Add TNG field (#108)

* Add TNG catalogue script

* Add imoprt

* Add TNG box

* Add import

* Fix little bug

* Add TNG300-1

* Add shell scripts

* Organize .gitignore

* Add scatter to file name

* Add argument scatter

* Add threshold on mass

* Update nb

* Add scatter argument

* Add scattering of radial positions

* Update nb

* Update script

scripts_independent/catalogue_tng.py

@@ -0,0 +1,64 @@
+# Copyright (C) 2023 Richard Stiskalek
+# This program is free software; you can redistribute it and/or modify it
+# under the terms of the GNU 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 General Public License along
+# with this program; if not, write to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+"""
+Script to iteratively load particles of a TNG simulation and construct the DM
+density field.
+"""
+from os.path import join
+import numpy as np
+from h5py import File
+import illustris_python as il
+
+
+if __name__ == "__main__":
+    fdir = "/mnt/extraspace/rstiskalek/TNG300-1/"
+    basepath = join(fdir, "output")
+    out_fname = join(fdir, "postprocessing/subhalo_catalogue_099.hdf5")
+
+    # SUBFIND catalogue
+    fields = ["SubhaloFlag", "SubhaloPos", "SubhaloMassType",
+              "SubhaloGasMetallicity", "SubhaloStarMetallicity",
+              "SubhaloSFR", "SubhaloSpin", "SubhaloStellarPhotometrics"]
+
+    print("Loading the data.....")
+    data = il.groupcat.loadSubhalos(basepath, 99, fields=fields)
+    data["SubhaloPos"] /= 1000.  # Convert to Mpc/h
+    print("Finished loading!")
+
+    # Take only galaxies with stellar mass more than 10^9 Msun / h
+    mask = (data["SubhaloFlag"] == 1) & (data["SubhaloMassType"][:, 4] > 0.1)
+
+    print(f"Writing the subfind dataset to '{out_fname}'")
+    with File(out_fname, 'w') as f:
+        for key in fields:
+            if key == "SubhaloFlag":
+                continue
+
+            f.create_dataset(key, data=data[key][mask])
+
+    # HIH2 supplemetary catalogue
+    print("Loading the HI & H2 supplementary catalogue.")
+    fname = join(fdir, "postprocessing/hih2/hih2_galaxy_099.hdf5")
+    with File(fname, "r") as f:
+        _m_neutral_H = f["m_neutral_H"][:]
+        _id_subhalo = np.array(f["id_subhalo"][:], dtype=int)
+
+    m_neutral_H = np.full(data["count"], np.nan, dtype=float)
+    for i, j in enumerate(_id_subhalo):
+        m_neutral_H[j] = _m_neutral_H[i]
+
+    print("Adding the HI & H2 supplementary catalogue.")
+    with File(out_fname, 'r+') as f:
+        f.create_dataset("m_neutral_H", data=m_neutral_H[mask])