ScfIterationData"], [5, 1, 1, "", "SingleExcitation"], [5, 1, 1, "", "SmearingData"], [5, 1, 1, "", "SpinData"], [5, 1, 1, "", "StatptData"], [5, 1, 1, "", "SymmetryData"], [5, 1, 1, "", "TurbomoleData"]], "turbomoleio.output.data.AoforceNumericalIntegrationData": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.data.AoforceRotationalData": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.data.AoforceVibrationalData": [[5, 2, 1, "", "from_parser"], [5, 2, 1, "", "get_freqs_df"], [5, 2, 1, "", "n_negative_freqs"], [5, 2, 1, "", "n_positive_freqs"], [5, 2, 1, "", "n_zero_freqs"]], "turbomoleio.output.data.BaseData": [[5, 2, 1, "", "from_file"], [5, 2, 1, "", "from_parser"], [5, 2, 1, "", "from_string"]], "turbomoleio.output.data.BasisData": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.data.CosmoData": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.data.DFTData": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.data.DispersionCorrectionData": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.data.ElectrostaticMomentsData": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.data.EscfData": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.data.EscfIterationData": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.data.FunctionalData": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.data.GeometryData": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.data.IntegralData": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.data.MP2Data": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.data.MP2Results": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.data.PeriodicityData": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.data.RelaxConvergenceData": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.data.RelaxData": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.data.RelaxGradientsData": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.data.RiData": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.data.RunData": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.data.ScfData": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.data.ScfEnergiesData": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.data.ScfIterationData": [[5, 2, 1, "", "from_parser"], [5, 2, 1, "", "plot_energies"]], "turbomoleio.output.data.SmearingData": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.data.SpinData": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.data.StatptData": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.data.SymmetryData": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.data.TurbomoleData": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.files": [[5, 1, 1, "", "AoforceOutput"], [5, 1, 1, "", "EgradOutput"], [5, 1, 1, "", "EscfOnlyOutput"], [5, 1, 1, "", "EscfOutput"], [5, 1, 1, "", "GradOutput"], [5, 1, 1, "", "JobexOutput"], [5, 1, 1, "", "MP2Output"], [5, 1, 1, "", "RelaxOutput"], [5, 1, 1, "", "Ricc2Output"], [5, 1, 1, "", "ScfOutput"], [5, 1, 1, "", "StatptOutput"]], "turbomoleio.output.files.AoforceOutput": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.files.EgradOutput": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.files.EscfOnlyOutput": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.files.EscfOutput": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.files.GradOutput": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.files.JobexOutput": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.files.MP2Output": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.files.RelaxOutput": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.files.Ricc2Output": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.files.ScfOutput": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.files.StatptOutput": [[5, 2, 1, "", "from_parser"]], "turbomoleio.output.parser": [[5, 1, 1, "", "Parser"], [5, 3, 1, "", "convert_float"], [5, 3, 1, "", "convert_int"], [5, 3, 1, "", "convert_time_string"]], "turbomoleio.output.parser.Parser": [[5, 2, 1, "", "all_done"], [5, 2, 1, "", "aoforce_analysis"], [5, 2, 1, "", "aoforce_numerical_integration"], [5, 2, 1, "", "basis"], [5, 2, 1, "", "centers"], [5, 2, 1, "", "coordinates"], [5, 2, 1, "", "cosmo_header"], [5, 2, 1, "", "cosmo_results"], [5, 2, 1, "", "density_functional_data"], [5, 2, 1, "", "dftd"], [5, 2, 1, "", "egrad_excited_state"], [5, 2, 1, "", "electrostatic_moments"], [5, 2, 1, "", "escf_excitations"], [5, 2, 1, "", "escf_gs_total_en"], [5, 2, 1, "", "escf_iterations"], [5, 2, 1, "", "fermi"], [5, 2, 1, "", "from_file"], [5, 2, 1, "", "get_split_jobex_parsers"], [5, 2, 1, "", "get_value"], [5, 2, 1, "", "gradient"], [5, 2, 1, "", "grep_line"], [5, 2, 1, "", "header"], [5, 2, 1, "", "integral"], [5, 2, 1, "", "is_uhf"], [5, 2, 1, "", "mp2_data"], [5, 2, 1, "", "mp2_results"], [5, 2, 1, "", "periodicity_data"], [5, 2, 1, "", "pre_escf_run"], [5, 2, 1, "", "pre_scf_run"], [5, 2, 1, "", "rdgrad_memory"], [5, 2, 1, "", "relax_conv_info"], [5, 2, 1, "", "relax_gradient_values"], [5, 2, 1, "", "relax_info"], [5, 2, 1, "", "rij_info"], [5, 2, 1, "", "riper_scf_energies"], [5, 2, 1, "", "s2"], [5, 2, 1, "", "scf_energies"], [5, 2, 1, "", "scf_iterations"], [5, 2, 1, "", "statpt_info"], [5, 4, 1, "", "string"], [5, 2, 1, "", "symmetry"], [5, 2, 1, "", "timings"]], "turbomoleio.output.states": [[5, 1, 1, "", "EigerOutput"], [5, 1, 1, "", "EigerRunner"], [5, 1, 1, "", "State"], [5, 1, 1, "", "States"], [5, 3, 1, "", "get_mos_energies"]], "turbomoleio.output.states.EigerOutput": [[5, 2, 1, "", "compare_states"], [5, 2, 1, "", "from_file"], [5, 2, 1, "", "from_string"]], "turbomoleio.output.states.EigerRunner": [[5, 2, 1, "", "get_eiger_output"], [5, 2, 1, "", "run"], [5, 2, 1, "", "to_file"]], "turbomoleio.output.states.State": [[5, 2, 1, "", "as_dict"], [5, 2, 1, "", "from_dict"], [5, 4, 1, "", "has_fractional_occ"], [5, 4, 1, "", "max_occupation"]], "turbomoleio.output.states.States": [[5, 2, 1, "", "as_dict"], [5, 4, 1, "", "eigenvalues"], [5, 2, 1, "", "filter_states"], [5, 2, 1, "", "from_file"], [5, 4, 1, "", "gap"], [5, 2, 1, "", "generate_lowest_filled_states"], [5, 2, 1, "", "get_shells"], [5, 4, 1, "", "has_fractional_occ"], [5, 4, 1, "", "has_hole"], [5, 4, 1, "", "homo"], [5, 4, 1, "", "homo_index"], [5, 2, 1, "", "insert"], [5, 4, 1, "", "irrep_indices"], [5, 4, 1, "", "irreps"], [5, 4, 1, "", "is_uhf"], [5, 4, 1, "", "lumo"], [5, 4, 1, "", "lumo_index"], [5, 4, 1, "", "n_states"], [5, 4, 1, "", "occupations"], [5, 4, 1, "", "spins"], [5, 4, 1, "", "total_electrons"]], "turbomoleio.testing": [[6, 1, 1, "", "ItestConfig"], [6, 6, 1, "", "ItestError"], [6, 3, 1, "", "assert_MSONable"], [6, 3, 1, "", "assert_almost_equal"], [6, 3, 1, "", "compare_differences"], [6, 3, 1, "", "generate_control_for_test"], [6, 3, 1, "", "generate_reference_out_parser_files"], [6, 3, 1, "", "generate_reference_output"], [6, 3, 1, "", "get_control_integration"], [6, 3, 1, "", "get_sp"], [6, 3, 1, "", "get_test_data_dir"], [6, 3, 1, "", "get_tests_configs_tm_versions"], [6, 3, 1, "", "get_tfp"], [6, 3, 1, "", "gisnan"], [6, 3, 1, "", "has_matplotlib"], [6, 3, 1, "", "run_itest"], [6, 3, 1, "", "temp_dir"], [6, 3, 1, "", "touch_file"]], "turbomoleio.testing.ItestConfig": [[6, 5, 1, "", "define_timeout"], [6, 5, 1, "", "delete_tmp_dir"], [6, 5, 1, "", "dryrun"], [6, 5, 1, "", "dryrun_fpath"], [6, 5, 1, "", "dryrun_use_ref_control"], [6, 5, 1, "", "generate_ref"], [6, 5, 1, "", "tol"]]}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "class", "Python class"], "2": ["py", "method", "Python method"], "3": ["py", "function", "Python function"], "4": ["py", "property", "Python