From e9cc65ffeb0684a97618b67c2164d95ea497226c Mon Sep 17 00:00:00 2001 From: Luca Fedeli Date: Mon, 10 Oct 2022 20:36:14 +0200 Subject: Partial refactoring of the utils directory (#3404) * initial work to clean WarpX Utils * remove AMRCore from Ionization tables * progress * refactoring of a part of the utils directory * fix bug * fixed bug * fixed bug * remove debug line accidentally slipped into the code * remove debug line accidentally slipped into the code * remove debug line accidentally slipped into the code * cleaning * fixed bug --- Source/Utils/write_atomic_data_cpp.py | 87 ----------------------------------- 1 file changed, 87 deletions(-) delete mode 100644 Source/Utils/write_atomic_data_cpp.py (limited to 'Source/Utils/write_atomic_data_cpp.py') diff --git a/Source/Utils/write_atomic_data_cpp.py b/Source/Utils/write_atomic_data_cpp.py deleted file mode 100644 index 3b0538aa1..000000000 --- a/Source/Utils/write_atomic_data_cpp.py +++ /dev/null @@ -1,87 +0,0 @@ -#!/usr/bin/env python3 -# -# Copyright 2019-2021 Axel Huebl, Luca Fedeli, Maxence Thevenet -# -# -# This file is part of WarpX. -# -# License: BSD-3-Clause-LBNL - -''' -This python script reads ionization tables in atomic_data.txt (generated from -the NIST website) and extracts ionization levels into C++ file -IonizationEnergiesTable.H, which contains tables + metadata. -''' - -import os -import re - -import numpy as np - -filename = os.path.join( '.', 'atomic_data.txt' ) -with open(filename) as f: - text_data = f.read() - -# Read full table from file and get names, atomic numbers and offsets -# position in table of ionization energies for all species -regex_command = '\n\s+(\d+)\s+\|\s+([A-Z]+[a-z]*)\s+\w+\s+\|\s+\+*(\d+)\s+\|\s+\(*\[*(\d+\.*\d*)' -list_of_tuples = re.findall( regex_command, text_data ) -ion_atom_numbers = [int(i) for i in list(dict.fromkeys( [x[0] for x in list_of_tuples] ))] -ion_names = list(dict.fromkeys( [x[1] for x in list_of_tuples] )) -ion_offsets = np.concatenate(([0], np.cumsum(np.array(ion_atom_numbers)[:-1])), axis=0) - -# Head of CPP file -cpp_string = '// This script was automatically generated!\n' -cpp_string += '// Edit dev/Source/Utils/write_atomic_data_cpp.py instead!\n' -cpp_string += '#ifndef WARPX_IONIZATION_TABLE_H_\n' -cpp_string += '#define WARPX_IONIZATION_TABLE_H_\n\n' -cpp_string += '#include \n' -cpp_string += '#include \n\n' -cpp_string += '#include \n' -cpp_string += '#include \n\n' - -# Map each element to ID in table -cpp_string += 'static std::map const ion_map_ids = {' -for count, name in enumerate(ion_names): - cpp_string += '\n {"' + name + '", ' + str(count) + '},' -cpp_string = cpp_string[:-1] -cpp_string += ' };\n\n' - -# Atomic number of each species -cpp_string += 'constexpr int nelements = ' + str(len(ion_names)) + ';\n\n' -cpp_string += 'constexpr int ion_atomic_numbers[nelements] = {\n ' -for count, atom_num in enumerate(ion_atom_numbers): - if count%10==0 and count>0: cpp_string = cpp_string[:-2] + ',\n ' - cpp_string += str(atom_num) + ', ' -cpp_string = cpp_string[:-2] -cpp_string += '};\n\n' - -# Offset of each element in table of ionization energies -cpp_string += 'constexpr int ion_energy_offsets[nelements] = {\n ' -for count, offset in enumerate(ion_offsets): - if count%10==0 and count>0: cpp_string = cpp_string[:-2] + ',\n ' - cpp_string += str(offset) + ', ' -cpp_string = cpp_string[:-2] -cpp_string += '};\n\n' - -# Table of ionization energies -cpp_string += 'constexpr int energies_tab_length = ' + str(len(list_of_tuples)) + ';\n\n' -cpp_string += 'constexpr amrex::Real table_ionization_energies[energies_tab_length]{' -for element in ion_names: - cpp_string += '\n // ' + element + '\n ' - regex_command = \ - '\n\s+(\d+)\s+\|\s+%s\s+\w+\s+\|\s+\+*(\d+)\s+\|\s+\(*\[*(\d+\.*\d*)' \ - %element - list_of_tuples = re.findall( regex_command, text_data ) - for count, energy in enumerate([x[2] for x in list_of_tuples]): - if count%3==0 and count>0: cpp_string = cpp_string[:-2] + ',\n ' - cpp_string += "amrex::Real(" + energy + '), ' - cpp_string = cpp_string[:-1] -cpp_string = cpp_string[:-1] -cpp_string += '\n};\n\n' - -# Write the string to file -cpp_string += '#endif // #ifndef WARPX_IONIZATION_TABLE_H_\n' -f= open("IonizationEnergiesTable.H","w") -f.write(cpp_string) -f.close() -- cgit v1.2.3