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Calculate upglade redshifts (#128)
* Update redshift reading * Add helio to CMB redshift * Update imports * Update nb * Run for Quijote * Add script * Update * Update .gitignore * Update imports * Add Peery estimator * Add bulk flow scripts * Update typs * Add comment * Add blank space * Update submission script * Update description * Add barriers * Update nb * Update nb * Rename script * Move to old * Update imports * Add nb * Update script * Fix catalogue key * Update script * Update submit * Update comment * Update .gitignore * Update nb * Update for stationary obsrevers * Update submission * Add nb * Add better verbose control * Update nb * Update submit * Update nb * Add SN errors * Add draft of the script * Update verbosity flags * Add submission script * Debug script * Quickfix * Remove comment * Update nb * Update submission * Update nb * Processed UPGLADE
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Richard Stiskalek
GitHub
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commit
779f2e76ac
24 changed files with 2066 additions and 300 deletions
165
scripts/old/field_bulk_estimator.py
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165
scripts/old/field_bulk_estimator.py
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# Copyright (C) 2023 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 calculate the bulk flow in Quijote to compare the volume average
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definition to various estimators that rely on radial velocities (e.g. Nusser
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2014 and Peery+2018).
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"""
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from argparse import ArgumentParser
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from datetime import datetime
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from os import remove
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from os.path import join
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import csiborgtools
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import numpy as np
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from mpi4py import MPI
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from taskmaster import work_delegation # noqa
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###############################################################################
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# Read in information about the simulation #
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###############################################################################
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def t():
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return datetime.now()
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def get_reader(simname, paths, nsim):
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"""Get the appropriate snaspshot reader for the simulation."""
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# We only want Quijote because it has all particles of the same mass.
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if simname == "quijote":
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# We want the z = 0 snapshots
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reader = csiborgtools.read.QuijoteSnapshot(nsim, 4, paths)
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else:
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raise ValueError(f"Unknown simname: `{simname}`.")
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return reader
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def get_particles(reader, verbose=True):
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"""
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Get the distance of particles from the center of the box and their masses.
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"""
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if verbose:
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print(f"{t()},: reading coordinates and calculating radial distance.")
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pos = reader.coordinates().astype(np.float64)
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vel = reader.velocities().astype(np.float64)
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return pos, vel
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###############################################################################
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# Main & command line interface #
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###############################################################################
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def main(simname, nsim, folder, Rmax):
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observers = csiborgtools.read.fiducial_observers(boxsize, Rmax)
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distances = np.linspace(0, Rmax, 101)[1:]
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reader = get_reader(simname, paths, nsim)
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pos, vel = get_particles(reader, verbose=False)
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mass = np.ones(len(pos)) # Quijote has equal masses
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bf_volume = np.full((len(observers), len(distances), 3), np.nan)
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bf_peery = np.full_like(bf_volume, np.nan)
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bf_const = np.full_like(bf_volume, np.nan)
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for i in range(len(observers)):
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print(f"{t()}: Calculating bulk flow for observer {i + 1} of simulation {nsim}.") # noqa
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# Subtract the observer position.
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pos_current = pos - observers[i]
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# Get the distance of each particle from the observer and sort it.
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rdist = np.linalg.norm(pos_current, axis=1)
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indxs = np.argsort(rdist)
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pos_current = pos_current[indxs]
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vel_current = vel[indxs]
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rdist = rdist[indxs]
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# Volume average
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bf_volume[i, ...] = csiborgtools.field.particles_enclosed_momentum(
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rdist, mass, vel_current, distances)
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bf_volume[i, ...] /= csiborgtools.field.particles_enclosed_mass(
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rdist, mass, distances)[:, np.newaxis]
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# Peery 2018 1 / r^2 weighted
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bf_peery[i, ...] = csiborgtools.field.bulkflow_peery2018(
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rdist, mass, pos_current, vel_current, distances, "1/r^2",
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verbose=False)
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# Constant weight
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bf_const[i, ...] = csiborgtools.field.bulkflow_peery2018(
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rdist, mass, pos_current, vel_current, distances, "constant",
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verbose=False)
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# Finally save the output
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fname = join(folder, f"bf_estimators_addconstant_{simname}_{nsim}.npz")
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print(f"Saving to `{fname}`.")
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np.savez(fname, bf_volume=bf_volume, bf_peery=bf_peery, bf_const=bf_const,
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distances=distances)
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if __name__ == "__main__":
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parser = ArgumentParser()
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parser.add_argument("--simname", type=str, help="Simulation name.",
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choices=["quijote"]) # noqa
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args = parser.parse_args()
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Rmax = 150
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folder = "/mnt/extraspace/rstiskalek/csiborg_postprocessing/field_shells"
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comm = MPI.COMM_WORLD
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rank = comm.Get_rank()
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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boxsize = csiborgtools.simname2boxsize(args.simname)
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def main_wrapper(nsim):
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main(args.simname, nsim, folder, Rmax)
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nsims = list(paths.get_ics(args.simname))
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if rank == 0:
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print(f"Running with {len(nsims)} Quijote simulations.")
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comm.Barrier()
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work_delegation(main_wrapper, nsims, comm, master_verbose=True)
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comm.Barrier()
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# Collect the results
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if rank == 0:
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for i, nsim in enumerate(nsims):
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fname = join(folder, f"bf_estimators_{args.simname}_{nsim}.npz")
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data = np.load(fname)
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if i == 0:
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bf_volume = np.empty((len(nsims), *data["bf_volume"].shape))
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bf_peery = np.empty_like(bf_volume)
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bf_const = np.empty_like(bf_volume)
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distances = data["distances"]
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bf_volume[i, ...] = data["bf_volume"]
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bf_peery[i, ...] = data["bf_peery"]
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bf_const[i, ...] = data["bf_const"]
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# Remove file from this rank
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remove(fname)
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# Save the results
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fname = join(folder, f"bf_estimators_{args.simname}.npz")
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print(f"Saving final results to `{fname}`.")
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np.savez(fname, bf_volume=bf_volume, bf_peery=bf_peery,
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bf_const=bf_const, distances=distances)
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21
scripts/old/field_bulk_estimator.sh
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21
scripts/old/field_bulk_estimator.sh
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@ -0,0 +1,21 @@
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nthreads=20
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memory=24
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on_login=0
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queue="berg"
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env="/mnt/zfsusers/rstiskalek/csiborgtools/venv_csiborg/bin/python"
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file="field_bulk_estimator.py"
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simname="quijote"
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pythoncm="$env $file --simname $simname"
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if [ $on_login -eq 1 ]; then
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echo $pythoncm
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$pythoncm
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else
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cm="addqueue -q $queue -n $nthreads -m $memory $pythoncm"
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echo "Submitting:"
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echo $cm
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echo
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eval $cm
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fi
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