pyiron
pyiron-0.2.17
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A
abcproperty() (in module pyiron.atomistics.structure.atom)
accept_crash() (pyiron.base.server.generic.Server property)
add() (pyiron.table.datamining.TableJob property)
add_band() (pyiron.dft.waves.electronic.Kpoint method)
add_column() (pyiron.base.database.generic.DatabaseAccess method)
add_element() (pyiron.atomistics.structure.periodic_table.PeriodicTable method)
add_high_symmetry_path() (pyiron.atomistics.structure.atoms.Atoms method)
add_high_symmetry_points() (pyiron.atomistics.structure.atoms.Atoms method)
add_item_dict() (pyiron.base.database.filetable.FileTable method)
(pyiron.base.database.generic.DatabaseAccess method)
add_kpoint() (pyiron.dft.waves.electronic.ElectronicStructure method)
add_new_element() (pyiron.sphinx.potential.SphinxJTHPotentialFile method)
(pyiron.vasp.potential.VaspPotentialFile method)
add_tag() (pyiron.atomistics.structure.atoms.Atoms method)
(pyiron.atomistics.structure.sparse_list.SparseArray method)
add_tags() (pyiron.atomistics.structure.periodic_table.ChemicalElement method)
always_true() (in module pyiron.table.datamining)
always_true_pandas() (in module pyiron.table.datamining)
analyse_minimized_structure() (in module pyiron.thermodynamics.interfacemethod)
analyse_ovito_centro_symmetry() (pyiron.atomistics.structure.atoms.Atoms method)
analyse_ovito_cna_adaptive() (pyiron.atomistics.structure.atoms.Atoms method)
analyse_ovito_voronoi_volume() (pyiron.atomistics.structure.atoms.Atoms method)
analyse_phonopy_equivalent_atoms() (pyiron.atomistics.structure.atoms.Atoms method)
analyse_pyscal_steinhardt_parameter() (pyiron.atomistics.structure.atoms.Atoms method)
analysis_project() (pyiron.table.datamining.TableJob property)
animate_nma_mode() (pyiron.atomistics.nma.nma.NMA method)
animate_structure() (pyiron.atomistics.job.atomistic.AtomisticGenericJob method)
append() (pyiron.atomistics.job.structurecontainer.StructureContainer method)
(pyiron.atomistics.structure.atoms.Atoms method)
(pyiron.base.generic.inputlist.InputList method)
(pyiron.base.job.generic.GenericJob method)
(pyiron.base.master.generic.GenericMaster method)
(pyiron.base.master.list.ListMaster method)
(pyiron.base.pyio.parser.Logstatus method)
append_charge_density() (pyiron.vasp.base.VaspBase method)
append_eigenvalues() (pyiron.dft.waves.bandstructure.Bandstructure method)
append_wave_function() (pyiron.vasp.base.VaspBase method)
apply_func() (pyiron.base.pyio.parser.LogTag method)
apply_strain() (pyiron.atomistics.structure.atoms.Atoms method)
arg() (pyiron.base.pyio.parser.LogTag method)
ase_to_pyiron() (in module pyiron.atomistics.structure.atoms)
AseAdapter (class in pyiron.gpaw.pyiron_ase)
AseJob (class in pyiron.gpaw.pyiron_ase)
Atom (class in pyiron.atomistics.structure.atom)
atomic_number_to_abbreviation() (pyiron.atomistics.structure.periodic_table.PeriodicTable method)
AtomisticExampleJob (class in pyiron.testing.randomatomistic)
AtomisticGenericJob (class in pyiron.atomistics.job.atomistic)
AtomisticParallelMaster (class in pyiron.atomistics.master.parallel)
atomproperty() (in module pyiron.atomistics.structure.atom)
Atoms (class in pyiron.atomistics.structure.atoms)
atoms() (pyiron.atomistics.volumetric.generic.VolumetricData property)
atoms_from_string() (in module pyiron.vasp.structure)
attribute (pyiron.base.job.script.ScriptJob attribute)
AutorestoredConnection (class in pyiron.base.database.generic)
available_versions() (pyiron.base.job.executable.Executable property)
B
Band (class in pyiron.dft.waves.electronic)
BandPath (class in pyiron.dft.waves.bandstructure)
bands (pyiron.dft.waves.electronic.Kpoint attribute)
bands() (pyiron.vasp.base.GenericOutput property)
Bandstructure (class in pyiron.dft.waves.bandstructure)
base_name (pyiron.base.generic.hdfio.FileHDFio attribute)
base_name() (pyiron.base.generic.hdfio.FileHDFio property)
(pyiron.base.generic.hdfio.ProjectHDFio property)
(pyiron.base.job.path.JobPathBase property)
(pyiron.base.project.path.GenericPath property)
birch() (in module pyiron.atomistics.master.murnaghan)
(pyiron.atomistics.master.murnaghan.EnergyVolumeFit static method)
birchmurnaghan_energy() (in module pyiron.atomistics.master.murnaghan)
(pyiron.atomistics.master.murnaghan.EnergyVolumeFit static method)
bond_dict() (pyiron.lammps.base.LammpsBase property)
bsse_to_pandas() (pyiron.gaussian.gaussian.Gaussian method)
C
calc_md() (pyiron.atomistics.job.atomistic.AtomisticGenericJob method)
(pyiron.dft.job.generic.GenericDFTJob method)
(pyiron.gaussian.gaussian.Gaussian method)
(pyiron.lammps.base.LammpsBase method)
(pyiron.lammps.control.LammpsControl method)
(pyiron.lammps.interactive.LammpsInteractive method)
(pyiron.sphinx.base.SphinxBase method)
(pyiron.vasp.base.VaspBase method)
(pyiron.vasp.interactive.VaspInteractive method)
(pyiron.yaff.yaff.Yaff method)
calc_minimize() (pyiron.atomistics.job.atomistic.AtomisticGenericJob method)
(pyiron.dft.job.generic.GenericDFTJob method)
(pyiron.gaussian.gaussian.Gaussian method)
(pyiron.lammps.base.LammpsBase method)
(pyiron.lammps.control.LammpsControl method)
(pyiron.lammps.interactive.LammpsInteractive method)
(pyiron.sphinx.base.SphinxBase method)
(pyiron.sphinx.interactive.SphinxInteractive method)
(pyiron.vasp.base.VaspBase method)
(pyiron.vasp.interactive.VaspInteractive method)
(pyiron.yaff.yaff.Yaff method)
calc_static() (pyiron.atomistics.job.atomistic.AtomisticGenericJob method)
(pyiron.dft.job.generic.GenericDFTJob method)
(pyiron.gaussian.gaussian.Gaussian method)
(pyiron.lammps.base.LammpsBase method)
(pyiron.lammps.control.LammpsControl method)
(pyiron.sphinx.base.SphinxBase method)
(pyiron.sphinx.interactive.SphinxInteractive method)
(pyiron.vasp.base.VaspBase method)
(pyiron.yaff.yaff.Yaff method)
calc_temp_iteration() (in module pyiron.thermodynamics.interfacemethod)
calc_vcsgc() (pyiron.lammps.base.LammpsBase method)
(pyiron.lammps.control.LammpsControl method)
calculate_forces() (pyiron.thermodynamics.hessian.HessianJob method)
cbm() (pyiron.dft.waves.electronic.ElectronicStructure property)
cell() (pyiron.atomistics.structure.atoms.Atoms property)
cells() (pyiron.atomistics.job.atomistic.GenericOutput property)
(pyiron.atomistics.job.interactive.GenericInteractiveOutput property)
(pyiron.atomistics.job.interactivewrapper.ReferenceJobOutput property)
center() (pyiron.atomistics.structure.atoms.Atoms method)
center_coordinates_in_unit_cell() (pyiron.atomistics.structure.atoms.Atoms method)
change_column_type() (pyiron.base.database.generic.DatabaseAccess method)
charge_density (pyiron.vasp.base.Output attribute)
(pyiron.vasp.interactive.Output attribute)
check_band_occupancy() (pyiron.sphinx.interactive.SphinxOutput method)
check_consistency() (pyiron.atomistics.structure.sparse_list.SparseArray method)
check_for_holes() (in module pyiron.thermodynamics.interfacemethod)
check_if_job_exists() (pyiron.base.job.core.JobCore method)
check_setup() (pyiron.atomistics.job.interactivewrapper.InteractiveWrapper method)
(pyiron.base.job.generic.GenericJob method)
(pyiron.sphinx.base.SphinxBase method)
check_vasp_potentials() (pyiron.sphinx.base.SphinxBase static method)
ChemicalElement (class in pyiron.atomistics.structure.periodic_table)
child_id_lst() (pyiron.thermodynamics.sxphonons.SxDynMat property)
child_ids() (pyiron.base.generic.template.PyironObject property)
(pyiron.base.job.core.JobCore property)
(pyiron.base.master.generic.GenericMaster property)
child_lst() (pyiron.thermodynamics.sxphonons.SxDynMat property)
child_names() (pyiron.base.master.generic.GenericMaster property)
clean_character() (in module pyiron.vasp.vasprun)
clean_key() (in module pyiron.vasp.vasprun)
cleanup() (pyiron.vasp.base.VaspBase method)
clear() (pyiron.base.generic.inputlist.InputList method)
clear_all() (pyiron.base.generic.parameters.GenericParameters method)
clear_job() (pyiron.base.job.generic.GenericJob method)
close() (pyiron.atomistics.structure.atoms.Atoms method)
(pyiron.base.database.generic.AutorestoredConnection method)
(pyiron.base.generic.hdfio.FileHDFio method)
(pyiron.base.job.path.JobPathBase method)
(pyiron.base.project.path.ProjectPath method)
close_connection() (pyiron.base.settings.generic.Settings method)
cluster_analysis() (pyiron.atomistics.structure.atoms.Atoms method)
coarse_run() (pyiron.sphinx.interactive.SphinxInteractive property)
col_to_value() (pyiron.table.datamining.PyironTable method)
collect() (pyiron.sphinx.base.Output method)
(pyiron.vasp.base.Output method)
(pyiron.vasp.metadyn.MetadynOutput method)
collect_charge_density() (pyiron.sphinx.base.Output method)
collect_dump_file() (pyiron.lammps.base.LammpsBase method)
collect_electrostatic_potential() (pyiron.sphinx.base.Output method)
collect_energy_dat() (pyiron.sphinx.base.Output method)
collect_energy_struct() (pyiron.sphinx.base.Output method)
collect_eps_dat() (pyiron.sphinx.base.Output method)
collect_errors() (pyiron.lammps.base.LammpsBase method)
(pyiron.sphinx.base.SphinxBase method)
(pyiron.vasp.base.VaspBase method)
collect_h5md_file() (pyiron.lammps.base.LammpsBase method)
collect_logfiles() (pyiron.atomistics.job.interactivewrapper.InteractiveWrapper method)
(pyiron.base.job.generic.GenericJob method)
(pyiron.base.job.script.ScriptJob method)
(pyiron.base.master.parallel.ParallelMaster method)
(pyiron.base.master.serial.SerialMasterBase method)
(pyiron.base.project.store.ProjectStore method)
(pyiron.lammps.base.LammpsBase method)
(pyiron.sphinx.base.SphinxBase method)
(pyiron.testing.randomatomistic.ExampleJob method)
(pyiron.thermodynamics.sxphonons.SxDynMat method)
(pyiron.vasp.base.VaspBase method)
collect_output() (in module pyiron.gaussian.gaussian)
(in module pyiron.quickff.quickff)
(in module pyiron.yaff.yaff)
(pyiron.atomistics.job.interactivewrapper.InteractiveWrapper method)
(pyiron.atomistics.master.murnaghan.Murnaghan method)
(pyiron.atomistics.master.parallel.MapMaster method)
(pyiron.atomistics.master.structure.StructureListMaster method)
(pyiron.base.job.generic.GenericJob method)
(pyiron.base.job.script.ScriptJob method)
(pyiron.base.master.flexible.FlexibleMaster method)
(pyiron.base.master.generic.GenericMaster method)
(pyiron.base.master.list.ListMaster method)
(pyiron.base.master.parallel.ParallelMaster method)
(pyiron.base.master.serial.SerialMasterBase method)
(pyiron.base.project.store.ProjectStore method)
(pyiron.dft.master.convergence_encut_parallel.ConvEncutParallel method)
(pyiron.dft.master.convergence_kpoint_parallel.ConvKpointParallel method)
(pyiron.gaussian.gaussian.Gaussian method)
(pyiron.gpaw.gpaw.GpawJob method)
(pyiron.interactive.scipy_minimizer.ScipyMinimizer method)
(pyiron.lammps.base.LammpsBase method)
(pyiron.lammps.interactive.LammpsInteractive method)
(pyiron.quickff.quickff.QuickFF method)
(pyiron.sphinx.base.SphinxBase method)
(pyiron.sphinx.interactive.SphinxInteractive method)
(pyiron.testing.randomatomistic.ExampleJob method)
(pyiron.thermodynamics.sxphonons.SxDynMat method)
(pyiron.thermodynamics.sxphonons.SxHarmPotTst method)
(pyiron.thermodynamics.sxphonons.SxPhonons method)
(pyiron.thermodynamics.sxphonons.SxUniqDispl method)
(pyiron.vasp.base.VaspBase method)
(pyiron.yaff.yaff.Yaff method)
collect_output_log() (pyiron.lammps.base.LammpsBase method)
(pyiron.testing.randomatomistic.ExampleJob method)
collect_relaxed_hist() (pyiron.sphinx.base.Output method)
collect_residue_dat() (pyiron.sphinx.base.Output method)
collect_sphinx_log() (pyiron.sphinx.base.Output method)
collect_spins_dat() (pyiron.sphinx.base.Output method)
collect_warnings() (pyiron.sphinx.base.SphinxBase method)
(pyiron.testing.randomatomistic.ExampleJob method)
(pyiron.vasp.base.VaspBase method)
combine_mat() (pyiron.base.pyio.parser.Logstatus method)
combine_xyz() (pyiron.base.pyio.parser.Logstatus method)
comment_char() (pyiron.base.generic.parameters.GenericParameters property)
communicator() (pyiron.gpaw.pyiron_ase.AseAdapter property)
compress() (pyiron.base.job.core.JobCore method)
(pyiron.lammps.base.LammpsBase method)
(pyiron.sphinx.base.SphinxBase method)
(pyiron.vasp.base.VaspBase method)
compress_jobs() (pyiron.base.project.generic.Project method)
computation_time() (pyiron.atomistics.job.atomistic.GenericOutput property)
content() (pyiron.base.job.core.JobCore property)
continue_with_final_structure() (pyiron.atomistics.job.atomistic.AtomisticGenericJob method)
continue_with_restart_files() (pyiron.atomistics.job.atomistic.AtomisticGenericJob method)
contour_entropy() (pyiron.atomistics.thermodynamics.thermo_bulk.ThermoBulk method)
contour_pressure() (pyiron.atomistics.thermodynamics.thermo_bulk.ThermoBulk method)
ConvEncutParallel (class in pyiron.dft.master.convergence_encut_parallel)
ConvEncutSerial (class in pyiron.dft.master.convergence_encut_serial)
converged() (pyiron.interactive.sxextoptint.SxExtOpt property)
convergence_check() (pyiron.base.job.generic.GenericJob method)
(pyiron.interactive.sxextoptint.SxExtOptInteractive method)
(pyiron.lammps.base.LammpsBase method)
(pyiron.sphinx.base.SphinxBase method)
(pyiron.vasp.base.VaspBase method)
convergence_goal() (in module pyiron.atomistics.master.convergence_volume)
(in module pyiron.dft.master.convergence_encut_serial)
ConvergenceVolume (class in pyiron.atomistics.master.convergence_volume)
convert_database_config() (pyiron.base.settings.generic.Settings static method)
convert_dict() (pyiron.table.datamining.PyironTable method)
convert_element() (pyiron.atomistics.structure.atoms.Atoms method)
convert_formula() (pyiron.atomistics.structure.atoms.Atoms static method)
convert_path() (in module pyiron.base.settings.generic)
convert_str_to_class() (pyiron.base.job.jobtype.JobType static method)
convert_to_object() (pyiron.table.datamining.TableJob property)
convert_unit() (pyiron.base.pyio.parser.Logstatus method)
ConvKpointParallel (class in pyiron.dft.master.convergence_kpoint_parallel)
copy() (pyiron.atomistics.structure.atoms.Atoms method)
(pyiron.atomistics.thermodynamics.thermo_bulk.ThermoBulk method)
(pyiron.base.generic.hdfio.FileHDFio method)
(pyiron.base.generic.hdfio.ProjectHDFio method)
(pyiron.base.generic.inputlist.InputList method)
(pyiron.base.generic.template.PyironObject method)
(pyiron.base.job.core.JobCore method)
(pyiron.base.job.generic.GenericJob method)
(pyiron.base.master.list.ListMaster method)
(pyiron.base.master.parallel.ParallelMaster method)
(pyiron.base.master.serial.SerialMasterBase method)
(pyiron.base.project.generic.Project method)
(pyiron.base.project.path.GenericPath method)
(pyiron.base.project.path.ProjectPath method)
(pyiron.project.Project method)
copy_file_to_working_directory() (pyiron.base.job.generic.GenericJob method)
copy_hamiltonian() (pyiron.vasp.base.VaspBase method)
copy_pot_files() (pyiron.lammps.potential.LammpsPotential method)
copy_potentials() (pyiron.sphinx.base.InputWriter method)
copy_template() (pyiron.base.job.generic.GenericJob method)
copy_to() (pyiron.atomistics.job.atomistic.AtomisticGenericJob method)
(pyiron.base.generic.hdfio.FileHDFio method)
(pyiron.base.generic.template.PyironObject method)
(pyiron.base.job.core.JobCore method)
(pyiron.base.job.generic.GenericJob method)
(pyiron.base.master.generic.GenericMaster method)
(pyiron.base.master.parallel.ParallelMaster method)
(pyiron.base.project.generic.Project method)
cores() (pyiron.base.server.generic.Server property)
create_ase_bulk() (in module pyiron.atomistics.structure.generator)
(pyiron.project.Project static method)
