irradiapy.srim package

Subpackages

• irradiapy.srim.ofiles package
  • Submodules
  • irradiapy.srim.ofiles.backscat module
    • Backscat
      • Backscat.get_nions()
      • Backscat.merge()
      • Backscat.process_file()
      • Backscat.read()
  • irradiapy.srim.ofiles.collision module
    • Collision
      • Collision.read()
  • irradiapy.srim.ofiles.e2recoil module
    • E2Recoil
      • E2Recoil.read()
  • irradiapy.srim.ofiles.ioniz module
    • Ioniz
      • Ioniz.merge()
      • Ioniz.process_file()
      • Ioniz.read()
  • irradiapy.srim.ofiles.lateral module
    • Lateral
      • Lateral.merge()
      • Lateral.process_file()
      • Lateral.read()
  • irradiapy.srim.ofiles.novac module
    • Novac
      • Novac.merge()
      • Novac.process_file()
      • Novac.read()
  • irradiapy.srim.ofiles.phonon module
    • Phonon
      • Phonon.merge()
      • Phonon.process_file()
      • Phonon.read()
  • irradiapy.srim.ofiles.range module
    • Range
      • Range.read()
  • irradiapy.srim.ofiles.range3d module
    • Range3D
      • Range3D.merge()
      • Range3D.process_file()
      • Range3D.read()
  • irradiapy.srim.ofiles.sputter module
    • Sputter
      • Sputter.get_natoms()
      • Sputter.merge()
      • Sputter.process_file()
      • Sputter.read()
  • irradiapy.srim.ofiles.srimfile module
    • SRIMFile
      • SRIMFile.commit()
      • SRIMFile.cursor()
      • SRIMFile.srim
  • irradiapy.srim.ofiles.subcollision module
    • Subcollision
      • Subcollision.empty()
      • Subcollision.read()
  • irradiapy.srim.ofiles.transmit module
    • Transmit
      • Transmit.get_nions()
      • Transmit.merge()
      • Transmit.process_file()
      • Transmit.read()
  • irradiapy.srim.ofiles.trimdat module
    • Trimdat
      • Trimdat.merge()
      • Trimdat.process_file()
      • Trimdat.read()
  • irradiapy.srim.ofiles.vacancy module
    • Vacancy
      • Vacancy.read()
  • Module contents
• irradiapy.srim.target package
  • Submodules
  • irradiapy.srim.target.element module
    • Element
      • Element.symbol
      • Element.atomic_number
      • Element.atomic_mass
      • Element.e_d
      • Element.e_l
      • Element.e_s
      • Element.density
      • Element.atomic_mass
      • Element.atomic_number
      • Element.density
      • Element.e_d
      • Element.e_l
      • Element.e_s
      • Element.symbol
  • irradiapy.srim.target.layer module
    • Layer
      • Layer.width
      • Layer.phase
      • Layer.density
      • Layer.elements
      • Layer.stoichs
      • Layer.bragg
      • Layer.bragg
      • Layer.density
      • Layer.elements
      • Layer.nelements
      • Layer.phase
      • Layer.stoichs
      • Layer.width
  • irradiapy.srim.target.target module
    • Target
      • Target.layers
      • Target.nelements
      • Target.nlayers
      • Target.layers
      • Target.nelements
      • Target.nlayers
      • Target.trimin_bragg()
      • Target.trimin_description()
      • Target.trimin_displacement()
      • Target.trimin_lattice()
      • Target.trimin_phases()
      • Target.trimin_surface()
      • Target.trimin_target_elements()
      • Target.trimin_target_layers()
  • Module contents

Submodules

irradiapy.srim.analysis module

Utility functions related to SRIM data analysis and debris production.

irradiapy.srim.analysis.generate_debris(srimdb, dir_mddb, compute_tdam, path_debris, tdam_mode, dpa_mode, energy_tolerance, add_injected, outsiders, seed=None, depth_offset=0.0, ylo=None, yhi=None, zlo=None, zhi=None)

Turns SRIM’s collisions into .xyz files for the given database of cascades’ debris.

Warning

Assumes a monolayer monoatomic target and same element for all ions.

Parameters:

• srimdb (SRIMDB) – SRIM database class.

• dir_mddb (Path) – Directory where the database of cascades’ debris is stored.

• compute_tdam (bool) – Whether to transform the PKA energies into damage energies. It should be True for MD simulations without electronic stopping.

