Index

A

a0 (irradiapy.analysis.defectsidentifier.DefectsIdentifier attribute) AnalysisDB (class in irradiapy.analysis.analysisdb) ap_rm_file() (in module irradiapy.utils.mpi) append_output() (irradiapy.srim.srimdb.SRIMDB method) apply_boundary_conditions() (in module irradiapy.utils.math) apply_boundary_conditions_to_lammps() (in module irradiapy.utils.io) ARC (irradiapy.enums.DisplacementMode attribute) args (irradiapy.lammps.commands.atom_style.AtomStyle attribute) (irradiapy.lammps.commands.compute.Compute attribute) (irradiapy.lammps.commands.create_atoms.CreateAtoms attribute) (irradiapy.lammps.commands.create_box.CreateBox attribute) (irradiapy.lammps.commands.fix.Fix attribute) (irradiapy.lammps.commands.group.Group attribute) (irradiapy.lammps.commands.pair_coeff.PairCoeff attribute) (irradiapy.lammps.commands.pair_style.PairStyle attribute) (irradiapy.lammps.commands.region.Region attribute) (irradiapy.lammps.commands.thermo_style.ThermoStyle attribute) (irradiapy.lammps.commands.timer.Timer attribute) (irradiapy.lammps.commands.variable.Variable attribute) (irradiapy.lammps.commands.velocity.Velocity attribute)

atom_to_object() (in module irradiapy.analysis.clusters) atomic_density (irradiapy.materials.component.Component attribute) atomic_number (irradiapy.materials.element.Element attribute) atomic_symbols (irradiapy.lammps.cascadebase.CascadeBase attribute) atomic_weight (irradiapy.materials.element.Element attribute) AtomModify (class in irradiapy.lammps.commands.atom_modify) AtomStyle (class in irradiapy.lammps.commands.atom_style) attributes (irradiapy.lammps.commands.dump.Dump attribute) autosave (irradiapy.spectrapka.spectra2srim.Spectra2SRIM attribute) (irradiapy.srim.py2srim.Py2SRIM attribute) (irradiapy.srim.srimdb.SRIMDB attribute) ax (irradiapy.materials.component.Component attribute) ay (irradiapy.materials.component.Component attribute) az (irradiapy.materials.component.Component attribute)

B

b_arc (irradiapy.materials.component.Component attribute) (irradiapy.materials.element.Element attribute) Backscat (class in irradiapy.srim.backscat) backscat (irradiapy.srim.srimdb.SRIMDB attribute) Boundary (class in irradiapy.lammps.commands.boundary) bragg (irradiapy.spectrapka.spectra2srim.Spectra2SRIM attribute) (irradiapy.srim.py2srim.Py2SRIM attribute) (irradiapy.srim.srimdb.SRIMDB attribute)

broadcast_variables() (in module irradiapy.utils.mpi) BZIP2LAMMPSReader (class in irradiapy.io) (class in irradiapy.io.bzip2lammpsreader) BZIP2LAMMPSReaderMPI (class in irradiapy.io) (class in irradiapy.io.bzip2lammpsreadermpi) BZIP2LAMMPSWriter (class in irradiapy.io) (class in irradiapy.io.bzip2lammpswriter) BZIP2LAMMPSWriterMPI (class in irradiapy.io) (class in irradiapy.io.bzip2lammpswritermpi)

C

c (irradiapy.materials.component.Component attribute) c_arc (irradiapy.materials.component.Component attribute) (irradiapy.materials.element.Element attribute) calculate_energies (irradiapy.materials.component.Component attribute) calculation (irradiapy.srim.py2srim.Py2SRIM attribute) (irradiapy.srim.srimdb.SRIMDB attribute) Cascade (class in irradiapy.lammps.cascade) CascadeBase (class in irradiapy.lammps.cascadebase) check_interval (irradiapy.spectrapka.spectra2srim.Spectra2SRIM attribute) (irradiapy.srim.py2srim.Py2SRIM attribute) clear_debris_database() (in module irradiapy.config) clear_srim_dir() (in module irradiapy.config) close() (irradiapy.io.BZIP2LAMMPSReader method) (irradiapy.io.bzip2lammpsreader.BZIP2LAMMPSReader method) (irradiapy.io.BZIP2LAMMPSReaderMPI method) (irradiapy.io.bzip2lammpsreadermpi.BZIP2LAMMPSReaderMPI method) (irradiapy.io.BZIP2LAMMPSWriter method) (irradiapy.io.bzip2lammpswriter.BZIP2LAMMPSWriter method) (irradiapy.io.BZIP2LAMMPSWriterMPI method) (irradiapy.io.bzip2lammpswritermpi.BZIP2LAMMPSWriterMPI method) (irradiapy.io.LAMMPSReader method) (irradiapy.io.lammpsreader.LAMMPSReader method) (irradiapy.io.LAMMPSReaderMPI method) (irradiapy.io.lammpsreadermpi.LAMMPSReaderMPI method) (irradiapy.io.LAMMPSWriter method) (irradiapy.io.lammpswriter.LAMMPSWriter method) (irradiapy.io.LAMMPSWriterMPI method) (irradiapy.io.lammpswritermpi.LAMMPSWriterMPI method) (irradiapy.io.XYZWriter method) (irradiapy.io.xyzwriter.XYZWriter method) cluster_size_scaling_law() (in module irradiapy.analysis.clusters) cluster_size_scaling_law_plot() (in module irradiapy.analysis.clusters) cluster_sizes_plot() (irradiapy.analysis.debrismanager.DebrisManager method) clusterize_atoms() (in module irradiapy.analysis.clusters) clusterize_file() (in module irradiapy.analysis.clusters) cmds_cascade (irradiapy.lammps.cascadebase.CascadeBase attribute) cmds_ions_grouping (irradiapy.lammps.cascade.Cascade attribute) cmds_preamble (irradiapy.lammps.cascadebase.CascadeBase attribute) cmds_rerun (irradiapy.lammps.cascadebase.CascadeBase attribute) cmds_therma (irradiapy.lammps.cascadebase.CascadeBase attribute) CMonitorBorders (class in irradiapy.lammps.commands.cmonitor_borders) collection (irradiapy.lammps.commands.cmonitor_borders.CMonitorBorders attribute) (irradiapy.lammps.commands.crdf.CRDF attribute) (irradiapy.lammps.commands.cruntime.CRunTime attribute) Collision (class in irradiapy.srim.collision) collision (irradiapy.srim.srimdb.SRIMDB attribute) comm (irradiapy.io.BZIP2LAMMPSReaderMPI attribute) (irradiapy.io.bzip2lammpsreadermpi.BZIP2LAMMPSReaderMPI attribute) (irradiapy.io.BZIP2LAMMPSWriterMPI attribute) (irradiapy.io.bzip2lammpswritermpi.BZIP2LAMMPSWriterMPI attribute) (irradiapy.io.LAMMPSReaderMPI attribute) (irradiapy.io.lammpsreadermpi.LAMMPSReaderMPI attribute) (irradiapy.io.LAMMPSWriterMPI attribute) (irradiapy.io.lammpswritermpi.LAMMPSWriterMPI attribute) (irradiapy.lammps.cascadebase.CascadeBase attribute) Command (class in irradiapy.lammps.commands.command) command() (irradiapy.lammps.commands.atom_modify.AtomModify method) (irradiapy.lammps.commands.atom_style.AtomStyle method) (irradiapy.lammps.commands.boundary.Boundary method) (irradiapy.lammps.commands.comm_modify.CommModify method) (irradiapy.lammps.commands.command.Command method) (irradiapy.lammps.commands.compute.Compute method) (irradiapy.lammps.commands.compute_modify.ComputeModify method) (irradiapy.lammps.commands.create_atoms.CreateAtoms method) (irradiapy.lammps.commands.create_box.CreateBox method) (irradiapy.lammps.commands.dump.Dump method) (irradiapy.lammps.commands.dump_modify.DumpModify method) (irradiapy.lammps.commands.echo.Echo method) (irradiapy.lammps.commands.fix.Fix method) (irradiapy.lammps.commands.fix_modify.FixModify method) (irradiapy.lammps.commands.group.Group method) (irradiapy.lammps.commands.lattice.Lattice method) (irradiapy.lammps.commands.log.Log method) (irradiapy.lammps.commands.pair_coeff.PairCoeff method) (irradiapy.lammps.commands.pair_style.PairStyle method) (irradiapy.lammps.commands.print.Print method) (irradiapy.lammps.commands.read_data.ReadData method) (irradiapy.lammps.commands.read_restart.ReadRestart method) (irradiapy.lammps.commands.region.Region method) (irradiapy.lammps.commands.reset_timestep.ResetTimestep method) (irradiapy.lammps.commands.run.Run method) (irradiapy.lammps.commands.thermo.Thermo method) (irradiapy.lammps.commands.thermo_modify.ThermoModify method) (irradiapy.lammps.commands.thermo_style.ThermoStyle method) (irradiapy.lammps.commands.timer.Timer method) (irradiapy.lammps.commands.uncompute.Uncompute method) (irradiapy.lammps.commands.undump.Undump method) (irradiapy.lammps.commands.unfix.Unfix method) (irradiapy.lammps.commands.units.Units method) (irradiapy.lammps.commands.variable.Variable method) (irradiapy.lammps.commands.velocity.Velocity method) (irradiapy.lammps.commands.write_data.WriteData method) (irradiapy.lammps.commands.write_dump.WriteDump method) (irradiapy.lammps.commands.write_restart.WriteRestart method)