create_atoms() (pyiron.project.Project static method)
create_child_job() (pyiron.base.master.parallel.ParallelMaster method)
create_element() (pyiron.project.Project static method)
create_from_job() (pyiron.base.project.generic.Project method)
create_group() (pyiron.base.generic.hdfio.FileHDFio method)
(pyiron.base.generic.inputlist.InputList method)
(pyiron.base.job.path.JobPathBase method)
(pyiron.base.project.generic.Project method)
create_hdf() (pyiron.base.generic.hdfio.ProjectHDFio method)
(pyiron.base.project.generic.Project static method)
create_hkl_surface() (in module pyiron.atomistics.structure.generator)
create_job() (pyiron.base.job.generic.GenericJob method)
(pyiron.base.project.generic.Project method)
(pyiron.project.Project method)
create_job_template() (in module pyiron.thermodynamics.interfacemethod)
create_line_mode_structure() (pyiron.atomistics.structure.atoms.Atoms method)
create_next() (pyiron.atomistics.master.convergence_volume.ConvergenceVolume method)
(pyiron.base.master.serial.SerialMasterBase method)
(pyiron.dft.master.convergence_encut_serial.ConvEncutSerial method)
create_object() (pyiron.base.generic.hdfio.ProjectHDFio method)
(pyiron.project.Project static method)
create_pipeline() (pyiron.base.job.generic.GenericJob method)
(pyiron.project.Project method)
create_structure() (in module pyiron.atomistics.structure.generator)
(pyiron.project.Project static method)
create_surface() (in module pyiron.atomistics.structure.generator)
(pyiron.project.Project static method)
create_table() (pyiron.project.Project method)
(pyiron.table.datamining.PyironTable method)
create_working_directory() (pyiron.base.generic.hdfio.ProjectHDFio method)
CrystalStructure (class in pyiron.atomistics.structure.atoms)
current() (pyiron.base.pyio.parser.LogTag property)
current_structure() (pyiron.atomistics.job.interactive.GenericInteractive property)
cut_reference_to_atoms() (pyiron.atomistics.structure.atom.Atom method)
cutoff_radius() (pyiron.lammps.base.LammpsBase property)
cylindrical_average_potential() (pyiron.atomistics.volumetric.generic.VolumetricData method)
D
database() (in module pyiron.base.settings.update)
(pyiron.base.job.jobstatus.JobStatus property)
(pyiron.base.master.submissionstatus.SubmissionStatus property)
(pyiron.base.settings.generic.Settings property)
database_entry() (pyiron.base.job.core.JobCore property)
database_is_disabled() (pyiron.base.settings.generic.Settings property)
DatabaseAccess (class in pyiron.base.database.generic)
DatabaseProperties (class in pyiron.base.job.core)
dataset() (pyiron.lammps.control.LammpsControl property)
db() (pyiron.base.generic.hdfio.ProjectHDFio property)
db_entry() (pyiron.atomistics.job.atomistic.AtomisticGenericJob method)
(pyiron.atomistics.job.interactivewrapper.InteractiveWrapper method)
(pyiron.base.job.generic.GenericJob method)
(pyiron.base.server.generic.Server method)
db_filter_function() (pyiron.table.datamining.PyironTable property)
(pyiron.table.datamining.TableJob property)
debye_function() (in module pyiron.atomistics.master.murnaghan)
debye_integral() (in module pyiron.atomistics.master.murnaghan)
debye_temperature() (pyiron.atomistics.master.murnaghan.DebyeModel property)
DebyeModel (class in pyiron.atomistics.master.murnaghan)
decompress() (pyiron.base.job.core.JobCore method)
default() (in module pyiron.atomistics.structure.atoms)
(pyiron.lammps.potential.LammpsPotentialFile method)
(pyiron.vasp.potential.VaspPotentialAbstract method)
default_version() (pyiron.base.job.executable.Executable property)
define_blocks() (pyiron.base.generic.parameters.GenericParameters method)
define_bonds() (pyiron.lammps.base.LammpsBase method)
delete_item() (pyiron.base.database.filetable.FileTable method)
(pyiron.base.database.generic.DatabaseAccess method)
delete_output_files_jobs() (pyiron.base.project.generic.Project method)
detect_ffatypes() (pyiron.quickff.quickff.QuickFF method)
(pyiron.yaff.yaff.Yaff method)
df() (pyiron.lammps.potential.LammpsPotential property)
DFTOutput (class in pyiron.vasp.base)
(class in pyiron.vasp.interactive)
diff_data() (pyiron.sphinx.volumetric_data.SphinxVolumetricData property)
(pyiron.vasp.volumetric_data.VaspVolumetricData property)
displacements() (pyiron.atomistics.job.atomistic.GenericOutput property)
dist_between_two_grid_points() (pyiron.atomistics.volumetric.generic.VolumetricData static method)
dist_between_two_grid_points_cyl() (pyiron.atomistics.volumetric.generic.VolumetricData static method)
distances() (pyiron.atomistics.structure.atoms.Neighbors property)
Dos (class in pyiron.dft.waves.dos)
dos_densities() (pyiron.dft.waves.electronic.ElectronicStructure property)
dos_energies() (pyiron.dft.waves.electronic.ElectronicStructure property)
dos_idensities() (pyiron.dft.waves.electronic.ElectronicStructure property)
drop_status_to_aborted() (pyiron.base.job.generic.GenericJob method)
dyn_tags() (pyiron.base.pyio.parser.LogTag property)
E
efermi() (pyiron.dft.waves.electronic.ElectronicStructure property)
eg() (pyiron.dft.waves.electronic.ElectronicStructure property)
eig_occ_matrix() (pyiron.dft.waves.electronic.Kpoint property)
eigenvalue() (pyiron.dft.waves.electronic.Band property)
eigenvalue_matrix() (pyiron.dft.waves.electronic.ElectronicStructure property)
eigenvalues() (pyiron.dft.waves.electronic.ElectronicStructure property)
el_eam_lst() (pyiron.lammps.structure.LammpsStructure property)
electronic_structure (pyiron.vasp.base.Output attribute)
(pyiron.vasp.interactive.Output attribute)
ElectronicStructure (class in pyiron.dft.waves.electronic)
electrostatic_potential (pyiron.vasp.base.Output attribute)
(pyiron.vasp.interactive.Output attribute)
element() (pyiron.atomistics.structure.periodic_table.PeriodicTable method)
ElementColorDictionary (class in pyiron.atomistics.structure.periodic_table)
elementColors (pyiron.atomistics.structure.periodic_table.ElementColorDictionary attribute)
elements() (pyiron.atomistics.structure.atoms.Atoms property)
enable_h5md() (pyiron.lammps.base.LammpsBase method)
encut() (pyiron.dft.job.generic.GenericDFTJob property)
(pyiron.gpaw.gpaw.GpawJob property)
EncutConvergenceJobGenerator (class in pyiron.dft.master.convergence_encut_parallel)
end() (pyiron.interactive.sxextoptint.SxExtOpt method)
end_value_char() (pyiron.base.generic.parameters.GenericParameters property)
energies() (pyiron.atomistics.thermodynamics.thermo_bulk.ThermoBulk property)
energy_lst() (pyiron.atomistics.master.murnaghan.EnergyVolumeFit property)
energy_pot() (pyiron.atomistics.job.atomistic.GenericOutput property)
(pyiron.atomistics.job.interactive.GenericInteractiveOutput property)
(pyiron.atomistics.job.interactivewrapper.ReferenceJobOutput property)
energy_pot_per_atom() (pyiron.lammps.control.LammpsControl method)
energy_tot() (pyiron.atomistics.job.atomistic.GenericOutput property)
(pyiron.atomistics.job.interactive.GenericInteractiveOutput property)
(pyiron.atomistics.job.interactivewrapper.ReferenceJobOutput property)
energy_vib() (pyiron.atomistics.master.murnaghan.DebyeModel method)
EnergyVolumeFit (class in pyiron.atomistics.master.murnaghan)
enforce_update() (pyiron.table.datamining.TableJob property)
entropy() (pyiron.atomistics.thermodynamics.thermo_bulk.ThermoBulk property)
equilibrium_energy() (pyiron.atomistics.master.murnaghan.Murnaghan property)
equilibrium_volume() (pyiron.atomistics.master.murnaghan.Murnaghan property)
eV_to_J_per_mol (pyiron.atomistics.thermodynamics.thermo_bulk.ThermoBulk attribute)
ExampleExecutable (class in pyiron.testing.executable)
ExampleInput (class in pyiron.testing.randomatomistic)
ExampleJob (class in pyiron.testing.randomatomistic)
exchange_correlation_functional() (pyiron.dft.job.generic.GenericDFTJob property)
(pyiron.sphinx.base.SphinxBase property)
(pyiron.vasp.base.VaspBase property)
exclude_groups_hdf() (pyiron.base.job.generic.GenericJob property)
exclude_nodes_hdf() (pyiron.base.job.generic.GenericJob property)
Executable (class in pyiron.base.job.executable)
executable() (pyiron.base.job.generic.GenericJob property)
executable_path() (pyiron.base.job.executable.Executable property)
execute() (pyiron.base.database.generic.AutorestoredConnection method)
extend() (pyiron.atomistics.structure.atoms.Atoms method)
(pyiron.base.generic.inputlist.InputList method)
extract_data_from_file() (in module pyiron.base.pyio.parser)
extract_data_from_str_lst() (in module pyiron.base.pyio.parser)
extract_file() (pyiron.base.pyio.parser.Logstatus method)
extract_from_list() (pyiron.base.pyio.parser.Logstatus method)
extract_item() (pyiron.base.pyio.parser.Logstatus static method)
extract_structure() (pyiron.thermodynamics.sxphonons.SxUniqDispl method)
F
f2qdec() (pyiron.lammps.structure.UnfoldingPrism method)
f2s() (pyiron.lammps.structure.UnfoldingPrism method)
fchk2dict() (in module pyiron.gaussian.gaussian)
file_exists (pyiron.base.generic.hdfio.FileHDFio attribute)
file_exists() (pyiron.base.generic.hdfio.FileHDFio property)
file_name (pyiron.base.generic.hdfio.FileHDFio attribute)
file_name() (pyiron.base.generic.hdfio.FileHDFio property)
(pyiron.base.generic.parameters.GenericParameters property)
file_path (pyiron.base.generic.hdfio.FileHDFio attribute)
file_path() (pyiron.base.generic.hdfio.FileHDFio property)
(pyiron.base.job.path.JobPathBase property)
file_size() (pyiron.base.generic.hdfio.FileHDFio static method)
FileHDFio (class in pyiron.base.generic.hdfio)
files() (pyiron.lammps.potential.LammpsPotential property)
FileTable (class in pyiron.base.database.filetable)
filter() (pyiron.table.datamining.PyironTable property)
(pyiron.table.datamining.TableJob property)
filter_function() (in module pyiron.base.database.filetable)
(pyiron.table.datamining.PyironTable property)
(pyiron.table.datamining.TableJob property)
find() (pyiron.atomistics.job.potentials.PotentialAbstract method)
(pyiron.vasp.potential.VaspPotentialAbstract method)
find_by_name() (pyiron.atomistics.job.potentials.PotentialAbstract method)
find_default() (pyiron.lammps.potential.LammpsPotentialFile method)
(pyiron.vasp.potential.VaspPotentialAbstract method)
find_neighbors_by_vector() (pyiron.atomistics.structure.atoms.Atoms method)
find_potential_file() (in module pyiron.sphinx.potential)
(in module pyiron.vasp.potential)
find_potential_file_base() (in module pyiron.atomistics.job.potentials)
finished() (pyiron.base.master.submissionstatus.SubmissionStatus property)
first_child_name() (pyiron.base.master.generic.GenericMaster method)
fit() (pyiron.atomistics.master.murnaghan.Murnaghan property)
fit_birch_murnaghan() (pyiron.atomistics.master.murnaghan.Murnaghan method)
fit_dict() (pyiron.atomistics.master.murnaghan.EnergyVolumeFit property)
fit_energy() (pyiron.atomistics.master.murnaghan.EnergyVolumeFit method)
fit_eos_general() (pyiron.atomistics.master.murnaghan.EnergyVolumeFit method)
fit_eos_general_intern() (pyiron.atomistics.master.murnaghan.EnergyVolumeFit method)
fit_leastsq() (in module pyiron.atomistics.master.murnaghan)
fit_murnaghan() (pyiron.atomistics.master.murnaghan.Murnaghan method)
fit_polynomial() (pyiron.atomistics.master.murnaghan.EnergyVolumeFit method)
(pyiron.atomistics.master.murnaghan.Murnaghan method)
fit_vinet() (pyiron.atomistics.master.murnaghan.Murnaghan method)
fitfunction() (in module pyiron.atomistics.master.murnaghan)
fix_ipython_autocomplete() (in module pyiron.base.generic.jedi)
fix_iso() (in module pyiron.thermodynamics.interfacemethod)
fix_spin_constraint() (pyiron.dft.job.generic.GenericDFTJob property)
(pyiron.sphinx.base.SphinxBase property)
(pyiron.vasp.base.VaspBase property)
fix_symmetry() (pyiron.dft.job.generic.GenericDFTJob property)
(pyiron.vasp.base.VaspBase property)
fix_z_dir() (in module pyiron.thermodynamics.interfacemethod)
FlexibleMaster (class in pyiron.base.master.flexible)
force_max() (pyiron.atomistics.job.atomistic.GenericOutput property)
force_reset() (pyiron.base.database.filetable.FileTable method)
forces() (pyiron.atomistics.job.atomistic.GenericOutput property)
(pyiron.atomistics.job.interactive.GenericInteractiveOutput property)
(pyiron.atomistics.job.interactivewrapper.ReferenceJobOutput property)
format_docstring_with_statuses() (in module pyiron.base.job.jobstatus)
freeze_one_half() (in module pyiron.thermodynamics.interfacemethod)
from_directory() (pyiron.sphinx.base.SphinxBase method)
(pyiron.vasp.base.VaspBase method)
from_file() (pyiron.sphinx.volumetric_data.SphinxVolumetricData method)
(pyiron.vasp.outcar.Outcar method)
(pyiron.vasp.procar.Procar method)
(pyiron.vasp.report.Report method)
(pyiron.vasp.vasprun.Vasprun method)
(pyiron.vasp.volumetric_data.VaspVolumetricData method)
from_hdf() (pyiron.atomistics.job.atomistic.AtomisticGenericJob method)
(pyiron.atomistics.job.interactivewrapper.InteractiveWrapper method)
(pyiron.atomistics.job.structurecontainer.StructureContainer method)
(pyiron.atomistics.master.parallel.MapMaster method)
(pyiron.atomistics.master.structure.StructureListMaster method)
(pyiron.atomistics.structure.atoms.Atoms method)
(pyiron.atomistics.structure.periodic_table.ChemicalElement method)
(pyiron.atomistics.structure.periodic_table.PeriodicTable method)
(pyiron.atomistics.volumetric.generic.VolumetricData method)
(pyiron.base.generic.inputlist.InputList method)
(pyiron.base.generic.parameters.GenericParameters method)
(pyiron.base.generic.template.PyironObject method)
(pyiron.base.job.core.JobCore method)
(pyiron.base.job.generic.GenericJob method)
(pyiron.base.job.interactive.InteractiveBase method)
(pyiron.base.job.script.ScriptJob method)
(pyiron.base.job.template.TemplateJob method)
(pyiron.base.master.flexible.FlexibleMaster method)
(pyiron.base.master.generic.GenericMaster method)
(pyiron.base.master.parallel.ParallelMaster method)
(pyiron.base.master.serial.SerialMasterBase method)
(pyiron.base.project.store.ProjectStore method)
(pyiron.base.server.generic.Server method)
(pyiron.dft.waves.bandstructure.Bandstructure method)
(pyiron.dft.waves.electronic.ElectronicStructure method)
(pyiron.gaussian.gaussian.Gaussian method)
(pyiron.gpaw.gpaw.GpawJob method)
(pyiron.gpaw.pyiron_ase.AseJob method)
(pyiron.interactive.scipy_minimizer.ScipyMinimizerOutput method)
(pyiron.lammps.base.Input method)
(pyiron.lammps.base.LammpsBase method)
(pyiron.lammps.interactive.LammpsInteractive method)
(pyiron.lammps.potential.LammpsPotential method)
(pyiron.quickff.quickff.QuickFF method)
(pyiron.sphinx.base.Output method)
(pyiron.sphinx.base.SphinxBase method)
(pyiron.sphinx.volumetric_data.SphinxVolumetricData method)
(pyiron.table.datamining.PyironTable method)
(pyiron.table.datamining.TableJob method)
(pyiron.testing.randomatomistic.AtomisticExampleJob method)
(pyiron.testing.randomatomistic.ExampleJob method)
(pyiron.thermodynamics.hessian.HessianJob method)
(pyiron.thermodynamics.sxphonons.SxHarmPotTst method)
(pyiron.thermodynamics.sxphonons.SxUniqDispl method)
(pyiron.vasp.base.DFTOutput method)
(pyiron.vasp.base.GenericOutput method)
(pyiron.vasp.base.Input method)
(pyiron.vasp.base.Kpoints method)
(pyiron.vasp.base.Output method)
(pyiron.vasp.base.VaspBase method)
(pyiron.vasp.metadyn.MetadynInput method)
(pyiron.vasp.metadyn.VaspMetadyn method)
(pyiron.vasp.outcar.Outcar method)
(pyiron.vasp.volumetric_data.VaspVolumetricData method)
(pyiron.yaff.yaff.Yaff method)
from_hdf_old() (pyiron.dft.waves.electronic.ElectronicStructure method)
function_lst() (pyiron.base.master.flexible.FlexibleMaster property)
FunctionContainer (class in pyiron.table.datamining)
G
