csiborgtools/scripts/run_fit_halos.py

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Within halo work and NFW fit (#4) * add listing of snapshots * change distance to comoving * ignore cp files * rename nb * add str to list * add NFW profile shapes * add fits imports * Rename to Nsnap * in clumps_read only select props * make clumpid int * expand doc * add import * edit readme * distribute halos * add profile & posterior * add import * add import * add documentation * add rvs and init guess * update todo * update nb * add file * return end index too * change clump_ids format to int32 * skeleton of dump particle * update nb * add func to drop 0 clump indxs parts * add import * add halo dump * switch to float32 * Update TODO * update TODO * add func that loads a split * add halo object * Rename to clump * make post work with a clump * add optimiser * add Nsplits * ignore submission scripts * ignore .out * add dumppath * add job splitting * add split halos script * rename file * renaem files * rm file * rename imports * edit desc * add pick clump * add number of particles * update TODO * update todo * add script * add dumping * change dumpdir structure * change dumpdir * add import * Remove tqdm * Increase the number of splits * rm shuffle option * Change to remove split * add emojis * fix part counts in splits * change num of splits * rm with particle cut * keep splits * fit only if 10 part and more * add min distance * rm warning about not set vels * update TODO * calculate rho0 too * add results collection * add import * add func to combine splits * update TODO * add extract cols * update nb * update TODO
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# Copyright (C) 2022 Richard Stiskalek
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option) any later version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
# Public License for more details.
#
# You should have received a copy of the GNU General Public License along
# with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
"""
A script to fit halos (concentration, ...). The particle array of each CSiBORG
realisation must have been split in advance by `run_split_halos`.
"""
import numpy
from datetime import datetime
Within halo work and NFW fit (#4) * add listing of snapshots * change distance to comoving * ignore cp files * rename nb * add str to list * add NFW profile shapes * add fits imports * Rename to Nsnap * in clumps_read only select props * make clumpid int * expand doc * add import * edit readme * distribute halos * add profile & posterior * add import * add import * add documentation * add rvs and init guess * update todo * update nb * add file * return end index too * change clump_ids format to int32 * skeleton of dump particle * update nb * add func to drop 0 clump indxs parts * add import * add halo dump * switch to float32 * Update TODO * update TODO * add func that loads a split * add halo object * Rename to clump * make post work with a clump * add optimiser * add Nsplits * ignore submission scripts * ignore .out * add dumppath * add job splitting * add split halos script * rename file * renaem files * rm file * rename imports * edit desc * add pick clump * add number of particles * update TODO * update todo * add script * add dumping * change dumpdir structure * change dumpdir * add import * Remove tqdm * Increase the number of splits * rm shuffle option * Change to remove split * add emojis * fix part counts in splits * change num of splits * rm with particle cut * keep splits * fit only if 10 part and more * add min distance * rm warning about not set vels * update TODO * calculate rho0 too * add results collection * add import * add func to combine splits * update TODO * add extract cols * update nb * update TODO
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from os.path import join
from mpi4py import MPI
try:
import csiborgtools
except ModuleNotFoundError:
import sys
sys.path.append("../")
import csiborgtools
import utils
F64 = numpy.float64
I64 = numpy.int64
# Get MPI things
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
nproc = comm.Get_size()
dumpdir = utils.dumpdir
loaddir = join(utils.dumpdir, "temp")
cols_collect = [("npart", I64), ("totpartmass", F64), ("Rs", F64),
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("vx", F64), ("vy", F64), ("vz", F64),
("rho0", F64), ("conc", F64), ("rmin", F64),
("rmax", F64), ("r200", F64), ("r500", F64),
("m200", F64), ("m500", F64)]
paths = csiborgtools.read.CSiBORGPaths()
for i, n_sim in enumerate(paths.ic_ids):
if rank == 0:
print("{}: calculating {}th simulation.".format(datetime.now(), i))
