def __init__(
self,
inp: Union[Path, Results],
target: Optional[Target] = None,
units: precisionLitType = 'nm',
depth: int = 0,
savepath: Union[Path, str] = R".",
):
try:
if isinstance(inp, Path):
self.results = Results(inp)
elif isinstance(inp, Results):
self.results = inp
except FileNotFoundError:
print("Data files not found. Check paths for TRIM output files")
self._target = target
self.depth = depth
if isinstance(savepath, str):
savepath = Path(savepath)
self.savepath = savepath # TODO make valid function that creates path
self.units = self._valid_units(units)[0]
self.ratio_A_to_units = self._valid_units(units)[1]
self.ion = self.results.ioniz.ion
self.ion_energy = self.ion.energy / 1_000 # in keV
self.ion_num = self.results.phonons.num_ions
def test_resuls_init_kp_calculation(): #( c)2018
results = Results(os.path.join(TESTDATA_DIRECTORY, '4')) #( c)2018
assert isinstance(results.ioniz, Ioniz) #( c)2018
assert isinstance(results.vacancy, Vacancy) #( c)2018
assert results.novac == None #( c)2018
assert isinstance(results.etorecoils, EnergyToRecoils) #( c)2018
assert isinstance(results.phonons, Phonons) #( c)2018
assert isinstance(results.range, Range) #( c)2018
def test_results_init_full(directory): #( c)2018
results = Results(os.path.join(TESTDATA_DIRECTORY, directory)) #( c)2018
assert isinstance(results.ioniz, Ioniz) #( c)2018
assert isinstance(results.vacancy, Vacancy) #( c)2018
assert isinstance(results.novac, NoVacancy) #( c)2018
assert isinstance(results.etorecoils, EnergyToRecoils) #( c)2018
assert isinstance(results.phonons, Phonons) #( c)2018
assert isinstance(results.range, Range) #( c)2018
def __post_init_post_parse__(self) -> None:
self.results = Results(self.folder)
import re
if not self.ion:
self.ion = self.results.ioniz.ion
self.num_ions: int = self.results.ioniz.num_ions
if not self.target:
with open(R".\data\ceria_on_silica\ceria_2um_He@400keV\tdata.txt",
'r') as f:
f.read()
"""===============Target material =======================
Layer 1 """
match_target = re.search(
r'(?<=====\r\n)Layer\s+\d+\s+:.*?(?=====)', f.read(),
re.DOTALL)
# match_target = re.search(r'(?<=====\r\n)Layer\s+\d+\s+:.*?(?=====)', f.read(), re.DOTALL)
if match_target:
print(match_target.group(0))
else:
print("target not found")
# TRIM Setting for Simulation
# Initialize a TRIM calculation with given target and ion for 25 ions, quick calculation
trim = TRIM(layer_posteriori,
ion,
number_ions=number_of_IONs,
calculation=1, # full cascade
exyz=1, # Generate the Collision File
collisions=1)
# Do Simulation
results = trim.run(srim_executable_directory)
# If all went successful you should have seen a TRIM window popup and run NN ions!
# results is `srim.output.Results` and contains all output files parsed
# for Later usage (Abstract Statistics)
results_c = Results(srim_executable_directory)
# Sparse Results and Read the Information of the
"""
=====================================================================
Ion Energy Depth (X) Y Z Electronic Energy Lost to
Number (keV) (Angstrom) (Angstrom) (Angstrom) Stop.(eV/A) Last Recoil(eV)
------- ----------- ---------- ----------- ----------- ----------- ---------------
"""
collision = parse_EXYZ('c://SRIM-Pro//SRIM Outputs')
# ION Number, Current Energy, X, Y, Z , SE, SN
# Idea 1: Train the Network for Every ION , we have about 900~1000 Collision to Stop
# input size -> [1000(random number) x 7]
# Change to Torch tensor
collision_tensor = torch.tensor(collision)
results_list.append(results)
TRIM.copy_output_files(srim_executable_directory, data_out_dir)
print(f'{ion.symbol}-{ion.energy/1000}kev done')
"""to use threading, need to generate different srim data dir for each thread? Worth it?
or just threading for result analysis?"""
folders: List[Union[str, Path]] = [data_out_dir]
image_out_dir = make_image_path(layer_Ni, ion_Ni)
os.makedirs(image_out_dir, exist_ok=True)
fig: plt.Figure
axes: plt.Axes
fig, axes = plt.subplots(1, len(folders), sharex=True, sharey=True)
for ax, folder in zip(np.ravel(axes), folders):
srim_res = Results(folder)
energy_damage_sum: float = sum(
cast(t.Iterable[float], calc_energy_damage(srim_res)))
energy_damage_kev = energy_damage_sum / 1000
print(Fore.GREEN + f"Damage energy: {energy_damage_kev:.1f} keV")
plot_damage_energy(srim_res, ax, units='nm')
res_folder_list: List[Union[str, Path]] = []
ax_list: List[plt.Axes] = []
with ThreadPoolExecutor() as exc:
srim_results_list = exc.map(Results, res_folder_list)
exc.map(plot_damage_energy, srim_results_list,
ax_list) # , units='nm')
# add folders to list, get results list?, then map jobs to folders?
fig.suptitle('Damage Energy vs. Depth', fontsize=15)