Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z A A (nexus.qmcpack_property_analyzers.Bspline attribute) (nexus.unit_converter.UnitConverter attribute) absmin() (in module nexus.numerics) accumulate() (nexus.hdfreader.HDFgroup method) accumulate_data() (nexus.qmcpack_quantity_analyzers.TracesAnalyzer method) accumulate_scalars() (nexus.qmcpack_quantity_analyzers.TracesFileHDF method) accumulated_scalars() (nexus.qmcpack_quantity_analyzers.TracesFileHDF method) acquire_dependents() (nexus.simulation.Simulation method) Actinium (nexus.periodic_table.Elements attribute) active() (nexus.simulation.Simulation method) adapted_fermi_level() (nexus.qmcpack.GCTA method) add() (nexus.generic.obj method) (nexus.machines.Machine static method) (nexus.machines.Options method) (nexus.pwscf_input.Element method) (nexus.qmcpack_input.collection method) (nexus.qmcpack_input.QmcpackInputCollections method) add_all_attributes() (nexus.qmcpack_quantity_analyzers.SpaceGridBase method) add_atoms() (nexus.structure.Structure method) add_cascade() (nexus.project_manager.ProjectManager method) add_dataset() (nexus.hdfreader.HDFreader method) add_density() (nexus.fileio.XsfFile method) add_group() (nexus.hdfreader.HDFreader method) add_include() (nexus.qmcpack_input.QmcpackInput method) add_job() (nexus.machines.Machine method) add_kmesh() (nexus.structure.Structure method) add_kpoints() (nexus.structure.Structure method) add_L2() (nexus.pseudopotential.SemilocalPP method) add_local() (nexus.pseudopotential.SemilocalPP method) add_new_dyn_procs() (nexus.project_manager.DynamicWorkflowManager method) add_nonlocal() (nexus.pseudopotential.SemilocalPP method) add_optional() (nexus.generic.obj method) add_particles() (nexus.physical_system.Particles method) (nexus.physical_system.PhysicalSystem method) add_simulations() (nexus.project_manager.ProjectManager method) add_symmetrized_kmesh() (nexus.structure.Structure method) add_to_image() (nexus.fileio.XsfFile method) addbs() (nexus.basisset.BasisSets method) added_keys (nexus.quantum_package_input.QuantumPackageInput attribute) addpp() (nexus.pseudopotential.Pseudopotentials method) adjust_axes() (nexus.structure.Structure method) advance() (nexus.vasp_analyzer.VaspLines method) advance_line() (nexus.vasp_analyzer.VaspLines method) advance_token() (nexus.vasp_analyzer.VaspLines method) ae_pp_species() (nexus.physical_system.PhysicalSystem method) afqmc_expanded_names (nexus.qmcpack_input.Names attribute) afqmc_mode (nexus.qmcpack_input.QIobj attribute) ALCF_Machine (class in nexus.machines) alias (nexus.observables.StatFile attribute) all_children() (in module nexus.memory) all_dp (nexus.project_manager.DynamicWorkflowManager attribute) all_dynamic_processes (nexus.simulation.DynamicProcess attribute) all_group_aliases (nexus.gamess_input.GamessInput attribute) all_groups (nexus.gamess_input.GamessInput attribute) all_inputs (nexus.vasp_input.VaspInput attribute) all_keywords (nexus.gamess_input.GamessInput attribute) all_name_aliases (nexus.gamess_input.GamessInput attribute) all_names (nexus.gamess_input.GamessInput attribute) all_outputs (nexus.vasp_input.VaspInput attribute) all_periodic() (nexus.structure.Structure method) all_sims (nexus.project_manager.DynamicWorkflowManager attribute) (nexus.simulation.Simulation attribute) all_variables (nexus.pwscf_input.PwscfInputBase attribute) allow_no_assign() (nexus.simulation.SimulationInputTemplateDev method) allow_overlapping_files (nexus.quantum_package.QuantumPackage attribute) (nexus.simulation.Simulation attribute) (nexus.vasp.Vasp attribute) allow_warnings (nexus.machines.Machine attribute) allowed_inputs (nexus.simulation.GenericSimulation attribute) (nexus.simulation.Simulation attribute) allowed_requirements (nexus.pwscf.Pwscf attribute) (nexus.qmcpack.Qmcpack attribute) (nexus.simulation.DynamicProcess attribute) allowed_settings (nexus.qmcpack_quantity_analyzers.DensityMatricesAnalyzer attribute) allowed_types (nexus.pyscf_input.PyscfInput attribute) allowed_user_info (nexus.machines.Machine attribute) allowed_values (nexus.gamess_input.BasisGroup attribute) (nexus.gamess_input.CidrtGroup attribute) (nexus.gamess_input.ContrlGroup attribute) (nexus.gamess_input.DetGroup attribute) (nexus.gamess_input.DftGroup attribute) (nexus.gamess_input.DrtGroup attribute) (nexus.gamess_input.GuessGroup attribute) (nexus.gamess_input.KeywordSpecGroup attribute) (nexus.gamess_input.McscfGroup attribute) (nexus.gamess_input.ScfGroup attribute) (nexus.gamess_input.SystemGroup attribute) Aluminum (nexus.periodic_table.Elements attribute) Amber (class in nexus.machines) Americium (nexus.periodic_table.Elements attribute) Amos (class in nexus.machines) amu (nexus.unit_converter.UnitConverter attribute) analysis_succeeded (nexus.rmg_analyzer.RmgAnalyzer property) analyze() (nexus.bundle.SimulationBundle method) (nexus.gamess_analyzer.GamessAnalyzer method) (nexus.pwscf_analyzer.PwscfAnalyzer method) (nexus.pwscf_postprocessors.HpAnalyzer method) (nexus.pwscf_postprocessors.ProjwfcAnalyzer method) (nexus.qmcpack_analyzer.QmcpackAnalyzer method) (nexus.rmg_analyzer.RmgAnalyzer method) (nexus.simulation.NullSimulationAnalyzer method) (nexus.simulation.Simulation method) (nexus.simulation.SimulationAnalyzer method) (nexus.vasp_analyzer.VaspAnalyzer method) analyze_local() (nexus.qmcpack_property_analyzers.WavefunctionAnalyzer method) (nexus.qmcpack_quantity_analyzers.DatAnalyzer method) (nexus.qmcpack_quantity_analyzers.DensityAnalyzer method) (nexus.qmcpack_quantity_analyzers.DensityMatricesAnalyzer method) (nexus.qmcpack_quantity_analyzers.DmcDatAnalyzer method) (nexus.qmcpack_quantity_analyzers.EnergyDensityAnalyzer method) (nexus.qmcpack_quantity_analyzers.ScalarsDatAnalyzer method) (nexus.qmcpack_quantity_analyzers.ScalarsHDFAnalyzer method) (nexus.qmcpack_quantity_analyzers.SpinDensityAnalyzer method) (nexus.qmcpack_quantity_analyzers.StructureFactorAnalyzer method) (nexus.qmcpack_quantity_analyzers.TracesAnalyzer method) (nexus.qmcpack_result_analyzers.OptimizationAnalyzer method) (nexus.qmcpack_result_analyzers.TimestepStudyAnalyzer method) analyze_local_orig() (nexus.qmcpack_quantity_analyzers.DensityMatricesAnalyzer method) analyze_log() (nexus.gamess_analyzer.GamessAnalyzer method) analyze_outcar() (nexus.vasp_analyzer.VaspAnalyzer method) analyze_punch() (nexus.gamess_analyzer.GamessAnalyzer method) analyzed (nexus.rmg_analyzer.RmgAnalyzer property) (nexus.simulation.DynamicProcess property) analyzer_image (nexus.simulation.DynamicProcess property) analyzer_imagefile (nexus.simulation.Simulation attribute) analyzer_type (nexus.bundle.SimulationBundle attribute) (nexus.gamess.Gamess attribute) (nexus.pwscf.Pwscf attribute) (nexus.pwscf_postprocessors.Hp attribute) (nexus.pwscf_postprocessors.PostProcessSimulation attribute) (nexus.pwscf_postprocessors.Projwfc attribute) (nexus.pyscf_sim.Pyscf attribute) (nexus.qmcpack.Qmcpack attribute) (nexus.quantum_package.QuantumPackage attribute) (nexus.rmg.Rmg attribute) (nexus.simulation.Simulation attribute) (nexus.vasp.Vasp attribute) Andes (class in nexus.machines) angstrom (nexus.unit_converter.UnitConverter attribute) angular_channels() (nexus.pseudopotential.SemilocalPP method) angular_terms (nexus.basisset.gaussBasisFile attribute) Antimony (nexus.periodic_table.Elements attribute) any_functions (nexus.vasp_analyzer.OutcarData attribute) any_periodic() (nexus.structure.Structure method) app_command() (nexus.bundle.SimulationBundle method) (nexus.gamess.Gamess method) (nexus.pwscf.Pwscf method) (nexus.pwscf_postprocessors.PostProcessSimulation method) (nexus.pyscf_sim.Pyscf method) (nexus.qmcpack.Qmcpack method) (nexus.quantum_package.QuantumPackage method) (nexus.rmg.Rmg method) (nexus.simulation.GenericSimulation method) (nexus.simulation.Simulation method) (nexus.vasp.Vasp method) append() (nexus.generic.obj method) append_list() (nexus.gamess_input.CardGroup method) append_text() (nexus.gamess_input.CardGroup method) append_to_component() (nexus.pseudopotential.GaussianPP method) application (nexus.gamess.Gamess attribute) (nexus.pwscf.Pwscf attribute) (nexus.pwscf_postprocessors.Bands attribute) (nexus.pwscf_postprocessors.Cppp attribute) (nexus.pwscf_postprocessors.Dos attribute) (nexus.pwscf_postprocessors.Hp attribute) (nexus.pwscf_postprocessors.PP attribute) (nexus.pwscf_postprocessors.Projwfc attribute) (nexus.pwscf_postprocessors.Pwexport attribute) (nexus.pyscf_sim.Pyscf attribute) (nexus.qmcpack.Qmcpack attribute) (nexus.quantum_package.QuantumPackage attribute) (nexus.rmg.Rmg attribute) (nexus.simulation.Simulation attribute) (nexus.vasp.Vasp attribute) application_properties (nexus.gamess.Gamess attribute) (nexus.pwscf.Pwscf attribute) (nexus.pyscf_sim.Pyscf attribute) (nexus.qmcpack.Qmcpack attribute) (nexus.quantum_package.QuantumPackage attribute) (nexus.rmg.Rmg attribute) (nexus.simulation.Simulation attribute) (nexus.vasp.Vasp attribute) application_results (nexus.gamess.Gamess attribute) (nexus.pwscf.Pwscf attribute) (nexus.pwscf_postprocessors.Hp attribute) (nexus.pyscf_sim.Pyscf attribute) (nexus.qmcpack.Qmcpack attribute) (nexus.quantum_package.QuantumPackage attribute) (nexus.rmg.Rmg attribute) (nexus.simulation.Simulation attribute) (nexus.vasp.Vasp attribute) aprun_options (nexus.machines.Supercomputer attribute) Archer2 (class in nexus.machines) Argon (nexus.periodic_table.Elements attribute) array_from_lines() (in module nexus.pwscf_input) array_keys (nexus.pwscf_data_reader.QEXML attribute) array_keywords (nexus.vasp_input.Incar attribute) (nexus.vasp_input.Stopcar attribute) array_options (nexus.rmg_input.AtomsKeyword attribute) (nexus.rmg_input.FormattedTableRmgKeyword attribute) (nexus.rmg_input.KpointsBandstructureKeyword attribute) (nexus.rmg_input.KpointsKeyword attribute) (nexus.rmg_input.PseudopotentialKeyword attribute) array_to_string() (in module nexus.pwscf_input) array_types (nexus.rmg_input.AtomsKeyword attribute) (nexus.rmg_input.FormattedTableRmgKeyword attribute) (nexus.rmg_input.KpointsBandstructureKeyword attribute) (nexus.rmg_input.KpointsKeyword attribute) (nexus.rmg_input.PseudopotentialKeyword attribute) arrays (nexus.gamess_input.BasisGroup attribute) (nexus.gamess_input.DetGroup attribute) (nexus.gamess_input.GuessGroup attribute) (nexus.gamess_input.GugdiaGroup attribute) (nexus.gamess_input.KeywordSpecGroup attribute) (nexus.gamess_input.McscfGroup attribute) (nexus.gamess_input.ScfGroup attribute) (nexus.gamess_input.SystemGroup attribute) Arsenic (nexus.periodic_table.Elements attribute) assert_numeric() (nexus.pseudopotential.SemilocalPP method) assign() (nexus.pwscf_input.Section method) (nexus.qmcpack_input.QIxml method) (nexus.qmcpack_input.QmcpackInput method) (nexus.rmg_input.FormattedRmgKeyword method) (nexus.rmg_input.FormattedTableRmgKeyword method) (nexus.rmg_input.HubbardUKeyword method) (nexus.rmg_input.RmgInput method) (nexus.rmg_input.RmgKeyword method) (nexus.simulation.SimulationInputTemplateDev method) (nexus.vasp_input.VKeywordFile method) assign_bool() (in module nexus.vasp_input) assign_bool_array() (in module nexus.vasp_input) assign_defaults() (nexus.fileio.PoscarFile method) assign_int_array() (in module nexus.vasp_input) assign_real_array() (in module nexus.vasp_input) assign_string() (in module nexus.vasp_input) assign_value (nexus.vasp_input.Incar attribute) (nexus.vasp_input.Stopcar attribute) assign_value() (in module nexus.gamess_analyzer) assign_values() (nexus.pwscf_postprocessors.Namelist method) Astatine (nexus.periodic_table.Elements attribute) at_Gpoint() (nexus.structure.Structure method) at_Lpoint() (nexus.structure.Structure method) at_real_kpoint() (nexus.structure.Structure method) atm (nexus.unit_converter.UnitConverter attribute) atmosphere (nexus.unit_converter.UnitConverter attribute) atomic_forces (class in nexus.pwscf_input) atomic_mass_unit (nexus.unit_converter.UnitConverter attribute) atomic_number (nexus.periodic_table.ElementData attribute) atomic_positions (class in nexus.pwscf_input) atomic_species (class in nexus.pwscf_input) atomic_variables (nexus.pwscf_input.system attribute) atomic_weight (nexus.periodic_table.ElementData attribute) AtomsKeyword (class in nexus.rmg_input) Attaway (class in nexus.machines) attempt_files() (nexus.quantum_package.QuantumPackage method) (nexus.simulation.Simulation method) attribute_definitions (nexus.observables.Density attribute) (nexus.observables.MomentumDistribution attribute) (nexus.observables.MomentumDistributionDFT attribute) (nexus.observables.Observable attribute) attribute_to_value() (in module nexus.qmcpack_input) AttributeProperties (class in nexus.observables) Aurora (class in nexus.machines) available() (in module nexus.developer) available_specifiers (nexus.pwscf_input.hubbard attribute) average_bundle_data() (nexus.qmcpack_analyzer.QmcpackAnalyzer method) axindex (nexus.qmcpack_quantity_analyzers.SpaceGridBase attribute) axlabel_n2s (nexus.qmcpack_quantity_analyzers.SpaceGridBase attribute) axlabel_s2n (nexus.qmcpack_quantity_analyzers.SpaceGridBase attribute) B B (nexus.unit_converter.UnitConverter attribute) backfold() (nexus.observables.MomentumDistribution method) Bands (class in nexus.pwscf_postprocessors) BandsInput (class in nexus.pwscf_postprocessors) BandsNamelist (class in nexus.pwscf_postprocessors) bar (nexus.unit_converter.UnitConverter attribute) Barium (nexus.periodic_table.Elements attribute) base_partition (nexus.machines.ALCF_Machine attribute) (nexus.machines.Cetus attribute) (nexus.machines.Mira attribute) (nexus.machines.Vesta attribute) Baseline (class in nexus.machines) bases_by_atom() (nexus.basisset.BasisSets method) basic_types (nexus.pyscf_input.PyscfInput attribute) (nexus.vasp_analyzer.VXML attribute) basis_size() (nexus.basisset.GaussianBasisSet method) BasisFile (class in nexus.basisset) BasisGroup (class in nexus.gamess_input) BasisSets (class in nexus.basisset) batch_capable (nexus.machines.ALCF_Machine attribute) (nexus.machines.Amos attribute) (nexus.machines.Andes attribute) (nexus.machines.Archer2 attribute) (nexus.machines.Aurora attribute) (nexus.machines.Baseline attribute) (nexus.machines.Besms attribute) (nexus.machines.BlueWatersXE attribute) (nexus.machines.BlueWatersXK attribute) (nexus.machines.CadesMoab attribute) (nexus.machines.CadesSlurm attribute) (nexus.machines.Cooley attribute) (nexus.machines.EOS attribute) (nexus.machines.Frontier attribute) (nexus.machines.ICMP_Machine attribute) (nexus.machines.Improv attribute) (nexus.machines.Inti attribute) (nexus.machines.Kagayaki attribute) (nexus.machines.Kestrel attribute) (nexus.machines.Lassen attribute) (nexus.machines.Leonardo attribute) (nexus.machines.Lonestar attribute) (nexus.machines.Machine attribute) (nexus.machines.NerscMachine attribute) (nexus.machines.OIC5 attribute) (nexus.machines.Polaris attribute) (nexus.machines.Rhea attribute) (nexus.machines.Ruby attribute) (nexus.machines.SnlMachine attribute) (nexus.machines.Stampede2 attribute) (nexus.machines.Summit attribute) (nexus.machines.Supercomputer attribute) (nexus.machines.SuperMUC attribute) (nexus.machines.SuperMUC_NG attribute) (nexus.machines.Theta attribute) (nexus.machines.Titan attribute) (nexus.machines.Tomcat3 attribute) (nexus.machines.Workstation attribute) become_primitive() (nexus.structure.Structure method) Berkelium (nexus.periodic_table.Elements attribute) Beryllium (nexus.periodic_table.Elements attribute) Besms (class in nexus.machines) birch() (in module nexus.numerics) birch_pressure() (in module nexus.numerics) Bismuth (nexus.periodic_table.Elements attribute) block (nexus.simulation.DynamicProcess property) block_dependents() (nexus.simulation.Simulation method) BlueWatersXE (class in nexus.machines) BlueWatersXK (class in nexus.machines) bohr (nexus.unit_converter.UnitConverter attribute) Bohrium (nexus.periodic_table.Elements attribute) bond_compression() (nexus.structure.Structure method) bonds() (nexus.structure.Structure method) bool_arrays (nexus.vasp_input.Incar attribute) (nexus.vasp_input.Stopcar attribute) bool_map (nexus.vasp_input.Poscar attribute) booldict (nexus.gamess_input.KeywordGroup attribute) bools (nexus.gamess_input.BasisGroup attribute) (nexus.gamess_input.CidrtGroup attribute) (nexus.gamess_input.ContrlGroup attribute) (nexus.gamess_input.DetGroup attribute) (nexus.gamess_input.DftGroup attribute) (nexus.gamess_input.DrtGroup attribute) (nexus.gamess_input.GuessGroup attribute) (nexus.gamess_input.KeywordSpecGroup attribute) (nexus.gamess_input.McscfGroup attribute) (nexus.gamess_input.ScfGroup attribute) (nexus.gamess_input.SystemGroup attribute) (nexus.pwscf_input.PwscfInputBase attribute) (nexus.vasp_input.Incar attribute) (nexus.vasp_input.Stopcar attribute) booster_qos (nexus.machines.Leonardo attribute) Boron (nexus.periodic_table.Elements attribute) boundary() (nexus.structure.Structure method) bounding_box() (nexus.structure.Structure method) bravais_lattice_name() (nexus.structure.Structure method) broken_docs (nexus.vasp_input.Incar attribute) Bromine (nexus.periodic_table.Elements attribute) Bspline (class in nexus.qmcpack_property_analyzers) bundle() (in module nexus.bundle) (nexus.qmcpack_analyzer.QmcpackAnalyzer method) (nexus.qmcpack_input.QmcpackInput method) bundle_dependencies() (nexus.bundle.SimulationBundle method) bundle_inputs() (nexus.qmcpack_input.TracedQmcpackInput method) bundle_jobs() (nexus.bundle.SimulationBundle method) BundledQmcpackInput (class in nexus.qmcpack_input) C c (in module nexus.qmcpack_input) (nexus.pseudopotential.SemilocalPP attribute) C (nexus.unit_converter.UnitConverter attribute) CadesMoab (class in nexus.machines) CadesSlurm (class in nexus.machines) Cadmium (nexus.periodic_table.Elements attribute) Calcium (nexus.periodic_table.Elements attribute) calculation_mode (nexus.rmg_analyzer.RmgAnalyzer property) calculation_shortmode (nexus.rmg_analyzer.RmgAnalyzer property) Californium (nexus.periodic_table.Elements attribute) Carbon (nexus.periodic_table.Elements attribute) Card (class in nexus.pwscf_input) card_groups (nexus.gamess_input.GamessInput attribute) card_types (nexus.pwscf_input.PwscfInput attribute) CardGroup (class in nexus.gamess_input) cards (nexus.pwscf_input.PwscfInput attribute) cartesian (nexus.qmcpack_quantity_analyzers.SpaceGridBase attribute) carve() (nexus.structure.Structure method) case_map (nexus.pwscf_input.cell attribute) (nexus.pwscf_input.control