mirror of
https://github.com/Richard-Sti/csiborgtools.git
synced 2024-10-18 20:15:05 +02:00
fb4b4edf19
* Renaming * Edit docs * Delete old function * Add a blank space * Rename particle reader * Add comments * Rename * Rename * edit get_snapshots * More renaming * Remove old correction * Add import * Add basics of the Quijote reader * Add a blank space * Fix paths * Rename function * Fix HID and path * Add more FoF reading * Move definition * Adding arguments * Renaming * Add kwargs for backward comp * FoF Quijote return only hids * Add sorting of quijote * Add path to CSiBORG ICs snapshot * Add support for Quijote * initmatch paths for quijote * Add kwargs * Fix blank lines * Rename kwarg * Remove unused import * Remove hardcoded numbers * Update for Quijote * Do not store velocities in QUijote ICs * Box units mass Quijote * Fix typo * Ensure particles are not right at the edge * Add structfit paths for QUuijote * Basic CSiBORG units * Add more quijote halo reading * Add Quijote fitting * Docs changes * Docs changes
122 lines
4.2 KiB
Python
122 lines
4.2 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 sort the initial snapshot particles according to their final
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snapshot ordering, which is sorted by the halo IDs.
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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 taskmaster import work_delegation
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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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def _main(nsim, simname, verbose):
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"""
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Sort the initial snapshot particles according to their final snapshot
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ordering and dump them into a HDF5 file.
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Parameters
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----------
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nsim : int
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IC realisation index.
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simname : str
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Simulation name.
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verbose : bool
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Verbosity flag.
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"""
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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if simname == "csiborg":
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partreader = csiborgtools.read.CSiBORGReader(paths)
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else:
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partreader = csiborgtools.read.QuijoteReader(paths)
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if verbose:
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print(f"{datetime.now()}: reading and processing simulation `{nsim}`.",
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flush=True)
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# We first load the particle IDs in the final snapshot.
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pidf = csiborgtools.read.read_h5(paths.particles(nsim, simname))
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pidf = pidf["particle_ids"]
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# Then we load the particles in the initil snapshot and make sure that
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# their particle IDs are sorted as in the final snapshot. Again, because of
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# precision this must be read as structured.
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if simname == "csiborg":
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pars_extract = ["x", "y", "z", "M", "ID"]
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# CSiBORG's initial snapshot ID
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nsnap = 1
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else:
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pars_extract = None
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# Use this to point the reader to the ICs snapshot
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nsnap = -1
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part0, pid0 = partreader.read_particle(
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nsnap, nsim, pars_extract, return_structured=False, verbose=verbose)
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# Quijote's initial snapshot information also contains velocities but we
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# don't need those.
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if simname == "quijote":
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part0 = part0[:, [0, 1, 2, 6]]
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# In Quijote some particles are position precisely at the edge of the
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# box. Move them to be just inside.
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pos = part0[:, :3]
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mask = pos >= 1
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if numpy.any(mask):
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spacing = numpy.spacing(pos[mask])
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assert numpy.max(spacing) <= 1e-5
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pos[mask] -= spacing
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# First enforce them to already be sorted and then apply reverse
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# sorting from the final snapshot.
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part0 = part0[numpy.argsort(pid0)]
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del pid0
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collect()
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part0 = part0[numpy.argsort(numpy.argsort(pidf))]
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fout = paths.initmatch(nsim, simname, "particles")
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if verbose:
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print(f"{datetime.now()}: dumping particles for `{nsim}` to `{fout}`",
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flush=True)
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with h5py.File(fout, "w") as f:
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f.create_dataset("particles", data=part0)
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if __name__ == "__main__":
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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.")
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args = parser.parse_args()
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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nsims = get_nsims(args, paths)
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def main(nsim):
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_main(nsim, args.simname, MPI.COMM_WORLD.Get_size() == 1)
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work_delegation(main, nsims, MPI.COMM_WORLD)
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