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 _ __init__() (pyiron_atomistics.atomistics.generic.object_type.ObjectType method) (pyiron_atomistics.atomistics.generic.object_type.ObjectTypeChoice method) (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.atomistic.GenericInput method) (pyiron_atomistics.atomistics.job.atomistic.GenericOutput method) (pyiron_atomistics.atomistics.job.atomistic.MapFunctions method) (pyiron_atomistics.atomistics.job.atomistic.Trajectory method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractiveOutput method) (pyiron_atomistics.atomistics.job.interactive.InteractiveInterface method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.interactivewrapper.ReferenceJobOutput method) (pyiron_atomistics.atomistics.job.potentials.PotentialAbstract method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticJobGenerator method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixCalculator method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.murnaghan.MurnaghanDebyeModel method) (pyiron_atomistics.atomistics.master.murnaghan.MurnaghanJobGenerator method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.GenericOutput method) (pyiron_atomistics.atomistics.master.parallel.MapJobGenerator method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJobGenerator method) (pyiron_atomistics.atomistics.master.phonopy.Thermal method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSJobGenerator method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureJobGenerator method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.atomistics.structure.analyse.Analyse method) (pyiron_atomistics.atomistics.structure.atom.Atom method) (pyiron_atomistics.atomistics.structure.atoms.Atoms method) (pyiron_atomistics.atomistics.structure.atoms.CrystalStructure method) (pyiron_atomistics.atomistics.structure.atoms.Symbols method) (pyiron_atomistics.atomistics.structure.factories.aimsgb.AimsgbFactory method) (pyiron_atomistics.atomistics.structure.factories.ase.AseFactory method) (pyiron_atomistics.atomistics.structure.factories.atomsk.AtomskBuilder method) (pyiron_atomistics.atomistics.structure.factories.atomsk.AtomskFactory method) (pyiron_atomistics.atomistics.structure.factories.compound.CompoundFactory method) (pyiron_atomistics.atomistics.structure.factories.materialsproject.MaterialsProjectFactory method) (pyiron_atomistics.atomistics.structure.factories.materialsproject.MPQueryResults method) (pyiron_atomistics.atomistics.structure.factory.StructureFactory method) (pyiron_atomistics.atomistics.structure.has_structure.HasStructure method) (pyiron_atomistics.atomistics.structure.has_structure.TransformStructure method) (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) (pyiron_atomistics.atomistics.structure.periodic_table.ChemicalElement method) (pyiron_atomistics.atomistics.structure.periodic_table.PeriodicTable method) (pyiron_atomistics.atomistics.structure.structurestorage.StructurePlots method) (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage method) (pyiron_atomistics.atomistics.thermodynamics.thermo_bulk.ThermoBulk method) (pyiron_atomistics.atomistics.volumetric.generic.VolumetricData method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.bader.Bader method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.job.generic.MapFunctions method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_encut_parallel.EncutConvergenceJobGenerator method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.KpointConvergenceJobGenerator method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.dft.waves.bandstructure.BandPath method) (pyiron_atomistics.dft.waves.bandstructure.Bandstructure method) (pyiron_atomistics.dft.waves.electronic.ElectronicStructure method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.gpaw.GpawInput method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.activation_relaxation_technique.ARTInteractive method) (pyiron_atomistics.interactive.activation_relaxation_technique.ARTIntOutput method) (pyiron_atomistics.interactive.quasi_newton.Input method) (pyiron_atomistics.interactive.quasi_newton.Output method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewtonInteractive method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizerInput method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizerOutput method) (pyiron_atomistics.interactive.sxextoptint.Input method) (pyiron_atomistics.interactive.sxextoptint.SxExtOpt method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.Input method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.control.LammpsControl method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.lammps.potential.LammpsPotential method) (pyiron_atomistics.lammps.potential.LammpsPotentialFile method) (pyiron_atomistics.lammps.potential.PotentialAvailable method) (pyiron_atomistics.lammps.structure.LammpsStructure method) (pyiron_atomistics.project.AtomisticsLocalMaintenance method) (pyiron_atomistics.project.AtomisticsMaintenance method) (pyiron_atomistics.project.Creator method) (pyiron_atomistics.project.Project method) (pyiron_atomistics.sphinx.base.Output method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.input_writer.Group method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.interactive.SphinxOutput method) (pyiron_atomistics.sphinx.potential.SphinxJTHPotentialFile method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.sphinx.volumetric_data.SphinxVolumetricData method) (pyiron_atomistics.testing.executable.ExampleExecutable method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleInput method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.toolkit.AtomisticsTools method) (pyiron_atomistics.toolkit.JobFactory method) (pyiron_atomistics.vasp.base.Incar method) (pyiron_atomistics.vasp.base.Input method) (pyiron_atomistics.vasp.base.Kpoints method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.MetadynInput method) (pyiron_atomistics.vasp.metadyn.MetadynOutput method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.output.DFTOutput method) (pyiron_atomistics.vasp.output.GenericOutput method) (pyiron_atomistics.vasp.output.Output method) (pyiron_atomistics.vasp.potential.Potcar method) (pyiron_atomistics.vasp.potential.VaspPotential method) (pyiron_atomistics.vasp.potential.VaspPotentialAbstract method) (pyiron_atomistics.vasp.potential.VaspPotentialFile method) (pyiron_atomistics.vasp.potential.VaspPotentialSetter method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vasprun.Vasprun method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) (pyiron_atomistics.vasp.volumetric_data.VaspVolumetricData method) _get_structure() (pyiron_atomistics.atomistics.structure.has_structure.HasStructure method) _number_of_structures() (pyiron_atomistics.atomistics.structure.has_structure.HasStructure method) _translate_frame() (pyiron_atomistics.atomistics.structure.has_structure.HasStructure method) A a (pyiron_atomistics.atomistics.structure.atom.Atom property) add_array() (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage method) add_chunk() (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage method) add_element() (pyiron_atomistics.atomistics.structure.periodic_table.PeriodicTable method) add_high_symmetry_path() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) add_high_symmetry_points() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) add_kpoint() (pyiron_atomistics.dft.waves.electronic.ElectronicStructure method) add_new_element() (pyiron_atomistics.sphinx.potential.SphinxJTHPotentialFile method) (pyiron_atomistics.vasp.potential.VaspPotentialFile method) add_structure() (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage method) add_tag() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) add_tags() (pyiron_atomistics.atomistics.structure.periodic_table.ChemicalElement method) aimsgb_build() (pyiron_atomistics.atomistics.structure.factory.StructureFactory method) aimsgb_info() (pyiron_atomistics.atomistics.structure.factory.StructureFactory method) AimsgbFactory (class in pyiron_atomistics.atomistics.structure.factories.aimsgb) Analyse (class in pyiron_atomistics.atomistics.structure.analyse) analyse_centro_symmetry() (in module pyiron_atomistics.atomistics.structure.pyscal) analyse_cna_adaptive() (in module pyiron_atomistics.atomistics.structure.pyscal) analyse_diamond_structure() (in module pyiron_atomistics.atomistics.structure.pyscal) analyse_find_solids() (in module pyiron_atomistics.atomistics.structure.pyscal) analyse_minimized_structure() (in module pyiron_atomistics.thermodynamics.interfacemethod) analyse_ovito_centro_symmetry() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) analyse_ovito_cna_adaptive() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) analyse_ovito_voronoi_volume() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) analyse_phonopy_equivalent_atoms() (in module pyiron_atomistics.atomistics.structure.phonopy) analyse_pyscal_centro_symmetry() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) analyse_pyscal_cna_adaptive() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) analyse_pyscal_diamond_structure() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) analyse_pyscal_steinhardt_parameter() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) analyse_pyscal_voronoi_volume() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) analyse_structure() (in module pyiron_atomistics.thermodynamics.interfacemethod) analyse_structures() (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixCalculator method) analyse_voronoi_volume() (in module pyiron_atomistics.atomistics.structure.pyscal) animate_structure() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) animate_structures() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.atomistic.Trajectory method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.structure.factories.materialsproject.MPQueryResults method) (pyiron_atomistics.atomistics.structure.has_structure.HasStructure method) (pyiron_atomistics.atomistics.structure.has_structure.TransformStructure method) (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) append() (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.atomistics.structure.atoms.Atoms method) (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.sphinx.input_writer.Group method) append_charge_density() (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) append_wave_function() (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) apply_strain() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) ART (class in pyiron_atomistics.interactive.activation_relaxation_technique) ARTInteractive (class in pyiron_atomistics.interactive.activation_relaxation_technique) ARTIntOutput (class in pyiron_atomistics.interactive.activation_relaxation_technique) ase_bulk() (pyiron_atomistics.atomistics.structure.factory.StructureFactory method) ase_read() (pyiron_atomistics.atomistics.structure.factory.StructureFactory method) ase_to_pyiron() (in module pyiron_atomistics.atomistics.structure.atom) (in module pyiron_atomistics.atomistics.structure.atoms) AseFactory (class in pyiron_atomistics.atomistics.structure.factories.ase) AseJob (class in pyiron_atomistics.gpaw.pyiron_ase) Atom (class in pyiron_atomistics.atomistics.structure.atom) atomic_number_to_abbreviation() (pyiron_atomistics.atomistics.structure.periodic_table.PeriodicTable method) AtomisticExampleJob (class in pyiron_atomistics.testing.randomatomistic) AtomisticGenericJob (class in pyiron_atomistics.atomistics.job.atomistic) AtomisticParallelMaster (class in pyiron_atomistics.atomistics.master.parallel) AtomisticsLocalMaintenance (class in pyiron_atomistics.project) AtomisticsMaintenance (class in pyiron_atomistics.project) AtomisticsTools (class in pyiron_atomistics.toolkit) Atoms (class in pyiron_atomistics.atomistics.structure.atoms) atoms (pyiron_atomistics.atomistics.volumetric.generic.VolumetricData property) (pyiron_atomistics.sphinx.volumetric_data.SphinxVolumetricData property) (pyiron_atomistics.vasp.volumetric_data.VaspVolumetricData property) atoms() (pyiron_atomistics.atomistics.structure.factory.StructureFactory static method) (pyiron_atomistics.atomistics.structure.structurestorage.StructurePlots method) atoms_from_string() (in module pyiron_atomistics.vasp.structure) AtomskBuilder (class in pyiron_atomistics.atomistics.structure.factories.atomsk) AtomskError AtomskFactory (class in pyiron_atomistics.atomistics.structure.factories.atomsk) B b (pyiron_atomistics.atomistics.structure.atom.Atom property) B2() (pyiron_atomistics.atomistics.structure.factories.compound.CompoundFactory static method) Bader (class in pyiron_atomistics.dft.bader) BandPath (class in pyiron_atomistics.dft.waves.bandstructure) Bandstructure (class in pyiron_atomistics.dft.waves.bandstructure) base_name (pyiron_atomistics.project.Project attribute) (pyiron_atomistics.project.Project property) bond_dict (pyiron_atomistics.lammps.base.LammpsBase property) (pyiron_atomistics.lammps.interactive.LammpsInteractive property) (pyiron_atomistics.lammps.lammps.Lammps property) build() (pyiron_atomistics.atomistics.structure.factories.aimsgb.AimsgbFactory static method) (pyiron_atomistics.atomistics.structure.factories.atomsk.AtomskBuilder method) bulk() (pyiron_atomistics.atomistics.structure.factories.ase.AseFactory method) (pyiron_atomistics.atomistics.structure.factory.StructureFactory method) by_id() (pyiron_atomistics.atomistics.structure.factories.materialsproject.MaterialsProjectFactory static method) C c (pyiron_atomistics.atomistics.structure.atom.Atom property) C14() (pyiron_atomistics.atomistics.structure.factories.compound.CompoundFactory static method) C15() (pyiron_atomistics.atomistics.structure.factories.compound.CompoundFactory static method) C36() (pyiron_atomistics.atomistics.structure.factories.compound.CompoundFactory static method) calc (pyiron_atomistics.atomistics.structure.atoms.Atoms property) calc_free_energy() (pyiron_atomistics.calphy.job.Calphy method) calc_md() (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.control.LammpsControl method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) calc_minimize() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.control.LammpsControl method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) calc_mode_alchemy() (pyiron_atomistics.calphy.job.Calphy method) calc_mode_fe() (pyiron_atomistics.calphy.job.Calphy method) calc_mode_pscale() (pyiron_atomistics.calphy.job.Calphy method) calc_mode_ts() (pyiron_atomistics.calphy.job.Calphy method) calc_static() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) calc_temp_iteration() (in module pyiron_atomistics.thermodynamics.interfacemethod) calc_v0_from_fit_funct() (in module pyiron_atomistics.atomistics.master.quasi) calc_vcsgc() (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.control.LammpsControl method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) calculate_kwargs (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob property) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive property) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper property) (pyiron_atomistics.atomistics.job.sqs.SQSJob property) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer property) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob property) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan property) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster property) (pyiron_atomistics.atomistics.master.parallel.MapMaster property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster property) (pyiron_atomistics.atomistics.master.structure.StructureListMaster property) (pyiron_atomistics.calphy.job.Calphy property) (pyiron_atomistics.dft.job.generic.GenericDFTJob property) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel property) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT property) (pyiron_atomistics.gpaw.gpaw.Gpaw property) (pyiron_atomistics.gpaw.pyiron_ase.AseJob property) (pyiron_atomistics.interactive.activation_relaxation_technique.ART property) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton property) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer property) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive property) (pyiron_atomistics.lammps.base.LammpsBase property) (pyiron_atomistics.lammps.interactive.LammpsInteractive property) (pyiron_atomistics.lammps.lammps.Lammps property) (pyiron_atomistics.sphinx.base.SphinxBase property) (pyiron_atomistics.sphinx.interactive.SphinxInt2 property) (pyiron_atomistics.sphinx.interactive.SphinxInteractive property) (pyiron_atomistics.sphinx.sphinx.Sphinx property) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob property) (pyiron_atomistics.testing.randomatomistic.ExampleJob property) (pyiron_atomistics.thermodynamics.hessian.HessianJob property) (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) Calphy (class in pyiron_atomistics.calphy.job) cbm (pyiron_atomistics.dft.waves.electronic.ElectronicStructure property) cell (pyiron_atomistics.atomistics.structure.atoms.Atoms property) cell() (pyiron_atomistics.atomistics.structure.structurestorage.StructurePlots method) center() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) center_coordinates_in_unit_cell() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) charge (pyiron_atomistics.atomistics.structure.atom.Atom property) check_band_occupancy() (pyiron_atomistics.sphinx.interactive.SphinxOutput method) check_diamond() (in module pyiron_atomistics.thermodynamics.interfacemethod) check_for_holes() (in module pyiron_atomistics.thermodynamics.interfacemethod) check_if_job_exists() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) check_setup() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) chemical_element_dict_to_hdf() (in module pyiron_atomistics.atomistics.structure.periodic_table) chemical_formula() (in module pyiron_atomistics.atomistics.job.sqs) ChemicalElement (class in pyiron_atomistics.atomistics.structure.periodic_table) child_hdf() (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) child_ids (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob property) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive property) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper property) (pyiron_atomistics.atomistics.job.sqs.SQSJob property) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer property) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob property) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan property) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster property) (pyiron_atomistics.atomistics.master.parallel.MapMaster property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster property) (pyiron_atomistics.atomistics.master.structure.StructureListMaster property) (pyiron_atomistics.calphy.job.Calphy property) (pyiron_atomistics.dft.job.generic.GenericDFTJob property) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel property) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT property) (pyiron_atomistics.gpaw.gpaw.Gpaw property) (pyiron_atomistics.gpaw.pyiron_ase.AseJob property) (pyiron_atomistics.interactive.activation_relaxation_technique.ART property) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton property) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer property) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive property) (pyiron_atomistics.lammps.base.LammpsBase property) (pyiron_atomistics.lammps.interactive.LammpsInteractive property) (pyiron_atomistics.lammps.lammps.Lammps property) (pyiron_atomistics.sphinx.base.SphinxBase property) (pyiron_atomistics.sphinx.interactive.SphinxInt2 property) (pyiron_atomistics.sphinx.interactive.SphinxInteractive property) (pyiron_atomistics.sphinx.sphinx.Sphinx property) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob property) (pyiron_atomistics.testing.randomatomistic.ExampleJob property) (pyiron_atomistics.thermodynamics.hessian.HessianJob property) (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) child_names (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper property) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob property) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan property) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster property) (pyiron_atomistics.atomistics.master.parallel.MapMaster property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster property) (pyiron_atomistics.atomistics.master.structure.StructureListMaster property) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel property) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT property) (pyiron_atomistics.interactive.activation_relaxation_technique.ART property) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton property) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer property) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive property) child_project (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper property) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob property) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan property) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster property) (pyiron_atomistics.atomistics.master.parallel.MapMaster property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster property) (pyiron_atomistics.atomistics.master.structure.StructureListMaster property) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel property) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT property) (pyiron_atomistics.interactive.activation_relaxation_technique.ART property) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton property) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer property) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive property) cleanup() (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) clear() (pyiron_atomistics.atomistics.master.parallel.GenericOutput method) (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) (pyiron_atomistics.sphinx.base.Output method) (pyiron_atomistics.sphinx.input_writer.Group method) (pyiron_atomistics.sphinx.interactive.SphinxOutput method) clear_all() (pyiron_atomistics.atomistics.job.atomistic.GenericInput method) (pyiron_atomistics.gpaw.gpaw.GpawInput method) (pyiron_atomistics.interactive.quasi_newton.Input method) (pyiron_atomistics.interactive.sxextoptint.Input method) (pyiron_atomistics.lammps.control.LammpsControl method) (pyiron_atomistics.lammps.potential.LammpsPotential method) (pyiron_atomistics.testing.randomatomistic.ExampleInput method) (pyiron_atomistics.vasp.base.Incar method) (pyiron_atomistics.vasp.base.Kpoints method) (pyiron_atomistics.vasp.potential.Potcar method) clear_bonds() (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) clear_job() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) close() (pyiron_atomistics.project.Project method) cluster_analysis() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) cluster_positions() (pyiron_atomistics.atomistics.structure.analyse.Analyse method) collect() (pyiron_atomistics.sphinx.base.Output method) (pyiron_atomistics.sphinx.interactive.SphinxOutput method) (pyiron_atomistics.vasp.metadyn.MetadynOutput method) (pyiron_atomistics.vasp.output.Output method) collect_energy_dat() (pyiron_atomistics.sphinx.base.Output method) (pyiron_atomistics.sphinx.interactive.SphinxOutput method) collect_energy_struct() (pyiron_atomistics.sphinx.base.Output method) (pyiron_atomistics.sphinx.interactive.SphinxOutput method) collect_eps_dat() (pyiron_atomistics.sphinx.base.Output method) (pyiron_atomistics.sphinx.interactive.SphinxOutput