attribute) (nexus.pwscf_input.ee attribute) (nexus.pwscf_input.electrons attribute) (nexus.pwscf_input.ions attribute) (nexus.pwscf_input.phonon attribute) (nexus.pwscf_input.system attribute) CasinoPP (class in nexus.pseudopotential) cdesc (nexus.structure.Crystal attribute) cell (class in nexus.pwscf_input) (nexus.structure.Crystal attribute) cell_aliases (nexus.structure.Crystal attribute) cell_allowed (nexus.pyscf_input.PyscfInput attribute) cell_classes (nexus.structure.Crystal attribute) cell_image() (nexus.structure.Structure method) cell_order (nexus.pyscf_input.PyscfInput attribute) cell_parameters (class in nexus.pwscf_input) cell_types (nexus.structure.Crystal attribute) celsius (nexus.unit_converter.UnitConverter attribute) center_distances() (nexus.structure.Structure method) center_molecule() (nexus.structure.Structure method) center_solid() (nexus.structure.Structure method) centering_options (nexus.vasp_input.Kpoints attribute) centering_types (nexus.structure.Crystal attribute) centerings (nexus.structure.Crystal attribute) Cerium (nexus.periodic_table.Elements attribute) Cesium (nexus.periodic_table.Elements attribute) Cetus (class in nexus.machines) change_density_units() (nexus.observables.Density method) change_distance_units() (nexus.observables.Density method) change_local() (nexus.pseudopotential.SemilocalPP method) change_option() (nexus.pwscf_input.Card method) change_request() (nexus.qmcpack_analyzer.QmcpackAnalyzer method) change_specifier() (nexus.pwscf_input.atomic_positions method) (nexus.pwscf_input.Card method) (nexus.pwscf_input.cell_parameters method) (nexus.pwscf_input.k_points method) (nexus.vasp_input.Poscar method) change_units() (nexus.fileio.XsfFile method) (nexus.physical_system.PhysicalSystem method) (nexus.structure.Structure method) channel_colors (nexus.pseudopotential.SemilocalPP attribute) channel_indices (nexus.pseudopotential.SemilocalPP attribute) charge_density (nexus.simulation.DynamicProcess property) charge_dict (nexus.unit_converter.UnitConverter attribute) ChargeDensity (class in nexus.observables) check_allowed() (nexus.bundle.SimulationBundle method) check_attributes() (nexus.observables.DefinedAttributeBase method) check_charge_neutrality() (nexus.qmcpack.GCTA method) check_complete() (nexus.qmcpack_quantity_analyzers.SpaceGridBase method) (nexus.qmcpack_quantity_analyzers.SpaceGridInitializer method) (nexus.vasp_input.Poscar method) check_consistency() (nexus.vasp_input.VKeywordFile class method) check_consistent() (nexus.physical_system.PhysicalSystem method) (nexus.structure.Structure method) check_dependencies() (nexus.project_manager.ProjectManager method) (nexus.simulation.Simulation method) check_dmc() (nexus.qmcpack_quantity_analyzers.TracesAnalyzer method) check_dmc_old() (nexus.qmcpack_quantity_analyzers.TracesAnalyzer method) check_excitation_type() (in module nexus.qmcpack_input) check_final_state() (in module nexus.testing) check_first_gen() (nexus.simulation.DynamicProcess class method) check_folded_system() (nexus.physical_system.PhysicalSystem method) check_implementation() (nexus.qmcpack.GCTA method) check_jackknife_inputs() (in module nexus.numerics) check_junk() (nexus.qmcpack_input.QIxml method) check_keyspec_groups() (in module nexus.gamess_input) check_kmesh_size() (nexus.qmcpack.GCTA method) check_kpoint_consistency() (nexus.qmcpack.GCTA method) check_magnetization_accuracy() (nexus.qmcpack.GCTA method) check_names() (nexus.pwscf_postprocessors.Namelist method) check_new_variables() (in module nexus.pwscf_input) check_object_eq() (in module nexus.testing) check_on_write (nexus.rmg_input.RmgInputSettings attribute) check_particle_sums() (nexus.qmcpack_quantity_analyzers.TracesAnalyzer method) (nexus.qmcpack_quantity_analyzers.TracesFileHDF method) check_point_group_operations() (nexus.structure.Structure method) check_required() (nexus.generic.obj method) check_result() (nexus.gamess.Gamess method) (nexus.pwscf.Pwscf method) (nexus.pwscf_postprocessors.Hp method) (nexus.pwscf_postprocessors.PostProcessSimulation method) (nexus.pyscf_sim.Pyscf method) (nexus.qmcpack.Qmcpack method) (nexus.quantum_package.QuantumPackage method) (nexus.rmg.Rmg method) (nexus.simulation.Simulation method) (nexus.vasp.Vasp method) check_scalars() (nexus.qmcpack_quantity_analyzers.TracesAnalyzer method) check_scalars_old() (nexus.qmcpack_quantity_analyzers.TracesAnalyzer method) check_section_classes() (in module nexus.pwscf_input) check_sim_status() (nexus.bundle.SimulationBundle method) (nexus.gamess.Gamess method) (nexus.pwscf.Pwscf method) (nexus.pwscf_postprocessors.PostProcessSimulation method) (nexus.pyscf_sim.Pyscf method) (nexus.qmcpack.Qmcpack method) (nexus.quantum_package.QuantumPackage method) (nexus.rmg.Rmg method) (nexus.simulation.GenericSimulation method) (nexus.simulation.Simulation method) (nexus.vasp.Vasp method) check_status() (nexus.simulation.Simulation method) check_subcascade() (nexus.simulation.Simulation method) check_tiling() (nexus.structure.Structure method) check_traces() (nexus.qmcpack_analyzer.QmcpackAnalyzer method) (nexus.qmcpack_method_analyzers.MethodAnalyzer method) check_types() (nexus.generic.obj method) check_types_optional() (nexus.generic.obj method) check_unassigned() (nexus.observables.DefinedAttributeBase method) check_valid() (nexus.fileio.StandardFile method) (nexus.quantum_package_input.QuantumPackageInput method) (nexus.rmg_input.RmgInput method) check_value_eq() (in module nexus.testing) checked_particle_sums() (nexus.qmcpack_quantity_analyzers.TracesFileHDF method) chemical_coordination() (nexus.structure.Structure method) ChgcarFile (class in nexus.fileio) Chlorine (nexus.periodic_table.Elements attribute) Chromium (nexus.periodic_table.Elements attribute) ci() (in module nexus.debug) CidrtGroup (class in nexus.gamess_input) class_error() (nexus.generic.object_interface class method) class_get() (nexus.generic.object_interface class method) class_has() (nexus.generic.object_interface class method) class_init() (nexus.pwscf_input.Section class method) (nexus.pwscf_postprocessors.Namelist class method) (nexus.pwscf_postprocessors.NamelistInput class method) (nexus.vasp_input.VKeywordFile class method) class_items() (nexus.generic.object_interface class method) class_keys() (nexus.generic.object_interface class method) class_log() (nexus.generic.object_interface class method) class_set() (nexus.generic.object_interface class method) class_set_optional() (nexus.generic.object_interface class method) class_set_single() (nexus.generic.object_interface class method) class_warn() (nexus.generic.object_interface class method) classcollection (class in nexus.qmcpack_input) cleaned_text() (nexus.basisset.BasisFile method) (nexus.basisset.gaussBasisFile method) clear() (nexus.generic.hobj method) (nexus.generic.object_interface method) (nexus.simulation.SimulationInputTemplateDev method) clear_all_sims() (in module nexus.testing) (nexus.simulation.Simulation class method) clear_kpoints() (nexus.structure.Structure method) cleave() (nexus.structure.Structure method) climbing_images (class in nexus.pwscf_input) clone() (nexus.machines.Job method) clone_from() (nexus.structure.Structure method) close() (nexus.fileio.TextFile method) close_hubbard_dat() (nexus.pwscf_postprocessors.HpAnalyzer method) close_log() (nexus.generic.hidden method) (nexus.generic.object_interface method) (nexus.pwscf_postprocessors.ProjwfcAnalyzer method) cls (in module nexus.pwscf_postprocessors) (in module nexus.vasp_input) (nexus.observables.StatFile attribute) cnames (nexus.qmcpack_quantity_analyzers.SpaceGridBase attribute) Cobalt (nexus.periodic_table.Elements attribute) code_name() (nexus.simulation.Simulation class method) collect_profile() (nexus.qmcpack_input.QIxml method) collection (class in nexus.qmcpack_input) collective_vars (class in nexus.pwscf_input) combine() (nexus.qmcpack_input.QIxml method) compare() (nexus.structure.DefectStructure method) complete() (nexus.qmcpack_analyzer.QmcpackAnalysisRequest method) completed() (nexus.bundle.SimulationBundle method) (nexus.simulation.Simulation method) component() (nexus.observables.ObservableWithComponents method) component_names (nexus.observables.Density attribute) (nexus.observables.MomentumDistribution attribute) (nexus.observables.ObservableWithComponents attribute) components() (nexus.observables.ObservableWithComponents method) condense() (nexus.xmlreader.XMLelement method) condense_name() (nexus.observables.StatFile method) (nexus.qmcpack_input.Names method) (nexus.simulation.Simulation method) condense_names() (nexus.qmcpack_input.Names method) condensed_name_report() (nexus.qmcpack_input.Names method) condensed_names (nexus.qmcpack_input.Names attribute) connected_graphs() (nexus.structure.Structure method) constraints (class in nexus.pwscf_input) contracted() (nexus.basisset.GaussianBasisSet method) contracted_basis_size() (nexus.basisset.GaussianBasisSet method) ContrlGroup (class in nexus.gamess_input) control (class in nexus.pwscf_input) convert() (in module nexus.unit_converter) (nexus.pseudopotential.Pseudopotential method) (nexus.unit_converter.UnitConverter static method) convert_numeric() (nexus.xmlreader.XMLelement method) convert_scalar_to_all() (nexus.unit_converter.UnitConverter static method) convex_hull() (in module nexus.numerics) Cooley (class in nexus.machines) coord_n2s (nexus.qmcpack_quantity_analyzers.SpaceGridBase attribute) coord_options() (nexus.vasp_input.Kpoints method) coord_s2n (nexus.qmcpack_quantity_analyzers.SpaceGridBase attribute) Copernicium (nexus.periodic_table.Elements attribute) Copper (nexus.periodic_table.Elements attribute) copy() (nexus.generic.object_interface method) (nexus.physical_system.PhysicalSystem method) (nexus.qmcpack_quantity_analyzers.RectilinearGrid method) (nexus.qmcpack_quantity_analyzers.SpaceGridBase method) (nexus.qmcpack_quantity_analyzers.VoronoiGrid method) copy_file() (nexus.simulation.Simulation method) copy_from() (nexus.generic.obj method) copy_to() (nexus.generic.obj method) Cori (class in nexus.machines) corners() (nexus.structure.Structure method) correct() (nexus.qmcpack_quantity_analyzers.ScalarsHDFAnalyzer method) corrections (nexus.qmcpack_quantity_analyzers.ScalarsHDFAnalyzer attribute) coulomb (nexus.unit_converter.UnitConverter attribute) count_electrons() (nexus.physical_system.Particles method) count_ions() (nexus.physical_system.Particles method) count_jastrow_params() (in module nexus.qmcpack_input) count_kshells() (nexus.structure.Structure method) Cppp (class in nexus.pwscf_postprocessors) CpppInput (class in nexus.pwscf_postprocessors) CpppInputppNamelist (class in nexus.pwscf_postprocessors) create_directories() (nexus.bundle.SimulationBundle method) (nexus.simulation.Simulation method) creating_fake_sims (nexus.simulation.Simulation attribute) Crystal (class in nexus.structure) crystal_lmap (nexus.basisset.GaussianBasisSet attribute) crystal_lmap_reverse (nexus.basisset.GaussianBasisSet attribute) cube_deviation() (nexus.structure.Structure method) cumulative_radial_density() (nexus.observables.Density method) Curium (nexus.periodic_table.Elements attribute) curve_fit() (in module nexus.numerics) cusp_correction() (nexus.qmcpack_input.QmcpackInput method) cylindrical (nexus.qmcpack_quantity_analyzers.SpaceGridBase attribute) D d2A (nexus.qmcpack_property_analyzers.Bspline attribute) dA (nexus.qmcpack_property_analyzers.Bspline attribute) Da (nexus.unit_converter.UnitConverter attribute) dalton (nexus.unit_converter.UnitConverter attribute) Darmstadtium (nexus.periodic_table.Elements attribute) data_repr() (nexus.generic.object_interface method) data_types (nexus.vasp_analyzer.VXML attribute) DatAnalyzer (class in nexus.qmcpack_quantity_analyzers) decrement() (nexus.observables.VLog method) decrement_level() (nexus.hdfreader.HDFreader method) (nexus.xmlreader.XMLreader method) deepcopy_attributes (nexus.observables.Density attribute) (nexus.observables.MomentumDistribution attribute) (nexus.observables.MomentumDistributionDFT attribute) (nexus.observables.Observable attribute) default_component() (nexus.observables.ObservableWithComponents method) default_component_name (nexus.observables.Density attribute) (nexus.observables.MomentumDistribution attribute) (nexus.observables.ObservableWithComponents attribute) default_extensions (nexus.pseudopotential.PPset attribute) default_metadata (nexus.qmcpack_input.QmcpackInput attribute) default_specifier (nexus.pwscf_input.hubbard attribute) defect_from_bond_compression() (nexus.structure.DefectStructure method) defect_from_displacement() (nexus.structure.DefectStructure method) DefectStructure (class in nexus.structure) define_attributes() (nexus.observables.DefinedAttributeBase class method) DefinedAttributeBase (class in nexus.observables) degC (nexus.unit_converter.UnitConverter attribute) degC_shift (nexus.unit_converter.UnitConverter attribute) degF (nexus.unit_converter.UnitConverter attribute) degF_shift (nexus.unit_converter.UnitConverter attribute) delete() (nexus.generic.obj method) (nexus.quantum_package_input.QuantumPackageInput method) delete_optional() (nexus.generic.obj method) delete_required() (nexus.generic.obj method) Density (class in nexus.observables) density() (nexus.structure.Jellium method) DensityAnalyzer (class in nexus.qmcpack_quantity_analyzers) DensityAnalyzerBase (class in nexus.qmcpack_quantity_analyzers) DensityMatricesAnalyzer (class in nexus.qmcpack_quantity_analyzers) depends() (nexus.simulation.Simulation method) deprecated (nexus.vasp_input.Incar attribute) desc (nexus.structure.Crystal attribute) determine_end_status() (nexus.machines.Job method) DetGroup (class in nexus.gamess_input) DevBase (class in nexus.developer) devlog (nexus.generic.generic_settings attribute) DftGroup (class in nexus.gamess_input) dict() (nexus.generic.obj method) dict_cmp() (in module nexus.utilities) difference() (nexus.qmcpack_input.QIxml method) (nexus.qmcpack_input.QmcpackInput method) dimension() (nexus.fileio.XsfFile method) dimensions (nexus.fileio.XsfFile attribute) displacement() (nexus.structure.Structure method) distance_dict (nexus.unit_converter.UnitConverter attribute) distance_table() (in module nexus.numerics) (nexus.structure.Structure method) distances() (nexus.structure.Structure method) distortion() (nexus.structure.Structure method) divert_out_err() (nexus.machines.Job method) dlog() (nexus.nexus_base.NexusCore method) DmcAnalyzer (class in nexus.qmcpack_method_analyzers) DmcDatAnalyzer (class in nexus.qmcpack_quantity_analyzers) DMSettings (class in nexus.qmcpack_quantity_analyzers) done (nexus.simulation.DynamicProcess property) Dos (class in nexus.pwscf_postprocessors) DosInput (class in nexus.pwscf_postprocessors) DosNamelist (class in nexus.pwscf_postprocessors) downstream_simids() (nexus.simulation.Simulation method) DrtGroup (class in nexus.gamess_input) Dubnium (nexus.periodic_table.Elements attribute) DynamicProcess (class in nexus.simulation) DynamicWorkflowManager (class in nexus.project_manager) Dysprosium (nexus.periodic_table.Elements attribute) E e (nexus.unit_converter.UnitConverter attribute) Eclipse (class in nexus.machines) ee (class in nexus.pwscf_input) Einsteinium (nexus.periodic_table.Elements attribute) elast_functions (nexus.vasp_analyzer.OutcarData attribute) electron_charge (nexus.unit_converter.UnitConverter attribute) electron_counts() (nexus.physical_system.Particles method) electron_mass (nexus.unit_converter.UnitConverter attribute) electron_volt (nexus.unit_converter.UnitConverter attribute) electrons (class in nexus.pwscf_input) Element (class in nexus.pwscf_input) element_types (nexus.pwscf_input.PwscfInput attribute) ElementData (class in nexus.periodic_table) Elements (class in nexus.periodic_table) elements (nexus.physical_system.Matter attribute) eliminate() (nexus.simulation.Simulation method) embed() (nexus.structure.Structure method) energy_dict (nexus.unit_converter.UnitConverter attribute) EnergyDensity (class in nexus.observables) EnergyDensityAnalyzer (class in nexus.qmcpack_quantity_analyzers) enforce_allowed (nexus.rmg_input.RmgInputSettings attribute) enforce_max_value (nexus.rmg_input.RmgInputSettings attribute) enforce_min_value (nexus.rmg_input.RmgInputSettings attribute) enter() (nexus.nexus_base.NexusCore method) EOS (class in nexus.machines) eos_B() (in module nexus.numerics) eos_Bp() (in module nexus.numerics) eos_Einf() (in module nexus.numerics) eos_eval() (in module nexus.numerics) eos_fit() (in module nexus.numerics) eos_param() (in module nexus.numerics) eos_V() (in module nexus.numerics) equality() (in module nexus.vasp_input) equate() (in module nexus.structure) equilibration_length() (in module nexus.numerics) equivalent_atoms() (nexus.structure.Structure method) Erbium (nexus.periodic_table.Elements attribute) ericfmt (nexus.gamess.Gamess attribute) errfile_extension (nexus.machines.ALCF_Machine attribute) (nexus.machines.Amos attribute) (nexus.machines.Andes attribute) (nexus.machines.Archer2 attribute) (nexus.machines.Cooley attribute) (nexus.machines.ICMP_Machine attribute) (nexus.machines.Leonardo attribute) (nexus.machines.Machine attribute) (nexus.machines.Rhea attribute) (nexus.machines.SnlMachine attribute) (nexus.machines.Stampede2 attribute) (nexus.machines.Theta attribute) (nexus.simulation.Simulation attribute) errfile_text() (nexus.simulation.Simulation method) error() (in module nexus.generic) (nexus.generic.object_interface method) escape_names (nexus.qmcpack_input.Names attribute) escaped_names (nexus.qmcpack_input.Names attribute) etest() (nexus.qmcpack_quantity_analyzers.EnergyDensityAnalyzer method) Europium (nexus.periodic_table.Elements attribute) eV (nexus.unit_converter.UnitConverter attribute) evaluate() (nexus.qmcpack_property_analyzers.Bspline method) (nexus.qmcpack_property_analyzers.RadialJastrow method) evaluate_channel() (nexus.pseudopotential.SemilocalPP method) evaluate_comp() (nexus.pseudopotential.SemilocalPP method) evaluate_comp_rV() (nexus.pseudopotential.CasinoPP method) (nexus.pseudopotential.GaussianPP method) (nexus.pseudopotential.QmcpackPP method) (nexus.pseudopotential.SemilocalPP method) evaluate_component() (nexus.pseudopotential.SemilocalPP method) evaluate_L2() (nexus.pseudopotential.SemilocalPP method) evaluate_local() (nexus.pseudopotential.SemilocalPP method) evaluate_nonlocal() (nexus.pseudopotential.SemilocalPP method) exclude_fields (nexus.rmg_input.AtomsKeyword attribute) (nexus.rmg_input.FormattedTableRmgKeyword attribute) executable_subfile (nexus.machines.ALCF_Machine attribute) (nexus.machines.Amos attribute) (nexus.machines.Cooley attribute) (nexus.machines.ICMP_Machine attribute) (nexus.machines.Machine attribute) (nexus.machines.Theta attribute) execute() (in module nexus.execute) (in module nexus.testing) (nexus.simulation.Simulation method) Exhcar (class in nexus.vasp_input) exists() (nexus.machines.Machine static method) expand_array() (in module nexus.vasp_input) expand_L2() (nexus.pseudopotential.SemilocalPP method) expand_name() (nexus.qmcpack_input.Names method) expanded_names (nexus.qmcpack_input.Names attribute) extract() (nexus.generic.obj method) extract_added_keys() (nexus.quantum_package_input.QuantumPackageInput method) extract_input_specification() (in module nexus.quantum_package_input) extract_optional() (nexus.generic.obj method) F face_distances() (nexus.structure.Structure method) face_vectors() (nexus.structure.Structure method) fahrenheit (nexus.unit_converter.UnitConverter attribute) fail (nexus.simulation.DynamicProcess property) failed (nexus.simulation.DynamicProcess property) failed() (in module nexus.testing) FailedTest fake() (nexus.simulation.Simulation method) femtometer (nexus.unit_converter.UnitConverter attribute) femtosecond (nexus.unit_converter.UnitConverter attribute) Fermium (nexus.periodic_table.Elements attribute) file_units (nexus.gamess_input.GamessInput attribute) filetypes (nexus.fileio.XsfFile attribute) fill_produces() (nexus.pwscf.Pwscf method) (nexus.qmcpack.Qmcpack method) (nexus.simulation.Simulation method) fill_products() (nexus.pwscf.Pwscf method) (nexus.qmcpack.Qmcpack method) (nexus.simulation.Simulation method) filter_raw_data() (nexus.observables.MomentumDistribution method) finalize() (nexus.pwscf_data_reader.QEXML method) find() (nexus.fileio.TextFile method) find_class() (nexus.generic.NexusUnpickler method) find_pair() (in module nexus.xmlreader) find_r_rng() (nexus.pseudopotential.SemilocalPP method) find_rcut() (nexus.pseudopotential.SemilocalPP method) finished (nexus.simulation.DynamicProcess property) first() (nexus.generic.obj method) Flerovium (nexus.periodic_table.Elements attribute) Flight (class in nexus.machines) float_diff() (in module nexus.testing) floats (nexus.pwscf_input.PwscfInputBase attribute) Fluorine (nexus.periodic_table.Elements attribute) flush() (nexus.fileio.TextFile method) fm (nexus.unit_converter.UnitConverter attribute) fold() (nexus.structure.Structure method) fold_pos() (nexus.structure.Structure method) force_dict (nexus.unit_converter.UnitConverter attribute) form_diagnostic_data() (nexus.qmcpack_quantity_analyzers.TracesAnalyzer method) (nexus.qmcpack_quantity_analyzers.TracesFileHDF method) formats (nexus.basisset.GaussianBasisSet attribute) (nexus.pseudopotential.GaussianPP attribute) (nexus.pseudopotential.Pseudopotential attribute) (nexus.pseudopotential.SemilocalPP attribute) (nexus.rmg_input.AtomsKeyword attribute) formatted_groups (nexus.gamess_input.GamessInput attribute) FormattedGroup (class in nexus.gamess_input) FormattedRmgKeyword (class in nexus.rmg_input) FormattedTableRmgKeyword (class in nexus.rmg_input) formed_diagnostic_data() (nexus.qmcpack_quantity_analyzers.TracesFileHDF method) found_attribute() (nexus.xmlreader.XMLreader method) found_element_end() (nexus.xmlreader.XMLreader method) found_element_start() (nexus.xmlreader.XMLreader method) found_text() (nexus.xmlreader.XMLreader method) Francium (nexus.periodic_table.Elements attribute) freeze() (nexus.structure.Structure method) Frontier (class in nexus.machines) fs (nexus.unit_converter.UnitConverter attribute) full_mode() (nexus.rmg_input.RmgCalcModes method) func_fit() (in module nexus.numerics) G g (nexus.gamess_input.GamessInput attribute) Gadolinium (nexus.periodic_table.Elements attribute) Gallium (nexus.periodic_table.Elements attribute) Gamess (class in nexus.gamess) GamessAnalyzer (class in nexus.gamess_analyzer) gamessBasisFile (class in nexus.basisset) GamessInput (class in nexus.gamess_input) gamessPPFile (class in nexus.pseudopotential) gaussBasisFile (class in nexus.basisset) GaussianBasisSet (class in nexus.basisset) GaussianPP (class in nexus.pseudopotential) gc (nexus.nexus_base.NexusCore attribute) GCTA (class in nexus.qmcpack) gcta_converter_kmapping() (nexus.qmcpack.GCTA method) gen_calculations() (nexus.qmcpack_input.QmcpackInput method) gen_jastrows() (nexus.qmcpack_input.QmcpackInput method) generate_any_gamess_input() (in module nexus.gamess_input) generate_any_pwscf_input() (in module nexus.pwscf_input) generate_any_rmg_input() (in module nexus.rmg_input) generate_any_vasp_input() (in module nexus.vasp_input) generate_atom_structure() (in module nexus.structure) generate_bands() (in module nexus.pwscf_postprocessors) generate_bands_input (in module nexus.pwscf_postprocessors) generate_basic_afqmc_input() (in module nexus.qmcpack_input) generate_basic_input() (in module nexus.qmcpack_input) generate_batched_dmc_calculations() (in module nexus.qmcpack_input) generate_batched_opt_calculations() (in module nexus.qmcpack_input) generate_batched_vmc_calculations() (in module nexus.qmcpack_input) generate_bspline_builder() (in module nexus.qmcpack_input) generate_bspline_jastrow2() (in module nexus.qmcpack_input) generate_cell() (in module nexus.structure) generate_cppp() (in module nexus.pwscf_postprocessors) generate_cppp_input (in module nexus.pwscf_postprocessors) generate_crystal_structure() (in module nexus.structure) generate_cusp_correction() (in module nexus.qmcpack) generate_defect_structure() (in module nexus.structure) generate_determinantset() (in module nexus.qmcpack_input) generate_determinantset_old() (in module nexus.qmcpack_input) generate_dimer_structure() (in module nexus.structure) generate_dmc_calculations() (in module nexus.qmcpack_input) generate_dos() (in module nexus.pwscf_postprocessors) generate_dos_input (in module nexus.pwscf_postprocessors) generate_electrons() (nexus.physical_system.PhysicalSystem method) generate_energydensity() (in module nexus.qmcpack_input) generate_estimators_batched() (in module nexus.qmcpack_input) generate_filenames() (nexus.qmcpack_input.BundledQmcpackInput method) (nexus.qmcpack_input.TracedQmcpackInput method) generate_gamess() (in module nexus.gamess) generate_gamess_input() (in module nexus.gamess_input) generate_hamiltonian() (in module nexus.qmcpack_input) generate_heg_builder() (in module nexus.qmcpack_input) generate_hp() (in module nexus.pwscf_postprocessors) generate_hp_input() (in module nexus.pwscf_postprocessors) generate_jastrow() (in module nexus.qmcpack_input) generate_jastrow1() (in module nexus.qmcpack_input) generate_jastrow2() (in module nexus.qmcpack_input) generate_jastrow3() (in module nexus.qmcpack_input) generate_jastrows() (in module nexus.qmcpack_input) (nexus.qmcpack_input.QmcpackInput method) generate_jastrows_alt() (in module nexus.qmcpack_input) generate_jellium_structure() (in module nexus.structure) generate_jobid() (nexus.machines.Job static method) generate_kspace_jastrow() (in module nexus.qmcpack_input) generate_legacy_dmc_calculations() (in module nexus.qmcpack_input) generate_legacy_opt_calculations() (in module nexus.qmcpack_input) generate_legacy_vmc_calculations() (in module nexus.qmcpack_input) generate_multi_template_input() (in module nexus.simulation) generate_nscf_input() (in module nexus.pwscf_input) generate_opt() (in module nexus.qmcpack_input) generate_opt_calculations() (in module nexus.qmcpack_input) generate_opt_jastrow_input() (in module nexus.qmcpack_input) generate_opts() (in module nexus.qmcpack_input) generate_pade_jastrow2() (in module nexus.qmcpack_input) generate_particlesets() (in module nexus.qmcpack_input) generate_physical_system() (in module nexus.physical_system) generate_poscar() (in module nexus.vasp_input) generate_pp() (in module nexus.pwscf_postprocessors) generate_pp_input (in module nexus.pwscf_postprocessors) generate_ppsim() (in module nexus.pwscf_postprocessors) generate_projwfc() (in module nexus.pwscf_postprocessors) generate_projwfc_input() (in module nexus.pwscf_postprocessors) generate_pwexport() (in module nexus.pwscf_postprocessors) generate_pwexport_input (in module nexus.pwscf_postprocessors) generate_pwscf() (in module nexus.pwscf) generate_pwscf_input() (in module nexus.pwscf_input) generate_pyscf() (in module nexus.pyscf_sim) generate_pyscf_input() (in module nexus.pyscf_input) generate_qmcpack() (in module nexus.qmcpack) generate_qmcpack_input() (in module nexus.qmcpack_input) generate_quantum_package() (in module nexus.quantum_package) generate_quantum_package_input() (in module nexus.quantum_package_input) generate_relax_input() (in module nexus.pwscf_input) generate_rmg() (in module nexus.rmg) generate_rmg_input() (in module nexus.rmg_input) generate_scf_input() (in module nexus.pwscf_input) generate_simulation() (in module nexus.simulation) generate_simulationcell() (in module nexus.qmcpack_input) generate_sposet_builder() (in module nexus.qmcpack_input) generate_sposets() (in module nexus.qmcpack_input) generate_structure() (in module nexus.structure) generate_template_input() (in module nexus.simulation) generate_trimer_structure() (in module nexus.structure) generate_vasp() (in module nexus.vasp) generate_vasp_input() (in module nexus.vasp_input) generate_vcrelax_input() (in module nexus.pwscf_input) generate_vmc_calculations() (in module nexus.qmcpack_input) generic_identifier (nexus.bundle.SimulationBundle attribute) (nexus.gamess.Gamess attribute) (nexus.pwscf.Pwscf attribute) (nexus.pwscf_postprocessors.Bands attribute) (nexus.pwscf_postprocessors.Cppp attribute) (nexus.pwscf_postprocessors.Dos attribute) (nexus.pwscf_postprocessors.Hp attribute) (nexus.pwscf_postprocessors.PP attribute) (nexus.pwscf_postprocessors.Projwfc attribute) (nexus.pwscf_postprocessors.Pwexport attribute) (nexus.pyscf_sim.Pyscf attribute) (nexus.qmcpack.Qmcpack attribute) (nexus.quantum_package.QuantumPackage attribute) (nexus.rmg.Rmg attribute) (nexus.simulation.Simulation attribute) (nexus.vasp.Vasp attribute) generic_settings (class in nexus.generic) GenericSimulation (class in nexus.simulation) GenericSimulationInput (class in nexus.simulation) Germanium (nexus.periodic_table.Elements attribute) get() (nexus.generic.obj method) (nexus.machines.Machine static method) (nexus.physical_system.Particles method) (nexus.pseudopotential.PPset method) (nexus.qmcpack_input.QIxml method) (nexus.qmcpack_input.QmcpackInput method) (nexus.qmcpack_input.QmcpackInputCollections method) (nexus.quantum_package_input.QuantumPackageInput method) get_atomic_numbers() (nexus.structure.Structure method) get_attribute() (nexus.observables.DefinedAttributeBase method) get_band_tiling() (in module nexus.structure) get_base() (nexus.qmcpack_input.QmcpackInput method) get_basename() (nexus.qmcpack_input.QmcpackInput method) get_basis() (nexus.pseudopotential.GaussianPP method) get_calculations() (nexus.qmcpack_input.QmcpackInput method) get_cell() (nexus.structure.Structure method) get_children() (in module nexus.memory) get_common_vars() (nexus.pwscf_input.PwscfInput method) get_component() (nexus.pseudopotential.SemilocalPP method) get_conventional_cell() (in module nexus.structure) get_cpu_cores() (in module nexus.machines) get_density() (nexus.fileio.XsfFile method) get_dependencies() (nexus.bundle.SimulationBundle method) (nexus.simulation.Simulation method) get_driver() (nexus.qmcpack_input.QmcpackInput method) get_electron_particle_set() (nexus.qmcpack_input.QmcpackInput method) get_electrons() (nexus.physical_system.Particles method) get_host() (nexus.qmcpack_input.QIxml method) (nexus.qmcpack_input.QmcpackInput method) get_hostname() (nexus.machines.Machine static method) get_ion_particlesets() (nexus.qmcpack_input.QmcpackInput method) get_ions() (nexus.physical_system.Particles method) get_jastrows() (nexus.qmcpack_input.QmcpackInput method) get_keys() (nexus.hdfreader.HDFgroup method) get_kpath() (in module nexus.structure) get_L2() (nexus.pseudopotential.SemilocalPP method) get_line() (nexus.vasp_analyzer.VaspLines method) get_line_ahead() (nexus.vasp_analyzer.VaspLines method) get_local() (nexus.pseudopotential.SemilocalPP method) get_machine() (in module nexus.machines) (nexus.machines.Job method) get_machine_name() (in module nexus.machines) get_magnetic_moments() (nexus.structure.Structure method) get_multidet() (nexus.qmcpack_input.QmcpackInput method) get_nblocks_exclude() (nexus.qmcpack_quantity_analyzers.DmcDatAnalyzer method) (nexus.qmcpack_quantity_analyzers.QuantityAnalyzer method) get_nonlocal() (nexus.pseudopotential.SemilocalPP method) get_number_of_atoms() (nexus.structure.Structure method) get_optional() (nexus.generic.obj method) get_output() (nexus.bundle.SimulationBundle method) (nexus.gamess_analyzer.GamessAnalyzer method) (nexus.simulation.Simulation method) get_output_files() (nexus.bundle.SimulationBundle method) (nexus.gamess.Gamess method) (nexus.pwscf.Pwscf method) (nexus.pwscf_postprocessors.PostProcessSimulation method) (nexus.pyscf_sim.Pyscf method) (nexus.qmcpack.Qmcpack method) (nexus.quantum_package.QuantumPackage method) (nexus.rmg.Rmg method) (nexus.simulation.GenericSimulation method) (nexus.simulation.Simulation method) (nexus.vasp.Vasp method) get_output_info() (nexus.qmcpack_input.BundledQmcpackInput method) (nexus.qmcpack_input.QmcpackInput method) (nexus.qmcpack_input.QmcpackInputTemplate method) get_particle() (nexus.physical_system.Particles method) get_path() (nexus.generic.obj method) (nexus.vasp_input.Vobj method) get_pp_files() (nexus.qmcpack_input.QmcpackInput method) get_precision() (nexus.qmcpack_input.QIxml method) get_primitive_cell() (in module nexus.structure) get_qmc() (nexus.qmcpack_input.QmcpackInput method) get_raw_data() (nexus.observables.MomentumDistribution method) get_required() (nexus.generic.obj method) get_result() (nexus.gamess.Gamess method) (nexus.pwscf.Pwscf method) (nexus.pwscf_postprocessors.Hp method) (nexus.pyscf_sim.Pyscf method) (nexus.qmcpack.Qmcpack method) (nexus.quantum_package.QuantumPackage method) (nexus.rmg.Rmg method) (nexus.simulation.Simulation method) (nexus.vasp.Vasp method) get_scaled_positions() (nexus.structure.Structure method) get_seekpath_full() (in module nexus.structure) get_single() (nexus.qmcpack_input.collection method) (nexus.qmcpack_input.QIxml method) get_slave() (nexus.quantum_package.QuantumPackage method) get_smallest() (nexus.physical_system.PhysicalSystem method) (nexus.structure.Structure method) get_specifier() (nexus.pwscf_input.Card method) get_structure_with_bands() (in module nexus.structure) get_symmetry() (in module nexus.structure) (nexus.structure.Structure method) get_symmetry_dataset() (nexus.structure.Structure method) get_time() (nexus.machines.Job method) get_unboundedness() (nexus.pseudopotential.GaussianPP method) Ghost (class in nexus.machines) ghost_atoms() (in module nexus.physical_system) GIarray (class in nexus.gamess_input) GIbase (class in nexus.gamess_input) gigapascal (nexus.unit_converter.UnitConverter attribute) gname (nexus.gamess_input.GamessInput attribute) Gold (nexus.periodic_table.Elements attribute) Golub (class in nexus.machines) got_output (nexus.simulation.DynamicProcess property) GPa (nexus.unit_converter.UnitConverter attribute) gpu_machine (nexus.machines.Hops attribute) (nexus.machines.SnlMachine attribute) gpus_per_node (nexus.machines.Hops attribute) graph_sims() (in module nexus.simulation) Group (class in nexus.gamess_input) group (nexus.periodic_table.ElementData attribute) group_aliases (nexus.gamess_input.GamessInput attribute) group_atoms() (nexus.physical_system.PhysicalSystem method) (nexus.structure.Structure method) group_keyword_overlap (nexus.gamess_input.GamessInput attribute) group_order (nexus.gamess_input.GamessInput attribute) GuessGroup (class in nexus.gamess_input) GugdiaGroup (class in nexus.gamess_input) H Ha (nexus.unit_converter.UnitConverter attribute) Hafnium (nexus.periodic_table.Elements attribute) hartree (nexus.unit_converter.UnitConverter attribute) has_afqmc_input() (nexus.qmcpack.Qmcpack method) has_animation() (nexus.fileio.XsfFile method) has_attribute() (nexus.observables.DefinedAttributeBase method) has_axes() (nexus.structure.Structure method) has_bands() (nexus.fileio.XsfFile method) has_calculations() (nexus.qmcpack_input.QmcpackInput method) has_component() (nexus.pseudopotential.SemilocalPP method) has_data() (nexus.fileio.XsfFile method) has_energy_matrix() (nexus.qmcpack_quantity_analyzers.DensityMatricesAnalyzer method) has_folded() (nexus.physical_system.PhysicalSystem method) (nexus.structure.Structure method) has_folded_structure() (nexus.structure.Structure method) has_generic_input() (nexus.simulation.Simulation method) has_jastrows() (nexus.qmcpack_input.QmcpackInput method) has_L2() (nexus.pseudopotential.SemilocalPP method) has_lcao_orbitals() (nexus.qmcpack_input.QmcpackInput method) has_local() (nexus.pseudopotential.SemilocalPP method) has_multidet() (nexus.qmcpack_input.QmcpackInput method) has_nonlocal() (nexus.pseudopotential.SemilocalPP method) has_qmc() (nexus.qmcpack_input.QmcpackInput method) has_set() (nexus.pseudopotential.PPset method) has_structure() (nexus.fileio.XsfFile method) has_tmatrix() (nexus.structure.Structure method) Hassium (nexus.periodic_table.Elements attribute) HDFAnalyzer (class in nexus.qmcpack_quantity_analyzers) HDFglobals (class in nexus.hdfreader) HDFgroup (class in nexus.hdfreader) HDFreader (class in nexus.hdfreader) Helium (nexus.periodic_table.Elements attribute) hidden (class in nexus.generic) hidden() (nexus.generic.hidden method) hobj (class in nexus.generic) Holmium (nexus.periodic_table.Elements attribute) Hops (class in nexus.machines) Hp (class in nexus.pwscf_postprocessors) HpAnalyzer (class in nexus.pwscf_postprocessors) HpInput (class in nexus.pwscf_postprocessors) HpNamelist (class in nexus.pwscf_postprocessors) hubbard (class in nexus.pwscf_input) HubbardUKeyword (class in nexus.rmg_input) Hydrogen (nexus.periodic_table.Elements attribute) I i (nexus.pseudopotential.SemilocalPP attribute) (nexus.qmcpack_input.Names attribute) (nexus.qmcpack_quantity_analyzers.SpaceGridBase attribute) ICMP_Machine (class in nexus.machines) Iconst (class in nexus.vasp_input) identifier (nexus.simulation.DynamicProcess