property"], "5": ["py", "attribute", "Python attribute"], "6": ["py", "exception", "Python exception"], "7": ["py", "data", "Python data"]}, "objtypes": {"0": "py:module", "1": "py:class", "2": "py:method", "3": "py:function", "4": "py:property", "5": "py:attribute", "6": "py:exception", "7": "py:data"}, "terms": {"": [2, 5, 13, 15, 18, 19], "0": [2, 3, 5, 6, 10, 16, 17, 18, 19, 20], "00000000000000": 10, "0001": [2, 6], "01": [5, 16], "03717448857876": 10, "06": 5, "07": 6, "0x7fb15f425eb8": 20, "0x7fd37d6282b0": 20, "1": [2, 5, 6, 10, 12, 16, 17, 18, 19, 20], "10": [6, 12, 19], "100": 11, "11": [5, 18, 19], "12": [5, 19], "120": 12, "123d": 5, "123e": 5, "13": 19, "14": 19, "15": [18, 19], "16": [6, 18, 19], "17": 19, "17616323936717": 10, "1996": 19, "1d": [2, 5], "1e": [5, 6], "2": [2, 3, 5, 6, 10, 12, 16, 18, 19], "20": [18, 19], "200": 3, "2007": 19, "2021": 18, "2022": 18, "2024": 18, "23": 5, "24": 18, "27": 18, "28": 19, "29": 19, "2d": [2, 5], "3": [2, 5, 10, 12, 14, 16, 17, 18, 19], "30": 19, "35232647873438": 10, "3d": [2, 5], "3x3": 5, "4": [2, 3, 5, 10, 12, 17, 18, 19], "42945116692": 20, "49586861429": 20, "5": [2, 10, 12, 17, 18, 19], "55": 5, "589": 12, "6": [2, 5, 12, 16, 18, 19], "60": [3, 12, 19], "6b": 19, "6d": 19, "7": [2, 9, 12, 16, 17, 18, 19], "8": [9, 14, 16, 18, 19], "89": 16, "9": [3, 12, 16, 19], "99": 16, "A": [2, 5, 9, 11, 12, 14, 15, 16, 19], "AND": 19, "AS": 19, "And": 19, "As": [10, 11, 12, 15, 16], "At": [12, 20], "BE": 19, "BEING": 19, "BUT": 19, "BY": 19, "Being": [12, 13], "But": 19, "By": [6, 12, 16, 19], "FOR": 19, "For": [2, 5, 8, 10, 11, 12, 13, 15, 16, 17, 19, 20], "IF": 19, "IN": 19, "If": [2, 3, 5, 6, 11, 12, 13, 15, 16, 19, 20], "In": [2, 5, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20], "It": [1, 2, 5, 11, 12, 14, 15, 16, 19], "NO": 19, "NOT": 19, "No": 19, "Not": 19, "OF": 19, "OR": 19, "Of": [12, 19], "On": 15, "One": [2, 5], "SUCH": 19, "Such": 19, "THE": 19, "THERE": 19, "TO": 19, "The": [2, 3, 5, 6, 13, 14, 15, 17, 18, 19], "Their": [10, 16], "There": 13, "These": [10, 11, 12, 16, 19, 20], "To": [2, 11, 16, 17, 19], "WILL": 19, "WITH": 19, "Will": [5, 6], "With": 14, "_": 13, "__init__": [15, 17], "__version__": 17, "_expect": 13, "_privat": 6, "_sendlin": 13, "a1": [2, 5, 12], "a2": 5, "a3": 5, "ab": 5, "abc": [2, 5, 20], "abil": 19, "abl": 15, "abnorm": [3, 12], "about": [2, 5, 8, 10, 12, 13, 15, 16, 18, 19, 20], "abov": [11, 12, 15, 16, 19, 20], "absenc": 19, "absent": [2, 5], "absolut": [6, 12, 16, 19], "abstract": [2, 5, 14, 15], "abus": 19, "accept": [2, 12, 13, 14, 15, 19], "access": [5, 12, 13, 15, 16, 17, 18, 19, 20], "accompani": 19, "accord": [2, 3, 5, 11, 12, 13, 14, 19], "account": 5, "accuraci": 12, "aceton_dftd3_tzvp": 16, "aceton_ful": 16, "achiev": [5, 16, 19], "acknowledg": 19, "acoust": 16, "acquir": 19, "across": [5, 16, 19], "act": [1, 11], "action": [16, 19], "activ": [5, 12, 19], "actual": [2, 5, 6, 12, 16, 19], "ad": [2, 11, 12, 13, 15, 16, 18, 19], "adapt": [9, 19], "adc": [3, 12], "add": [2, 5, 11, 12, 13, 15, 16, 17, 19], "add_bond_angl": [1, 2, 10], "add_cosmo": [1, 2, 13], "add_data_group": [1, 2, 11], "add_dihedr": [1, 2], "add_dist": [1, 2, 10], "add_user_def_bond": 2, "addit": [2, 6, 9, 10, 11, 12, 13, 15, 16, 17, 19, 20], "additionn": 16, "address": [15, 19], "adg": [1, 2, 11], "adopt": [17, 19], "advanc": [13, 18], "advantag": [10, 12, 13, 14, 15], "advers": 19, "advis": [14, 18, 19], "affect": 19, "affero": 19, "affirm": 19, "aforc": 5, "after": [2, 5, 11, 12, 13, 15, 16, 19], "after_end": 2, "afterward": [3, 10, 12], "again": [10, 15, 20], "against": [13, 19], "aggreg": 19, "agre": [14, 15, 19], "agreement": 19, "aim": [5, 12, 16, 19], "align": 5, "all": [2, 3, 5, 6, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20], "all_don": [1, 5], "alleg": 19, "alloc": 5, "allow": [1, 2, 3, 5, 6, 10, 11, 12, 13, 15, 16, 19], "allow_fract": 5, "almost": 6, "alon": [16, 20], "along": [19, 20], "alpha": [2, 5, 11, 12], "alreadi": [2, 3, 11, 12, 13, 15, 16, 19], "also": [2, 3, 5, 8, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20], "altern": [12, 13, 19], "although": [14, 19, 20], "altogeth": 16, "alwai": [2, 3, 5, 6, 10, 11, 13, 15, 16], "ambigu": 11, "among": [3, 5, 11, 12, 16, 19], "amount": [2, 16, 18], "ampran": 5, "an": [1, 2, 3, 5, 6, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20], "analys": 11, "analysi": [5, 16, 20], "analyz": [15, 16], "ancillari": 19, "angl": [2, 5], "angstrom": [2, 5, 10, 12], "ani": [2, 5, 6, 11, 12, 13, 16, 19], "anisotropi": 5, "anneal": 5, "annealing_factor": 5, "annealing_homo_lumo_gap_limit": 5, "anot": 5, "anoth": [2, 11, 16], "anti": 19, "anymor": 15, "anyon": 19, "anyth": [2, 19], "anywai": [2, 12, 16], "aoforc": [5, 9, 16, 20], "aoforce_analysi": [1, 5], "aoforce_numerical_integr": [1, 5], "aoforcenumericalintegrationdata": [1, 5, 20], "aoforceoutput": [1, 5, 20], "aoforcerotationaldata": [1, 5, 20], "aoforcevibrationaldata": [1, 5, 20], "api": [9, 10, 11, 14, 17, 20], "appar": 11, "appear": 15, "append": [2, 6, 10, 16], "appendix": 18, "appli": [2, 9, 11, 12, 16, 19], "applic": [12, 16, 19], "approach": [15, 20], "appropri": [2, 15, 16, 19], "approxim": [5, 19], "ar": [2, 3, 5, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20], "arbitrari": 16, "area": [5, 19], "argument": [2, 3, 5, 6, 11, 12, 16], "aris": [16, 19], "arrai": 6, "arrang": 19, "articl": 19, "artifici": 2, "as_dict": [1, 2, 5, 20], "ascend": [5, 20], "ascii": 2, "asid": [2, 16], "ask": [11, 19], "aspect": [13, 14], "assert": [6, 19], "assert_allclos": 6, "assert_almost_equ": [1, 6, 16], "assert_equ": 6, "assert_mson": [1, 6], "assertionerror": 6, "asset": 19, "associ": [2, 5, 19, 20], "assum": [16, 19], "assumpt": 19, "assur": 19, "asterisk": 5, "atol": [2, 6], "atom": [2, 5, 9, 10, 12], "atom1": [2, 10], "atom2": [2, 10], "atom3": 2, "atom4": 2, "atoms_per_loop": 5, "attach": 19, "attempt": [2, 19], "attent": 11, "attribut": [2, 6, 10, 11, 12, 13, 15, 16, 19, 20], "author": 19, "autom": 12, "automat": [2, 5, 9, 10, 11, 13, 14, 16, 19], "aux_basis_per_speci": 5, "auxialiari": 5, "auxiliari": [5, 6], "avail": [2, 3, 4, 5, 9, 10, 11, 12, 13, 15, 16, 18, 19, 20], "available_templ": [3, 4], "avoid": [3, 5, 11, 13, 16, 19], "awai": 19, "ax": [2, 5], "ax_annot": [2, 5], "ax_grid": [2, 5], "axi": 5, "b": [2, 3, 5, 11, 12, 19], "b1": [2, 5], "b2": [2, 5], "b3": 5, "back": [2, 6, 16, 20], "backup": 2, "backup_fil": 2, "backup_suffix": 2, "backward": [14, 15, 16, 18], "base": [0, 1, 3, 5, 6, 10, 11, 12, 13, 15, 16, 18, 19, 20], "basedata": [1, 5, 6, 15], "baseexcept": 6, "basesystem": [1, 2], "basi": [1, 2, 3, 5, 12, 15, 20], "basic": [2, 5, 11, 14, 16, 19, 20], "basis_atom": [3, 12], "basis_per_speci": 5, "basisdata": [1, 5, 20], "becaus": [5, 15, 19], "becom": 15, "been": [2, 3, 5, 9, 12, 13, 15, 16, 18, 19, 20], "befor": [2, 3, 5, 6, 11, 12, 13, 15, 16, 18, 20], "before_first_dollar": 2, "begin": [2, 11], "behalf": 19, "behav": 16, "behavior": [3, 11, 13, 16], "being": [3, 5, 11, 12, 16, 19], "believ": 19, "below": [2, 10, 11, 15, 16, 19, 20], "bend": [2, 10], "benefit": 19, "benzen": 16, "benzene_myxc": 16, "besid": 11, "best": [11, 13, 16, 19], "beta": [2, 5, 11, 12], "better": [5, 16], "between": [2, 5, 6, 11, 12, 16, 18, 19], "beyond": [16, 19], "bit": 12, "bj": [2, 3, 12], "blank": [2, 11], "blank_lin": 2, "block": [2, 11], "bodi": 19, "bohr": [2, 10], "bond": [2, 10], "bondangl": [1, 2], "bool": [2, 3, 5, 6, 12], "boolean": [3, 5, 16], "both": [2, 6, 11, 15, 16, 19, 20], "bottom": 15, "box": 19, "brief": 19, "briefli": 13, "bring": [10, 13], "brought": 12, "bug": [15, 16, 17, 18], "build": [5, 