• path_debris (Path) – Directory where the ions debris will be stored as .xyz files.

• tdam_mode (materials.Material.TdamMode) – Mode to convert the PKA energy into damage energy.

• dpa_mode (materials.Material.DpaMode) – Formula to convert the residual energy into Frenkel pairs.

• energy_tolerance (float (default=0.1)) – Tolerance for energy decomposition. For example, if this value if 0.1, the PKA energy is 194 keV and the database contains an energy of 200 keV, then 194 will be in the range 200 +/- 20 keV, therefore a cascade of 200 keV will be used, instead of decomposing 194 keV into, for example, 100x1 + 50x1 + 20x2 + 3x1 + 1xFP (Frenkel pairs). This fixes biases towards smaller clusters (lower energies) and helps reducing cascade overlapping. Set to 0.0 to disable this feature.

• add_injected (bool) – Whether to add the injected interstitial.

• outsiders (bool) – Whether to include defects generated outside the material (PKAs close to surfaces). This can cause an inmbalance between the number of vacancies and interstitials.

• seed (int, optional) – Random seed for reproducibility.

• depth_offset (float, optional (default=0.0)) – Offset to add to the depth of the defects.

• ylo (float, optional (default=None)) – Minimum y-coordinate for the defects. If None, will be set to minus the target width.

• yhi (float, optional (default=None)) – Maximum y-coordinate for the defects. If None, will be set to the target width.

• zlo (float, optional (default=None)) – Minimum z-coordinate for the defects. If None, will be set to minus the target width.

• zhi (float, optional (default=None)) – Maximum z-coordinate for the defects. If None, will be set to the target width.

Return type:

None

irradiapy.srim.analysis.plot_distances(srimdb, pka_e_lim=5000.0, dist_bins=100, energy_bins=100, plot_path=None, dpi=300)

Plots a 2D histogram of pairwise distances and sum of PKA energies for each ion.

Parameters:

• srimdb (SRIMDB) – SRIM database class.

• pka_elim (float, optional (default=5e3)) – Minimum recoil energy to consider.

• dist_bins (int, optional (default=100)) – Number of bins for the distance histogram.

• energy_bins (int, optional (default=100)) – Number of bins for the energy histogram.

• plot_path (Path, optional (default=None)) – Output path for the plot. If None, the plot is shown.

• dpi (int, optional (default=300)) – Dots per inch for the plot.

Return type:

None

irradiapy.srim.analysis.plot_energy_depth(srimdb, depth_bins=100, pka_ebins=100, pka_e_max=200, plot_high_path=None, plot_low_path=None, dpi=300)

Plots the depth-energy distribution of PKAs.

Parameters:

• srimdb (SRIMDB) – SRIM database class.

• depth_bins (int, optional (default=100)) – Number of bins for depth histogram.

• pka_ebins (int, optional (default=100)) – Number of bins for PKA energy histogram.

• pka_e_max (float, optional (default=200)) – Maximum PKA energy.

• plot_high_path (Path, optional (default=None)) – Output path for the high energy plot. If None, the plot is shown.

• plot_low_path (Path, optional (default=None)) – Output path for the low energy plot. If None, the plot is shown.

• dpi (int, optional (default=300)) – Dots per inch for the plot.

Return type:

None

irradiapy.srim.analysis.plot_injected(srimdb, bins=100, plot_path=None, path_fit=None, p0=None, asymmetry=1.0, dpi=300)

Plot injected ions final depth distribution.

Parameters:

• srimdb (SRIMDB) – SRIM database class.

• bins (int, optional (default=100)) – Depth bins.

• plot_path (Path, optional (default=None)) – Output path for the plot. If None, the plot is shown.

• path_fit (Path, optional (default=None)) – Output path for the fit parameters.

• p0 (float, optional (default=None)) – Initial guess of fit parameters.

• asymmetry (float, optional (default=1.0)) – Asymmetry fit parameter bound.

• dpi (int, optional (default=300)) – Dots per inch.

Return type:

None

irradiapy.srim.analysis.plot_pka_distribution(srimdb, bins=100, plot_path=None, fit_path=None, dpi=300)

Plot the PKA energy distribution and tries to fit it.

Parameters:

• srimdb (SRIMDB) – SRIM database class.

• bins (int, optional (default=100)) – Energy bins. The fit will be done over non-empty bins.