gauss_f() (pyiron.atomistics.volumetric.generic.VolumetricData static method)
Gaussian (class in pyiron.gaussian.gaussian)
GaussianInput (class in pyiron.gaussian.gaussian)
generate_from_matrices() (pyiron.dft.waves.electronic.ElectronicStructure method)
generate_random_seed() (in module pyiron.thermodynamics.interfacemethod)
generate_seed_from_job() (pyiron.lammps.control.LammpsControl static method)
generate_structure() (in module pyiron.thermodynamics.interfacemethod)
GenericDFTJob (class in pyiron.dft.job.generic)
GenericError (class in pyiron.base.job.generic)
GenericInput (class in pyiron.atomistics.job.atomistic)
GenericInteractive (class in pyiron.atomistics.job.interactive)
GenericInteractiveOutput (class in pyiron.atomistics.job.interactive)
GenericJob (class in pyiron.base.job.generic)
GenericMaster (class in pyiron.base.master.generic)
GenericOutput (class in pyiron.atomistics.job.atomistic)
(class in pyiron.atomistics.master.parallel)
(class in pyiron.atomistics.master.serial)
(class in pyiron.base.master.parallel)
(class in pyiron.base.master.serial)
(class in pyiron.vasp.base)
(class in pyiron.vasp.interactive)
GenericParameters (class in pyiron.base.generic.parameters)
GenericPath (class in pyiron.base.project.path)
get() (pyiron.atomistics.structure.atom.Atom method)
(pyiron.base.generic.hdfio.FileHDFio method)
(pyiron.base.generic.inputlist.InputList method)
(pyiron.base.generic.parameters.GenericParameters method)
(pyiron.base.job.core.JobCore method)
get_all_total_energies() (pyiron.vasp.outcar.Outcar static method)
get_angular_momentum() (pyiron.gpaw.pyiron_ase.AseAdapter method)
get_array() (pyiron.atomistics.structure.atoms.Atoms method)
get_atomic_numbers() (pyiron.atomistics.structure.atoms.Atoms method)
get_attribute() (pyiron.base.generic.parameters.GenericParameters method)
get_average_along_axis() (pyiron.atomistics.volumetric.generic.VolumetricData method)
get_average_waves() (in module pyiron.table.funct)
get_band_gap() (pyiron.dft.waves.electronic.ElectronicStructure method)
get_bonds() (pyiron.atomistics.structure.atoms.Atoms method)
get_boundary_region() (pyiron.atomistics.structure.atoms.Atoms method)
get_broyden_mixing_mesh() (pyiron.vasp.outcar.Outcar static method)
get_bsse_array() (in module pyiron.gaussian.gaussian)
get_calculator() (pyiron.atomistics.structure.atoms.Atoms method)
get_cbm() (pyiron.dft.waves.electronic.ElectronicStructure method)
get_cell() (pyiron.atomistics.job.interactive.InteractiveInterface method)
(pyiron.atomistics.structure.atoms.Atoms method)
get_cells() (pyiron.vasp.outcar.Outcar method)
get_center_of_mass() (pyiron.atomistics.structure.atoms.Atoms method)
(pyiron.gpaw.pyiron_ase.AseAdapter method)
get_center_point() (in module pyiron.thermodynamics.interfacemethod)
get_charge() (pyiron.lammps.potential.LammpsPotential method)
get_charge_density() (pyiron.sphinx.base.SphinxBase method)
(pyiron.vasp.base.VaspBase method)
get_chemical_elements() (pyiron.atomistics.structure.atoms.Atoms method)
get_chemical_formula() (pyiron.atomistics.structure.atoms.Atoms method)
get_chemical_indices() (pyiron.atomistics.structure.atoms.Atoms method)
get_chemical_symbols() (pyiron.atomistics.structure.atoms.Atoms method)
get_child_cores() (pyiron.base.master.generic.GenericMaster method)
get_child_ids() (in module pyiron.base.database.jobtable)
(pyiron.base.database.filetable.FileTable method)
(pyiron.base.project.generic.Project method)
get_config_from_environment() (pyiron.base.settings.generic.Settings static method)
get_constraint() (pyiron.atomistics.structure.atoms.Atoms method)
get_convergence_check() (in module pyiron.table.funct)
get_custom_dict() (pyiron.base.job.external.Notebook static method)
get_dataframe() (pyiron.table.datamining.PyironTable method)
(pyiron.table.datamining.TableJob method)
get_db_columns() (in module pyiron.base.database.jobtable)
(pyiron.base.database.filetable.FileTable method)
(pyiron.base.project.generic.Project method)
get_density() (pyiron.atomistics.structure.atoms.Atoms method)
get_dipole_moments() (pyiron.vasp.outcar.Outcar static method)
get_displacements() (pyiron.atomistics.job.atomistic.GenericOutput static method)
get_distance() (pyiron.atomistics.structure.atoms.Atoms method)
get_distance_matrix() (pyiron.atomistics.structure.atoms.Atoms method)
get_distances() (pyiron.atomistics.structure.atoms.Atoms method)
get_dos() (pyiron.dft.waves.electronic.ElectronicStructure method)
get_e_band() (in module pyiron.table.funct)
get_e_conv_level() (in module pyiron.table.funct)
get_eddrmm_handling() (pyiron.vasp.base.VaspBase method)
get_ekin_error() (in module pyiron.table.funct)
get_electronic_structure() (pyiron.vasp.base.VaspBase method)
(pyiron.vasp.vasprun.Vasprun method)
get_electrostatic_potential() (pyiron.sphinx.base.SphinxBase method)
(pyiron.vasp.base.VaspBase method)
get_element_id() (pyiron.lammps.potential.LammpsPotential method)
get_element_lst() (pyiron.lammps.potential.LammpsPotential method)
get_elements() (in module pyiron.table.funct)
get_encut() (in module pyiron.table.funct)
(pyiron.atomistics.job.atomistic.AtomisticGenericJob method)
(pyiron.dft.job.generic.GenericDFTJob method)
(pyiron.dft.master.murnaghan_dft.MurnaghanDFT method)
(pyiron.gpaw.gpaw.GpawJob method)
get_energy() (pyiron.testing.executable.ExampleExecutable method)
get_energy_free() (in module pyiron.table.funct)
get_energy_free_per_atom() (in module pyiron.table.funct)
get_energy_int() (in module pyiron.table.funct)
get_energy_int_per_atom() (in module pyiron.table.funct)
get_energy_pot() (pyiron.atomistics.job.interactive.InteractiveInterface method)
get_energy_sigma_0() (pyiron.vasp.outcar.Outcar static method)
get_energy_tot() (in module pyiron.table.funct)
(pyiron.atomistics.job.interactive.InteractiveInterface method)
get_energy_tot_per_atom() (in module pyiron.table.funct)
get_energy_without_entropy() (pyiron.vasp.outcar.Outcar static method)
get_enmax_among_species() (in module pyiron.vasp.potential)
get_entropy_p() (pyiron.atomistics.thermodynamics.thermo_bulk.ThermoBulk method)
get_entropy_v() (pyiron.atomistics.thermodynamics.thermo_bulk.ThermoBulk method)
get_equilibrium_parameters() (in module pyiron.table.funct)
get_equivalent_points() (pyiron.atomistics.structure.atoms.Atoms method)
get_equivalent_voronoi_vertices() (pyiron.atomistics.structure.atoms.Atoms method)
get_error() (pyiron.atomistics.master.murnaghan.EnergyVolumeFit static method)
get_external_input() (pyiron.base.project.generic.Project static method)
get_extract() (pyiron.base.database.filetable.FileTable static method)
get_f_states() (in module pyiron.table.funct)
get_fermi_level() (pyiron.vasp.outcar.Outcar static method)
get_final_structure() (pyiron.atomistics.job.atomistic.AtomisticGenericJob method)
(pyiron.atomistics.job.interactivewrapper.InteractiveWrapper method)
(pyiron.lammps.base.LammpsBase method)
(pyiron.vasp.vasprun.Vasprun method)
get_final_structure_from_file() (pyiron.vasp.base.VaspBase method)
get_forces() (in module pyiron.table.funct)
(pyiron.atomistics.job.interactive.InteractiveInterface method)
(pyiron.gpaw.pyiron_ase.AseAdapter method)
(pyiron.interactive.sxextoptint.SxExtOptInteractive method)
(pyiron.vasp.outcar.Outcar method)
get_free_energy() (pyiron.atomistics.thermodynamics.thermo_bulk.ThermoBulk method)
get_free_energy_p() (pyiron.atomistics.thermodynamics.thermo_bulk.ThermoBulk method)
get_from_childs() (pyiron.base.master.serial.SerialMasterBase method)
get_from_table() (pyiron.base.generic.hdfio.FileHDFio method)
(pyiron.base.job.core.JobCore method)
get_function_from_string() (in module pyiron.base.master.generic)
get_hamilton_from_file() (in module pyiron.base.database.filetable)
get_hamilton_version_from_file() (in module pyiron.base.database.filetable)
get_hesse_matrix() (pyiron.thermodynamics.sxphonons.SxDynMat method)
(pyiron.thermodynamics.sxphonons.SxHarmPotTst method)
(pyiron.thermodynamics.sxphonons.SxPhonons method)
get_high_symmetry_path() (pyiron.atomistics.structure.atoms.Atoms method)
get_high_symmetry_points() (pyiron.atomistics.structure.atoms.Atoms method)
get_icharg_value() (pyiron.vasp.base.VaspBase method)
get_incar() (in module pyiron.table.funct)
get_initial_child_name() (pyiron.base.master.serial.SerialMasterBase method)
get_initial_magnetic_moments() (pyiron.atomistics.structure.atoms.Atoms method)
get_initial_melting_temperature_guess() (in module pyiron.thermodynamics.interfacemethod)
get_initial_structure() (pyiron.vasp.vasprun.Vasprun method)
get_ir_reciprocal_mesh() (pyiron.atomistics.structure.atoms.Atoms method)
get_irreducible_kpoints() (pyiron.vasp.outcar.Outcar static method)
get_ismear() (in module pyiron.table.funct)
get_item() (pyiron.base.pyio.parser.LogTag method)
get_item_by_id() (pyiron.base.database.filetable.FileTable method)
(pyiron.base.database.generic.DatabaseAccess method)
get_items_dict() (pyiron.base.database.filetable.FileTable method)
(pyiron.base.database.generic.DatabaseAccess method)
get_items_sql() (pyiron.base.database.generic.DatabaseAccess method)
get_job_id() (in module pyiron.base.database.jobtable)
(in module pyiron.table.funct)
(pyiron.base.database.filetable.FileTable method)
(pyiron.base.generic.hdfio.ProjectHDFio method)
(pyiron.base.job.core.JobCore method)
(pyiron.base.project.generic.Project method)
get_job_ids() (in module pyiron.base.database.jobtable)
(pyiron.base.database.filetable.FileTable method)
(pyiron.base.project.generic.Project method)
get_job_name() (in module pyiron.table.funct)
get_job_status() (in module pyiron.base.database.jobtable)
(pyiron.base.database.filetable.FileTable method)
(pyiron.base.project.generic.Project method)
get_job_status_from_file() (in module pyiron.base.database.filetable)
get_job_working_directory() (in module pyiron.base.database.jobtable)
(pyiron.base.database.filetable.FileTable method)
(pyiron.base.project.generic.Project method)
get_jobs() (in module pyiron.base.database.jobtable)
(pyiron.base.database.filetable.FileTable method)
(pyiron.base.project.generic.Project method)
get_jobs_status() (pyiron.base.project.generic.Project method)
get_k_mesh_by_cell() (in module pyiron.vasp.base)
(pyiron.dft.job.generic.GenericDFTJob method)
(pyiron.gpaw.gpaw.GpawJob method)
get_kinetic_energy() (pyiron.gpaw.pyiron_ase.AseAdapter method)
get_kinetic_energy_error() (pyiron.vasp.outcar.Outcar static method)
get_lammps_prism_str() (pyiron.lammps.structure.UnfoldingPrism method)
get_magnetic_moments() (pyiron.dft.job.generic.GenericDFTJob method)
(pyiron.vasp.base.VaspBase method)
get_magnetic_structure() (in module pyiron.table.funct)
get_magnetization() (pyiron.vasp.outcar.Outcar static method)
get_majority() (in module pyiron.table.funct)
get_majority_crystal_structure() (in module pyiron.table.funct)
get_majority_species() (in module pyiron.table.funct)
(pyiron.atomistics.structure.atoms.Atoms method)
get_masses() (pyiron.atomistics.structure.atoms.Atoms method)
(pyiron.gpaw.pyiron_ase.AseAdapter method)
get_masses_dof() (pyiron.atomistics.structure.atoms.Atoms method)
get_minimum_energy_path() (pyiron.atomistics.thermodynamics.thermo_bulk.ThermoBulk method)
get_momenta() (pyiron.gpaw.pyiron_ase.AseAdapter method)
get_n_equ_kpts() (in module pyiron.table.funct)
get_n_ir_reciprocal_points() (pyiron.sphinx.base.SphinxBase method)
get_n_kpts() (in module pyiron.table.funct)
get_neighborhood() (pyiron.atomistics.structure.atoms.Atoms method)
get_neighbors() (pyiron.atomistics.structure.atoms.Atoms method)
get_nelect() (pyiron.vasp.base.VaspBase method)
(pyiron.vasp.outcar.Outcar static method)
get_number_of_atoms() (pyiron.atomistics.structure.atoms.Atoms method)
(pyiron.gpaw.pyiron_ase.AseAdapter method)
(pyiron.vasp.outcar.Outcar static method)
get_number_of_degrees_of_freedom() (pyiron.atomistics.structure.atoms.Atoms method)
get_number_of_final_electronic_steps() (in module pyiron.table.funct)
get_number_of_ionic_steps() (in module pyiron.table.funct)
get_number_of_species() (in module pyiron.table.funct)
(pyiron.atomistics.structure.atoms.Atoms method)
get_number_species_atoms() (pyiron.atomistics.structure.atoms.Atoms method)
get_nve_job_name() (in module pyiron.thermodynamics.interfacemethod)
get_orbital_resolved_dos() (pyiron.dft.waves.dos.Dos method)
get_pandas() (pyiron.base.generic.hdfio.FileHDFio method)
(pyiron.base.generic.parameters.GenericParameters method)
(pyiron.base.job.core.JobCore method)
get_parent_basis() (pyiron.atomistics.structure.atoms.Atoms method)
get_parent_symbols() (pyiron.atomistics.structure.atoms.Atoms method)
get_path() (pyiron.dft.waves.bandstructure.Bandstructure method)
get_pathes() (pyiron.dft.waves.bandstructure.Bandstructure method)
get_pbc() (pyiron.atomistics.structure.atoms.Atoms method)
get_plane_waves() (in module pyiron.table.funct)
get_positions() (pyiron.atomistics.job.interactive.InteractiveInterface method)
(pyiron.atomistics.structure.atoms.Atoms method)
(pyiron.gpaw.pyiron_ase.AseAdapter method)
(pyiron.interactive.sxextoptint.SxExtOpt method)
(pyiron.vasp.outcar.Outcar method)
get_positions_and_forces() (pyiron.vasp.outcar.Outcar method)
get_potentials_for_structure() (pyiron.lammps.base.LammpsBase method)
get_press() (in module pyiron.thermodynamics.interfacemethod)
get_pressure() (pyiron.atomistics.job.interactive.InteractiveInterface method)
get_primitive_cell() (pyiron.atomistics.structure.atoms.Atoms method)
get_project_size() (pyiron.base.project.generic.Project method)
get_repository_status() (pyiron.base.project.generic.Project static method)
get_resolved_dos() (pyiron.dft.waves.electronic.ElectronicStructure method)
get_rwigs() (pyiron.vasp.base.VaspBase method)
get_scaled_positions() (pyiron.atomistics.structure.atoms.Atoms method)
get_scf_group() (pyiron.sphinx.base.SphinxBase method)
get_shell_matrix() (pyiron.atomistics.structure.atoms.Atoms method)
get_shell_radius() (pyiron.atomistics.structure.atoms.Atoms method)
get_shells() (pyiron.atomistics.structure.atoms.Atoms method)
get_sigma() (in module pyiron.table.funct)
get_size() (pyiron.base.generic.hdfio.FileHDFio method)
get_spacegroup() (pyiron.atomistics.structure.atoms.Atoms method)
get_spatial_orbital_resolved_dos() (pyiron.dft.waves.dos.Dos method)
get_spatially_resolved_dos() (pyiron.dft.waves.dos.Dos method)
get_species_list_from_potcar() (in module pyiron.vasp.structure)
get_species_objects() (pyiron.atomistics.structure.atoms.Atoms method)
get_species_symbols() (pyiron.atomistics.structure.atoms.Atoms method)
get_spherical_coordinates() (pyiron.atomistics.structure.atoms.Atoms method)
get_spin_resolved_dos() (pyiron.dft.waves.dos.Dos method)
(pyiron.dft.waves.electronic.ElectronicStructure method)
get_steinhardt_parameter_job() (in module pyiron.atomistics.structure.pyscal)
get_steinhardt_parameter_structure() (in module pyiron.atomistics.structure.pyscal)
get_steps() (pyiron.vasp.outcar.Outcar static method)
get_strain_lst() (in module pyiron.thermodynamics.interfacemethod)
get_stresses() (pyiron.vasp.outcar.Outcar static method)
get_string_lst() (pyiron.base.generic.parameters.GenericParameters method)
get_structure() (in module pyiron.table.funct)
(pyiron.atomistics.job.atomistic.AtomisticGenericJob method)
(pyiron.atomistics.job.interactive.GenericInteractive method)
(pyiron.atomistics.master.murnaghan.Murnaghan method)
(pyiron.atomistics.master.parallel.AtomisticParallelMaster method)
(pyiron.atomistics.master.serial.SerialMaster method)
(pyiron.dft.job.generic.GenericDFTJob method)
