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https://github.com/Richard-Sti/csiborgtools_public.git
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Particle init CM separation (#17)
* Rename * rename module * add new_ic_ids * Add to_new support * rm unnecessary comment * Remove JUlia! * add new package attempt * add dump script * simplify positions getter * Remove unused code * change dumpdirs * update project * Add sorting * fix indexing bug * add comment * Add particle dumping * Delete blank line * Delete Julia things * Update README * add working script * fix assignment bug * fix bug * save temp to temp folder * fix indexing bug & path * do not always crreate folder * Rename file * add initcm reader * add x0, y0, z0 transforms * add initcm to halo cat * docs update * add initial KNN * add attempt at init match * add initial fiducial radius * rm blank space * Add further KNN Init pos support * Add init radius support * Remove message about the bug * Get rid of an error msg * purge mention of knn_init * Add init CM distance calc
This commit is contained in:
Richard Stiskalek
GitHub
parent
c3c686fa60
commit
13a9d11afe
12 changed files with 409 additions and 525 deletions
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# 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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using Pkg: activate, build
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activate("../JuliaCSiBORGTools/")
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using JuliaCSiBORGTools
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using NPZ: npzread
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using PyCall: pyimport
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csiborgtools = pyimport("csiborgtools")
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verbose = true
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paths = csiborgtools.read.CSiBORGPaths()
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nsims = paths.ic_ids[:1]
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for nsim in nsims
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nsnap_min = convert(Int64, paths.get_minimum_snapshot(nsim))
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nsnap_max = convert(Int64, paths.get_maximum_snapshot(nsim))
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# Get the maximum snapshot properties
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verbose ? println("Loading snapshot $nsnap_max from simulation $nsim") : nothing
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pids, ppos, pmass, clumpids = csiborgtools.read.get_positions(nsim, nsnap_max, get_clumpid=true, verbose=false)
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println("Sizes are: ")
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println(size(pids))
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println(size(ppos))
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println(size(pmass))
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# # Get the minimum snapshot properties
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# verbose ? println("Loading snapshot $nsnap_min from simulation $nsim") : nothing
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# pids, ppos, pmass = csiborgtools.read.get_positions(nsim, nsnap_max, get_clumpid=false, verbose=false)
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JuliaCSiBORGTools.halo_parts(0, partids, clumpids)
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end
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143
scripts/run_initmatch.py
Normal file
143
scripts/run_initmatch.py
Normal file
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# 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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A script to calculate the centre of mass of particles at redshift 70 that
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are grouped in a clump at present redshift.
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Optionally also dumps the clumps information, however watch out as this will
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eat up a lot of memory.
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"""
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from argparse import ArgumentParser
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import numpy
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from datetime import datetime
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from mpi4py import MPI
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from distutils.util import strtobool
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from os.path import join, isdir
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from os import mkdir
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from os import remove
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from sys import stdout
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from gc import collect
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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("--dump_clumps", default=False,
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type=lambda x: bool(strtobool(x)))
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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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init_paths = csiborgtools.read.CSiBORGPaths(to_new=True)
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fin_paths = csiborgtools.read.CSiBORGPaths(to_new=False)
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nsims = init_paths.ic_ids
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# Output files
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dumpdir = "/mnt/extraspace/rstiskalek/csiborg/initmatch"
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ftemp = join(dumpdir, "temp", "temp_{}_{}.npy")
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fperm = join(dumpdir, "clump_cm_{}.npy")
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for nsim in nsims:
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if rank == 0:
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print("{}: reading simulation {}.".format(datetime.now(), nsim))
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stdout.flush()
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# Check that the output folder for this sim exists
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clumpdumpdir = join(dumpdir, "out_{}".format(nsim))
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if args.dump_clumps and rank == 0 and not isdir(clumpdumpdir):
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mkdir(clumpdumpdir)
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# Barrier to make sure we created the directory with the rank 0
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comm.Barrier()
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# Set the snapshot numbers
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init_paths.set_info(nsim, init_paths.get_minimum_snapshot(nsim))
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fin_paths.set_info(nsim, fin_paths.get_maximum_snapshot(nsim))
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# Set the readers
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init_reader = csiborgtools.read.ParticleReader(init_paths)
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fin_reader = csiborgtools.read.ParticleReader(fin_paths)
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# Read and sort the initial particle files by their particle IDs
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part0 = init_reader.read_particle(["x", "y", "z", "M", "ID"],
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verbose=False)
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part0 = part0[numpy.argsort(part0["ID"])]
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# Order the final snapshot clump IDs by the particle IDs
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pid = fin_reader.read_particle(["ID"], verbose=False)["ID"]
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clump_ids = fin_reader.read_clumpid(verbose=False)
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clump_ids = clump_ids[numpy.argsort(pid)]
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del pid
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collect()
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# Get rid of the clumps whose index is 0 -- those are unassigned
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mask = clump_ids > 0
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clump_ids = clump_ids[mask]
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part0 = part0[mask]
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del mask
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collect()
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if rank == 0:
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print("{}: dumping clumps for simulation.".format(datetime.now()))
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stdout.flush()
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# Grab unique clump IDs and loop over them
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unique_clumpids = numpy.unique(clump_ids)
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njobs = unique_clumpids.size
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jobs = csiborgtools.fits.split_jobs(njobs, nproc)[rank]
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for i in jobs:
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n = unique_clumpids[i]
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x0 = part0[clump_ids == n]
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# Center of mass
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cm = numpy.asanyarray(
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[numpy.average(x0[p], weights=x0["M"]) for p in ('x', 'y', 'z')])
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# Dump the center of mass
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with open(ftemp.format(nsim, n), 'wb') as f:
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numpy.save(f, cm)
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# Optionally dump the entire clump
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if args.dump_clumps:
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fout = join(clumpdumpdir, "clump_{}.npy".format(n))
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stdout.flush()
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with open(fout, "wb") as f:
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numpy.save(f, x0)
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comm.Barrier()
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if rank == 0:
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print("Collecting CM files...")
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stdout.flush()
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# Collect the centre of masses and dump them
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dtype = {"names": ['x', 'y', 'z', "ID"],
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"formats": [numpy.float32] * 3 + [numpy.int32]}
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out = numpy.full(njobs, numpy.nan, dtype=dtype)
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for i, n in enumerate(unique_clumpids):
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with open(ftemp.format(nsim, n), 'rb') as f:
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fin = numpy.load(f)
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out['x'][i] = fin[0]
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out['y'][i] = fin[1]
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out['z'][i] = fin[2]
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out["ID"][i] = n
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remove(ftemp.format(nsim, n))
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print("Dumping CM files to .. `{}`.".format(fperm.format(nsim)))
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with open(fperm.format(nsim), 'wb') as f:
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numpy.save(f, out)
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