commit() (irradiapy.srim.srimfile.SRIMFile method) CommModify (class in irradiapy.lammps.commands.comm_modify) Component (class in irradiapy.materials.component) component (irradiapy.analysis.debrismanager.DebrisManager attribute) compress_file_bz2() (in module irradiapy.utils.io) compresslevel (irradiapy.io.BZIP2LAMMPSWriter attribute) (irradiapy.io.bzip2lammpswriter.BZIP2LAMMPSWriter attribute) (irradiapy.io.BZIP2LAMMPSWriterMPI attribute) (irradiapy.io.bzip2lammpswritermpi.BZIP2LAMMPSWriterMPI attribute) Compute (class in irradiapy.lammps.commands.compute) compute (irradiapy.lammps.commands.cmonitor_borders.CMonitorBorders attribute) (irradiapy.lammps.commands.crdf.CRDF attribute) compute_damage_energy (irradiapy.analysis.debrismanager.DebrisManager attribute) compute_id (irradiapy.lammps.commands.cmonitor_borders.CMonitorBorders attribute) (irradiapy.lammps.commands.compute_modify.ComputeModify attribute) (irradiapy.lammps.commands.crdf.CRDF attribute) (irradiapy.lammps.commands.uncompute.Uncompute attribute) ComputeModify (class in irradiapy.lammps.commands.compute_modify) contributors (irradiapy.debris_database.DebrisDatabase attribute) (irradiapy.debris_dataset.DebrisDataset attribute) cp_file() (in module irradiapy.utils.mpi) CRDF (class in irradiapy.lammps.commands.crdf) create_tables() (irradiapy.recoilsdb.RecoilsDB method) CreateAtoms (class in irradiapy.lammps.commands.create_atoms) CreateBox (class in irradiapy.lammps.commands.create_box) CRunTime (class in irradiapy.lammps.commands.cruntime) cursor() (irradiapy.srim.srimfile.SRIMFile method) CustomEnum (class in irradiapy.enums)

D

damage_energy_mode (irradiapy.analysis.debrismanager.DebrisManager attribute) damage_energy_to_displacements() (irradiapy.materials.component.Component method) DamageEnergyMode (class in irradiapy.enums) data (irradiapy.io.LAMMPSLogReader attribute) (irradiapy.io.lammpslogreader.LAMMPSLogReader attribute) Database (class in irradiapy.database) datasets (irradiapy.debris_database.DebrisDatabase attribute) debris_database (irradiapy.analysis.debrismanager.DebrisManager attribute) DebrisDatabase (class in irradiapy.debris_database) DebrisDataset (class in irradiapy.debris_dataset) DebrisManager (class in irradiapy.analysis.debrismanager) debug (irradiapy.analysis.defectsidentifier.DefectsIdentifier attribute) decompress_file_bz2() (in module irradiapy.utils.io) DefectsIdentifier (class in irradiapy.analysis.defectsidentifier) delete() (irradiapy.lammps.commands.compute.Compute method) (irradiapy.lammps.commands.dump.Dump method) (irradiapy.lammps.commands.fix.Fix method) (irradiapy.lammps.commands.group.Group method) (irradiapy.lammps.commands.variable.Variable method) delete_all_arrays() (in module irradiapy.utils.sqlite) delete_array() (in module irradiapy.utils.sqlite) density (irradiapy.materials.component.Component attribute) depth_cluster_sizes_plot() (in module irradiapy.analysis.clusters) depth_clustering_fraction_hist() (in module irradiapy.analysis.clusters) depth_clustering_fraction_hist_plot() (in module irradiapy.analysis.clusters) depth_dpa_hist() (in module irradiapy.analysis.dpa) depth_dpa_hist_plot() (in module irradiapy.analysis.dpa) depth_injected_ions_hist() (in module irradiapy.analysis.recoils) depth_injected_ions_hist_plot() (in module irradiapy.analysis.recoils)