method) collect_errors() (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) collect_general_output() (pyiron_atomistics.calphy.job.Calphy method) collect_logfiles() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) collect_output() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) collect_output_log() (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) collect_relaxed_hist() (pyiron_atomistics.sphinx.base.Output method) (pyiron_atomistics.sphinx.interactive.SphinxOutput method) collect_residue_dat() (pyiron_atomistics.sphinx.base.Output method) (pyiron_atomistics.sphinx.interactive.SphinxOutput method) collect_sphinx_log() (pyiron_atomistics.sphinx.base.Output method) (pyiron_atomistics.sphinx.interactive.SphinxOutput method) collect_spins_dat() (pyiron_atomistics.sphinx.base.Output method) (pyiron_atomistics.sphinx.interactive.SphinxOutput method) collect_structures() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.atomistic.Trajectory method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.structure.factories.materialsproject.MPQueryResults method) (pyiron_atomistics.atomistics.structure.has_structure.HasStructure method) (pyiron_atomistics.atomistics.structure.has_structure.TransformStructure method) (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) collect_warnings() (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) comment_char (pyiron_atomistics.atomistics.job.atomistic.GenericInput property) (pyiron_atomistics.gpaw.gpaw.GpawInput property) (pyiron_atomistics.interactive.quasi_newton.Input property) (pyiron_atomistics.interactive.sxextoptint.Input property) (pyiron_atomistics.lammps.control.LammpsControl property) (pyiron_atomistics.lammps.potential.LammpsPotential property) (pyiron_atomistics.testing.randomatomistic.ExampleInput property) (pyiron_atomistics.vasp.base.Incar property) (pyiron_atomistics.vasp.base.Kpoints property) (pyiron_atomistics.vasp.potential.Potcar property) CompoundFactory (class in pyiron_atomistics.atomistics.structure.factories.compound) compress() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) compress_jobs() (pyiron_atomistics.project.Project method) compute_bader_charges() (pyiron_atomistics.dft.bader.Bader method) compute_neighbors() (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) concentration() (pyiron_atomistics.atomistics.structure.structurestorage.StructurePlots method) constraints (pyiron_atomistics.atomistics.structure.atoms.Atoms property) continue_with_final_structure() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) continue_with_restart_files() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) contour_entropy() (pyiron_atomistics.atomistics.thermodynamics.thermo_bulk.ThermoBulk method) contour_pressure() (pyiron_atomistics.atomistics.thermodynamics.thermo_bulk.ThermoBulk method) ConvEncutParallel (class in pyiron_atomistics.dft.master.convergence_encut_parallel) convergence_check() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) convert_element() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) convert_formula() (pyiron_atomistics.atomistics.structure.atoms.Atoms static method) ConvKpointParallel (class in pyiron_atomistics.dft.master.convergence_kpoint_parallel) coordination() (pyiron_atomistics.atomistics.structure.structurestorage.StructurePlots method) copy() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.GenericOutput method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.atomistics.structure.atoms.Atoms method) (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage method) (pyiron_atomistics.atomistics.thermodynamics.thermo_bulk.ThermoBulk method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.project.Project method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.input_writer.Group method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) copy_file_to_working_directory() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) copy_hamiltonian() (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) copy_potentials() (in module pyiron_atomistics.sphinx.input_writer) copy_template() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) copy_to() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.project.Project method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) count() (pyiron_atomistics.atomistics.structure.atoms.Symbols method) create() (pyiron_atomistics.atomistics.structure.factories.atomsk.AtomskBuilder class method) (pyiron_atomistics.atomistics.structure.factories.atomsk.AtomskFactory method) create_ase_bulk() (pyiron_atomistics.project.Project method) create_atoms() (pyiron_atomistics.project.Project method) create_child_job() (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) create_element() (pyiron_atomistics.project.Project method) create_from_job() (pyiron_atomistics.project.Project method) create_group() (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) (pyiron_atomistics.project.Project method) (pyiron_atomistics.sphinx.input_writer.Group method) create_hdf() (pyiron_atomistics.project.Project static method) create_job() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.project.Project method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) create_job_class() (pyiron_atomistics.project.Project static method) create_job_template() (in module pyiron_atomistics.thermodynamics.interfacemethod) create_line_mode_structure() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) create_object() (pyiron_atomistics.project.Project static method) create_pipeline() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.project.Project method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) create_structure() (pyiron_atomistics.project.Project method) create_surface() (pyiron_atomistics.project.Project method) create_table() (pyiron_atomistics.project.Project method) Creator (class in pyiron_atomistics.project) crystal() (pyiron_atomistics.atomistics.structure.factories.ase.AseFactory method) (pyiron_atomistics.atomistics.structure.factory.StructureFactory static method) CrystalStructure (class in pyiron_atomistics.atomistics.structure.atoms) cut() (pyiron_atomistics.atomistics.structure.factories.ase.AseFactory method) (pyiron_atomistics.atomistics.structure.factory.StructureFactory method) cut_reference_to_atoms() (pyiron_atomistics.atomistics.structure.atom.Atom method) cutoff_radius (pyiron_atomistics.lammps.base.LammpsBase property) (pyiron_atomistics.lammps.interactive.LammpsInteractive property) (pyiron_atomistics.lammps.lammps.Lammps property) cylindrical_average_potential() (pyiron_atomistics.atomistics.volumetric.generic.VolumetricData method) (pyiron_atomistics.sphinx.volumetric_data.SphinxVolumetricData method) (pyiron_atomistics.vasp.volumetric_data.VaspVolumetricData method) D D03() (pyiron_atomistics.atomistics.structure.factories.compound.CompoundFactory static method) db_entry() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) debye_temperature (pyiron_atomistics.atomistics.master.murnaghan.MurnaghanDebyeModel property) decompress() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) default() (in module pyiron_atomistics.atomistics.structure.atoms) define_blocks() (pyiron_atomistics.atomistics.job.atomistic.GenericInput method) (pyiron_atomistics.gpaw.gpaw.GpawInput method) (pyiron_atomistics.interactive.quasi_newton.Input method) (pyiron_atomistics.interactive.sxextoptint.Input method) (pyiron_atomistics.lammps.control.LammpsControl method) (pyiron_atomistics.lammps.potential.LammpsPotential method) (pyiron_atomistics.testing.randomatomistic.ExampleInput method) (pyiron_atomistics.vasp.base.Incar method) (pyiron_atomistics.vasp.base.Kpoints method) (pyiron_atomistics.vasp.potential.Potcar method) define_bonds() (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) defragment_storage() (pyiron_atomistics.project.AtomisticsLocalMaintenance method) del_array() (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage method) delete() (pyiron_atomistics.atomistics.structure.atom.Atom method) delete_output_files_jobs() (pyiron_atomistics.project.Project method) DFTOutput (class in pyiron_atomistics.vasp.output) dict_group_to_hdf() (in module pyiron_atomistics.atomistics.structure.atoms) diff_data (pyiron_atomistics.sphinx.volumetric_data.SphinxVolumetricData property) (pyiron_atomistics.vasp.volumetric_data.VaspVolumetricData property) displacements (pyiron_atomistics.atomistics.job.atomistic.GenericOutput property) (pyiron_atomistics.atomistics.job.interactive.GenericInteractiveOutput property) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizerOutput property) (pyiron_atomistics.sphinx.interactive.SphinxOutput property) dist_between_two_grid_points() (pyiron_atomistics.atomistics.volumetric.generic.VolumetricData static method) (pyiron_atomistics.sphinx.volumetric_data.SphinxVolumetricData static method) (pyiron_atomistics.vasp.volumetric_data.VaspVolumetricData static method) dist_between_two_grid_points_cyl() (pyiron_atomistics.atomistics.volumetric.generic.VolumetricData static method) (pyiron_atomistics.sphinx.volumetric_data.SphinxVolumetricData static method) (pyiron_atomistics.vasp.volumetric_data.VaspVolumetricData static method) distances (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory property) distances() (pyiron_atomistics.atomistics.structure.structurestorage.StructurePlots method) dos_densities (pyiron_atomistics.dft.waves.electronic.ElectronicStructure property) dos_energies (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) (pyiron_atomistics.dft.waves.electronic.ElectronicStructure property) dos_idensities (pyiron_atomistics.dft.waves.electronic.ElectronicStructure property) dos_total (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) drop_status_to_aborted() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) duplicate() (pyiron_atomistics.atomistics.structure.factories.atomsk.AtomskBuilder method) dynamical_matrix (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) dynamical_matrix_at_q() (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) E edit() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) efermi (pyiron_atomistics.dft.waves.electronic.ElectronicStructure property) eg (pyiron_atomistics.dft.waves.electronic.ElectronicStructure property) eigenvalue_matrix (pyiron_atomistics.dft.waves.electronic.ElectronicStructure property) eigenvalues (pyiron_atomistics.dft.waves.electronic.ElectronicStructure property) el_eam_lst (pyiron_atomistics.lammps.structure.LammpsStructure property) ElasticJobGenerator (class in pyiron_atomistics.atomistics.master.elasticmatrix) ElasticMatrixCalculator (class in pyiron_atomistics.atomistics.master.elasticmatrix) ElasticMatrixJob (class in pyiron_atomistics.atomistics.master.elasticmatrix) electronic_structure_dict_to_hdf() (in module pyiron_atomistics.dft.waves.electronic) ElectronicStructure (class in pyiron_atomistics.dft.waves.electronic) element() (in module pyiron_atomistics.atomistics.structure.periodic_table) (pyiron_atomistics.atomistics.structure.factory.StructureFactory static method) (pyiron_atomistics.atomistics.structure.periodic_table.PeriodicTable method) elements (pyiron_atomistics.atomistics.structure.atoms.Atoms property) enable_h5md() (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) EncutConvergenceJobGenerator (class in pyiron_atomistics.dft.master.convergence_encut_parallel) end_value_char (pyiron_atomistics.atomistics.job.atomistic.GenericInput property) (pyiron_atomistics.gpaw.gpaw.GpawInput property) (pyiron_atomistics.interactive.quasi_newton.Input property) (pyiron_atomistics.interactive.sxextoptint.Input property) (pyiron_atomistics.lammps.control.LammpsControl property) (pyiron_atomistics.lammps.potential.LammpsPotential property) (pyiron_atomistics.testing.randomatomistic.ExampleInput property) (pyiron_atomistics.vasp.base.Incar property) (pyiron_atomistics.vasp.base.Kpoints property) (pyiron_atomistics.vasp.potential.Potcar property) energies (pyiron_atomistics.atomistics.thermodynamics.thermo_bulk.ThermoBulk property) energy_kin_per_atom() (pyiron_atomistics.lammps.control.LammpsControl method) energy_pot_per_atom() (pyiron_atomistics.lammps.control.LammpsControl method) energy_vib() (pyiron_atomistics.atomistics.master.murnaghan.MurnaghanDebyeModel method) entropy (pyiron_atomistics.atomistics.thermodynamics.thermo_bulk.ThermoBulk property) euler_rotate() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) ExampleExecutable (class in pyiron_atomistics.testing.executable) ExampleInput (class in pyiron_atomistics.testing.randomatomistic) ExampleJob (class in pyiron_atomistics.testing.randomatomistic) exchange_correlation_functional (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) exclude_groups_hdf (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob property) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive property) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper property) (pyiron_atomistics.atomistics.job.sqs.SQSJob property) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer property) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob property) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan property) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster property) (pyiron_atomistics.atomistics.master.parallel.MapMaster property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster property) (pyiron_atomistics.atomistics.master.structure.StructureListMaster property) (pyiron_atomistics.calphy.job.Calphy property) (pyiron_atomistics.dft.job.generic.GenericDFTJob property) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel property) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT property) (pyiron_atomistics.gpaw.gpaw.Gpaw property) (pyiron_atomistics.gpaw.pyiron_ase.AseJob property) (pyiron_atomistics.interactive.activation_relaxation_technique.ART property) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton property) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer property) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive property) (pyiron_atomistics.lammps.base.LammpsBase property) (pyiron_atomistics.lammps.interactive.LammpsInteractive property) (pyiron_atomistics.lammps.lammps.Lammps property) (pyiron_atomistics.sphinx.base.SphinxBase property) (pyiron_atomistics.sphinx.interactive.SphinxInt2 property) (pyiron_atomistics.sphinx.interactive.SphinxInteractive property) (pyiron_atomistics.sphinx.sphinx.Sphinx property) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob property) (pyiron_atomistics.testing.randomatomistic.ExampleJob property) (pyiron_atomistics.thermodynamics.hessian.HessianJob property) (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) exclude_nodes_hdf (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob property) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive property) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper property) (pyiron_atomistics.atomistics.job.sqs.SQSJob property) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer property) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob property) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan property) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster property) (pyiron_atomistics.atomistics.master.parallel.MapMaster property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster property) (pyiron_atomistics.atomistics.master.structure.StructureListMaster property) (pyiron_atomistics.calphy.job.Calphy property) (pyiron_atomistics.dft.job.generic.GenericDFTJob property) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel property) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT property) (pyiron_atomistics.gpaw.gpaw.Gpaw property) (pyiron_atomistics.gpaw.pyiron_ase.AseJob property) (pyiron_atomistics.interactive.activation_relaxation_technique.ART property) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton property) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer property) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive property) (pyiron_atomistics.lammps.base.LammpsBase property) (pyiron_atomistics.lammps.interactive.LammpsInteractive property) (pyiron_atomistics.lammps.lammps.Lammps property) (pyiron_atomistics.sphinx.base.SphinxBase property) (pyiron_atomistics.sphinx.interactive.SphinxInt2 property) (pyiron_atomistics.sphinx.interactive.SphinxInteractive property) (pyiron_atomistics.sphinx.sphinx.Sphinx property) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob property) (pyiron_atomistics.testing.randomatomistic.ExampleJob property) (pyiron_atomistics.thermodynamics.hessian.HessianJob property) (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) executable (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob property) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive property) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper property) (pyiron_atomistics.atomistics.job.sqs.SQSJob property) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer property) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob property) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan property) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster property) (pyiron_atomistics.atomistics.master.parallel.MapMaster property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster property) (pyiron_atomistics.atomistics.master.structure.StructureListMaster property) (pyiron_atomistics.calphy.job.Calphy property) (pyiron_atomistics.dft.job.generic.GenericDFTJob property) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel property) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT property) (pyiron_atomistics.gpaw.gpaw.Gpaw property) (pyiron_atomistics.gpaw.pyiron_ase.AseJob property) (pyiron_atomistics.interactive.activation_relaxation_technique.ART property) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton property) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer property) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive property) (pyiron_atomistics.lammps.base.LammpsBase property) (pyiron_atomistics.lammps.interactive.LammpsInteractive property) (pyiron_atomistics.lammps.lammps.Lammps property) (pyiron_atomistics.sphinx.base.SphinxBase property) (pyiron_atomistics.sphinx.interactive.SphinxInt2 property) (pyiron_atomistics.sphinx.interactive.SphinxInteractive property) (pyiron_atomistics.sphinx.sphinx.Sphinx property) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob property) (pyiron_atomistics.testing.randomatomistic.ExampleJob property) (pyiron_atomistics.thermodynamics.hessian.HessianJob property) (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) extend() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage method) (pyiron_atomistics.sphinx.input_writer.Group method) F file_name (pyiron_atomistics.atomistics.job.atomistic.GenericInput property) (pyiron_atomistics.gpaw.gpaw.GpawInput property) (pyiron_atomistics.interactive.quasi_newton.Input property) (pyiron_atomistics.interactive.sxextoptint.Input property) (pyiron_atomistics.lammps.control.LammpsControl property) (pyiron_atomistics.lammps.potential.LammpsPotential property) (pyiron_atomistics.testing.randomatomistic.ExampleInput property) (pyiron_atomistics.vasp.base.Incar property) (pyiron_atomistics.vasp.base.Kpoints property) (pyiron_atomistics.vasp.potential.Potcar property) files (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob property) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive property) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper property) (pyiron_atomistics.atomistics.job.sqs.SQSJob property) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer property) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob property) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan property) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster property) (pyiron_atomistics.atomistics.master.parallel.MapMaster property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster property) (pyiron_atomistics.atomistics.master.structure.StructureListMaster property) (pyiron_atomistics.calphy.job.Calphy property) (pyiron_atomistics.dft.job.generic.GenericDFTJob property) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel property) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT property) (pyiron_atomistics.gpaw.gpaw.Gpaw property) (pyiron_atomistics.gpaw.pyiron_ase.AseJob property) (pyiron_atomistics.interactive.activation_relaxation_technique.ART property) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton property) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer property) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive property) (pyiron_atomistics.lammps.base.LammpsBase property) (pyiron_atomistics.lammps.interactive.LammpsInteractive property) (pyiron_atomistics.lammps.lammps.Lammps property) (pyiron_atomistics.sphinx.base.SphinxBase property) (pyiron_atomistics.sphinx.interactive.SphinxInt2 property) (pyiron_atomistics.sphinx.interactive.SphinxInteractive property) (pyiron_atomistics.sphinx.sphinx.Sphinx property) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob property) (pyiron_atomistics.testing.randomatomistic.ExampleJob property) (pyiron_atomistics.thermodynamics.hessian.HessianJob property) (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) find() (pyiron_atomistics.atomistics.job.potentials.PotentialAbstract method) (pyiron_atomistics.lammps.potential.LammpsPotentialFile method) (pyiron_atomistics.sphinx.potential.SphinxJTHPotentialFile method) (pyiron_atomistics.vasp.potential.VaspPotentialAbstract method) (pyiron_atomistics.vasp.potential.VaspPotentialFile method) find_chunk() (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage method) find_default() (pyiron_atomistics.lammps.potential.LammpsPotentialFile method) find_mic() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) find_neighbors_by_vector() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) first_child_name() (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) fix_iso() (in module pyiron_atomistics.thermodynamics.interfacemethod) fix_move_linear_by_id() (pyiron_atomistics.lammps.control.LammpsControl method) fix_setforce_by_id() (pyiron_atomistics.lammps.control.LammpsControl method) fix_spin_constraint (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) fix_z_dir() (in module pyiron_atomistics.thermodynamics.interfacemethod) force_max (pyiron_atomistics.atomistics.job.atomistic.GenericOutput property) (pyiron_atomistics.atomistics.job.interactive.GenericInteractiveOutput property) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizerOutput property) (pyiron_atomistics.sphinx.interactive.SphinxOutput property) formula (pyiron_atomistics.atomistics.structure.atoms.Symbols property) freeze_one_half() (in module pyiron_atomistics.thermodynamics.interfacemethod) from_ase() (pyiron_atomistics.atomistics.structure.factory.StructureFactory static method) from_dict() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.atomistic.GenericInput method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.gpaw.GpawInput method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.Input method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.Input method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.control.LammpsControl method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.lammps.potential.LammpsPotential method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.input_writer.Group method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleInput method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.Incar method) (pyiron_atomistics.vasp.base.Kpoints method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.potential.Potcar