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JAX and fix conc (#6)

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* change to log10 initlogRs

* add uncertainty

* add check if hessian negative

* update TODO

* update TODO

* output the error too

* save e_logRs

* add concentration calculation

* calcul concentration

* missed comma in a list

* Update TODO

* fix bug

* add box units and pretty status

* make uncertainty optional

* add BIC function

* remove BIC again

* add new overdensity calculation

* change defualt values to max dist and mass

* change to r200

* new halo find

* speed up the calculation

* add commented fucn

* update TODO

* add check whether too close to outside boundary

* Update TODO

* extract velocity as well

* calculate m200 and m500

* update nb

* update TODO
This commit is contained in:
Richard Stiskalek 2022-11-05 21:17:05 +00:00 • committed by GitHub
parent ee84c12a55
commit 7f58b1f78c
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GPG key ID: 4AEE18F83AFDEB23
6 changed files with 278 additions and 594 deletions
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498
scripts/plot_concentration.ipynb
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File diff suppressed because one or more lines are too long

47
scripts/run_fit_halos.py
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@ -18,6 +18,7 @@ realisation must have been split in advance by `run_split_halos`.
"""
import numpy
from datetime import datetime
from os.path import join
from mpi4py import MPI
try:
@ -43,52 +44,56 @@ nproc = comm.Get_size()
dumpdir = utils.dumpdir
loaddir = join(utils.dumpdir, "temp")
cols_collect = [("npart", I64), ("totpartmass", F64), ("logRs", F64),
("rho0", F64), ("rmin", F64), ("rmax", F64),
("r200", F64), ("r178", F64), ("r500", F64),
("m200", F64), ("m178", F64), ("m500", F64)]
cols_collect = [("npart", I64), ("totpartmass", F64), ("Rs", F64),
("rho0", F64), ("conc", F64), ("rmin", F64),
("rmax", F64), ("r200", F64), ("r500", F64),
("m200", F64), ("m500", F64)]
# NOTE later loop over sims too
Nsim = Nsims[0]
simpath = csiborgtools.io.get_sim_path(Nsim)
box = csiborgtools.units.BoxUnits(Nsnap, simpath)
jobs = csiborgtools.fits.split_jobs(utils.Nsplits, nproc)[rank]
for Nsplit in jobs:
print("Rank {} working on {}.".format(rank, Nsplit))
for icount, Nsplit in enumerate(jobs):
print("{}: rank {} working {} / {} jobs.".format(datetime.now(), rank,
icount + 1, len(jobs)))
parts, part_clumps, clumps = csiborgtools.fits.load_split_particles(
Nsplit, loaddir, Nsim, Nsnap, remove_split=False)
N = clumps.size
cols = [("index", I64), ("npart", I64), ("totpartmass", F64),
("logRs", F64), ("rho0", F64), ("rmin", F64), ("rmax", F64),
("r200", F64), ("r178", F64), ("r500", F64),
("m200", F64), ("m178", F64), ("m500", F64)]
("Rs", F64), ("rho0", F64), ("conc", 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)
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["r200"][n] = clump.r200
out["r178"][n] = clump.r178
out["r500"][n] = clump.r500
out["m200"][n] = clump.m200
out["m178"][n] = clump.m178
out["m500"][n] = clump.m200
# 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]):
# NOTE here it calculates the r200 again, but its fast so does not
# matter anyway.
nfwpost = csiborgtools.fits.NFWPosterior(clump)
logRs = nfwpost.maxpost_logRs()
logRs, __ = nfwpost.maxpost_logRs()
Rs = 10**logRs
if not numpy.isnan(logRs):
out["logRs"][n] = logRs
out["rho0"][n] = nfwpost.rho0_from_logRs(logRs)
out["Rs"][n] = Rs
out["rho0"][n] = nfwpost.rho0_from_Rs(Rs)
out["conc"][n] = out["r200"][n] / Rs
csiborgtools.io.dump_split(out, Nsplit, Nsim, Nsnap, dumpdir)

2
scripts/run_split_halos.py
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@ -29,7 +29,7 @@ import utils
Nsims = [9844]
Nsnap = 1016
partcols = ["x", "y", "z", "M", "level"]
partcols = ["x", "y", "z", "vx", "vy", "vz", "M", "level"]
dumpdir = join(utils.dumpdir, "temp")
for Nsim in tqdm(Nsims):