depth_recoil_energy_hist_plot() (in module irradiapy.analysis.recoils) dir_parent (irradiapy.lammps.cascadebase.CascadeBase attribute) displacement_mode (irradiapy.analysis.debrismanager.DebrisManager attribute) DisplacementMode (class in irradiapy.enums) displacements_number_plot() (irradiapy.analysis.debrismanager.DebrisManager method) do_backscatt (irradiapy.spectrapka.spectra2srim.Spectra2SRIM attribute) (irradiapy.srim.py2srim.Py2SRIM attribute) (irradiapy.srim.srimdb.SRIMDB attribute) do_collisions (irradiapy.spectrapka.spectra2srim.Spectra2SRIM attribute) (irradiapy.srim.py2srim.Py2SRIM attribute) (irradiapy.srim.srimdb.SRIMDB attribute) do_ranges (irradiapy.spectrapka.spectra2srim.Spectra2SRIM attribute) (irradiapy.srim.py2srim.Py2SRIM attribute) (irradiapy.srim.srimdb.SRIMDB attribute) do_sputtered (irradiapy.spectrapka.spectra2srim.Spectra2SRIM attribute) (irradiapy.srim.py2srim.Py2SRIM attribute) (irradiapy.srim.srimdb.SRIMDB attribute) do_transmit (irradiapy.spectrapka.spectra2srim.Spectra2SRIM attribute) (irradiapy.srim.py2srim.Py2SRIM attribute) (irradiapy.srim.srimdb.SRIMDB attribute) doi (irradiapy.debris_database.DebrisDatabase attribute) (irradiapy.debris_dataset.DebrisDataset attribute) dpa() (in module irradiapy.analysis.dpa) dtype (irradiapy.io.XYZReader attribute) (irradiapy.io.xyzreader.XYZReader attribute) Dump (class in irradiapy.lammps.commands.dump) dump_args (irradiapy.lammps.commands.write_dump.WriteDump attribute) dump_id (irradiapy.lammps.commands.undump.Undump attribute) dump_modify_kw_vals (irradiapy.lammps.commands.write_dump.WriteDump attribute) DumpModify (class in irradiapy.lammps.commands.dump_modify)

E

E2Recoil (class in irradiapy.srim.e2recoil) e2recoil (irradiapy.srim.srimdb.SRIMDB attribute) Echo (class in irradiapy.lammps.commands.echo) ed_avr (irradiapy.materials.component.Component attribute) (irradiapy.materials.element.Element attribute) ed_min (irradiapy.materials.component.Component attribute) (irradiapy.materials.element.Element attribute) electronic_interactions (irradiapy.debris_database.DebrisDatabase attribute) (irradiapy.debris_dataset.DebrisDataset attribute) Element (class in irradiapy.materials.element) elements (irradiapy.materials.component.Component attribute) ENCODING (in module irradiapy.config) encoding (irradiapy.io.BZIP2LAMMPSReader attribute) (irradiapy.io.bzip2lammpsreader.BZIP2LAMMPSReader attribute) (irradiapy.io.BZIP2LAMMPSReaderMPI attribute) (irradiapy.io.bzip2lammpsreadermpi.BZIP2LAMMPSReaderMPI attribute) (irradiapy.io.BZIP2LAMMPSWriter attribute) (irradiapy.io.bzip2lammpswriter.BZIP2LAMMPSWriter attribute) (irradiapy.io.BZIP2LAMMPSWriterMPI attribute) (irradiapy.io.bzip2lammpswritermpi.BZIP2LAMMPSWriterMPI attribute) (irradiapy.io.LAMMPSReader attribute) (irradiapy.io.lammpsreader.LAMMPSReader attribute) (irradiapy.io.LAMMPSReaderMPI attribute) (irradiapy.io.lammpsreadermpi.LAMMPSReaderMPI attribute) (irradiapy.io.LAMMPSWriter attribute) (irradiapy.io.lammpswriter.LAMMPSWriter attribute) (irradiapy.io.LAMMPSWriterMPI attribute) (irradiapy.io.lammpswritermpi.LAMMPSWriterMPI attribute) (irradiapy.io.XYZReader attribute) (irradiapy.io.xyzreader.XYZReader attribute) (irradiapy.io.XYZWriter attribute) (irradiapy.io.xyzwriter.XYZWriter attribute)

energy_tolerance (irradiapy.analysis.debrismanager.DebrisManager attribute) EXCLUDED_ITEMS (in module irradiapy.config) excluded_items (irradiapy.io.BZIP2LAMMPSWriter attribute) (irradiapy.io.bzip2lammpswriter.BZIP2LAMMPSWriter attribute) (irradiapy.io.BZIP2LAMMPSWriterMPI attribute) (irradiapy.io.bzip2lammpswritermpi.BZIP2LAMMPSWriterMPI attribute) (irradiapy.io.LAMMPSWriter attribute) (irradiapy.io.lammpswriter.LAMMPSWriter attribute) (irradiapy.io.LAMMPSWriterMPI attribute) (irradiapy.io.lammpswritermpi.LAMMPSWriterMPI attribute) exec_cmds() (irradiapy.lammps.cascadebase.CascadeBase method) exyz (irradiapy.spectrapka.spectra2srim.Spectra2SRIM attribute) (irradiapy.srim.py2srim.Py2SRIM attribute) (irradiapy.srim.srimdb.SRIMDB attribute)

F

FERARC (irradiapy.enums.DisplacementMode attribute) file (irradiapy.io.XYZReader attribute) (irradiapy.io.xyzreader.XYZReader attribute) (irradiapy.io.XYZWriter attribute) (irradiapy.io.xyzwriter.XYZWriter attribute) (irradiapy.lammps.commands.dump.Dump attribute) (irradiapy.lammps.commands.log.Log attribute) (irradiapy.lammps.commands.read_data.ReadData attribute) (irradiapy.lammps.commands.read_restart.ReadRestart attribute) (irradiapy.lammps.commands.write_data.WriteData attribute) (irradiapy.lammps.commands.write_dump.WriteDump attribute) (irradiapy.lammps.commands.write_restart.WriteRestart attribute) file_path (irradiapy.io.BZIP2LAMMPSReader attribute) (irradiapy.io.bzip2lammpsreader.BZIP2LAMMPSReader attribute) (irradiapy.io.BZIP2LAMMPSReaderMPI attribute) (irradiapy.io.bzip2lammpsreadermpi.BZIP2LAMMPSReaderMPI attribute) (irradiapy.io.BZIP2LAMMPSWriter attribute) (irradiapy.io.bzip2lammpswriter.BZIP2LAMMPSWriter attribute) (irradiapy.io.BZIP2LAMMPSWriterMPI attribute) (irradiapy.io.bzip2lammpswritermpi.BZIP2LAMMPSWriterMPI attribute) (irradiapy.io.LAMMPSReader attribute) (irradiapy.io.lammpsreader.LAMMPSReader attribute) (irradiapy.io.LAMMPSReaderMPI attribute) (irradiapy.io.lammpsreadermpi.LAMMPSReaderMPI attribute) (irradiapy.io.LAMMPSWriter attribute) (irradiapy.io.lammpswriter.LAMMPSWriter attribute) (irradiapy.io.LAMMPSWriterMPI attribute) (irradiapy.io.lammpswritermpi.LAMMPSWriterMPI attribute) (irradiapy.io.XYZReader attribute) (irradiapy.io.xyzreader.XYZReader attribute) (irradiapy.io.XYZWriter attribute) (irradiapy.io.xyzwriter.XYZWriter attribute)

