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Particle match & file system & phase space (#11)

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* Create file system

* add doc

* add n_sim n_snap directly to paths

* Move things to a single particle reader for consistency

* add docstring

* add srdcir, dumpdir and mmain_path

* make boxunits work with paths

* switch to using paths

* add tempdumpdir

* rm dependence on old functions

* rm comment

* rm unused import

* go back to all imports

* fix import bug

* rm dependence on old functions

* modernize code!

* fix typo

* fix typo

* update fits to new data structureing

* change docs

* add julia repo

* add setup

* add install commands

* ignore install files

* add array flattening

* update dependene

* add positions reader

* update manifest and projects

* add func

* update gitignore

* pos matching progress

* move file

* rm comment

* add velocities getter

* fix bug

* fix name bug

* fix path bug

* fix args func

* add redshift calculation to catalogues

* add shortcut to set n_sim and n_snap

* if cond bug

* add the cosine similarity

* add verbosit iterator

* add docs

* update README

* update README

* update README
This commit is contained in:
Richard Stiskalek 2022-11-25 10:44:08 +00:00 • committed by GitHub
parent c748c87e45
commit 161c27d995
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GPG key ID: 4AEE18F83AFDEB23
22 changed files with 1443 additions and 4178 deletions
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3633
scripts/playground.ipynb
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File diff suppressed because one or more lines are too long

49
scripts/run_find_initpos.jl Normal file
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@ -0,0 +1,49 @@
# 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.
using Pkg: activate, build
activate("../JuliaCSiBORGTools/")
using JuliaCSiBORGTools
using NPZ: npzread
using PyCall: pyimport
csiborgtools = pyimport("csiborgtools")
verbose = true
paths = csiborgtools.read.CSiBORGPaths()
nsims = paths.ic_ids[:1]
for nsim in nsims
nsnap_min = convert(Int64, paths.get_minimum_snapshot(nsim))
nsnap_max = convert(Int64, paths.get_maximum_snapshot(nsim))
# Get the maximum snapshot properties
verbose ? println("Loading snapshot $nsnap_max from simulation $nsim") : nothing
pids, ppos, pmass, clumpids = csiborgtools.read.get_positions(nsim, nsnap_max, get_clumpid=true, verbose=false)
println("Sizes are: ")
println(size(pids))
println(size(ppos))
println(size(pmass))
# # Get the minimum snapshot properties
# verbose ? println("Loading snapshot $nsnap_min from simulation $nsim") : nothing
# pids, ppos, pmass = csiborgtools.read.get_positions(nsim, nsnap_max, get_clumpid=false, verbose=false)
JuliaCSiBORGTools.halo_parts(0, partids, clumpids)
end

