mirror of
https://github.com/Richard-Sti/csiborgtools.git
synced 2024-12-22 18:38:02 +00:00
56e39a8b1d
* 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
110 lines
3.8 KiB
Python
110 lines
3.8 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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# 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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f = csiborgtools.read.read_h5(paths.particles_path(nsim))
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particles = f["particles"]
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clump_map = f["clumpmap"]
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clid2map = {clid: i for i, clid in enumerate(clump_map[:, 0])}
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clumps_cat = csiborgtools.read.ClumpsCatalogue(nsim, paths, 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 = csiborgtools.read.load_parent_particles(
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clumpid, particles, clump_map, clid2map, 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(clumpid)] = _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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