(pyiron.dft.master.murnaghan_dft.MurnaghanDFT method)
(pyiron.lammps.interactive.LammpsInteractive method)
(pyiron.project.Project method)
(pyiron.quickff.quickff.QuickFF method)
(pyiron.sphinx.interactive.SphinxInteractive method)
(pyiron.testing.randomatomistic.AtomisticExampleJob method)
(pyiron.vasp.interactive.VaspInteractive method)
(pyiron.yaff.yaff.Yaff method)
get_structure_group() (pyiron.sphinx.base.SphinxBase method)
get_symmetry() (pyiron.atomistics.structure.atoms.Atoms method)
get_symmetry_dataset() (pyiron.atomistics.structure.atoms.Atoms method)
get_table_headings() (pyiron.base.database.filetable.FileTable method)
(pyiron.base.database.generic.DatabaseAccess method)
get_tags() (pyiron.atomistics.structure.atoms.Atoms method)
get_temperature() (pyiron.atomistics.job.interactive.InteractiveInterface method)
get_temperatures() (pyiron.vasp.outcar.Outcar static method)
get_time() (pyiron.vasp.outcar.Outcar method)
get_total_energies() (pyiron.vasp.outcar.Outcar static method)
get_total_number_of_atoms() (in module pyiron.table.funct)
get_vbm() (pyiron.dft.waves.electronic.ElectronicStructure method)
get_velocities() (pyiron.gpaw.pyiron_ase.AseAdapter method)
get_version_float() (pyiron.sphinx.base.SphinxBase method)
get_volume() (in module pyiron.table.funct)
(pyiron.atomistics.structure.atoms.Atoms method)
get_volume_per_atom() (in module pyiron.table.funct)
get_voronoi_volume() (in module pyiron.thermodynamics.interfacemethod)
(pyiron.atomistics.structure.atoms.Atoms method)
get_yaff_ff() (pyiron.quickff.quickff.QuickFF method)
(pyiron.yaff.yaff.Yaff method)
get_yaff_system() (pyiron.quickff.quickff.QuickFF method)
(pyiron.yaff.yaff.Yaff method)
GpawInput (class in pyiron.gpaw.gpaw)
GpawJob (class in pyiron.gpaw.gpaw)
grand_dos_matrix() (pyiron.dft.waves.electronic.ElectronicStructure property)
Group (class in pyiron.sphinx.base)
group_points_by_symmetry() (pyiron.atomistics.structure.atoms.Atoms method)
groups() (pyiron.base.generic.hdfio.FileHDFio method)
(pyiron.base.job.path.JobPathBase method)
(pyiron.base.project.generic.Project method)
gui() (pyiron.atomistics.job.atomistic.AtomisticGenericJob method)
(pyiron.project.Project method)
H
h5() (pyiron.base.pyio.parser.LogTag method)
h5_dict() (pyiron.base.pyio.parser.LogTag property)
h5_path (pyiron.base.generic.hdfio.FileHDFio attribute)
h5_path() (pyiron.base.generic.hdfio.FileHDFio property)
(pyiron.base.job.path.JobPathBase property)
half_velocity() (in module pyiron.thermodynamics.interfacemethod)
has() (pyiron.gpaw.pyiron_ase.AseAdapter method)
has_keys() (pyiron.base.generic.inputlist.InputList method)
hd_copy() (pyiron.base.generic.hdfio.FileHDFio method)
hdf2dict() (in module pyiron.yaff.yaff)
HDF5Content (class in pyiron.base.job.core)
HDFStoreIO (class in pyiron.base.generic.hdfio)
HessianJob (class in pyiron.thermodynamics.hessian)
history (pyiron.base.generic.hdfio.FileHDFio attribute)
history() (pyiron.base.project.path.ProjectPath property)
I
id() (pyiron.base.generic.template.PyironObject property)
(pyiron.base.job.core.JobCore property)
id_pyi_to_spx() (pyiron.sphinx.base.InputWriter property)
(pyiron.sphinx.base.SphinxBase property)
(pyiron.thermodynamics.sxphonons.SxUniqDispl property)
id_spx_to_pyi() (pyiron.sphinx.base.InputWriter property)
(pyiron.sphinx.base.SphinxBase property)
(pyiron.thermodynamics.sxphonons.SxUniqDispl property)
import_from_path() (pyiron.project.Project method)
import_single_calculation() (pyiron.project.Project method)
Incar (class in pyiron.vasp.base)
incar (pyiron.vasp.base.Input attribute)
indices (pyiron.atomistics.structure.atoms.Atoms attribute)
indices() (pyiron.atomistics.job.atomistic.GenericOutput property)
(pyiron.atomistics.job.interactive.GenericInteractiveOutput property)
(pyiron.atomistics.job.interactivewrapper.ReferenceJobOutput property)
(pyiron.atomistics.structure.atoms.Neighbors property)
info() (pyiron.atomistics.structure.atoms.Atoms property)
init_table() (pyiron.base.database.filetable.FileTable method)
initial_structure() (pyiron.atomistics.job.interactive.GenericInteractive property)
initialise_iterators() (in module pyiron.thermodynamics.interfacemethod)
initialized() (pyiron.base.master.submissionstatus.SubmissionStatus property)
Input (class in pyiron.interactive.scipy_minimizer)
(class in pyiron.interactive.sxextoptint)
(class in pyiron.lammps.base)
(class in pyiron.sphinx.base)
(class in pyiron.vasp.base)
input (pyiron.lammps.base.LammpsBase attribute)
(pyiron.lammps.lammps.Lammps attribute)
(pyiron.vasp.base.VaspBase attribute)
input() (pyiron.base.master.serial.SerialMasterBase property)
InputList (class in pyiron.base.generic.inputlist)
InputWriter (class in pyiron.sphinx.base)
insert() (pyiron.base.generic.inputlist.InputList method)
inspect() (pyiron.base.generic.hdfio.ProjectHDFio method)
(pyiron.base.generic.template.PyironObject method)
(pyiron.base.job.core.JobCore method)
(pyiron.base.project.generic.Project method)
inspect_emperical_potentials() (pyiron.project.Project static method)
inspect_periodic_table() (pyiron.project.Project static method)
inspect_pseudo_potentials() (pyiron.project.Project static method)
install() (in module pyiron)
install_dialog() (in module pyiron.base.settings.install)
install_pyiron() (in module pyiron.base.settings.install)
interactive_atom_spin_constraints_getter() (pyiron.atomistics.job.interactive.GenericInteractive method)
interactive_atom_spins_getter() (pyiron.atomistics.job.interactive.GenericInteractive method)
interactive_cell_organizer() (pyiron.atomistics.job.interactive.GenericInteractive method)
interactive_cells_getter() (pyiron.atomistics.job.interactive.GenericInteractive method)
(pyiron.gpaw.pyiron_ase.AseJob method)
(pyiron.lammps.interactive.LammpsInteractive method)
(pyiron.sphinx.interactive.SphinxInteractive method)
interactive_cells_setter() (pyiron.atomistics.job.interactive.GenericInteractive method)
(pyiron.lammps.interactive.LammpsInteractive method)
interactive_close() (pyiron.base.job.generic.GenericJob method)
(pyiron.base.job.interactive.InteractiveBase method)
(pyiron.base.master.generic.GenericMaster method)
(pyiron.gpaw.pyiron_ase.AseAdapter method)
(pyiron.gpaw.pyiron_ase.AseJob method)
(pyiron.interactive.scipy_minimizer.ScipyMinimizer method)
(pyiron.interactive.sxextoptint.SxExtOpt method)
(pyiron.lammps.interactive.LammpsInteractive method)
(pyiron.sphinx.interactive.SphinxInteractive method)
(pyiron.testing.randomatomistic.ExampleJob method)
(pyiron.thermodynamics.hessian.HessianJob method)
(pyiron.vasp.interactive.VaspInteractive method)
interactive_collect() (pyiron.atomistics.job.interactive.GenericInteractive method)
(pyiron.gpaw.pyiron_ase.AseJob method)
interactive_computation_time_getter() (pyiron.atomistics.job.interactive.GenericInteractive method)
interactive_energy_pot_getter() (pyiron.atomistics.job.interactive.GenericInteractive method)
(pyiron.gpaw.pyiron_ase.AseJob method)
(pyiron.lammps.interactive.LammpsInteractive method)
(pyiron.sphinx.interactive.SphinxInteractive method)
(pyiron.vasp.interactive.VaspInteractive method)
interactive_energy_tot_getter() (pyiron.atomistics.job.interactive.GenericInteractive method)
(pyiron.lammps.interactive.LammpsInteractive method)
(pyiron.sphinx.interactive.SphinxInteractive method)
(pyiron.vasp.interactive.VaspInteractive method)
interactive_enforce_structure_reset() (pyiron.atomistics.job.interactive.GenericInteractive property)
(pyiron.vasp.interactive.VaspInteractive property)
interactive_execute() (pyiron.lammps.interactive.LammpsInteractive method)
interactive_fetch() (pyiron.base.job.generic.GenericJob method)
(pyiron.base.master.generic.GenericMaster method)
(pyiron.lammps.interactive.LammpsInteractive method)
(pyiron.sphinx.interactive.SphinxInteractive method)
(pyiron.vasp.interactive.VaspInteractive method)
interactive_flush() (pyiron.atomistics.job.interactive.GenericInteractive method)
(pyiron.base.job.generic.GenericJob method)
(pyiron.base.job.interactive.InteractiveBase method)
(pyiron.base.master.generic.GenericMaster method)
interactive_flush_frequency() (pyiron.base.job.interactive.InteractiveBase property)
interactive_forces_getter() (pyiron.atomistics.job.interactive.GenericInteractive method)
(pyiron.gpaw.pyiron_ase.AseJob method)
(pyiron.lammps.interactive.LammpsInteractive method)
(pyiron.sphinx.interactive.SphinxInteractive method)
(pyiron.vasp.interactive.VaspInteractive method)
interactive_index_organizer() (pyiron.atomistics.job.interactive.GenericInteractive method)
interactive_indices_getter() (pyiron.atomistics.job.interactive.GenericInteractive method)
(pyiron.gpaw.pyiron_ase.AseJob method)
(pyiron.lammps.interactive.LammpsInteractive method)
interactive_indices_setter() (pyiron.atomistics.job.interactive.GenericInteractive method)
(pyiron.lammps.interactive.LammpsInteractive method)
interactive_initialize_interface() (pyiron.atomistics.job.interactive.GenericInteractive method)
(pyiron.lammps.interactive.LammpsInteractive method)
(pyiron.sphinx.interactive.SphinxInteractive method)
(pyiron.vasp.interactive.VaspInteractive method)
interactive_is_activated() (pyiron.base.job.interactive.InteractiveBase method)
(pyiron.interactive.sxextoptint.SxExtOpt method)
interactive_magmom_organizer() (pyiron.atomistics.job.interactive.GenericInteractive method)
interactive_magnetic_forces_getter() (pyiron.atomistics.job.interactive.GenericInteractive method)
(pyiron.sphinx.interactive.SphinxInteractive method)
interactive_open() (pyiron.base.job.interactive.InteractiveBase method)
interactive_position_setter() (pyiron.thermodynamics.hessian.HessianJob method)
interactive_positions_getter() (pyiron.atomistics.job.interactive.GenericInteractive method)
(pyiron.gpaw.pyiron_ase.AseJob method)
(pyiron.lammps.interactive.LammpsInteractive method)
(pyiron.sphinx.interactive.SphinxInteractive method)
interactive_positions_organizer() (pyiron.atomistics.job.interactive.GenericInteractive method)
interactive_positions_setter() (pyiron.atomistics.job.interactive.GenericInteractive method)
(pyiron.lammps.interactive.LammpsInteractive method)
(pyiron.sphinx.interactive.SphinxInteractive method)
(pyiron.vasp.interactive.VaspInteractive method)
interactive_pressures_getter() (pyiron.atomistics.job.interactive.GenericInteractive method)
(pyiron.lammps.interactive.LammpsInteractive method)
interactive_ref_job_initialize() (pyiron.base.master.parallel.ParallelMaster method)
interactive_spin_constraints_getter() (pyiron.atomistics.job.interactive.GenericInteractive method)
(pyiron.sphinx.interactive.SphinxInteractive method)
interactive_spin_constraints_setter() (pyiron.atomistics.job.interactive.GenericInteractive method)
(pyiron.sphinx.interactive.SphinxInteractive method)
interactive_spins_getter() (pyiron.atomistics.job.interactive.GenericInteractive method)
(pyiron.sphinx.interactive.SphinxInteractive method)
interactive_steps_getter() (pyiron.atomistics.job.interactive.GenericInteractive method)
(pyiron.gpaw.pyiron_ase.AseJob method)
(pyiron.lammps.interactive.LammpsInteractive method)
interactive_store_in_cache() (pyiron.base.job.interactive.InteractiveBase method)
interactive_stress_getter() (pyiron.atomistics.job.interactive.GenericInteractive method)
(pyiron.lammps.interactive.LammpsInteractive method)
interactive_structure_setter() (pyiron.atomistics.job.interactive.GenericInteractive method)
(pyiron.lammps.interactive.LammpsInteractive method)
interactive_temperatures_getter() (pyiron.atomistics.job.interactive.GenericInteractive method)
(pyiron.lammps.interactive.LammpsInteractive method)
interactive_time_getter() (pyiron.atomistics.job.interactive.GenericInteractive method)
(pyiron.gpaw.pyiron_ase.AseJob method)
interactive_unwrapped_positions_getter() (pyiron.atomistics.job.interactive.GenericInteractive method)
interactive_volume_getter() (pyiron.atomistics.job.interactive.GenericInteractive method)
(pyiron.gpaw.pyiron_ase.AseJob method)
(pyiron.lammps.interactive.LammpsInteractive method)
interactive_write_frequency() (pyiron.base.job.interactive.InteractiveBase property)
InteractiveBase (class in pyiron.base.job.interactive)
InteractiveInterface (class in pyiron.atomistics.job.interactive)
InteractiveWrapper (class in pyiron.atomistics.job.interactivewrapper)
interpolate_volume() (pyiron.atomistics.thermodynamics.thermo_bulk.ThermoBulk method)
is_compressed() (pyiron.base.job.core.JobCore method)
is_element() (pyiron.atomistics.structure.periodic_table.PeriodicTable method)
is_empty (pyiron.base.generic.hdfio.FileHDFio attribute)
is_empty() (pyiron.base.generic.hdfio.FileHDFio property)
(pyiron.base.job.path.JobPathBase property)
is_finished() (pyiron.base.master.flexible.FlexibleMaster method)
(pyiron.base.master.list.ListMaster method)
(pyiron.base.master.parallel.ParallelMaster method)
is_func() (pyiron.base.pyio.parser.LogTag method)
is_item() (pyiron.base.pyio.parser.LogTag method)
is_master_id() (pyiron.base.job.core.JobCore method)
is_metal() (pyiron.dft.waves.electronic.ElectronicStructure property)
is_open (pyiron.base.generic.hdfio.FileHDFio attribute)
is_root (pyiron.base.generic.hdfio.FileHDFio attribute)
is_root() (pyiron.base.generic.hdfio.FileHDFio property)
(pyiron.base.job.path.JobPathBase property)
is_self_archived() (pyiron.base.job.core.JobCore method)
item_update() (pyiron.base.database.filetable.FileTable method)
(pyiron.base.database.generic.DatabaseAccess method)
items() (pyiron.atomistics.structure.sparse_list.SparseArray method)
(pyiron.atomistics.structure.sparse_list.SparseList method)
(pyiron.base.generic.hdfio.FileHDFio method)
(pyiron.base.job.path.JobPathBase method)
(pyiron.base.project.generic.Project method)
(pyiron.base.project.store.ProjectStore property)
(pyiron.sphinx.base.Group method)
iter_groups() (pyiron.base.project.generic.Project method)
iter_jobs() (pyiron.base.master.list.ListMaster method)
(pyiron.base.master.parallel.ParallelMaster method)
(pyiron.base.master.serial.SerialMasterBase method)
(pyiron.base.project.generic.Project method)
iter_output() (pyiron.base.project.generic.Project method)
J
job_class_dict() (pyiron.base.job.jobtype.JobTypeChoice property)
job_file_name() (pyiron.base.job.generic.GenericJob method)
job_id() (pyiron.base.job.core.JobCore property)
(pyiron.base.job.jobstatus.JobStatus property)
job_info_str() (pyiron.base.job.core.JobCore property)
job_name() (pyiron.atomistics.master.murnaghan.MurnaghanJobGenerator static method)
(pyiron.atomistics.master.structure.StructureJobGenerator static method)
(pyiron.base.job.core.JobCore property)
(pyiron.dft.master.convergence_encut_parallel.EncutConvergenceJobGenerator static method)
(pyiron.dft.master.convergence_kpoint_parallel.KpointConvergenceJobGenerator static method)
(pyiron.thermodynamics.sxphonons.SxPhononsJobGenerator static method)
job_name_contains() (pyiron.table.datamining.JobFilters static method)
job_object_dict() (pyiron.base.master.generic.GenericMaster property)
job_table() (in module pyiron.base.database.jobtable)
(pyiron.base.database.filetable.FileTable method)
(pyiron.base.project.generic.Project method)
job_type() (pyiron.base.job.generic.GenericJob property)
(pyiron.table.datamining.JobFilters static method)
job_wrap_function() (in module pyiron.base.master.parallel)
job_wrapper_function() (in module pyiron.base.job.wrapper)
JobCore (class in pyiron.base.job.core)
JobFilters (class in pyiron.table.datamining)
JobGenerator (class in pyiron.base.master.parallel)
JobPath (class in pyiron.base.job.path)