33
scripts/run_fit_halos.py
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@ -46,20 +46,21 @@ cols_collect = [("npart", I64), ("totpartmass", F64), ("Rs", F64),
("rho0", F64), ("conc", F64), ("rmin", F64),
("rmax", F64), ("r200", F64), ("r500", F64),
("m200", F64), ("m500", F64)]
paths = csiborgtools.read.CSiBORGPaths()
Nsims = csiborgtools.read.get_csiborg_ids("/mnt/extraspace/hdesmond")
for i, Nsim in enumerate(Nsims):
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)
simpath = csiborgtools.read.get_sim_path(Nsim)
Nsnap = csiborgtools.read.get_maximum_snapshot(simpath)
box = csiborgtools.units.BoxUnits(Nsnap, simpath)
box = csiborgtools.units.BoxUnits(paths)
jobs = csiborgtools.fits.split_jobs(utils.Nsplits, nproc)[rank]
for Nsplit in jobs:
for n_split in jobs:
parts, part_clumps, clumps = csiborgtools.fits.load_split_particles(
Nsplit, loaddir, Nsim, Nsnap, remove_split=False)
n_split, paths, remove_split=False)
N = clumps.size
cols = [("index", I64), ("npart", I64), ("totpartmass", F64),
@ -79,9 +80,9 @@ for i, Nsim in enumerate(Nsims):
out["rmin"][n] = clump.rmin
out["rmax"][n] = clump.rmax
out["totpartmass"][n] = clump.total_particle_mass
out["vx"] = numpy.average(clump.vel[:, 0], weights=clump.m)
out["vy"] = numpy.average(clump.vel[:, 1], weights=clump.m)
out["vz"] = numpy.average(clump.vel[:, 2], weights=clump.m)
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])
@ -100,7 +101,7 @@ for i, Nsim in enumerate(Nsims):
out["rho0"][n] = nfwpost.rho0_from_Rs(Rs)
out["conc"][n] = out["r200"][n] / Rs
csiborgtools.read.dump_split(out, Nsplit, Nsim, Nsnap, dumpdir)
csiborgtools.read.dump_split(out, n_split, paths)
# Wait until all jobs finished before moving to another simulation
comm.Barrier()
@ -108,11 +109,13 @@ for i, Nsim in enumerate(Nsims):
# 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, Nsim, Nsnap, utils.dumpdir, cols_collect,
remove_splits=True, verbose=False)
fname = join(utils.dumpdir, "ramses_out_{}_{}.npy"
.format(str(Nsim).zfill(5), str(Nsnap).zfill(5)))
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)

28
scripts/run_split_halos.py
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@ -18,7 +18,6 @@ membership for faster manipulation. Currently does this for the maximum
snapshot of each simulation. Running this will require a lot of memory.
"""
from os.path import join
from mpi4py import MPI
from datetime import datetime
try:
@ -34,29 +33,28 @@ comm = MPI.COMM_WORLD
rank = comm.Get_rank()
nproc = comm.Get_size()
Nsims = csiborgtools.read.get_csiborg_ids("/mnt/extraspace/hdesmond")
paths = csiborgtools.read.CSiBORGPaths()
n_sims = paths.ic_ids[:1]
partcols = ["x", "y", "z", "vx", "vy", "vz", "M", "level"]
dumpdir = join(utils.dumpdir, "temp")
jobs = csiborgtools.fits.split_jobs(len(Nsims), nproc)[rank]
jobs = csiborgtools.fits.split_jobs(len(n_sims), nproc)[rank]
for icount, sim_index in enumerate(jobs):
print("{}: rank {} working {} / {} jobs.".format(datetime.now(), rank,
icount + 1, len(jobs)))
Nsim = Nsims[sim_index]
simpath = csiborgtools.read.get_sim_path(Nsim)
Nsnap = csiborgtools.read.get_maximum_snapshot(simpath)
n_sim = n_sims[sim_index]
n_snap = paths.get_maximum_snapshot(n_sim)
# Set paths and inifitalise a particle reader
paths.set_info(n_sim, n_snap)
partreader = csiborgtools.read.ParticleReader(paths)
# Load the clumps, particles' clump IDs and particles.
clumps = csiborgtools.read.read_clumps(Nsnap, simpath)
particle_clumps = csiborgtools.read.read_clumpid(Nsnap, simpath,
verbose=False)
particles = csiborgtools.read.read_particle(partcols, Nsnap, simpath,
verbose=False)
clumps = partreader.read_clumps()
particle_clumps = partreader.read_clumpid(verbose=False)
particles = partreader.read_particle(partcols, verbose=False)
# Drop all particles whose clump index is 0 (not assigned to any halo)
particle_clumps, particles = csiborgtools.read.drop_zero_indx(
particle_clumps, particles = partreader.drop_zero_indx(
particle_clumps, particles)
# Dump it!
csiborgtools.fits.dump_split_particles(particles, particle_clumps, clumps,
utils.Nsplits, dumpdir, Nsim, Nsnap,
verbose=False)
utils.Nsplits, paths, verbose=False)
print("All finished!")