Overlap fixing and more (#107)

* Update README

* Update density field reader

* Update name of SDSSxALFAFA

* Fix quick bug

* Add little fixes

* Update README

* Put back fit_init

* Add paths to initial snapshots

* Add export

* Remove some choices

* Edit README

* Add Jens' comments

* Organize imports

* Rename snapshot

* Add additional print statement

* Add paths to initial snapshots

* Add masses to the initial files

* Add normalization

* Edit README

* Update README

* Fix bug in CSiBORG1 so that does not read fof_00001

* Edit README

* Edit README

* Overwrite comments

* Add paths to init lag

* Fix Quijote path

* Add lagpatch

* Edit submits

* Update README

* Fix numpy int problem

* Update README

* Add a flag to keep the snapshots open when fitting

* Add a flag to keep snapshots open

* Comment out some path issue

* Keep snapshots open

* Access directly snasphot

* Add lagpatch for CSiBORG2

* Add treatment of x-z coordinates flipping

* Add radial velocity field loader

* Update README

* Add lagpatch to Quijote

* Fix typo

* Add setter

* Fix typo

* Update README

* Add output halo cat as ASCII

* Add import

* Add halo plot

* Update README

* Add evaluating field at radial distanfe

* Add field shell evaluation

* Add enclosed mass computation

* Add BORG2 import

* Add BORG boxsize

* Add BORG paths

* Edit run

* Add BORG2 overdensity field

* Add bulk flow clauclation

* Update README

* Add new plots

* Add nbs

* Edit paper

* Update plotting

* Fix overlap paths to contain simname

* Add normalization of positions

* Add default paths to CSiBORG1

* Add overlap path simname

* Fix little things

* Add CSiBORG2 catalogue

* Update README

* Add import

* Add TNG density field constructor

* Add TNG density

* Add draft of calculating BORG ACL

* Fix bug

* Add ACL of enclosed density

* Add nmean acl

* Add galaxy bias calculation

* Add BORG acl notebook

* Add enclosed mass calculation

* Add TNG300-1 dir

* Add TNG300 and BORG1 dir

* Update nb

scripts_independent/density_field_tng.py

@@ -0,0 +1,56 @@
+# 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 glob import glob
+from os.path import join
+
+import MAS_library as MASL
+import numpy as np
+from h5py import File
+from tqdm import trange
+
+
+if __name__ == "__main__":
+    # Some parameters
+    basepath = "/mnt/extraspace/rstiskalek/TNG300-1"
+    snap = str(99).zfill(3)
+    grid = 1024
+    boxsize = 205000.0  # kpc/h
+    mpart = 0.00398342749867548 * 1e10  # Msun/h, DM particles mass
+    MAS = "PCS"
+
+    # Get the snapshot files
+    files = glob(join(basepath, "output", f"snapdir_{snap}", f"snap_{snap}.*"))
+    print(f"Found {len(files)} snapshot files.")
+
+    # Iterate over the snapshot files and construct the density field
+    rho = np.zeros((grid, grid, grid), dtype=np.float32)
+    for i in trange(len(files), desc="Reading snapshot files"):
+        with File(files[i], 'r') as f:
+            pos = f["PartType1/Coordinates"][...].astype(np.float32)
+
+        MASL.MA(pos, rho, boxsize, MAS, verbose=False)
+
+    # Convert to units h^2 Msun / kpc^3
+    rho *= mpart / (boxsize / grid)**3
+
+    # Save to file
+    fname = join(basepath, "postprocessing", "density_field",
+                 f"rho_dm_{snap}_{grid}_{MAS}.npy")
+    print(f"Saving to {fname}.", flush=True)
+    np.save(fname, rho)