method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) from_directory() (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) from_file() (pyiron_atomistics.sphinx.volumetric_data.SphinxVolumetricData method) (pyiron_atomistics.vasp.vasprun.Vasprun method) (pyiron_atomistics.vasp.volumetric_data.VaspVolumetricData method) from_hdf() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.atomistic.GenericInput method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.atomistics.structure.atoms.Atoms method) (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) (pyiron_atomistics.atomistics.structure.periodic_table.ChemicalElement method) (pyiron_atomistics.atomistics.structure.periodic_table.PeriodicTable method) (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage method) (pyiron_atomistics.atomistics.volumetric.generic.VolumetricData method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.dft.waves.electronic.ElectronicStructure method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.gpaw.GpawInput method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.Input method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizerInput method) (pyiron_atomistics.interactive.sxextoptint.Input method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.Input method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.control.LammpsControl method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.lammps.potential.LammpsPotential method) (pyiron_atomistics.sphinx.base.Output method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.input_writer.Group method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.interactive.SphinxOutput method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.sphinx.volumetric_data.SphinxVolumetricData method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleInput method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.Incar method) (pyiron_atomistics.vasp.base.Kpoints method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.MetadynOutput method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.output.DFTOutput method) (pyiron_atomistics.vasp.output.GenericOutput method) (pyiron_atomistics.vasp.output.Output method) (pyiron_atomistics.vasp.potential.Potcar method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) (pyiron_atomistics.vasp.volumetric_data.VaspVolumetricData method) from_hdf_args() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob class method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive class method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper class method) (pyiron_atomistics.atomistics.job.sqs.SQSJob class method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer class method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob class method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan class method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster class method) (pyiron_atomistics.atomistics.master.parallel.MapMaster class method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob class method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob class method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster class method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster class method) (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory class method) (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage class method) (pyiron_atomistics.calphy.job.Calphy class method) (pyiron_atomistics.dft.job.generic.GenericDFTJob class method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel class method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel class method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT class method) (pyiron_atomistics.gpaw.gpaw.Gpaw class method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob class method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART class method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton class method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer class method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizerInput class method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive class method) (pyiron_atomistics.lammps.base.LammpsBase class method) (pyiron_atomistics.lammps.interactive.LammpsInteractive class method) (pyiron_atomistics.lammps.lammps.Lammps class method) (pyiron_atomistics.sphinx.base.SphinxBase class method) (pyiron_atomistics.sphinx.input_writer.Group class method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 class method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive class method) (pyiron_atomistics.sphinx.sphinx.Sphinx class method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob class method) (pyiron_atomistics.testing.randomatomistic.ExampleJob class method) (pyiron_atomistics.thermodynamics.hessian.HessianJob class method) (pyiron_atomistics.vasp.base.VaspBase class method) (pyiron_atomistics.vasp.interactive.VaspInteractive class method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn class method) (pyiron_atomistics.vasp.vasp.Vasp class method) (pyiron_atomistics.vasp.vaspsol.VaspSol class method) from_hdf_old() (pyiron_atomistics.dft.waves.electronic.ElectronicStructure method) from_ovito() (pyiron_atomistics.atomistics.structure.factory.StructureFactory static method) from_pymatgen() (pyiron_atomistics.atomistics.structure.factory.StructureFactory static method) fromdict() (pyiron_atomistics.atomistics.structure.atoms.Atoms class method) fromkeys() (pyiron_atomistics.atomistics.master.parallel.GenericOutput method) G gauss_f() (pyiron_atomistics.atomistics.volumetric.generic.VolumetricData static method) (pyiron_atomistics.sphinx.volumetric_data.SphinxVolumetricData static method) (pyiron_atomistics.vasp.volumetric_data.VaspVolumetricData static method) generate_from_matrices() (pyiron_atomistics.dft.waves.electronic.ElectronicStructure method) generate_random_seed() (in module pyiron_atomistics.thermodynamics.interfacemethod) generate_seed_from_job() (pyiron_atomistics.lammps.control.LammpsControl static method) generate_structure() (in module pyiron_atomistics.thermodynamics.interfacemethod) generate_structures() (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixCalculator method) generic_output_dict_to_hdf() (in module pyiron_atomistics.vasp.output) GenericDFTJob (class in pyiron_atomistics.dft.job.generic) GenericInput (class in pyiron_atomistics.atomistics.job.atomistic) GenericInteractive (class in pyiron_atomistics.atomistics.job.interactive) GenericInteractiveOutput (class in pyiron_atomistics.atomistics.job.interactive) GenericOutput (class in pyiron_atomistics.atomistics.job.atomistic) (class in pyiron_atomistics.atomistics.master.parallel) (class in pyiron_atomistics.vasp.output) get() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.atomistic.GenericInput method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.GenericOutput method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.atomistics.structure.atom.Atom method) (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.gpaw.GpawInput method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.Input method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.Input method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.control.LammpsControl method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.lammps.potential.LammpsPotential method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.input_writer.Group method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleInput method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.Incar method) (pyiron_atomistics.vasp.base.Kpoints method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.potential.Potcar method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) get_all_distances() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_angle() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_angles() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_angular_momentum() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_array() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage method) get_array_filled() (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage method) get_array_ragged() (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage method) get_atomic_numbers() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_attribute() (pyiron_atomistics.atomistics.job.atomistic.GenericInput method) (pyiron_atomistics.gpaw.gpaw.GpawInput method) (pyiron_atomistics.interactive.quasi_newton.Input method) (pyiron_atomistics.interactive.sxextoptint.Input method) (pyiron_atomistics.lammps.control.LammpsControl method) (pyiron_atomistics.lammps.potential.LammpsPotential method) (pyiron_atomistics.testing.randomatomistic.ExampleInput method) (pyiron_atomistics.vasp.base.Incar method) (pyiron_atomistics.vasp.base.Kpoints method) (pyiron_atomistics.vasp.potential.Potcar method) get_average_along_axis() (pyiron_atomistics.atomistics.volumetric.generic.VolumetricData method) (pyiron_atomistics.sphinx.volumetric_data.SphinxVolumetricData method) (pyiron_atomistics.vasp.volumetric_data.VaspVolumetricData method) get_average_waves() (in module pyiron_atomistics.table.funct) get_bader_charges() (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) get_bader_volumes() (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) get_band_gap() (pyiron_atomistics.dft.waves.electronic.ElectronicStructure method) get_band_structure() (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) get_BFGS() (in module pyiron_atomistics.interactive.quasi_newton) get_bonds() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_calculate_function() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) get_calculator() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_cbm() (pyiron_atomistics.dft.waves.electronic.ElectronicStructure method) get_cell() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_cell_lengths_and_angles() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_celldisp() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_center_of_mass() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_center_point() (in module pyiron_atomistics.thermodynamics.interfacemethod) get_charge() (pyiron_atomistics.lammps.potential.LammpsPotential method) get_charge_density() (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) get_charges() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_chemical_elements() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_chemical_formula() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) (pyiron_atomistics.atomistics.structure.atoms.Symbols method) get_chemical_indices() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_chemical_symbols() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_child_cores() (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) get_child_ids() (pyiron_atomistics.project.Project method) get_convergence_check() (in module pyiron_atomistics.table.funct) get_db_columns() (pyiron_atomistics.project.Project method) get_delaunay_neighbors() (pyiron_atomistics.atomistics.structure.analyse.Analyse method) get_density() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_density_of_states() (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) get_dihedral() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_dihedrals() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_dipole_moment() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_displacements() (pyiron_atomistics.atomistics.job.atomistic.GenericOutput static method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractiveOutput static method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizerOutput static method) (pyiron_atomistics.sphinx.interactive.SphinxOutput static method) get_distance() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_distances() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_distances_array() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_dos() (pyiron_atomistics.dft.waves.electronic.ElectronicStructure method) get_e_band() (in module pyiron_atomistics.table.funct) get_e_conv_level() (in module pyiron_atomistics.table.funct) get_eddrmm_handling() (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) get_ekin_error() (in module pyiron_atomistics.table.funct) get_electronic_structure() (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vasprun.Vasprun method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) get_electrostatic_potential() (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) get_element_id() (pyiron_atomistics.lammps.potential.LammpsPotential method) get_elements() (in module pyiron_atomistics.table.funct) (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage method) get_encut() (in module pyiron_atomistics.table.funct) get_energy() (pyiron_atomistics.testing.executable.ExampleExecutable method) get_energy_free() (in module pyiron_atomistics.table.funct) get_energy_free_per_atom() (in module pyiron_atomistics.table.funct) get_energy_int() (in module pyiron_atomistics.table.funct) get_energy_int_per_atom() (in module pyiron_atomistics.table.funct) get_energy_pot() (in module pyiron_atomistics.table.funct) get_energy_pot_per_atom() (in module pyiron_atomistics.table.funct) get_energy_tot() (in module pyiron_atomistics.table.funct) get_energy_tot_per_atom() (in module pyiron_atomistics.table.funct) get_enmax_among_potentials() (in module pyiron_atomistics.vasp.potential) get_enmax_among_species() (in module pyiron_atomistics.vasp.potential) get_entropy_p() (pyiron_atomistics.atomistics.thermodynamics.thermo_bulk.ThermoBulk method) get_entropy_v() (pyiron_atomistics.atomistics.thermodynamics.thermo_bulk.ThermoBulk method) get_equilibrium_parameters() (in module pyiron_atomistics.table.funct) get_equivalent_points() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_extended_positions() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_external_input() (pyiron_atomistics.project.Project static method) get_f_states() (in module pyiron_atomistics.table.funct) get_final_structure() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vasprun.Vasprun method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) get_final_structure_from_file() (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) get_forces() (in module pyiron_atomistics.table.funct) (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_free_energy() (pyiron_atomistics.atomistics.thermodynamics.thermo_bulk.ThermoBulk method) get_free_energy_p() (pyiron_atomistics.atomistics.thermodynamics.thermo_bulk.ThermoBulk method) get_from_table() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) get_global_number_of_atoms() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_hesse_matrix() (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) get_high_symmetry_path() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_high_symmetry_points() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_icharg_value() (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) get_incar() (in module pyiron_atomistics.table.funct) get_initial_charges() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_initial_magnetic_moments() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_initial_melting_temperature_guess() (in module pyiron_atomistics.thermodynamics.interfacemethod) get_initial_structure() (pyiron_atomistics.vasp.vasprun.Vasprun method) get_input_parameter_dict() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.Input method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.MetadynInput method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) get_ir_reciprocal_mesh() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_ismear() (in module pyiron_atomistics.table.funct) get_job_id() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.project.Project method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) get_job_ids() (pyiron_atomistics.project.Project method) get_job_name() (in module pyiron_atomistics.table.funct) get_job_status() (pyiron_atomistics.project.Project method) get_job_working_directory() (pyiron_atomistics.project.Project method) get_jobs() (pyiron_atomistics.project.Project method) get_jobs_status() (pyiron_atomistics.project.Project method) get_k_mesh_by_cell() (in module pyiron_atomistics.vasp.base) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) get_k_mesh_by_density() (in module pyiron_atomistics.dft.job.generic) get_kinetic_energy() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_kinetic_stress() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_kinetic_stresses() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_layers() (pyiron_atomistics.atomistics.structure.analyse.Analyse method) get_magnetic_moment() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_magnetic_moments() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) get_magnetic_structure() (in module pyiron_atomistics.table.funct) get_majority() (in module pyiron_atomistics.table.funct) get_majority_crystal_structure() (in module pyiron_atomistics.table.funct) get_majority_species() (in module pyiron_atomistics.table.funct) (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_masses() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_masses_dof() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_minimum_energy_path() (pyiron_atomistics.atomistics.thermodynamics.thermo_bulk.ThermoBulk method) get_momenta() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_moments_of_inertia() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_n_equ_kpts() (in module pyiron_atomistics.table.funct) get_n_kpts() (in module pyiron_atomistics.table.funct) get_neighborhood() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_neighbors() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.atomistic.Trajectory method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.structure.atoms.Atoms method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) get_neighbors_by_distance() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_neighbors_snapshots() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.atomistic.Trajectory method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) get_nelect() (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) get_number_of_atoms() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_number_of_degrees_of_freedom() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_number_of_final_electronic_steps() (in module pyiron_atomistics.table.funct) get_number_of_ionic_steps() (in module pyiron_atomistics.table.funct) get_number_of_species() (in module pyiron_atomistics.table.funct) (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_number_species_atoms() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_numbers_of_neighbors_in_sphere() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_nve_job_name() (in module pyiron_atomistics.thermodynamics.interfacemethod) get_pandas() (pyiron_atomistics.atomistics.job.atomistic.GenericInput method) (pyiron_atomistics.gpaw.gpaw.GpawInput method) (pyiron_atomistics.interactive.quasi_newton.Input method) (pyiron_atomistics.interactive.sxextoptint.Input method) (pyiron_atomistics.lammps.control.LammpsControl method) (pyiron_atomistics.lammps.potential.LammpsPotential method) (pyiron_atomistics.testing.randomatomistic.ExampleInput method) (pyiron_atomistics.vasp.base.Incar method) (pyiron_atomistics.vasp.base.Kpoints method) (pyiron_atomistics.vasp.potential.Potcar method) get_parent_basis() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_parent_symbols() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_pathes() (pyiron_atomistics.dft.waves.bandstructure.Bandstructure method) get_pbc() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_plane_waves() (in module pyiron_atomistics.table.funct) get_poscar_content() (in module pyiron_atomistics.vasp.structure) get_positions() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_potential_energies() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_potential_energy() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_potentials() (pyiron_atomistics.calphy.job.Calphy method) get_potentials_for_structure() (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) get_potentiostat_output() (pyiron_atomistics.vasp.vasprun.Vasprun method) get_press() (in module pyiron_atomistics.thermodynamics.interfacemethod) get_primitive_cell() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_project_size() (pyiron_atomistics.project.Project method) get_properties() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_PSB() (in module pyiron_atomistics.interactive.quasi_newton) get_raw() (pyiron_atomistics.atomistics.structure.atom.Atom method) get_reciprocal_cell() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_repository_status() (pyiron_atomistics.project.AtomisticsMaintenance static method) get_resolved_dos() (pyiron_atomistics.dft.waves.electronic.ElectronicStructure method) get_rwigs() (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) get_scaled_positions() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_scf_group() (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) get_shell_matrix() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_sigma() (in module pyiron_atomistics.table.funct) get_spacegroup() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_species_objects() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_species_symbols() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_spherical_coordinates() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_spin_resolved_dos() (pyiron_atomistics.dft.waves.electronic.ElectronicStructure method) get_SR() (in module pyiron_atomistics.interactive.quasi_newton) get_steinhardt_parameter_structure() (in module pyiron_atomistics.atomistics.structure.pyscal) get_strain() (pyiron_atomistics.atomistics.structure.analyse.Analyse method) get_strain_lst() (in module pyiron_atomistics.thermodynamics.interfacemethod) get_stress() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_stresses() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_string_lst() (pyiron_atomistics.atomistics.job.atomistic.GenericInput method) (pyiron_atomistics.gpaw.gpaw.GpawInput method) (pyiron_atomistics.interactive.quasi_newton.Input method) (pyiron_atomistics.interactive.sxextoptint.Input method) (pyiron_atomistics.lammps.control.LammpsControl method) (pyiron_atomistics.lammps.potential.LammpsPotential method) (pyiron_atomistics.testing.randomatomistic.ExampleInput method) (pyiron_atomistics.vasp.base.Incar method) (pyiron_atomistics.vasp.base.Kpoints method) (pyiron_atomistics.vasp.potential.Potcar method) get_structure() (in module pyiron_atomistics.table.funct) (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.atomistic.Trajectory method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.structure.factories.materialsproject.MPQueryResults method) (pyiron_atomistics.atomistics.structure.has_structure.HasStructure method) (pyiron_atomistics.atomistics.structure.has_structure.TransformStructure method) (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.project.Project method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) get_structure_group() (in module pyiron_atomistics.sphinx.input_writer) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) get_symmetry() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_symmetry_dataset() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_tags() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_temperature() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_thermal_properties() (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) get_total_energy() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_total_number_of_atoms() (in module