mirror of
https://github.com/Richard-Sti/csiborgtools.git
synced 2024-10-18 20:25:07 +02:00
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
105 lines
3.6 KiB
Python
105 lines
3.6 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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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("--ics", 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.CSiBORGPaths(**csiborgtools.paths_glamdring)
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partreader = csiborgtools.read.ParticleReader(paths)
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if args.ics is None or args.ics[0] == -1:
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ics = paths.get_ics(tonew=True)
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else:
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ics = args.ics
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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", numpy.float32),]
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# MPI loop over simulations
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jobs = csiborgtools.fits.split_jobs(len(ics), nproc)[rank]
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for nsim in [ics[i] for i in jobs]:
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nsnap = max(paths.get_snapshots(nsim))
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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_path(nsim, "particles"))
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parts = parts['particles']
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clump_map = csiborgtools.read.read_h5(paths.particles_path(nsim))
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clump_map = clump_map["clumpmap"]
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clumps_cat = csiborgtools.read.ClumpsCatalogue(nsim, paths, rawdata=True,
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load_fitted=False)
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clid2map = {clid: i for i, clid in enumerate(clump_map[:, 0])}
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ismain = clumps_cat.ismain
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out = csiborgtools.read.cols_to_structured(len(clumps_cat), cols_collect)
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indxs = clumps_cat["index"]
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for i, hid in enumerate(tqdm(indxs) if verbose else indxs):
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out["index"][i] = hid
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if not ismain[i]:
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continue
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part = csiborgtools.read.load_parent_particles(hid, parts, clump_map,
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clid2map, clumps_cat)
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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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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"][i] = patchsize
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out = out[ismain]
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# Now save it
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fout = paths.initmatch_path(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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