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Add pynbody and other support (#92)
* Simplify box units * Move old scripts * Add printing * Update readers * Disable boundscheck * Add new ordering * Clean up imports * Enforce dtype and add mass to quijote * Simplify print statements * Fix little typos * Fix key bug * Bug fixing * Delete boring comments * Improve ultimate clumps for PHEW * Delete boring comments * Add basic reading * Remove 0th index HID * Add flipping of X and Z * Updates to halo catalogues * Add ordered caching * Fix flipping * Add new flags * Fix PHEW empty clumps * Stop over-wrriting * Little improvements to angular neighbours * Add catalogue masking * Change if-else statements * Cache only filtered data * Add PHEW cats * Add comments * Sort imports * Get Quijote workign * Docs * Add HMF calculation * Move to old * Fix angular * Add great circle distance * Update imports * Update impotrts * Update docs * Remove unused import * Fix a quick bug * Update compatibility * Rename files * Renaming * Improve compatiblity * Rename snapsht * Fix snapshot bug * Update interface * Finish updating interface * Update all paths * Add old scripts * Add basic halo * Update imports * Improve snapshot processing * Update ordering * Fix how CM positions accessed * Add merger paths * Add imports * Add merger reading * Add making a merger tree * Add a basic merger tree reader * Add imports * Add main branch walking + comments + debuggin * Get tree running * Add working merger tree walking along main branch * Add units conversion for merger data * Add hid_to_array_index * Update merger tree * Add mergertree mass to PHEWcat * Edit comments * Add this to track changes... * Fix a little bug * Add mergertree mass * Add cache clearing * Improve summing substructure code * Littbe bug * Little updates to the merger tree reader * Update .giignore * Add box selection * Add optional deletingf of a group * add to keep track of changes * Update changes * Remove * Add manual tracker * Fix bug * Add m200c_to_r200c * Add manual halo tracking * Remove skipped snapshots * update cosmo params to match csiborg * remove old comments * Add SDSSxALFALFA * Fix bugs * Rename * Edit paths * Updates * Add comments * Add comment * Add hour conversion * Add imports * Add new observation class * Add selection * Add imports * Fix small bug * Add field copying for safety * Add matching to survey without masking * Add P(k) calculation * Add nb * Edit comment * Move files * Remove merger import * Edit setup.yp * Fix typo * Edit import warnigns * update nb * Update README * Update README * Update README * Add skeleton * Add skeleton
This commit is contained in:
Richard Stiskalek
GitHub
parent
5500fbd2b9
commit
e972f8e3f2
53 changed files with 4627 additions and 1774 deletions
159
old/cluster_crosspk.py
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159
old/cluster_crosspk.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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MPI script to calculate the matter cross power spectrum between CSiBORG
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IC realisations. Units are Mpc/h.
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"""
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raise NotImplementedError("This script is currently not working.")
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from argparse import ArgumentParser
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from datetime import datetime
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from gc import collect
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from itertools import combinations
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from os import remove
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from os.path import join
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import joblib
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import numpy
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import Pk_library as PKL
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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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dumpdir = "/mnt/extraspace/rstiskalek/csiborg/"
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parser = ArgumentParser()
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parser.add_argument("--grid", type=int)
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parser.add_argument("--halfwidth", type=float, default=0.5)
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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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MAS = "CIC" # mass asignment scheme
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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box = csiborgtools.read.CSiBORGBox(paths)
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reader = csiborgtools.read.CSiBORGReader(paths)
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ics = paths.get_ics("csiborg")
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nsims = len(ics)
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# File paths
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ftemp = join(dumpdir, "temp_crosspk",
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"out_{}_{}" + "_{}".format(args.halfwidth))
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fout = join(dumpdir, "crosspk",
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"out_{}_{}" + "_{}.p".format(args.halfwidth))
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jobs = csiborgtools.utils.split_jobs(nsims, nproc)[rank]
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for n in jobs:
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print(f"Rank {rank} at {datetime.now()}: saving {n}th delta.", flush=True)
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nsim = ics[n]
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particles = reader.read_snapshot(max(paths.get_snapshots(nsim, "csiborg")),
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nsim, ["x", "y", "z", "M"], verbose=False)
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# Halfwidth -- particle selection
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if args.halfwidth < 0.5:
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particles = csiborgtools.read.halfwidth_select(
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args.halfwidth, particles)
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length = box.box2mpc(2 * args.halfwidth) * box.h # Mpc/h
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else:
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length = box.box2mpc(1) * box.h # Mpc/h
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# Calculate the overdensity field
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field = csiborgtools.field.DensityField(particles, length, box, MAS)
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delta = field.overdensity_field(args.grid, verbose=False)
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aexp = box._aexp
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# Try to clean up memory
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del field, particles, box, reader
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collect()
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# Dump the results
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with open(ftemp.format(nsim, "delta") + ".npy", "wb") as f:
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numpy.save(f, delta)
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joblib.dump([aexp, length], ftemp.format(nsim, "lengths") + ".p")
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# Try to clean up memory
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del delta
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collect()
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comm.Barrier()
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# Get off-diagonal elements and append the diagoal
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combs = [c for c in combinations(range(nsims), 2)]
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for i in range(nsims):
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combs.append((i, i))
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prev_delta = [-1, None, None, None] # i, delta, aexp, length
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jobs = csiborgtools.utils.split_jobs(len(combs), nproc)[rank]
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for n in jobs:
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i, j = combs[n]
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print("Rank {}@{}: combination {}.".format(rank, datetime.now(), (i, j)))
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# If i same as last time then don't have to load it
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if prev_delta[0] == i:
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delta_i = prev_delta[1]
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aexp_i = prev_delta[2]
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length_i = prev_delta[3]
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else:
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with open(ftemp.format(ics[i], "delta") + ".npy", "rb") as f:
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delta_i = numpy.load(f)
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aexp_i, length_i = joblib.load(ftemp.format(ics[i], "lengths") + ".p")
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# Store in prev_delta
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prev_delta[0] = i
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prev_delta[1] = delta_i
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prev_delta[2] = aexp_i
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prev_delta[3] = length_i
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# Get jth delta
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with open(ftemp.format(ics[j], "delta") + ".npy", "rb") as f:
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delta_j = numpy.load(f)
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aexp_j, length_j = joblib.load(ftemp.format(ics[j], "lengths") + ".p")
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# Verify the difference between the scale factors! Say more than 1%
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daexp = abs((aexp_i - aexp_j) / aexp_i)
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if daexp > 0.01:
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raise ValueError(
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"Boxes {} and {} final snapshot scale factors disagree by "
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"`{}` percent!".format(ics[i], ics[j], daexp * 100))
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# Check how well the boxsizes agree
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dlength = abs((length_i - length_j) / length_i)
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if dlength > 0.001:
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raise ValueError("Boxes {} and {} box sizes disagree by `{}` percent!"
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.format(ics[i], ics[j], dlength * 100))
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# Calculate the cross power spectrum
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Pk = PKL.XPk([delta_i, delta_j], length_i, axis=1, MAS=[MAS, MAS],
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threads=1)
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joblib.dump(Pk, fout.format(ics[i], ics[j]))
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del delta_i, delta_j, Pk
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collect()
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# Clean up the temp files
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comm.Barrier()
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if rank == 0:
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print("Cleaning up the temporary files...")
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for ic in ics:
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remove(ftemp.format(ic, "delta") + ".npy")
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remove(ftemp.format(ic, "lengths") + ".p")
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print("All finished!")
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