files_by_energy (irradiapy.debris_dataset.DebrisDataset attribute) finalize (irradiapy.lammps.cascadebase.CascadeBase attribute) fit_gaussian() (in module irradiapy.utils.math) fit_linear() (in module irradiapy.utils.math) fit_lorentzian() (in module irradiapy.utils.math) fit_offset_power_law() (in module irradiapy.utils.math) fit_power_law() (in module irradiapy.utils.math) Fix (class in irradiapy.lammps.commands.fix) fix (irradiapy.lammps.commands.cmonitor_borders.CMonitorBorders attribute) (irradiapy.lammps.commands.crdf.CRDF attribute) (irradiapy.lammps.commands.cruntime.CRunTime attribute) fix_id (irradiapy.lammps.commands.fix_modify.FixModify attribute) (irradiapy.lammps.commands.unfix.Unfix attribute) FixModify (class in irradiapy.lammps.commands.fix_modify) FLOAT_FORMAT (in module irradiapy.config) float_format (irradiapy.io.BZIP2LAMMPSWriter attribute) (irradiapy.io.bzip2lammpswriter.BZIP2LAMMPSWriter attribute) (irradiapy.io.BZIP2LAMMPSWriterMPI attribute) (irradiapy.io.bzip2lammpswritermpi.BZIP2LAMMPSWriterMPI attribute) (irradiapy.io.LAMMPSWriter attribute) (irradiapy.io.lammpswriter.LAMMPSWriter attribute) (irradiapy.io.LAMMPSWriterMPI attribute) (irradiapy.io.lammpswritermpi.LAMMPSWriterMPI attribute) (irradiapy.io.XYZWriter attribute) (irradiapy.io.xyzwriter.XYZWriter attribute) fp_dist (irradiapy.analysis.debrismanager.DebrisManager attribute) fp_energy_abs (irradiapy.analysis.debrismanager.DebrisManager attribute) from_int() (irradiapy.enums.CustomEnum class method)

G

GAS (irradiapy.enums.Phases attribute) gaussian() (in module irradiapy.utils.math) generate_debris() (in module irradiapy.analysis.debris) get_debris_database() (in module irradiapy.config) get_last_reader() (in module irradiapy.utils.io) get_natoms() (irradiapy.srim.sputter.Sputter method) get_nevents() (irradiapy.recoilsdb.RecoilsDB method) get_nions() (irradiapy.srim.backscat.Backscat method) (irradiapy.srim.srimdb.SRIMDB method) (irradiapy.srim.transmit.Transmit method) get_nrecoils() (irradiapy.recoilsdb.RecoilsDB method) get_pka_data() (irradiapy.io.LAMMPSLogReader method) (irradiapy.io.lammpslogreader.LAMMPSLogReader method)

get_pka_properties() (irradiapy.lammps.cascadebase.CascadeBase method) get_pkas_properties() (irradiapy.lammps.cascadebase.CascadeBase method) get_properties_from_group() (in module irradiapy.lammps.utils) get_recoil_debris() (irradiapy.analysis.debrismanager.DebrisManager method) get_simulation_dirs() (irradiapy.lammps.cascadebase.CascadeBase method) get_srim_dir() (in module irradiapy.config) get_tag() (irradiapy.utils.mpi.MPITagAllocator class method) Group (class in irradiapy.lammps.commands.group) group (irradiapy.lammps.commands.crdf.CRDF attribute) group_id (irradiapy.lammps.commands.compute.Compute attribute) (irradiapy.lammps.commands.dump.Dump attribute) (irradiapy.lammps.commands.fix.Fix attribute) (irradiapy.lammps.commands.velocity.Velocity attribute) (irradiapy.lammps.commands.write_dump.WriteDump attribute)

H

has_matches() (irradiapy.debris_database.DebrisDatabase method)

height (irradiapy.materials.component.Component attribute)

I

i (irradiapy.lammps.commands.pair_coeff.PairCoeff attribute) id (irradiapy.lammps.commands.compute.Compute attribute) (irradiapy.lammps.commands.dump.Dump attribute) (irradiapy.lammps.commands.dump_modify.DumpModify attribute) (irradiapy.lammps.commands.fix.Fix attribute) (irradiapy.lammps.commands.group.Group attribute) (irradiapy.lammps.commands.region.Region attribute) identify() (irradiapy.analysis.defectsidentifier.DefectsIdentifier method) identify_defects() (in module irradiapy.analysis.defects) identify_lammps_dump() (in module irradiapy.analysis.defects) insert_array() (in module irradiapy.utils.sqlite) insert_ion_vac() (irradiapy.recoilsdb.RecoilsDB method) insert_recoil() (irradiapy.recoilsdb.RecoilsDB method) INT_FORMAT (in module irradiapy.config) int_format (irradiapy.io.BZIP2LAMMPSWriter attribute) (irradiapy.io.bzip2lammpswriter.BZIP2LAMMPSWriter attribute) (irradiapy.io.BZIP2LAMMPSWriterMPI attribute) (irradiapy.io.bzip2lammpswritermpi.BZIP2LAMMPSWriterMPI attribute) (irradiapy.io.LAMMPSWriter attribute) (irradiapy.io.lammpswriter.LAMMPSWriter attribute) (irradiapy.io.LAMMPSWriterMPI attribute) (irradiapy.io.lammpswritermpi.LAMMPSWriterMPI attribute) (irradiapy.io.XYZWriter attribute) (irradiapy.io.xyzwriter.XYZWriter attribute) interatomic_potentials (irradiapy.debris_database.DebrisDatabase attribute) (irradiapy.debris_dataset.DebrisDataset attribute) ion_energy (irradiapy.lammps.cascade.Cascade attribute) Ioniz (class in irradiapy.srim.ioniz) ioniz (irradiapy.srim.srimdb.SRIMDB attribute) irradiapy module irradiapy.analysis module irradiapy.analysis.analysisdb module irradiapy.analysis.clusters module irradiapy.analysis.debris module irradiapy.analysis.debrismanager module irradiapy.analysis.defects module irradiapy.analysis.defectsidentifier module irradiapy.analysis.dpa module irradiapy.analysis.recoils module irradiapy.config module irradiapy.database module irradiapy.debris_database module irradiapy.debris_dataset module irradiapy.dtypes module irradiapy.enums module irradiapy.io module irradiapy.io.bzip2lammpsreader module irradiapy.io.bzip2lammpsreadermpi module irradiapy.io.bzip2lammpswriter module irradiapy.io.bzip2lammpswritermpi module irradiapy.io.lammpslogreader module irradiapy.io.lammpsreader module irradiapy.io.lammpsreadermpi module irradiapy.io.lammpswriter module irradiapy.io.lammpswritermpi module irradiapy.io.xyzreader module irradiapy.io.xyzwriter module irradiapy.lammps module irradiapy.lammps.cascade module irradiapy.lammps.cascadebase module irradiapy.lammps.commands module irradiapy.lammps.commands.atom_modify module irradiapy.lammps.commands.atom_style module irradiapy.lammps.commands.boundary module irradiapy.lammps.commands.cmonitor_borders module irradiapy.lammps.commands.comm_modify module irradiapy.lammps.commands.command module irradiapy.lammps.commands.compute module irradiapy.lammps.commands.compute_modify module irradiapy.lammps.commands.crdf module irradiapy.lammps.commands.create_atoms module irradiapy.lammps.commands.create_box module irradiapy.lammps.commands.cruntime module irradiapy.lammps.commands.dump module