pyiron_atomistics.table.funct) get_valence_and_total_charge_density() (in module pyiron_atomistics.dft.bader) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) get_valence_electrons_per_atom() (pyiron_atomistics.vasp.vasprun.Vasprun method) get_vbm() (pyiron_atomistics.dft.waves.electronic.ElectronicStructure method) get_velocities() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_vertical_length() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_volume() (in module pyiron_atomistics.table.funct) (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_volume_per_atom() (in module pyiron_atomistics.table.funct) get_voronoi_neighbors() (pyiron_atomistics.atomistics.structure.analyse.Analyse method) get_voronoi_vertices() (pyiron_atomistics.atomistics.structure.analyse.Analyse method) get_voronoi_volume() (in module pyiron_atomistics.thermodynamics.interfacemethod) (pyiron_atomistics.atomistics.structure.atoms.Atoms method) get_workdir_file() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) get_wrapped_coordinates() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) Gpaw (class in pyiron_atomistics.gpaw.gpaw) GpawInput (class in pyiron_atomistics.gpaw.gpaw) grand_dos_matrix (pyiron_atomistics.dft.waves.electronic.ElectronicStructure property) Group (class in pyiron_atomistics.sphinx.input_writer) group_points_by_symmetry() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) groups() (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) (pyiron_atomistics.project.Project method) (pyiron_atomistics.sphinx.input_writer.Group method) gui() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.project.Project method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) H half_velocity() (in module pyiron_atomistics.thermodynamics.interfacemethod) has() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) has_array() (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage method) has_keys() (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) (pyiron_atomistics.sphinx.input_writer.Group method) HasStructure (class in pyiron_atomistics.atomistics.structure.has_structure) HessianJob (class in pyiron_atomistics.thermodynamics.hessian) high_index_surface() (pyiron_atomistics.atomistics.structure.factory.StructureFactory method) high_index_surface_info() (pyiron_atomistics.atomistics.structure.factory.StructureFactory method) history (pyiron_atomistics.project.Project attribute) (pyiron_atomistics.project.Project property) I id (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob property) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive property) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper property) (pyiron_atomistics.atomistics.job.sqs.SQSJob property) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer property) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob property) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan property) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster property) (pyiron_atomistics.atomistics.master.parallel.MapMaster property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster property) (pyiron_atomistics.atomistics.master.structure.StructureListMaster property) (pyiron_atomistics.calphy.job.Calphy property) (pyiron_atomistics.dft.job.generic.GenericDFTJob property) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel property) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT property) (pyiron_atomistics.gpaw.gpaw.Gpaw property) (pyiron_atomistics.gpaw.pyiron_ase.AseJob property) (pyiron_atomistics.interactive.activation_relaxation_technique.ART property) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton property) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer property) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive property) (pyiron_atomistics.lammps.base.LammpsBase property) (pyiron_atomistics.lammps.interactive.LammpsInteractive property) (pyiron_atomistics.lammps.lammps.Lammps property) (pyiron_atomistics.sphinx.base.SphinxBase property) (pyiron_atomistics.sphinx.interactive.SphinxInt2 property) (pyiron_atomistics.sphinx.interactive.SphinxInteractive property) (pyiron_atomistics.sphinx.sphinx.Sphinx property) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob property) (pyiron_atomistics.testing.randomatomistic.ExampleJob property) (pyiron_atomistics.thermodynamics.hessian.HessianJob property) (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) import_from_path() (pyiron_atomistics.project.Project method) import_single_calculation() (pyiron_atomistics.project.Project method) Incar (class in pyiron_atomistics.vasp.base) incar (pyiron_atomistics.vasp.base.Input attribute) index() (pyiron_atomistics.atomistics.structure.atoms.Symbols method) indices (pyiron_atomistics.atomistics.structure.atoms.Atoms attribute) (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory property) indices() (pyiron_atomistics.atomistics.structure.atoms.Symbols method) info() (pyiron_atomistics.atomistics.structure.factories.aimsgb.AimsgbFactory static method) initialise_iterators() (in module pyiron_atomistics.thermodynamics.interfacemethod) Input (class in pyiron_atomistics.interactive.quasi_newton) (class in pyiron_atomistics.interactive.sxextoptint) (class in pyiron_atomistics.lammps.base) (class in pyiron_atomistics.vasp.base) input (pyiron_atomistics.lammps.base.LammpsBase attribute) (pyiron_atomistics.lammps.lammps.Lammps attribute) (pyiron_atomistics.vasp.base.VaspBase attribute) insert() (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) (pyiron_atomistics.sphinx.input_writer.Group method) inspect() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) inspect_emperical_potentials() (pyiron_atomistics.project.Project static method) install() (in module pyiron_atomistics) instantiate() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob class method) (pyiron_atomistics.atomistics.job.atomistic.GenericInput class method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive class method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper class method) (pyiron_atomistics.atomistics.job.sqs.SQSJob class method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer class method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob class method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan class method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster class method) (pyiron_atomistics.atomistics.master.parallel.MapMaster class method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob class method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob class method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster class method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster class method) (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory class method) (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage class method) (pyiron_atomistics.calphy.job.Calphy class method) (pyiron_atomistics.dft.job.generic.GenericDFTJob class method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel class method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel class method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT class method) (pyiron_atomistics.gpaw.gpaw.Gpaw class method) (pyiron_atomistics.gpaw.gpaw.GpawInput class method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob class method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART class method) (pyiron_atomistics.interactive.quasi_newton.Input class method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton class method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer class method) (pyiron_atomistics.interactive.sxextoptint.Input class method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive class method) (pyiron_atomistics.lammps.base.LammpsBase class method) (pyiron_atomistics.lammps.control.LammpsControl class method) (pyiron_atomistics.lammps.interactive.LammpsInteractive class method) (pyiron_atomistics.lammps.lammps.Lammps class method) (pyiron_atomistics.lammps.potential.LammpsPotential class method) (pyiron_atomistics.sphinx.base.SphinxBase class method) (pyiron_atomistics.sphinx.input_writer.Group class method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 class method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive class method) (pyiron_atomistics.sphinx.sphinx.Sphinx class method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob class method) (pyiron_atomistics.testing.randomatomistic.ExampleInput class method) (pyiron_atomistics.testing.randomatomistic.ExampleJob class method) (pyiron_atomistics.thermodynamics.hessian.HessianJob class method) (pyiron_atomistics.vasp.base.Incar class method) (pyiron_atomistics.vasp.base.Kpoints class method) (pyiron_atomistics.vasp.base.VaspBase class method) (pyiron_atomistics.vasp.interactive.VaspInteractive class method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn class method) (pyiron_atomistics.vasp.potential.Potcar class method) (pyiron_atomistics.vasp.vasp.Vasp class method) (pyiron_atomistics.vasp.vaspsol.VaspSol class method) interactive_close() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) interactive_fetch() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) interactive_flush() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) interactive_is_activated() (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) interactive_open() (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) interactive_prepare() (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) interactive_ref_job_initialize() (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) interactive_store_in_cache() (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) interactive_stress_getter() (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) InteractiveInterface (class in pyiron_atomistics.atomistics.job.interactive) InteractiveWrapper (class in pyiron_atomistics.atomistics.job.interactivewrapper) interpolate() (pyiron_atomistics.atomistics.master.murnaghan.MurnaghanDebyeModel method) interpolate_volume() (pyiron_atomistics.atomistics.thermodynamics.thermo_bulk.ThermoBulk method) ionic_energy_tolerance (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizerInput property) ionic_force_tolerance (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizerInput property) ionic_steps (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizerInput property) is_compressed() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) is_element() (pyiron_atomistics.atomistics.structure.periodic_table.PeriodicTable method) is_finished() (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) is_master_id() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) is_metal (pyiron_atomistics.dft.waves.electronic.ElectronicStructure property) is_self_archived() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) is_skewed() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) items() (pyiron_atomistics.atomistics.master.parallel.GenericOutput method) (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) (pyiron_atomistics.project.Project method) (pyiron_atomistics.sphinx.input_writer.Group method) iter_groups() (pyiron_atomistics.project.Project method) iter_jobs() (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.project.Project method) iter_output() (pyiron_atomistics.project.Project method) iter_structures() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.atomistic.Trajectory method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.structure.factories.materialsproject.MPQueryResults method) (pyiron_atomistics.atomistics.structure.has_structure.HasStructure method) (pyiron_atomistics.atomistics.structure.has_structure.TransformStructure method) (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) J job_file_name() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) job_id (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob property) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive property) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper property) (pyiron_atomistics.atomistics.job.sqs.SQSJob property) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer property) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob property) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan property) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster property) (pyiron_atomistics.atomistics.master.parallel.MapMaster property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster property) (pyiron_atomistics.atomistics.master.structure.StructureListMaster property) (pyiron_atomistics.calphy.job.Calphy property) (pyiron_atomistics.dft.job.generic.GenericDFTJob property) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel property) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT property) (pyiron_atomistics.gpaw.gpaw.Gpaw property) (pyiron_atomistics.gpaw.pyiron_ase.AseJob property) (pyiron_atomistics.interactive.activation_relaxation_technique.ART property) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton property) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer property) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive property) (pyiron_atomistics.lammps.base.LammpsBase property) (pyiron_atomistics.lammps.interactive.LammpsInteractive property) (pyiron_atomistics.lammps.lammps.Lammps property) (pyiron_atomistics.sphinx.base.SphinxBase property) (pyiron_atomistics.sphinx.interactive.SphinxInt2 property) (pyiron_atomistics.sphinx.interactive.SphinxInteractive property) (pyiron_atomistics.sphinx.sphinx.Sphinx property) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob property) (pyiron_atomistics.testing.randomatomistic.ExampleJob property) (pyiron_atomistics.thermodynamics.hessian.HessianJob property) (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) job_info_str (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob property) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive property) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper property) (pyiron_atomistics.atomistics.job.sqs.SQSJob property) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer property) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob property) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan property) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster property) (pyiron_atomistics.atomistics.master.parallel.MapMaster property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster property) (pyiron_atomistics.atomistics.master.structure.StructureListMaster property) (pyiron_atomistics.calphy.job.Calphy property) (pyiron_atomistics.dft.job.generic.GenericDFTJob property) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel property) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT property) (pyiron_atomistics.gpaw.gpaw.Gpaw property) (pyiron_atomistics.gpaw.pyiron_ase.AseJob property) (pyiron_atomistics.interactive.activation_relaxation_technique.ART property) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton property) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer property) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive property) (pyiron_atomistics.lammps.base.LammpsBase property) (pyiron_atomistics.lammps.interactive.LammpsInteractive property) (pyiron_atomistics.lammps.lammps.Lammps property) (pyiron_atomistics.sphinx.base.SphinxBase property) (pyiron_atomistics.sphinx.interactive.SphinxInt2 property) (pyiron_atomistics.sphinx.interactive.SphinxInteractive property) (pyiron_atomistics.sphinx.sphinx.Sphinx property) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob property) (pyiron_atomistics.testing.randomatomistic.ExampleJob property) (pyiron_atomistics.thermodynamics.hessian.HessianJob property) (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) job_name (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob property) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive property) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper property) (pyiron_atomistics.atomistics.job.sqs.SQSJob property) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer property) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob property) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan property) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster property) (pyiron_atomistics.atomistics.master.parallel.MapMaster property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster property) (pyiron_atomistics.atomistics.master.structure.StructureListMaster property) (pyiron_atomistics.calphy.job.Calphy property) (pyiron_atomistics.dft.job.generic.GenericDFTJob property) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel property) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT property) (pyiron_atomistics.gpaw.gpaw.Gpaw property) (pyiron_atomistics.gpaw.pyiron_ase.AseJob property) (pyiron_atomistics.interactive.activation_relaxation_technique.ART property) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton property) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer property) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive property) (pyiron_atomistics.lammps.base.LammpsBase property) (pyiron_atomistics.lammps.interactive.LammpsInteractive property) (pyiron_atomistics.lammps.lammps.Lammps property) (pyiron_atomistics.sphinx.base.SphinxBase property) (pyiron_atomistics.sphinx.interactive.SphinxInt2 property) (pyiron_atomistics.sphinx.interactive.SphinxInteractive property) (pyiron_atomistics.sphinx.sphinx.Sphinx property) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob property) (pyiron_atomistics.testing.randomatomistic.ExampleJob property) (pyiron_atomistics.thermodynamics.hessian.HessianJob property) (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) job_name() (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticJobGenerator static method) (pyiron_atomistics.atomistics.master.murnaghan.MurnaghanJobGenerator method) (pyiron_atomistics.atomistics.master.parallel.MapJobGenerator method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJobGenerator static method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSJobGenerator static method) (pyiron_atomistics.atomistics.master.structure.StructureJobGenerator static method) (pyiron_atomistics.dft.master.convergence_encut_parallel.EncutConvergenceJobGenerator static method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.KpointConvergenceJobGenerator static method) (pyiron_atomistics.project.Creator static method) job_object_dict (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper property) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob property) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan property) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster property) (pyiron_atomistics.atomistics.master.parallel.MapMaster property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster property) (pyiron_atomistics.atomistics.master.structure.StructureListMaster property) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel property) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT property) (pyiron_atomistics.interactive.activation_relaxation_technique.ART property) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton property) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer property) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive property) job_table() (pyiron_atomistics.project.Project method) job_type (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob property) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive property) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper property) (pyiron_atomistics.atomistics.job.sqs.SQSJob property) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer property) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob property) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan property) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster property) (pyiron_atomistics.atomistics.master.parallel.MapMaster property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster property) (pyiron_atomistics.atomistics.master.structure.StructureListMaster property) (pyiron_atomistics.calphy.job.Calphy property) (pyiron_atomistics.dft.job.generic.GenericDFTJob property) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel property) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT property) (pyiron_atomistics.gpaw.gpaw.Gpaw property) (pyiron_atomistics.gpaw.pyiron_ase.AseJob property) (pyiron_atomistics.interactive.activation_relaxation_technique.ART property) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton property) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer property) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive property) (pyiron_atomistics.lammps.base.LammpsBase property) (pyiron_atomistics.lammps.interactive.LammpsInteractive property) (pyiron_atomistics.lammps.lammps.Lammps property) (pyiron_atomistics.sphinx.base.SphinxBase property) (pyiron_atomistics.sphinx.interactive.SphinxInt2 property) (pyiron_atomistics.sphinx.interactive.SphinxInteractive property) (pyiron_atomistics.sphinx.sphinx.Sphinx property) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob property) (pyiron_atomistics.testing.randomatomistic.ExampleJob property) (pyiron_atomistics.thermodynamics.hessian.HessianJob property) (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) JobFactory (class in pyiron_atomistics.toolkit) join() (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage method) K k_mesh_center_shift (pyiron_atomistics.dft.job.generic.GenericDFTJob property) (pyiron_atomistics.gpaw.gpaw.Gpaw property) (pyiron_atomistics.sphinx.base.SphinxBase property) (pyiron_atomistics.sphinx.interactive.SphinxInt2 property) (pyiron_atomistics.sphinx.interactive.SphinxInteractive property) (pyiron_atomistics.sphinx.sphinx.Sphinx property) (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) k_mesh_spacing (pyiron_atomistics.dft.job.generic.GenericDFTJob property) (pyiron_atomistics.gpaw.gpaw.Gpaw property) (pyiron_atomistics.sphinx.base.SphinxBase property) (pyiron_atomistics.sphinx.interactive.SphinxInt2 property) (pyiron_atomistics.sphinx.interactive.SphinxInteractive property) (pyiron_atomistics.sphinx.sphinx.Sphinx property) (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) keys() (pyiron_atomistics.atomistics.job.atomistic.GenericInput method) (pyiron_atomistics.atomistics.master.parallel.GenericOutput method) (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) (pyiron_atomistics.gpaw.gpaw.GpawInput method) (pyiron_atomistics.interactive.quasi_newton.Input method) (pyiron_atomistics.interactive.sxextoptint.Input method) (pyiron_atomistics.lammps.control.LammpsControl method) (pyiron_atomistics.lammps.potential.LammpsPotential method) (pyiron_atomistics.project.Project method) (pyiron_atomistics.sphinx.input_writer.Group method) (pyiron_atomistics.testing.randomatomistic.ExampleInput method) (pyiron_atomistics.vasp.base.Incar method) (pyiron_atomistics.vasp.base.Kpoints method) (pyiron_atomistics.vasp.potential.Potcar method) kill() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) kpoint_list (pyiron_atomistics.dft.waves.electronic.ElectronicStructure property) kpoint_weights (pyiron_atomistics.dft.waves.electronic.ElectronicStructure property) KpointConvergenceJobGenerator (class in pyiron_atomistics.dft.master.convergence_kpoint_parallel) Kpoints (class in pyiron_atomistics.vasp.base) kpoints (pyiron_atomistics.vasp.base.Input attribute) L Lammps (class in pyiron_atomistics.lammps.lammps) lammps_function() (in module pyiron_atomistics.lammps.lammps) LammpsBase (class in pyiron_atomistics.lammps.base) LammpsControl (class in