#!/usr/bin/env python3 ############################################################################### # This file is part of SWIFT. # Copyright (c) 2023 Yolan Uyttenhove (yolan.uyttenhove@ugent.be) # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published # by the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU Lesser General Public License # along with this program. If not, see . # ############################################################################## import math # --------------------------------------------------------------------- # Test the diffusion/advection of metals by creating regions with/without # initial metallicities. Run with EAGLE chemistry. # --------------------------------------------------------------------- import numpy as np import h5py GAMMA = 5 / 3 RHO = 1 P = 1 VELOCITY = 2.5 ELEMENT_COUNT = 9 outputfilename = "advect_metals.hdf5" def get_masks(boxsize, pos): masks = dict() x = boxsize[0] y = boxsize[1] right_half_mask = pos[:, 0] > x / 2 masks["TotalMetallicity"] = right_half_mask masks["He"] = pos[:, 0] * 2 % x > x / 2 masks["C"] = right_half_mask & (pos[:, 0] < 0.75 * x) masks["N"] = right_half_mask & (pos[:, 0] > 0.75 * x) masks["O"] = right_half_mask & (pos[:, 1] > 0.5 * y) masks["Ne"] = right_half_mask & (pos[:, 1] < 0.5 * y) masks["Mg"] = right_half_mask & (pos[:, 0] < 0.75 * x) & (pos[:, 1] > 0.5 * y) masks["Si"] = right_half_mask & (pos[:, 0] > 0.75 * x) & (pos[:, 1] > 0.5 * y) masks["Fe"] = right_half_mask & (pos[:, 0] < 0.75 * x) & (pos[:, 1] < 0.5 * y) return masks def get_element_abundances_metallicity(pos, boxsize): elements = ["He", "C", "N", "O", "Ne", "Mg", "Si", "Fe"] abundances = [0.2, 0.2, 0.2, 0.2, 0.2, 0.1, 0.1, 0.1] masks = get_masks(boxsize, pos) total_metallicity = np.where(masks["TotalMetallicity"], 0.7, 0.1) element_abundances = [ np.where(masks[k], v, 0) for k, v in zip(elements, abundances) ] # Finally add H so that H + He + TotalMetallicity = 1 return ( np.stack( [1 - element_abundances[0] - total_metallicity] + element_abundances, axis=1 ), total_metallicity, ) if __name__ == "__main__": glass = h5py.File("glassPlane_64.hdf5", "r") parts = glass["PartType0"] pos = parts["Coordinates"][:] pos = np.concatenate([pos, pos + np.array([1, 0, 0])]) h = parts["SmoothingLength"][:] h = np.concatenate([h, h]) glass.close() # Set up metadata boxsize = np.array([2.0, 1.0, 1.0]) n_part = len(h) ids = np.arange(n_part) + 1 # Setup other particle quantities rho = RHO * np.ones_like(h) rho[pos[:, 1] < 0.5 * boxsize[1]] *= 0.5 masses = rho * np.prod(boxsize) / n_part velocities = np.zeros((n_part, 3)) velocities[:, :] = 0.5 * math.sqrt(2) * VELOCITY * np.array([1.0, 1.0, 0.0]) internal_energy = P / (rho * (GAMMA - 1)) # Setup metallicities element_abundances, metallicities = get_element_abundances_metallicity(pos, boxsize) # Now open the file and write the data. file = h5py.File(outputfilename, "w") # Header grp = file.create_group("/Header") grp.attrs["BoxSize"] = boxsize grp.attrs["NumPart_Total"] = [n_part, 0, 0, 0, 0, 0] grp.attrs["NumPart_Total_HighWord"] = [0, 0, 0, 0, 0, 0] grp.attrs["NumPart_ThisFile"] = [n_part, 0, 0, 0, 0, 0] grp.attrs["Time"] = 0.0 grp.attrs["NumFilesPerSnapshot"] = 1 grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0] grp.attrs["Flag_Entropy_ICs"] = 0 grp.attrs["Dimension"] = 2 # Units grp = file.create_group("/Units") grp.attrs["Unit length in cgs (U_L)"] = 1.0 grp.attrs["Unit mass in cgs (U_M)"] = 1.0 grp.attrs["Unit time in cgs (U_t)"] = 1.0 grp.attrs["Unit current in cgs (U_I)"] = 1.0 grp.attrs["Unit temperature in cgs (U_T)"] = 1.0 # Particle group grp = file.create_group("/PartType0") grp.create_dataset("Coordinates", data=pos, dtype="d") grp.create_dataset("Velocities", data=velocities, dtype="f") grp.create_dataset("Masses", data=masses, dtype="f") grp.create_dataset("SmoothingLength", data=h, dtype="f") grp.create_dataset("InternalEnergy", data=internal_energy, dtype="f") grp.create_dataset("ParticleIDs", data=ids, dtype="L") grp.create_dataset("Metallicity", data=metallicities, dtype="f") grp.create_dataset("ElementAbundance", data=element_abundances, dtype="f") file.close() # close up, and we're done! file.close()