irradiapy.lammps.commands.dump_modify module irradiapy.lammps.commands.echo module irradiapy.lammps.commands.fix module irradiapy.lammps.commands.fix_modify module irradiapy.lammps.commands.group module irradiapy.lammps.commands.lattice module irradiapy.lammps.commands.log module irradiapy.lammps.commands.mboost_ion module irradiapy.lammps.commands.pair_coeff module irradiapy.lammps.commands.pair_style module irradiapy.lammps.commands.print module irradiapy.lammps.commands.read_data module irradiapy.lammps.commands.read_restart module irradiapy.lammps.commands.region module irradiapy.lammps.commands.reset_timestep module irradiapy.lammps.commands.run module irradiapy.lammps.commands.thermo module irradiapy.lammps.commands.thermo_modify module irradiapy.lammps.commands.thermo_style module irradiapy.lammps.commands.timer module irradiapy.lammps.commands.uncompute module irradiapy.lammps.commands.undump module irradiapy.lammps.commands.unfix module irradiapy.lammps.commands.units module irradiapy.lammps.commands.variable module irradiapy.lammps.commands.velocity module irradiapy.lammps.commands.write_data module irradiapy.lammps.commands.write_dump module irradiapy.lammps.commands.write_restart module irradiapy.lammps.utils module irradiapy.materials module irradiapy.materials.component module irradiapy.materials.element module irradiapy.recoilsdb module irradiapy.spectrapka module irradiapy.spectrapka.matrices module irradiapy.spectrapka.spectra2srim module irradiapy.srim module irradiapy.srim.backscat module irradiapy.srim.collision module irradiapy.srim.e2recoil module irradiapy.srim.ioniz module irradiapy.srim.lateral module irradiapy.srim.novac module irradiapy.srim.phonon module irradiapy.srim.py2srim module irradiapy.srim.range module irradiapy.srim.range3d module irradiapy.srim.sputter module irradiapy.srim.srimdb module irradiapy.srim.srimfile module irradiapy.srim.transmit module irradiapy.srim.trimdat module irradiapy.srim.vacancy module irradiapy.utils module irradiapy.utils.io module irradiapy.utils.math module irradiapy.utils.mpi module irradiapy.utils.sqlite module

J

j (irradiapy.lammps.commands.pair_coeff.PairCoeff attribute)

K

kemax (irradiapy.lammps.commands.cmonitor_borders.CMonitorBorders attribute) keyword (irradiapy.lammps.commands.log.Log attribute) kw_vals (irradiapy.lammps.commands.atom_modify.AtomModify attribute) (irradiapy.lammps.commands.comm_modify.CommModify attribute) (irradiapy.lammps.commands.compute_modify.ComputeModify attribute) (irradiapy.lammps.commands.create_atoms.CreateAtoms attribute) (irradiapy.lammps.commands.create_box.CreateBox attribute) (irradiapy.lammps.commands.dump_modify.DumpModify attribute) (irradiapy.lammps.commands.fix.Fix attribute) (irradiapy.lammps.commands.fix_modify.FixModify attribute) (irradiapy.lammps.commands.group.Group attribute) (irradiapy.lammps.commands.lattice.Lattice attribute) (irradiapy.lammps.commands.print.Print attribute) (irradiapy.lammps.commands.read_data.ReadData attribute) (irradiapy.lammps.commands.region.Region attribute) (irradiapy.lammps.commands.reset_timestep.ResetTimestep attribute) (irradiapy.lammps.commands.run.Run attribute) (irradiapy.lammps.commands.thermo_modify.ThermoModify attribute) (irradiapy.lammps.commands.velocity.Velocity attribute) (irradiapy.lammps.commands.write_data.WriteData attribute) (irradiapy.lammps.commands.write_restart.WriteRestart attribute)

L

lammps_to_mmonca() (in module irradiapy.utils.io) LAMMPSLogReader (class in irradiapy.io) (class in irradiapy.io.lammpslogreader) LAMMPSReader (class in irradiapy.io) (class in irradiapy.io.lammpsreader) LAMMPSReaderMPI (class in irradiapy.io) (class in irradiapy.io.lammpsreadermpi) LAMMPSUnavailableError LAMMPSWriter (class in irradiapy.io) (class in irradiapy.io.lammpswriter) LAMMPSWriterMPI (class in irradiapy.io) (class in irradiapy.io.lammpswritermpi) Lateral (class in irradiapy.srim.lateral) lateral (irradiapy.srim.srimdb.SRIMDB attribute) Lattice (class in irradiapy.lammps.commands.lattice) lattice (irradiapy.analysis.defectsidentifier.DefectsIdentifier attribute) (irradiapy.debris_database.DebrisDatabase attribute) (irradiapy.debris_dataset.DebrisDataset attribute) (irradiapy.lammps.commands.crdf.CRDF attribute) length (irradiapy.materials.component.Component attribute) LINDHARD (irradiapy.enums.DamageEnergyMode attribute) linear() (in module irradiapy.utils.math) LIQUID (irradiapy.enums.Phases attribute) load_cluster_size_hist() (irradiapy.analysis.analysisdb.AnalysisDB method)

load_cluster_size_hist_fit_errors() (irradiapy.analysis.analysisdb.AnalysisDB method) load_cluster_size_hist_fit_function() (irradiapy.analysis.analysisdb.AnalysisDB method) load_cluster_size_hist_fit_parameters() (irradiapy.analysis.analysisdb.AnalysisDB method) load_clustering_fraction_hist() (irradiapy.analysis.analysisdb.AnalysisDB method) load_depth_dpa_hist() (irradiapy.analysis.analysisdb.AnalysisDB method) load_depth_dpa_hist_fit_errors() (irradiapy.analysis.analysisdb.AnalysisDB method) load_depth_dpa_hist_fit_functions() (irradiapy.analysis.analysisdb.AnalysisDB method) load_depth_dpa_hist_fit_parameters() (irradiapy.analysis.analysisdb.AnalysisDB method) load_depth_ions_hist() (irradiapy.analysis.analysisdb.AnalysisDB method) load_depth_ions_hist_fit_errors() (irradiapy.analysis.analysisdb.AnalysisDB method) load_depth_ions_hist_fit_function() (irradiapy.analysis.analysisdb.AnalysisDB method) load_depth_ions_hist_fit_parameters() (irradiapy.analysis.analysisdb.AnalysisDB method) load_dpa() (irradiapy.analysis.analysisdb.AnalysisDB method) load_lammps_class() (in module irradiapy.lammps.utils) load_recoil_energies_hist() (irradiapy.analysis.analysisdb.AnalysisDB method) load_recoil_energies_hist_fit_errors() (irradiapy.analysis.analysisdb.AnalysisDB method) load_recoil_energies_hist_fit_function() (irradiapy.analysis.analysisdb.AnalysisDB method) load_recoil_energies_hist_fit_parameters() (irradiapy.analysis.analysisdb.AnalysisDB method) load_target() (irradiapy.recoilsdb.RecoilsDB method) load_target_calculation() (irradiapy.srim.srimdb.SRIMDB method) Log (class in irradiapy.lammps.commands.log) log_path (irradiapy.io.LAMMPSLogReader attribute) (irradiapy.io.lammpslogreader.LAMMPSLogReader attribute) lorentzian() (in module irradiapy.utils.math)