JobPathBase (class in pyiron.base.job.path)
JobStatus (class in pyiron.base.job.jobstatus)
JobType (class in pyiron.base.job.jobtype)
JobTypeChoice (class in pyiron.base.job.jobtype)
JobWrapper (class in pyiron.base.job.wrapper)
K
kB (pyiron.atomistics.thermodynamics.thermo_bulk.ThermoBulk attribute)
key_dict() (pyiron.base.pyio.parser.LogTag property)
keys() (pyiron.atomistics.structure.sparse_list.SparseArray method)
(pyiron.atomistics.structure.sparse_list.SparseList method)
(pyiron.base.generic.hdfio.FileHDFio method)
(pyiron.base.generic.parameters.GenericParameters method)
(pyiron.base.job.path.JobPathBase method)
(pyiron.base.project.generic.Project method)
(pyiron.base.project.store.ProjectStore property)
kill() (pyiron.base.job.generic.GenericJob method)
Kpoint (class in pyiron.dft.waves.electronic)
kpoint_list() (pyiron.dft.waves.electronic.ElectronicStructure property)
kpoint_weights() (pyiron.dft.waves.electronic.ElectronicStructure property)
KpointConvergenceJobGenerator (class in pyiron.dft.master.convergence_kpoint_parallel)
Kpoints (class in pyiron.vasp.base)
kpoints (pyiron.vasp.base.Input attribute)
L
Lammps (class in pyiron.lammps.lammps)
LammpsBase (class in pyiron.lammps.base)
LammpsControl (class in pyiron.lammps.control)
LammpsInteractive (class in pyiron.lammps.interactive)
LammpsPotential (class in pyiron.lammps.potential)
LammpsPotentialFile (class in pyiron.lammps.potential)
LammpsStructure (class in pyiron.lammps.structure)
line_skip() (pyiron.base.pyio.parser.LogTag method)
list() (pyiron.atomistics.job.potentials.PotentialAbstract method)
(pyiron.atomistics.structure.sparse_list.SparseList method)
(pyiron.vasp.potential.VaspPotentialAbstract method)
list_all() (pyiron.base.generic.hdfio.FileHDFio method)
(pyiron.base.job.core.JobCore method)
(pyiron.base.job.generic.GenericJob method)
(pyiron.base.project.generic.Project method)
list_childs() (pyiron.base.job.core.JobCore method)
list_dirs() (pyiron.base.generic.hdfio.FileHDFio method)
(pyiron.base.job.path.JobPathBase method)
(pyiron.base.project.generic.Project method)
list_executables() (pyiron.base.job.executable.Executable method)
list_files() (pyiron.base.job.core.JobCore method)
(pyiron.base.project.generic.Project method)
list_groups() (pyiron.base.generic.hdfio.FileHDFio method)
(pyiron.base.job.core.JobCore method)
(pyiron.base.project.generic.Project method)
(pyiron.table.datamining.PyironTable method)
list_nodes() (pyiron.base.generic.hdfio.FileHDFio method)
(pyiron.base.job.core.JobCore method)
(pyiron.base.project.generic.Project method)
(pyiron.table.datamining.PyironTable method)
list_potential_names() (pyiron.vasp.potential.VaspPotentialAbstract method)
list_potentials() (pyiron.lammps.base.LammpsBase method)
(pyiron.vasp.base.VaspBase method)
list_publications() (pyiron.project.Project static method)
list_queues() (pyiron.base.server.generic.Server static method)
list_structures() (pyiron.atomistics.master.murnaghan.Murnaghan method)
(pyiron.thermodynamics.sxphonons.SxUniqDispl method)
listdir() (pyiron.base.project.path.ProjectPath method)
listdirs() (pyiron.base.generic.hdfio.FileHDFio method)
(pyiron.base.job.path.JobPathBase method)
ListMaster (class in pyiron.base.master.list)
load() (pyiron.base.generic.hdfio.ProjectHDFio method)
(pyiron.base.generic.template.PyironObject method)
(pyiron.base.job.core.JobCore method)
(pyiron.base.project.generic.Project method)
(pyiron.table.datamining.PyironTable method)
load_basis_group() (pyiron.sphinx.base.SphinxBase method)
load_chk() (pyiron.yaff.yaff.Yaff method)
load_default() (pyiron.atomistics.job.atomistic.GenericInput method)
(pyiron.base.generic.parameters.GenericParameters method)
(pyiron.gaussian.gaussian.GaussianInput method)
(pyiron.gpaw.gpaw.GpawInput method)
(pyiron.interactive.scipy_minimizer.Input method)
(pyiron.interactive.sxextoptint.Input method)
(pyiron.lammps.control.LammpsControl method)
(pyiron.lammps.structure.LammpsStructure method)
(pyiron.quickff.quickff.QuickFFInput method)
(pyiron.sphinx.base.Input method)
(pyiron.testing.randomatomistic.ExampleInput method)
(pyiron.vasp.base.Incar method)
(pyiron.vasp.base.Kpoints method)
(pyiron.vasp.potential.Potcar method)
(pyiron.yaff.yaff.YaffInput method)
load_default_groups() (pyiron.sphinx.base.SphinxBase method)
load_from_jobpath() (pyiron.base.generic.hdfio.ProjectHDFio method)
(pyiron.base.project.generic.Project method)
(pyiron.project.Project method)
load_from_jobpath_string() (pyiron.base.project.generic.Project static method)
(pyiron.project.Project method)
load_guess_group() (pyiron.sphinx.base.SphinxBase method)
load_hamilton_group() (pyiron.sphinx.base.SphinxBase method)
load_main_group() (pyiron.sphinx.base.SphinxBase method)
(pyiron.sphinx.interactive.SphinxInteractive method)
load_object() (pyiron.base.job.core.JobCore method)
load_species_group() (pyiron.sphinx.base.SphinxBase method)
load_string() (pyiron.base.generic.parameters.GenericParameters method)
load_structure_group() (pyiron.sphinx.base.SphinxBase method)
log() (pyiron.gaussian.gaussian.Gaussian method)
(pyiron.quickff.quickff.QuickFF method)
(pyiron.yaff.yaff.Yaff method)
log_dict (pyiron.vasp.base.DFTOutput attribute)
(pyiron.vasp.base.GenericOutput attribute)
(pyiron.vasp.interactive.DFTOutput attribute)
(pyiron.vasp.interactive.GenericOutput attribute)
logger() (pyiron.base.job.generic.GenericJob property)
login_user() (pyiron.base.settings.generic.Settings property)
Logstatus (class in pyiron.base.pyio.parser)
LogTag (class in pyiron.base.pyio.parser)
M
main() (in module pyiron.cli)
(in module pyiron.cli.install)
(in module pyiron.cli.ls)
(in module pyiron.cli.reloadfile)
(in module pyiron.cli.rm)
(in module pyiron.cli.wrapper)
manip_contcar() (in module pyiron.vasp.structure)
map() (pyiron.atomistics.job.atomistic.AtomisticGenericJob method)
MapFunctions (class in pyiron.atomistics.job.atomistic)
MapJobGenerator (class in pyiron.atomistics.master.parallel)
MapMaster (class in pyiron.atomistics.master.parallel)
mark() (pyiron.base.generic.inputlist.InputList method)
mass() (pyiron.atomistics.structure.atom.Atom property)
master_id() (pyiron.base.generic.template.PyironObject property)
(pyiron.base.job.core.JobCore property)
matrix_to_str() (pyiron.thermodynamics.sxphonons.SxDynMat static method)
md_job() (pyiron.thermodynamics.sxphonons.SxHarmPotTst property)
measure_mean_value() (pyiron.lammps.control.LammpsControl method)
memory_limit() (pyiron.base.server.generic.Server property)
meshgrid() (pyiron.atomistics.thermodynamics.thermo_bulk.ThermoBulk method)
MetadynInput (class in pyiron.vasp.metadyn)
MetadynOutput (class in pyiron.vasp.metadyn)
minimize_pos() (in module pyiron.thermodynamics.interfacemethod)
minimize_vol() (in module pyiron.thermodynamics.interfacemethod)
minimizer() (pyiron.interactive.scipy_minimizer.ScipyMinimizer property)
mode() (pyiron.base.server.runmode.Runmode property)
modify() (pyiron.base.generic.parameters.GenericParameters method)
(pyiron.vasp.potential.Potcar method)
modify_function() (pyiron.atomistics.master.parallel.MapMaster property)
modify_job() (pyiron.atomistics.master.murnaghan.MurnaghanJobGenerator method)
(pyiron.atomistics.master.parallel.MapJobGenerator method)
(pyiron.atomistics.master.structure.StructureJobGenerator method)
(pyiron.base.master.parallel.JobGenerator static method)
(pyiron.dft.master.convergence_encut_parallel.EncutConvergenceJobGenerator static method)
(pyiron.dft.master.convergence_kpoint_parallel.KpointConvergenceJobGenerator static method)
(pyiron.thermodynamics.sxphonons.SxPhononsJobGenerator method)
module
pyiron
pyiron.atomistics
pyiron.atomistics.generic
pyiron.atomistics.generic.object_type
pyiron.atomistics.job
pyiron.atomistics.job.atomistic
pyiron.atomistics.job.interactive
pyiron.atomistics.job.interactivewrapper
pyiron.atomistics.job.potentials
pyiron.atomistics.job.structurecontainer
pyiron.atomistics.master
pyiron.atomistics.master.convergence_volume
pyiron.atomistics.master.murnaghan
pyiron.atomistics.master.parallel
pyiron.atomistics.master.serial
pyiron.atomistics.master.structure
pyiron.atomistics.nma
pyiron.atomistics.nma.nma
pyiron.atomistics.structure
pyiron.atomistics.structure.atom
pyiron.atomistics.structure.atoms
pyiron.atomistics.structure.generator
pyiron.atomistics.structure.periodic_table
pyiron.atomistics.structure.pyironase
pyiron.atomistics.structure.pyscal
pyiron.atomistics.structure.sparse_list
pyiron.atomistics.thermodynamics
pyiron.atomistics.thermodynamics.thermo_bulk
pyiron.atomistics.volumetric
pyiron.atomistics.volumetric.generic
pyiron.base
pyiron.base.database
pyiron.base.database.filetable
pyiron.base.database.generic
pyiron.base.database.jobtable
pyiron.base.generic
pyiron.base.generic.hdfio
pyiron.base.generic.inputlist
pyiron.base.generic.jedi
pyiron.base.generic.parameters
pyiron.base.generic.template
pyiron.base.generic.util
pyiron.base.job
pyiron.base.job.core
pyiron.base.job.executable
pyiron.base.job.external
pyiron.base.job.generic
pyiron.base.job.interactive
pyiron.base.job.jobstatus
pyiron.base.job.jobtype
pyiron.base.job.path
pyiron.base.job.script
pyiron.base.job.template
pyiron.base.job.wrapper
pyiron.base.master
pyiron.base.master.flexible
pyiron.base.master.generic
pyiron.base.master.list
pyiron.base.master.parallel
pyiron.base.master.serial
pyiron.base.master.submissionstatus
pyiron.base.project
pyiron.base.project.generic
pyiron.base.project.path
pyiron.base.project.store
pyiron.base.pyio
pyiron.base.pyio.parser
pyiron.base.server
pyiron.base.server.generic
pyiron.base.server.queuestatus
pyiron.base.server.runmode
pyiron.base.settings
pyiron.base.settings.generic
pyiron.base.settings.install
pyiron.base.settings.logger
pyiron.base.settings.update
pyiron.cli
pyiron.cli.install
pyiron.cli.ls
pyiron.cli.reloadfile
pyiron.cli.rm
pyiron.cli.wrapper
pyiron.dft
pyiron.dft.job
pyiron.dft.job.generic
pyiron.dft.master
pyiron.dft.master.convergence_encut_parallel
pyiron.dft.master.convergence_encut_serial
pyiron.dft.master.convergence_kpoint_parallel
pyiron.dft.master.murnaghan_dft
pyiron.dft.waves
pyiron.dft.waves.bandstructure
pyiron.dft.waves.dos
pyiron.dft.waves.electronic
pyiron.gaussian
pyiron.gaussian.gaussian
pyiron.gpaw
pyiron.gpaw.gpaw
pyiron.gpaw.pyiron_ase
pyiron.interactive
pyiron.interactive.scipy_minimizer
pyiron.interactive.sxextoptint
pyiron.lammps
pyiron.lammps.base
pyiron.lammps.control
pyiron.lammps.interactive
pyiron.lammps.lammps
pyiron.lammps.potential
pyiron.lammps.structure
pyiron.project
pyiron.quickff
pyiron.quickff.quickff
pyiron.sphinx
pyiron.sphinx.base
pyiron.sphinx.interactive
pyiron.sphinx.potential
pyiron.sphinx.sphinx
pyiron.sphinx.structure
pyiron.sphinx.volumetric_data
pyiron.table
pyiron.table.datamining
pyiron.table.funct
pyiron.testing
pyiron.testing.executable
pyiron.testing.randomatomistic
pyiron.thermodynamics
pyiron.thermodynamics.hessian
pyiron.thermodynamics.interfacemethod
pyiron.thermodynamics.sxphonons
pyiron.vasp
pyiron.vasp.base
pyiron.vasp.interactive
pyiron.vasp.metadyn
pyiron.vasp.outcar
pyiron.vasp.potential
pyiron.vasp.procar
pyiron.vasp.report
pyiron.vasp.structure
pyiron.vasp.vasp
pyiron.vasp.vasprun
pyiron.vasp.vaspsol
pyiron.vasp.volumetric_data
pyiron.yaff
pyiron.yaff.yaff
move_to() (pyiron.base.generic.template.PyironObject method)
(pyiron.base.job.core.JobCore method)
(pyiron.base.master.generic.GenericMaster method)
(pyiron.base.project.generic.Project method)
mpi() (pyiron.base.job.executable.Executable property)
mtd_sum_hills_1d() (pyiron.yaff.yaff.Yaff method)
multi_word_separator() (pyiron.base.generic.parameters.GenericParameters property)
multiprocess_wrapper() (in module pyiron.base.job.generic)
Murnaghan (class in pyiron.atomistics.master.murnaghan)
murnaghan() (in module pyiron.atomistics.master.murnaghan)
(pyiron.atomistics.master.murnaghan.EnergyVolumeFit static method)
MurnaghanDFT (class in pyiron.dft.master.murnaghan_dft)
MurnaghanJobGenerator (class in pyiron.atomistics.master.murnaghan)
N
name() (pyiron.base.generic.hdfio.ProjectHDFio property)
(pyiron.base.job.core.JobCore property)
(pyiron.base.project.generic.Project property)
(pyiron.table.datamining.PyironTable property)
Neighbors (class in pyiron.atomistics.structure.atoms)
new_array() (pyiron.atomistics.structure.atoms.Atoms method)
(pyiron.gpaw.pyiron_ase.AseAdapter method)
new_hdf() (pyiron.base.server.generic.Server property)
next() (pyiron.base.master.parallel.JobGenerator method)
(pyiron.lammps.base.LammpsBase method)
next_calc() (in module pyiron.thermodynamics.interfacemethod)
next_step_funct() (in module pyiron.thermodynamics.interfacemethod)
NMA (class in pyiron.atomistics.nma.nma)
nodes() (pyiron.base.generic.hdfio.FileHDFio method)
(pyiron.base.job.path.JobPathBase method)
(pyiron.base.project.generic.Project method)
NoResolvedDosError
Notebook (class in pyiron.base.job.external)
npt_liquid() (in module pyiron.thermodynamics.interfacemethod)
npt_solid() (in module pyiron.thermodynamics.interfacemethod)
num_atoms() (pyiron.atomistics.thermodynamics.thermo_bulk.ThermoBulk property)
num_steps() (pyiron.atomistics.master.murnaghan.DebyeModel property)
number() (pyiron.atomistics.structure.atom.Atom property)
number_jobs_total() (pyiron.base.master.parallel.ParallelMaster property)
numbers_to_elements() (pyiron.atomistics.structure.atoms.Atoms method)
O
ObjectType (class in pyiron.atomistics.generic.object_type)
ObjectTypeChoice (class in pyiron.atomistics.generic.object_type)
occupancies() (pyiron.dft.waves.electronic.ElectronicStructure property)
occupancy() (pyiron.dft.waves.electronic.Band property)
occupancy_matrix() (pyiron.dft.waves.electronic.ElectronicStructure property)
occupy_lattice() (pyiron.atomistics.structure.atoms.Atoms method)
open() (pyiron.base.generic.hdfio.FileHDFio method)
(pyiron.base.generic.hdfio.HDFStoreIO method)
(pyiron.base.job.path.JobPathBase method)
(pyiron.base.project.path.ProjectPath method)
open_connection() (pyiron.base.settings.generic.Settings method)
orbital_dict() (pyiron.dft.waves.electronic.ElectronicStructure property)
Outcar (class in pyiron.vasp.outcar)
Output (class in pyiron.sphinx.base)
(class in pyiron.vasp.base)
(class in pyiron.vasp.interactive)
output_to_pandas() (pyiron.base.master.parallel.ParallelMaster method)
ovito_to_pyiron() (in module pyiron.atomistics.structure.atoms)
P
ParallelMaster (class in pyiron.base.master.parallel)
parameter_list() (pyiron.atomistics.master.murnaghan.MurnaghanJobGenerator property)
(pyiron.atomistics.master.parallel.MapJobGenerator property)
(pyiron.atomistics.master.structure.StructureJobGenerator property)
(pyiron.base.master.parallel.JobGenerator property)
(pyiron.dft.master.convergence_encut_parallel.EncutConvergenceJobGenerator property)
(pyiron.dft.master.convergence_kpoint_parallel.KpointConvergenceJobGenerator property)
(pyiron.thermodynamics.sxphonons.SxPhononsJobGenerator property)
parameter_list_cached() (pyiron.base.master.parallel.JobGenerator property)
parent_group() (pyiron.base.project.generic.Project property)
parent_id() (pyiron.base.generic.template.PyironObject property)
(pyiron.base.job.core.JobCore property)
parse_atom_information_to_dict() (pyiron.vasp.vasprun.Vasprun method)
parse_calc_to_dict() (pyiron.vasp.vasprun.Vasprun method)
parse_dict (pyiron.vasp.outcar.Outcar attribute)
parse_eigenvalues_to_dict() (pyiron.vasp.vasprun.Vasprun method)
parse_fermi_level_to_dict() (pyiron.vasp.vasprun.Vasprun method)