15, 20], "busi": 19, "c": [2, 5, 11, 12, 19], "c1": 11, "calc_typ": 5, "calcul": [2, 5, 6, 9, 10, 12, 13, 15, 16, 18, 20], "call": [2, 5, 10, 11, 12, 13, 15, 16, 19, 20], "callabl": 5, "caller": 2, "can": [2, 3, 5, 6, 8, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20], "cannot": [5, 11, 12, 16, 19], "cao": 5, "capabl": 10, "care": [12, 15, 16, 18], "carefulli": [13, 15, 16, 18], "carri": 19, "cartesian": [2, 5, 10], "case": [2, 3, 5, 6, 11, 12, 13, 14, 15, 16, 19], "caus": [2, 19], "caviti": [2, 3, 5, 12], "cc2": 20, "ccsd": [3, 12], "ccsdapprox": 12, "ccsdt": [3, 12], "cd": 6, "cdg": [1, 2, 6, 11, 12], "ceas": 19, "cell": 2, "cell_str": 2, "center": [1, 5, 20], "center_of_charg": 5, "center_of_mass": 5, "cerberu": [3, 12, 13], "certain": [12, 19], "cessat": 19, "challeng": 12, "chang": [2, 3, 5, 10, 11, 14, 15, 17, 18, 19], "change_data_group": [1, 2, 11, 13], "changedir": 6, "changelog": 18, "charact": 2, "character": [5, 19], "charg": [2, 3, 5, 12, 15, 19, 20], "check": [2, 3, 5, 6, 9, 11, 12, 13, 15, 16, 20], "check_all_don": 5, "chemic": 16, "child": 12, "choos": 19, "chosen": [5, 15], "chunk": [2, 5], "ci": [3, 12], "circumst": 19, "circumvent": 19, "ciss": 12, "cist": 12, "civil": 19, "claim": 19, "class": [2, 3, 5, 6, 15, 16, 19, 20], "classmethod": [2, 5], "clean": [2, 9, 11], "cleanup": 2, "cleanup_str": [1, 2], "cleanup_typ": 2, "clear": [14, 19], "clearli": [14, 19], "close": [2, 5, 11, 12, 19], "cls_dict_path": 15, "cm": 5, "code": [2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20], "coeff": 5, "coeffici": 5, "coexist": 2, "collect": [2, 16, 19, 20], "collinear": 2, "collinearbendingangl": [1, 2], "column": 5, "com": 8, "combin": [2, 5, 12, 15, 19], "come": [2, 5, 12, 15, 16, 19, 20], "command": [3, 5, 6, 11, 12, 13, 16, 19], "comment": [2, 11, 12, 14], "comment_typ": 2, "commerci": 19, "commit": [9, 19], "common": [2, 5, 12, 15, 18, 19], "commonli": 10, "commun": [3, 15, 19], "compar": [1, 2, 5, 6, 15, 16], "compare_datagroup_str": [1, 2], "compare_differ": [1, 6], "compare_st": [1, 5], "comparison": [2, 6, 16], "compat": [5, 15, 16, 18], "compil": 19, "complet": [2, 3, 5, 10, 11, 12, 13, 20], "complex": 12, "compli": [14, 19], "complianc": 19, "complic": [10, 13], "compon": [5, 16, 19], "compos": [5, 20], "compromis": 12, "comput": [16, 19], "compute_valu": [1, 2], "concern": [5, 13, 14, 15, 19], "concret": 2, "condit": [5, 15, 16, 19], "conf": 17, "config": 6, "configur": [6, 16, 17], "conflict": 6, "conftest": 16, "connect": [11, 16, 18, 19], "consequ": 19, "consequenti": 19, "consid": [2, 3, 5, 11, 12, 13, 15, 16, 19, 20], "consider": 15, "consist": [2, 9, 19], "conspicu": 19, "constant": 5, "constantli": 19, "constitut": 19, "constraint": [2, 15], "constru": 19, "construct": [2, 3, 5, 12], "construction_tim": 5, "consum": 19, "contact": 19, "contain": [2, 5, 6, 8, 9, 10, 11, 12, 13, 15, 16, 18, 19, 20], "content": [0, 11, 19, 20], "context": [6, 15, 16, 19], "continu": 19, "contractu": 19, "contradict": 19, "contrast": 19, "contribut": [2, 5, 8, 13, 16, 20], "contributor": 19, "control": [0, 1, 3, 5, 6, 9, 12, 13, 16, 18, 19, 20], "control_dir": 2, "control_reference_filenam": 6, "conv": 5, "conv_one_e_en": 5, "conv_tot_en": 5, "convei": 19, "conveni": 19, "convent": [2, 10, 11, 13, 14, 16], "converg": [5, 9, 20], "convern": 5, "convers": 10, "convert": [2, 3, 5, 6, 11, 14, 15, 20], "convert_float": [1, 5], "convert_int": [1, 5], "convert_time_str": [1, 5], "convey": 19, "coord": [2, 3, 5, 6, 11, 12, 16, 18], "coord_fil": [3, 12], "coord_filenam": 6, "coord_lin": [1, 2], "coord_str": [1, 2], "coord_typ": [1, 2], "coordin": [1, 2, 3, 5, 9, 10, 12], "copi": [2, 3, 12, 19], "copyleft": 19, "copymo": [3, 12], "copyright": 19, "core": [0, 1, 5, 10, 11, 13], "core_memory_dft": 5, "correct": [2, 5, 6, 9, 11, 12, 13, 16, 19, 20], "correctli": [2, 15, 16], "correl": [5, 16, 20], "correspond": [2, 5, 10, 11, 13, 15, 16, 17, 19], "cosmo": [2, 5, 12, 20], "cosmo_head": [1, 5], "cosmo_out": 12, "cosmo_result": [1, 5], "cosmodata": [1, 5, 20], "cost": 19, "could": [2, 5, 10, 13, 15, 16, 19, 20], "coulomb": 5, "coulomb_energi": 5, "count": 2, "counterclaim": 19, "countri": 19, "cours": [12, 16, 19], "court": 19, "cov": 16, "coven": 19, "cover": [12, 16, 19], "coverag": [16, 19], "coverage_html": 16, "coveragerc_integr": 16, "coveragerc_unit": 16, "cpc": [1, 2, 11], "cpu": 5, "cpu_tim": 5, "crash": 5, "creat": [2, 3, 5, 6, 9, 12, 13, 15, 16, 17, 20], "creation": 16, "criteria": 20, "criterion": [5, 19], "criterium": 5, "critic": 16, "cross": 19, "crucial": 12, "crystallograph": 5, "cumbersom": 16, "cure": 19, "current": [2, 3, 5, 9, 11, 12, 14, 15, 16, 18], "current_level": 6, "custom": [16, 19], "customarili": 19, "d": [2, 5, 16, 19], "d1": [2, 3, 5, 12], "d2": [2, 3, 5, 12], "d3": [2, 3, 12], "dai": [5, 19], "damag": 19, "damp": 5, "danger": 19, "data": [0, 1, 2, 9, 10, 12, 13, 15, 18, 19], "data_block": [2, 11], "data_group": [2, 11], "data_path": 5, "databas": 18, "datafram": 5, "datagroup": [0, 1, 5, 6, 9, 17, 18, 20], "datagroup_nam": 6, "datagroup_valu": 6, "datagroups_opt": 6, "date": [16, 19], "datetim": 5, "davidson": 5, "ddip_dq": 5, "de": 5, "deactiv": 6, "deal": [15, 20], "dealt": 5, "decemb": 19, "decid": [15, 19], "declin": 19, "decomposit": 20, "deem": 19, "def2": 12, "default": [1, 2, 3, 5, 6, 11, 12, 15, 16], "default_sett": 3, "defect": 19, "defens": 19, "defin": [0, 1, 2, 4, 5, 6, 9, 10, 11, 14, 16, 17, 18, 19], "define_command": 3, "define_opt": 6, "define_parameters_valid": 12, "define_quit": [1, 2], "define_timeout": [1, 6], "defineerror": [1, 3, 12, 13], "defineexpecterror": [1, 3, 12], "defineirederror": [1, 3], "defineparametererror": [1, 3], "definerunn": [1, 3, 6, 13, 16, 18], "definit": [2, 5, 6, 9, 10, 12, 16, 19], "degeneraci": 5, "degre": 2, "delet": [6, 16], "delete_tmp_dir": [1, 6, 16], "delta_": [1, 2], "deni": 19, "denomin": 19, "density_functional_data": [1, 5], "depend": [2, 3, 5, 12, 15, 16], "dependeci": 13, "depriv": 19, "depth": 15, "deriv": 5, "describ": [2, 3, 5, 11, 13, 14, 15, 16, 20], "descript": [2, 5, 13, 16, 20], "deseri": 15, "desi": [3, 12], "design": [11, 15, 16, 18, 19, 20], "desir": [6, 13], "dest_dir": 2, "destin": 2, "desy_ep": [3, 12], "detail": [5, 14, 15, 16, 18, 19, 20], "determin": [2, 5, 6, 10, 11, 12, 16, 19, 20], "dev_script": 16, "develop": [13, 14, 15, 16, 19, 20], "deviat": 14, "devic": 19, "dft": [2, 3, 5, 11, 12, 20], "dftd": [1, 5], "dftdata": [1, 5, 20], "dg": 11, "dg1": 2, "dg2": 2, "dg_list": [2, 11], "dg_string": 5, "dg_to_remov": 2, "dict": [2, 3, 5, 6, 12], "dictionari": [2, 3, 5, 6, 11, 12, 13, 15, 20], "dielectr": 5, "dielectric_energi": 5, "dielectric_energy_oc_corr": 5, "differ": [2, 5, 6, 10, 11, 12, 13, 15, 16, 17, 19, 20], "dig": 20, "dihedr": 2, "dihedralangl": [1, 2], "dii": [5, 20], "diis_error_vect": 5, "dimens": 5, "dimension": [2, 9, 10], "dipol": [5, 20], "dipole_mo": 5, "dipole_norm": 5, "dipole_vector": 5, "dir": 2, "direct": [2, 5, 16, 19], "direct_space_vector": 5, "directli": [2, 5, 11, 12, 13, 15, 16, 19, 20], "directori": [2, 3, 5, 6, 9, 11, 12, 16], "disabl": [3, 12], "disappear": 15, "disclaim": 19, "discourag": [14, 16], "discov": 16, "discriminatori": 19, "discuss": [13, 15, 16], "disex": [2, 3, 5, 12], "disex2": 5, "disp": [2, 3, 12], "dispers": [2, 5, 11, 12, 20], "dispersion_correct": [2, 5], "dispersioncorrectiondata": [1, 5, 20], "displac": 5, "displai": [2, 5, 19], "dispos": 15, "disrupt": 13, "distanc": [1, 2, 5, 10, 12], "distinct": 11, "distinguish": [12, 19], "distribut": [11, 13, 16, 19], "divid": [11, 16], "do": [3, 6, 13, 14, 15, 18, 19], "doc": [14, 17], "docs_rst": 