M

matches() (irradiapy.debris_dataset.DebrisDataset method) matching_datasets() (irradiapy.debris_database.DebrisDatabase method) matching_files_by_energy() (irradiapy.debris_database.DebrisDatabase method) matdict (irradiapy.spectrapka.spectra2srim.Spectra2SRIM attribute) max_energy (irradiapy.debris_dataset.DebrisDataset attribute) max_steps (irradiapy.lammps.commands.cruntime.CRunTime attribute) max_time (irradiapy.lammps.commands.cruntime.CRunTime attribute) MBoostIon (class in irradiapy.lammps.commands.mboost_ion) merge_lammps_snapshots() (in module irradiapy.utils.io) minimize_window (irradiapy.srim.py2srim.Py2SRIM attribute) mode (irradiapy.io.BZIP2LAMMPSWriter attribute) (irradiapy.io.bzip2lammpswriter.BZIP2LAMMPSWriter attribute) (irradiapy.io.BZIP2LAMMPSWriterMPI attribute) (irradiapy.io.bzip2lammpswritermpi.BZIP2LAMMPSWriterMPI attribute) (irradiapy.io.LAMMPSWriter attribute) (irradiapy.io.lammpswriter.LAMMPSWriter attribute) (irradiapy.io.LAMMPSWriterMPI attribute) (irradiapy.io.lammpswritermpi.LAMMPSWriterMPI attribute) (irradiapy.io.XYZWriter attribute) (irradiapy.io.xyzwriter.XYZWriter attribute) (irradiapy.lammps.commands.crdf.CRDF attribute) module irradiapy irradiapy.analysis irradiapy.analysis.analysisdb irradiapy.analysis.clusters irradiapy.analysis.debris irradiapy.analysis.debrismanager irradiapy.analysis.defects irradiapy.analysis.defectsidentifier irradiapy.analysis.dpa irradiapy.analysis.recoils irradiapy.config irradiapy.database irradiapy.debris_database irradiapy.debris_dataset irradiapy.dtypes irradiapy.enums irradiapy.io irradiapy.io.bzip2lammpsreader irradiapy.io.bzip2lammpsreadermpi irradiapy.io.bzip2lammpswriter irradiapy.io.bzip2lammpswritermpi irradiapy.io.lammpslogreader irradiapy.io.lammpsreader irradiapy.io.lammpsreadermpi irradiapy.io.lammpswriter irradiapy.io.lammpswritermpi irradiapy.io.xyzreader irradiapy.io.xyzwriter irradiapy.lammps irradiapy.lammps.cascade irradiapy.lammps.cascadebase irradiapy.lammps.commands irradiapy.lammps.commands.atom_modify irradiapy.lammps.commands.atom_style irradiapy.lammps.commands.boundary irradiapy.lammps.commands.cmonitor_borders irradiapy.lammps.commands.comm_modify irradiapy.lammps.commands.command irradiapy.lammps.commands.compute irradiapy.lammps.commands.compute_modify irradiapy.lammps.commands.crdf irradiapy.lammps.commands.create_atoms irradiapy.lammps.commands.create_box irradiapy.lammps.commands.cruntime irradiapy.lammps.commands.dump irradiapy.lammps.commands.dump_modify irradiapy.lammps.commands.echo irradiapy.lammps.commands.fix irradiapy.lammps.commands.fix_modify irradiapy.lammps.commands.group irradiapy.lammps.commands.lattice irradiapy.lammps.commands.log irradiapy.lammps.commands.mboost_ion irradiapy.lammps.commands.pair_coeff irradiapy.lammps.commands.pair_style irradiapy.lammps.commands.print irradiapy.lammps.commands.read_data irradiapy.lammps.commands.read_restart irradiapy.lammps.commands.region irradiapy.lammps.commands.reset_timestep irradiapy.lammps.commands.run irradiapy.lammps.commands.thermo irradiapy.lammps.commands.thermo_modify irradiapy.lammps.commands.thermo_style irradiapy.lammps.commands.timer irradiapy.lammps.commands.uncompute irradiapy.lammps.commands.undump irradiapy.lammps.commands.unfix irradiapy.lammps.commands.units irradiapy.lammps.commands.variable irradiapy.lammps.commands.velocity irradiapy.lammps.commands.write_data irradiapy.lammps.commands.write_dump irradiapy.lammps.commands.write_restart irradiapy.lammps.utils irradiapy.materials irradiapy.materials.component irradiapy.materials.element irradiapy.recoilsdb irradiapy.spectrapka irradiapy.spectrapka.matrices irradiapy.spectrapka.spectra2srim irradiapy.srim irradiapy.srim.backscat irradiapy.srim.collision irradiapy.srim.e2recoil irradiapy.srim.ioniz irradiapy.srim.lateral irradiapy.srim.novac irradiapy.srim.phonon irradiapy.srim.py2srim irradiapy.srim.range irradiapy.srim.range3d irradiapy.srim.sputter irradiapy.srim.srimdb irradiapy.srim.srimfile irradiapy.srim.transmit irradiapy.srim.trimdat irradiapy.srim.vacancy irradiapy.utils irradiapy.utils.io irradiapy.utils.math irradiapy.utils.mpi irradiapy.utils.sqlite

mpi_safe_method() (in module irradiapy.utils.mpi) mpi_subdomains_decomposition() (in module irradiapy.utils.mpi) MPIExceptionHandlerMixin (class in irradiapy.utils.mpi) MPITagAllocator (class in irradiapy.utils.mpi) mv_file() (in module irradiapy.utils.mpi)

N

n (irradiapy.lammps.commands.cmonitor_borders.CMonitorBorders attribute) (irradiapy.lammps.commands.crdf.CRDF attribute) (irradiapy.lammps.commands.create_box.CreateBox attribute) (irradiapy.lammps.commands.dump.Dump attribute) (irradiapy.lammps.commands.reset_timestep.ResetTimestep attribute) (irradiapy.lammps.commands.run.Run attribute) (irradiapy.lammps.commands.thermo.Thermo attribute) name (irradiapy.lammps.commands.variable.Variable attribute) (irradiapy.materials.component.Component attribute) nbins (irradiapy.lammps.commands.crdf.CRDF attribute) nelements (irradiapy.materials.component.Component attribute)

NEWLINE (in module irradiapy.config) newline (irradiapy.io.BZIP2LAMMPSWriter attribute) (irradiapy.io.bzip2lammpswriter.BZIP2LAMMPSWriter attribute) (irradiapy.io.LAMMPSWriter attribute) (irradiapy.io.lammpswriter.LAMMPSWriter attribute) (irradiapy.io.LAMMPSWriterMPI attribute) (irradiapy.io.lammpswritermpi.LAMMPSWriterMPI attribute) nions (irradiapy.srim.srimdb.SRIMDB attribute) Novac (class in irradiapy.srim.novac) NRT (irradiapy.enums.DisplacementMode attribute) nsims (irradiapy.lammps.cascadebase.CascadeBase attribute)