parse_item_to_dict() (pyiron.vasp.vasprun.Vasprun static method)
parse_kpoints_to_dict() (pyiron.vasp.vasprun.Vasprun method)
parse_parameters() (pyiron.vasp.vasprun.Vasprun method)
parse_partial_dos_to_dict() (pyiron.vasp.vasprun.Vasprun method)
parse_projected_dos_to_dict() (pyiron.vasp.vasprun.Vasprun method)
parse_recursively() (pyiron.vasp.vasprun.Vasprun method)
parse_root_to_dict() (pyiron.vasp.vasprun.Vasprun method)
parse_scf() (pyiron.vasp.vasprun.Vasprun method)
parse_structure_to_dict() (pyiron.vasp.vasprun.Vasprun method)
parse_total_dos_to_dict() (pyiron.vasp.vasprun.Vasprun method)
path() (pyiron.base.generic.hdfio.ProjectHDFio property)
(pyiron.base.job.core.JobCore property)
(pyiron.base.project.path.GenericPath property)
path_dict() (pyiron.dft.waves.bandstructure.Bandstructure property)
pbc() (pyiron.atomistics.structure.atoms.Atoms property)
PeriodicTable (class in pyiron.atomistics.structure.periodic_table)
pipe() (in module pyiron.atomistics.master.parallel)
plane_wave_cutoff() (pyiron.dft.job.generic.GenericDFTJob property)
(pyiron.gpaw.gpaw.GpawJob property)
(pyiron.sphinx.base.SphinxBase property)
(pyiron.vasp.base.VaspBase property)
plot() (pyiron.atomistics.master.murnaghan.Murnaghan method)
(pyiron.dft.master.convergence_encut_parallel.ConvEncutParallel method)
(pyiron.dft.master.convergence_kpoint_parallel.ConvKpointParallel method)
(pyiron.dft.waves.bandstructure.Bandstructure method)
(pyiron.yaff.yaff.Yaff method)
plot3d() (pyiron.atomistics.structure.atoms.Atoms method)
plot3d_ase() (pyiron.atomistics.structure.atoms.Atoms method)
plot_contourf() (pyiron.atomistics.thermodynamics.thermo_bulk.ThermoBulk method)
plot_entropy() (pyiron.atomistics.thermodynamics.thermo_bulk.ThermoBulk method)
plot_equilibration() (in module pyiron.thermodynamics.interfacemethod)
plot_fermi_dirac() (pyiron.dft.waves.electronic.ElectronicStructure method)
plot_free_energy() (pyiron.atomistics.thermodynamics.thermo_bulk.ThermoBulk method)
plot_heat_capacity() (pyiron.atomistics.thermodynamics.thermo_bulk.ThermoBulk method)
plot_IR_spectrum() (pyiron.atomistics.nma.nma.NMA method)
plot_melting_point_prediction() (in module pyiron.thermodynamics.interfacemethod)
plot_min_energy_path() (pyiron.atomistics.thermodynamics.thermo_bulk.ThermoBulk method)
plot_multi() (pyiron.yaff.yaff.Yaff method)
plot_orbital_resolved_dos() (pyiron.dft.waves.dos.Dos method)
plot_solid_liquid_ratio() (in module pyiron.thermodynamics.interfacemethod)
plot_total_dos() (pyiron.dft.waves.dos.Dos method)
poly_fit() (pyiron.atomistics.master.murnaghan.Murnaghan method)
polynomial() (pyiron.atomistics.master.murnaghan.DebyeModel method)
pop() (pyiron.atomistics.structure.atoms.Atoms method)
(pyiron.base.master.generic.GenericMaster method)
pos_to_lammps() (pyiron.lammps.structure.UnfoldingPrism method)
pos_xyz() (pyiron.atomistics.structure.atoms.Atoms method)
position() (pyiron.atomistics.structure.atom.Atom property)
positions() (pyiron.atomistics.job.atomistic.GenericOutput property)
(pyiron.atomistics.job.interactive.GenericInteractiveOutput property)
(pyiron.atomistics.job.interactivewrapper.ReferenceJobOutput property)
pot_path_dict (pyiron.vasp.potential.Potcar attribute)
Potcar (class in pyiron.vasp.potential)
potcar (pyiron.vasp.base.Input attribute)
potcar_set_structure() (pyiron.vasp.potential.Potcar method)
potential() (pyiron.lammps.base.LammpsBase property)
(pyiron.lammps.structure.LammpsStructure property)
(pyiron.vasp.base.VaspBase property)
potential_available() (pyiron.lammps.base.LammpsBase property)
(pyiron.vasp.base.VaspBase property)
potential_list() (pyiron.lammps.base.LammpsBase property)
(pyiron.vasp.base.VaspBase property)
potential_view() (pyiron.lammps.base.LammpsBase property)
(pyiron.vasp.base.VaspBase property)
PotentialAbstract (class in pyiron.atomistics.job.potentials)
PotentialAvailable (class in pyiron.lammps.potential)
pouriertarantola() (in module pyiron.atomistics.master.murnaghan)
(pyiron.atomistics.master.murnaghan.EnergyVolumeFit static method)
pressure() (pyiron.atomistics.thermodynamics.thermo_bulk.ThermoBulk property)
pressure_to_lammps() (pyiron.lammps.control.LammpsControl method)
pressures() (pyiron.atomistics.job.atomistic.GenericOutput property)
(pyiron.atomistics.job.interactive.GenericInteractiveOutput property)
(pyiron.atomistics.job.interactivewrapper.ReferenceJobOutput property)
print_message() (pyiron.base.job.generic.GenericError method)
print_MO() (pyiron.gaussian.gaussian.Gaussian method)
print_queue() (pyiron.base.job.generic.GenericError method)
Procar (class in pyiron.vasp.procar)
Project (class in pyiron.base.project.generic)
(class in pyiron.project)
project() (pyiron.base.generic.hdfio.ProjectHDFio property)
(pyiron.base.job.core.JobCore property)
project_check_enabled() (pyiron.base.settings.generic.Settings property)
project_hdf5() (pyiron.base.job.core.JobCore property)
project_level() (pyiron.table.datamining.TableJob property)
project_path() (pyiron.base.generic.hdfio.ProjectHDFio property)
(pyiron.base.project.path.GenericPath property)
ProjectHDFio (class in pyiron.base.generic.hdfio)
ProjectPath (class in pyiron.base.project.path)
ProjectStore (class in pyiron.base.project.store)
publication() (in module pyiron.atomistics.structure.pyironase)
(pyiron.base.settings.generic.Settings property)
(pyiron.lammps.base.LammpsBase property)
(pyiron.vasp.base.VaspBase property)
publication_add() (pyiron.base.settings.generic.Settings method)
publication_lst() (pyiron.base.settings.generic.Settings property)
put() (pyiron.base.generic.hdfio.FileHDFio method)
(pyiron.base.job.path.JobPathBase method)
pyiron
module
pyiron.atomistics
module
pyiron.atomistics.generic
module
pyiron.atomistics.generic.object_type
module
pyiron.atomistics.job
module
pyiron.atomistics.job.atomistic
module
pyiron.atomistics.job.interactive
module
pyiron.atomistics.job.interactivewrapper
module
pyiron.atomistics.job.potentials
module
pyiron.atomistics.job.structurecontainer
module
pyiron.atomistics.master
module
pyiron.atomistics.master.convergence_volume
module
pyiron.atomistics.master.murnaghan
module
pyiron.atomistics.master.parallel
module
pyiron.atomistics.master.serial
module
pyiron.atomistics.master.structure
module
pyiron.atomistics.nma
module
pyiron.atomistics.nma.nma
module
pyiron.atomistics.structure
module
pyiron.atomistics.structure.atom
module
pyiron.atomistics.structure.atoms
module
pyiron.atomistics.structure.generator
module
pyiron.atomistics.structure.periodic_table
module
pyiron.atomistics.structure.pyironase
module
pyiron.atomistics.structure.pyscal
module
pyiron.atomistics.structure.sparse_list
module
pyiron.atomistics.thermodynamics
module
pyiron.atomistics.thermodynamics.thermo_bulk
module
pyiron.atomistics.volumetric
module
pyiron.atomistics.volumetric.generic
module
pyiron.base
module
pyiron.base.database
module
pyiron.base.database.filetable
module
pyiron.base.database.generic
module
pyiron.base.database.jobtable
module
pyiron.base.generic
module
pyiron.base.generic.hdfio
module
pyiron.base.generic.inputlist
module
pyiron.base.generic.jedi
module
pyiron.base.generic.parameters
module
pyiron.base.generic.template
module
pyiron.base.generic.util
module
pyiron.base.job
module
pyiron.base.job.core
module
pyiron.base.job.executable
module
pyiron.base.job.external
module
pyiron.base.job.generic
module
pyiron.base.job.interactive
module
pyiron.base.job.jobstatus
module
pyiron.base.job.jobtype
module
pyiron.base.job.path
module
pyiron.base.job.script
module
pyiron.base.job.template
module
pyiron.base.job.wrapper
module
pyiron.base.master
module
pyiron.base.master.flexible
module
pyiron.base.master.generic
module
pyiron.base.master.list
module
pyiron.base.master.parallel
module
pyiron.base.master.serial
module
pyiron.base.master.submissionstatus
module
pyiron.base.project
module
pyiron.base.project.generic
module
pyiron.base.project.path
module
pyiron.base.project.store
module
pyiron.base.pyio
module
pyiron.base.pyio.parser
module
pyiron.base.server
module
pyiron.base.server.generic
module
pyiron.base.server.queuestatus
module
pyiron.base.server.runmode
module
pyiron.base.settings
module
pyiron.base.settings.generic
module
pyiron.base.settings.install
module
pyiron.base.settings.logger
module
pyiron.base.settings.update
module
pyiron.cli
module
pyiron.cli.install
module
pyiron.cli.ls
module
pyiron.cli.reloadfile
module
pyiron.cli.rm
module
pyiron.cli.wrapper
module
pyiron.dft
module
pyiron.dft.job
module
pyiron.dft.job.generic
module
pyiron.dft.master
module
pyiron.dft.master.convergence_encut_parallel
module
pyiron.dft.master.convergence_encut_serial
module
pyiron.dft.master.convergence_kpoint_parallel
module
pyiron.dft.master.murnaghan_dft
module
pyiron.dft.waves
module
pyiron.dft.waves.bandstructure
module
pyiron.dft.waves.dos
module
pyiron.dft.waves.electronic
module
pyiron.gaussian
module
pyiron.gaussian.gaussian
module
pyiron.gpaw
module
pyiron.gpaw.gpaw
module
pyiron.gpaw.pyiron_ase
module
pyiron.interactive
module
pyiron.interactive.scipy_minimizer
module
pyiron.interactive.sxextoptint
module
pyiron.lammps
module
pyiron.lammps.base
module
pyiron.lammps.control
module
pyiron.lammps.interactive
module
pyiron.lammps.lammps
module
pyiron.lammps.potential
module
pyiron.lammps.structure
module
pyiron.project
module
pyiron.quickff
module
pyiron.quickff.quickff
module
pyiron.sphinx
module
pyiron.sphinx.base
module
pyiron.sphinx.interactive
module
pyiron.sphinx.potential
module
pyiron.sphinx.sphinx
module
pyiron.sphinx.structure
module
pyiron.sphinx.volumetric_data
module
pyiron.table
module
pyiron.table.datamining
module
pyiron.table.funct
module
pyiron.testing
module
pyiron.testing.executable
module
pyiron.testing.randomatomistic
module
pyiron.thermodynamics
module
pyiron.thermodynamics.hessian
module
pyiron.thermodynamics.interfacemethod
module
pyiron.thermodynamics.sxphonons
module
pyiron.vasp
module
pyiron.vasp.base
module
pyiron.vasp.interactive
module
pyiron.vasp.metadyn
module
pyiron.vasp.outcar
module
pyiron.vasp.potential
module
pyiron.vasp.procar
module
pyiron.vasp.report
module
pyiron.vasp.structure
module
pyiron.vasp.vasp
module
pyiron.vasp.vasprun
module
pyiron.vasp.vaspsol
module
pyiron.vasp.volumetric_data
module
pyiron.yaff
module
pyiron.yaff.yaff
module
pyiron_table() (pyiron.table.datamining.TableJob property)
pyiron_to_ase() (in module pyiron.atomistics.structure.atoms)
pyiron_to_ovito() (in module pyiron.atomistics.structure.atoms)
pyiron_to_pymatgen() (in module pyiron.atomistics.structure.atoms)
PyironObject (class in pyiron.base.generic.template)
PyironTable (class in pyiron.table.datamining)
pymatgen_to_pyiron() (in module pyiron.atomistics.structure.atoms)
Q
query_for_element() (pyiron.base.database.generic.DatabaseAccess method)
queue() (pyiron.base.server.generic.Server property)
queue_adapter() (pyiron.base.settings.generic.Settings property)
queue_check_job_is_waiting_or_running() (in module pyiron.base.server.queuestatus)
(pyiron.base.project.generic.Project static method)
queue_delete_job() (in module pyiron.base.server.queuestatus)
(pyiron.base.project.generic.Project method)
queue_enable_reservation() (in module pyiron.base.server.queuestatus)
(pyiron.base.project.generic.Project static method)
queue_id() (pyiron.base.job.generic.GenericJob property)
(pyiron.base.server.generic.Server property)
queue_info_by_job_id() (in module pyiron.base.server.queuestatus)
queue_is_empty() (in module pyiron.base.server.queuestatus)
(pyiron.base.project.generic.Project static method)
queue_list() (pyiron.base.server.generic.Server property)
queue_table() (in module pyiron.base.server.queuestatus)
(pyiron.base.project.generic.Project method)
queue_table_global() (pyiron.base.project.generic.Project method)
queue_view() (pyiron.base.server.generic.Server property)
QuickFF (class in pyiron.quickff.quickff)
QuickFFInput (class in pyiron.quickff.quickff)
R
raise_iter() (pyiron.base.pyio.parser.Logstatus method)
ratio_selection() (in module pyiron.thermodynamics.interfacemethod)
read_abinitio() (pyiron.quickff.quickff.QuickFF method)
read_atoms() (in module pyiron.sphinx.structure)
(in module pyiron.vasp.structure)
read_bsse() (in module pyiron.gaussian.gaussian)
read_colvar() (in module pyiron.yaff.yaff)
read_cube_file() (pyiron.atomistics.volumetric.generic.VolumetricData method)
read_EmpiricalDispersion() (in module pyiron.gaussian.gaussian)
read_input() (pyiron.base.generic.parameters.GenericParameters method)
read_NMA() (pyiron.gaussian.gaussian.Gaussian method)
read_restart() (pyiron.testing.executable.ExampleExecutable method)
read_restart_file() (pyiron.lammps.base.LammpsBase method)
ref_job() (pyiron.atomistics.job.interactivewrapper.InteractiveWrapper property)
(pyiron.base.master.parallel.ParallelMaster property)
(pyiron.base.master.serial.SerialMasterBase property)
ref_job_initialize() (pyiron.atomistics.job.interactivewrapper.InteractiveWrapper method)
ref_project() (pyiron.table.datamining.TableJob property)
ReferenceJobOutput (class in pyiron.atomistics.job.interactivewrapper)
refill_dict() (pyiron.table.datamining.PyironTable method)
refine_cell() (pyiron.atomistics.structure.atoms.Atoms method)
refresh() (pyiron.base.master.submissionstatus.SubmissionStatus method)
refresh_job_status() (pyiron.base.job.generic.GenericJob method)
refresh_job_status_based_on_job_id() (pyiron.base.project.generic.Project method)
refresh_job_status_based_on_queue_status() (pyiron.base.project.generic.Project method)
refresh_status() (pyiron.base.job.jobstatus.JobStatus method)
refresh_submission_status() (pyiron.base.master.list.ListMaster method)
(pyiron.base.master.parallel.ParallelMaster method)
regexp() (pyiron.base.database.generic.DatabaseAccess static method)
register() (in module pyiron.cli.install)
(in module pyiron.cli.ls)
(in module pyiron.cli.reloadfile)
(in module pyiron.cli.rm)
(in module pyiron.cli.wrapper)
remap_indices() (pyiron.lammps.base.LammpsBase method)
remove() (pyiron.base.generic.template.PyironObject method)
(pyiron.base.job.core.JobCore method)
(pyiron.base.project.generic.Project method)
(pyiron.sphinx.base.Group method)
remove_child() (pyiron.base.job.core.JobCore method)
(pyiron.base.job.generic.GenericJob method)
remove_file() (pyiron.base.generic.hdfio.FileHDFio method)
(pyiron.base.job.path.JobPathBase method)
(pyiron.base.project.generic.Project method)
remove_group() (pyiron.base.generic.hdfio.FileHDFio method)
remove_job() (pyiron.base.generic.hdfio.ProjectHDFio method)
(pyiron.base.project.generic.Project method)
remove_jobs() (pyiron.base.project.generic.Project method)
remove_keys() (pyiron.base.generic.parameters.GenericParameters method)
remove_selective_dynamics() (in module pyiron.thermodynamics.interfacemethod)
remove_structure_block() (pyiron.lammps.potential.LammpsPotential method)
remove_tag() (pyiron.atomistics.structure.sparse_list.SparseArray method)
removedirs() (pyiron.base.project.path.ProjectPath method)
rename() (pyiron.base.job.core.JobCore method)
repeat() (pyiron.atomistics.structure.atoms.Atoms method)
repeat_points() (pyiron.atomistics.structure.atoms.Atoms method)
replace_char_dict() (pyiron.base.generic.parameters.GenericParameters property)
Report (class in pyiron.vasp.report)
reset_absolute() (pyiron.atomistics.structure.atoms.Atoms method)
reset_iter() (pyiron.base.pyio.parser.Logstatus method)
reset_job_id() (pyiron.base.job.core.JobCore method)
(pyiron.base.job.generic.GenericJob method)
(pyiron.base.master.list.ListMaster method)