14, "docstr": 14, "document": [9, 13, 14, 16, 17, 19, 20], "doe": [2, 11, 12, 19, 20], "dollar": [2, 11], "domain": 19, "domin": 5, "dominant_contribut": 5, "done": [2, 5, 10, 11, 12, 13, 16], "doublet": [3, 12], "doubt": 19, "down": [15, 18], "downstream": 19, "dp": 12, "dr": 12, "dr_data": 13, "dry": 16, "dryrun": [1, 6, 16], "dryrun_fpath": [1, 6], "dryrun_itest": [6, 16], "dryrun_use_ref_control": [1, 6], "dscf": [5, 9, 12, 16, 20], "due": 16, "dummi": [2, 11], "dump": [3, 5], "dump_command_fil": [1, 3], "duplic": 2, "durabl": 19, "dure": [3, 10, 11, 15], "dwell": 19, "dynam": [2, 6, 10, 12, 19], "dynpol": [3, 12], "e": [2, 3, 5, 8, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20], "each": [2, 5, 6, 10, 11, 12, 15, 16, 19, 20], "earlier": 19, "eas": [16, 17], "easiest": 16, "easili": [1, 5, 12, 15, 16, 20], "ecp_atom": 3, "edit": 3, "effect": [3, 11, 16, 19], "effort": 19, "egrad": [5, 9, 20], "egrad_excited_st": [1, 5], "egradoutput": [1, 5, 20], "eht": 12, "eigenst": [5, 20], "eigenvalu": [1, 5, 16, 20], "eigenvector": [5, 16], "eiger": [5, 20], "eigeroutput": [1, 5], "eigerrunn": [1, 5], "either": [2, 15, 16, 19], "elaps": 16, "electr": 5, "electric_dipol": 5, "electric_quadrupol": 5, "electron": [2, 5, 12, 19], "electrostat": [5, 20], "electrostatic_mo": [1, 5], "electrostaticmomentsdata": [1, 5, 20], "element": [2, 5, 6, 11, 12], "element_radiu": 5, "elimin": 2, "embodi": 19, "employ": 19, "empti": [1, 2, 5, 11, 12, 20], "en_corr": 5, "enabl": [3, 12, 18, 19], "encapsul": 15, "encount": [11, 12], "end": [2, 3, 5, 6, 10, 11, 12, 15, 19], "end_tim": 5, "energi": [1, 2, 5, 11, 12, 15, 18, 20], "energy_chang": 5, "energy_data": 20, "energy_onli": 5, "enforc": [12, 14, 19], "enough": [16, 20], "ensur": [13, 19], "enter": [3, 19], "entir": [2, 11, 15, 16, 19], "entiti": 19, "entrop": 5, "environ": [3, 8, 16], "eof": 3, "ep": [2, 5], "epsilon": [2, 3, 5, 12], "equal": [5, 6, 14], "equival": [2, 5, 6, 11, 15, 16, 19], "err_msg": 6, "erron": 19, "error": [2, 3, 5, 6, 11, 12, 13, 16], "escf": [5, 9, 15, 20], "escf_excit": [1, 5], "escf_gs_total_en": [1, 5], "escf_iter": [1, 5], "escfdata": [1, 5, 20], "escfiterationdata": [1, 5, 20], "escfonlyoutput": [1, 5, 15, 20], "escfoutput": [1, 5, 20], "essenti": [14, 16, 19], "establish": 2, "etc": 2, "euclidean": 5, "even": [2, 3, 5, 6, 12, 13, 16, 19], "event": 19, "ever": 19, "everi": [12, 19], "everyon": 19, "everyth": [2, 11], "evolut": [2, 5, 11], "ex_all_st": [3, 12], "ex_exopt": [3, 12], "ex_frequ": [3, 12], "ex_frequency_unit": [3, 12], "ex_irrep_st": [3, 12], "ex_method": [3, 12], "ex_mp2": [3, 12], "ex_multi": [3, 12], "ex_sett": [1, 3], "ex_stat": 5, "exact": [2, 11, 15, 19], "exactli": [2, 15, 16], "exampl": [2, 5, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20], "except": [2, 3, 5, 6, 11, 12, 14, 16, 19], "excerpt": 16, "exchang": [5, 16, 20], "exci": 12, "excit": [2, 3, 5, 12], "exclud": [16, 19], "exclus": 19, "excus": 19, "exec_en": 5, "exec_grad": 5, "exec_relax": 5, "exec_to_out_obj": 15, "execut": [2, 3, 5, 6, 11, 12, 13, 15, 16, 17, 18, 19, 20], "exercis": 19, "exhaust": 16, "exist": [2, 6, 10, 11, 12, 13, 15, 16], "exit": 2, "exopt": [5, 12], "expect": [2, 3, 5, 6, 9, 12, 13, 16, 19], "experi": 16, "experiment": [3, 9, 10, 12, 13], "explain": [15, 16, 19], "explan": [13, 14, 15], "explicit": [2, 6, 11, 16], "explicitli": [11, 12, 19], "exploit": 10, "explor": 13, "exponenti": 5, "expos": 6, "express": [15, 19, 20], "expressli": 19, "extend": [3, 12, 19], "extens": [12, 19], "extent": 19, "extern": [2, 8, 16, 20], "extract": [2, 5, 9, 11, 12, 15, 16, 18, 20], "extrem": [15, 16], "f": [2, 5, 10, 19], "f12": 12, "facil": 19, "facilit": 16, "factor": [2, 5, 12], "fail": [2, 3, 5, 6, 12, 13, 16, 19, 20], "failur": [6, 12, 13, 16, 19], "fair": 19, "fals": [2, 3, 5, 6, 11, 12, 16], "famili": 19, "fashion": [2, 19], "favor": 19, "featur": [3, 8, 10, 12, 13, 14, 16, 17, 18, 19], "feb": 18, "fee": 19, "fepsi": 5, "fermi": [1, 5], "few": [10, 11, 13, 14, 20], "fig": [2, 5], "fig_clos": [2, 5], "figur": [2, 5, 12], "file": [0, 1, 2, 3, 6, 8, 9, 12, 13, 14, 15, 16, 17, 18, 19], "file_class": 6, "file_nam": 6, "filenam": [2, 5, 6], "filepath": [2, 3, 5], "files_list": 15, "fill": [5, 10], "filter": 5, "filter_st": [1, 5], "final": [5, 11, 14, 15, 19, 20], "final_elec_temp": 5, "final_step_radiu": 5, "find": [5, 19], "firework": 18, "first": [2, 3, 5, 6, 9, 11, 13, 15, 16, 19, 20], "first_index": 5, "fit": 19, "five": 2, "fix": [2, 13, 16, 17, 18, 19], "fixtur": [13, 15, 16], "float": [2, 3, 5, 6, 12, 15], "flow": [13, 19], "fmt": 2, "focu": [15, 20], "focus": [12, 20], "folder": [2, 3, 6, 9, 11, 12, 14, 15, 16], "follow": [2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20], "forbid": 19, "forc": [12, 19], "force_overwrit": 2, "foreseen": 12, "form": [2, 6, 10, 12, 19, 20], "formal": 2, "format": [2, 5, 10, 11, 14, 16, 18, 19], "fortran": 5, "found": [2, 3, 5, 6, 11, 14, 15, 16, 18, 19, 20], "foundat": 19, "four": 2, "fourth": 2, "fpath": 16, "fraction": [2, 5, 16], "free": [5, 19], "free_energi": 5, "freedom": 19, "frequenc": [2, 5, 12], "frequent": 11, "from": [2, 3, 5, 6, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20], "from_dict": [1, 2, 5, 20], "from_fil": [1, 2, 5, 10, 11, 15, 20], "from_metr": [1, 2], "from_pars": [1, 5, 15, 20], "from_str": [1, 2, 5, 15], "frozen": [2, 5, 10], "frozen_indic": [2, 10], "fsf": 19, "fulfil": 19, "full": [2, 5, 6, 11, 12, 13, 18, 19], "fulli": 16, "func_typ": 5, "function": [2, 3, 5, 6, 10, 11, 12, 13, 15, 16, 17, 19, 20], "functional_msg": 5, "functional_nam": 5, "functional_typ": 5, "functionaldata": [1, 5, 20], "fundament": 19, "further": [10, 19, 20], "futur": [14, 19], "g": [2, 3, 5, 8, 11, 12, 15, 16, 17, 20], "gain": 16, "gamma": [2, 5], "gap": [1, 5, 20], "gather": 20, "gdii": 5, "gener": [1, 2, 3, 5, 6, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20], "generate_control": 16, "generate_control_for_test": [1, 6], "generate_fil": 15, "generate_lowest_filled_st": [1, 5], "generate_output_fil": 16, "generate_ref": [1, 6], "generate_reference_out_parser_fil": [1, 6], "generate_reference_output": [1, 6], "geometri": [2, 3, 5, 10, 11, 12, 20], "geometrydata": [1, 5, 20], "geoopt": 12, "get": [2, 4, 5, 6, 11, 15, 16, 19], "get_charg": [1, 2, 11], "get_control_integr": [1, 6], "get_coord_lin": [1, 2], "get_define_templ": [1, 3, 12], "get_eiger_output": [1, 5], "get_freqs_df": [1, 5], "get_int_def_inconsist": [1, 2], "get_mol_and_indices_frozen": [1, 2], "get_mos_energi": [1, 5], "get_shel": [1, 2, 5, 11], "get_sp": [1, 6], "get_split_jobex_pars": [1, 5], "get_subclass_from_str": [1, 2], "get_subfiles_list": [1, 2], "get_test_data_dir": [1, 6], "get_tests_configs_tm_vers": [1, 6], "get_tfp": [1, 6], "get_tm_vers": [1, 2], "get_valu": [1, 5], "gga": 5, "gisnan": [1, 6], "github": [8, 9], "give": [2, 8, 16, 19], "given": [2, 3, 5, 6, 10, 11, 12, 13, 15, 16, 17, 19, 20], "global": [2, 16], "gnu": 19, "go": [3, 12, 16], "good": [12, 13, 15, 16, 20], "googl": 14, "govern": 19, "gpl": [9, 19], "grad": [2, 5, 9, 20], "gradien": 5, "gradient": [1, 2, 5, 9, 11, 20], "gradlatt": 2, "gradoutput": [1, 5, 20], "grant": 19, "grati": 19, "greater": 14, "greatest": 19, "grep": 5, "grep_lin": [1, 5], "grid": [2, 5, 12, 20], "gridpoint": 5, "gridsiz": [3, 11, 12], "ground": 5, "group": [2, 10, 12, 13, 15, 16, 18, 20], "gs_tot_en": 5, "guarante": [2, 19], "guess": [3, 12], "gui": 19, "guid": [13, 14, 15, 16, 20], "guidelin": 14, "h": [2, 5], "h2_numforc": 16, "h2o_std": 16, "h2o_uhf": 16, "ha": [3, 5, 9, 10, 11, 12, 13, 15, 16, 19, 20], "had": 19, "hand": 15, "handl": [2, 3, 5, 9, 15], "happen": [3, 11, 