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kNN-CDF secondary halo bias (#40)
* Add seperate autoknn script & config file * edit ics * Edit submission script * Add threshold values * Edit batch sizign * Remove print * edit * Rename files * Rename * Update nb * edit runs * Edit submit * Add median threshold * add new auto reader * editt submit * edit submit * Edit submit * Add mean prk * Edit runs * Remove correlation file * Move split to clutering * Add init * Remove import * Add the file * Add correlation reading * Edit scripts * Add below and above median permutation for cross * Update imports * Move rvs_in_sphere * Create utils * Split * Add import * Add normalised marks * Add import * Edit readme * Clean up submission file * Stop tracking submit files * Update gitignore * Add poisson field analytical expression * Add abstract generators * Add generators * Pass in the generator * Add a check for if there are any files * Start saving average density * Update nb * Update readme * Update units * Edit jobs * Update submits * Update reader * Add random crossing * Update crossing script * Add crossing with random * Update readme * Update notebook
This commit is contained in:
Richard Stiskalek
GitHub
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826ab61d2d
commit
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28 changed files with 2563 additions and 486 deletions
129
scripts/fit_halos.py
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129
scripts/fit_halos.py
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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 fit halos (concentration, ...). The particle array of each CSiBORG
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realisation must have been split in advance by `runsplit_halos`.
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"""
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from os.path import join
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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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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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import utils
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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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paths = csiborgtools.read.CSiBORGPaths()
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dumpdir = "/mnt/extraspace/rstiskalek/csiborg/"
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loaddir = join(dumpdir, "temp")
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cols_collect = [("npart", numpy.int64), ("totpartmass", numpy.float64),
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("Rs", numpy.float64), ("vx", numpy.float64),
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("vy", numpy.float64), ("vz", numpy.float64),
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("Lx", numpy.float64), ("Ly", numpy.float64),
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("Lz", numpy.float64), ("rho0", numpy.float64),
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("conc", numpy.float64), ("rmin", numpy.float64),
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("rmax", numpy.float64), ("r200", numpy.float64),
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("r500", numpy.float64), ("m200", numpy.float64),
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("m500", numpy.float64), ("lambda200c", numpy.float64)]
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for i, nsim in enumerate(paths.ic_ids(tonew=False)):
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if rank == 0:
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print("{}: calculating {}th simulation.".format(datetime.now(), i))
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nsnap = max(paths.get_snapshots(nsim))
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box = csiborgtools.units.BoxUnits(nsnap, nsim, paths)
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jobs = csiborgtools.fits.split_jobs(utils.Nsplits, nproc)[rank]
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for nsplit in jobs:
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parts, part_clumps, clumps = csiborgtools.fits.load_split_particles(
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nsplit, nsnap, nsim, paths, remove_split=False)
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N = clumps.size
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cols = [("index", numpy.int64), ("npart", numpy.int64),
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("totpartmass", numpy.float64), ("Rs", numpy.float64),
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("rho0", numpy.float64), ("conc", numpy.float64),
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("lambda200c", numpy.float64), ("vx", numpy.float64),
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("vy", numpy.float64), ("vz", numpy.float64),
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("Lx", numpy.float64), ("Ly", numpy.float64),
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("Lz", numpy.float64), ("rmin", numpy.float64),
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("rmax", numpy.float64), ("r200", numpy.float64),
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("r500", numpy.float64), ("m200", numpy.float64),
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("m500", numpy.float64)]
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out = csiborgtools.utils.cols_to_structured(N, cols)
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out["index"] = clumps["index"]
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for n in range(N):
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# Pick clump and its particles
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xs = csiborgtools.fits.pick_single_clump(n, parts, part_clumps,
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clumps)
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clump = csiborgtools.fits.Clump.from_arrays(
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*xs, rhoc=box.box_rhoc, G=box.box_G)
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out["npart"][n] = clump.Npart
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out["rmin"][n] = clump.rmin
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out["rmax"][n] = clump.rmax
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out["totpartmass"][n] = clump.total_particle_mass
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out["vx"][n] = numpy.average(clump.vel[:, 0], weights=clump.m)
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out["vy"][n] = numpy.average(clump.vel[:, 1], weights=clump.m)
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out["vz"][n] = numpy.average(clump.vel[:, 2], weights=clump.m)
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out["Lx"][n], out["Ly"][n], out["Lz"][n] = clump.angular_momentum
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# Spherical overdensity radii and masses
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rs, ms = clump.spherical_overdensity_mass([200, 500])
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out["r200"][n] = rs[0]
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out["r500"][n] = rs[1]
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out["m200"][n] = ms[0]
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out["m500"][n] = ms[1]
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out["lambda200c"][n] = clump.lambda200c
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# NFW profile fit
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if clump.Npart > 10 and numpy.isfinite(out["r200"][n]):
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nfwpost = csiborgtools.fits.NFWPosterior(clump)
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logRs, __ = nfwpost.maxpost_logRs()
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Rs = 10**logRs
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if not numpy.isnan(logRs):
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out["Rs"][n] = Rs
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out["rho0"][n] = nfwpost.rho0_from_Rs(Rs)
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out["conc"][n] = out["r200"][n] / Rs
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csiborgtools.read.dump_split(out, nsplit, nsnap, nsim, paths)
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# Wait until all jobs finished before moving to another simulation
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comm.Barrier()
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# Use the rank 0 to combine outputs for this CSiBORG realisation
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if rank == 0:
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print("Collecting results!")
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partreader = csiborgtools.read.ParticleReader(paths)
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out_collected = csiborgtools.read.combine_splits(
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utils.Nsplits, nsnap, nsim, partreader, cols_collect,
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remove_splits=True, verbose=False)
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fname = join(paths.dumpdir, "ramses_out_{}_{}.npy"
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.format(str(nsim).zfill(5), str(nsnap).zfill(5)))
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print("Saving results to `{}`.".format(fname))
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numpy.save(fname, out_collected)
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comm.Barrier()
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if rank == 0:
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print("All finished! See ya!")
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