Overlapper improvements (#53)

* Store indices as f32

* Fix init sorting

* Organise imports

* Rename pathing

* Add particle loading

* Improve particle reading

* Add h5py reader

* edit particle path

* Update particles loading

* update particles loading

* Fix particle dumping

* Add init fitting

* Fix bug due to insufficient precision

* Add commnet

* Add comment

* Add clumps catalogue to halo cat

* Add comment

* Make sure PIDS never forced to float32

* fix pid reading

* fix pid reading

* Update matching to work with new arrays

* Stop using cubical sub boxes, turn off nshift if no smoothing

* Improve caching

* Move function definitions

* Simplify calculation

* Add import

* Small updates to the halo

* Simplify calculation

* Simplify looping calculation

* fix tonew

* Add initial data

* Add skip condition

* Add unit conversion

* Add loading background in batches

* Rename mmain index

* Switch overlaps to h5

* Add finite lagpatch check

* fix column name

* Add verbosity flags

* Save halo IDs instead.

* Switch back to npz

* Delte nbs

* Reduce size of the box

* Load correct bckg of halos being matched

* Remove verbosity

* verbosity edits

* Change lower thresholds

scripts/pre_sortinit.py

@@ -0,0 +1,82 @@
+# Copyright (C) 2022 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 sort the initial snapshot particles according to their final
+snapshot ordering, which is sorted by the clump IDs.
+"""
+from argparse import ArgumentParser
+from datetime import datetime
+
+import h5py
+from gc import collect
+import numpy
+from mpi4py import MPI
+
+try:
+    import csiborgtools
+except ModuleNotFoundError:
+    import sys
+
+    sys.path.append("../")
+    import csiborgtools
+
+
+# Get MPI things
+comm = MPI.COMM_WORLD
+rank = comm.Get_rank()
+nproc = comm.Get_size()
+verbose = nproc == 1
+
+# Argument parser
+parser = ArgumentParser()
+parser.add_argument("--ics", type=int, nargs="+", default=None,
+                    help="IC realisations. If `-1` processes all simulations.")
+args = parser.parse_args()
+paths = csiborgtools.read.CSiBORGPaths(**csiborgtools.paths_glamdring)
+partreader = csiborgtools.read.ParticleReader(paths)
+# NOTE: ID has to be the last column.
+pars_extract = ["x", "y", "z", "M", "ID"]
+
+if args.ics is None or args.ics[0] == -1:
+    ics = paths.get_ics(tonew=True)
+else:
+    ics = args.ics
+
+# We loop over simulations. Each simulation is then procesed with MPI, rank 0
+# loads the data and broadcasts it to other ranks.
+jobs = csiborgtools.fits.split_jobs(len(ics), nproc)[rank]
+for i in jobs:
+    nsim = ics[i]
+    nsnap = max(paths.get_snapshots(nsim))
+
+    print(f"{datetime.now()}: reading and processing simulation {nsim}.",
+          flush=True)
+    # We first load the particle IDs in the final snapshot.
+    pidf = csiborgtools.read.read_h5(paths.particles_path(nsim))
+    pidf = pidf["particle_ids"]
+    # Then we load the particles in the initil snapshot and make sure that
+    # their particle IDs are sorted as in the final snapshot.
+    # Again, because of precision this must be read as structured.
+    part0, pid0 = partreader.read_particle(
+        1, nsim, pars_extract, return_structured=False, verbose=verbose)
+    # First enforce them to already be sorted and then apply reverse
+    # sorting from the final snapshot.
+    part0 = part0[numpy.argsort(pid0)]
+    del pid0
+    collect()
+    part0 = part0[numpy.argsort(numpy.argsort(pidf))]
+    print(f"{datetime.now()}: dumping particles for {nsim}.", flush=True)
+    with h5py.File(paths.initmatch_path(nsim, "particles"), "w") as f:
+        f.create_dataset("particles", data=part0)