pyiron_atomistics.lammps.control) LammpsInteractive (class in pyiron_atomistics.lammps.interactive) LammpsPotential (class in pyiron_atomistics.lammps.potential) LammpsPotentialFile (class in pyiron_atomistics.lammps.potential) LammpsStructure (class in pyiron_atomistics.lammps.structure) list() (pyiron_atomistics.atomistics.job.potentials.PotentialAbstract method) (pyiron_atomistics.lammps.potential.LammpsPotentialFile method) (pyiron_atomistics.sphinx.potential.SphinxJTHPotentialFile method) (pyiron_atomistics.vasp.potential.VaspPotentialAbstract method) (pyiron_atomistics.vasp.potential.VaspPotentialFile method) list_all() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.project.Project method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.input_writer.Group method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) list_arrays() (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage method) list_childs() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) list_clusters() (pyiron_atomistics.project.Project static method) list_dirs() (pyiron_atomistics.project.Project method) list_files() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.project.Project method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) list_groups() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.project.Project method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.input_writer.Group method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) list_nodes() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.project.Project method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.input_writer.Group method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) list_of_structures (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster property) list_potentials() (in module pyiron_atomistics.lammps.potential) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) list_publications() (pyiron_atomistics.project.Project static method) list_structures() (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) listdir() (pyiron_atomistics.project.Project method) load (pyiron_atomistics.project.Project property) load() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) load_basis_group() (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) load_default() (pyiron_atomistics.atomistics.job.atomistic.GenericInput method) (pyiron_atomistics.gpaw.gpaw.GpawInput method) (pyiron_atomistics.interactive.quasi_newton.Input method) (pyiron_atomistics.interactive.sxextoptint.Input method) (pyiron_atomistics.lammps.control.LammpsControl method) (pyiron_atomistics.lammps.potential.LammpsPotential method) (pyiron_atomistics.testing.randomatomistic.ExampleInput method) (pyiron_atomistics.vasp.base.Incar method) (pyiron_atomistics.vasp.base.Kpoints method) (pyiron_atomistics.vasp.potential.Potcar method) load_default_groups() (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) load_default_input() (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) load_from_jobpath() (pyiron_atomistics.project.Project method) load_from_jobpath_string() (pyiron_atomistics.project.Project method) load_guess_group() (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) load_hamilton_group() (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) load_main_group() (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) load_species_group() (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) load_string() (pyiron_atomistics.atomistics.job.atomistic.GenericInput method) (pyiron_atomistics.gpaw.gpaw.GpawInput method) (pyiron_atomistics.interactive.quasi_newton.Input method) (pyiron_atomistics.interactive.sxextoptint.Input method) (pyiron_atomistics.lammps.control.LammpsControl method) (pyiron_atomistics.lammps.potential.LammpsPotential method) (pyiron_atomistics.testing.randomatomistic.ExampleInput method) (pyiron_atomistics.vasp.base.Incar method) (pyiron_atomistics.vasp.base.Kpoints method) (pyiron_atomistics.vasp.potential.Potcar method) load_structure_group() (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) lock() (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage method) (pyiron_atomistics.sphinx.input_writer.Group method) log_dict (pyiron_atomistics.vasp.output.DFTOutput attribute) (pyiron_atomistics.vasp.output.GenericOutput attribute) logger (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob property) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive property) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper property) (pyiron_atomistics.atomistics.job.sqs.SQSJob property) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer property) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob property) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan property) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster property) (pyiron_atomistics.atomistics.master.parallel.MapMaster property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster property) (pyiron_atomistics.atomistics.master.structure.StructureListMaster property) (pyiron_atomistics.calphy.job.Calphy property) (pyiron_atomistics.dft.job.generic.GenericDFTJob property) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel property) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT property) (pyiron_atomistics.gpaw.gpaw.Gpaw property) (pyiron_atomistics.gpaw.pyiron_ase.AseJob property) (pyiron_atomistics.interactive.activation_relaxation_technique.ART property) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton property) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer property) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive property) (pyiron_atomistics.lammps.base.LammpsBase property) (pyiron_atomistics.lammps.interactive.LammpsInteractive property) (pyiron_atomistics.lammps.lammps.Lammps property) (pyiron_atomistics.sphinx.base.SphinxBase property) (pyiron_atomistics.sphinx.interactive.SphinxInt2 property) (pyiron_atomistics.sphinx.interactive.SphinxInteractive property) (pyiron_atomistics.sphinx.sphinx.Sphinx property) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob property) (pyiron_atomistics.testing.randomatomistic.ExampleJob property) (pyiron_atomistics.thermodynamics.hessian.HessianJob property) (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) M magmom (pyiron_atomistics.atomistics.structure.atom.Atom property) map() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) map_dict() (in module pyiron_atomistics.atomistics.job.sqs) MapFunctions (class in pyiron_atomistics.atomistics.job.atomistic) (class in pyiron_atomistics.dft.job.generic) MapJobGenerator (class in pyiron_atomistics.atomistics.master.parallel) MapMaster (class in pyiron_atomistics.atomistics.master.parallel) mark() (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) (pyiron_atomistics.sphinx.input_writer.Group method) mass (pyiron_atomistics.atomistics.structure.atom.Atom property) master (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticJobGenerator property) (pyiron_atomistics.atomistics.master.murnaghan.MurnaghanJobGenerator property) (pyiron_atomistics.atomistics.master.parallel.MapJobGenerator property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJobGenerator property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSJobGenerator property) (pyiron_atomistics.atomistics.master.structure.StructureJobGenerator property) (pyiron_atomistics.dft.master.convergence_encut_parallel.EncutConvergenceJobGenerator property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.KpointConvergenceJobGenerator property) master_id (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob property) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive property) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper property) (pyiron_atomistics.atomistics.job.sqs.SQSJob property) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer property) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob property) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan property) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster property) (pyiron_atomistics.atomistics.master.parallel.MapMaster property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster property) (pyiron_atomistics.atomistics.master.structure.StructureListMaster property) (pyiron_atomistics.calphy.job.Calphy property) (pyiron_atomistics.dft.job.generic.GenericDFTJob property) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel property) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT property) (pyiron_atomistics.gpaw.gpaw.Gpaw property) (pyiron_atomistics.gpaw.pyiron_ase.AseJob property) (pyiron_atomistics.interactive.activation_relaxation_technique.ART property) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton property) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer property) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive property) (pyiron_atomistics.lammps.base.LammpsBase property) (pyiron_atomistics.lammps.interactive.LammpsInteractive property) (pyiron_atomistics.lammps.lammps.Lammps property) (pyiron_atomistics.sphinx.base.SphinxBase property) (pyiron_atomistics.sphinx.interactive.SphinxInt2 property) (pyiron_atomistics.sphinx.interactive.SphinxInteractive property) (pyiron_atomistics.sphinx.sphinx.Sphinx property) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob property) (pyiron_atomistics.testing.randomatomistic.ExampleJob property) (pyiron_atomistics.thermodynamics.hessian.HessianJob property) (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) MaterialsProjectFactory (class in pyiron_atomistics.atomistics.structure.factories.materialsproject) measure_mean_value() (pyiron_atomistics.lammps.control.LammpsControl method) meshgrid() (pyiron_atomistics.atomistics.thermodynamics.thermo_bulk.ThermoBulk method) MetadynInput (class in pyiron_atomistics.vasp.metadyn) MetadynOutput (class in pyiron_atomistics.vasp.metadyn) minimize_pos() (in module pyiron_atomistics.thermodynamics.interfacemethod) minimize_vol() (in module pyiron_atomistics.thermodynamics.interfacemethod) minimizer (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizerInput property) modify() (pyiron_atomistics.atomistics.job.atomistic.GenericInput method) (pyiron_atomistics.atomistics.structure.factories.atomsk.AtomskBuilder class method) (pyiron_atomistics.atomistics.structure.factories.atomsk.AtomskFactory method) (pyiron_atomistics.gpaw.gpaw.GpawInput method) (pyiron_atomistics.interactive.quasi_newton.Input method) (pyiron_atomistics.interactive.sxextoptint.Input method) (pyiron_atomistics.lammps.control.LammpsControl method) (pyiron_atomistics.lammps.potential.LammpsPotential method) (pyiron_atomistics.testing.randomatomistic.ExampleInput method) (pyiron_atomistics.vasp.base.Incar method) (pyiron_atomistics.vasp.base.Kpoints method) (pyiron_atomistics.vasp.potential.Potcar method) modify_job() (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticJobGenerator method) (pyiron_atomistics.atomistics.master.murnaghan.MurnaghanJobGenerator method) (pyiron_atomistics.atomistics.master.parallel.MapJobGenerator method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJobGenerator method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSJobGenerator method) (pyiron_atomistics.atomistics.master.structure.StructureJobGenerator method) (pyiron_atomistics.dft.master.convergence_encut_parallel.EncutConvergenceJobGenerator static method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.KpointConvergenceJobGenerator static method) module pyiron_atomistics pyiron_atomistics.atomistics pyiron_atomistics.atomistics.generic pyiron_atomistics.atomistics.generic.object_type pyiron_atomistics.atomistics.job pyiron_atomistics.atomistics.job.atomistic pyiron_atomistics.atomistics.job.interactive pyiron_atomistics.atomistics.job.interactivewrapper pyiron_atomistics.atomistics.job.potentials pyiron_atomistics.atomistics.job.sqs pyiron_atomistics.atomistics.job.structurecontainer pyiron_atomistics.atomistics.master pyiron_atomistics.atomistics.master.elasticmatrix pyiron_atomistics.atomistics.master.murnaghan pyiron_atomistics.atomistics.master.parallel pyiron_atomistics.atomistics.master.phonopy pyiron_atomistics.atomistics.master.quasi pyiron_atomistics.atomistics.master.sqsmaster pyiron_atomistics.atomistics.master.structure pyiron_atomistics.atomistics.structure pyiron_atomistics.atomistics.structure.analyse pyiron_atomistics.atomistics.structure.atom pyiron_atomistics.atomistics.structure.atoms pyiron_atomistics.atomistics.structure.factories pyiron_atomistics.atomistics.structure.factories.aimsgb pyiron_atomistics.atomistics.structure.factories.ase pyiron_atomistics.atomistics.structure.factories.atomsk pyiron_atomistics.atomistics.structure.factories.compound pyiron_atomistics.atomistics.structure.factories.materialsproject pyiron_atomistics.atomistics.structure.factory pyiron_atomistics.atomistics.structure.has_structure pyiron_atomistics.atomistics.structure.neighbors pyiron_atomistics.atomistics.structure.periodic_table pyiron_atomistics.atomistics.structure.phonopy pyiron_atomistics.atomistics.structure.pyironase pyiron_atomistics.atomistics.structure.pyscal pyiron_atomistics.atomistics.structure.pyxtal pyiron_atomistics.atomistics.structure.structurestorage pyiron_atomistics.atomistics.thermodynamics pyiron_atomistics.atomistics.thermodynamics.thermo_bulk pyiron_atomistics.atomistics.volumetric pyiron_atomistics.atomistics.volumetric.generic pyiron_atomistics.calphy pyiron_atomistics.calphy.job pyiron_atomistics.dft pyiron_atomistics.dft.bader pyiron_atomistics.dft.job pyiron_atomistics.dft.job.generic pyiron_atomistics.dft.master pyiron_atomistics.dft.master.convergence_encut_parallel pyiron_atomistics.dft.master.convergence_kpoint_parallel pyiron_atomistics.dft.master.murnaghan_dft pyiron_atomistics.dft.waves pyiron_atomistics.dft.waves.bandstructure pyiron_atomistics.dft.waves.electronic pyiron_atomistics.gpaw pyiron_atomistics.gpaw.gpaw pyiron_atomistics.gpaw.pyiron_ase pyiron_atomistics.interactive pyiron_atomistics.interactive.activation_relaxation_technique pyiron_atomistics.interactive.quasi_newton pyiron_atomistics.interactive.scipy_minimizer pyiron_atomistics.interactive.sxextoptint pyiron_atomistics.lammps pyiron_atomistics.lammps.base pyiron_atomistics.lammps.control pyiron_atomistics.lammps.interactive pyiron_atomistics.lammps.lammps pyiron_atomistics.lammps.output pyiron_atomistics.lammps.potential pyiron_atomistics.lammps.structure pyiron_atomistics.project pyiron_atomistics.sphinx pyiron_atomistics.sphinx.base pyiron_atomistics.sphinx.input_writer pyiron_atomistics.sphinx.interactive pyiron_atomistics.sphinx.potential pyiron_atomistics.sphinx.sphinx pyiron_atomistics.sphinx.structure pyiron_atomistics.sphinx.util pyiron_atomistics.sphinx.volumetric_data pyiron_atomistics.table pyiron_atomistics.table.datamining pyiron_atomistics.table.funct pyiron_atomistics.testing pyiron_atomistics.testing.executable pyiron_atomistics.testing.randomatomistic pyiron_atomistics.thermodynamics pyiron_atomistics.thermodynamics.hessian pyiron_atomistics.thermodynamics.interfacemethod pyiron_atomistics.toolkit pyiron_atomistics.vasp pyiron_atomistics.vasp.base pyiron_atomistics.vasp.interactive pyiron_atomistics.vasp.metadyn pyiron_atomistics.vasp.output pyiron_atomistics.vasp.potential pyiron_atomistics.vasp.structure pyiron_atomistics.vasp.vasp pyiron_atomistics.vasp.vasprun pyiron_atomistics.vasp.vaspsol pyiron_atomistics.vasp.volumetric_data mole_fractions_to_composition() (in module pyiron_atomistics.atomistics.job.sqs) molecule() (pyiron_atomistics.atomistics.structure.factories.ase.AseFactory method) momentum (pyiron_atomistics.atomistics.structure.atom.Atom property) move_to() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.project.Project method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) move_to_end() (pyiron_atomistics.atomistics.master.parallel.GenericOutput method) MPQueryResults (class in pyiron_atomistics.atomistics.structure.factories.materialsproject) multi_word_separator (pyiron_atomistics.atomistics.job.atomistic.GenericInput property) (pyiron_atomistics.gpaw.gpaw.GpawInput property) (pyiron_atomistics.interactive.quasi_newton.Input property) (pyiron_atomistics.interactive.sxextoptint.Input property) (pyiron_atomistics.lammps.control.LammpsControl property) (pyiron_atomistics.lammps.potential.LammpsPotential property) (pyiron_atomistics.testing.randomatomistic.ExampleInput property) (pyiron_atomistics.vasp.base.Incar property) (pyiron_atomistics.vasp.base.Kpoints property) (pyiron_atomistics.vasp.potential.Potcar property) Murnaghan (class in pyiron_atomistics.atomistics.master.murnaghan) MurnaghanDebyeModel (class in pyiron_atomistics.atomistics.master.murnaghan) MurnaghanDFT (class in pyiron_atomistics.dft.master.murnaghan_dft) MurnaghanJobGenerator (class in pyiron_atomistics.atomistics.master.murnaghan) N name (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob property) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive property) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper property) (pyiron_atomistics.atomistics.job.sqs.SQSJob property) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer property) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob property) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan property) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster property) (pyiron_atomistics.atomistics.master.parallel.MapMaster property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster property) (pyiron_atomistics.atomistics.master.structure.StructureListMaster property) (pyiron_atomistics.calphy.job.Calphy property) (pyiron_atomistics.dft.job.generic.GenericDFTJob property) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel property) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT property) (pyiron_atomistics.gpaw.gpaw.Gpaw property) (pyiron_atomistics.gpaw.pyiron_ase.AseJob property) (pyiron_atomistics.interactive.activation_relaxation_technique.ART property) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton property) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer property) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive property) (pyiron_atomistics.lammps.base.LammpsBase property) (pyiron_atomistics.lammps.interactive.LammpsInteractive property) (pyiron_atomistics.lammps.lammps.Lammps property) (pyiron_atomistics.project.Project property) (pyiron_atomistics.sphinx.base.SphinxBase property) (pyiron_atomistics.sphinx.interactive.SphinxInt2 property) (pyiron_atomistics.sphinx.interactive.SphinxInteractive property) (pyiron_atomistics.sphinx.sphinx.Sphinx property) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob property) (pyiron_atomistics.testing.randomatomistic.ExampleJob property) (pyiron_atomistics.thermodynamics.hessian.HessianJob property) (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) nbands_convergence_check() (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) NeighborsTrajectory (class in pyiron_atomistics.atomistics.structure.neighbors) new_array() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) next() (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticJobGenerator method) (pyiron_atomistics.atomistics.master.murnaghan.MurnaghanJobGenerator method) (pyiron_atomistics.atomistics.master.parallel.MapJobGenerator method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJobGenerator method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSJobGenerator method) (pyiron_atomistics.atomistics.master.structure.StructureJobGenerator method) (pyiron_atomistics.dft.master.convergence_encut_parallel.EncutConvergenceJobGenerator method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.KpointConvergenceJobGenerator method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) next_calc() (in module pyiron_atomistics.thermodynamics.interfacemethod) next_step_funct() (in module pyiron_atomistics.thermodynamics.interfacemethod) nodes() (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) (pyiron_atomistics.project.Project method) (pyiron_atomistics.sphinx.input_writer.Group method) npt_liquid() (in module pyiron_atomistics.thermodynamics.interfacemethod) npt_solid() (in module pyiron_atomistics.thermodynamics.interfacemethod) num_atoms (pyiron_atomistics.atomistics.thermodynamics.thermo_bulk.ThermoBulk property) num_neighbors (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory property) num_steps (pyiron_atomistics.atomistics.master.murnaghan.MurnaghanDebyeModel property) number (pyiron_atomistics.atomistics.structure.atom.Atom property) number_jobs_total (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob property) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan property) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster property) (pyiron_atomistics.atomistics.master.parallel.MapMaster property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster property) (pyiron_atomistics.atomistics.master.structure.StructureListMaster property) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel property) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT property) number_of_lattice_vectors (pyiron_atomistics.atomistics.structure.atoms.Atoms property) number_of_structures (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob property) (pyiron_atomistics.atomistics.job.atomistic.Trajectory property) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive property) (pyiron_atomistics.atomistics.job.sqs.SQSJob property) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer property) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob property) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan property) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster property) (pyiron_atomistics.atomistics.master.parallel.MapMaster property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster property) (pyiron_atomistics.atomistics.structure.factories.materialsproject.MPQueryResults property) (pyiron_atomistics.atomistics.structure.has_structure.HasStructure property) (pyiron_atomistics.atomistics.structure.has_structure.TransformStructure property) (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage property) (pyiron_atomistics.calphy.job.Calphy property) (pyiron_atomistics.dft.job.generic.GenericDFTJob property) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel property) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT property) (pyiron_atomistics.gpaw.gpaw.Gpaw property) (pyiron_atomistics.gpaw.pyiron_ase.AseJob property) (pyiron_atomistics.lammps.base.LammpsBase property) (pyiron_atomistics.lammps.interactive.LammpsInteractive property) (pyiron_atomistics.lammps.lammps.Lammps property) (pyiron_atomistics.sphinx.base.SphinxBase property) (pyiron_atomistics.sphinx.interactive.SphinxInt2 property) (pyiron_atomistics.sphinx.interactive.SphinxInteractive property) (pyiron_atomistics.sphinx.sphinx.Sphinx property) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob property) (pyiron_atomistics.thermodynamics.hessian.HessianJob property) (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) numbers (pyiron_atomistics.atomistics.structure.atoms.Atoms property) numbers_to_elements() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) O ObjectType (class in pyiron_atomistics.atomistics.generic.object_type) ObjectTypeChoice (class in pyiron_atomistics.atomistics.generic.object_type) occupancies (pyiron_atomistics.dft.waves.electronic.ElectronicStructure property) occupancy_matrix (pyiron_atomistics.dft.waves.electronic.ElectronicStructure property) occupy_lattice() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) open() (pyiron_atomistics.project.Project method) optimise_volume() (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) orbital_dict (pyiron_atomistics.dft.waves.electronic.ElectronicStructure property) Output (class in pyiron_atomistics.interactive.quasi_newton) (class in pyiron_atomistics.sphinx.base) (class in pyiron_atomistics.vasp.output) output_dict_to_hdf() (in module pyiron_atomistics.vasp.output) output_to_pandas() (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) ovito_to_pyiron() (in module pyiron_atomistics.atomistics.structure.atoms) P pack() (pyiron_atomistics.project.Project method) parameter_list (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticJobGenerator property) (pyiron_atomistics.atomistics.master.murnaghan.MurnaghanJobGenerator property) (pyiron_atomistics.atomistics.master.parallel.MapJobGenerator property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJobGenerator property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSJobGenerator property) (pyiron_atomistics.atomistics.master.structure.StructureJobGenerator property) (pyiron_atomistics.dft.master.convergence_encut_parallel.EncutConvergenceJobGenerator property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.KpointConvergenceJobGenerator property) parent_group (pyiron_atomistics.project.Project property) parent_id (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob property) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive property) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper property) (pyiron_atomistics.atomistics.job.sqs.SQSJob property) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer property) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob property) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan property) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster property) (pyiron_atomistics.atomistics.master.parallel.MapMaster property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster property) (pyiron_atomistics.atomistics.master.structure.StructureListMaster property) (pyiron_atomistics.calphy.job.Calphy property) (pyiron_atomistics.dft.job.generic.GenericDFTJob property) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel property) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT property) (pyiron_atomistics.gpaw.gpaw.Gpaw property) (pyiron_atomistics.gpaw.pyiron_ase.AseJob property) (pyiron_atomistics.interactive.activation_relaxation_technique.ART property) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton property) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer property) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive property) (pyiron_atomistics.lammps.base.LammpsBase property) (pyiron_atomistics.lammps.interactive.LammpsInteractive property) (pyiron_atomistics.lammps.lammps.Lammps property) (pyiron_atomistics.sphinx.base.SphinxBase property) (pyiron_atomistics.sphinx.interactive.SphinxInt2 property) (pyiron_atomistics.sphinx.interactive.SphinxInteractive property) (pyiron_atomistics.sphinx.sphinx.Sphinx property) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob property) (pyiron_atomistics.testing.randomatomistic.ExampleJob property) (pyiron_atomistics.thermodynamics.hessian.HessianJob property) (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) parse_atom_information_to_dict() (pyiron_atomistics.vasp.vasprun.Vasprun method) parse_calc_to_dict() (pyiron_atomistics.vasp.vasprun.Vasprun method) parse_eigenvalues_to_dict() (pyiron_atomistics.vasp.vasprun.Vasprun method) parse_fermi_level_to_dict() (pyiron_atomistics.vasp.vasprun.Vasprun method) parse_item_to_dict() (pyiron_atomistics.vasp.vasprun.Vasprun static method) parse_kpoints_to_dict() (pyiron_atomistics.vasp.vasprun.Vasprun method) parse_parameters() (pyiron_atomistics.vasp.vasprun.Vasprun method) parse_partial_dos_to_dict() (pyiron_atomistics.vasp.vasprun.Vasprun method) parse_projected_dos_to_dict() (pyiron_atomistics.vasp.vasprun.Vasprun method) parse_recursively() (pyiron_atomistics.vasp.vasprun.Vasprun method) parse_root_to_dict() (pyiron_atomistics.vasp.vasprun.Vasprun method) parse_scf() (pyiron_atomistics.vasp.vasprun.Vasprun method) parse_structure_to_dict() (pyiron_atomistics.vasp.vasprun.Vasprun method) parse_total_dos_to_dict() (pyiron_atomistics.vasp.vasprun.Vasprun method) path (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob property) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive property) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper property) (pyiron_atomistics.atomistics.job.sqs.SQSJob property) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer property) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob property) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan property) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster property) (pyiron_atomistics.atomistics.master.parallel.MapMaster property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster property) (pyiron_atomistics.atomistics.master.structure.StructureListMaster property) (pyiron_atomistics.calphy.job.Calphy property) (pyiron_atomistics.dft.job.generic.GenericDFTJob property) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel property) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT property) (pyiron_atomistics.gpaw.gpaw.Gpaw property) (pyiron_atomistics.gpaw.pyiron_ase.AseJob property) (pyiron_atomistics.interactive.activation_relaxation_technique.ART property) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton property) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer property) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive property) (pyiron_atomistics.lammps.base.LammpsBase property) (pyiron_atomistics.lammps.interactive.LammpsInteractive property) (pyiron_atomistics.lammps.lammps.Lammps property) (pyiron_atomistics.project.Project attribute) (pyiron_atomistics.project.Project property) (pyiron_atomistics.sphinx.base.SphinxBase property) (pyiron_atomistics.sphinx.interactive.SphinxInt2 property) (pyiron_atomistics.sphinx.interactive.SphinxInteractive property) (pyiron_atomistics.sphinx.sphinx.Sphinx property) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob property) (pyiron_atomistics.testing.randomatomistic.ExampleJob property) (pyiron_atomistics.thermodynamics.hessian.HessianJob property) (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) pbc (pyiron_atomistics.atomistics.structure.atoms.Atoms property) PeriodicTable (class in pyiron_atomistics.atomistics.structure.periodic_table) PhonopyJob (class in pyiron_atomistics.atomistics.master.phonopy) PhonopyJobGenerator (class in pyiron_atomistics.atomistics.master.phonopy) pipe() (in module pyiron_atomistics.atomistics.master.parallel) plane_wave_cutoff (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) plot (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer property) (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage property) plot() (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) plot3d() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) plot_band_structure() (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) plot_contourf() (pyiron_atomistics.atomistics.thermodynamics.thermo_bulk.ThermoBulk method) plot_dos() (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) plot_entropy() (pyiron_atomistics.atomistics.thermodynamics.thermo_bulk.ThermoBulk method) plot_equilibration() (in module pyiron_atomistics.thermodynamics.interfacemethod) plot_fermi_dirac() (pyiron_atomistics.dft.waves.electronic.ElectronicStructure method) plot_free_energy() (pyiron_atomistics.atomistics.thermodynamics.thermo_bulk.ThermoBulk method) plot_free_energy_volume_temperature() (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) plot_heat_capacity() (pyiron_atomistics.atomistics.thermodynamics.thermo_bulk.ThermoBulk method) plot_melting_point_prediction() (in module pyiron_atomistics.thermodynamics.interfacemethod) plot_min_energy_path() (pyiron_atomistics.atomistics.thermodynamics.thermo_bulk.ThermoBulk method) plot_solid_liquid_ratio() (in module pyiron_atomistics.thermodynamics.interfacemethod) pop() (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.GenericOutput method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.atomistics.structure.atoms.Atoms method) (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.sphinx.input_writer.Group method) popitem() (pyiron_atomistics.atomistics.master.parallel.GenericOutput method) (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) (pyiron_atomistics.sphinx.input_writer.Group method) pos_xyz() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) position (pyiron_atomistics.atomistics.structure.atom.Atom property) positions (pyiron_atomistics.atomistics.structure.atoms.Atoms property) Potcar (class in pyiron_atomistics.vasp.potential) potcar (pyiron_atomistics.vasp.base.Input attribute) potential (pyiron_atomistics.lammps.base.LammpsBase property) (pyiron_atomistics.lammps.interactive.LammpsInteractive property) (pyiron_atomistics.lammps.lammps.Lammps property) potential_list (pyiron_atomistics.lammps.base.LammpsBase property) (pyiron_atomistics.lammps.interactive.LammpsInteractive property) (pyiron_atomistics.lammps.lammps.Lammps property) potential_view (pyiron_atomistics.lammps.base.LammpsBase property) (pyiron_atomistics.lammps.interactive.LammpsInteractive property) (pyiron_atomistics.lammps.lammps.Lammps property) PotentialAbstract (class in pyiron_atomistics.atomistics.job.potentials) PotentialAvailable (class in pyiron_atomistics.lammps.potential) pressure (pyiron_atomistics.atomistics.thermodynamics.thermo_bulk.ThermoBulk property) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizerInput property) pressure_to_lammps() (pyiron_atomistics.lammps.control.LammpsControl method) pressure_tolerance (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizerInput property) Project (class in pyiron_atomistics.project) project (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob property) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive property) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper property) (pyiron_atomistics.atomistics.job.sqs.SQSJob property) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer property) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob property) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan property) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster property) (pyiron_atomistics.atomistics.master.parallel.MapMaster property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster property) (pyiron_atomistics.atomistics.master.structure.StructureListMaster property) (pyiron_atomistics.calphy.job.Calphy property) (pyiron_atomistics.dft.job.generic.GenericDFTJob property) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel property) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT property) (pyiron_atomistics.gpaw.gpaw.Gpaw property) (pyiron_atomistics.gpaw.pyiron_ase.AseJob property) (pyiron_atomistics.interactive.activation_relaxation_technique.ART property) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton property) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer property) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive property) (pyiron_atomistics.lammps.base.LammpsBase property) (pyiron_atomistics.lammps.interactive.LammpsInteractive property) (pyiron_atomistics.lammps.lammps.Lammps property) (pyiron_atomistics.sphinx.base.SphinxBase property) (pyiron_atomistics.sphinx.interactive.SphinxInt2 property) (pyiron_atomistics.sphinx.interactive.SphinxInteractive property) (pyiron_atomistics.sphinx.sphinx.Sphinx property) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob property) (pyiron_atomistics.testing.randomatomistic.ExampleJob property) (pyiron_atomistics.thermodynamics.hessian.HessianJob property) (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) project_hdf5 (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob property) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive property) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper property) (pyiron_atomistics.atomistics.job.sqs.SQSJob property) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer property) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob property) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan property) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster property) (pyiron_atomistics.atomistics.master.parallel.MapMaster property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster property) (pyiron_atomistics.atomistics.master.structure.StructureListMaster property) (pyiron_atomistics.calphy.job.Calphy property) (pyiron_atomistics.dft.job.generic.GenericDFTJob property) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel property) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT property) (pyiron_atomistics.gpaw.gpaw.Gpaw property) (pyiron_atomistics.gpaw.pyiron_ase.AseJob property) (pyiron_atomistics.interactive.activation_relaxation_technique.ART property) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton property) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer property) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive property) (pyiron_atomistics.lammps.base.LammpsBase property) (pyiron_atomistics.lammps.interactive.LammpsInteractive property) (pyiron_atomistics.lammps.lammps.Lammps property) (pyiron_atomistics.sphinx.base.SphinxBase property) (pyiron_atomistics.sphinx.interactive.SphinxInt2 property) (pyiron_atomistics.sphinx.interactive.SphinxInteractive property) (pyiron_atomistics.sphinx.sphinx.Sphinx property) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob property) (pyiron_atomistics.testing.randomatomistic.ExampleJob property) (pyiron_atomistics.thermodynamics.hessian.HessianJob property) (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) project_path (pyiron_atomistics.project.Project attribute) (pyiron_atomistics.project.Project property) publication() (in module pyiron_atomistics.atomistics.structure.phonopy) (in module pyiron_atomistics.atomistics.structure.pyironase) (in module pyiron_atomistics.atomistics.structure.pyscal) pyiron_atomistics module pyiron_atomistics.atomistics module pyiron_atomistics.atomistics.generic module pyiron_atomistics.atomistics.generic.object_type module pyiron_atomistics.atomistics.job module pyiron_atomistics.atomistics.job.atomistic module pyiron_atomistics.atomistics.job.interactive module pyiron_atomistics.atomistics.job.interactivewrapper module pyiron_atomistics.atomistics.job.potentials module pyiron_atomistics.atomistics.job.sqs module pyiron_atomistics.atomistics.job.structurecontainer module pyiron_atomistics.atomistics.master module pyiron_atomistics.atomistics.master.elasticmatrix module pyiron_atomistics.atomistics.master.murnaghan module pyiron_atomistics.atomistics.master.parallel module pyiron_atomistics.atomistics.master.phonopy module pyiron_atomistics.atomistics.master.quasi module pyiron_atomistics.atomistics.master.sqsmaster module pyiron_atomistics.atomistics.master.structure module pyiron_atomistics.atomistics.structure module pyiron_atomistics.atomistics.structure.analyse module pyiron_atomistics.atomistics.structure.atom module pyiron_atomistics.atomistics.structure.atoms module pyiron_atomistics.atomistics.structure.factories module pyiron_atomistics.atomistics.structure.factories.aimsgb module pyiron_atomistics.atomistics.structure.factories.ase module pyiron_atomistics.atomistics.structure.factories.atomsk module pyiron_atomistics.atomistics.structure.factories.compound module pyiron_atomistics.atomistics.structure.factories.materialsproject module pyiron_atomistics.atomistics.structure.factory module pyiron_atomistics.atomistics.structure.has_structure module pyiron_atomistics.atomistics.structure.neighbors module pyiron_atomistics.atomistics.structure.periodic_table module pyiron_atomistics.atomistics.structure.phonopy module pyiron_atomistics.atomistics.structure.pyironase module pyiron_atomistics.atomistics.structure.pyscal module pyiron_atomistics.atomistics.structure.pyxtal module pyiron_atomistics.atomistics.structure.structurestorage module pyiron_atomistics.atomistics.thermodynamics module pyiron_atomistics.atomistics.thermodynamics.thermo_bulk module pyiron_atomistics.atomistics.volumetric module pyiron_atomistics.atomistics.volumetric.generic module pyiron_atomistics.calphy module pyiron_atomistics.calphy.job module pyiron_atomistics.dft module pyiron_atomistics.dft.bader module pyiron_atomistics.dft.job module pyiron_atomistics.dft.job.generic module pyiron_atomistics.dft.master module pyiron_atomistics.dft.master.convergence_encut_parallel module pyiron_atomistics.dft.master.convergence_kpoint_parallel module pyiron_atomistics.dft.master.murnaghan_dft module pyiron_atomistics.dft.waves module pyiron_atomistics.dft.waves.bandstructure module pyiron_atomistics.dft.waves.electronic module pyiron_atomistics.gpaw module pyiron_atomistics.gpaw.gpaw module pyiron_atomistics.gpaw.pyiron_ase module pyiron_atomistics.interactive module pyiron_atomistics.interactive.activation_relaxation_technique module pyiron_atomistics.interactive.quasi_newton module pyiron_atomistics.interactive.scipy_minimizer module pyiron_atomistics.interactive.sxextoptint module pyiron_atomistics.lammps module pyiron_atomistics.lammps.base module pyiron_atomistics.lammps.control module pyiron_atomistics.lammps.interactive module pyiron_atomistics.lammps.lammps module pyiron_atomistics.lammps.output module pyiron_atomistics.lammps.potential module pyiron_atomistics.lammps.structure module pyiron_atomistics.project module pyiron_atomistics.sphinx module pyiron_atomistics.sphinx.base module pyiron_atomistics.sphinx.input_writer module pyiron_atomistics.sphinx.interactive module pyiron_atomistics.sphinx.potential module pyiron_atomistics.sphinx.sphinx module pyiron_atomistics.sphinx.structure module pyiron_atomistics.sphinx.util module pyiron_atomistics.sphinx.volumetric_data module pyiron_atomistics.table module pyiron_atomistics.table.datamining module pyiron_atomistics.table.funct module pyiron_atomistics.testing module pyiron_atomistics.testing.executable module pyiron_atomistics.testing.randomatomistic module pyiron_atomistics.thermodynamics module pyiron_atomistics.thermodynamics.hessian module pyiron_atomistics.thermodynamics.interfacemethod module pyiron_atomistics.toolkit module pyiron_atomistics.vasp module pyiron_atomistics.vasp.base module pyiron_atomistics.vasp.interactive module pyiron_atomistics.vasp.metadyn module pyiron_atomistics.vasp.output module pyiron_atomistics.vasp.potential module pyiron_atomistics.vasp.structure module pyiron_atomistics.vasp.vasp module pyiron_atomistics.vasp.vasprun module pyiron_atomistics.vasp.vaspsol module pyiron_atomistics.vasp.volumetric_data module pyiron_to_ase() (in module pyiron_atomistics.atomistics.structure.atoms) pyiron_to_ovito() (in module pyiron_atomistics.atomistics.structure.atoms) pyiron_to_pymatgen() (in module pyiron_atomistics.atomistics.structure.atoms) pyiron_to_pyscal_system() (in module pyiron_atomistics.atomistics.structure.pyscal) pymatgen_to_pyiron() (in module pyiron_atomistics.atomistics.structure.atoms) pyscal_centro_symmetry() (pyiron_atomistics.atomistics.structure.analyse.Analyse method) pyscal_cna_adaptive() (pyiron_atomistics.atomistics.structure.analyse.Analyse method) pyscal_diamond_structure() (pyiron_atomistics.atomistics.structure.analyse.Analyse method) pyscal_find_solids() (pyiron_atomistics.atomistics.structure.analyse.Analyse method) pyscal_steinhardt_parameter() (pyiron_atomistics.atomistics.structure.analyse.Analyse method) pyscal_voronoi_volume() (pyiron_atomistics.atomistics.structure.analyse.Analyse method) pyxtal() (in module pyiron_atomistics.atomistics.structure.pyxtal) (pyiron_atomistics.atomistics.structure.factory.StructureFactory static method) Q QuasiHarmonicJob (class in pyiron_atomistics.atomistics.master.quasi) QuasiNewton (class in pyiron_atomistics.interactive.quasi_newton) QuasiNewtonInteractive (class in pyiron_atomistics.interactive.quasi_newton) queue_check_job_is_waiting_or_running() (pyiron_atomistics.project.Project static method) queue_delete_job() (pyiron_atomistics.project.Project method) queue_enable_reservation() (pyiron_atomistics.project.Project static method) queue_id (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob property) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive property) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper property) (pyiron_atomistics.atomistics.job.sqs.SQSJob property) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer property) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob property) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan property) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster property) (pyiron_atomistics.atomistics.master.parallel.MapMaster property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster property) (pyiron_atomistics.atomistics.master.structure.StructureListMaster property) (pyiron_atomistics.calphy.job.Calphy property) (pyiron_atomistics.dft.job.generic.GenericDFTJob property) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel property) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT property) (pyiron_atomistics.gpaw.gpaw.Gpaw property) (pyiron_atomistics.gpaw.pyiron_ase.AseJob property) (pyiron_atomistics.interactive.activation_relaxation_technique.ART property) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton property) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer property) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive property) (pyiron_atomistics.lammps.base.LammpsBase property) (pyiron_atomistics.lammps.interactive.LammpsInteractive property) (pyiron_atomistics.lammps.lammps.Lammps property) (pyiron_atomistics.sphinx.base.SphinxBase property) (pyiron_atomistics.sphinx.interactive.SphinxInt2 property) (pyiron_atomistics.sphinx.interactive.SphinxInteractive property) (pyiron_atomistics.sphinx.sphinx.Sphinx property) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob property) (pyiron_atomistics.testing.randomatomistic.ExampleJob property) (pyiron_atomistics.thermodynamics.hessian.HessianJob property) (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) queue_is_empty() (pyiron_atomistics.project.Project static method) queue_table() (pyiron_atomistics.project.Project method) queue_table_global() (pyiron_atomistics.project.Project method) R ratio_selection() (in module pyiron_atomistics.thermodynamics.interfacemethod) rattle() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) read() (pyiron_atomistics.atomistics.structure.factories.ase.AseFactory method) (pyiron_atomistics.atomistics.structure.factory.StructureFactory method) (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) (pyiron_atomistics.sphinx.input_writer.Group method) read_atoms() (in module pyiron_atomistics.sphinx.structure) (in module pyiron_atomistics.vasp.structure) read_cube_file() (pyiron_atomistics.atomistics.volumetric.generic.VolumetricData method) (pyiron_atomistics.sphinx.volumetric_data.SphinxVolumetricData method) (pyiron_atomistics.vasp.volumetric_data.VaspVolumetricData method) read_input() (pyiron_atomistics.atomistics.job.atomistic.GenericInput method) (pyiron_atomistics.gpaw.gpaw.GpawInput method) (pyiron_atomistics.interactive.quasi_newton.Input method) (pyiron_atomistics.interactive.sxextoptint.Input method) (pyiron_atomistics.lammps.control.LammpsControl method) (pyiron_atomistics.lammps.potential.LammpsPotential method) (pyiron_atomistics.testing.randomatomistic.ExampleInput method) (pyiron_atomistics.vasp.base.Incar method) (pyiron_atomistics.vasp.base.Kpoints method) (pyiron_atomistics.vasp.potential.Potcar method) read_only (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory property) (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage property) (pyiron_atomistics.sphinx.input_writer.Group property) read_restart() (pyiron_atomistics.testing.executable.ExampleExecutable method) read_restart_file() (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) reduce_kpoint_symmetry (pyiron_atomistics.dft.job.generic.GenericDFTJob property) (pyiron_atomistics.gpaw.gpaw.Gpaw property) (pyiron_atomistics.sphinx.base.SphinxBase property) (pyiron_atomistics.sphinx.interactive.SphinxInt2 property) (pyiron_atomistics.sphinx.interactive.SphinxInteractive property) (pyiron_atomistics.sphinx.sphinx.Sphinx property) (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) ref_job (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper property) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob property) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan property) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster property) (pyiron_atomistics.atomistics.master.parallel.MapMaster property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster property) (pyiron_atomistics.atomistics.master.structure.StructureListMaster property) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel property) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT property) (pyiron_atomistics.interactive.activation_relaxation_technique.ART property) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton property) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer property) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive property) ReferenceJobOutput (class in pyiron_atomistics.atomistics.job.interactivewrapper) refine_cell() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) refresh_job_status() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.project.Project method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) refresh_job_status_based_on_job_id() (pyiron_atomistics.project.Project method) refresh_job_status_based_on_queue_status() (pyiron_atomistics.project.Project method) refresh_submission_status() (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) register_tools() (pyiron_atomistics.project.Project class method) relocate_hdf5() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) remap_indices() (in module pyiron_atomistics.lammps.output) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) remove() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.project.Project method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) remove_and_reset_id() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) remove_child() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) remove_file() (pyiron_atomistics.project.Project method) remove_job() (pyiron_atomistics.project.Project method) remove_jobs() (pyiron_atomistics.project.Project method) remove_keys() (pyiron_atomistics.atomistics.job.atomistic.GenericInput method) (pyiron_atomistics.gpaw.gpaw.GpawInput method) (pyiron_atomistics.interactive.quasi_newton.Input method) (pyiron_atomistics.interactive.sxextoptint.Input method) (pyiron_atomistics.lammps.control.LammpsControl method) (pyiron_atomistics.lammps.potential.LammpsPotential method) (pyiron_atomistics.testing.randomatomistic.ExampleInput method) (pyiron_atomistics.vasp.base.Incar method) (pyiron_atomistics.vasp.base.Kpoints method) (pyiron_atomistics.vasp.potential.Potcar method) remove_selective_dynamics() (in module pyiron_atomistics.thermodynamics.interfacemethod) removedirs() (pyiron_atomistics.project.Project method) rename() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) repeat() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) repeat_points() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) replace_char_dict (pyiron_atomistics.atomistics.job.atomistic.GenericInput property) (pyiron_atomistics.gpaw.gpaw.GpawInput property) (pyiron_atomistics.interactive.quasi_newton.Input property) (pyiron_atomistics.interactive.sxextoptint.Input property) (pyiron_atomistics.lammps.control.LammpsControl property) (pyiron_atomistics.lammps.potential.LammpsPotential property) (pyiron_atomistics.testing.randomatomistic.ExampleInput property) (pyiron_atomistics.vasp.base.Incar property) (pyiron_atomistics.vasp.base.Kpoints property) (pyiron_atomistics.vasp.potential.Potcar property) reset_job_id() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) reset_output() (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) resolve_hierachical_dict() (in module pyiron_atomistics.lammps.base) resolved_densities (pyiron_atomistics.dft.waves.electronic.ElectronicStructure property) resource_plugin_name (pyiron_atomistics.atomistics.job.potentials.PotentialAbstract property) restart() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) restart_file_dict (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob property) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive property) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper property) (pyiron_atomistics.atomistics.job.sqs.SQSJob property) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer property) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob property) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan property) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster property) (pyiron_atomistics.atomistics.master.parallel.MapMaster property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster property) (pyiron_atomistics.atomistics.master.structure.StructureListMaster property) (pyiron_atomistics.calphy.job.Calphy property) (pyiron_atomistics.dft.job.generic.GenericDFTJob property) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel property) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT property) (pyiron_atomistics.gpaw.gpaw.Gpaw property) (pyiron_atomistics.gpaw.pyiron_ase.AseJob property) (pyiron_atomistics.interactive.activation_relaxation_technique.ART property) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton property) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer property) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive property) (pyiron_atomistics.lammps.base.LammpsBase property) (pyiron_atomistics.lammps.interactive.LammpsInteractive property) (pyiron_atomistics.lammps.lammps.Lammps property) (pyiron_atomistics.sphinx.base.SphinxBase property) (pyiron_atomistics.sphinx.interactive.SphinxInt2 property) (pyiron_atomistics.sphinx.interactive.SphinxInteractive property) (pyiron_atomistics.sphinx.sphinx.Sphinx property) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob property) (pyiron_atomistics.testing.randomatomistic.ExampleJob property) (pyiron_atomistics.thermodynamics.hessian.HessianJob property) (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) restart_file_list (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob property) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive property) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper property) (pyiron_atomistics.atomistics.job.sqs.SQSJob property) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer property) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob property) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan property) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster property) (pyiron_atomistics.atomistics.master.parallel.MapMaster property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster property) (pyiron_atomistics.atomistics.master.structure.StructureListMaster property) (pyiron_atomistics.calphy.job.Calphy property) (pyiron_atomistics.dft.job.generic.GenericDFTJob property) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel property) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT property) (pyiron_atomistics.gpaw.gpaw.Gpaw property) (pyiron_atomistics.gpaw.pyiron_ase.AseJob property) (pyiron_atomistics.interactive.activation_relaxation_technique.ART property) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton property) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer property) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive property) (pyiron_atomistics.lammps.base.LammpsBase property) (pyiron_atomistics.lammps.interactive.LammpsInteractive property) (pyiron_atomistics.lammps.lammps.Lammps property) (pyiron_atomistics.sphinx.base.SphinxBase property) (pyiron_atomistics.sphinx.interactive.SphinxInt2 property) (pyiron_atomistics.sphinx.interactive.SphinxInteractive property) (pyiron_atomistics.sphinx.sphinx.Sphinx property) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob property) (pyiron_atomistics.testing.randomatomistic.ExampleJob property) (pyiron_atomistics.thermodynamics.hessian.HessianJob property) (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) restart_for_band_structure_calculations() (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) restart_from_charge_density() (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) restart_from_wave_and_charge() (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) restart_from_wave_functions() (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) rewrite_hdf() (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizerInput method) (pyiron_atomistics.sphinx.input_writer.Group method) root_path (pyiron_atomistics.project.Project attribute) (pyiron_atomistics.project.Project property) rotate() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) rotate_dihedral() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) rotate_positions() (pyiron_atomistics.lammps.structure.LammpsStructure method) rotate_velocities() (pyiron_atomistics.lammps.structure.LammpsStructure method) round_temperature_next() (in module pyiron_atomistics.thermodynamics.interfacemethod) run() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.executable.ExampleExecutable method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) run_addon() (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) run_if_interactive() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) run_if_interactive_non_modal() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) run_if_modal() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) run_if_refresh() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) run_if_scheduler() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) run_lib() (pyiron_atomistics.testing.executable.ExampleExecutable method) run_qn() (in module pyiron_atomistics.interactive.quasi_newton) run_static() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) run_time_to_db() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) S sample() (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage method) save() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) save_output() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) scaled_pos_xyz() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) ScipyMinimizer (class in pyiron_atomistics.interactive.scipy_minimizer) ScipyMinimizerInput (class in pyiron_atomistics.interactive.scipy_minimizer) ScipyMinimizerOutput (class in pyiron_atomistics.interactive.scipy_minimizer) search() (pyiron_atomistics.atomistics.structure.atoms.Symbols method) (pyiron_atomistics.atomistics.structure.factories.materialsproject.MaterialsProjectFactory static method) (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) (pyiron_atomistics.sphinx.input_writer.Group method) select_index() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) select_parent_index() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) self_archive() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) self_unarchive() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) separator_char (pyiron_atomistics.atomistics.job.atomistic.GenericInput property) (pyiron_atomistics.gpaw.gpaw.GpawInput property) (pyiron_atomistics.interactive.quasi_newton.Input property) (pyiron_atomistics.interactive.sxextoptint.Input property) (pyiron_atomistics.lammps.control.LammpsControl property) (pyiron_atomistics.lammps.potential.LammpsPotential property) (pyiron_atomistics.testing.randomatomistic.ExampleInput property) (pyiron_atomistics.vasp.base.Incar property) (pyiron_atomistics.vasp.base.Kpoints property) (pyiron_atomistics.vasp.potential.Potcar property) server (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob property) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive property) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper property) (pyiron_atomistics.atomistics.job.sqs.SQSJob property) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer property) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob property) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan property) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster property) (pyiron_atomistics.atomistics.master.parallel.MapMaster property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster property) (pyiron_atomistics.atomistics.master.structure.StructureListMaster property) (pyiron_atomistics.calphy.job.Calphy property) (pyiron_atomistics.dft.job.generic.GenericDFTJob property) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel property) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT property) (pyiron_atomistics.gpaw.gpaw.Gpaw property) (pyiron_atomistics.gpaw.pyiron_ase.AseJob property) (pyiron_atomistics.interactive.activation_relaxation_technique.ART property) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton property) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer property) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive property) (pyiron_atomistics.lammps.base.LammpsBase property) (pyiron_atomistics.lammps.interactive.LammpsInteractive property) (pyiron_atomistics.lammps.lammps.Lammps property) (pyiron_atomistics.sphinx.base.SphinxBase property) (pyiron_atomistics.sphinx.interactive.SphinxInt2 property) (pyiron_atomistics.sphinx.interactive.SphinxInteractive property) (pyiron_atomistics.sphinx.sphinx.Sphinx property) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob property) (pyiron_atomistics.testing.randomatomistic.ExampleJob property) (pyiron_atomistics.thermodynamics.hessian.HessianJob property) (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) set() (pyiron_atomistics.atomistics.job.atomistic.GenericInput method) (pyiron_atomistics.atomistics.structure.atom.Atom method) (pyiron_atomistics.gpaw.gpaw.GpawInput method) (pyiron_atomistics.interactive.quasi_newton.Input method) (pyiron_atomistics.interactive.sxextoptint.Input method) (pyiron_atomistics.lammps.control.LammpsControl method) (pyiron_atomistics.lammps.potential.LammpsPotential method) (pyiron_atomistics.testing.randomatomistic.ExampleInput method) (pyiron_atomistics.vasp.base.Incar method) (pyiron_atomistics.vasp.base.Kpoints method) (pyiron_atomistics.vasp.potential.Potcar method) set_algorithm() (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) set_angle() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) set_array() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage method) set_atomic_numbers() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) set_calculator() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) set_cell() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) set_celldisp() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) set_center_of_mass() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) set_check_overlap() (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) set_chemical_symbols() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) set_child_id_func() (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) set_complex_constraint() (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) set_constraint() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) set_convergence_precision() (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) set_coulomb_interactions() (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) set_dict() (pyiron_atomistics.atomistics.job.atomistic.GenericInput method) (pyiron_atomistics.gpaw.gpaw.GpawInput method) (pyiron_atomistics.interactive.quasi_newton.Input method) (pyiron_atomistics.interactive.sxextoptint.Input method) (pyiron_atomistics.lammps.control.LammpsControl method) (pyiron_atomistics.lammps.potential.LammpsPotential method) (pyiron_atomistics.testing.randomatomistic.ExampleInput method) (pyiron_atomistics.vasp.base.Incar method) (pyiron_atomistics.vasp.base.Kpoints method) (pyiron_atomistics.vasp.potential.Potcar method) set_dihedral() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) set_dipole_correction() (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) set_distance() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) set_eddrmm_handling() (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) set_electric_field() (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) set_empty_states() (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) set_encut() (in module pyiron_atomistics.dft.job.generic) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) set_fft_mesh() (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) set_fix_external() (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) set_for_band_structure_calc() (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) set_initial_charges() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) set_initial_magnetic_moments() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) set_initial_velocity() (pyiron_atomistics.lammps.control.LammpsControl method) set_input_to_read_only() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) set_job_status() (pyiron_atomistics.project.Project method) set_kpoints() (in module pyiron_atomistics.dft.job.generic) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) set_kpoints_file() (pyiron_atomistics.vasp.base.Kpoints method) set_logging_level() (pyiron_atomistics.project.Project static method) set_masses() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) set_mixing_parameters() (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) set_momenta() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) set_occupancy_smearing() (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) set_pbc() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) set_positions() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) set_potential() (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) set_potentials() (pyiron_atomistics.calphy.job.Calphy method) set_primitive_constraint() (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) set_rwigs() (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) set_scaled_positions() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) set_server() (in module pyiron_atomistics.thermodynamics.interfacemethod) set_species() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) set_spin_constraint() (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) set_structure() (in module pyiron_atomistics.atomistics.job.atomistic) set_tags() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) set_temperatures() (pyiron_atomistics.atomistics.thermodynamics.thermo_bulk.ThermoBulk method) set_value() (pyiron_atomistics.atomistics.job.atomistic.GenericInput method) (pyiron_atomistics.gpaw.gpaw.GpawInput method) (pyiron_atomistics.interactive.quasi_newton.Input method) (pyiron_atomistics.interactive.sxextoptint.Input method) (pyiron_atomistics.lammps.control.LammpsControl method) (pyiron_atomistics.lammps.potential.LammpsPotential method) (pyiron_atomistics.testing.randomatomistic.ExampleInput method) (pyiron_atomistics.vasp.base.Incar method) (pyiron_atomistics.vasp.base.Kpoints method) (pyiron_atomistics.vasp.potential.Potcar method) set_velocities() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) set_volumes() (pyiron_atomistics.atomistics.thermodynamics.thermo_bulk.ThermoBulk method) setdefault() (pyiron_atomistics.atomistics.master.parallel.GenericOutput method) (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) (pyiron_atomistics.sphinx.input_writer.Group method) setup_liquid_job() (in module pyiron_atomistics.thermodynamics.interfacemethod) shell_distances() (pyiron_atomistics.atomistics.structure.structurestorage.StructurePlots method) shells (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory property) show_hdf() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) signal_intercept() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) simulation_cell() (pyiron_atomistics.lammps.structure.LammpsStructure method) size (pyiron_atomistics.project.Project property) sorted_indices (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) spacegroups() (pyiron_atomistics.atomistics.structure.structurestorage.StructurePlots method) species (pyiron_atomistics.atomistics.structure.atoms.Atoms property) species() (pyiron_atomistics.atomistics.structure.atoms.Symbols method) species_indices() (pyiron_atomistics.atomistics.structure.atoms.Symbols method) spherical_average_potential() (pyiron_atomistics.atomistics.volumetric.generic.VolumetricData method) (pyiron_atomistics.sphinx.volumetric_data.SphinxVolumetricData method) (pyiron_atomistics.vasp.volumetric_data.VaspVolumetricData method) Sphinx (class in pyiron_atomistics.sphinx.sphinx) SphinxBase (class in pyiron_atomistics.sphinx.base) SphinxInt2 (class in pyiron_atomistics.sphinx.interactive) SphinxInteractive (class in pyiron_atomistics.sphinx.interactive) SphinxJTHPotentialFile (class in pyiron_atomistics.sphinx.potential) SphinxOutput (class in pyiron_atomistics.sphinx.interactive) SphinxVolumetricData (class in pyiron_atomistics.sphinx.volumetric_data) spin_constraints (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) spins (pyiron_atomistics.atomistics.structure.atoms.Atoms property) split() (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage method) SQSJob (class in pyiron_atomistics.atomistics.job.sqs) SQSJobGenerator (class in pyiron_atomistics.atomistics.master.sqsmaster) SQSMaster (class in pyiron_atomistics.atomistics.master.sqsmaster) stack() (pyiron_atomistics.atomistics.structure.factories.ase.AseFactory method) (pyiron_atomistics.atomistics.structure.factory.StructureFactory method) status (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob property) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive property) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper property) (pyiron_atomistics.atomistics.job.sqs.SQSJob property) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer property) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob property) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan property) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster property) (pyiron_atomistics.atomistics.master.parallel.MapMaster property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster property) (pyiron_atomistics.atomistics.master.structure.StructureListMaster property) (pyiron_atomistics.calphy.job.Calphy property) (pyiron_atomistics.dft.job.generic.GenericDFTJob property) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel property) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT property) (pyiron_atomistics.gpaw.gpaw.Gpaw property) (pyiron_atomistics.gpaw.pyiron_ase.AseJob property) (pyiron_atomistics.interactive.activation_relaxation_technique.ART property) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton property) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer property) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive property) (pyiron_atomistics.lammps.base.LammpsBase property) (pyiron_atomistics.lammps.interactive.LammpsInteractive property) (pyiron_atomistics.lammps.lammps.Lammps property) (pyiron_atomistics.sphinx.base.SphinxBase property) (pyiron_atomistics.sphinx.interactive.SphinxInt2 property) (pyiron_atomistics.sphinx.interactive.SphinxInteractive