property) idstr() (nexus.simulation.Simulation method) ilast_functions (nexus.vasp_analyzer.OutcarData attribute) image_directory (nexus.bundle.SimulationBundle attribute) (nexus.simulation.Simulation attribute) Improv (class in nexus.machines) in_batch_mode() (nexus.machines.Machine method) Incar (class in nexus.vasp_input) include_files() (nexus.xmlreader.XMLreader method) include_xml() (nexus.qmcpack_input.QmcpackInput method) incorporate() (nexus.basisset.GaussianBasisSet method) (nexus.structure.Structure method) incorporate_defaults() (nexus.qmcpack_input.QIxml method) (nexus.qmcpack_input.QmcpackInput method) incorporate_hubbard() (nexus.pwscf_input.PwscfInput method) incorporate_result() (nexus.gamess.Gamess method) (nexus.pwscf.Pwscf method) (nexus.pyscf_sim.Pyscf method) (nexus.qmcpack.Qmcpack method) (nexus.quantum_package.QuantumPackage method) (nexus.rmg.Rmg method) (nexus.simulation.Simulation method) (nexus.vasp.Vasp method) incorporate_structure() (nexus.fileio.XsfFile method) incorporate_system() (nexus.gamess_input.GamessInput method) (nexus.pwscf_input.PwscfInput method) (nexus.qmcpack_input.QmcpackInput method) (nexus.quantum_package_input.QuantumPackageInput method) (nexus.simulation.NullSimulationInput method) (nexus.simulation.SimulationInput method) (nexus.vasp_input.VaspInput method) incorporate_system_old() (nexus.pwscf_input.PwscfInput method) incorporate_user_info() (nexus.machines.Machine method) incorporate_xsf() (nexus.fileio.ChgcarFile method) (nexus.fileio.PoscarFile method) increment() (nexus.observables.VLog method) increment_level() (nexus.hdfreader.HDFreader method) (nexus.xmlreader.XMLreader method) index_by_layer_1d() (in module nexus.numerics) Indium (nexus.periodic_table.Elements attribute) infile_extension (nexus.gamess.Gamess attribute) (nexus.pyscf_sim.Pyscf attribute) (nexus.qmcpack.Qmcpack attribute) (nexus.quantum_package.QuantumPackage attribute) (nexus.simulation.Simulation attribute) init_cascades() (nexus.project_manager.ProjectManager method) init_class() (nexus.qmcpack_input.Param method) (nexus.qmcpack_input.QIxml class method) (nexus.qmcpack_input.QIxmlFactory method) init_from_args() (nexus.machines.InteractiveCluster method) (nexus.qmcpack_input.QIxml method) init_from_hdfgroup() (nexus.qmcpack_quantity_analyzers.RectilinearGrid method) (nexus.qmcpack_quantity_analyzers.SpaceGridBase method) init_from_initializer() (nexus.qmcpack_quantity_analyzers.RectilinearGrid method) (nexus.qmcpack_quantity_analyzers.SpaceGridBase method) init_from_inputs() (nexus.qmcpack_input.QIxml method) init_from_kwargs() (nexus.qmcpack_input.QIxml method) init_from_spacegrid() (nexus.qmcpack_quantity_analyzers.RectilinearGrid method) (nexus.qmcpack_quantity_analyzers.SpaceGridBase method) init_from_supercomputer() (nexus.machines.InteractiveCluster method) init_from_xml() (nexus.qmcpack_input.QIxml method) init_from_xmlelement() (nexus.qmcpack_quantity_analyzers.RectilinearGrid method) (nexus.qmcpack_quantity_analyzers.SpaceGridBase method) init_job() (nexus.simulation.Simulation method) init_job_extra() (nexus.gamess.Gamess method) (nexus.simulation.Simulation method) init_special() (nexus.qmcpack_quantity_analyzers.RectilinearGrid method) (nexus.qmcpack_quantity_analyzers.SpaceGridBase method) init_sub_analyzers() (nexus.qmcpack_analyzer.QmcpackAnalyzer method) (nexus.qmcpack_method_analyzers.MethodAnalyzer method) (nexus.qmcpack_method_analyzers.OptAnalyzer method) (nexus.qmcpack_quantity_analyzers.QuantityAnalyzer method) (nexus.qmcpack_quantity_analyzers.TracesAnalyzer method) (nexus.qmcpack_result_analyzers.OptimizationAnalyzer method) (nexus.qmcpack_result_analyzers.TimestepStudyAnalyzer method) init_trace() (nexus.qmcpack_quantity_analyzers.TracesFileHDF method) initialize() (nexus.machines.Job method) (nexus.observables.DefinedAttributeBase method) (nexus.observables.Observable method) (nexus.qmcpack_quantity_analyzers.RectilinearGrid method) initialized (nexus.rmg_analyzer.RmgAnalyzer property) initialized() (nexus.fileio.XsfFile method) input (nexus.simulation.DynamicProcess property) input_files (nexus.vasp_input.VaspInput attribute) input_imagefile (nexus.simulation.Simulation attribute) input_template() (in module nexus.simulation) input_template_dev() (in module nexus.simulation) input_type (nexus.bundle.SimulationBundle attribute) (nexus.gamess.Gamess attribute) (nexus.pwscf.Pwscf attribute) (nexus.pwscf_postprocessors.Bands attribute) (nexus.pwscf_postprocessors.Cppp attribute) (nexus.pwscf_postprocessors.Dos attribute) (nexus.pwscf_postprocessors.Hp attribute) (nexus.pwscf_postprocessors.PP attribute) (nexus.pwscf_postprocessors.Projwfc attribute) (nexus.pwscf_postprocessors.Pwexport attribute) (nexus.pyscf_sim.Pyscf attribute) (nexus.qmcpack.Qmcpack attribute) (nexus.quantum_package.QuantumPackage attribute) (nexus.rmg.Rmg attribute) (nexus.simulation.Simulation attribute) (nexus.vasp.Vasp attribute) inside() (nexus.structure.Structure method) instance_counter (nexus.pseudopotential.PPset attribute) int_arrays (nexus.vasp_input.Incar attribute) (nexus.vasp_input.Stopcar attribute) int_kpoint_weight() (nexus.qmcpack.GCTA static method) integers (nexus.gamess_input.BasisGroup attribute) (nexus.gamess_input.CidrtGroup attribute) (nexus.gamess_input.ContrlGroup attribute) (nexus.gamess_input.DetGroup attribute) (nexus.gamess_input.DftGroup attribute) (nexus.gamess_input.DrtGroup attribute) (nexus.gamess_input.GuessGroup attribute) (nexus.gamess_input.GugdiaGroup attribute) (nexus.gamess_input.KeywordSpecGroup attribute) (nexus.gamess_input.McscfGroup attribute) (nexus.gamess_input.ScfGroup attribute) (nexus.gamess_input.SystemGroup attribute) integrate() (nexus.qmcpack_quantity_analyzers.SpaceGridBase method) integrate_data() (nexus.qmcpack_quantity_analyzers.SpaceGridBase method) interact() (in module nexus.debug) interactive_representation() (nexus.machines.Supercomputer method) InteractiveCluster (class in nexus.machines) interpolatable (nexus.pseudopotential.CasinoPP attribute) (nexus.pseudopotential.QmcpackPP attribute) (nexus.pseudopotential.SemilocalPP attribute) interpolate() (nexus.qmcpack_property_analyzers.RadialJastrow method) (nexus.qmcpack_quantity_analyzers.RectilinearGrid method) (nexus.structure.Structure method) interpolate_across() (nexus.qmcpack_quantity_analyzers.RectilinearGrid method) interpolate_plane() (nexus.fileio.XsfFile method) interpolate_structures() (in module nexus.structure) Inti (class in nexus.machines) ints (nexus.pwscf_input.PwscfInputBase attribute) (nexus.vasp_input.Incar attribute) (nexus.vasp_input.Stopcar attribute) inverse() (nexus.generic.obj method) inversion_symmetrize_kpoints() (nexus.structure.Structure method) Iodine (nexus.periodic_table.Elements attribute) Ion (class in nexus.physical_system) ions (class in nexus.pwscf_input) Iridium (nexus.periodic_table.Elements attribute) Iron (nexus.periodic_table.Elements attribute) is_afqmc_input() (nexus.qmcpack_input.QmcpackInput method) is_array() (in module nexus.qmcpack_input) is_bundle (nexus.bundle.SimulationBundle attribute) (nexus.simulation.Simulation attribute) is_consistent() (nexus.gamess_input.KeywordSpecGroup method) is_element() (nexus.periodic_table.Elements static method) (nexus.physical_system.Matter method) is_empty() (nexus.vasp_input.VFormattedFile method) is_float() (in module nexus.qmcpack_input) is_frozen() (nexus.structure.Structure method) is_full_mode() (nexus.rmg_input.RmgCalcModes method) is_int() (in module nexus.qmcpack_input) is_integer() (in module nexus.qmcpack_quantity_analyzers) is_magnetic() (nexus.physical_system.PhysicalSystem method) (nexus.structure.Structure method) is_number() (in module nexus.pwscf_analyzer) is_open() (nexus.structure.Structure method) is_periodic() (nexus.structure.Structure method) is_relative_path() (in module nexus.utilities) is_short_mode() (nexus.rmg_input.RmgCalcModes method) is_tiled() (nexus.structure.Structure method) is_truncated_L2() (nexus.pseudopotential.GaussianPP method) is_unique() (nexus.machines.Machine static method) is_valid() (nexus.fileio.StandardFile method) (nexus.gamess_input.KeywordSpecGroup method) (nexus.physical_system.PhysicalSystem method) (nexus.quantum_package_input.QuantumPackageInput method) (nexus.rmg_input.RmgInput method) (nexus.simulation.NullSimulationInput method) (nexus.simulation.SimulationInput method) is_valid_filename() (in module nexus.utilities) is_valid_path() (in module nexus.utilities) isosurface() (nexus.qmcpack_quantity_analyzers.EnergyDensityAnalyzer method) (nexus.qmcpack_quantity_analyzers.RectilinearGrid method) isotopes (nexus.periodic_table.ElementData attribute) items() (nexus.generic.hobj method) (nexus.generic.object_interface method) J J (nexus.unit_converter.UnitConverter attribute) jackknife() (in module nexus.numerics) jackknife_aux() (in module nexus.numerics) Jaguar (class in nexus.machines) jastrow (nexus.simulation.DynamicProcess property) Jastrow1B (class in nexus.qmcpack_property_analyzers) Jastrow2B (class in nexus.qmcpack_property_analyzers) jastrow_types (nexus.qmcpack_property_analyzers.WavefunctionAnalyzer attribute) Jellium (class in nexus.structure) Job (class in nexus.machines) job (in module nexus.machines) (nexus.simulation.DynamicProcess property) job_command() (nexus.machines.Workstation method) job_count (nexus.machines.Job attribute) join() (nexus.vasp_input.VFormattedFile method) joule (nexus.unit_converter.UnitConverter attribute) K k (nexus.pyscf_input.PyscfInput attribute) K (nexus.unit_converter.UnitConverter attribute) k_points (class in nexus.pwscf_input) Kagayaki (class in nexus.machines) kb (nexus.unit_converter.UnitConverter attribute) kcal_mol (nexus.unit_converter.UnitConverter attribute) kcal_mole (nexus.unit_converter.UnitConverter attribute) kelvin (nexus.unit_converter.UnitConverter attribute) Kestrel (class in nexus.machines) key_groups (nexus.gamess_input.GamessInput attribute) keys() (nexus.generic.hobj method) (nexus.generic.object_interface method) keyspec_group_order (nexus.gamess_input.GamessInput attribute) keyspec_groups (nexus.gamess_input.GamessInput attribute) keyword_classification (nexus.vasp_input.Incar attribute) (nexus.vasp_input.VKeywordFile attribute) keyword_files (nexus.vasp_input.VaspInput attribute) KeywordGroup (class in nexus.gamess_input) keywords (nexus.gamess_input.BasisGroup attribute) (nexus.gamess_input.CidrtGroup attribute) (nexus.gamess_input.ContrlGroup attribute) (nexus.gamess_input.DetGroup attribute) (nexus.gamess_input.DftGroup attribute) (nexus.gamess_input.DrtGroup attribute) (nexus.gamess_input.GuessGroup attribute) (nexus.gamess_input.GugdiaGroup attribute) (nexus.gamess_input.KeywordSpecGroup attribute) (nexus.gamess_input.McscfGroup attribute) (nexus.gamess_input.ScfGroup attribute) (nexus.gamess_input.SystemGroup attribute) (nexus.vasp_input.Incar attribute) (nexus.vasp_input.Stopcar attribute) KeywordSpecGroup (class in nexus.gamess_input) kf_rpa() (nexus.physical_system.PhysicalSystem method) kfold() (nexus.structure.Structure method) kg (nexus.unit_converter.UnitConverter attribute) kgrid_from_kspacing() (nexus.structure.Structure method) kilogram (nexus.unit_converter.UnitConverter attribute) kJ_mol (nexus.unit_converter.UnitConverter attribute) kJ_mole (nexus.unit_converter.UnitConverter attribute) kmap() (nexus.structure.Structure method) kmesh() (in module nexus.structure) known_codes (nexus.pseudopotential.PPset attribute) known_crystals (nexus.structure.Crystal attribute) Komodo (class in nexus.machines) Kpoints (class in nexus.vasp_input) kpoints_qmcpack() (nexus.structure.Structure method) kpoints_reduced() (nexus.structure.Structure method) kpoints_unit() (nexus.structure.Structure method) KpointsBandstructureKeyword (class in nexus.rmg_input) KpointsKeyword (class in nexus.rmg_input) Kraken (class in nexus.machines) Krypton (nexus.periodic_table.Elements attribute) kw_arrays (nexus.vasp_input.Incar attribute) (nexus.vasp_input.Stopcar attribute) kw_fields (nexus.vasp_input.Incar attribute) (nexus.vasp_input.Stopcar attribute) kw_scalars (nexus.vasp_input.Incar attribute) (nexus.vasp_input.Stopcar attribute) L l (nexus.gamess_analyzer.GamessAnalyzer attribute) l_channels (nexus.pseudopotential.SemilocalPP attribute) label_to_potcar_name() (nexus.vasp_input.Potcar method) Lanthanum (nexus.periodic_table.Elements attribute) large_Zeff_elem() (nexus.physical_system.PhysicalSystem method) Lassen (class in nexus.machines) last() (nexus.generic.obj method) lattice (nexus.structure.Crystal attribute) lattice_centerings (nexus.structure.Crystal attribute) lattice_constants (nexus.structure.Crystal attribute) lattices (nexus.structure.Crystal attribute) Lawrencium (nexus.periodic_table.Elements attribute) layer_composition() (nexus.structure.Structure method) layer_means_1d() (in module nexus.numerics) layers() (nexus.structure.Structure method) layers_1d() (in module nexus.numerics) lbasis() (nexus.basisset.GaussianBasisSet method) lcount() (nexus.basisset.GaussianBasisSet method) Lead (nexus.periodic_table.Elements attribute) least_squares() (in module nexus.numerics) leave() (nexus.nexus_base.NexusCore method) Leonardo (class in nexus.machines) line_data() (nexus.fileio.XsfFile method) line_plot() (nexus.fileio.XsfFile method) lineindent (nexus.gamess_input.KeywordGroup attribute) lines() (nexus.fileio.TextFile method) linewrap (nexus.gamess_input.KeywordGroup attribute) list() (nexus.gamess_input.CardGroup method) (nexus.generic.obj method) (nexus.qmcpack_input.collection method) list_optional() (nexus.generic.obj method) Lithium (nexus.periodic_table.Elements attribute) Livermorium (nexus.periodic_table.Elements attribute) ll_walltime() (nexus.machines.Job method) load() (nexus.generic.object_interface method) (nexus.physical_system.PhysicalSystem method) (nexus.qmcpack_analyzer.QmcpackAnalyzer method) (nexus.qmcpack_quantity_analyzers.TracesFileHDF method) (nexus.vasp_input.Potcar method) load_analyzer_image() (nexus.simulation.Simulation method) load_cascades() (nexus.project_manager.ProjectManager method) load_data() (nexus.qmcpack_analyzer.QmcpackAnalyzer method) load_data_local() (nexus.qmcpack_method_analyzers.MethodAnalyzer method) (nexus.qmcpack_property_analyzers.WavefunctionAnalyzer method) (nexus.qmcpack_quantity_analyzers.DensityAnalyzer method) (nexus.qmcpack_quantity_analyzers.DensityMatricesAnalyzer method) (nexus.qmcpack_quantity_analyzers.DmcDatAnalyzer method) (nexus.qmcpack_quantity_analyzers.EnergyDensityAnalyzer method) (nexus.qmcpack_quantity_analyzers.ScalarsDatAnalyzer method) (nexus.qmcpack_quantity_analyzers.ScalarsHDFAnalyzer method) (nexus.qmcpack_quantity_analyzers.SpinDensityAnalyzer method) (nexus.qmcpack_quantity_analyzers.StructureFactorAnalyzer method) (nexus.qmcpack_quantity_analyzers.TracesAnalyzer method) load_fields (nexus.simulation.SimulationImage attribute) load_image() (nexus.simulation.Simulation method) (nexus.simulation.SimulationImage method) load_jastrow_data() (nexus.qmcpack_property_analyzers.WavefunctionAnalyzer method) loaded() (nexus.qmcpack_quantity_analyzers.TracesFileHDF method) locate() (nexus.structure.Structure method) locate_simple() (nexus.structure.Structure method) log() (in module nexus.generic) (nexus.generic.hidden method) (nexus.generic.object_interface method) (nexus.nexus_base.NexusCore method) Lonestar (class in nexus.machines) lset() (nexus.basisset.GaussianBasisSet method) lset_full (nexus.basisset.GaussianBasisSet attribute) (nexus.gamess_analyzer.GamessAnalyzer attribute) lsf_walltime() (nexus.machines.Job method) lsort() (nexus.basisset.GaussianBasisSet method) lstyles (nexus.basisset.GaussianBasisSet attribute) Lutetium (nexus.periodic_table.Elements attribute) lxyz (nexus.gamess_analyzer.GamessAnalyzer attribute) lxyz_reverse (nexus.gamess_analyzer.GamessAnalyzer attribute) M m (nexus.unit_converter.UnitConverter attribute) Machine (class in nexus.machines) machine (nexus.machines.Job attribute) (nexus.project_manager.ProjectManager attribute) machines (nexus.machines.Machine attribute) madelung() (nexus.structure.Structure method) madmin() (in module nexus.numerics) Magnesium (nexus.periodic_table.Elements attribute) make_collection() (in module nexus.qmcpack_input) make_L2_bounded() (nexus.pseudopotential.GaussianPP method) make_movie() (nexus.pwscf_analyzer.PwscfAnalyzer method) makov_payne() (nexus.structure.Structure method) Manganese (nexus.periodic_table.Elements attribute) Manzano (class in nexus.machines) map_raw_data_onto_grid() (nexus.observables.MomentumDistribution method) MaskFilter (class in nexus.structure) mass_dict (nexus.unit_converter.UnitConverter attribute) Matisse (class in nexus.machines) matrix_transform() (nexus.structure.Structure method) Matter (class in nexus.physical_system) max_time() (nexus.machines.Job method) Mbar (nexus.unit_converter.UnitConverter attribute) mcppath (nexus.gamess.Gamess attribute) McscfGroup (class in nexus.gamess_input) md_plots() (nexus.pwscf_analyzer.PwscfAnalyzer method) md_statistics() (nexus.pwscf_analyzer.PwscfAnalyzer method) me (nexus.unit_converter.UnitConverter attribute) megabar (nexus.unit_converter.UnitConverter attribute) Meitnerium (nexus.periodic_table.Elements attribute) mem_usage() (nexus.nexus_base.NexusCore method) memory() (in module nexus.memory) Mendelevium (nexus.periodic_table.Elements attribute) Mercury (nexus.periodic_table.Elements attribute) mesh() (nexus.qmcpack_quantity_analyzers.EnergyDensityAnalyzer method) message() (in module nexus.generic) (nexus.gamess_input.GIbase method) meta (class in nexus.qmcpack_input) metadata (nexus.qmcpack_input.Param attribute) meter (nexus.unit_converter.UnitConverter attribute) MethodAnalyzer (class in nexus.qmcpack_method_analyzers) miller_direction() (nexus.structure.Structure method) miller_normal() (nexus.structure.Structure method) millisecond (nexus.unit_converter.UnitConverter attribute) min_image_centroid() (nexus.structure.Structure method) min_image_centroids() (nexus.structure.Structure method) min_image_distances() (nexus.structure.Structure method) min_image_norms() (nexus.structure.Structure method) min_image_vectors() (nexus.structure.Structure method) minsize() (nexus.hdfreader.HDFgroup method) minsize_data() (nexus.qmcpack_quantity_analyzers.TracesAnalyzer method) Mira (class in nexus.machines) Missing (class in nexus.observables) mode (nexus.machines.Machine