irradiapy.srim.py2srim module

This module contains the Py2SRIM class.

class irradiapy.srim.py2srim.Py2SRIM(seed=0, srim_dir=<factory>, wineprefix=<factory>, wine_cmd=<factory>, check_interval=0.2, minimize_window=False, 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, autosave=0)[source]

Bases: object

Base class for running SRIM calculations from Python.

Variables:

  • seed (int (default=0)) – Seed for SRIM randomness.

  • root_dir (Path) – Root directory where all calculations will be stored.

  • target (list[Component]) – List of target components.

  • calculation (str) – SRIM calculation.

  • srim_dir (Path (default=config.get_srim_dir())) – Directory where SRIM is installed.

  • wineprefix (Path (default=Path(os.environ.get("WINEPREFIX", Path.home() / ".wine-srim2013")))) – Wine prefix to use for running SRIM on Linux. By default, it uses the WINEPREFIX environment variable if set, or ~/.wine-srim2013 otherwise.

  • wine_cmd (str (default=os.environ.get("WINE", "wine"))) – Command to run Wine on Linux. By default, it uses the WINE environment variable if set, or wine otherwise.

  • recoilsdb (RecoilsDB) – Database to store all recoils collected from SPECTRA-PKA and SRIM calculations.

  • check_interval (float (default=0.2)) – Interval to check for SRIM window/popups.

  • minimize_window (bool (default=False)) – Whether to minimize the SRIM/TRIM window while calculations run.

  • plot_type (int (default=5)) – Plot type during SRIM calculations. 5 for no plots (faster calculations).

  • xmin (float (default=0.0)) – Minimum x for plots and depth-dependent means during SRIM calculations. Particularly important for large targets, since SRIM divides it in 100 segments.

  • xmax (float (default=0.0)) – Maximum x for plots and depth-dependent means during SRIM calculations. Particularly important for large targets, since SRIM divides it in 100 segments. 0.0 for full target.

  • do_ranges (int (default=1)) – Whether to save RANGE.txt file. Disabling this might cause errors afterwards because of missing tables.

  • do_backscatt (int (default=1)) – Whether to save BACKSCAT.txt file. Disabling this might cause errors afterwards because of missing tables.

  • do_transmit (int (default=1)) – Whether to save TRANSMIT.txt file. Disabling this might cause errors afterwards because of missing tables.

  • do_sputtered (int (default=1)) – Whether to save SPUTTER.txt file. Disabling this might cause errors afterwards because of missing tables.

  • do_collisions (int (default=1)) – Whether to save COLLISON.txt file. Disabling this might cause errors afterwards because of missing tables.

  • exyz (float (default=0.0)) – Whether to save ions position every time they loose exyz energy in the EXYZ.txt file.

  • autosave (int (default=0)) – Autosave every this number of ions. 0 to disable.

autosave: int = 0
bragg: int = 1
calculation: str
check_interval: float = 0.2
do_backscatt: int = 1
do_collisions: int = 1
do_ranges: int = 1
do_sputtered: int = 1
do_transmit: int = 1
exyz: float = 0.0
minimize_window: bool = False
plot_type: int = 5
recoilsdb: RecoilsDB
reminders: int = 0
root_dir: Path
run(root_dir, target, calculation, atomic_numbers, energies, depths, ys, zs, cosxs, cosys, coszs, max_energy_rel, max_srim_iters, fail_on_transmit, fail_on_backscatt, fp_energy_abs=1000.0, ignore_32bit_warning=True, minimize_window=None)[source]

Run SRIM iteratively, creating a folder tree driven by a recoil-energy threshold.

  • Group ions by atomic number, keeping only those that should be sent to SRIM.

  • Create a directory tree under root_dir where each branch holds a srim.db file.

  • Run SRIM once per branch.

  • Recursively spawn new SRIM runs for recoils from the collision table whose energy is above the relative maximum of their matching MD debris datasets.

  • Stop at depth max_srim_iters. Depth is len(tree); for example, (26, 76, 26) has depth 3.

Parameters:

  • root_dir (Path) – Root directory where all calculations will be stored.

  • target (list[Component]) – SRIM target.

  • calculation (str) – SRIM calculation.

  • atomic_numbers (GenericAlias[int_]) – Ion atomic numbers.

  • energies (GenericAlias[double]) – Ion energies.

  • depths (GenericAlias[double]) – Ion initial depths.

  • ys (GenericAlias[double]) – Ion initial y positions.

  • zs (GenericAlias[double]) – Ion initial z positions.

  • cosxs (GenericAlias[double]) – Ion initial x directions.

  • cosys (GenericAlias[double]) – Ion initial y directions.

  • coszs (GenericAlias[double]) – Ion initial z directions.

  • max_energy_rel (float) – Relative recoil energy threshold for matching MD debris datasets. Recoils above max_dataset_energy * max_energy_rel spawn further SRIM branches, where max_dataset_energy is the highest recoil energy available in the matching dataset data. Must be at least 1.0.

  • max_srim_iters (int) – Maximum number of SRIM iterations.

  • fail_on_transmit (bool) – If True, raise if any ion is transmitted (TRANSMIT.txt non-empty).

  • fail_on_backscatt (bool) – If True, raise if any ion is backscattered (BACKSCAT.txt non-empty).

  • fp_energy_abs (float) – Absolute recoil energy below which unmatched recoils are represented by Frenkel pairs instead of being sent to SRIM, in eV.

  • ignore_32bit_warning (bool) – Whether to ignore the 32-bit warning when using 32-bit SRIM with 64-bit Python.

  • minimize_window (bool | None) – Whether to minimize the SRIM/TRIM window while calculations run. If None, use the instance-level minimize_window setting. The default instance setting is False.

Returns:

Database with all recoils collected.

Return type:

RecoilsDB

seed: int = 0
srim_dir: Path
target: list[Component]
wine_cmd: str
wineprefix: Path
xmax: float = 0.0
xmin: float = 0.0