mirror of
https://github.com/Richard-Sti/csiborgtools.git
synced 2024-10-19 00:15:06 +02:00
eb8d070fff
* Add moving FoF membership files * add FoF membership path * Add notes where its PHEW * Add FoF catalogue path * Correct typo * Add more functionalities * Make work with halo IDs from FoF * Edit print statement * Fix copy bug * copy * Add FoF catalogue reading * Clean up script * Fix typo * Little edits * Fix naming convention * Rename key * Remove loading substructure particles * Rename CSiBORG Cat * Rename clumps cat * Rename cat * Remove misplaced import * Switch to halos * rm import * structfit of only halos * Add FoF halo reading * Add a short comment * Fix __getitem__ to work with int * Fix problems * Improve __getitem__ * Add more conversion * Fix indexing * Fix __getitem__ assertion * Fix numbers * Rename * Fix verbosity flags * Add full Quijote HMF option * Add plot of Quijote only * Add quijote full paths * Fix the fit_init script * Renam arg * Update .gitignore * add default argument name * Change default verbosity flag * Modernise script structure * Fix dictionary * Fix reading to include m200c * Modernise script * Add args
108 lines
3.9 KiB
Python
108 lines
3.9 KiB
Python
# Copyright (C) 2022 Richard Stiskalek
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# This program is free software; you can redistribute it and/or modify it
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# under the terms of the GNU General Public License as published by the
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# Free Software Foundation; either version 3 of the License, or (at your
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# option) any later version.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
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# Public License for more details.
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#
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# You should have received a copy of the GNU General Public License along
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# with this program; if not, write to the Free Software Foundation, Inc.,
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# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
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"""
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Script to calculate the particle centre of mass, Lagrangian patch size in the
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initial snapshot. The initial snapshot particles are read from the sorted
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files.
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"""
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from argparse import ArgumentParser
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from datetime import datetime
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import numpy
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from mpi4py import MPI
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from tqdm import tqdm
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from utils import get_nsims
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try:
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import csiborgtools
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except ModuleNotFoundError:
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import sys
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sys.path.append("../")
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import csiborgtools
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# Get MPI things
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comm = MPI.COMM_WORLD
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rank = comm.Get_rank()
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nproc = comm.Get_size()
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verbose = nproc == 1
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# Argument parser
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parser = ArgumentParser()
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parser.add_argument("--simname", type=str, default="csiborg",
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choices=["csiborg", "quijote"],
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help="Simulation name")
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parser.add_argument("--nsims", type=int, nargs="+", default=None,
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help="IC realisations. If `-1` processes all simulations.")
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args = parser.parse_args()
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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partreader = csiborgtools.read.ParticleReader(paths)
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nsims = get_nsims(args, paths)
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cols_collect = [("index", numpy.int32),
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("x", numpy.float32),
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("y", numpy.float32),
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("z", numpy.float32),
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("lagpatch_size", numpy.float32),
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("lagpatch_ncells", numpy.int32),]
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# MPI loop over simulations
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jobs = csiborgtools.fits.split_jobs(len(nsims), nproc)[rank]
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for nsim in [nsims[i] for i in jobs]:
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nsnap = max(paths.get_snapshots(nsim))
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overlapper = csiborgtools.match.ParticleOverlap()
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print(f"{datetime.now()}: rank {rank} calculating simulation `{nsim}`.",
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flush=True)
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parts = csiborgtools.read.read_h5(paths.initmatch(nsim, "particles"))
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parts = parts['particles']
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halo_map = csiborgtools.read.read_h5(paths.particles(nsim))
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halo_map = halo_map["halomap"]
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cat = csiborgtools.read.CSiBORGHaloCatalogue(
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nsim, paths, rawdata=True, load_fitted=False, load_initial=False)
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hid2map = {hid: i for i, hid in enumerate(halo_map[:, 0])}
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out = csiborgtools.read.cols_to_structured(len(cat), cols_collect)
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for i, hid in enumerate(tqdm(cat["index"]) if verbose else cat["index"]):
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out["index"][i] = hid
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part = csiborgtools.read.load_halo_particles(hid, parts, halo_map,
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hid2map)
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# Skip if the halo is too small.
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if part is None or part.size < 100:
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continue
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# Calculate the centre of mass and the Lagrangian patch size.
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dist, cm = csiborgtools.fits.dist_centmass(part)
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# We enforce a maximum patchsize of 0.075 in box coordinates.
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patchsize = min(numpy.percentile(dist, 99), 0.075)
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out["x"][i], out["y"][i], out["z"][i] = cm
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out["lagpatch_size"][i] = patchsize
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# Calculate the number of cells with > 0 density.
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delta = overlapper.make_delta(part[:, :3], part[:, 3], subbox=True)
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out["lagpatch_ncells"][i] = csiborgtools.fits.delta2ncells(delta)
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# Now save it
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fout = paths.initmatch(nsim, "fit")
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print(f"{datetime.now()}: dumping fits to .. `{fout}`.",
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flush=True)
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with open(fout, "wb") as f:
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numpy.save(f, out)
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