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Add pynbody and other support (#92)

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* Simplify box units

* Move old scripts

* Add printing

* Update readers

* Disable boundscheck

* Add new ordering

* Clean up imports

* Enforce dtype and add mass to quijote

* Simplify print statements

* Fix little typos

* Fix key bug

* Bug fixing

* Delete boring comments

* Improve ultimate clumps for PHEW

* Delete boring comments

* Add basic reading

* Remove 0th index HID

* Add flipping of X and Z

* Updates to halo catalogues

* Add ordered caching

* Fix flipping

* Add new flags

* Fix PHEW empty clumps

* Stop over-wrriting

* Little improvements to angular neighbours

* Add catalogue masking

* Change if-else statements

* Cache only filtered data

* Add PHEW cats

* Add comments

* Sort imports

* Get Quijote workign

* Docs

* Add HMF calculation

* Move to old

* Fix angular

* Add great circle distance

* Update imports

* Update impotrts

* Update docs

* Remove unused import

* Fix a quick bug

* Update compatibility

* Rename files

* Renaming

* Improve compatiblity

* Rename snapsht

* Fix snapshot bug

* Update interface

* Finish updating interface

* Update all paths

* Add old scripts

* Add basic halo

* Update imports

* Improve snapshot processing

* Update ordering

* Fix how CM positions accessed

* Add merger paths

* Add imports

* Add merger reading

* Add making a merger tree

* Add a basic merger tree reader

* Add imports

* Add main branch walking + comments + debuggin

* Get tree running

* Add working merger tree walking along main branch

* Add units conversion for merger data

* Add hid_to_array_index

* Update merger tree

* Add mergertree mass to PHEWcat

* Edit comments

* Add this to track changes...

* Fix a little bug

* Add mergertree mass

* Add cache clearing

* Improve summing substructure code

* Littbe bug

* Little updates to the merger tree reader

* Update .giignore

* Add box selection

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* Add manual tracker

* Fix bug

* Add m200c_to_r200c

* Add manual halo tracking

* Remove skipped snapshots

* update cosmo params to match csiborg

* remove old comments

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* Fix bugs

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* Updates

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* Add imports

* Add new observation class

* Add selection

* Add imports

* Fix small bug

* Add field copying for safety

* Add matching to survey without masking

* Add P(k) calculation

* Add nb

* Edit comment

* Move files

* Remove merger import

* Edit setup.yp

* Fix typo

* Edit import warnigns

* update nb

* Update README

* Update README

* Update README

* Add skeleton

* Add skeleton
This commit is contained in:
Richard Stiskalek 2023-12-07 14:23:32 +00:00 • committed by GitHub
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commit e972f8e3f2
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scripts/fit_init.py
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# 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 calculate the particle centre of mass, Lagrangian patch size in the
initial snapshot.
The initial snapshot particles are read from the sorted files.
"""
from argparse import ArgumentParser
from datetime import datetime
import numpy
from mpi4py import MPI
from taskmaster import work_delegation
from tqdm import tqdm
from utils import get_nsims
try:
import csiborgtools
except ModuleNotFoundError:
import sys
sys.path.append("../")
import csiborgtools
def _main(nsim, simname, verbose):
"""
Calculate the Lagrangian halo centre of mass and Lagrangian patch size in
the initial snapshot.
"""
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
cols = [("index", numpy.int32),
("x", numpy.float32),
("y", numpy.float32),
("z", numpy.float32),
("lagpatch_size", numpy.float32),
("lagpatch_ncells", numpy.int32),]
fname = paths.initmatch(nsim, simname, "particles")
parts = csiborgtools.read.read_h5(fname)
parts = parts['particles']
halo_map = csiborgtools.read.read_h5(paths.particles(nsim, simname))
halo_map = halo_map["halomap"]
if simname == "csiborg":
cat = csiborgtools.read.CSiBORGHaloCatalogue(
nsim, paths, bounds=None, load_fitted=False, load_initial=False)
else:
cat = csiborgtools.read.QuijoteHaloCatalogue(
nsim, paths, nsnap=4, load_fitted=False, load_initial=False)
hid2map = {hid: i for i, hid in enumerate(halo_map[:, 0])}
# Initialise the overlapper.
if simname == "csiborg":
kwargs = {"box_size": 2048, "bckg_halfsize": 512}
else:
kwargs = {"box_size": 512, "bckg_halfsize": 256}
overlapper = csiborgtools.match.ParticleOverlap(**kwargs)
out = csiborgtools.read.cols_to_structured(len(cat), cols)
for i, hid in enumerate(tqdm(cat["index"]) if verbose else cat["index"]):
out["index"][i] = hid
part = csiborgtools.read.load_halo_particles(hid, parts, halo_map,
hid2map)
# Skip if the halo has no particles or is too small.
if part is None or part.size < 40:
continue
pos, mass = part[:, :3], part[:, 3]
# Calculate the centre of mass and the Lagrangian patch size.
cm = csiborgtools.center_of_mass(pos, mass, boxsize=1.0)
distances = csiborgtools.periodic_distance(pos, cm, boxsize=1.0)
out["x"][i], out["y"][i], out["z"][i] = cm
out["lagpatch_size"][i] = numpy.percentile(distances, 99)
# Calculate the number of cells with > 0 density.
delta = overlapper.make_delta(pos, mass, subbox=True)
out["lagpatch_ncells"][i] = csiborgtools.delta2ncells(delta)
# Now save it
fout = paths.initmatch(nsim, simname, "fit")
if verbose:
print(f"{datetime.now()}: dumping fits to .. `{fout}`.", flush=True)
with open(fout, "wb") as f:
numpy.save(f, out)
if __name__ == "__main__":
parser = ArgumentParser()
parser.add_argument("--simname", type=str, default="csiborg",
choices=["csiborg", "quijote"],
help="Simulation name")
parser.add_argument("--nsims", type=int, nargs="+", default=None,
help="IC realisations. If `-1` processes all.")
args = parser.parse_args()
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
nsims = get_nsims(args, paths)
def main(nsim):
_main(nsim, args.simname, MPI.COMM_WORLD.Get_size() == 1)
work_delegation(main, nsims, MPI.COMM_WORLD)