# Correctly set the paths!
n_snap = paths.get_maximum_snapshot(n_sim)
paths.set_info(n_sim, n_snap)
box = csiborgtools.units.BoxUnits(paths)
jobs = csiborgtools.fits.split_jobs(utils.Nsplits, nproc)[rank]
for n_split in jobs:
parts, part_clumps, clumps = csiborgtools.fits.load_split_particles(
n_split, paths, remove_split=False)
N = clumps.size
cols = [("index", I64), ("npart", I64), ("totpartmass", F64),
("Rs", F64), ("rho0", F64), ("conc", F64),
("vx", F64), ("vy", F64), ("vz", F64),
("rmin", F64), ("rmax", F64),
("r200", F64), ("r500", F64), ("m200", F64), ("m500", F64)]
out = csiborgtools.utils.cols_to_structured(N, cols)
out["index"] = clumps["index"]
for n in range(N):
# Pick clump and its particles
xs = csiborgtools.fits.pick_single_clump(n, parts, part_clumps,
clumps)
clump = csiborgtools.fits.Clump.from_arrays(*xs, rhoc=box.box_rhoc)
out["npart"][n] = clump.Npart
out["rmin"][n] = clump.rmin
out["rmax"][n] = clump.rmax
out["totpartmass"][n] = clump.total_particle_mass
out["vx"][n] = numpy.average(clump.vel[:, 0], weights=clump.m)
out["vy"][n] = numpy.average(clump.vel[:, 1], weights=clump.m)
out["vz"][n] = numpy.average(clump.vel[:, 2], weights=clump.m)
# Spherical overdensity radii and masses
rs, ms = clump.spherical_overdensity_mass([200, 500])
out["r200"][n] = rs[0]
out["r500"][n] = rs[1]
out["m200"][n] = ms[0]
out["m500"][n] = ms[1]
# NFW profile fit
if clump.Npart > 10 and numpy.isfinite(out["r200"][n]):
nfwpost = csiborgtools.fits.NFWPosterior(clump)
logRs, __ = nfwpost.maxpost_logRs()
Rs = 10**logRs
if not numpy.isnan(logRs):
out["Rs"][n] = Rs
out["rho0"][n] = nfwpost.rho0_from_Rs(Rs)
out["conc"][n] = out["r200"][n] / Rs
csiborgtools.read.dump_split(out, n_split, paths)
# Wait until all jobs finished before moving to another simulation
comm.Barrier()
# Use the rank 0 to combine outputs for this CSiBORG realisation
if rank == 0:
print("Collecting results!")
partreader = csiborgtools.read.ParticleReader(paths)
out_collected = csiborgtools.read.combine_splits(
utils.Nsplits, partreader, cols_collect, remove_splits=True,
verbose=False)
fname = join(paths.dumpdir, "ramses_out_{}_{}.npy"
.format(str(paths.n_sim).zfill(5),
str(paths.n_snap).zfill(5)))
print("Saving results to `{}`.".format(fname))
numpy.save(fname, out_collected)
comm.Barrier()
Within halo work and NFW fit (#4) * add listing of snapshots * change distance to comoving * ignore cp files * rename nb * add str to list * add NFW profile shapes * add fits imports * Rename to Nsnap * in clumps_read only select props * make clumpid int * expand doc * add import * edit readme * distribute halos * add profile & posterior * add import * add import * add documentation * add rvs and init guess * update todo * update nb * add file * return end index too * change clump_ids format to int32 * skeleton of dump particle * update nb * add func to drop 0 clump indxs parts * add import * add halo dump * switch to float32 * Update TODO * update TODO * add func that loads a split * add halo object * Rename to clump * make post work with a clump * add optimiser * add Nsplits * ignore submission scripts * ignore .out * add dumppath * add job splitting * add split halos script * rename file * renaem files * rm file * rename imports * edit desc * add pick clump * add number of particles * update TODO * update todo * add script * add dumping * change dumpdir structure * change dumpdir * add import * Remove tqdm * Increase the number of splits * rm shuffle option * Change to remove split * add emojis * fix part counts in splits * change num of splits * rm with particle cut * keep splits * fit only if 10 part and more * add min distance * rm warning about not set vels * update TODO * calculate rho0 too * add results collection * add import * add func to combine splits * update TODO * add extract cols * update nb * update TODO
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if rank == 0:
print("All finished! See ya!")