attribute) (nexus.machines.Supercomputer attribute) (nexus.machines.Workstation attribute) mode_match() (nexus.rmg_input.RmgCalcModes method) modes (nexus.machines.Machine attribute) modify() (nexus.qmcpack_input.QmcpackInput method) module nexus.basisset nexus.bundle nexus.debug nexus.developer nexus.execute nexus.fileio nexus.gamess nexus.gamess_analyzer nexus.gamess_input nexus.generic nexus.hdfreader nexus.machines nexus.memory nexus.nexus_base nexus.numerics nexus.numpy_extensions nexus.observables nexus.periodic_table nexus.physical_system nexus.project_manager nexus.pseudopotential nexus.pwscf nexus.pwscf_analyzer nexus.pwscf_data_reader nexus.pwscf_input nexus.pwscf_postprocessors nexus.pyscf_analyzer nexus.pyscf_input nexus.pyscf_sim nexus.qmcpack nexus.qmcpack_analyzer nexus.qmcpack_input nexus.qmcpack_method_analyzers nexus.qmcpack_property_analyzers nexus.qmcpack_quantity_analyzers nexus.qmcpack_result_analyzers nexus.quantum_package nexus.quantum_package_analyzer nexus.quantum_package_input nexus.rmg nexus.rmg_analyzer nexus.rmg_input nexus.simulation nexus.structure nexus.testing nexus.unit_converter nexus.utilities nexus.vasp nexus.vasp_analyzer nexus.vasp_input nexus.xmlreader mol (nexus.unit_converter.UnitConverter attribute) mole_allowed (nexus.pyscf_input.PyscfInput attribute) mole_order (nexus.pyscf_input.PyscfInput attribute) Molybdenum (nexus.periodic_table.Elements attribute) MomentumDistribution (class in nexus.observables) MomentumDistributionDFT (class in nexus.observables) MomentumDistributionQMC (class in nexus.observables) morse() (in module nexus.numerics) morse_a() (in module nexus.numerics) morse_De() (in module nexus.numerics) morse_depth() (in module nexus.numerics) morse_E0() (in module nexus.numerics) morse_Ee() (in module nexus.numerics) morse_Einf() (in module nexus.numerics) morse_En() (in module nexus.numerics) morse_fit() (in module nexus.numerics) morse_fit_fine() (in module nexus.numerics) morse_freq() (in module nexus.numerics) morse_harmfreq() (in module nexus.numerics) morse_harmonic_potential() (in module nexus.numerics) morse_k() (in module nexus.numerics) morse_params() (in module nexus.numerics) morse_rDw_fit() (in module nexus.numerics) morse_re() (in module nexus.numerics) morse_reduced_mass() (in module nexus.numerics) morse_spect_fit() (in module nexus.numerics) morse_w() (in module nexus.numerics) morse_width() (in module nexus.numerics) morse_wX() (in module nexus.numerics) morse_zero_point() (in module nexus.numerics) Moscovium (nexus.periodic_table.Elements attribute) move() (nexus.fileio.TextFile method) (nexus.qmcpack_input.QIxml method) (nexus.qmcpack_input.QmcpackInput method) move_from() (nexus.generic.obj method) move_from_optional() (nexus.generic.obj method) move_to() (nexus.generic.obj method) move_to_optional() (nexus.generic.obj method) mp (nexus.unit_converter.UnitConverter attribute) ms (nexus.unit_converter.UnitConverter attribute) mtest() (nexus.qmcpack_quantity_analyzers.EnergyDensityAnalyzer method) multi_input_template() (in module nexus.simulation) multi_input_template_dev() (in module nexus.simulation) multidimensional_arrays (nexus.pwscf_input.PwscfInputBase attribute) murnaghan() (in module nexus.numerics) murnaghan_pressure() (in module nexus.numerics) N N (nexus.unit_converter.UnitConverter attribute) name (nexus.machines.Amber attribute) (nexus.machines.Amos attribute) (nexus.machines.Andes attribute) (nexus.machines.Archer2 attribute) (nexus.machines.Attaway attribute) (nexus.machines.Aurora attribute) (nexus.machines.Baseline attribute) (nexus.machines.Besms attribute) (nexus.machines.BlueWatersXE attribute) (nexus.machines.BlueWatersXK attribute) (nexus.machines.CadesMoab attribute) (nexus.machines.CadesSlurm attribute) (nexus.machines.Cetus attribute) (nexus.machines.Cooley attribute) (nexus.machines.Cori attribute) (nexus.machines.Eclipse attribute) (nexus.machines.EOS attribute) (nexus.machines.Flight attribute) (nexus.machines.Frontier attribute) (nexus.machines.Ghost attribute) (nexus.machines.Golub attribute) (nexus.machines.Hops attribute) (nexus.machines.Improv attribute) (nexus.machines.Inti attribute) (nexus.machines.Jaguar attribute) (nexus.machines.Kagayaki attribute) (nexus.machines.Kestrel attribute) (nexus.machines.Komodo attribute) (nexus.machines.Kraken attribute) (nexus.machines.Lassen attribute) (nexus.machines.Leonardo attribute) (nexus.machines.Lonestar attribute) (nexus.machines.Manzano attribute) (nexus.machines.Matisse attribute) (nexus.machines.Mira attribute) (nexus.machines.OIC5 attribute) (nexus.machines.Perlmutter attribute) (nexus.machines.Polaris attribute) (nexus.machines.Rhea attribute) (nexus.machines.Ruby attribute) (nexus.machines.Solo attribute) (nexus.machines.Stampede2 attribute) (nexus.machines.Summit attribute) (nexus.machines.Supercomputer attribute) (nexus.machines.SuperMUC attribute) (nexus.machines.SuperMUC_NG attribute) (nexus.machines.Theta attribute) (nexus.machines.Titan attribute) (nexus.machines.Tomcat3 attribute) (nexus.machines.Vesta attribute) (nexus.observables.StatFile attribute) (nexus.pwscf_input.atomic_forces attribute) (nexus.pwscf_input.atomic_positions attribute) (nexus.pwscf_input.atomic_species attribute) (nexus.pwscf_input.cell attribute) (nexus.pwscf_input.cell_parameters attribute) (nexus.pwscf_input.climbing_images attribute) (nexus.pwscf_input.collective_vars attribute) (nexus.pwscf_input.constraints attribute) (nexus.pwscf_input.control attribute) (nexus.pwscf_input.ee attribute) (nexus.pwscf_input.electrons attribute) (nexus.pwscf_input.Element attribute) (nexus.pwscf_input.hubbard attribute) (nexus.pwscf_input.ions attribute) (nexus.pwscf_input.k_points attribute) (nexus.pwscf_input.occupations attribute) (nexus.pwscf_input.phonon attribute) (nexus.pwscf_input.system attribute) (nexus.qmcpack_quantity_analyzers.SpaceGridBase attribute) (nexus.structure.Crystal attribute) name_map (nexus.pwscf_postprocessors.BandsInput attribute) (nexus.pwscf_postprocessors.CpppInput attribute) (nexus.pwscf_postprocessors.DosInput attribute) (nexus.pwscf_postprocessors.HpInput attribute) (nexus.pwscf_postprocessors.NamelistInput attribute) (nexus.pwscf_postprocessors.PPInput attribute) (nexus.pwscf_postprocessors.ProjwfcInput attribute) (nexus.pwscf_postprocessors.PwexportInput attribute) name_set (nexus.pwscf_postprocessors.BandsNamelist attribute) (nexus.pwscf_postprocessors.CpppInputppNamelist attribute) (nexus.pwscf_postprocessors.DosNamelist attribute) (nexus.pwscf_postprocessors.HpNamelist attribute) (nexus.pwscf_postprocessors.Namelist attribute) (nexus.pwscf_postprocessors.PPInputppNamelist attribute) (nexus.pwscf_postprocessors.PPPlotNamelist attribute) (nexus.pwscf_postprocessors.ProjwfcNamelist attribute) (nexus.pwscf_postprocessors.PwexportInputppNamelist attribute) Namelist (class in nexus.pwscf_postprocessors) namelist (nexus.pwscf_postprocessors.BandsNamelist attribute) (nexus.pwscf_postprocessors.CpppInputppNamelist attribute) (nexus.pwscf_postprocessors.DosNamelist attribute) (nexus.pwscf_postprocessors.HpNamelist attribute) (nexus.pwscf_postprocessors.Namelist attribute) (nexus.pwscf_postprocessors.PPInputppNamelist attribute) (nexus.pwscf_postprocessors.PPPlotNamelist attribute) (nexus.pwscf_postprocessors.ProjwfcNamelist attribute) (nexus.pwscf_postprocessors.PwexportInputppNamelist attribute) namelist_classes (nexus.pwscf_postprocessors.BandsInput attribute) (nexus.pwscf_postprocessors.CpppInput attribute) (nexus.pwscf_postprocessors.DosInput attribute) (nexus.pwscf_postprocessors.HpInput attribute) (nexus.pwscf_postprocessors.NamelistInput attribute) (nexus.pwscf_postprocessors.PPInput attribute) (nexus.pwscf_postprocessors.ProjwfcInput attribute) (nexus.pwscf_postprocessors.PwexportInput attribute) namelist_set (nexus.pwscf_postprocessors.BandsInput attribute) (nexus.pwscf_postprocessors.CpppInput attribute) (nexus.pwscf_postprocessors.DosInput attribute) (nexus.pwscf_postprocessors.HpInput attribute) (nexus.pwscf_postprocessors.NamelistInput attribute) (nexus.pwscf_postprocessors.PPInput attribute) (nexus.pwscf_postprocessors.ProjwfcInput attribute) (nexus.pwscf_postprocessors.PwexportInput attribute) NamelistInput (class in nexus.pwscf_postprocessors) namelists (nexus.pwscf_postprocessors.BandsInput attribute) (nexus.pwscf_postprocessors.CpppInput attribute) (nexus.pwscf_postprocessors.DosInput attribute) (nexus.pwscf_postprocessors.HpInput attribute) (nexus.pwscf_postprocessors.NamelistInput attribute) (nexus.pwscf_postprocessors.PPInput attribute) (nexus.pwscf_postprocessors.ProjwfcInput attribute) (nexus.pwscf_postprocessors.PwexportInput attribute) Names (class in nexus.qmcpack_input) names (nexus.pwscf_postprocessors.BandsNamelist attribute) (nexus.pwscf_postprocessors.CpppInputppNamelist attribute) (nexus.pwscf_postprocessors.DosNamelist attribute) (nexus.pwscf_postprocessors.HpNamelist attribute) (nexus.pwscf_postprocessors.Namelist attribute) (nexus.pwscf_postprocessors.PPInputppNamelist attribute) (nexus.pwscf_postprocessors.PPPlotNamelist attribute) (nexus.pwscf_postprocessors.ProjwfcNamelist attribute) (nexus.pwscf_postprocessors.PwexportInputppNamelist attribute) nanometer (nexus.unit_converter.UnitConverter attribute) nanosecond (nexus.unit_converter.UnitConverter attribute) ndgrid() (in module nexus.numerics) nearest_neighbors() (in module nexus.numerics) (nexus.structure.Structure method) NebPoscars (class in nexus.vasp_input) negate() (in module nexus.structure) neighbor_table() (nexus.structure.Structure method) Neodymium (nexus.periodic_table.Elements attribute) Neon (nexus.periodic_table.Elements attribute) Neptunium (nexus.periodic_table.Elements attribute) NerscMachine (class in nexus.machines) neutrons() (nexus.periodic_table.ElementData method) new_particles() (nexus.physical_system.Matter class method) new_variables (nexus.pwscf_input.cell attribute) (nexus.pwscf_input.control attribute) (nexus.pwscf_input.electrons attribute) (nexus.pwscf_input.ions attribute) (nexus.pwscf_input.system attribute) newton (nexus.unit_converter.UnitConverter attribute) nexus.basisset module nexus.bundle module nexus.debug module nexus.developer module nexus.execute module nexus.fileio module nexus.gamess module nexus.gamess_analyzer module nexus.gamess_input module nexus.generic module nexus.hdfreader module nexus.machines module nexus.memory module nexus.nexus_base module nexus.numerics module nexus.numpy_extensions module nexus.observables module nexus.periodic_table module nexus.physical_system module nexus.project_manager module nexus.pseudopotential module nexus.pwscf module nexus.pwscf_analyzer module nexus.pwscf_data_reader module nexus.pwscf_input module nexus.pwscf_postprocessors module nexus.pyscf_analyzer module nexus.pyscf_input module nexus.pyscf_sim module nexus.qmcpack module nexus.qmcpack_analyzer module nexus.qmcpack_input module nexus.qmcpack_method_analyzers module nexus.qmcpack_property_analyzers module nexus.qmcpack_quantity_analyzers module nexus.qmcpack_result_analyzers module nexus.quantum_package module nexus.quantum_package_analyzer module nexus.quantum_package_input module nexus.rmg module nexus.rmg_analyzer module nexus.rmg_input module nexus.simulation module nexus.structure module nexus.testing module nexus.unit_converter module nexus.utilities module nexus.vasp module nexus.vasp_analyzer module nexus.vasp_input module nexus.xmlreader module NexusCore (class in nexus.nexus_base) NexusDevWarning NexusError NexusUnpickler (class in nexus.generic) NexusUserWarning Nickel (nexus.periodic_table.Elements attribute) Nihonium (nexus.periodic_table.Elements attribute) Niobium (nexus.periodic_table.Elements attribute) Nitrogen (nexus.periodic_table.Elements attribute) nm (nexus.unit_converter.UnitConverter attribute) Nobelium (nexus.periodic_table.Elements attribute) noconv() (in module nexus.pwscf_input) nocopy() (in module nexus.generic) norm() (nexus.fileio.XsfFile method) (nexus.observables.Density method) normalize() (nexus.hdfreader.HDFgroup method) normalize_data() (nexus.qmcpack_quantity_analyzers.TracesAnalyzer method) normalize_time() (nexus.machines.Job method) not_implemented() (nexus.developer.DevBase method) ns (nexus.unit_converter.UnitConverter attribute) NullSimulationAnalyzer (class in nexus.simulation) NullSimulationInput (class in nexus.simulation) num_elements() (nexus.periodic_table.Elements static method) numeric (nexus.pseudopotential.CasinoPP attribute) (nexus.pseudopotential.QmcpackPP attribute) (nexus.pseudopotential.SemilocalPP attribute) numeric_channel() (nexus.pseudopotential.SemilocalPP method) numerics_jackknife() (in module nexus.numerics) nxs_deprecate() (in module nexus.generic) O obj (class in nexus.generic) obj() (nexus.generic.obj method) object_diff() (in module nexus.testing) object_eq() (in module nexus.testing) object_interface (class in nexus.generic) object_neq() (in module nexus.testing) Observable (class in nexus.observables) observable (nexus.observables.StatFile attribute) observable_aliases (nexus.observables.StatFile attribute) observable_class_to_stat_group (nexus.observables.StatFile attribute) observable_classes (nexus.observables.StatFile attribute) observable_groups() (nexus.observables.StatFile method) ObservableWithComponents (class in nexus.observables) obtain_attributes() (nexus.observables.DefinedAttributeBase class method) occupations (class in nexus.pwscf_input) Oganesson (nexus.periodic_table.Elements attribute) OIC5 (class in nexus.machines) onezero() (in module nexus.qmcpack_input) open() (nexus.fileio.TextFile method) open_hubbard_dat() (nexus.pwscf_postprocessors.HpAnalyzer method) open_log() (nexus.generic.hidden method) (nexus.generic.object_interface method) (nexus.pwscf_postprocessors.ProjwfcAnalyzer method) operate() (nexus.structure.Structure method) operations (nexus.structure.Structure attribute) opt_methods (nexus.qmcpack_input.QmcpackInput attribute) opt_tilematrix() (nexus.structure.Structure method) OptAnalyzer (class in nexus.qmcpack_method_analyzers) optimal_tilematrix() (in module nexus.structure) OptimizationAnalyzer (class in nexus.qmcpack_result_analyzers) optimize_jastrows() (nexus.qmcpack_input.QmcpackInput method) optimize_multidet() (nexus.qmcpack_input.QmcpackInput method) Options (class in nexus.machines) orbitals (nexus.simulation.DynamicProcess property) order_by_species() (nexus.structure.Structure method) ordered_species() (nexus.structure.Structure method) Osmium (nexus.periodic_table.Elements attribute) our_load_source() (in module nexus.machines) OutcarData (class in nexus.vasp_analyzer) outfile_extension (nexus.machines.ALCF_Machine attribute) (nexus.machines.Amos attribute) (nexus.machines.Andes attribute) (nexus.machines.Archer2 attribute) (nexus.machines.Cooley attribute) (nexus.machines.ICMP_Machine attribute) (nexus.machines.Leonardo attribute) (nexus.machines.Machine attribute) (nexus.machines.Rhea attribute) (nexus.machines.SnlMachine attribute) (nexus.machines.Stampede2 attribute) (nexus.machines.Theta attribute) (nexus.simulation.Simulation attribute) outfile_text() (nexus.simulation.Simulation method) output_filename() (nexus.gamess.Gamess method) output_filepath() (nexus.gamess.Gamess method) Oxygen (nexus.periodic_table.Elements attribute) P Pa (nexus.unit_converter.UnitConverter attribute) pairlist() (nexus.qmcpack_input.collection method) Palladium (nexus.periodic_table.Elements attribute) Param (class in nexus.qmcpack_input) parse_string() (in module nexus.xmlreader) Particle (class in nexus.physical_system) particle_collection (nexus.physical_system.Matter attribute) Particles (class in nexus.physical_system) partition_sposets() (in module nexus.qmcpack_input) pascal (nexus.unit_converter.UnitConverter attribute) path_exists() (nexus.generic.obj method) path_string() (in module nexus.utilities) pbs_walltime() (nexus.machines.Job method) Penaltypot (class in nexus.vasp_input) per_type_cmp() (in module nexus.utilities) performing_neb() (nexus.vasp_input.VaspInput method) performing_relax() (nexus.vasp_input.VaspInput method) periodicities (nexus.fileio.XsfFile attribute) Perlmutter (class in nexus.machines) permissive_init (nexus.qmcpack_input.QIobj attribute) permissive_read (nexus.qmcpack_input.QIobj attribute) permissive_write (nexus.qmcpack_input.QIobj attribute) permute() (nexus.structure.Structure method) phonon (class in nexus.pwscf_input) Phosphorus (nexus.periodic_table.Elements attribute) PhysicalSystem (class in nexus.physical_system) picometer (nexus.unit_converter.UnitConverter attribute) piconewton (nexus.unit_converter.UnitConverter attribute) picosecond (nexus.unit_converter.UnitConverter attribute) plabel (nexus.qmcpack_quantity_analyzers.SpaceGridBase attribute) Platinum (nexus.periodic_table.Elements attribute) plot() (nexus.basisset.GaussianBasisSet method) (nexus.pseudopotential.Pseudopotential method) (nexus.pseudopotential.SemilocalPP method) (nexus.qmcpack_property_analyzers.RadialJastrow method) plot2d() (nexus.structure.Structure method) plot2d_ax() (nexus.structure.Structure method) plot2d_kax() (nexus.structure.Structure method) plot2d_kp() (nexus.structure.Structure method) plot2d_points() (nexus.structure.Structure method) plot2d_pos() (nexus.structure.Structure method) plot_axes() (nexus.qmcpack_quantity_analyzers.RectilinearGrid method) plot_bandstructure() (nexus.pwscf_analyzer.PwscfAnalyzer method) plot_box() (nexus.qmcpack_quantity_analyzers.RectilinearGrid method) plot_channels() (nexus.pseudopotential.SemilocalPP method) plot_components() (nexus.pseudopotential.SemilocalPP method) plot_directional_raw() (nexus.observables.MomentumDistribution method) plot_jastrow_convergence() (nexus.qmcpack_result_analyzers.OptimizationAnalyzer method) plot_jastrow_data() (nexus.qmcpack_property_analyzers.WavefunctionAnalyzer method) plot_jastrows() (nexus.qmcpack_property_analyzers.WavefunctionAnalyzer method) plot_L2() (nexus.pseudopotential.SemilocalPP method) plot_nonlocal_polar() (nexus.pseudopotential.SemilocalPP method) plot_opt_convergence() (nexus.qmcpack_result_analyzers.OptimizationAnalyzer method) plot_plane_contours() (nexus.observables.MomentumDistribution method) plot_positive_definite() (nexus.pseudopotential.SemilocalPP method) plot_prim_widths() (nexus.basisset.GaussianBasisSet method) plot_primitives() (nexus.basisset.GaussianBasisSet method) plot_radial_density() (nexus.observables.Density