12, 13, 15, 16], "has_fractional_occ": [1, 5], "has_hol": [1, 5, 20], "has_inconsist": [1, 2], "has_matplotlib": [1, 6], "hash": 2, "hash_inlin": 2, "hash_start": 2, "have": [2, 10, 11, 12, 14, 15, 16, 18, 19, 20], "he": 15, "header": [1, 2, 5, 15], "heavili": [5, 13], "help": [12, 14, 16], "helper": [10, 13, 15, 16, 20], "here": [2, 5, 6, 11, 13, 14, 15, 16, 20], "hereaft": [16, 19], "hessian": 5, "hessian_update_method": 5, "hf": [3, 12], "high": 16, "higher": [5, 9, 18, 20], "highlight": 14, "histori": [12, 13], "hoc": 13, "hold": 15, "holder": 19, "hole": 5, "homo": [1, 5], "homo_index": [1, 5], "hook": 9, "hope": 19, "host": [5, 19], "hour": 5, "household": 19, "how": [5, 13, 15, 16, 18, 19, 20], "howev": [10, 11, 12, 13, 15, 19, 20], "html": [14, 16, 19], "http": [8, 19], "hueckel": [3, 12], "human": 2, "hypothet": 19, "i": [1, 2, 3, 5, 6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20], "idea": [13, 19, 20], "ident": 20, "identifi": [2, 5, 6, 11, 13, 16, 17, 19], "ignor": [2, 5, 12], "ignored_dg": 2, "ignored_valu": 6, "impact": 15, "implement": [2, 3, 6, 11, 12, 13, 14, 15, 16, 19, 20], "impli": 19, "import": [6, 10, 11, 12, 14, 16, 19, 20], "impos": 19, "imposs": 16, "impract": 16, "improv": 13, "inabl": 19, "inaccur": 19, "inc": 19, "incident": 19, "includ": [2, 5, 11, 13, 18, 19], "inclus": 19, "incompat": [3, 14, 16, 17, 19], "incomplet": 3, "inconsist": 2, "incorpor": 19, "incorrectli": 2, "increas": [5, 11, 12, 18], "increment": [5, 17], "inddic": 5, "inde": 16, "indemnif": 19, "independ": 19, "index": [2, 5, 18, 20], "index1": [2, 10], "index2": [2, 10], "indic": [2, 5, 10, 19], "individu": 19, "industri": 19, "inevit": 16, "infer": 2, "info": 5, "inform": [2, 3, 5, 8, 9, 10, 15, 16, 19, 20], "infrastructur": [6, 16], "infring": 19, "inherit": 14, "init_trust_radiu": 5, "initi": [2, 5, 11, 16, 19, 20], "initial_elec_temp": 5, "inlin": [2, 11], "inner": 5, "input": [0, 1, 2, 5, 9, 11, 12, 13, 15, 16, 17, 18, 20], "insensit": 2, "insert": [1, 5, 12], "insid": [2, 6, 12, 13, 15, 16, 19], "inspect": [15, 16], "inspir": 11, "instal": [6, 16, 19], "instanc": [2, 5, 6, 10, 11, 12, 13, 15, 20], "instanti": [15, 20], "instead": [5, 6, 10, 11, 13, 15, 16, 19, 20], "int": [2, 3, 5, 12], "int_def": [2, 10], "intact": 19, "intdef": [2, 10], "integ": [2, 3], "integr": [1, 5, 6, 13, 14, 18, 20], "integral_neglect_threshold": 5, "integraldata": [1, 5, 20], "integrations_test": 16, "intend": [2, 16, 19], "intens": 5, "intensities_perc": 5, "intent": [11, 19], "interact": [2, 11, 12, 19, 20], "interatom": 5, "intercept": 13, "interchang": 19, "interconnected": 13, "interest": [11, 19], "interf": 19, "interfac": [1, 3, 6, 9, 18, 19], "interfer": 2, "intern": [2, 3, 5, 10, 11, 12, 13, 20], "internaldefinit": [1, 2, 10], "interpret": 19, "interrupt": 12, "intersect": [2, 12], "intim": 19, "introduc": [13, 15, 16], "introduct": [13, 16], "invalid": 19, "invers": 2, "inversedist": [1, 2], "invok": 14, "involv": [2, 15], "invr": 2, "ir": [3, 5, 10, 12], "irreduc": [2, 5, 11, 20], "irrep": [1, 2, 5, 12], "irrep_data": 5, "irrep_index": [2, 5], "irrep_indic": [1, 5], "irrevoc": 19, "is_uhf": [1, 2, 5], "is_valid": [1, 2], "isnan": 6, "isol": [10, 15], "isotop": 5, "issu": 8, "item": 19, "iter": [5, 12, 20], "itest": [6, 16], "itestconfig": [1, 6], "itesterror": [1, 6], "its": [2, 3, 5, 10, 11, 12, 13, 16, 19, 20], "itself": [16, 19], "job": [3, 5, 6, 12], "jobex": [5, 9, 20], "jobexoutput": [1, 5, 20], "join": 11, "json": [2, 5, 6, 12, 15, 16, 18], "june": 19, "just": [2, 11, 12, 15, 20], "k": [2, 10, 16], "kb": 5, "kdg": [1, 2, 11], "keep": [5, 11, 13, 16, 19], "kei": [2, 5, 6, 11, 12, 19], "kept": [2, 15, 16], "kernel": 19, "keysrul": 3, "keyword": [2, 5, 6, 11, 12], "keywork": 12, "kill_data_group": [1, 2, 11], "kind": [11, 12, 15, 16, 19, 20], "kinet": [2, 5], "kinetic_energi": 5, "km": 5, "know": [16, 19], "knowingli": 19, "knowledg": 19, "known": 13, "kwarg": [2, 5], "label": [2, 5], "lack": 11, "languag": 19, "larg": [2, 12], "larger": [12, 19], "largest": 2, "last": [2, 5, 10, 20], "last_grad_max": [1, 2], "last_grad_norm": [1, 2], "lastli": [11, 15, 16, 20], "later": [16, 19], "latest": 17, "latter": 15, "lattic": [2, 5, 9], "lattice_gradi": 2, "lattice_param": 5, "lattice_str": 2, "lattice_vector": 2, "law": 19, "lawsuit": 19, "layout": 9, "lazi": [5, 15, 20], "lazy_properti": 15, "lda": 5, "lead": [5, 11, 12, 14, 16], "leading_spaces_dollar": 2, "leading_spaces_hash": 2, "learn": 13, "least": [3, 13, 15, 16, 19], "leav": [2, 12, 16], "left": [2, 5], "legal": 19, "length": [2, 5], "less": [2, 20], "lesser": 19, "let": [10, 15], "level": [6, 13, 15, 16, 20], "lgpl": 19, "liabil": 19, "liabl": 19, "librari": [18, 19], "licens": [9, 18], "license": 19, "licensor": 19, "light": 16, "like": [2, 3, 5, 6, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20], "likewis": 19, "limit": [10, 11, 12, 16, 19], "linc": 2, "line": [2, 5, 10, 11, 12, 15, 16, 19], "linear": 2, "link": [19, 20], "linp": 2, "lint": 9, "list": [2, 3, 4, 5, 6, 10, 11, 12, 13, 15, 16, 19, 20], "litig": 19, "littl": [13, 16], "local": [3, 19], "locat": [2, 14, 16], "log": [3, 9, 17, 18], "log_filepath": 3, "log_fpath": 6, "logfil": 6, "long": 19, "look": [6, 10, 11, 16, 20], "loop": 5, "loos": 15, "looser": 16, "loss": 19, "low": 12, "lower": [2, 5, 16, 20], "lowest": [5, 20], "ltol": 2, "lumo": [1, 5], "lumo_index": [1, 5], "ly": 5, "m": [5, 10, 16], "m3": 11, "machin": [5, 16, 19], "machine_precis": 5, "made": [2, 15, 19], "magnet": 5, "magnetic_dipol": 5, "mai": [2, 5, 9, 11, 15, 16, 19], "mail": 19, "main": [5, 13, 15, 16, 18], "mainli": [10, 12, 14, 15, 16, 20], "maintain": [14, 19], "major": [17, 19], "make": [6, 8, 11, 13, 14, 15, 16, 17, 19], "manag": [6, 15, 16, 18], "mandatori": 11, "mani": 2, "manipul": 2, "manner": [15, 17, 19, 20], "manual": [2, 12], "manufactur": 19, "map": 2, "mar": 18, "march": 19, "marij": [3, 5, 12], "mark": [11, 15, 16, 19], "mask": 19, "mass": [5, 20], "match": [2, 5, 11, 16], "materi": 19, "matgenix": 8, "matplotlib": [2, 5, 6], "matrix": [2, 5, 12], "max": [3, 5], "max_cao_basis_vector": 5, "max_core_mem": 5, "max_davidson_it": 5, "max_displ": 5, "max_grad": 5, "max_gradi": [1, 2], "max_intern": 5, "max_occup": [1, 5], "max_treated_vector": 5, "max_trust_radiu": 5, "maxcor": [3, 12], "maximum": [2, 3, 5, 12], "maxit": [3, 12], "mayb": 15, "mb": 5, "mdgo": [1, 2, 11], "mean": [2, 5, 9, 11, 15, 16, 19, 20], "meaning": 16, "meaningless": 16, "meant": 15, "measur": [16, 19], "medium": 19, "meet": [16, 19], "memori": [5, 12], "memory_per_atom": 5, "mention": [11, 12, 16], "menu": [3, 12, 13, 19], "merchant": 19, "mere": 19, "merg": 19, "messag": [2, 3, 5, 6], "met": 19, "method": [2, 3, 5, 6, 10, 11, 12, 13, 15, 16, 19, 20], "metric": [1, 2, 3, 12], "might": [5, 9, 10, 11, 12, 13, 15, 16, 18, 19], "mimic": 13, "min": 3, "min_grad_norm_for_gdii": 5, "min_trust_radiu": 5, "mind": [13, 15], "minim": 5, "minimum": [5, 12], "minor": [16, 17], "minut": 5, "miscellan": 2, "misrepresent": 19, "miss": [2, 5, 11, 12, 15], "mix": 15, "mkdtemp": 6, "mo": [2, 5, 12], "mock": [13, 16], "mode": [5, 16, 19], "model": [2, 19], "modif": [2, 6, 9, 16, 17, 19], "modifi": [2, 5, 12, 13, 15, 16, 17, 18, 19], "modify_data_group_opt": [1, 2, 11], "modul": [0, 9, 11, 12, 13, 16, 17, 18, 20], "mol": 5, "molecul": [0, 1, 5, 10, 12, 16, 18, 20], "molecular": [2, 3, 5, 12], "molecule_or_structur": 2, "moleculesystem": [1, 2, 10, 18], "moment": [5, 12, 13, 20], "moments_column": 5, "mongodb": 18, "mongomock": 16, "monti": [6, 15, 18, 20], "more": [2, 10, 11, 13, 14, 15, 16, 18, 19, 20], "moreov": 