mirror of
https://github.com/Richard-Sti/csiborgtools.git
synced 2024-10-19 00:15:06 +02:00
1a9e6177d7
* Edit the particle paths * Remove script * Add h5py to dumping * Minor adjustments * add h5py support * remove split path * h5py support * Type * Edit initmatch paths * Shorten func * dist_centmass to work with 2D arrays * Forgot to return the centre of mass * Fixed code * Fix halo bug * Start MPI broadcasting * Mini bug * Remove commenting * Remove test statement * Fix index * Printing from rank 0 only * Move where clump index stored * Add dtype options * Add dtype options
140 lines
4.6 KiB
Python
140 lines
4.6 KiB
Python
# Copyright (C) 2023 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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A script to calculate the particle's separation from the CM and save it.
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Currently MPI is not supported.
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"""
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from argparse import ArgumentParser
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from datetime import datetime
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from gc import collect
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import h5py
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import numpy
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from mpi4py import MPI
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from tqdm import trange
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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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parser = ArgumentParser()
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parser.add_argument("--ics", type=int, nargs="+", default=None,
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help="IC realisatiosn. If `-1` processes all simulations.")
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args = parser.parse_args()
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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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if nproc > 1:
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raise NotImplementedError("MPI is not implemented implemented yet.")
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paths = csiborgtools.read.CSiBORGPaths(**csiborgtools.paths_glamdring)
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cols_collect = [("r", numpy.float32), ("M", numpy.float32)]
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if args.ics is None or args.ics == -1:
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nsims = paths.get_ics(tonew=False)
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else:
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nsims = args.ics
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def load_clump_particles(clumpid, particles, clump_map):
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"""
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Load a clump's particles. If it is not there, i.e clump has no associated
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particles, return `None`.
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"""
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try:
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return particles[clump_map[clumpid], :]
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except KeyError:
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return None
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def load_parent_particles(clumpid, particles, clump_map, clumps_cat):
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"""
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Load a parent halo's particles.
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"""
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indxs = clumps_cat["index"][clumps_cat["parent"] == clumpid]
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# We first load the particles of each clump belonging to this parent
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# and then concatenate them for further analysis.
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clumps = []
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for ind in indxs:
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parts = load_clump_particles(ind, particles, clump_map)
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if parts is not None:
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clumps.append(parts)
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if len(clumps) == 0:
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return None
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return numpy.concatenate(clumps)
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# We loop over simulations. Here later optionally add MPI.
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for i, nsim in enumerate(nsims):
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if rank == 0:
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now = datetime.now()
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print(f"{now}: calculating {i}th simulation `{nsim}`.", flush=True)
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nsnap = max(paths.get_snapshots(nsim))
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box = csiborgtools.read.BoxUnits(nsnap, nsim, paths)
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particles = h5py.File(paths.particle_h5py_path(nsim), 'r')["particles"]
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clump_map = h5py.File(paths.particle_h5py_path(nsim, "clumpmap"), 'r')
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clumps_cat = csiborgtools.read.ClumpsCatalogue(nsim, paths, maxdist=None,
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minmass=None, rawdata=True,
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load_fitted=False)
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ismain = clumps_cat.ismain
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ntasks = len(clumps_cat)
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# We loop over halos and add ther particle positions to this dictionary,
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# which we will later save as an archive.
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out = {}
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for j in trange(ntasks) if nproc == 1 else range(ntasks):
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# If we are fitting halos and this clump is not a main, then continue.
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if not ismain[j]:
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continue
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clumpid = clumps_cat["index"][j]
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parts = load_parent_particles(clumpid, particles, clump_map,
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clumps_cat)
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# If we have no particles, then do not save anything.
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if parts is None:
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continue
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obj = csiborgtools.fits.Clump(parts, clumps_cat[j], box)
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r200m, m200m = obj.spherical_overdensity_mass(200, npart_min=10,
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kind="matter")
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r = obj.r()
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mask = r <= r200m
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_out = csiborgtools.read.cols_to_structured(numpy.sum(mask),
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cols_collect)
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_out["r"] = r[mask]
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_out["M"] = obj["M"][mask]
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out[str(clumps_cat["index"][j])] = _out
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# Finished, so we save everything.
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fout = paths.radpos_path(nsnap, nsim)
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now = datetime.now()
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print(f"{now}: saving radial profiles for simulation {nsim} to `{fout}`",
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flush=True)
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numpy.savez(fout, **out)
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# Clean up the memory just to be sure.
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del out
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collect()
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