method) plot_radial_raw() (nexus.observables.MomentumDistribution method) plot_timestep_convergence() (nexus.qmcpack_result_analyzers.TimestepStudyAnalyzer method) plot_trace() (nexus.qmcpack_analyzer.QmcpackAnalyzer method) (nexus.qmcpack_quantity_analyzers.QuantityAnalyzer method) pluralize() (nexus.qmcpack_input.QIxml method) (nexus.qmcpack_input.QmcpackInput method) Plutonium (nexus.periodic_table.Elements attribute) pm (nexus.unit_converter.UnitConverter attribute) pN (nexus.unit_converter.UnitConverter attribute) point2unit_cartesian() (nexus.qmcpack_quantity_analyzers.RectilinearGrid method) point2unit_cylindrical() (nexus.qmcpack_quantity_analyzers.RectilinearGrid method) point2unit_spherical() (nexus.qmcpack_quantity_analyzers.RectilinearGrid method) point_defect() (nexus.structure.Structure method) point_group_operations() (nexus.structure.Structure method) points2domains_cartesian() (nexus.qmcpack_quantity_analyzers.RectilinearGrid method) points2domains_cylindrical() (nexus.qmcpack_quantity_analyzers.RectilinearGrid method) points2domains_spherical() (nexus.qmcpack_quantity_analyzers.RectilinearGrid method) Polaris (class in nexus.machines) poll() (nexus.project_manager.DynamicWorkflowManager method) Polonium (nexus.periodic_table.Elements attribute) pos_to_cartesian() (nexus.structure.Structure method) pos_to_str() (nexus.structure.Structure method) pos_unit() (nexus.structure.Structure method) Poscar (class in nexus.vasp_input) PoscarFile (class in nexus.fileio) post_analyze() (nexus.pwscf_postprocessors.Projwfc method) (nexus.qmcpack.Qmcpack method) (nexus.simulation.Simulation method) post_init() (nexus.qmcpack.Qmcpack method) (nexus.quantum_package.QuantumPackage method) (nexus.simulation.Simulation method) post_process_job() (nexus.machines.ALCF_Machine method) (nexus.machines.Andes method) (nexus.machines.Archer2 method) (nexus.machines.Aurora method) (nexus.machines.CadesMoab method) (nexus.machines.Cooley method) (nexus.machines.EOS method) (nexus.machines.Frontier method) (nexus.machines.Improv method) (nexus.machines.Lassen method) (nexus.machines.Leonardo method) (nexus.machines.Polaris method) (nexus.machines.Rhea method) (nexus.machines.Summit method) (nexus.machines.Supercomputer method) (nexus.machines.Theta method) post_process_read() (nexus.pwscf_input.Element method) (nexus.pwscf_input.system method) post_submit() (nexus.simulation.Simulation method) PostProcessSimulation (class in nexus.pwscf_postprocessors) pot_info() (nexus.vasp_input.Potcar method) Potassium (nexus.periodic_table.Elements attribute) Potcar (class in nexus.vasp_input) PP (class in nexus.pwscf_postprocessors) pp_elem_label() (in module nexus.pseudopotential) ppconvert() (nexus.pseudopotential.GaussianPP method) PPInput (class in nexus.pwscf_postprocessors) PPInputppNamelist (class in nexus.pwscf_postprocessors) PPPlotNamelist (class in nexus.pwscf_postprocessors) PPset (class in nexus.pseudopotential) Praseodymium (nexus.periodic_table.Elements attribute) pre_check_status() (nexus.simulation.Simulation method) pre_create_directories() (nexus.simulation.Simulation method) pre_init() (nexus.quantum_package.QuantumPackage method) (nexus.simulation.Simulation method) pre_process_job() (nexus.machines.Aurora method) (nexus.machines.Cori method) (nexus.machines.Frontier method) (nexus.machines.Perlmutter method) (nexus.machines.Supercomputer method) pre_send_files() (nexus.simulation.Simulation method) pre_write_inputs() (nexus.qmcpack.Qmcpack method) (nexus.simulation.Simulation method) prefactors (nexus.structure.Jellium attribute) prefixed_output (nexus.machines.ALCF_Machine attribute) (nexus.machines.Amos attribute) (nexus.machines.Andes attribute) (nexus.machines.Archer2 attribute) (nexus.machines.Cooley attribute) (nexus.machines.ICMP_Machine attribute) (nexus.machines.Leonardo attribute) (nexus.machines.Machine attribute) (nexus.machines.Rhea attribute) (nexus.machines.SnlMachine attribute) (nexus.machines.Stampede2 attribute) (nexus.machines.Theta attribute) preprocess() (nexus.qmcpack_input.QmcpackInputTemplate method) (nexus.simulation.SimulationInputTemplateDev method) preprocess_multiline_strings() (nexus.vasp_input.VFile method) present() (nexus.quantum_package_input.QuantumPackageInput method) pressure_dict (nexus.unit_converter.UnitConverter attribute) prevent_average_load() (nexus.qmcpack_analyzer.QmcpackAnalyzer method) prim_expons() (nexus.basisset.GaussianBasisSet method) prim_kpoints() (nexus.qmcpack.GCTA method) prim_widths() (nexus.basisset.GaussianBasisSet method) primitive() (nexus.structure.Structure method) principle_isotope() (nexus.periodic_table.ElementData method) print_current_keyword_differences() (nexus.vasp_input.VKeywordFile class method) print_diff() (in module nexus.testing) process() (nexus.machines.Job method) process_component_name() (nexus.observables.ObservableWithComponents method) process_dm1b_estimator() (in module nexus.qmcpack_input) process_float() (nexus.basisset.GaussianBasisSet static method) (nexus.pseudopotential.GaussianPP static method) process_gaussian_text() (in module nexus.basisset) process_job() (nexus.machines.InteractiveCluster method) (nexus.machines.Machine method) (nexus.machines.Supercomputer method) (nexus.machines.Workstation method) process_job_options() (nexus.machines.Kagayaki method) (nexus.machines.Machine method) (nexus.machines.Supercomputer method) (nexus.machines.Workstation method) process_line() (nexus.gamess_input.GamessInput method) process_options() (nexus.machines.Job method) producing_structure() (nexus.vasp_input.VaspInput method) products (nexus.simulation.DynamicProcess property) profile_collection (nexus.qmcpack_input.QmcpackInput attribute) progress() (nexus.bundle.SimulationBundle method) (nexus.simulation.Simulation method) progress_cascades() (nexus.project_manager.ProjectManager method) project_plane() (nexus.structure.Structure method) ProjectManager (class in nexus.project_manager) Projwfc (class in nexus.pwscf_postprocessors) ProjwfcAnalyzer (class in nexus.pwscf_postprocessors) ProjwfcInput (class in nexus.pwscf_postprocessors) ProjwfcNamelist (class in nexus.pwscf_postprocessors) Promethium (nexus.periodic_table.Elements attribute) promote_local() (nexus.pseudopotential.SemilocalPP method) propagate_blockages() (nexus.project_manager.ProjectManager method) propagate_identifier() (nexus.qmcpack.Qmcpack method) (nexus.simulation.Simulation method) PropertyAnalyzer (class in nexus.qmcpack_property_analyzers) Protactinium (nexus.periodic_table.Elements attribute) proton_mass (nexus.unit_converter.UnitConverter attribute) protons() (nexus.periodic_table.ElementData method) ps (nexus.unit_converter.UnitConverter attribute) pseudize() (nexus.physical_system.Ion method) (nexus.physical_system.PhysicalSystem method) PseudoFile (class in nexus.pseudopotential) PseudoIon (class in nexus.physical_system) Pseudopotential (class in nexus.pseudopotential) PseudopotentialKeyword (class in nexus.rmg_input) Pseudopotentials (class in nexus.pseudopotential) pseudos_by_atom() (nexus.pseudopotential.Pseudopotentials method) public() (nexus.generic.hidden method) Pwexport (class in nexus.pwscf_postprocessors) PwexportInput (class in nexus.pwscf_postprocessors) PwexportInputppNamelist (class in nexus.pwscf_postprocessors) Pwscf (class in nexus.pwscf) pwscf_fermi() (nexus.qmcpack.GCTA static method) pwscf_orbitals (nexus.simulation.DynamicProcess property) pwscf_time() (in module nexus.pwscf_analyzer) pwscf_tot_magnet() (nexus.qmcpack.GCTA static method) PwscfAnalyzer (class in nexus.pwscf_analyzer) PwscfInput (class in nexus.pwscf_input) PwscfInputBase (class in nexus.pwscf_input) Pyscf (class in nexus.pyscf_sim) PyscfAnalyzer (class in nexus.pyscf_analyzer) PyscfInput (class in nexus.pyscf_input) python2_sort_key (class in nexus.utilities) Q QEXML (class in nexus.pwscf_data_reader) QIobj (class in nexus.qmcpack_input) QIxml (class in nexus.qmcpack_input) QIxmlFactory (class in nexus.qmcpack_input) Qmcpack (class in nexus.qmcpack) QmcpackAnalysisRequest (class in nexus.qmcpack_analyzer) QmcpackAnalyzer (class in nexus.qmcpack_analyzer) QmcpackAnalyzerCapabilities (class in nexus.qmcpack_analyzer) QmcpackInput (class in nexus.qmcpack_input) QmcpackInputCollections (class in nexus.qmcpack_input) QmcpackInputTemplate (class in nexus.qmcpack_input) QmcpackPP (class in nexus.pseudopotential) qprc (nexus.quantum_package.QuantumPackage attribute) quantities (nexus.qmcpack_quantity_analyzers.SpaceGridBase attribute) QuantityAnalyzer (class in nexus.qmcpack_quantity_analyzers) QuantumPackage (class in nexus.quantum_package) QuantumPackageAnalyzer (class in nexus.quantum_package_analyzer) QuantumPackageInput (class in nexus.quantum_package_input) query_queue() (nexus.machines.Machine method) (nexus.machines.Supercomputer method) (nexus.machines.Workstation method) query_with_username (nexus.machines.Machine attribute) (nexus.machines.SuperMUC attribute) (nexus.machines.SuperMUC_NG attribute) queue_configs (nexus.machines.Baseline attribute) (nexus.machines.Besms attribute) (nexus.machines.Frontier attribute) (nexus.machines.Machine attribute) R radial_density() (nexus.observables.Density method) RadialJastrow (class in nexus.qmcpack_property_analyzers) Radium (nexus.periodic_table.Elements attribute) Radon (nexus.periodic_table.Elements attribute) raise_error (nexus.generic.generic_settings attribute) random_key() (nexus.generic.obj method) rcell() (nexus.structure.Structure method) rcore_max() (nexus.structure.Structure method) read() (nexus.basisset.gaussBasisFile method) (nexus.basisset.GaussianBasisSet method) (nexus.fileio.StandardFile method) (nexus.fileio.TextFile method) (nexus.gamess_input.CardGroup method) (nexus.gamess_input.FormattedGroup method) (nexus.gamess_input.Group method) (nexus.gamess_input.KeywordGroup method) (nexus.machines.Options method) (nexus.observables.StatFile method) (nexus.pseudopotential.CasinoPP method) (nexus.pseudopotential.gamessPPFile method) (nexus.pseudopotential.PseudoFile method) (nexus.pseudopotential.Pseudopotential method) (nexus.pseudopotential.QmcpackPP method) (nexus.pseudopotential.SemilocalPP method) (nexus.pwscf_input.Card method) (nexus.pwscf_input.Element method) (nexus.pwscf_input.Section method) (nexus.qmcpack_input.Param method) (nexus.qmcpack_input.QmcpackInput method) (nexus.quantum_package_input.QuantumPackageInput method) (nexus.rmg_input.AtomsKeyword method) (nexus.rmg_input.FormattedRmgKeyword method) (nexus.rmg_input.HubbardUKeyword method) (nexus.rmg_input.KpointsBandstructureKeyword method) (nexus.rmg_input.KpointsKeyword method) (nexus.rmg_input.PseudopotentialKeyword method) (nexus.rmg_input.RmgKeyword method) (nexus.simulation.NullSimulationInput method) (nexus.simulation.SimulationInput method) (nexus.simulation.SimulationInputMultiTemplateDev method) (nexus.structure.Structure method) (nexus.vasp_analyzer.OutcarData method) (nexus.vasp_input.NebPoscars method) (nexus.vasp_input.VaspInput method) (nexus.vasp_input.VFile method) read_ao_populations() (nexus.gamess_analyzer.GamessAnalyzer method) read_arrays() (nexus.hdfreader.HDFgroup method) read_bandinfo_dat() (nexus.qmcpack.Qmcpack method) read_bool() (in module nexus.pwscf_input) (in module nexus.vasp_input) read_bool_array() (in module nexus.vasp_input) read_boolean() (in module nexus.rmg_input) read_byte() (nexus.fileio.TextFile method) read_cif() (in module nexus.structure) (nexus.structure.Structure method) read_cif_cell() (in module nexus.structure) read_cif_celldata() (in module nexus.structure) read_double() (in module nexus.rmg_input) read_double_array() (in module nexus.rmg_input) read_energy_components() (nexus.gamess_analyzer.GamessAnalyzer method) read_eshdf() (nexus.observables.MomentumDistributionDFT method) read_eshdf_data() (nexus.qmcpack.GCTA method) read_eshdf_nofk_data() (in module nexus.observables) read_fhi_aims() (nexus.structure.Structure method) read_file() (nexus.basisset.gamessBasisFile method) (nexus.basisset.gaussBasisFile method) read_file_text() (nexus.simulation.SimulationInput method) read_float() (in module nexus.pwscf_input) read_hdf() (in module nexus.hdfreader) read_hubbard_dat() (nexus.pwscf_postprocessors.HpAnalyzer method) read_int() (in module nexus.pwscf_input) (in module nexus.vasp_input) read_int_array() (in module nexus.vasp_input) read_integer() (in module nexus.rmg_input) read_integer_array() (in module nexus.rmg_input) read_jastrows() (in module nexus.qmcpack_input) read_line_tokens() (nexus.gamess_input.CardGroup method) read_lines() (nexus.basisset.GaussianBasisSet method) (nexus.vasp_input.VFormattedFile method) read_lowdin() (nexus.pwscf_postprocessors.ProjwfcAnalyzer method) read_orbitals() (nexus.gamess_analyzer.GamessAnalyzer method) read_outcar_accounting() (in module nexus.vasp_analyzer) read_outcar_bands() (in module nexus.vasp_analyzer) read_outcar_cell() (in module nexus.vasp_analyzer) read_outcar_charge_mag() (in module nexus.vasp_analyzer) read_outcar_core_potentials() (in module nexus.vasp_analyzer) read_outcar_fermi_energy() (in module nexus.vasp_analyzer) read_outcar_functions (nexus.vasp_analyzer.OutcarData attribute) read_outcar_header_values() (in module nexus.vasp_analyzer) read_outcar_magnetization() (in module nexus.vasp_analyzer) read_outcar_position_force() (in module nexus.vasp_analyzer) read_outcar_stress() (in module nexus.vasp_analyzer) read_outcar_total_charge() (in module nexus.vasp_analyzer) read_poscar() (nexus.structure.Structure method) read_poscar_chgcar() (in module nexus.fileio) read_process_id() (nexus.machines.Lassen method) (nexus.machines.Lonestar method) (nexus.machines.OIC5 method) (nexus.machines.Summit method) (nexus.machines.Supercomputer method) read_qexml() (in module nexus.pwscf_data_reader) read_qp_value() (in module nexus.quantum_package_input) read_qp_value_type() (in module nexus.quantum_package_input) read_real() (in module nexus.vasp_input) read_real_array() (in module nexus.vasp_input) read_results() (nexus.rmg_analyzer.RmgAnalyzer method) read_setup_info() (nexus.rmg_analyzer.RmgAnalyzer method) read_stat_h5() (nexus.observables.MomentumDistributionQMC method) read_states() (nexus.pwscf_postprocessors.ProjwfcAnalyzer method) read_str() (in module nexus.pwscf_input) read_string() (in module nexus.rmg_input) (in module nexus.vasp_input) read_structure() (in module nexus.structure) read_text() (nexus.basisset.GaussianBasisSet method) (nexus.fileio.ChgcarFile method) (nexus.fileio.PoscarFile method) (nexus.fileio.StandardFile method) (nexus.fileio.XsfFile method) (nexus.gamess_input.GamessInput method) (nexus.pseudopotential.GaussianPP method) (nexus.pseudopotential.Pseudopotential method) (nexus.pwscf_input.atomic_forces method) (nexus.pwscf_input.atomic_positions method) (nexus.pwscf_input.atomic_species method) (nexus.pwscf_input.Card method) (nexus.pwscf_input.cell_parameters method) (nexus.pwscf_input.climbing_images method) (nexus.pwscf_input.collective_vars method) (nexus.pwscf_input.constraints method) (nexus.pwscf_input.hubbard method) (nexus.pwscf_input.k_points method) (nexus.pwscf_input.occupations method) (nexus.pwscf_input.PwscfInput method) (nexus.pwscf_postprocessors.Namelist method) (nexus.pwscf_postprocessors.NamelistInput method) (nexus.quantum_package_input.QuantumPackageInput method) (nexus.rmg_input.RmgInput method) (nexus.simulation.NullSimulationInput method) (nexus.simulation.SimulationInput method) (nexus.simulation.SimulationInputTemplateDev method) (nexus.vasp_input.Kpoints method) (nexus.vasp_input.Poscar method) (nexus.vasp_input.Potcar method) (nexus.vasp_input.VFile method) (nexus.vasp_input.VKeywordFile method) read_text_tokens() (in module nexus.testing) read_text_value() (in module nexus.testing) read_tokens() (nexus.gamess_input.CardGroup method) read_value (nexus.vasp_input.Incar attribute) (nexus.vasp_input.Stopcar attribute) read_vxml() (in module nexus.vasp_analyzer) read_xml() (nexus.qmcpack_input.QmcpackInput method) read_xsf() (nexus.observables.Density method) (nexus.structure.Structure method) read_xyz() (nexus.structure.Structure method) readbs() (nexus.basisset.BasisSets method) readline() (nexus.fileio.TextFile method) readpp() (nexus.pseudopotential.Pseudopotentials method) readtokens() (nexus.fileio.TextFile method) readtokensf() (nexus.fileio.TextFile method) readval() (in module nexus.pwscf_data_reader) (in module nexus.pwscf_postprocessors) (in module nexus.vasp_analyzer) (nexus.gamess_input.CardGroup method) (nexus.gamess_input.KeywordGroup method) readxml() (in module nexus.xmlreader) ready() (nexus.simulation.Simulation method) real_arrays (nexus.pwscf_input.PwscfInputBase attribute) (nexus.vasp_input.Incar attribute) (nexus.vasp_input.Stopcar attribute) real_equality() (in module nexus.vasp_input) reals (nexus.gamess_input.ContrlGroup attribute) (nexus.gamess_input.DetGroup attribute) (nexus.gamess_input.DftGroup attribute) (nexus.gamess_input.GuessGroup attribute) (nexus.gamess_input.GugdiaGroup attribute) (nexus.gamess_input.KeywordSpecGroup attribute) (nexus.gamess_input.McscfGroup attribute) (nexus.gamess_input.ScfGroup attribute) (nexus.gamess_input.SystemGroup attribute) (nexus.vasp_input.Incar attribute) (nexus.vasp_input.Stopcar attribute) receive_charge_density() (nexus.pwscf.Pwscf method) receive_jastrow() (nexus.qmcpack.Qmcpack method) receive_pwscf_orbitals() (nexus.qmcpack.Qmcpack method) receive_structure() (nexus.pwscf.Pwscf method) (nexus.qmcpack.Qmcpack method) receive_wavefunction() (nexus.qmcpack.Qmcpack method) recenter() (nexus.structure.Structure method) recenter_k() (nexus.structure.Structure method) recenter_points() (in module nexus.structure) reconstruct_cascade() (nexus.simulation.Simulation method) recorner() (nexus.structure.Structure method) RectilinearGrid (class in nexus.qmcpack_quantity_analyzers) RectilinearGridInitializer (class in nexus.qmcpack_quantity_analyzers) redirect_output (nexus.machines.Machine attribute) (nexus.machines.Tomcat3 attribute) reduce_tilematrix() (in module nexus.structure) reenter_queue() (nexus.machines.Job method) remainder() (nexus.vasp_analyzer.VaspLines method) remove() (nexus.qmcpack_input.collection method) (nexus.qmcpack_input.QIxml method) (nexus.qmcpack_input.QmcpackInput method) (nexus.structure.Structure method) remove_calculations() (nexus.qmcpack_input.QmcpackInput method) remove_channels() (nexus.basisset.GaussianBasisSet