O

offset_power_law() (in module irradiapy.utils.math)

optimize() (irradiapy.database.Database method)

P

PairCoeff (class in irradiapy.lammps.commands.pair_coeff) PairStyle (class in irradiapy.lammps.commands.pair_style) parallelization (irradiapy.io.BZIP2LAMMPSReaderMPI attribute) (irradiapy.io.bzip2lammpsreadermpi.BZIP2LAMMPSReaderMPI attribute) path (irradiapy.database.Database attribute) (irradiapy.debris_dataset.DebrisDataset attribute) path_log_cwd (irradiapy.lammps.cascadebase.CascadeBase attribute) phase (irradiapy.materials.component.Component attribute) Phases (class in irradiapy.enums) Phonon (class in irradiapy.srim.phonon) phonon (irradiapy.srim.srimdb.SRIMDB attribute) pka_target (irradiapy.lammps.cascade.Cascade attribute) plot_all() (in module irradiapy.spectrapka.matrices) plot_type (irradiapy.spectrapka.spectra2srim.Spectra2SRIM attribute) (irradiapy.srim.py2srim.Py2SRIM attribute) (irradiapy.srim.srimdb.SRIMDB attribute)

power_law() (in module irradiapy.utils.math) Print (class in irradiapy.lammps.commands.print) process_config_events() (irradiapy.recoilsdb.RecoilsDB method) process_file() (irradiapy.srim.backscat.Backscat method) (irradiapy.srim.ioniz.Ioniz method) (irradiapy.srim.lateral.Lateral method) (irradiapy.srim.novac.Novac method) (irradiapy.srim.phonon.Phonon method) (irradiapy.srim.range3d.Range3D method) (irradiapy.srim.sputter.Sputter method) (irradiapy.srim.transmit.Transmit method) (irradiapy.srim.trimdat.Trimdat method) Py2SRIM (class in irradiapy.srim.py2srim)

R

Range (class in irradiapy.srim.range) range (irradiapy.srim.srimdb.SRIMDB attribute) Range3D (class in irradiapy.srim.range3d) range3d (irradiapy.srim.srimdb.SRIMDB attribute) rank (irradiapy.lammps.cascadebase.CascadeBase attribute) read() (in module irradiapy.spectrapka.matrices) (irradiapy.database.Database method) read_array() (in module irradiapy.utils.sqlite) read_chunk() (irradiapy.database.Database method) read_numpy() (irradiapy.database.Database method) ReadData (class in irradiapy.lammps.commands.read_data) ReadRestart (class in irradiapy.lammps.commands.read_restart) recoil (irradiapy.analysis.debrismanager.DebrisManager attribute) (irradiapy.debris_dataset.DebrisDataset attribute) recoil_energies_hist() (in module irradiapy.analysis.recoils) recoil_energies_hist_plot() (in module irradiapy.analysis.recoils) recoil_energy_to_damage_energy() (irradiapy.materials.component.Component method) recoils_distances_hist_plot() (in module irradiapy.analysis.recoils) RecoilsDB (class in irradiapy.recoilsdb) recoilsdb (irradiapy.spectrapka.spectra2srim.Spectra2SRIM attribute) (irradiapy.srim.py2srim.Py2SRIM attribute)

recombine_in_radius() (in module irradiapy.utils.math) Region (class in irradiapy.lammps.commands.region) region_id (irradiapy.lammps.commands.cmonitor_borders.CMonitorBorders attribute) (irradiapy.lammps.commands.crdf.CRDF attribute) (irradiapy.lammps.commands.create_box.CreateBox attribute) reminders (irradiapy.spectrapka.spectra2srim.Spectra2SRIM attribute) (irradiapy.srim.py2srim.Py2SRIM attribute) (irradiapy.srim.srimdb.SRIMDB attribute) repeated_prime_factors() (in module irradiapy.utils.math) ResetTimestep (class in irradiapy.lammps.commands.reset_timestep) rm_file() (in module irradiapy.utils.mpi) root (irradiapy.debris_database.DebrisDatabase attribute) root_dir (irradiapy.spectrapka.spectra2srim.Spectra2SRIM attribute) (irradiapy.srim.py2srim.Py2SRIM attribute) Run (class in irradiapy.lammps.commands.run) run (irradiapy.lammps.commands.cruntime.CRunTime attribute) run() (irradiapy.lammps.cascade.Cascade method) (irradiapy.lammps.cascadebase.CascadeBase method) (irradiapy.spectrapka.spectra2srim.Spectra2SRIM method) (irradiapy.srim.py2srim.Py2SRIM method) run_kw_vals (irradiapy.lammps.commands.cruntime.CRunTime attribute)

S

save_cluster_size_hist() (irradiapy.analysis.analysisdb.AnalysisDB method) save_cluster_size_hist_fit_errors() (irradiapy.analysis.analysisdb.AnalysisDB method) save_cluster_size_hist_fit_params() (irradiapy.analysis.analysisdb.AnalysisDB method) save_clustering_fraction_hist() (irradiapy.analysis.analysisdb.AnalysisDB method) save_depth_dpa_hist() (irradiapy.analysis.analysisdb.AnalysisDB method) save_depth_dpa_hist_fit_errors() (irradiapy.analysis.analysisdb.AnalysisDB method) save_depth_dpa_hist_fit_params() (irradiapy.analysis.analysisdb.AnalysisDB method) save_depth_ions_hist() (irradiapy.analysis.analysisdb.AnalysisDB method) save_depth_ions_hist_fit_errors() (irradiapy.analysis.analysisdb.AnalysisDB method) save_depth_ions_hist_fit_params() (irradiapy.analysis.analysisdb.AnalysisDB method) save_dpa() (irradiapy.analysis.analysisdb.AnalysisDB method) save_recoil_energies_hist() (irradiapy.analysis.analysisdb.AnalysisDB method) save_recoil_energies_hist_fit_errors() (irradiapy.analysis.analysisdb.AnalysisDB method) save_recoil_energies_hist_fit_params() (irradiapy.analysis.analysisdb.AnalysisDB method) save_target() (irradiapy.recoilsdb.RecoilsDB method) scale (irradiapy.lammps.commands.lattice.Lattice attribute) seed (irradiapy.analysis.debrismanager.DebrisManager attribute) (irradiapy.lammps.cascadebase.CascadeBase attribute) (irradiapy.spectrapka.spectra2srim.Spectra2SRIM attribute) (irradiapy.srim.py2srim.Py2SRIM attribute) (irradiapy.srim.srimdb.SRIMDB attribute) set_debris_database() (in module irradiapy.config) set_srim_dir() (in module irradiapy.config) skip (irradiapy.lammps.cascadebase.CascadeBase attribute) SOLID (irradiapy.enums.Phases attribute) Spectra2SRIM (class in irradiapy.spectrapka.spectra2srim) spectrapka_events_path (irradiapy.spectrapka.spectra2srim.Spectra2SRIM attribute) spectrapka_in_path (irradiapy.spectrapka.spectra2srim.Spectra2SRIM attribute) Sputter (class in irradiapy.srim.sputter) sputter (irradiapy.srim.srimdb.SRIMDB attribute) SRIM (irradiapy.enums.DamageEnergyMode attribute)