• plot_path (Path, optional (default=None)) – Output path for the plot. If None, the plot is shown.

• fit_path (Path, optional (default=None)) – Output path for the fit parameters.

• dpi (int, optional (default=300)) – Dots per inch.

Returns:

Fit parameters and function or None if fit failed.

Return type:

tuple[float, float, Callable] | None

irradiapy.srim.srimdb module

This module contains the SRIMDB class.

class irradiapy.srim.srimdb.SRIMDB(*, path_db, calculation=None, target=None, check_interval=0.2, seed=0, reminders=0, plot_type=5, xmin=0.0, xmax=0.0, do_ranges=1, do_backscatt=1, do_transmit=1, do_sputtered=1, do_collisions=1, exyz=0.0, bragg=1, autosave=0, dir_srim=<factory>)

Bases: Connection

Base class for running SRIM calculations and storing the output data in a SQLite database.

path_db

Output database path.

Type:

Path

target

SRIM target.

Type:

Target, optional

calculation

SRIM calculation.

Type:

str, optional

check_interval

Interval to check for SRIM window/popups.

Type:

float

srim_path

Where all SRIM output files are. If given, it will automatically add all those files into the database.

Type:

Path

con

Database connection.

Type:

sqlite3.Connection

backscat

Class storing BACKSCAT.txt data.

Type:

Backscat

e2recoil

Class storing E2RECOIL.txt data.

Type:

E2Recoil

ioniz

Class storing IONIZ.txt data.

Type:

Ioniz

lateral

Class storing LATERAL.txt data.

Type:

Lateral

phonon

Class storing PHONON.txt data.

Type:

Phonon

range

Class storing RANGE.txt data.

Type:

Range

range3d

Class storing RANGE_3D.txt data.

Type:

Range3D

sputter

Class storing SPUTTER.txt data.

Type:

Sputter

transmit

Class storing TRANSMIT.txt data.

Type:

Transmit

trimdat

Class storing TRIM.DAT data.

Type:

Trimdat

vacancy

Class storing VACANCY.txt data.

Type:

Vacancy

append_backscat(backscat_path)

Appends BACKSCAT.txt into the database.

Parameters:

backscat_path (Path) – BACKSCAT.txt path.

Return type:

None

append_e2recoil(e2recoil_path)

Appends E2RECOIL.txt into the database.

Parameters:

e2recoil_path (Path) – E2RECOIL.txt path.

Return type:

None

append_ioniz(ioniz_path)

Appends IONIZ.txt into the database.

Parameters:

ioniz_path (Path) – IONIZ.txt path.

Return type:

None

append_lateral(lateral_path)

Appends LATERAL.txt into the database.

Parameters:

lateral_path (Path) – LATERAL.txt path.

Return type:

None

append_novac(novac_path)

Appends NOVAC.txt into the database.

Parameters:

novac_path (Path) – NOVAC.txt path.

Return type:

None

append_phonon(phonon_path)

Appends PHONON.txt into the database.

Parameters:

phonon_path (Path) – PHONON.txt path.

Return type:

None

append_range(range_path)

Appends RANGE.txt into the database.

Parameters:

range_path (Path) – RANGE.txt path.

Return type:

None

append_range3d(range3d_path)

Appends RANGE_3D.txt into the database.

Parameters:

range3d_path (Path) – RANGE_3D.txt path.

Return type:

None

append_sputter(sputter_path)

Appends SPUTTER.txt into the database.

Parameters:

sputter_path (Path) – SPUTTER.txt path.

Return type:

None

append_subcollision(collision_path)

Appends currect iteration COLLISON.txt into the database.

Parameters:

collision_path (Path) – COLLISON.txt path.

Return type:

None

append_transmit(transmit_path)

Appends TRANSMIT.txt into the database.

Parameters:

transmit_path (Path) – TRANSMIT.txt path.

Return type:

None

append_trimdat(trimdat_path)

Appends TRIM.DAT into the database.

Parameters:

trimdat_path (Path) – TRIM.DAT path.

Return type:

None

append_vacancy(vacancy_path)

Appends VACANCY.txt into the database.

Parameters:

vacancy_path (Path) – VACANCY.txt path.

Return type:

None

autosave: int = 0

bragg: int = 1

calculation: None | str = None

check_interval: float = 0.2

dir_srim: Path

do_backscatt: int = 1

do_collisions: int = 1

do_ranges: int = 1

do_sputtered: int = 1

do_transmit: int = 1

exyz: float = 0.0

generate_trimdat(atomic_numbers, energies, depths=None, ys=None, zs=None, cosxs=None, cosys=None, coszs=None)

Generates TRIM.DAT file.

