"""This module contains the `Vacancy` class."""
from pathlib import Path
from typing import TYPE_CHECKING, Generator
import numpy as np
from irradiapy.srim.ofiles.srimfile import SRIMFile
if TYPE_CHECKING:
from irradiapy.srim.srimdb import SRIMDB
[docs]
class Vacancy(SRIMFile):
"""Class to handle `VACANCY.txt` file."""
def __init__(self, srimdb: "SRIMDB") -> None:
"""Initializes the `Vacancy` object.
Parameters
----------
srimdb : SRIMDB
`SRIMDB` object.
"""
super().__init__(srimdb)
if self.srim.calculation == "quick":
self.process_file = self.__process_file_qc
self.merge = self.__merge_qc
else:
self.process_file = self.__process_file_fc
self.merge = self.__merge_fc
def __process_file_qc(self, vacancy_path: Path) -> None:
"""Processes `VACANCY.txt` file in Quick-Calculation mode.
Parameters
----------
vacancy_path : Path
`VACANCY.txt` path.
"""
cur = self.cursor()
cur.execute(
(
"CREATE TABLE vacancy"
"(depth REAL, vacancies_ions REAL, vacancies_recoils REAL)"
)
)
with open(vacancy_path, "r", encoding="utf-8") as file:
for line in file:
if line.startswith(" TARGET"):
break
next(file)
next(file)
next(file)
for _ in range(100):
line = next(file)
data = list(map(float, line[:-1].split()))
depth = data[0]
vacancies_ions = data[1]
vacancies_recoils = data[2]
cur.execute(
(
"INSERT INTO vacancy"
"(depth, vacancies_ions, vacancies_recoils)"
"VALUES(?, ?, ?)"
),
[depth, vacancies_ions, vacancies_recoils],
)
cur.close()
self.srim.commit()
def __process_file_fc(self, vacancy_path: Path) -> None:
"""Processes `VACANCY.txt` file in Full-Calculation mode.
Parameters
----------
vacancy_path : Path
`VACANCY.txt` path.
"""
vacancies_1 = ", ".join(
f"vacancies_{i}_{j} REAL"
for i, layer in enumerate(self.srim.target.layers)
for j in range(len(layer.elements))
)
vacancies_2 = ", ".join(
f"vacancies_{i}_{j}"
for i, layer in enumerate(self.srim.target.layers)
for j in range(len(layer.elements))
)
vacancies_3 = ", ".join(["?" for _ in range(len(vacancies_1.split(", ")))])
cur = self.cursor()
cur.execute(
("CREATE TABLE vacancy" f"(depth REAL, knock_ons REAL, {vacancies_1})")
)
with open(vacancy_path, "r", encoding="utf-8") as file:
for line in file:
if line.startswith(" TARGET"):
break
next(file)
next(file)
next(file)
for _ in range(100):
line = next(file)
data = list(map(float, line[:-1].split()))
depth = data[0]
knock_ons = data[1]
vacancies = data[2:]
cur.execute(
(
"INSERT INTO vacancy"
f"(depth, knock_ons, {vacancies_2})"
f"VALUES(?, ?, {vacancies_3})"
),
[depth, knock_ons, *vacancies],
)
cur.close()
self.srim.commit()
def __merge_qc(self, srimdb2: "SRIMDB") -> None:
"""Merges the e2recoil table with another database for Quick-Calculation mode.
Parameters
----------
srimdb2 : SRIMDB
SRIM database to merge with.
"""
nions1 = self.srim.nions
nions2 = srimdb2.nions
nions = nions1 + nions2
vacancy1 = np.array(list(self.read()))
vacancy2 = np.array(list(srimdb2.vacancy.read()))
vacancy1[:, 1:] *= nions1
vacancy2[:, 1:] *= nions2
vacancy1[:, 1:] += vacancy2[:, 1:]
vacancy1[:, 1:] /= nions
cur = self.cursor()
cur.execute("DELETE FROM vacancy")
cur.executemany(
(
"INSERT INTO vacancy(depth, vacancies_ions, vacancies_recoils)"
"VALUES(?, ?, ?)"
),
vacancy1,
)
cur.close()
self.srim.commit()
def __merge_fc(self, srimdb2: "SRIMDB") -> None:
"""Merges the vacancy table with another database for Full-Calculation mode.
Parameters
----------
srimdb2 : SRIMDB
SRIM database to merge with
"""
nions1 = self.srim.nions
nions2 = srimdb2.nions
nions = nions1 + nions2
vacancy1 = np.array(list(self.read()))
vacancy2 = np.array(list(srimdb2.vacancy.read()))
vacancy1[:, 1:] *= nions1
vacancy2[:, 1:] *= nions2
vacancy1[:, 1:] += vacancy2[:, 1:]
vacancy1[:, 1:] /= nions
vacancies_1 = ", ".join(
f"vacancies_{i}_{j} REAL"
for i, layer in enumerate(self.srim.target.layers)
for j in range(len(layer.elements))
)
vacancies_2 = ", ".join(
f"vacancies_{i}_{j}"
for i, layer in enumerate(self.srim.target.layers)
for j in range(len(layer.elements))
)
vacancies_3 = ", ".join(["?" for _ in range(len(vacancies_1.split(", ")))])
cur = self.cursor()
cur.execute("DELETE FROM vacancy")
cur.executemany(
(
f"INSERT INTO vacancy(depth, knock_ons, {vacancies_2})"
f"VALUES(?, ?, {vacancies_3})"
),
vacancy1,
)
cur.close()
self.srim.commit()
[docs]
def read(
self, what: str = "*", condition: str = ""
) -> Generator[tuple, None, None]:
"""Reads vacancy data from the database as a generator.
Parameters
----------
what : str
Columns to select.
condition : str
Condition to filter data.
Yields
------
Generator[tuple, None, None]
Data from the database.
"""
cur = self.cursor()
cur.execute(f"SELECT {what} FROM vacancy {condition}")
while True:
data = cur.fetchone()
if data:
yield data
else:
break
cur.close()