(pyiron.base.master.parallel.ParallelMaster method)
reset_output() (pyiron.vasp.base.VaspBase method)
resolve_dynamic_variable() (pyiron.base.pyio.parser.LogTag method)
resolved_densities() (pyiron.dft.waves.electronic.ElectronicStructure property)
resolved_dos_matrix() (pyiron.dft.waves.electronic.Band property)
resource_paths() (pyiron.base.settings.generic.Settings property)
restart() (pyiron.atomistics.job.atomistic.AtomisticGenericJob method)
(pyiron.base.job.generic.GenericJob method)
(pyiron.lammps.base.LammpsBase method)
(pyiron.sphinx.base.SphinxBase method)
(pyiron.vasp.base.VaspBase method)
restart_file_dict() (pyiron.base.job.generic.GenericJob property)
restart_file_list() (pyiron.base.job.generic.GenericJob property)
restart_for_band_structure_calculations() (pyiron.dft.job.generic.GenericDFTJob method)
(pyiron.sphinx.base.SphinxBase method)
(pyiron.vasp.base.VaspBase method)
restart_from_charge_density() (pyiron.sphinx.base.SphinxBase method)
(pyiron.vasp.base.VaspBase method)
restart_from_wave_and_charge() (pyiron.vasp.base.VaspBase method)
restart_from_wave_functions() (pyiron.sphinx.base.SphinxBase method)
(pyiron.vasp.base.VaspBase method)
rewrite_hdf5() (pyiron.base.generic.hdfio.FileHDFio method)
root_path() (pyiron.base.generic.hdfio.ProjectHDFio property)
(pyiron.base.project.path.GenericPath property)
rotate() (pyiron.atomistics.structure.atoms.Atoms method)
rotate_euler() (pyiron.atomistics.structure.atoms.Atoms method)
rotate_positions() (pyiron.lammps.structure.LammpsStructure method)
round_temperature_next() (in module pyiron.thermodynamics.interfacemethod)
rows() (pyiron.base.pyio.parser.LogTag method)
run() (pyiron.base.job.generic.GenericJob method)
(pyiron.base.job.wrapper.JobWrapper method)
(pyiron.testing.executable.ExampleExecutable method)
run_if_interactive() (pyiron.atomistics.job.interactive.GenericInteractive method)
(pyiron.atomistics.job.structurecontainer.StructureContainer method)
(pyiron.base.job.generic.GenericJob method)
(pyiron.base.job.interactive.InteractiveBase method)
(pyiron.base.master.flexible.FlexibleMaster method)
(pyiron.base.master.generic.GenericMaster method)
(pyiron.base.master.list.ListMaster method)
(pyiron.base.master.parallel.ParallelMaster method)
(pyiron.base.master.serial.SerialMasterBase method)
(pyiron.gpaw.gpaw.GpawJob method)
(pyiron.gpaw.pyiron_ase.AseJob method)
(pyiron.lammps.interactive.LammpsInteractive method)
(pyiron.sphinx.interactive.SphinxInteractive method)
(pyiron.testing.randomatomistic.AtomisticExampleJob method)
(pyiron.testing.randomatomistic.ExampleJob method)
(pyiron.thermodynamics.hessian.HessianJob method)
(pyiron.vasp.interactive.VaspInteractive method)
run_if_interactive_non_modal() (pyiron.atomistics.master.structure.StructureListMaster method)
(pyiron.base.job.generic.GenericJob method)
(pyiron.base.job.interactive.InteractiveBase method)
(pyiron.base.master.generic.GenericMaster method)
(pyiron.lammps.interactive.LammpsInteractive method)
(pyiron.sphinx.interactive.SphinxInteractive method)
(pyiron.vasp.interactive.VaspInteractive method)
run_if_lib() (pyiron.base.job.script.ScriptJob method)
(pyiron.base.project.store.ProjectStore method)
run_if_manually() (pyiron.base.job.generic.GenericJob method)
run_if_modal() (pyiron.base.job.generic.GenericJob method)
run_if_non_modal() (pyiron.base.job.generic.GenericJob method)
run_if_refresh() (pyiron.base.job.generic.GenericJob method)
(pyiron.base.master.flexible.FlexibleMaster method)
(pyiron.base.master.generic.GenericMaster method)
(pyiron.base.master.list.ListMaster method)
(pyiron.base.master.parallel.ParallelMaster method)
(pyiron.base.master.serial.SerialMasterBase method)
run_if_scheduler() (pyiron.base.job.generic.GenericJob method)
(pyiron.gpaw.gpaw.GpawJob method)
run_interactive() (pyiron.atomistics.job.interactive.InteractiveInterface method)
run_lib() (pyiron.testing.executable.ExampleExecutable method)
run_mode() (pyiron.base.server.generic.Server property)
run_static() (pyiron.base.job.generic.GenericJob method)
(pyiron.base.master.flexible.FlexibleMaster method)
(pyiron.base.master.list.ListMaster method)
(pyiron.base.master.parallel.ParallelMaster method)
(pyiron.base.master.serial.SerialMasterBase method)
(pyiron.gpaw.gpaw.GpawJob method)
(pyiron.gpaw.pyiron_ase.AseJob method)
(pyiron.interactive.scipy_minimizer.ScipyMinimizer method)
(pyiron.interactive.sxextoptint.SxExtOptInteractive method)
(pyiron.table.datamining.TableJob method)
(pyiron.thermodynamics.sxphonons.SxPhonons method)
run_time() (pyiron.base.server.generic.Server property)
Runmode (class in pyiron.base.server.runmode)
S
save() (pyiron.base.generic.template.PyironObject method)
(pyiron.base.job.core.JobCore method)
(pyiron.base.job.generic.GenericJob method)
(pyiron.base.master.list.ListMaster method)
(pyiron.base.master.parallel.ParallelMaster method)
(pyiron.table.datamining.PyironTable method)
scaled_pos_xyz() (pyiron.atomistics.structure.atoms.Atoms method)
scaled_positions() (pyiron.atomistics.structure.atoms.Atoms property)
ScipyMinimizer (class in pyiron.interactive.scipy_minimizer)
ScipyMinimizerOutput (class in pyiron.interactive.scipy_minimizer)
script_path() (pyiron.base.job.script.ScriptJob property)
ScriptJob (class in pyiron.base.job.script)
select_index() (pyiron.atomistics.structure.atoms.Atoms method)
select_parent_index() (pyiron.atomistics.structure.atoms.Atoms method)
self_archive() (pyiron.base.job.core.JobCore method)
self_unarchive() (pyiron.base.job.core.JobCore method)
send_to_database() (pyiron.base.job.generic.GenericJob method)
send_to_db() (pyiron.base.server.generic.Server property)
separator_char() (pyiron.base.generic.parameters.GenericParameters property)
SerialMaster (class in pyiron.atomistics.master.serial)
SerialMasterBase (class in pyiron.base.master.serial)
Server (class in pyiron.base.server.generic)
server() (pyiron.base.job.generic.GenericJob property)
set() (pyiron.atomistics.structure.atom.Atom method)
(pyiron.base.generic.parameters.GenericParameters method)
(pyiron.sphinx.base.Group method)
set_absolute() (pyiron.atomistics.structure.atoms.Atoms method)
set_algorithm() (pyiron.vasp.base.VaspBase method)
set_array() (pyiron.atomistics.structure.atoms.Atoms method)
(pyiron.gpaw.pyiron_ase.AseAdapter method)
set_calculator() (pyiron.atomistics.structure.atoms.Atoms method)
set_cell() (pyiron.atomistics.job.interactive.InteractiveInterface method)
(pyiron.atomistics.structure.atoms.Atoms method)
set_check_overlap() (pyiron.sphinx.base.SphinxBase method)
set_child_id_func() (pyiron.base.master.generic.GenericMaster method)
set_complex_constraint() (pyiron.vasp.metadyn.VaspMetadyn method)
set_constraint() (pyiron.atomistics.structure.atoms.Atoms method)
set_convergence_precision() (pyiron.sphinx.base.SphinxBase method)
(pyiron.vasp.base.VaspBase method)
set_coulomb_interactions() (pyiron.vasp.base.VaspBase method)
set_dict() (pyiron.base.generic.parameters.GenericParameters method)
set_dipole_correction() (pyiron.vasp.base.VaspBase method)
set_eddrmm_handling() (pyiron.vasp.base.VaspBase method)
set_ei() (pyiron.quickff.quickff.QuickFF method)
set_eigenvalues() (pyiron.dft.waves.bandstructure.Bandstructure method)
set_electric_field() (pyiron.vasp.base.VaspBase method)
set_empty_states() (pyiron.dft.job.generic.GenericDFTJob method)
(pyiron.sphinx.base.SphinxBase method)
(pyiron.vasp.base.VaspBase method)
set_encut() (in module pyiron.atomistics.job.atomistic)
(pyiron.atomistics.job.atomistic.AtomisticGenericJob method)
(pyiron.dft.job.generic.GenericDFTJob method)
(pyiron.dft.master.murnaghan_dft.MurnaghanDFT method)
(pyiron.gpaw.gpaw.GpawJob method)
set_energy_pot() (pyiron.atomistics.job.interactive.InteractiveInterface method)
set_energy_tot() (pyiron.atomistics.job.interactive.InteractiveInterface method)
set_exchange_correlation_functional() (pyiron.dft.job.generic.GenericDFTJob method)
set_fft_mesh() (pyiron.vasp.base.VaspBase method)
set_flag() (pyiron.sphinx.base.Group method)
set_for_band_structure_calc() (pyiron.vasp.base.VaspBase method)
set_force_constants() (pyiron.thermodynamics.hessian.HessianJob method)
set_forces() (pyiron.atomistics.job.interactive.InteractiveInterface method)
(pyiron.interactive.sxextoptint.SxExtOpt method)
set_goal() (pyiron.base.master.serial.SerialMasterBase method)
set_group() (pyiron.sphinx.base.Group method)
set_initial_magnetic_moments() (pyiron.atomistics.structure.atoms.Atoms method)
set_initial_velocity() (pyiron.lammps.control.LammpsControl method)
set_input_to_read_only() (pyiron.atomistics.job.atomistic.AtomisticGenericJob method)
(pyiron.atomistics.job.interactivewrapper.InteractiveWrapper method)
(pyiron.base.job.generic.GenericJob method)
(pyiron.base.job.script.ScriptJob method)
(pyiron.base.master.list.ListMaster method)
(pyiron.base.master.parallel.ParallelMaster method)
(pyiron.base.master.serial.SerialMasterBase method)
(pyiron.interactive.scipy_minimizer.ScipyMinimizer method)
(pyiron.interactive.sxextoptint.SxExtOptInteractive method)
(pyiron.lammps.base.LammpsBase method)
(pyiron.sphinx.base.SphinxBase method)
(pyiron.testing.randomatomistic.AtomisticExampleJob method)
(pyiron.testing.randomatomistic.ExampleJob method)
(pyiron.thermodynamics.sxphonons.SxHarmPotTst method)
(pyiron.thermodynamics.sxphonons.SxUniqDispl method)
(pyiron.vasp.base.VaspBase method)
set_item() (pyiron.base.pyio.parser.LogTag method)
set_job_status() (in module pyiron.base.database.jobtable)
(pyiron.base.database.filetable.FileTable method)
(pyiron.base.project.generic.Project method)
set_kmesh_by_density() (pyiron.vasp.base.Kpoints method)
set_kpoints() (in module pyiron.atomistics.job.atomistic)
(pyiron.atomistics.job.atomistic.AtomisticGenericJob method)
(pyiron.dft.job.generic.GenericDFTJob method)
(pyiron.dft.master.murnaghan_dft.MurnaghanDFT method)
(pyiron.gpaw.gpaw.GpawJob method)
set_kpoints_file() (pyiron.vasp.base.Kpoints method)
set_logging_level() (in module pyiron.base.settings.logger)
(pyiron.base.project.generic.Project static method)
set_mixing_parameters() (pyiron.dft.job.generic.GenericDFTJob method)
(pyiron.sphinx.base.SphinxBase method)
(pyiron.vasp.base.VaspBase method)
set_momenta() (pyiron.gpaw.pyiron_ase.AseAdapter method)
set_mtd() (pyiron.yaff.yaff.Yaff method)
set_occupancy_smearing() (pyiron.sphinx.base.SphinxBase method)
(pyiron.vasp.base.VaspBase method)
set_parameter() (pyiron.sphinx.base.Group method)
set_pbc() (pyiron.atomistics.structure.atoms.Atoms method)
set_positions() (pyiron.atomistics.job.interactive.InteractiveInterface method)
(pyiron.atomistics.structure.atoms.Atoms method)
(pyiron.gpaw.pyiron_ase.AseAdapter method)
set_potential() (pyiron.lammps.base.LammpsBase method)
set_pressure() (pyiron.atomistics.job.interactive.InteractiveInterface method)
set_primitive_constraint() (pyiron.vasp.metadyn.VaspMetadyn method)
set_reference_structure() (pyiron.thermodynamics.hessian.HessianJob method)
set_relative() (pyiron.atomistics.structure.atoms.Atoms method)
set_repeat() (pyiron.atomistics.structure.atoms.Atoms method)
set_rwigs() (pyiron.vasp.base.VaspBase method)
set_scaled_positions() (pyiron.atomistics.structure.atoms.Atoms method)
set_server() (in module pyiron.thermodynamics.interfacemethod)
set_species() (pyiron.atomistics.structure.atoms.Atoms method)
set_spin_constraint() (pyiron.vasp.base.VaspBase method)
set_structure() (in module pyiron.atomistics.job.atomistic)
set_temperature() (pyiron.atomistics.job.interactive.InteractiveInterface method)
set_temperatures() (pyiron.atomistics.thermodynamics.thermo_bulk.ThermoBulk method)
set_us() (pyiron.yaff.yaff.Yaff method)
set_value() (pyiron.base.generic.parameters.GenericParameters method)
set_vdw() (pyiron.quickff.quickff.QuickFF method)
set_velocities() (pyiron.gpaw.pyiron_ase.AseAdapter method)
set_volumes() (pyiron.atomistics.thermodynamics.thermo_bulk.ThermoBulk method)
Settings (class in pyiron.base.settings.generic)
setup_liquid_job() (in module pyiron.thermodynamics.interfacemethod)
setup_logger() (in module pyiron.base.settings.logger)
(pyiron.base.job.wrapper.JobWrapper static method)
shells() (pyiron.atomistics.structure.atoms.Neighbors property)
show() (pyiron.base.master.serial.SerialMasterBase method)
show_hdf() (pyiron.base.generic.hdfio.FileHDFio method)
(pyiron.base.job.core.JobCore method)
(pyiron.base.master.parallel.ParallelMaster method)
signal_intercept() (pyiron.base.job.generic.GenericJob method)
simulation_cell() (pyiron.lammps.structure.LammpsStructure method)
Singleton (class in pyiron.base.database.filetable)
(class in pyiron.base.job.jobtype)
(class in pyiron.base.settings.generic)
sorted_indices() (pyiron.vasp.base.VaspBase property)
sparse_index() (in module pyiron.atomistics.structure.sparse_list)
SparseArray (class in pyiron.atomistics.structure.sparse_list)
SparseArrayElement (class in pyiron.atomistics.structure.sparse_list)
SparseList (class in pyiron.atomistics.structure.sparse_list)
SparseListElement (class in pyiron.atomistics.structure.sparse_list)
species() (pyiron.atomistics.structure.atoms.Atoms property)
species_from_hdf() (pyiron.atomistics.job.interactive.GenericInteractive method)
spherical_average_potential() (pyiron.atomistics.volumetric.generic.VolumetricData method)
Sphinx (class in pyiron.sphinx.sphinx)
SphinxBase (class in pyiron.sphinx.base)
SphinxInt2 (class in pyiron.sphinx.interactive)
SphinxInteractive (class in pyiron.sphinx.interactive)
SphinxJTHPotentialFile (class in pyiron.sphinx.potential)
SphinxOutput (class in pyiron.sphinx.interactive)
SphinxVolumetricData (class in pyiron.sphinx.volumetric_data)
spin_constraints() (pyiron.dft.job.generic.GenericDFTJob property)
(pyiron.vasp.base.VaspBase property)
splitter() (pyiron.sphinx.base.Output static method)
sql_query() (pyiron.base.generic.hdfio.ProjectHDFio property)
start_job() (pyiron.base.master.serial.SerialMasterBase property)
static_isinstance() (in module pyiron.base.generic.util)
STATUS (pyiron.base.master.submissionstatus.SubmissionStatus attribute)
status() (pyiron.base.job.core.JobCore property)
steps() (pyiron.atomistics.job.atomistic.GenericOutput property)
(pyiron.atomistics.job.interactive.GenericInteractiveOutput property)
(pyiron.atomistics.job.interactivewrapper.ReferenceJobOutput property)
stop_calculation() (pyiron.vasp.base.VaspBase method)
store_custom_output_dict() (pyiron.base.job.external.Notebook static method)
store_structure() (pyiron.atomistics.job.atomistic.AtomisticGenericJob method)
str_to_value() (pyiron.table.datamining.PyironTable static method)
strain_circle() (in module pyiron.thermodynamics.interfacemethod)
string() (pyiron.base.job.jobstatus.JobStatus property)
(pyiron.base.master.submissionstatus.SubmissionStatus property)
string2symbols() (in module pyiron.atomistics.structure.atoms)
string2vector() (in module pyiron.atomistics.structure.atoms)
structure() (pyiron.atomistics.job.atomistic.AtomisticGenericJob property)
(pyiron.atomistics.job.interactive.GenericInteractive property)
(pyiron.atomistics.job.interactivewrapper.InteractiveWrapper property)
(pyiron.atomistics.job.structurecontainer.StructureContainer property)
(pyiron.atomistics.master.parallel.AtomisticParallelMaster property)
(pyiron.atomistics.master.serial.SerialMaster property)
(pyiron.dft.waves.bandstructure.Bandstructure property)
(pyiron.dft.waves.electronic.ElectronicStructure property)
(pyiron.gpaw.gpaw.GpawJob property)
(pyiron.gpaw.pyiron_ase.AseJob property)
(pyiron.lammps.interactive.LammpsInteractive property)