Parameters:

• atomic_numbers (npt.NDArray[np.int64]) – Atomic numbers.

• energies (npt.NDArray[np.float64]) – Energies.

• depths (npt.NDArray[np.float64], optional) – Depths.

• ys (npt.NDArray[np.float64], optional) – Y positions.

• zs (npt.NDArray[np.float64], optional) – Z positions.

• cosxs (npt.NDArray[np.float64], optional) – X directions.

• cosys (npt.NDArray[np.float64], optional) – Y directions.

• coszs (npt.NDArray[np.float64], optional) – Z directions.

Returns:

TRIM.DAT data.

Return type:

npt.NDArray[np.float64]

generate_trimin(atomic_numbers, energies, target)

Generates TRIM.IN file.

Return type:

None

get_nions()

Gets the number of ions in the simulation.

Return type:

int

load_target_calculation()

Loads the target and calculation parameters from the database.

Return type:

Target

merge(srimdb2, backscat=True, e2recoil=True, ioniz=True, lateral=True, phonon=True, range3d=True, range_=True, sputter=True, transmit=True, vacancy=True, collision=True, trimdat=True, novac=True)

Merges two databases.

Parameters:

• srimdb2 (SRIMDBIter) – SRIM database to merge.

• backscat (bool, optional) – Merge backscattering data.

• e2recoil (bool, optional) – Merge energy to recoil data.

• ioniz (bool, optional) – Merge ionization data.

• lateral (bool, optional) – Merge lateral data.

• phonon (bool, optional) – Merge phonon data.

• range3d (bool, optional) – Merge 3D range data.

• range (bool, optional) – Merge range data.

• sputter (bool, optional) – Merge sputtering data.

• transmit (bool, optional) – Merge transmission data.

• vacancy (bool, optional) – Merge vacancy data.

• collision (bool, optional) – Merge collision data.

• trimdat (bool, optional) – Merge TRIMDAT data.

• novac (bool, optional) – Merge NOVAC data.

Return type:

None

minimize_and_handle_popup()

Minimizes the SRIM window and handles the end of calculation popup.

optimize()

Optimize the SQLite database.

This method performs two operations to optimize the database: 1. Executes the “PRAGMA optimize” command to analyze and optimize the database. 2. Executes the “VACUUM” command to rebuild the database file, repacking it into a minimal amount of disk space.

Return type:

None

path_db: Path

plot_type: int = 5

reminders: int = 0

run(criterion, atomic_numbers, energies, remove_offsets, depths=None, ys=None, zs=None, cosxs=None, cosys=None, coszs=None, iter_max=None, ignore_32bit_warning=True)

Runs the SRIM simulation.

Parameters:

• criterion (Callable) – Criterion to repeat calculation, must return False to repeat calculation. Its signature is: criterion(nion, energy, depth, y, z, se, atom_hit, pka_e, target_disp). Recommended to be defined as def criterion(**kwargs: dict) -> bool:.

• atomic_numbers (npt.NDArray[np.int64]) – Ion atomic numbers.

• energies (npt.NDArray[np.float64]) – Ion energies.

• remove_offsets (bool) – Whether to remove initial depth offsets or not.

• depths (npt.NDArray[np.float64], optional) – Ion initial depths.

• ys (npt.NDArray[np.float64], optional) – Ion initial y positions.

• zs (npt.NDArray[np.float64], optional) – Ion initial z positions.

• cosxs (npt.NDArray[np.float64], optional) – Ion initial x directions.

• cosys (npt.NDArray[np.float64], optional) – Ion initial y directions.

• coszs (npt.NDArray[np.float64], optional) – Ion initial z directions.

• iter_max (int, optional (default=None)) – Maximum number of iterations.

Return type:

None

save_target_calculation()

Saves the target and calculation parameters into the database.

Return type:

None

seed: int = 0

table_exists(table_name)

Checks if the given table already exists in the database.

Parameters:

table_name (str) – Table’s name to check.

Returns:

Whether the table already exists or not.

Return type:

bool

target: None | Target = None

xmax: float = 0.0

xmin: float = 0.0

Module contents

This subpackage provides a Python interface for SRIM for simulating collisional cascades.