property) (pyiron_atomistics.sphinx.sphinx.Sphinx property) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob property) (pyiron_atomistics.testing.randomatomistic.ExampleJob property) (pyiron_atomistics.thermodynamics.hessian.HessianJob property) (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) stop_calculation() (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) store_structure() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) strain_circle() (in module pyiron_atomistics.thermodynamics.interfacemethod) string2symbols() (in module pyiron_atomistics.atomistics.structure.atoms) string2vector() (in module pyiron_atomistics.atomistics.structure.atoms) strip_xc_from_potential_name() (in module pyiron_atomistics.vasp.potential) structure (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob property) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive property) (pyiron_atomistics.atomistics.job.sqs.SQSJob property) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob property) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan property) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster property) (pyiron_atomistics.atomistics.master.parallel.MapMaster property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster property) (pyiron_atomistics.atomistics.structure.atoms.Symbols property) (pyiron_atomistics.dft.job.generic.GenericDFTJob property) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel property) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT property) (pyiron_atomistics.dft.waves.electronic.ElectronicStructure property) (pyiron_atomistics.gpaw.gpaw.Gpaw property) (pyiron_atomistics.gpaw.pyiron_ase.AseJob property) (pyiron_atomistics.lammps.base.LammpsBase property) (pyiron_atomistics.lammps.interactive.LammpsInteractive property) (pyiron_atomistics.lammps.lammps.Lammps property) (pyiron_atomistics.lammps.structure.LammpsStructure property) (pyiron_atomistics.sphinx.base.SphinxBase property) (pyiron_atomistics.sphinx.interactive.SphinxInt2 property) (pyiron_atomistics.sphinx.interactive.SphinxInteractive property) (pyiron_atomistics.sphinx.sphinx.Sphinx property) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob property) (pyiron_atomistics.thermodynamics.hessian.HessianJob property) (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.MetadynOutput property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.output.Output property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) structure_atomic() (pyiron_atomistics.lammps.structure.LammpsStructure method) structure_bond() (pyiron_atomistics.lammps.structure.LammpsStructure method) structure_charge() (pyiron_atomistics.lammps.structure.LammpsStructure method) structure_dict_to_hdf() (in module pyiron_atomistics.atomistics.structure.atoms) structure_full() (pyiron_atomistics.lammps.structure.LammpsStructure method) structure_lst (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer property) StructureContainer (class in pyiron_atomistics.atomistics.job.structurecontainer) StructureFactory (class in pyiron_atomistics.atomistics.structure.factory) StructureJobGenerator (class in pyiron_atomistics.atomistics.master.structure) StructureListMaster (class in pyiron_atomistics.atomistics.master.structure) StructurePlots (class in pyiron_atomistics.atomistics.structure.structurestorage) StructureStorage (class in pyiron_atomistics.atomistics.structure.structurestorage) subjob_name() (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixCalculator static method) surface() (pyiron_atomistics.atomistics.structure.factory.StructureFactory static method) surface_hkl() (pyiron_atomistics.atomistics.structure.factory.StructureFactory static method) suspend() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) switch_cluster() (pyiron_atomistics.project.Project static method) switch_to_central_database() (pyiron_atomistics.project.Project method) switch_to_local_database() (pyiron_atomistics.project.Project method) switch_to_user_mode() (pyiron_atomistics.project.Project method) switch_to_viewer_mode() (pyiron_atomistics.project.Project method) SxExtOpt (class in pyiron_atomistics.interactive.sxextoptint) SxExtOptInteractive (class in pyiron_atomistics.interactive.sxextoptint) sxversions() (in module pyiron_atomistics.sphinx.util) symbol (pyiron_atomistics.atomistics.structure.atom.Atom property) Symbols (class in pyiron_atomistics.atomistics.structure.atoms) symbols (pyiron_atomistics.atomistics.structure.atoms.Atoms property) symbols2numbers() (in module pyiron_atomistics.atomistics.structure.atoms) symlink() (pyiron_atomistics.project.Project method) symmetrize_vectors() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) T table() (pyiron_atomistics.project.Creator method) table_name (pyiron_atomistics.atomistics.job.atomistic.GenericInput property) (pyiron_atomistics.gpaw.gpaw.GpawInput property) (pyiron_atomistics.interactive.quasi_newton.Input property) (pyiron_atomistics.interactive.sxextoptint.Input property) (pyiron_atomistics.lammps.control.LammpsControl property) (pyiron_atomistics.lammps.potential.LammpsPotential property) (pyiron_atomistics.testing.randomatomistic.ExampleInput property) (pyiron_atomistics.vasp.base.Incar property) (pyiron_atomistics.vasp.base.Kpoints property) (pyiron_atomistics.vasp.potential.Potcar property) tag (pyiron_atomistics.atomistics.structure.atom.Atom property) temperatures (pyiron_atomistics.atomistics.thermodynamics.thermo_bulk.ThermoBulk property) Thermal (class in pyiron_atomistics.atomistics.master.phonopy) ThermoBulk (class in pyiron_atomistics.atomistics.thermodynamics.thermo_bulk) to_builtin() (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) (pyiron_atomistics.sphinx.input_writer.Group method) to_dict() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.atomistic.GenericInput method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.gpaw.GpawInput method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.Input method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.Input method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.control.LammpsControl method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.lammps.potential.LammpsPotential method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.input_writer.Group method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleInput method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.Incar method) (pyiron_atomistics.vasp.base.Kpoints method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.potential.Potcar method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) to_hdf() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.atomistic.GenericInput method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.atomistics.structure.atoms.Atoms method) (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) (pyiron_atomistics.atomistics.structure.periodic_table.ChemicalElement method) (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage method) (pyiron_atomistics.atomistics.volumetric.generic.VolumetricData method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.dft.waves.electronic.ElectronicStructure method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.gpaw.GpawInput method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.Input method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizerInput method) (pyiron_atomistics.interactive.sxextoptint.Input method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.Input method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.control.LammpsControl method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.lammps.potential.LammpsPotential method) (pyiron_atomistics.sphinx.base.Output method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.input_writer.Group method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.interactive.SphinxOutput method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.sphinx.volumetric_data.SphinxVolumetricData method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleInput method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.Incar method) (pyiron_atomistics.vasp.base.Kpoints method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.MetadynOutput method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.output.DFTOutput method) (pyiron_atomistics.vasp.output.GenericOutput method) (pyiron_atomistics.vasp.output.Output method) (pyiron_atomistics.vasp.potential.Potcar method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) (pyiron_atomistics.vasp.volumetric_data.VaspVolumetricData method) to_list() (pyiron_atomistics.atomistics.structure.factories.materialsproject.MPQueryResults method) to_object() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) to_pandas() (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage method) to_storage() (pyiron_atomistics.atomistics.structure.factories.materialsproject.MPQueryResults method) todict() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) total_data (pyiron_atomistics.atomistics.volumetric.generic.VolumetricData attribute) (pyiron_atomistics.atomistics.volumetric.generic.VolumetricData property) (pyiron_atomistics.sphinx.volumetric_data.SphinxVolumetricData property) (pyiron_atomistics.vasp.volumetric_data.VaspVolumetricData property) total_displacements (pyiron_atomistics.atomistics.job.atomistic.GenericOutput property) (pyiron_atomistics.atomistics.job.interactive.GenericInteractiveOutput property) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizerOutput property) (pyiron_atomistics.sphinx.interactive.SphinxOutput property) Trajectory (class in pyiron_atomistics.atomistics.job.atomistic) trajectory() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) transfer_from_remote() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) transform_structures() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.atomistic.Trajectory method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.structure.factories.materialsproject.MPQueryResults method) (pyiron_atomistics.atomistics.structure.has_structure.HasStructure method) (pyiron_atomistics.atomistics.structure.has_structure.TransformStructure method) (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) TransformStructure (class in pyiron_atomistics.atomistics.structure.has_structure) translate() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) U units (pyiron_atomistics.lammps.base.LammpsBase property) (pyiron_atomistics.lammps.interactive.LammpsInteractive property) (pyiron_atomistics.lammps.lammps.Lammps property) unlink() (pyiron_atomistics.project.Project method) unlocked() (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) (pyiron_atomistics.atomistics.structure.structurestorage.StructureStorage method) (pyiron_atomistics.sphinx.input_writer.Group method) unpack() (pyiron_atomistics.project.Project method) unpack_csv() (pyiron_atomistics.project.Project static method) update() (pyiron_atomistics.atomistics.master.parallel.GenericOutput method) (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) (pyiron_atomistics.sphinx.input_writer.Group method) update_from_remote() (pyiron_atomistics.project.Project method) update_hdf_types() (pyiron_atomistics.project.AtomisticsLocalMaintenance method) update_master() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) use_pressure (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizerInput property) V val_only (pyiron_atomistics.atomistics.job.atomistic.GenericInput property) (pyiron_atomistics.gpaw.gpaw.GpawInput property) (pyiron_atomistics.interactive.quasi_newton.Input property) (pyiron_atomistics.interactive.sxextoptint.Input property) (pyiron_atomistics.lammps.control.LammpsControl property) (pyiron_atomistics.lammps.potential.LammpsPotential property) (pyiron_atomistics.testing.randomatomistic.ExampleInput property) (pyiron_atomistics.vasp.base.Incar property) (pyiron_atomistics.vasp.base.Kpoints property) (pyiron_atomistics.vasp.potential.Potcar property) validate_convergence() (in module pyiron_atomistics.thermodynamics.interfacemethod) validate_ready_to_run() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) values() (pyiron_atomistics.atomistics.master.parallel.GenericOutput method) (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) (pyiron_atomistics.project.Project method) (pyiron_atomistics.sphinx.input_writer.Group method) Vasp (class in pyiron_atomistics.vasp.vasp) vasp_correct_energy_kin() (pyiron_atomistics.project.AtomisticsLocalMaintenance method) vasp_energy_pot_as_free_energy() (pyiron_atomistics.project.AtomisticsLocalMaintenance method) vasp_function() (in module pyiron_atomistics.vasp.vasp) VaspBase (class in pyiron_atomistics.vasp.base) VaspInteractive (class in pyiron_atomistics.vasp.interactive) VaspMetadyn (class in pyiron_atomistics.vasp.metadyn) VaspPotential (class in pyiron_atomistics.vasp.potential) VaspPotentialAbstract (class in pyiron_atomistics.vasp.potential) VaspPotentialFile (class in pyiron_atomistics.vasp.potential) VaspPotentialSetter (class in pyiron_atomistics.vasp.potential) Vasprun (class in pyiron_atomistics.vasp.vasprun) VaspSol (class in pyiron_atomistics.vasp.vaspsol) VaspVolumetricData (class in pyiron_atomistics.vasp.volumetric_data) vbm (pyiron_atomistics.dft.waves.electronic.ElectronicStructure property) vecs (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory property) version (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob property) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive property) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper property) (pyiron_atomistics.atomistics.job.sqs.SQSJob property) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer property) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob property) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan property) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster property) (pyiron_atomistics.atomistics.master.parallel.MapMaster property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster property) (pyiron_atomistics.atomistics.master.structure.StructureListMaster property) (pyiron_atomistics.calphy.job.Calphy property) (pyiron_atomistics.dft.job.generic.GenericDFTJob property) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel property) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT property) (pyiron_atomistics.gpaw.gpaw.Gpaw property) (pyiron_atomistics.gpaw.pyiron_ase.AseJob property) (pyiron_atomistics.interactive.activation_relaxation_technique.ART property) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton property) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer property) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive property) (pyiron_atomistics.lammps.base.LammpsBase property) (pyiron_atomistics.lammps.interactive.LammpsInteractive property) (pyiron_atomistics.lammps.lammps.Lammps property) (pyiron_atomistics.sphinx.base.SphinxBase property) (pyiron_atomistics.sphinx.interactive.SphinxInt2 property) (pyiron_atomistics.sphinx.interactive.SphinxInteractive property) (pyiron_atomistics.sphinx.sphinx.Sphinx property) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob property) (pyiron_atomistics.testing.randomatomistic.ExampleJob property) (pyiron_atomistics.thermodynamics.hessian.HessianJob property) (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) view_potentials() (in module pyiron_atomistics.lammps.potential) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) view_structure() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) volume (pyiron_atomistics.atomistics.master.murnaghan.MurnaghanDebyeModel property) volume_only (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizerInput property) volumes (pyiron_atomistics.atomistics.thermodynamics.thermo_bulk.ThermoBulk property) volumetric_data_dict_to_hdf() (in module pyiron_atomistics.vasp.volumetric_data) VolumetricData (class in pyiron_atomistics.atomistics.volumetric.generic) W wait_for_job() (pyiron_atomistics.project.Project static method) wait_for_jobs() (pyiron_atomistics.project.Project method) walk() (pyiron_atomistics.project.Project method) working_directory (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob property) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive property) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper property) (pyiron_atomistics.atomistics.job.sqs.SQSJob property) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer property) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob property) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan property) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster property) (pyiron_atomistics.atomistics.master.parallel.MapMaster property) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob property) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob property) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster property) (pyiron_atomistics.atomistics.master.structure.StructureListMaster property) (pyiron_atomistics.calphy.job.Calphy property) (pyiron_atomistics.dft.job.generic.GenericDFTJob property) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel property) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel property) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT property) (pyiron_atomistics.gpaw.gpaw.Gpaw property) (pyiron_atomistics.gpaw.pyiron_ase.AseJob property) (pyiron_atomistics.interactive.activation_relaxation_technique.ART property) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton property) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer property) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive property) (pyiron_atomistics.lammps.base.LammpsBase property) (pyiron_atomistics.lammps.interactive.LammpsInteractive property) (pyiron_atomistics.lammps.lammps.Lammps property) (pyiron_atomistics.sphinx.base.SphinxBase property) (pyiron_atomistics.sphinx.interactive.SphinxInt2 property) (pyiron_atomistics.sphinx.interactive.SphinxInteractive property) (pyiron_atomistics.sphinx.sphinx.Sphinx property) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob property) (pyiron_atomistics.testing.randomatomistic.ExampleJob property) (pyiron_atomistics.thermodynamics.hessian.HessianJob property) (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) wrap() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) wrap_executable() (pyiron_atomistics.project.Project method) wrap_python_function() (pyiron_atomistics.project.Project method) write() (pyiron_atomistics.atomistics.structure.atoms.Atoms method) (pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory method) (pyiron_atomistics.sphinx.input_writer.Group method) (pyiron_atomistics.vasp.base.Input method) (pyiron_atomistics.vasp.metadyn.MetadynInput method) write_charge_density (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) write_constraints() (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) write_cube_file() (pyiron_atomistics.atomistics.volumetric.generic.VolumetricData method) (pyiron_atomistics.sphinx.volumetric_data.SphinxVolumetricData method) (pyiron_atomistics.vasp.volumetric_data.VaspVolumetricData method) write_electrostatic_potential (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) write_file() (pyiron_atomistics.atomistics.job.atomistic.GenericInput method) (pyiron_atomistics.gpaw.gpaw.GpawInput method) (pyiron_atomistics.interactive.quasi_newton.Input method) (pyiron_atomistics.interactive.sxextoptint.Input method) (pyiron_atomistics.lammps.control.LammpsControl method) (pyiron_atomistics.lammps.potential.LammpsPotential method) (pyiron_atomistics.lammps.structure.LammpsStructure method) (pyiron_atomistics.testing.randomatomistic.ExampleInput method) (pyiron_atomistics.vasp.base.Incar method) (pyiron_atomistics.vasp.base.Kpoints method) (pyiron_atomistics.vasp.potential.Potcar method) write_input() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.interactivewrapper.InteractiveWrapper method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.job.structurecontainer.StructureContainer method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.atomistics.master.structure.StructureListMaster method) (pyiron_atomistics.calphy.job.Calphy method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.interactive.activation_relaxation_technique.ART method) (pyiron_atomistics.interactive.quasi_newton.QuasiNewton method) (pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizer method) (pyiron_atomistics.interactive.sxextoptint.SxExtOptInteractive method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.testing.randomatomistic.ExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) write_magmoms() (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) write_phonopy_force_constants() (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) write_poscar() (in module pyiron_atomistics.vasp.structure) write_resolved_dos (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) write_restart() (pyiron_atomistics.testing.executable.ExampleExecutable method) write_restart_file() (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) write_spin_constraints() (in module pyiron_atomistics.sphinx.input_writer) write_structure() (pyiron_atomistics.calphy.job.Calphy method) write_traj() (pyiron_atomistics.atomistics.job.atomistic.AtomisticGenericJob method) (pyiron_atomistics.atomistics.job.interactive.GenericInteractive method) (pyiron_atomistics.atomistics.job.sqs.SQSJob method) (pyiron_atomistics.atomistics.master.elasticmatrix.ElasticMatrixJob method) (pyiron_atomistics.atomistics.master.murnaghan.Murnaghan method) (pyiron_atomistics.atomistics.master.parallel.AtomisticParallelMaster method) (pyiron_atomistics.atomistics.master.parallel.MapMaster method) (pyiron_atomistics.atomistics.master.phonopy.PhonopyJob method) (pyiron_atomistics.atomistics.master.quasi.QuasiHarmonicJob method) (pyiron_atomistics.atomistics.master.sqsmaster.SQSMaster method) (pyiron_atomistics.dft.job.generic.GenericDFTJob method) (pyiron_atomistics.dft.master.convergence_encut_parallel.ConvEncutParallel method) (pyiron_atomistics.dft.master.convergence_kpoint_parallel.ConvKpointParallel method) (pyiron_atomistics.dft.master.murnaghan_dft.MurnaghanDFT method) (pyiron_atomistics.gpaw.gpaw.Gpaw method) (pyiron_atomistics.gpaw.pyiron_ase.AseJob method) (pyiron_atomistics.lammps.base.LammpsBase method) (pyiron_atomistics.lammps.interactive.LammpsInteractive method) (pyiron_atomistics.lammps.lammps.Lammps method) (pyiron_atomistics.sphinx.base.SphinxBase method) (pyiron_atomistics.sphinx.interactive.SphinxInt2 method) (pyiron_atomistics.sphinx.interactive.SphinxInteractive method) (pyiron_atomistics.sphinx.sphinx.Sphinx method) (pyiron_atomistics.testing.randomatomistic.AtomisticExampleJob method) (pyiron_atomistics.thermodynamics.hessian.HessianJob method) (pyiron_atomistics.vasp.base.VaspBase method) (pyiron_atomistics.vasp.interactive.VaspInteractive method) (pyiron_atomistics.vasp.metadyn.VaspMetadyn method) (pyiron_atomistics.vasp.vasp.Vasp method) (pyiron_atomistics.vasp.vaspsol.VaspSol method) write_vasp_volumetric() (pyiron_atomistics.atomistics.volumetric.generic.VolumetricData method) (pyiron_atomistics.sphinx.volumetric_data.SphinxVolumetricData method) (pyiron_atomistics.vasp.volumetric_data.VaspVolumetricData method) write_wave_funct (pyiron_atomistics.vasp.base.VaspBase property) (pyiron_atomistics.vasp.interactive.VaspInteractive property) (pyiron_atomistics.vasp.metadyn.VaspMetadyn property) (pyiron_atomistics.vasp.vasp.Vasp property) (pyiron_atomistics.vasp.vaspsol.VaspSol property) X x (pyiron_atomistics.atomistics.structure.atom.Atom property) Y y (pyiron_atomistics.atomistics.structure.atom.Atom property) Z z (pyiron_atomistics.atomistics.structure.atom.Atom property)