method) remove_comment() (in module nexus.vasp_input) (nexus.vasp_input.VFile method) remove_component() (nexus.pseudopotential.SemilocalPP method) remove_data() (nexus.qmcpack_quantity_analyzers.EnergyDensityAnalyzer method) remove_empty() (nexus.qmcpack_input.QIxml method) (nexus.qmcpack_input.QmcpackInput method) remove_empty_lines() (in module nexus.xmlreader) remove_folded() (nexus.physical_system.PhysicalSystem method) (nexus.structure.Structure method) remove_folded_structure() (nexus.structure.Structure method) remove_folded_system() (nexus.physical_system.PhysicalSystem method) remove_ghost() (nexus.fileio.XsfFile method) remove_hidden() (nexus.xmlreader.XMLelement method) remove_J1() (nexus.qmcpack_input.QmcpackInput method) remove_J2() (nexus.qmcpack_input.QmcpackInput method) remove_J3() (nexus.qmcpack_input.QmcpackInput method) remove_jastrows() (nexus.qmcpack_input.QmcpackInput method) remove_job() (nexus.machines.Supercomputer method) remove_L2() (nexus.pseudopotential.SemilocalPP method) remove_large_prims() (nexus.basisset.GaussianBasisSet method) remove_large_prims_rel() (nexus.basisset.GaussianBasisSet method) remove_local() (nexus.pseudopotential.SemilocalPP method) remove_nonlocal() (nexus.pseudopotential.SemilocalPP method) remove_pair_sections() (in module nexus.xmlreader) remove_physical_system() (nexus.qmcpack_input.QmcpackInput method) remove_prims() (nexus.basisset.GaussianBasisSet method) remove_qmc() (nexus.qmcpack_input.QmcpackInput method) remove_small_prims() (nexus.basisset.GaussianBasisSet method) remove_small_prims_rel() (nexus.basisset.GaussianBasisSet method) rename() (nexus.physical_system.Particles method) (nexus.physical_system.PhysicalSystem method) (nexus.structure.Structure method) render_array() (in module nexus.pyscf_input) render_bool() (in module nexus.qmcpack_input) (in module nexus.vasp_input) render_string() (in module nexus.pyscf_input) renew_app_command (nexus.simulation.Simulation attribute) renew_app_command() (nexus.machines.Job method) reorder() (nexus.structure.Structure method) reorder_atomic_data() (nexus.qmcpack_quantity_analyzers.EnergyDensityAnalyzer method) (nexus.qmcpack_quantity_analyzers.SpaceGridBase method) (nexus.qmcpack_quantity_analyzers.VoronoiGrid method) replace() (nexus.qmcpack_input.QIxml method) (nexus.qmcpack_input.QmcpackInput method) (nexus.structure.Structure method) replace_nearest() (nexus.structure.Structure method) requeue_job() (nexus.machines.Machine method) (nexus.machines.Supercomputer method) required_attributes (nexus.observables.Density attribute) (nexus.observables.MomentumDistribution attribute) (nexus.observables.MomentumDistributionDFT attribute) (nexus.observables.Observable attribute) required_elements (nexus.pwscf_input.PwscfInput attribute) required_inputs (nexus.machines.Supercomputer attribute) requirements_met() (nexus.simulation.DynamicProcess method) requires_account (nexus.machines.ALCF_Machine attribute) (nexus.machines.Andes attribute) (nexus.machines.Archer2 attribute) (nexus.machines.Aurora attribute) (nexus.machines.Baseline attribute) (nexus.machines.Besms attribute) (nexus.machines.BlueWatersXE attribute) (nexus.machines.BlueWatersXK attribute) (nexus.machines.CadesMoab attribute) (nexus.machines.CadesSlurm attribute) (nexus.machines.Cooley attribute) (nexus.machines.EOS attribute) (nexus.machines.Frontier attribute) (nexus.machines.Improv attribute) (nexus.machines.Inti attribute) (nexus.machines.Jaguar attribute) (nexus.machines.Kagayaki attribute) (nexus.machines.Kestrel attribute) (nexus.machines.Kraken attribute) (nexus.machines.Lassen attribute) (nexus.machines.Leonardo attribute) (nexus.machines.Lonestar attribute) (nexus.machines.Machine attribute) (nexus.machines.Polaris attribute) (nexus.machines.Rhea attribute) (nexus.machines.Ruby attribute) (nexus.machines.SnlMachine attribute) (nexus.machines.Stampede2 attribute) (nexus.machines.Summit attribute) (nexus.machines.SuperMUC attribute) (nexus.machines.SuperMUC_NG attribute) (nexus.machines.Theta attribute) (nexus.machines.Titan attribute) (nexus.machines.Tomcat3 attribute) requires_format (nexus.pseudopotential.CasinoPP attribute) (nexus.pseudopotential.GaussianPP attribute) (nexus.pseudopotential.Pseudopotential attribute) (nexus.pseudopotential.QmcpackPP attribute) rescale() (nexus.structure.Structure method) reservation_required (nexus.machines.Flight attribute) (nexus.machines.SnlMachine attribute) reset() (nexus.simulation.SimulationInputTemplateDev method) reset_axes() (nexus.structure.Structure method) reset_indicators() (nexus.simulation.Simulation method) reset_precision() (nexus.qmcpack_input.Param method) reset_wait_ids() (nexus.simulation.Simulation method) reshape_axes() (nexus.structure.Structure method) reshape_inplace() (in module nexus.numpy_extensions) resident() (in module nexus.memory) resize() (nexus.fileio.TextFile method) resolve_file_collisions() (nexus.project_manager.ProjectManager method) restore_added_keys() (nexus.quantum_package_input.QuantumPackageInput method) restore_default_settings() (nexus.gamess.Gamess static method) (nexus.machines.Job static method) (nexus.machines.Machine method) (nexus.project_manager.ProjectManager static method) (nexus.pwscf.Pwscf static method) (nexus.quantum_package.QuantumPackage static method) restore_nexus_core_defaults() (in module nexus.nexus_base) ResultAnalyzer (class in nexus.qmcpack_result_analyzers) return_initial_structure() (nexus.rmg_analyzer.RmgAnalyzer method) return_structure() (nexus.rmg_input.RmgInput method) (nexus.simulation.SimulationInput method) return_system() (nexus.pwscf_input.PwscfInput method) (nexus.qmcpack_input.QmcpackInput method) (nexus.simulation.NullSimulationInput method) (nexus.simulation.SimulationInput method) (nexus.vasp_input.VaspInput method) rewind() (nexus.vasp_analyzer.VaspLines method) rfind() (nexus.fileio.TextFile method) Rhea (class in nexus.machines) Rhenium (nexus.periodic_table.Elements attribute) Rhodium (nexus.periodic_table.Elements attribute) ring_graphs() (nexus.structure.Structure method) rinscribe() (nexus.structure.Structure method) rinscribe_cube() (nexus.structure.Structure method) rlabel (nexus.qmcpack_quantity_analyzers.SpaceGridBase attribute) Rmg (class in nexus.rmg) rmg_lattice() (nexus.structure.Structure method) rmg_lattices (nexus.structure.Structure attribute) rmg_transform() (nexus.structure.Structure method) RmgAnalyzer (class in nexus.rmg_analyzer) RmgCalcModes (class in nexus.rmg_input) RmgInput (class in nexus.rmg_input) RmgInputSettings (class in nexus.rmg_input) RmgInputSpec (class in nexus.rmg_input) RmgKeyword (class in nexus.rmg_input) rmin() (nexus.structure.Structure method) Roentgenium (nexus.periodic_table.Elements attribute) rotate() (nexus.structure.Structure method) rotate_plane() (in module nexus.structure) (nexus.structure.Structure method) rs() (nexus.structure.Jellium method) rsqmc_expanded_names (nexus.qmcpack_input.Names attribute) Rubidium (nexus.periodic_table.Elements attribute) Ruby (class in nexus.machines) run() (nexus.simulation.SimulationEmulator method) run_command() (nexus.machines.Job method) run_completed (nexus.rmg_analyzer.RmgAnalyzer property) run_project() (nexus.project_manager.ProjectManager method) run_type() (nexus.vasp_input.VaspInput method) run_types (nexus.quantum_package_input.QuantumPackageInput attribute) Ruthenium (nexus.periodic_table.Elements attribute) Rutherfordium (nexus.periodic_table.Elements attribute) rwigner() (nexus.structure.Structure method) rwigner_cube() (nexus.structure.Structure method) Ry (nexus.unit_converter.UnitConverter attribute) rydberg (nexus.unit_converter.UnitConverter attribute) S s (nexus.unit_converter.UnitConverter attribute) Samarium (nexus.periodic_table.Elements attribute) save() (nexus.generic.object_interface method) (nexus.qmcpack_analyzer.QmcpackAnalyzer method) save_analyzer_image() (nexus.simulation.Simulation method) save_attempt() (nexus.simulation.Simulation method) save_fields (nexus.simulation.SimulationImage attribute) save_image() (nexus.simulation.Simulation method) (nexus.simulation.SimulationImage method) save_only_fields (nexus.simulation.SimulationImage attribute) save_radial_density() (nexus.observables.Density method) sbatch_walltime() (nexus.machines.Job method) scalar_displacement() (nexus.structure.Structure method) scalar_keywords (nexus.vasp_input.Incar attribute) (nexus.vasp_input.Stopcar attribute) scalars (nexus.observables.StatFile attribute) ScalarsDatAnalyzer (class in nexus.qmcpack_quantity_analyzers) ScalarsHDFAnalyzer (class in nexus.qmcpack_quantity_analyzers) scale_component() (nexus.pseudopotential.GaussianPP method) Scandium (nexus.periodic_table.Elements attribute) ScfGroup (class in nexus.gamess_input) screen_fake_sims() (nexus.project_manager.ProjectManager method) Seaborgium (nexus.periodic_table.Elements attribute) sec (in module nexus.pwscf_input) second (nexus.unit_converter.UnitConverter attribute) seconds_to_walltime() (nexus.machines.Supercomputer static method) Section (class in nexus.pwscf_input) section (class in nexus.qmcpack_input) Section (class in nexus.quantum_package_input) section_aliases (nexus.pwscf_input.PwscfInputBase attribute) section_types (nexus.pwscf_input.PwscfInput attribute) sections (nexus.pwscf_input.PwscfInput attribute) seek() (nexus.fileio.TextFile method) select_random() (nexus.generic.obj method) select_twist() (nexus.structure.Structure method) Selenium (nexus.periodic_table.Elements attribute) SemilocalPP (class in nexus.pseudopotential) send_files() (nexus.bundle.SimulationBundle method) (nexus.simulation.Simulation method) sent_files (nexus.simulation.DynamicProcess property) separate_inputs() (nexus.simulation.Simulation class method) serial() (nexus.generic.obj method) serial_clone() (nexus.machines.Job method) serial_max_cores (nexus.machines.Leonardo attribute) serial_max_hours (nexus.machines.Leonardo attribute) serial_only() (nexus.machines.Job method) serial_partition (nexus.machines.Leonardo attribute) set() (nexus.generic.obj method) (nexus.quantum_package_input.QuantumPackageInput method) (nexus.simulation.Simulation method) (nexus.structure.MaskFilter method) set_afqmc_expanded_names() (nexus.qmcpack_input.Names static method) set_afqmc_mode() (in module nexus.qmcpack_input) set_app_name() (nexus.simulation.Simulation method) set_attribute() (nexus.observables.DefinedAttributeBase method) set_attributes() (nexus.observables.DefinedAttributeBase method) set_axes() (nexus.structure.Structure method) set_basis() (nexus.pseudopotential.GaussianPP method) set_bconds() (nexus.structure.Structure method) set_channel() (nexus.pseudopotential.SemilocalPP method) set_component() (nexus.pseudopotential.SemilocalPP method) set_count() (nexus.physical_system.Particle method) set_default_attributes() (nexus.observables.DefinedAttributeBase method) set_directories() (nexus.simulation.Simulation method) set_driver() (nexus.qmcpack_input.QmcpackInput method) set_elem() (nexus.structure.Structure method) set_elements() (nexus.physical_system.Matter class method) set_environment() (nexus.machines.Job method) set_expanded_names() (nexus.qmcpack_input.Names static method) set_files() (nexus.simulation.Simulation method) (nexus.vasp.Vasp method) set_folded() (nexus.structure.Structure method) set_folded_structure() (nexus.structure.Structure method) set_frozen() (nexus.structure.Structure method) set_gcta_occupations() (nexus.qmcpack.GCTA method) set_global_info() (nexus.qmcpack_analyzer.QmcpackAnalyzer method) (nexus.qmcpack_method_analyzers.MethodAnalyzer method) set_high() (nexus.observables.VLog method) set_id() (nexus.machines.Job method) set_lcao_orbital_file() (nexus.qmcpack_input.QmcpackInput method) set_low() (nexus.observables.VLog method) set_mag() (nexus.structure.Structure method) set_multidet_h5() (nexus.qmcpack_input.QmcpackInput method) set_multidet_params() (nexus.qmcpack_input.QmcpackInput method) set_none() (nexus.observables.VLog method) set_operations() (nexus.structure.Structure class method) set_optional() (nexus.generic.obj method) set_orbitals_h5() (nexus.qmcpack_input.QmcpackInput method) set_origin() (nexus.qmcpack_quantity_analyzers.RectilinearGrid method) set_particle_collection() (nexus.physical_system.Matter class method) set_path() (nexus.generic.obj method) set_pos() (nexus.structure.Structure method) set_potcar() (nexus.vasp_input.VaspInput method) set_precision() (nexus.qmcpack_input.Param method) set_processes() (nexus.machines.Job method) set_pseudo_files() (nexus.qmcpack_input.QmcpackInput method) set_rsqmc_mode() (in module nexus.qmcpack_input) set_templates() (nexus.simulation.SimulationInputMultiTemplateDev method) set_unassigned_default() (nexus.observables.DefinedAttributeBase class method) set_verbosity() (in module nexus.observables) (nexus.observables.VLog method) settings() (nexus.gamess.Gamess static method) (nexus.pwscf.Pwscf static method) (nexus.qmcpack_input.QIobj static method) (nexus.qmcpack_input.QmcpackInput static method) (nexus.quantum_package.QuantumPackage static method) setup (nexus.simulation.DynamicProcess property) setup_environment() (nexus.machines.Supercomputer method) setup_neb() (nexus.vasp_input.VaspInput method) sftype (nexus.fileio.ChgcarFile attribute) (nexus.fileio.PoscarFile attribute) (nexus.fileio.StandardFile attribute) (nexus.fileio.XsfFile attribute) shallow_copy() (nexus.generic.obj method) shell() (nexus.structure.Structure method) shells() (nexus.structure.Structure method) shift_origin() (nexus.qmcpack_quantity_analyzers.RectilinearGrid method) short_mode() (nexus.rmg_input.RmgCalcModes method) show() (nexus.structure.Structure method) show_input() (nexus.simulation.DynamicProcess method) (nexus.simulation.Simulation method) show_plots() (in module nexus.basisset) Silicon (nexus.periodic_table.Elements attribute) Silver (nexus.periodic_table.Elements attribute) sim_count (nexus.simulation.Simulation attribute) sim_directories (nexus.simulation.Simulation attribute) sim_imagefile (nexus.simulation.Simulation attribute) simid (nexus.simulation.DynamicProcess property) simple_surface() (in module nexus.numerics) simplestats() (in module nexus.numerics) simplify() (nexus.pseudopotential.GaussianPP method) simstats() (in module nexus.numerics) Simulation (class in nexus.simulation) simulation_type (nexus.qmcpack_input.QmcpackInput attribute) SimulationAnalyzer (class in nexus.simulation) SimulationBundle (class in nexus.bundle) SimulationBundleAnalyzer (class in nexus.bundle) SimulationBundleInput (class in nexus.bundle) SimulationEmulator (class in nexus.simulation) SimulationImage (class in nexus.simulation) SimulationInput (class in nexus.simulation) SimulationInputMultiTemplate (class in nexus.simulation) SimulationInputMultiTemplateDev (class in nexus.simulation) SimulationInputTemplate (class in nexus.simulation) SimulationInputTemplateDev (class in nexus.simulation) size() (nexus.basisset.GaussianBasisSet method) (nexus.fileio.TextFile method) (nexus.structure.Structure method) skew() (nexus.structure.Structure method) skip_submit (nexus.simulation.DynamicProcess property) slave_partners (nexus.quantum_package.QuantumPackage attribute) slide() (nexus.structure.Structure method) SnlMachine (class in nexus.machines) Sobj (class in nexus.structure) Sodium (nexus.periodic_table.Elements attribute) Solo (class in nexus.machines) sorted_keys() (nexus.generic.obj method) sorted_py2() (in module nexus.utilities) space_group_operations() (nexus.structure.Structure method) SpaceGrid() (in module nexus.qmcpack_quantity_analyzers) SpaceGridBase (class in nexus.qmcpack_quantity_analyzers) SpaceGridInitializer (class in nexus.qmcpack_quantity_analyzers) special_bundling (nexus.machines.Aurora attribute) (nexus.machines.Kagayaki attribute) (nexus.machines.Machine attribute) (nexus.machines.Polaris attribute) specialized_bundle_commands() (nexus.machines.Aurora method) (nexus.machines.Machine method) (nexus.machines.Polaris method) species() (nexus.structure.Structure method) species_array_indices (nexus.pwscf_input.PwscfInputBase attribute) species_arrays (nexus.pwscf_input.PwscfInputBase attribute) spglib_cell() (nexus.structure.Structure method) spherical (nexus.qmcpack_quantity_analyzers.SpaceGridBase attribute) spin_adapted_fermi_level() (nexus.qmcpack.GCTA method) spin_polarized_orbitals() (nexus.physical_system.PhysicalSystem method) SpinDensityAnalyzer (class in nexus.qmcpack_quantity_analyzers) split_nodes() (nexus.machines.Job method) stacksize() (in module nexus.memory) Stampede2 (class in nexus.machines) standard_placements() (nexus.qmcpack_input.QmcpackInput method) StandardFile (class in nexus.fileio) standardize_types() (nexus.pwscf_input.PwscfInput method) state_names (nexus.machines.Job attribute) states (nexus.machines.Job attribute) StatFile (class in nexus.observables) status_line() (nexus.project_manager.ProjectManager method) Stopcar (class in nexus.vasp_input) stretch() (nexus.structure.Structure method) strings (nexus.gamess_input.BasisGroup attribute) (nexus.gamess_input.CidrtGroup attribute) (nexus.gamess_input.ContrlGroup attribute) (nexus.gamess_input.DetGroup attribute) (nexus.gamess_input.DftGroup attribute) (nexus.gamess_input.DrtGroup attribute) (nexus.gamess_input.GuessGroup attribute) (nexus.gamess_input.KeywordSpecGroup attribute) (nexus.gamess_input.McscfGroup attribute) (nexus.gamess_input.SystemGroup attribute) (nexus.vasp_input.Incar attribute) (nexus.vasp_input.Stopcar attribute) Strontium (nexus.periodic_table.Elements attribute) strs (nexus.pwscf_input.PwscfInputBase attribute) Structure (class in nexus.structure) structure (nexus.simulation.DynamicProcess property) structure_animation() (in module nexus.structure) StructureFactorAnalyzer (class in nexus.qmcpack_quantity_analyzers) sub_command() (nexus.machines.Supercomputer method) sublevel_attributes (nexus.observables.Density attribute) (nexus.observables.MomentumDistribution attribute) (nexus.observables.MomentumDistributionDFT attribute) (nexus.observables.Observable attribute) submit() (nexus.bundle.SimulationBundle method) (nexus.machines.Job method) (nexus.simulation.Simulation method) submit_job() (nexus.machines.Machine method) (nexus.machines.Supercomputer method) (nexus.machines.Workstation method) submit_jobs() (nexus.machines.Machine method) (nexus.machines.Supercomputer method) (nexus.machines.Workstation