srim (irradiapy.srim.srimfile.SRIMFile attribute) srim_bragg (irradiapy.materials.component.Component attribute) srim_dir (irradiapy.srim.py2srim.Py2SRIM attribute) (irradiapy.srim.srimdb.SRIMDB attribute) srim_el (irradiapy.materials.component.Component attribute) (irradiapy.materials.element.Element attribute) srim_es (irradiapy.materials.component.Component attribute) (irradiapy.materials.element.Element attribute) srim_phase (irradiapy.materials.component.Component attribute) srim_width (irradiapy.spectrapka.spectra2srim.Spectra2SRIM attribute) SRIMDB (class in irradiapy.srim.srimdb) SRIMFile (class in irradiapy.srim.srimfile) stoichiometry_dict (irradiapy.materials.component.Component attribute) stoichs (irradiapy.materials.component.Component attribute) string (irradiapy.lammps.commands.print.Print attribute) structure (irradiapy.materials.component.Component attribute) style (irradiapy.lammps.commands.atom_style.AtomStyle attribute) (irradiapy.lammps.commands.compute.Compute attribute) (irradiapy.lammps.commands.create_atoms.CreateAtoms attribute) (irradiapy.lammps.commands.dump.Dump attribute) (irradiapy.lammps.commands.echo.Echo attribute) (irradiapy.lammps.commands.fix.Fix attribute) (irradiapy.lammps.commands.group.Group attribute) (irradiapy.lammps.commands.lattice.Lattice attribute) (irradiapy.lammps.commands.pair_style.PairStyle attribute) (irradiapy.lammps.commands.region.Region attribute) (irradiapy.lammps.commands.thermo_style.ThermoStyle attribute) (irradiapy.lammps.commands.units.Units attribute) (irradiapy.lammps.commands.variable.Variable attribute) (irradiapy.lammps.commands.velocity.Velocity attribute) (irradiapy.lammps.commands.write_dump.WriteDump attribute) symbol (irradiapy.materials.element.Element attribute)

T

table_exists() (irradiapy.database.Database method) table_has_column() (irradiapy.database.Database method) target (irradiapy.debris_database.DebrisDatabase attribute) (irradiapy.debris_dataset.DebrisDataset attribute) (irradiapy.recoilsdb.RecoilsDB attribute) (irradiapy.spectrapka.spectra2srim.Spectra2SRIM attribute) (irradiapy.srim.py2srim.Py2SRIM attribute) (irradiapy.srim.srimdb.SRIMDB attribute) target_matches_component() (irradiapy.debris_dataset.DebrisDataset static method) target_matches_metadata() (irradiapy.debris_dataset.DebrisDataset static method) Thermo (class in irradiapy.lammps.commands.thermo) thermo (irradiapy.io.LAMMPSLogReader attribute) (irradiapy.io.lammpslogreader.LAMMPSLogReader attribute)

ThermoModify (class in irradiapy.lammps.commands.thermo_modify) ThermoStyle (class in irradiapy.lammps.commands.thermo_style) Timer (class in irradiapy.lammps.commands.timer) timer (irradiapy.lammps.commands.cruntime.CRunTime attribute) to_int() (irradiapy.enums.CustomEnum method) Transmit (class in irradiapy.srim.transmit) transmit (irradiapy.srim.srimdb.SRIMDB attribute) Trimdat (class in irradiapy.srim.trimdat) trimdat (irradiapy.srim.srimdb.SRIMDB attribute) type (irradiapy.lammps.commands.create_atoms.CreateAtoms attribute) types_to_atomic_numbers() (irradiapy.lammps.cascadebase.CascadeBase method)

U

Uncompute (class in irradiapy.lammps.commands.uncompute) Undump (class in irradiapy.lammps.commands.undump) Unfix (class in irradiapy.lammps.commands.unfix) Units (class in irradiapy.lammps.commands.units) use_style() (in module irradiapy.config)

uttm_c (irradiapy.lammps.cascadebase.CascadeBase attribute) uttm_extent (irradiapy.lammps.cascadebase.CascadeBase attribute) uttm_k (irradiapy.lammps.cascadebase.CascadeBase attribute) uttm_nxyz (irradiapy.lammps.cascadebase.CascadeBase attribute) uttm_temperature (irradiapy.lammps.cascadebase.CascadeBase attribute)

V

Vacancy (class in irradiapy.srim.vacancy) vacancy (irradiapy.srim.srimdb.SRIMDB attribute) Variable (class in irradiapy.lammps.commands.variable)

variable (irradiapy.lammps.commands.cmonitor_borders.CMonitorBorders attribute) (irradiapy.lammps.commands.crdf.CRDF attribute) (irradiapy.lammps.commands.cruntime.CRunTime attribute) Velocity (class in irradiapy.lammps.commands.velocity)

W

width (irradiapy.materials.component.Component attribute) wine_cmd (irradiapy.srim.py2srim.Py2SRIM attribute) wineprefix (irradiapy.srim.py2srim.Py2SRIM attribute) write() (irradiapy.io.BZIP2LAMMPSWriter method) (irradiapy.io.bzip2lammpswriter.BZIP2LAMMPSWriter method) (irradiapy.io.BZIP2LAMMPSWriterMPI method) (irradiapy.io.bzip2lammpswritermpi.BZIP2LAMMPSWriterMPI method) (irradiapy.io.LAMMPSWriter method) (irradiapy.io.lammpswriter.LAMMPSWriter method) (irradiapy.io.LAMMPSWriterMPI method) (irradiapy.io.lammpswritermpi.LAMMPSWriterMPI method) (irradiapy.io.XYZWriter method) (irradiapy.io.xyzwriter.XYZWriter method)

WriteData (class in irradiapy.lammps.commands.write_data) WriteDump (class in irradiapy.lammps.commands.write_dump) WriteRestart (class in irradiapy.lammps.commands.write_restart)

X

x (irradiapy.lammps.commands.boundary.Boundary attribute) x0 (irradiapy.materials.component.Component attribute) xmax (irradiapy.spectrapka.spectra2srim.Spectra2SRIM attribute) (irradiapy.srim.py2srim.Py2SRIM attribute) (irradiapy.srim.srimdb.SRIMDB attribute) xmin (irradiapy.spectrapka.spectra2srim.Spectra2SRIM attribute) (irradiapy.srim.py2srim.Py2SRIM attribute) (irradiapy.srim.srimdb.SRIMDB attribute)

XYZReader (class in irradiapy.io) (class in irradiapy.io.xyzreader) XYZWriter (class in irradiapy.io) (class in irradiapy.io.xyzwriter)

Y

y (irradiapy.lammps.commands.boundary.Boundary attribute)

y0 (irradiapy.materials.component.Component attribute)

Z

z (irradiapy.lammps.commands.boundary.Boundary attribute)

z0 (irradiapy.materials.component.Component attribute)