19, "most": [5, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20], "mostli": 20, "move": [2, 9, 11, 16], "mp2": [2, 3, 5, 9, 12, 20], "mp2_data": [1, 5], "mp2_result": [1, 5], "mp2data": [1, 5, 20], "mp2energi": [3, 12], "mp2output": [1, 5, 20], "mp2result": [1, 5, 20], "mpgrad": [5, 9, 20], "msg": 5, "msonabl": [2, 5, 6, 18, 20], "much": [8, 11, 12, 13, 16, 20], "multipl": [2, 5, 12, 16], "multiplicity_int": 12, "must": [3, 19], "mutablesequ": [5, 20], "n": [2, 3, 10, 12], "n_atom": [1, 2], "n_negative_freq": [1, 5], "n_occupied_orbit": 5, "n_positive_freq": [1, 5], "n_rep": 5, "n_state": [1, 5], "n_step": [1, 2, 5], "n_zero_freq": [1, 5], "name": [2, 3, 5, 6, 11, 12, 13, 15, 16, 19, 20], "name_of_the_execut": 20, "namedtupl": [2, 5], "narrow": 15, "nativ": 5, "natom": [2, 5], "natur": [13, 15, 18, 19], "navig": 12, "ndg": [1, 2], "necessari": [16, 19], "need": [5, 11, 12, 13, 15, 16, 19, 20], "neg": 5, "neglect": 5, "neither": 19, "nelec": 5, "nest": 6, "network": 19, "never": [10, 11], "new": [2, 5, 8, 9, 11, 12, 13, 14, 17, 18, 19], "newest": 16, "newli": 15, "newlin": 2, "nexc": 12, "next": [11, 16, 19], "nh3_cosmo_fermi": 16, "nh3_dftd1": 16, "nline": 5, "nm": 12, "non": [2, 5, 19], "noncommerci": 19, "none": [2, 3, 5, 6, 11, 12, 15, 20], "nonetheless": 14, "nor": [10, 19], "norm": [1, 2, 5], "norm_cartesian": 5, "norm_intern": 5, "normal": [3, 5, 19, 20], "notabl": 2, "notat": [2, 5], "note": [2, 5, 6, 9, 10, 11, 12, 15, 16, 18, 20], "noth": 19, "notic": [3, 5, 9, 10, 16, 19], "notifi": 19, "notimpl": 2, "notimplementedtyp": 6, "notwithstand": 19, "now": 16, "nppa": [2, 3, 5, 12], "npspher": 5, "nspa": [2, 3, 5, 12], "nsph": 5, "nstep": 2, "nullabl": [3, 13], "num": 5, "num_exc_st": 12, "number": [2, 5, 6, 11, 12, 17, 19], "number_of_data_group": [1, 2], "number_scf_aux_basis_func": 5, "number_scf_basis_func": 5, "numer": [2, 5, 6, 11, 15, 16, 20], "numerical_integr": 5, "numforc": 5, "numpi": 6, "o": [6, 8, 10, 16], "obj": 6, "object": [2, 3, 5, 6, 9, 10, 12, 13, 14, 15, 16, 18, 19], "oblig": 19, "obtain": [2, 5, 11, 15, 20], "obvious": 16, "occ_orb": 5, "occasion": 19, "occup": [1, 2, 5, 20], "occupi": [2, 5, 11, 20], "occur": [16, 19], "occurr": [2, 5], "off": [2, 5, 13], "offer": [11, 19, 20], "offici": [9, 19], "often": [14, 16], "old": [15, 16], "older": [16, 17], "onc": [6, 15, 16], "one": [2, 3, 5, 6, 10, 11, 12, 13, 15, 16, 19, 20], "oneof": 3, "ones": [5, 12, 15, 16], "onli": [2, 3, 5, 6, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20], "onlin": 16, "only_occupi": 5, "open": [2, 8, 11, 12, 18], "oper": [5, 11, 13, 19, 20], "oppos": 10, "optic": 5, "optim": [2, 5, 10, 11], "option": [2, 3, 5, 6, 10, 11, 12, 13, 15, 16, 19, 20], "option_name1": 2, "option_name2": 2, "option_valu": 2, "orbit": [2, 3, 5, 12, 20], "orbital_character": 5, "order": [2, 5, 12, 13, 16, 19, 20], "org": 19, "organ": [11, 15, 16, 19, 20], "orient": 14, "origin": [2, 6, 11, 16, 19], "osc_str": 5, "oscil": 5, "other": [2, 3, 5, 6, 10, 11, 12, 13, 14, 15, 16, 19, 20], "otherwis": [2, 3, 5, 12, 15, 16, 19], "our": 19, "out": [2, 5, 12, 19, 20], "outcom": [12, 16], "outdir": 6, "outer": [2, 12], "outli": [2, 12], "outofplaneangl": [1, 2], "outp": 2, "output": [0, 1, 2, 3, 6, 9, 10, 11, 12, 17, 18, 19], "outright": 16, "outsid": 19, "over": [11, 16], "overal": 18, "overrid": [12, 16], "overwrit": [2, 15, 16], "overwritten": 2, "own": [16, 19], "p": [11, 12], "packag": [0, 7, 8, 9, 10, 12, 14, 15, 16, 17, 18, 19], "page": 18, "pair": 2, "panda": 5, "paper": 19, "paragraph": 19, "paramat": 12, "paramet": [2, 3, 5, 6, 13, 16, 18], "parametersvalidationerror": [1, 3], "pars": [1, 2, 5, 9, 10, 11, 13, 17, 18], "parser": [0, 1, 6, 15, 16, 18, 20], "parser_en": 5, "parser_grad": 5, "parser_method": [6, 15], "parser_relax": 5, "parsing_update_differ": 16, "part": [5, 9, 11, 15, 16, 19], "parti": 19, "partial": 15, "particular": [11, 12, 13, 15, 16, 17, 19, 20], "paser": 5, "pass": [2, 3, 5, 6, 11, 12, 13, 16, 19], "password": 19, "patch": [8, 17], "patent": 19, "path": [2, 3, 5, 6, 11, 12, 13, 16, 20], "pattern": [3, 12, 19], "pave": [2, 12], "payment": 19, "pbe": 11, "peer": 19, "pep": 14, "per": [2, 5, 12], "percentag": 5, "perform": [2, 5, 6, 9, 10, 11, 12, 13, 15, 16, 19, 20], "period": [0, 1, 5, 9, 18, 20], "periodic_extens": 2, "periodic_str": 2, "periodicity_data": [1, 5], "periodicitydata": [1, 5, 20], "periodicsystem": [1, 2, 9, 10], "perman": 19, "permiss": 19, "permit": 19, "permitt": [2, 12], "perpendicularbendingangl": [1, 2], "perpetu": 19, "person": 19, "pertin": 19, "pexpect": [3, 12], "phsran": 5, "physic": [2, 5, 16, 19], "pi": 5, "piec": [19, 20], "pip": 16, "place": [13, 16, 19, 20], "plan": [13, 16], "plane": [2, 5], "pleas": [8, 19], "plot": [1, 2, 5, 11, 20], "plot_energi": [1, 5, 20], "plu": [5, 12, 19], "png": [2, 5], "pno": 5, "pnoccsd": [5, 20], "poetri": 9, "point": [2, 5, 12, 13, 15, 16, 17], "pointer": 19, "polaris": 12, "polli": [3, 12], "popen": 3, "popen_spawn": 3, "popenspawn": 3, "portion": [5, 13, 15, 16, 19], "posit": [2, 5], "possess": 19, "possibl": [5, 11, 12, 13, 14, 15, 16, 19], "possibli": [14, 16, 20], "potenti": [2, 5, 10, 13, 15], "potential_energi": 5, "power": [13, 19], "practic": [16, 19], "pre": [5, 9], "pre_escf_run": [1, 5], "pre_scf_run": [1, 5], "preambl": 19, "prece": 5, "preced": [2, 5], "precis": [5, 10, 19], "predecessor": 19, "predefin": [2, 12], "prefer": [15, 19, 20], "preliminari": 9, "prepapar": 12, "prepar": [12, 16], "prepend": [2, 11], "presenc": [2, 11, 16], "present": [2, 3, 5, 10, 11, 12, 14, 16, 19], "preserv": [6, 19], "prev_steps_for_gdii": 5, "prevent": [12, 16, 19], "previou": [3, 5, 9, 12, 15, 16, 19, 20], "previous": [12, 16], "price": 19, "primarili": 19, "principl": [5, 14, 16], "print": [5, 6, 16, 20], "prior": [9, 10, 16, 19], "privat": 19, "probabl": [12, 13, 15, 20], "problem": [3, 5, 6, 8, 12, 13, 15, 19], "proce": [15, 16], "procedur": [5, 13, 19, 20], "proceed": 12, "process": 16, "procur": 19, "produc": [2, 5, 6, 10, 12, 13, 16, 19, 20], "product": 19, "program": [5, 6, 9, 14, 19], "programm": 19, "progress": [9, 10], "prohibit": 19, "project": 16, "promin": 19, "prone": 13, "propag": 19, "proper": [3, 5], "properli": 3, "properti": [2, 5, 10, 15, 19, 20], "proprietari": 19, "protect": [13, 19], "protocol": 19, "prove": 19, "provid": [2, 3, 5, 8, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20], "provis": 19, "provision": 19, "proxi": 19, "pty": 3, "public": [6, 19], "publicli": 19, "publish": 19, "punctual": 20, "purpos": [2, 19], "pursuant": 19, "py": [14, 16, 17], "pymatgen": [2, 10, 18], "pytest": [6, 16], "pytestmark": 16, "python": [8, 9, 10, 11, 14, 16, 17, 18], "qq": [2, 12], "quadrupol": [5, 20], "quadrupole_anisotropi": 5, "quadrupole_tensor": 5, "quadrupole_trac": 5, "qualifi": 19, "qualiti": 19, "quantiti": [5, 18, 20], "queri": 2, "quick": 18, "quickli": 15, "quit": [2, 3], "radiu": 5, "rais": [2, 3, 5, 6, 11, 12, 13, 16], "raise_if_missing_subfil": 2, "raise_if_multiple_subfil": 2, "raise_if_regular_and_subfil": 2, "raman": 5, "rang": 12, "rate": 16, "rather": 2, "rdgrad": [5, 20], "rdgrad_memori": [1, 5], "reach": 3, "read": [2, 5, 10, 11, 16, 17, 18, 19, 20], "readabl": [2, 19], "readi": 19, "readili": 19, "real": 13, "realli": [12, 16], "reason": [10, 11, 12, 16, 19], "receipt": 19, "receiv": [13, 19], "recipi": 19, "reciproc": 5, "reciprocal_space_vector": 5, "recogn": 19, "recommend": 15, "recov": 5, "recurs": 6, "redistribut": 19, "reduc": [5, 11], "reduced_mass": 5, "redund": [2, 10, 15], "redund_inp": 2, "ref": 16, "refer": [2, 6, 9, 10, 11, 13, 15, 16, 19], "referenc": [2, 16], "refind": [2, 3, 5], "refract": 2, "refrain": 19, "regard": 