method) submitted (nexus.simulation.DynamicProcess property) succ (nexus.simulation.DynamicProcess property) Sulfur (nexus.periodic_table.Elements attribute) sum() (nexus.hdfreader.HDFgroup method) sum_charge_twists() (nexus.qmcpack.GCTA method) sum_spin_twists() (nexus.qmcpack.GCTA method) summarize() (nexus.qmcpack_result_analyzers.OptimizationAnalyzer method) (nexus.qmcpack_result_analyzers.TimestepStudyAnalyzer method) Summit (class in nexus.machines) Supercomputer (class in nexus.machines) SuperMUC (class in nexus.machines) SuperMUC_NG (class in nexus.machines) supports_code() (nexus.pseudopotential.PPset method) supports_restarts (nexus.pwscf.Pwscf attribute) (nexus.simulation.Simulation attribute) surface_normals() (in module nexus.numerics) surface_slice() (nexus.qmcpack_quantity_analyzers.RectilinearGrid method) symbol (nexus.periodic_table.ElementData attribute) symmetry_data() (nexus.structure.Structure method) system (class in nexus.pwscf_input) (nexus.pwscf_input.hubbard attribute) (nexus.simulation.DynamicProcess property) SystemGroup (class in nexus.gamess_input) T Tantalum (nexus.periodic_table.Elements attribute) Technetium (nexus.periodic_table.Elements attribute) tell() (nexus.fileio.TextFile method) Tellurium (nexus.periodic_table.Elements attribute) Tennessine (nexus.periodic_table.Elements attribute) Terbium (nexus.periodic_table.Elements attribute) test() (nexus.qmcpack_quantity_analyzers.EnergyDensityAnalyzer method) test_structured() (nexus.qmcpack_quantity_analyzers.EnergyDensityAnalyzer method) text_diff() (in module nexus.testing) text_eq() (in module nexus.testing) text_neq() (in module nexus.testing) TextFile (class in nexus.fileio) Thallium (nexus.periodic_table.Elements attribute) therm_cond_dict (nexus.unit_converter.UnitConverter attribute) Theta (class in nexus.machines) Thorium (nexus.periodic_table.Elements attribute) Thulium (nexus.periodic_table.Elements attribute) tile() (nexus.physical_system.PhysicalSystem method) (nexus.structure.Jellium method) (nexus.structure.Structure method) tile_opt() (nexus.structure.Structure method) tile_points() (nexus.structure.Structure method) tile_points_brute() (nexus.structure.Structure method) tile_points_simple() (nexus.structure.Structure method) tilematrix() (nexus.structure.Structure method) TimestepStudyAnalyzer (class in nexus.qmcpack_result_analyzers) Tin (nexus.periodic_table.Elements attribute) Titan (class in nexus.machines) Titanium (nexus.periodic_table.Elements attribute) tlabel (nexus.qmcpack_quantity_analyzers.SpaceGridBase attribute) tlog() (nexus.nexus_base.NexusCore method) to_dict() (nexus.generic.obj method) to_obj() (nexus.generic.obj method) to_str() (in module nexus.utilities) tokens() (nexus.fileio.TextFile method) Tomcat3 (class in nexus.machines) toplevel_attributes (nexus.observables.Density attribute) (nexus.observables.MomentumDistribution attribute) (nexus.observables.MomentumDistributionDFT attribute) (nexus.observables.Observable attribute) total_days() (nexus.machines.Job method) total_hours() (nexus.machines.Job method) total_minutes() (nexus.machines.Job method) total_seconds() (nexus.machines.Job method) trace() (nexus.qmcpack_input.QmcpackInput method) traceback_dependency() (nexus.qmcpack.GCTA static method) TracedQmcpackInput (class in nexus.qmcpack_input) TracesAnalyzer (class in nexus.qmcpack_quantity_analyzers) TracesFileHDF (class in nexus.qmcpack_quantity_analyzers) transfer_core_from() (nexus.pseudopotential.Pseudopotential method) (nexus.pseudopotential.SemilocalPP method) transfer_from() (nexus.generic.obj method) transfer_to() (nexus.generic.obj method) transform_to_truncated_L2() (nexus.pseudopotential.GaussianPP method) translate() (nexus.structure.Structure method) traverse_cascade() (nexus.simulation.Simulation method) traverse_cascades() (nexus.project_manager.ProjectManager method) traverse_full_cascade() (nexus.simulation.Simulation method) tree() (nexus.generic.object_interface method) trivial() (in module nexus.project_manager) trivial_filter() (in module nexus.structure) truefalse() (in module nexus.qmcpack_input) ttest() (in module nexus.numerics) Tungsten (nexus.periodic_table.Elements attribute) tuple() (nexus.generic.obj method) twist_average() (nexus.qmcpack.Qmcpack method) (nexus.qmcpack_input.QmcpackInput method) type (nexus.vasp_input.Incar attribute) (nexus.vasp_input.Stopcar attribute) typed_attributes (nexus.observables.Density attribute) (nexus.observables.MomentumDistribution attribute) (nexus.observables.MomentumDistributionDFT attribute) (nexus.observables.Observable attribute) U unassigned (nexus.unit_converter.UnitConverter attribute) unassigned_default (nexus.observables.Observable attribute) unavailable() (in module nexus.developer) uncontract() (nexus.basisset.GaussianBasisSet method) (nexus.pseudopotential.GaussianPP method) uncontracted() (nexus.basisset.GaussianBasisSet method) uncontracted_basis_size() (nexus.basisset.GaussianBasisSet method) undo_depends() (nexus.simulation.Simulation method) unfolded_nelecs() (nexus.qmcpack.GCTA method) unfolded_nkpoints() (nexus.qmcpack.GCTA method) unique_kpoints() (nexus.structure.Structure method) unique_points() (nexus.structure.Structure method) unique_points_fast() (nexus.structure.Structure method) unique_positions() (nexus.structure.Structure method) Unit (class in nexus.unit_converter) unit_dict (nexus.unit_converter.UnitConverter attribute) unit_dicts (nexus.unit_converter.Unit attribute) UnitConverter (class in nexus.unit_converter) unitmap (nexus.pseudopotential.CasinoPP attribute) Unknown (nexus.periodic_table.Elements attribute) unload() (nexus.qmcpack_quantity_analyzers.TracesFileHDF method) unroll_calculations() (nexus.qmcpack_input.QmcpackInput method) unset_global_info() (nexus.qmcpack_analyzer.QmcpackAnalyzer method) (nexus.qmcpack_method_analyzers.MethodAnalyzer method) unsheared_axes() (nexus.structure.Structure method) unsupported (nexus.vasp_input.Incar attribute) (nexus.vasp_input.Stopcar attribute) upcast() (nexus.structure.Structure method) update() (nexus.physical_system.PhysicalSystem method) update_particles() (nexus.physical_system.PhysicalSystem method) update_process_id() (nexus.simulation.Simulation method) update_process_ids() (nexus.project_manager.ProjectManager method) update_rcut() (nexus.pseudopotential.SemilocalPP method) Uranium (nexus.periodic_table.Elements attribute) use_afqmc_expanded_names() (nexus.qmcpack_input.Names static method) use_rsqmc_expanded_names() (nexus.qmcpack_input.Names static method) V v (nexus.pwscf_input.PwscfInputBase attribute) v_at_zero() (nexus.pseudopotential.QmcpackPP method) valid() (nexus.rmg_input.FormattedRmgKeyword method) (nexus.rmg_input.HubbardUKeyword method) (nexus.rmg_input.RmgKeyword method) valid_no_msg() (nexus.rmg_input.FormattedRmgKeyword method) (nexus.rmg_input.FormattedTableRmgKeyword method) valid_variable_name() (in module nexus.developer) validate() (nexus.machines.Machine method) validate_queue_config() (nexus.machines.Supercomputer method) validity_checks() (nexus.fileio.ChgcarFile method) (nexus.fileio.PoscarFile method) (nexus.fileio.StandardFile method) (nexus.fileio.XsfFile method) value_diff() (in module nexus.testing) value_eq() (in module nexus.testing) value_neq() (in module nexus.testing) values() (nexus.generic.hobj method) (nexus.generic.object_interface method) Vanadium (nexus.periodic_table.Elements attribute) var_types (nexus.pwscf_input.PwscfInputBase attribute) variables (nexus.pwscf_input.cell attribute) (nexus.pwscf_input.control attribute) (nexus.pwscf_input.ee attribute) (nexus.pwscf_input.electrons attribute) (nexus.pwscf_input.ions attribute) (nexus.pwscf_input.phonon attribute) (nexus.pwscf_input.system attribute) varlist (nexus.pwscf_input.cell attribute) (nexus.pwscf_input.control attribute) (nexus.pwscf_input.ee attribute) (nexus.pwscf_input.electrons attribute) (nexus.pwscf_input.ions attribute) (nexus.pwscf_input.phonon attribute) (nexus.pwscf_input.system attribute) Vasp (class in nexus.vasp) vasp_save_files (nexus.vasp.Vasp attribute) (nexus.vasp_input.VaspInput attribute) vasp_to_nexus_elem() (in module nexus.vasp_input) VaspAnalyzer (class in nexus.vasp_analyzer) VaspInput (class in nexus.vasp_input) VaspLines (class in nexus.vasp_analyzer) vdw_table (nexus.pwscf.Pwscf attribute) vector_table() (nexus.structure.Structure method) verbosity_levels (nexus.observables.VLog attribute) Vesta (class in nexus.machines) VFile (class in nexus.vasp_input) VFormattedFile (class in nexus.vasp_input) view (nexus.hdfreader.HDFglobals attribute) vinet() (in module nexus.numerics) vinet_pressure() (in module nexus.numerics) VKeywordFile (class in nexus.vasp_input) VLog (class in nexus.observables) VmcAnalyzer (class in nexus.qmcpack_method_analyzers) Vobj (class in nexus.vasp_input) volume() (nexus.structure.Structure method) volume_normalize() (nexus.observables.Density method) voronoi (nexus.qmcpack_quantity_analyzers.SpaceGridBase attribute) voronoi_distances() (nexus.structure.Structure method) voronoi_neighbors() (in module nexus.numerics) (nexus.structure.Structure method) voronoi_radii() (nexus.structure.Structure method) voronoi_species_radii() (nexus.structure.Structure method) voronoi_vectors() (nexus.structure.Structure method) VoronoiGrid (class in nexus.qmcpack_quantity_analyzers) VoronoiGridInitializer (class in nexus.qmcpack_quantity_analyzers) VXML (class in nexus.vasp_analyzer) VXMLcoll (class in nexus.vasp_analyzer) W W_mK (nexus.unit_converter.UnitConverter attribute) W_per_mK (nexus.unit_converter.UnitConverter attribute) walltime_to_seconds() (nexus.machines.Supercomputer static method) warn() (in module nexus.generic) (nexus.generic.object_interface method) (nexus.machines.Machine method) wavefunction (nexus.simulation.DynamicProcess property) WavefunctionAnalyzer (class in nexus.qmcpack_property_analyzers) workflow_manager() (in module nexus.project_manager) working_directory (nexus.nexus_base.NexusCore attribute) Workstation (class in nexus.machines) write() (nexus.basisset.GaussianBasisSet method) (nexus.fileio.StandardFile method) (nexus.fileio.TextFile method) (nexus.gamess_input.CardGroup method) (nexus.gamess_input.FormattedGroup method) (nexus.gamess_input.Group method) (nexus.gamess_input.KeywordGroup method) (nexus.generic.hidden method) (nexus.generic.object_interface method) (nexus.machines.Job method) (nexus.machines.Options method) (nexus.pseudopotential.Pseudopotential method) (nexus.pwscf_input.Card method) (nexus.pwscf_input.Element method) (nexus.pwscf_input.Section method) (nexus.qmcpack_input.BundledQmcpackInput method) (nexus.qmcpack_input.Param method) (nexus.qmcpack_input.QIxml method) (nexus.quantum_package_input.QuantumPackageInput method) (nexus.rmg_input.AtomsKeyword method) (nexus.rmg_input.FormattedRmgKeyword method) (nexus.rmg_input.HubbardUKeyword method) (nexus.rmg_input.KpointsBandstructureKeyword method) (nexus.rmg_input.KpointsKeyword method) (nexus.rmg_input.PseudopotentialKeyword method) (nexus.rmg_input.RmgKeyword method) (nexus.simulation.NullSimulationInput method) (nexus.simulation.SimulationInput method) (nexus.simulation.SimulationInputMultiTemplateDev method) (nexus.structure.Structure method) (nexus.vasp_input.NebPoscars method) (nexus.vasp_input.VaspInput method) (nexus.vasp_input.VFile method) write_array() (in module nexus.vasp_input) write_axes() (nexus.structure.Structure method) write_band() (nexus.fileio.XsfFile method) write_basis() (nexus.pseudopotential.GaussianPP method) write_bool() (in module nexus.pwscf_input) (in module nexus.vasp_input) write_bool_array() (in module nexus.vasp_input) write_boolean() (in module nexus.rmg_input) write_byte() (nexus.fileio.TextFile method) write_cascade_dependents() (nexus.project_manager.ProjectManager method) write_casino() (nexus.pseudopotential.SemilocalPP method) write_coord() (nexus.fileio.XsfFile method) write_data() (nexus.fileio.XsfFile method) write_density() (nexus.qmcpack_quantity_analyzers.DensityAnalyzer method) (nexus.qmcpack_quantity_analyzers.DensityAnalyzerBase method) (nexus.qmcpack_quantity_analyzers.SpinDensityAnalyzer method) write_dependents() (nexus.simulation.Simulation method) write_double() (in module nexus.rmg_input) write_double_array() (in module nexus.rmg_input) write_electron_counts() (nexus.pwscf_analyzer.PwscfAnalyzer method) write_end_splash() (nexus.nexus_base.NexusCore static method) write_fhi_aims() (nexus.structure.Structure method) write_file_text() (nexus.simulation.SimulationInput method) write_files() (nexus.qmcpack_quantity_analyzers.DensityMatricesAnalyzer method) (nexus.qmcpack_quantity_analyzers.SpinDensityAnalyzer method) (nexus.qmcpack_quantity_analyzers.StructureFactorAnalyzer method) write_float() (in module nexus.pwscf_input) write_gcta_report() (nexus.qmcpack.GCTA method) write_inputs() (nexus.bundle.SimulationBundle method) (nexus.simulation.Simulation method) write_int() (in module nexus.pwscf_input) (in module nexus.vasp_input) write_int_array() (in module nexus.vasp_input) write_integer() (in module nexus.rmg_input) write_integer_array() (in module nexus.rmg_input) write_job() (nexus.machines.Machine method) (nexus.machines.Supercomputer method) (nexus.machines.Workstation method) write_job_header() (nexus.machines.ALCF_Machine method) (nexus.machines.Amos method) (nexus.machines.Andes method) (nexus.machines.Archer2 method) (nexus.machines.Aurora method) (nexus.machines.Baseline method) (nexus.machines.Besms method) (nexus.machines.BlueWatersXE method) (nexus.machines.BlueWatersXK method) (nexus.machines.CadesMoab method) (nexus.machines.CadesSlurm method) (nexus.machines.Cooley method) (nexus.machines.Cori method) (nexus.machines.EOS method) (nexus.machines.Frontier method) (nexus.machines.Golub method) (nexus.machines.ICMP_Machine method) (nexus.machines.Improv method) (nexus.machines.Inti method) (nexus.machines.Jaguar method) (nexus.machines.Kagayaki method) (nexus.machines.Kestrel method) (nexus.machines.Kraken method) (nexus.machines.Lassen method) (nexus.machines.Leonardo method) (nexus.machines.Lonestar method) (nexus.machines.NerscMachine method) (nexus.machines.OIC5 method) (nexus.machines.Perlmutter method) (nexus.machines.Polaris method) (nexus.machines.Rhea method) (nexus.machines.Ruby method) (nexus.machines.SnlMachine method) (nexus.machines.Stampede2 method) (nexus.machines.Summit method) (nexus.machines.Supercomputer method) (nexus.machines.SuperMUC method) (nexus.machines.SuperMUC_NG method) (nexus.machines.Theta method) (nexus.machines.Titan method) (nexus.machines.Tomcat3 method) write_job_states() (nexus.machines.Workstation method) write_lowdin() (nexus.pwscf_postprocessors.ProjwfcAnalyzer method) write_old() (nexus.pwscf_input.system method) write_poscar() (nexus.structure.Structure method) write_prep() (nexus.pwscf.Pwscf method) (nexus.qmcpack.Qmcpack method) (nexus.quantum_package.QuantumPackage method) (nexus.simulation.Simulation method) write_qmcpack() (nexus.pseudopotential.SemilocalPP method) write_qp_value() (in module nexus.quantum_package_input) write_real() (in module nexus.vasp_input) write_real_array() (in module nexus.vasp_input) write_scalar() (in module nexus.pwscf_input) write_sim_dependencies() (nexus.project_manager.ProjectManager method) write_simulation_status() (nexus.project_manager.ProjectManager method) write_single_density() (nexus.qmcpack_quantity_analyzers.DensityAnalyzerBase method) write_splash() (nexus.nexus_base.NexusCore static method) write_str() (in module nexus.pwscf_input) write_string() (in module nexus.rmg_input) (in module nexus.vasp_input) write_text() (nexus.basisset.GaussianBasisSet method) (nexus.fileio.ChgcarFile method) (nexus.fileio.PoscarFile method) (nexus.fileio.StandardFile method) (nexus.fileio.XsfFile method) (nexus.gamess_input.GamessInput method) (nexus.pseudopotential.GaussianPP method) (nexus.pseudopotential.Pseudopotential method) (nexus.pwscf_input.atomic_forces method) (nexus.pwscf_input.atomic_positions method) (nexus.pwscf_input.atomic_species method) (nexus.pwscf_input.Card method) (nexus.pwscf_input.cell_parameters method) (nexus.pwscf_input.climbing_images method) (nexus.pwscf_input.collective_vars method) (nexus.pwscf_input.constraints method) (nexus.pwscf_input.hubbard method) (nexus.pwscf_input.k_points method) (nexus.pwscf_input.occupations method) (nexus.pwscf_input.PwscfInput method) (nexus.pwscf_postprocessors.Namelist method) (nexus.pwscf_postprocessors.NamelistInput method) (nexus.pyscf_input.PyscfInput method) (nexus.qmcpack_input.QmcpackInput method) (nexus.quantum_package_input.QuantumPackageInput method) (nexus.rmg_input.RmgInput method) (nexus.simulation.NullSimulationInput method) (nexus.simulation.SimulationInput method) (nexus.simulation.SimulationInputTemplateDev method) (nexus.vasp_input.Kpoints method) (nexus.vasp_input.Poscar method) (nexus.vasp_input.Potcar method) (nexus.vasp_input.VFile method) (nexus.vasp_input.VKeywordFile method) write_val() (nexus.qmcpack_input.Param method) write_value (nexus.vasp_input.Incar attribute) (nexus.vasp_input.Stopcar attribute) write_vec() (nexus.fileio.XsfFile method) write_xsf() (nexus.structure.Structure method) write_xyz() (nexus.structure.Structure method) writeval() (in module nexus.pwscf_postprocessors) (nexus.gamess_input.CardGroup method) (nexus.gamess_input.KeywordGroup method) wrote_something (nexus.nexus_base.NexusCore attribute) wrote_splash (nexus.nexus_base.NexusCore attribute) X Xenon (nexus.periodic_table.Elements attribute) xlabel (nexus.qmcpack_quantity_analyzers.SpaceGridBase attribute) XMLelement (class in nexus.xmlreader) XMLreader (class in nexus.xmlreader) XsfFile (class in nexus.fileio) xyz (nexus.gamess_analyzer.GamessAnalyzer attribute) xyzs (nexus.gamess_analyzer.GamessAnalyzer attribute) Y yesno() (in module nexus.qmcpack_input) yesnostr() (in module nexus.qmcpack_input) ylabel (nexus.qmcpack_quantity_analyzers.SpaceGridBase attribute) Ytterbium (nexus.periodic_table.Elements attribute) Yttrium (nexus.periodic_table.Elements attribute) Z zero() (nexus.hdfreader.HDFgroup method) zero_corner() (nexus.structure.Structure method) zero_data() (nexus.qmcpack_quantity_analyzers.TracesAnalyzer method) zero_time() (nexus.machines.Job class method) Zinc (nexus.periodic_table.Elements attribute) Zirconium (nexus.periodic_table.Elements attribute) zlabel (nexus.qmcpack_quantity_analyzers.SpaceGridBase attribute)