(pyiron.lammps.structure.LammpsStructure property)
(pyiron.sphinx.interactive.SphinxInteractive property)
(pyiron.testing.randomatomistic.AtomisticExampleJob property)
(pyiron.vasp.base.Output property)
(pyiron.vasp.base.VaspBase property)
(pyiron.vasp.interactive.VaspInteractive property)
structure_atomic() (pyiron.lammps.structure.LammpsStructure method)
structure_bond() (pyiron.lammps.structure.LammpsStructure method)
structure_charge() (pyiron.lammps.structure.LammpsStructure method)
structure_full() (pyiron.lammps.structure.LammpsStructure method)
structure_id() (pyiron.base.server.generic.Server property)
structure_lst() (pyiron.atomistics.master.structure.StructureListMaster property)
StructureContainer (class in pyiron.atomistics.job.structurecontainer)
StructureJobGenerator (class in pyiron.atomistics.master.structure)
StructureListMaster (class in pyiron.atomistics.master.structure)
SubmissionStatus (class in pyiron.base.master.submissionstatus)
submit_next() (pyiron.base.master.submissionstatus.SubmissionStatus method)
submitted() (pyiron.base.master.submissionstatus.SubmissionStatus property)
submitted_jobs() (pyiron.base.master.submissionstatus.SubmissionStatus property)
suspend() (pyiron.base.job.generic.GenericJob method)
switch_to_central_database() (pyiron.base.project.generic.Project method)
(pyiron.base.settings.generic.Settings method)
switch_to_local_database() (pyiron.base.project.generic.Project method)
(pyiron.base.settings.generic.Settings method)
switch_to_user_mode() (pyiron.base.project.generic.Project method)
(pyiron.base.settings.generic.Settings method)
switch_to_viewer_mode() (pyiron.base.project.generic.Project method)
(pyiron.base.settings.generic.Settings method)
SxDynMat (class in pyiron.thermodynamics.sxphonons)
SxExtOpt (class in pyiron.interactive.sxextoptint)
SxExtOptInteractive (class in pyiron.interactive.sxextoptint)
SxExtOptOutput (class in pyiron.interactive.sxextoptint)
SxHarmPotTst (class in pyiron.thermodynamics.sxphonons)
SxPhonons (class in pyiron.thermodynamics.sxphonons)
SxPhononsJobGenerator (class in pyiron.thermodynamics.sxphonons)
SxUniqDispl (class in pyiron.thermodynamics.sxphonons)
symbol() (pyiron.atomistics.structure.atom.Atom property)
symbols2numbers() (in module pyiron.atomistics.structure.atoms)
symmetrize_vectors() (pyiron.atomistics.structure.atoms.Atoms method)
T
table_name() (pyiron.base.generic.parameters.GenericParameters property)
TableJob (class in pyiron.table.datamining)
tag_dict() (pyiron.base.pyio.parser.LogTag property)
tag_first_word() (pyiron.base.pyio.parser.LogTag property)
tag_name() (pyiron.base.pyio.parser.LogTag property)
tags() (pyiron.atomistics.structure.periodic_table.ChemicalElement property)
temperature() (pyiron.atomistics.job.atomistic.GenericOutput property)
(pyiron.atomistics.job.interactive.GenericInteractiveOutput property)
temperatures() (pyiron.atomistics.job.interactivewrapper.ReferenceJobOutput property)
(pyiron.atomistics.thermodynamics.thermo_bulk.ThermoBulk property)
TemplateJob (class in pyiron.base.job.template)
test_split() (pyiron.base.pyio.parser.LogTag method)
ThermoBulk (class in pyiron.atomistics.thermodynamics.thermo_bulk)
threads() (pyiron.base.server.generic.Server property)
time() (pyiron.atomistics.job.interactive.GenericInteractiveOutput property)
(pyiron.atomistics.job.interactivewrapper.ReferenceJobOutput property)
time_created() (pyiron.base.project.store.ProjectStore property)
time_modified() (pyiron.base.project.store.ProjectStore property)
to_amat() (in module pyiron.lammps.base)
to_builtin() (pyiron.base.generic.inputlist.InputList method)
to_dict() (pyiron.vasp.potential.VaspPotentialSetter method)
to_hdf() (pyiron.atomistics.job.atomistic.AtomisticGenericJob method)
(pyiron.atomistics.job.interactivewrapper.InteractiveWrapper method)
(pyiron.atomistics.job.structurecontainer.StructureContainer method)
(pyiron.atomistics.master.parallel.MapMaster method)
(pyiron.atomistics.master.structure.StructureListMaster method)
(pyiron.atomistics.structure.atoms.Atoms method)
(pyiron.atomistics.structure.periodic_table.ChemicalElement method)
(pyiron.atomistics.structure.sparse_list.SparseList method)
(pyiron.atomistics.volumetric.generic.VolumetricData method)
(pyiron.base.generic.inputlist.InputList method)
(pyiron.base.generic.parameters.GenericParameters method)
(pyiron.base.generic.template.PyironObject method)
(pyiron.base.job.core.JobCore method)
(pyiron.base.job.generic.GenericJob method)
(pyiron.base.job.interactive.InteractiveBase method)
(pyiron.base.job.script.ScriptJob method)
(pyiron.base.job.template.TemplateJob method)
(pyiron.base.master.flexible.FlexibleMaster method)
(pyiron.base.master.generic.GenericMaster method)
(pyiron.base.master.parallel.ParallelMaster method)
(pyiron.base.master.serial.SerialMasterBase method)
(pyiron.base.pyio.parser.Logstatus method)
(pyiron.base.server.generic.Server method)
(pyiron.dft.waves.bandstructure.Bandstructure method)
(pyiron.dft.waves.electronic.ElectronicStructure method)
(pyiron.gaussian.gaussian.Gaussian method)
(pyiron.gpaw.gpaw.GpawJob method)
(pyiron.gpaw.pyiron_ase.AseJob method)
(pyiron.interactive.scipy_minimizer.ScipyMinimizer method)
(pyiron.interactive.scipy_minimizer.ScipyMinimizerOutput method)
(pyiron.lammps.base.Input method)
(pyiron.lammps.base.LammpsBase method)
(pyiron.lammps.potential.LammpsPotential method)
(pyiron.quickff.quickff.QuickFF method)
(pyiron.sphinx.base.Output method)
(pyiron.sphinx.base.SphinxBase method)
(pyiron.sphinx.volumetric_data.SphinxVolumetricData method)
(pyiron.table.datamining.PyironTable method)
(pyiron.table.datamining.TableJob method)
(pyiron.testing.randomatomistic.AtomisticExampleJob method)
(pyiron.testing.randomatomistic.ExampleJob method)
(pyiron.thermodynamics.hessian.HessianJob method)
(pyiron.thermodynamics.sxphonons.SxHarmPotTst method)
(pyiron.thermodynamics.sxphonons.SxUniqDispl method)
(pyiron.vasp.base.DFTOutput method)
(pyiron.vasp.base.GenericOutput method)
(pyiron.vasp.base.Input method)
(pyiron.vasp.base.Kpoints method)
(pyiron.vasp.base.Output method)
(pyiron.vasp.base.VaspBase method)
(pyiron.vasp.interactive.DFTOutput method)
(pyiron.vasp.interactive.GenericOutput method)
(pyiron.vasp.metadyn.MetadynInput method)
(pyiron.vasp.metadyn.MetadynOutput method)
(pyiron.vasp.metadyn.VaspMetadyn method)
(pyiron.vasp.outcar.Outcar method)
(pyiron.vasp.volumetric_data.VaspVolumetricData method)
(pyiron.yaff.yaff.Yaff method)
to_hdf_minimal() (pyiron.vasp.outcar.Outcar method)
to_hdf_old() (pyiron.dft.waves.electronic.ElectronicStructure method)
to_lut() (pyiron.atomistics.structure.periodic_table.ElementColorDictionary method)
to_object() (pyiron.base.generic.hdfio.ProjectHDFio method)
(pyiron.base.job.core.JobCore method)
to_sphinx() (pyiron.sphinx.base.Group method)
top_path() (pyiron.base.settings.generic.Settings method)
total_data (pyiron.atomistics.volumetric.generic.VolumetricData attribute)
total_data() (pyiron.atomistics.volumetric.generic.VolumetricData property)
(pyiron.sphinx.volumetric_data.SphinxVolumetricData property)
(pyiron.vasp.volumetric_data.VaspVolumetricData property)
total_displacements() (pyiron.atomistics.job.atomistic.GenericOutput property)
total_jobs() (pyiron.base.master.submissionstatus.SubmissionStatus property)
total_lst_of_keys() (pyiron.table.datamining.PyironTable static method)
Trajectory (class in pyiron.atomistics.job.atomistic)
trajectory() (pyiron.atomistics.job.atomistic.AtomisticGenericJob method)
transfer_from_remote() (pyiron.base.job.generic.GenericJob method)
translate() (pyiron.atomistics.structure.atoms.Atoms method)
(pyiron.base.pyio.parser.LogTag method)
translate_to_pylab (pyiron.dft.waves.bandstructure.Bandstructure attribute)
U
unfold_cell() (pyiron.lammps.structure.UnfoldingPrism method)
UnfoldingPrism (class in pyiron.lammps.structure)
unwrapped_positions() (pyiron.atomistics.job.atomistic.GenericOutput property)
(pyiron.atomistics.job.interactive.GenericInteractiveOutput property)
(pyiron.atomistics.job.interactivewrapper.ReferenceJobOutput property)
update() (pyiron.base.database.filetable.FileTable method)
(pyiron.base.generic.inputlist.InputList method)
update_master() (pyiron.base.job.generic.GenericJob method)
update_potential() (pyiron.lammps.interactive.LammpsInteractive method)
update_table() (pyiron.table.datamining.TableJob method)
user() (pyiron.base.generic.hdfio.ProjectHDFio property)
V
val_only() (pyiron.base.generic.parameters.GenericParameters property)
validate_convergence() (in module pyiron.thermodynamics.interfacemethod)
validate_ready_to_run() (pyiron.atomistics.job.atomistic.AtomisticGenericJob method)
(pyiron.atomistics.job.interactivewrapper.InteractiveWrapper method)
(pyiron.base.job.generic.GenericJob method)
(pyiron.base.job.interactive.InteractiveBase method)
(pyiron.base.master.flexible.FlexibleMaster method)
(pyiron.base.master.generic.GenericMaster method)
(pyiron.lammps.base.LammpsBase method)
(pyiron.sphinx.base.SphinxBase method)
(pyiron.table.datamining.TableJob method)
(pyiron.thermodynamics.sxphonons.SxHarmPotTst method)
(pyiron.vasp.base.VaspBase method)
(pyiron.vasp.interactive.VaspInteractive method)
value() (pyiron.dft.waves.electronic.Kpoint property)
values() (pyiron.atomistics.structure.sparse_list.SparseList method)
(pyiron.base.generic.hdfio.FileHDFio method)
(pyiron.base.job.path.JobPathBase method)
(pyiron.base.project.generic.Project method)
(pyiron.base.project.store.ProjectStore property)
Vasp (class in pyiron.vasp.vasp)
vasp_sorter() (in module pyiron.vasp.structure)
VaspBase (class in pyiron.vasp.base)
VaspCollectError
VaspInteractive (class in pyiron.vasp.interactive)
VaspMetadyn (class in pyiron.vasp.metadyn)
VaspPotential (class in pyiron.vasp.potential)
VaspPotentialAbstract (class in pyiron.vasp.potential)
VaspPotentialFile (class in pyiron.vasp.potential)
VaspPotentialSetter (class in pyiron.vasp.potential)
Vasprun (class in pyiron.vasp.vasprun)
vasprun_dict (pyiron.vasp.vasprun.Vasprun attribute)
VasprunError
VaspSol (class in pyiron.vasp.vaspsol)
VaspVolumetricData (class in pyiron.vasp.volumetric_data)
vbm() (pyiron.dft.waves.electronic.ElectronicStructure property)
vecs() (pyiron.atomistics.structure.atoms.Neighbors property)
vector_to_str() (pyiron.thermodynamics.sxphonons.SxDynMat static method)
version() (pyiron.base.job.executable.Executable property)
(pyiron.base.job.generic.GenericJob property)
view_mode() (pyiron.base.project.generic.Project property)
view_potentials() (pyiron.lammps.base.LammpsBase method)
view_queues() (pyiron.base.server.generic.Server static method)
view_structure() (pyiron.atomistics.job.atomistic.AtomisticGenericJob method)
viewer_mode() (pyiron.base.database.generic.DatabaseAccess property)
vinet_energy() (in module pyiron.atomistics.master.murnaghan)
(pyiron.atomistics.master.murnaghan.EnergyVolumeFit static method)
visualize_MO() (pyiron.gaussian.gaussian.Gaussian method)
volume() (pyiron.atomistics.job.atomistic.GenericOutput property)
(pyiron.atomistics.job.interactive.GenericInteractiveOutput property)
(pyiron.atomistics.job.interactivewrapper.ReferenceJobOutput property)
(pyiron.atomistics.master.murnaghan.DebyeModel property)
volume_lst() (pyiron.atomistics.master.murnaghan.EnergyVolumeFit property)
volumes() (pyiron.atomistics.thermodynamics.thermo_bulk.ThermoBulk property)
VolumetricData (class in pyiron.atomistics.volumetric.generic)
W
wait_for_job() (in module pyiron.base.server.queuestatus)
(pyiron.base.project.generic.Project static method)
walk() (pyiron.base.project.path.ProjectPath method)
weight() (pyiron.dft.waves.electronic.Kpoint property)
working_directory() (pyiron.base.generic.hdfio.ProjectHDFio property)
(pyiron.base.job.core.JobCore property)
(pyiron.base.job.generic.GenericJob property)
wrap() (pyiron.atomistics.structure.atoms.Atoms method)
write() (pyiron.atomistics.structure.atoms.Atoms method)
(pyiron.vasp.base.Input method)
(pyiron.vasp.metadyn.MetadynInput method)
write_charge_density() (pyiron.vasp.base.VaspBase property)
write_chk() (in module pyiron.quickff.quickff)
(in module pyiron.yaff.yaff)
write_config() (in module pyiron.quickff.quickff)
write_constraints() (pyiron.vasp.metadyn.VaspMetadyn method)
write_cube_file() (pyiron.atomistics.volumetric.generic.VolumetricData method)
write_electrostatic_potential() (pyiron.vasp.base.VaspBase property)
write_file() (pyiron.base.generic.parameters.GenericParameters method)
(pyiron.vasp.potential.Potcar method)
write_harmpot() (pyiron.thermodynamics.sxphonons.SxHarmPotTst method)
write_input() (in module pyiron.gaussian.gaussian)
(pyiron.base.job.generic.GenericJob method)
(pyiron.base.job.script.ScriptJob method)
(pyiron.base.master.flexible.FlexibleMaster method)
(pyiron.base.master.generic.GenericMaster method)
(pyiron.base.master.list.ListMaster method)
(pyiron.base.master.parallel.ParallelMaster method)
(pyiron.base.master.serial.SerialMasterBase method)
(pyiron.base.project.store.ProjectStore method)
(pyiron.dft.master.convergence_kpoint_parallel.ConvKpointParallel method)
(pyiron.gaussian.gaussian.Gaussian method)
(pyiron.gpaw.gpaw.GpawJob method)
(pyiron.interactive.scipy_minimizer.ScipyMinimizer method)
(pyiron.interactive.sxextoptint.SxExtOptInteractive method)
(pyiron.lammps.base.LammpsBase method)
(pyiron.quickff.quickff.QuickFF method)
(pyiron.sphinx.base.SphinxBase method)
(pyiron.table.datamining.TableJob method)
(pyiron.testing.randomatomistic.ExampleJob method)
(pyiron.thermodynamics.sxphonons.SxDynMat method)
(pyiron.thermodynamics.sxphonons.SxHarmPotTst method)
(pyiron.thermodynamics.sxphonons.SxUniqDispl method)
(pyiron.vasp.base.VaspBase method)
(pyiron.vasp.metadyn.VaspMetadyn method)
(pyiron.yaff.yaff.Yaff method)
write_lammps_datafile() (in module pyiron.lammps.structure)
write_magmoms() (pyiron.vasp.base.VaspBase method)
write_pars() (in module pyiron.quickff.quickff)
(in module pyiron.yaff.yaff)
write_plumed_enhanced() (in module pyiron.yaff.yaff)
write_poscar() (in module pyiron.vasp.structure)
write_resolved_dos() (pyiron.vasp.base.VaspBase property)
write_restart() (pyiron.testing.executable.ExampleExecutable method)
write_restart_file() (pyiron.lammps.base.LammpsBase method)
write_spin_constraints() (pyiron.sphinx.base.InputWriter method)
write_structure() (pyiron.thermodynamics.sxphonons.SxHarmPotTst method)
(pyiron.thermodynamics.sxphonons.SxUniqDispl method)
write_sxdynmat() (pyiron.thermodynamics.sxphonons.SxDynMat method)
write_traj() (pyiron.atomistics.job.atomistic.AtomisticGenericJob method)
write_vasp_volumetric() (pyiron.atomistics.volumetric.generic.VolumetricData method)
write_wave_funct() (pyiron.vasp.base.VaspBase property)
write_yhess() (in module pyiron.yaff.yaff)
write_ynpt() (in module pyiron.yaff.yaff)
write_ynve() (in module pyiron.yaff.yaff)
write_ynvt() (in module pyiron.yaff.yaff)
write_yopt() (in module pyiron.yaff.yaff)
write_yopt_cell() (in module pyiron.yaff.yaff)
write_ysp() (in module pyiron.yaff.yaff)
X
x() (pyiron.atomistics.structure.atom.Atom property)
xc() (pyiron.dft.job.generic.GenericDFTJob property)
xyzproperty() (in module pyiron.atomistics.structure.atom)
Y
y() (pyiron.atomistics.structure.atom.Atom property)
Yaff (class in pyiron.yaff.yaff)
YaffInput (class in pyiron.yaff.yaff)
Z
z() (pyiron.atomistics.structure.atom.Atom property)
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v: pyiron-0.2.17
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