19, "regardless": 19, "regener": [3, 6, 9, 12, 16, 19], "regex": 5, "regular": [2, 15, 20], "reinstat": 19, "reintroduc": 16, "rel": [5, 6, 11, 13, 15], "relat": [2, 3, 9, 12, 20], "relationship": 19, "relax": [5, 9, 20], "relax_conv_info": [1, 5], "relax_gradient_valu": [1, 5], "relax_info": [1, 5], "relaxconvergencedata": [1, 5, 20], "relaxdata": [1, 5, 20], "relaxgradientsdata": [1, 5, 20], "relaxoutput": [1, 5, 20], "releas": [16, 17, 18, 19], "relev": [5, 11, 15, 16, 18, 19, 20], "reli": [5, 13, 14, 15, 16, 19, 20], "relicens": 19, "remain": [5, 11, 19], "remark": 14, "rememb": [13, 15], "remov": [2, 5, 6, 11, 15, 16, 19], "remove_com": [1, 2], "remove_comment_typ": 2, "remove_dg_from_list": [1, 2], "remove_last_energi": [1, 2], "remove_last_gradi": [1, 2], "renam": 16, "render": 19, "reorder_irrep_index": 5, "reorgan": 9, "rep": 5, "repair": 19, "repeat": [15, 16, 20], "replac": [2, 11, 16], "repli": [12, 13], "report": [16, 18], "repres": [2, 5, 10, 12, 16, 19], "represent": [2, 5, 11, 20], "reproduc": [8, 11, 16], "request": [5, 8], "requir": [6, 9, 10, 11, 12, 13, 14, 15, 16, 19], "residu": 5, "residuum": 5, "residuum_convergence_criterium": 5, "resolut": 20, "resolv": 19, "resourc": 16, "respect": [2, 5, 11, 16, 19, 20], "respond": 12, "respons": [2, 11, 12, 13, 19], "rest": [15, 20], "restart": 5, "restart_fil": 5, "restrict": 19, "restructuredtext": 14, "result": [2, 5, 10, 11, 12, 16, 19, 20], "retain": 19, "retriev": 12, "return": [2, 3, 5, 6, 11, 12, 13, 15, 16, 19, 20], "return_all_diff": 2, "reus": 13, "reusabl": 5, "review": 19, "revis": 19, "ri": [3, 5, 12, 20], "ricc2": [5, 9, 12, 20], "ricc2output": [1, 5, 20], "ricor": 5, "ridata": [1, 5, 20], "ridft": [5, 9, 12, 15, 16, 20], "right": [13, 19], "rij": 5, "rij_info": [1, 5], "rij_memori": 5, "rijk": [3, 12], "rik": 5, "rimp2": 9, "riper": [2, 5, 9, 20], "riper_scf_energi": [1, 5], "rir12": 12, "risk": 19, "rm": 5, "rms_displ": 5, "rms_grad": 5, "rom": 19, "root": [1, 5, 16, 20], "rot_str": 5, "rotat": [5, 20], "rotatori": 5, "routf": [2, 3, 5, 12], "royalti": 19, "rpa": [3, 5, 12], "rpat": 12, "rsolv": [2, 3, 5, 12], "rst": 14, "rtol": 6, "rubric": 6, "rule": 19, "run": [1, 2, 3, 5, 6, 9, 11, 13, 15, 16, 18, 19], "run_": 13, "run_ful": [1, 3, 12, 13], "run_generate_mo_fil": [1, 3, 12, 13], "run_itest": [1, 6, 16], "run_update_internal_coord": [1, 3, 12, 13], "rundata": [1, 5, 20], "runner": 18, "runtest": 16, "runtimeerror": [2, 5], "s2": [1, 5], "safe": 16, "safer": 2, "safest": 19, "sai": 19, "sake": 19, "sale": 19, "same": [2, 5, 10, 11, 15, 16, 19, 20], "satisfi": [5, 19], "save": [2, 5], "savefig": [2, 5], "scalar": 6, "scale": [2, 12], "scenario": 12, "scf": [2, 5, 12, 20], "scf_energi": [1, 5], "scf_iter": [1, 5], "scf_output": 20, "scfconv": [3, 11, 12], "scfdata": [1, 5, 20], "scfenergiesdata": [1, 5, 15, 20], "scfiterationdata": [1, 5, 20], "scfiterlimit": [3, 11, 12], "scfkin": 2, "scfmo": [2, 20], "scfoutput": [1, 5, 20], "scfpot": 2, "schema": [3, 12, 13], "schema_define_param": [1, 3, 13], "school": 19, "scope": [16, 19], "scratch": 3, "screen": [2, 5, 12], "screening_charg": 5, "script": [9, 11, 16, 19, 20], "sdg": [1, 2, 11], "sdgo": [1, 2, 11], "seam": [2, 12], "search": [3, 5, 18], "second": [2, 5, 12, 16, 20], "secondarili": 19, "section": [5, 12, 13, 14, 15, 16, 19, 20], "see": [10, 12, 13, 14, 16, 19, 20], "segment": [2, 12], "select": [2, 5, 11, 12], "self": [5, 8, 13], "sell": 19, "semant": 17, "semiconductor": 19, "send": [2, 12, 13], "sens": 20, "sent_command": [12, 13], "sep": 18, "separ": [2, 11, 16, 19], "sequenc": [5, 13], "seri": [2, 11, 15, 16, 17, 18, 20], "serial": [2, 9, 15, 16], "serializ": [2, 5], "serv": 19, "server": 19, "servic": 19, "set": [2, 3, 5, 6, 10, 11, 12, 13, 15, 16, 18, 20], "set_disp": [1, 2, 11, 13], "set_size_inch": [2, 5], "setter": 3, "setup": [2, 12, 16, 17], "setuptool": 9, "sever": [2, 5, 15, 16, 18, 20], "sh": 16, "shall": 19, "shape": [2, 5], "share": [13, 15, 19], "shell": [1, 2, 5, 11, 12], "shells_typ": 2, "shift": [5, 20], "short": [16, 19], "shortcut": [5, 11], "shortest": 5, "shortest_interatomic_dist": 5, "should": [2, 3, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20], "show": [2, 5, 19], "show_data_group": [1, 2, 11], "show_data_group_opt": [1, 2, 11], "show_from_subfil": [2, 11], "show_subfile_fnam": [1, 2], "shown": [2, 11, 16], "side": [3, 11, 16, 20], "sigma0": 5, "sigma0_energi": 5, "sign": [2, 11, 19], "signal": 13, "signific": 19, "similar": [3, 11, 15, 19, 20], "similarli": [5, 20], "simpl": [2, 5, 12], "simplest": [10, 12], "simpli": [2, 5, 11, 13, 15], "simplic": 11, "simul": 10, "simultan": [5, 19], "sinc": [2, 6, 11, 12, 13, 14, 15, 16, 20], "singl": [2, 5, 6, 11, 12, 15, 16, 17, 19, 20], "singleexcit": [1, 5], "singlet": [3, 5, 12], "site": 5, "situat": 12, "size": [2, 5, 12, 20], "size_kwarg": [2, 5], "skip": [2, 3, 6, 13], "slightli": [16, 17], "small": [8, 12, 15, 16], "smear": [5, 20], "smearing_de_limit": 5, "smearingdata": [1, 5, 20], "snippet": 8, "so": [2, 11, 12, 13, 15, 16, 18, 19, 20], "softwar": 19, "sold": 19, "sole": 19, "solv": [6, 12], "solvent": [2, 3, 12], "some": [2, 3, 5, 6, 9, 11, 12, 13, 15, 16, 19, 20], "sometim": 6, "somewhat": 16, "sort": [5, 20], "sourc": [2, 3, 4, 5, 6, 14, 16, 18, 19], "space": [2, 5, 11], "span": 2, "spare": 19, "spawn": [3, 12, 13], "speak": 19, "speci": 5, "special": 19, "specic": 12, "specif": [2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20], "specifi": [2, 5, 6, 8, 11, 12, 19], "speed": 12, "sphere": [2, 12], "spheric": 5, "spherical_grids": 5, "sphinx": 14, "spin": [1, 5, 20], "spindata": [1, 5, 20], "spirit": 19, "split": [2, 5, 11], "split_string_to_dg_list": [1, 2], "src": 9, "stand": 19, "standard": [2, 3, 5, 11, 12, 14, 19], "stapt": [5, 20], "start": [2, 5, 11, 12, 13, 15, 16, 17, 18, 19], "start_tim": 5, "state": [0, 1, 2, 3, 11, 12, 18, 19], "statement": 19, "static": 2, "statpt": [5, 9, 15, 20], "statpt_info": [1, 5], "statptdata": [1, 5, 20], "statptoutput": [1, 5, 20], "statu": [2, 10, 19], "stdout": [5, 6, 16, 20], "step": [2, 5, 11, 12, 19, 20], "stick": [14, 16], "still": [6, 10, 11, 15, 16], "storag": [5, 19], "store": [2, 5, 6, 9, 10, 11, 12, 15, 16, 17, 18, 20], "str": [2, 3, 5, 6, 12], "stre": [2, 10], "strength": 5, "stress": 10, "strict": [2, 11, 16], "strictli": [11, 14], "string": [1, 2, 3, 5, 6, 11, 12, 13, 15, 17, 20], "strongli": 14, "struc": 6, "structur": [1, 2, 5, 6, 9, 10, 11, 15, 16, 18], "style": 14, "subclass": [2, 5, 6, 10, 11, 12, 13, 15, 16, 20], "subdictionari": 5, "subdivid": 19, "subfil": [2, 11, 20], "subfold": 16, "subject": 19, "sublicens": 19, "sublist": 5, "submit": 12, "submodul": [0, 1], "subpackag": 0, "subplot": [2, 5], "subprogram": 19, "subroutin": 19, "subsect": [19, 20], "subsequ": 11, "subset": [5, 13], "substanti": 19, "succe": 13, "success": [6, 16], "successfulli": [3, 6], "sue": 19, "suffic": 19, "suit": 18, "suitabl": [2, 5, 13, 14, 15, 16], "sum": 16, "summar": 18, "superflu": 11, "supplement": 19, "support": [2, 5, 6, 11, 12, 14, 15, 16, 17, 19], "suppos": 2, "sure": [6, 11, 13, 19], "surrend": 19, "surviv": 19, "sustain": 19, "sv": 12, "switch": [5, 9, 16], "sy": 12, "sym": [3, 12], "sym_ep": [3, 12], "symbol": [2, 5, 10, 11], "symmetri": [0, 1, 5, 11, 12, 20], "symmetrydata": [1, 5, 20], "system": [2, 3, 5, 9, 11, 12, 16, 18, 19, 20], "systemat": [16, 19, 20], "t": [3, 12], "tab": [2, 11], "tailor": 20, "take": [5, 10, 12, 13, 15, 16, 19, 20], "taken": [3, 6, 16, 18], "tangibl": 19, "target": [13, 15, 16], "task": 14, "technolog": 19, "tell": 19, "temp_dir": [1, 6, 16], "temperatur": 5, "tempfil": 6, "templat": [1, 3, 9, 12], "temporari": [6, 16], "temporarili": 15, "tensor": 5, "term": 19, "termin": [3, 12, 19], "test": [0, 1, 2, 3, 12, 14, 18], "test_": 16, "test_data": 6, "test_data_dir": 6, "test_definit": 6, "test_dscf": 16, "test_fil": 15, "test_if_subclass": 6, "test_pars": 15, "test_run_dscf_hf": 16, "testcas": 16, "testexec": 16, "testfil": [6, 9, 15, 16], "testgen": 16, "testnam": 16, "tests_config": 16, "text": [5, 15, 18, 20], "th": [5, 12], "than": [2, 5, 11, 12, 15, 19, 20], "thei": [2, 3, 5, 6, 10, 11, 14, 15, 16, 18, 19, 20], "them": [3, 5, 10, 11, 13, 15, 16, 18, 19, 20], "theorem": 5, "therefor": 19, "thereof": 2, "thi": [1, 2, 3, 5, 6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20], "thime": [5, 11], "thing": [16, 19], "third": [2, 19], "thize": [5, 11], "those": [2, 10, 12, 15, 16, 19], "though": [6, 12, 15, 16, 19, 20], "thr": 5, "thr_energy_chang": 5, "thr_int_coord": 5, "thr_max_displ": 5, "thr_max_grad": 5, "thr_rms_displ": 5, "thr_rms_grad": 5, "threaten": 19, "three": [2, 5, 12, 19, 20], "threshold": [2, 5, 12, 20], "through": [3, 10, 11, 12, 13, 19, 20], "thu": [2, 12, 13, 15, 16, 17, 19, 20], "tight_layout": [2, 5], "time": [1, 3, 5, 11, 12, 16, 19, 20], "timeout": [3, 12], "timing_descript": 5, "titl": [2, 3, 5, 12], "tm": [2, 5, 6], "tm_build": 5, "tm_lattice_param": 5, "tm_v7": 16, "tm_version": 5, "tm_vx": 16, "tmpdir": 16, "to_coord_fil": [1, 2], "to_coord_str": [1, 2], "to_datagroup": [1, 2], "to_fil": [1, 2, 5, 11], "to_str": [1, 2], "togeth": [15, 20], "tol": [1, 2, 5, 6, 16], "tolear": 16, "toler": [2, 5, 6, 12, 15, 16], "too": [12, 19], "tool": [2, 3, 13, 16, 18, 19], "top": 20, "tor": [2, 10], "tot_en": 5, "total": [2, 5], "total_electron": [1, 2, 5], "total_energi": [5, 20], "total_energy_oc_corr": 5, "touch": 6, "touch_fil": [1, 6], "toward": 16, "trace": 5, "track": 13, "trade": 19, "trademark": 19, "transact": 19, "transfer": 19, "transit": 16, "translat": 10, "transmiss": 19, "treat": [5, 19], "treati": 19, "treatment": 12, "tree": 16, "tri": 6, "trigger": 16, "triplet": [3, 12], "trivial": [13, 16], "true": [2, 3, 5, 6, 10, 11, 12, 16], "trust": 5, "try": [2, 8, 11, 13], "ts_energi": 5, "tune": [12, 16], "tupl": [2, 5, 6, 10], "turbomol": [1, 2, 5, 6, 8, 9, 10, 11, 12, 13, 15, 17, 18, 20], "turbomoledata": [1, 5, 20], "turbomoleio": [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20], "turn": 13, "two": [2, 5, 6, 12, 16, 19], "type": [2, 3, 5, 6, 10, 11, 12, 13, 18, 19, 20], "typeerror": 6, "typeset": 14, "typic": [2, 11, 12, 19], "typo": 12, "u": [5, 10, 15, 16], "ufunc": 6, "uhf": [2, 5, 11, 12, 20], "uhfmo_alpha": 20, "uhfmo_beta": 20, "uht": 12, "unaccept": 19, "unambigu": 11, "unchang": [2, 5], "under": [11, 15, 16, 19], "underli": 16, "understand": [14, 16, 20], "unexpect": 3, "uniform": 11, "unit": [10, 12, 13, 14, 15, 18], "unittest": 16, "unless": 19, "unlimit": 19, "unmodifi": 19, "unnecessari": [2, 19], "unpack": 19, "unpair": 12, "unpaired_electron": [3, 12], "unrestrict": 5, "unrestricted_electron": 5, "unsupporteddefinestateerror": [1, 3], "untidi": [2, 12], "until": 19, "up": [2, 11, 12, 15, 16], "updat": [2, 3, 5, 9, 11, 12, 15, 16, 17, 19], "upon": 15, "us": [2, 3, 5, 6, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20], "usag": 2, "use_cosmo": [3, 12], "use_default": 5, "use_f12": [3, 12], "use_old_amat": [2, 3, 12], "use_popen": 3, "usemo": [3, 12], "user": [2, 10, 11, 12, 13, 14, 15, 19, 20], "user_defined_bond": [2, 10], "usual": [2, 5, 11, 12, 15, 20], "util": [0, 1, 5, 6, 12, 13, 16], "v": 5, "v3": 9, "v7": 16, "vacuum": 2, "val": 10, "valid": [2, 3, 5, 11, 18, 19], "validate_paramet": [1, 3, 12], "valu": [2, 3, 5, 6, 10, 12, 13, 15, 16, 18, 20], "valueerror": [2, 5], "valuesrul": 3, "vari": 16, "variabl": [3, 10], "variat": 2, "varieti": [2, 12], "variou": [13, 20], "vector": [2, 5], "verbatim": 19, "verbos": 6, "veri": [2, 13, 15, 16], "verifi": [11, 12, 16], "version": [2, 5, 6, 8, 9, 11, 14, 15, 18, 19, 20], "vertex": [2, 10], "vertic": 2, "vibrat": [5, 20], "view": [11, 15, 19], "violat": 19, "virial": 5, "virial_theorem": [5, 20], "virt_orb": 5, "virtual": [5, 20], "virtual_orbital_shift_limit": 5, "virtual_orbital_shift_on": 5, "visibl": 19, "void": 19, "volum": [5, 19], "w": [2, 5, 19], "wa": [5, 12, 19, 20], "wai": [2, 3, 5, 11, 12, 13, 15, 16, 18, 19, 20], "wait": 3, "waiv": 19, "waiver": 19, "wall": 5, "wall_tim": 5, "want": [11, 12, 13, 15, 18, 19], "warn": 15, "warranti": 19, "wast": [5, 15], "wavefunct": 5, "wavefunction_norm": 5, "we": [10, 11, 12, 13, 15, 16, 19, 20], "weight": 2, "welcom": [13, 19], "well": [2, 9, 10, 12, 15, 16, 17, 19, 20], "were": [3, 5, 11, 16, 19], "what": [5, 15, 16, 19], "whatev": 19, "when": [2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 19], "whenev": 16, "where": [2, 3, 5, 10, 11, 12, 13, 15, 16, 19, 20], "whether": [2, 5, 6, 16, 19], "which": [2, 5, 6, 8, 10, 11, 13, 15, 16, 19, 20], "while": [2, 10, 11, 12, 13, 15, 16], "who": [19, 20], "whole": [11, 12, 15, 16, 19], "whom": 19, "whose": [2, 11, 14, 19], "why": [16, 19], "wide": [16, 19], "window": 19, "wipo": 19, "wise": 16, "wish": [13, 16, 19, 20], "within": [2, 5, 6, 12, 19], "without": [2, 3, 9, 10, 11, 15, 16, 19], "word": [2, 11], "work": [5, 9, 10, 11, 12, 15, 16, 19], "workdir": 3, "workflow": [9, 12, 18], "worldwid": 19, "would": [2, 5, 10, 12, 13, 14, 15, 16, 19, 20], "wrapper": 6, "write": [2, 5, 11, 15, 18, 19], "written": [2, 3, 10, 11, 14, 16, 19, 20], "wrong": 5, "wrongli": 16, "www": 19, "x": [5, 6, 16, 17, 18], "xc": 5, "xc_energi": 5, "xcfun": 5, "xf": 5, "xxx": 2, "xy": 5, "y": [16, 17], "yaml": [3, 12, 16], "year": 19, "yet": [5, 16], "yield": 6, "you": [8, 10, 11, 12, 13, 15, 16, 17, 19, 20], "your": [8, 12, 13, 15, 16, 19, 20], "yourself": 19, "z": 16, "zero": 5, "zpve": 5}, "titles": ["turbomoleio", "turbomoleio package", "turbomoleio.core package", "turbomoleio.input package", "turbomoleio.input.templates package", "turbomoleio.output package", "turbomoleio.testing package", "Appendix", "Reporting bugs", "Changelog", "The coord file", "The data group files", "Running define", "Define runner", "Contributing", "Output logs parsing", "Testing", "Versioning", "turbomoleio", "License", "Outputs parsing"], "titleterms": {"0": 9, "1": 9, "11": 9, "15": 9, "16": 9, "2": 9, "20": 9, "2021": 9, "2022": 9, "2024": 9, "24": 9, "27": 9, "3": 9, "4": 9, "5": 9, "6": 9, "The": [10, 11, 12, 16, 20], "access": 11, "ad": 9, "addit": 18, "appendix": 7, "backward": 17, "base": 2, "bug": [8, 9], "chang": [9, 16], "changelog": 9, "common": 20, "compat": 17, "content": [1, 2, 3, 4, 5, 6], "contribut": [14, 18], "control": [2, 11], "coord": 10, "core": 2, "data": [5, 11, 20], "datagroup": [2, 11], "defin": [3, 12, 13], "definerunn": 12, "develop": [9, 18], "featur": 9, "feb": 9, "file": [5, 10, 11, 20], "fix": 9, "group": 11, "guid": 18, "indic": 18, "inform": 18, "input": [3, 4], "integr": 16, "licens": 19, "log": [15, 20], "mar": 9, "modifi": 11, "modul": [1, 2, 3, 4, 5, 6], "molecul": 2, "new": [15, 16], "object": [11, 20], "output": [5, 15, 16, 20], "overal": 20, "packag": [1, 2, 3, 4, 5, 6], "paramet": 12, "pars": [15, 16, 20], "parser": 5, "period": [2, 10], "procedur": 16, "quantiti": 15, "quick": 20, "releas": 9, "report": 8, "run": 12, "runner": 13, "sep": 9, "standard": 16, "start": 20, "state": [5, 20], "structur": 20, "submodul": [2, 3, 5], "subpackag": [1, 3], "suit": 16, "symmetri": 2, "system": 10, "tabl": 18, "templat": 4, "test": [6, 9, 13, 15, 16], "turbomol": 16, "turbomoleio": [0, 1, 2, 3, 4, 5, 6, 18], "type": 15, "unit": 16, "user": 18, "util": [2, 3], "valid": [12, 13], "valu": 11, "version": [16, 17], "write": 16}})