mirror of
https://github.com/Richard-Sti/csiborgtools.git
synced 2024-12-22 17:08:03 +00:00
9e4b34f579
* Update README * Update density field reader * Update name of SDSSxALFAFA * Fix quick bug * Add little fixes * Update README * Put back fit_init * Add paths to initial snapshots * Add export * Remove some choices * Edit README * Add Jens' comments * Organize imports * Rename snapshot * Add additional print statement * Add paths to initial snapshots * Add masses to the initial files * Add normalization * Edit README * Update README * Fix bug in CSiBORG1 so that does not read fof_00001 * Edit README * Edit README * Overwrite comments * Add paths to init lag * Fix Quijote path * Add lagpatch * Edit submits * Update README * Fix numpy int problem * Update README * Add a flag to keep the snapshots open when fitting * Add a flag to keep snapshots open * Comment out some path issue * Keep snapshots open * Access directly snasphot * Add lagpatch for CSiBORG2 * Add treatment of x-z coordinates flipping * Add radial velocity field loader * Update README * Add lagpatch to Quijote * Fix typo * Add setter * Fix typo * Update README * Add output halo cat as ASCII * Add import * Add halo plot * Update README * Add evaluating field at radial distanfe * Add field shell evaluation * Add enclosed mass computation * Add BORG2 import * Add BORG boxsize * Add BORG paths * Edit run * Add BORG2 overdensity field * Add bulk flow clauclation * Update README * Add new plots * Add nbs * Edit paper * Update plotting * Fix overlap paths to contain simname * Add normalization of positions * Add default paths to CSiBORG1 * Add overlap path simname * Fix little things * Add CSiBORG2 catalogue * Update README * Add import * Add TNG density field constructor * Add TNG density * Add draft of calculating BORG ACL * Fix bug * Add ACL of enclosed density * Add nmean acl * Add galaxy bias calculation * Add BORG acl notebook * Add enclosed mass calculation * Add TNG300-1 dir * Add TNG300 and BORG1 dir * Update nb
349 lines
13 KiB
Python
349 lines
13 KiB
Python
# 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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"""MPI script to calculate the various fields."""
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from argparse import ArgumentParser
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from datetime import datetime
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import numpy
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from mpi4py import MPI
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from taskmaster import work_delegation
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import csiborgtools
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from utils import get_nsims
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###############################################################################
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# Density field #
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###############################################################################
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def density_field(nsim, parser_args):
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"""
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Calculate and save the density field from the particle positions and
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masses.
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Parameters
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----------
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nsim : int
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Simulation index.
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parser_args : argparse.Namespace
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Command line arguments.
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Returns
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-------
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density_field : 3-dimensional array
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"""
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if parser_args.MAS == "SPH":
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raise NotImplementedError("SPH is not implemented here. Use cosmotool")
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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nsnap = max(paths.get_snapshots(nsim, parser_args.simname))
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# Read in the particle coordinates and masses
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if parser_args.simname == "csiborg1":
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snapshot = csiborgtools.read.CSiBORG1Snapshot(nsim, nsnap, paths)
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elif "csiborg2" in parser_args.simname:
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kind = parser_args.simname.split("_")[-1]
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snapshot = csiborgtools.read.CSiBORG2Snapshot(nsim, nsnap, paths, kind)
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elif parser_args.simname == "quijote":
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snapshot = csiborgtools.read.QuijoteSnapshot(nsim, nsnap, paths)
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else:
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raise RuntimeError(f"Unknown simulation name `{parser_args.simname}`.")
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pos = snapshot.coordinates()
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mass = snapshot.masses()
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# Run the field generator
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boxsize = csiborgtools.simname2boxsize(parser_args.simname)
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gen = csiborgtools.field.DensityField(boxsize, parser_args.MAS)
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field = gen(pos, mass, parser_args.grid)
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fout = paths.field("density", parser_args.MAS, parser_args.grid,
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nsim, parser_args.simname)
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print(f"{datetime.now()}: saving output to `{fout}`.")
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numpy.save(fout, field)
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return field
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###############################################################################
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# Velocity field #
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###############################################################################
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def velocity_field(nsim, parser_args):
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"""
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Calculate and save the velocity field from the particle positions,
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velocities and masses.
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Parameters
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----------
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nsim : int
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Simulation index.
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parser_args : argparse.Namespace
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Command line arguments.
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Returns
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-------
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velocity_field : 4-dimensional array
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"""
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if parser_args.MAS == "SPH":
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raise NotImplementedError("SPH is not implemented here. Use cosmotool")
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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nsnap = max(paths.get_snapshots(nsim, parser_args.simname))
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if parser_args.simname == "csiborg1":
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snapshot = csiborgtools.read.CSiBORG1Snapshot(nsim, nsnap, paths)
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elif "csiborg2" in parser_args.simname:
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kind = parser_args.simname.split("_")[-1]
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snapshot = csiborgtools.read.CSiBORG2Snapshot(nsim, nsnap, kind, paths)
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elif parser_args.simname == "quijote":
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snapshot = csiborgtools.read.QuijoteSnapshot(nsim, nsnap, paths)
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else:
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raise RuntimeError(f"Unknown simulation name `{parser_args.simname}`.")
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pos = snapshot.coordinates()
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vel = snapshot.velocities()
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mass = snapshot.masses()
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boxsize = csiborgtools.simname2boxsize(parser_args.simname)
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gen = csiborgtools.field.VelocityField(boxsize, parser_args.MAS)
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field = gen(pos, vel, mass, parser_args.grid)
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fout = paths.field("velocity", parser_args.MAS, parser_args.grid,
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nsim, parser_args.simname)
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print(f"{datetime.now()}: saving output to `{fout}`.")
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numpy.save(fout, field)
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return field
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###############################################################################
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# Radial velocity field #
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###############################################################################
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def radvel_field(nsim, parser_args):
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"""
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Calculate and save the radial velocity field.
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Parameters
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----------
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nsim : int
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Simulation index.
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parser_args : argparse.Namespace
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Command line arguments.
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Returns
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-------
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radvel_field : 3-dimensional array
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"""
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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if parser_args.simname == "csiborg1":
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field = csiborgtools.read.CSiBORG1Field(nsim, paths)
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elif "csiborg2" in parser_args.simname:
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kind = parser_args.simname.split("_")[-1]
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field = csiborgtools.read.CSiBORG2Field(nsim, kind, paths)
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elif parser_args.simname == "quijote":
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field = csiborgtools.read.QuijoteField(nsim, paths)
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else:
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raise RuntimeError(f"Unknown simulation name `{parser_args.simname}`.")
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vel = field.velocity_field(parser_args.MAS, parser_args.grid)
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observer_velocity = csiborgtools.field.observer_peculiar_velocity(vel)
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radvel = csiborgtools.field.radial_velocity(vel, observer_velocity)
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fout = paths.field("radvel", parser_args.MAS, parser_args.grid,
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nsim, parser_args.simname)
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print(f"{datetime.now()}: saving output to `{fout}`.")
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numpy.save(fout, radvel)
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return field
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def observer_peculiar_velocity(nsim, parser_args):
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"""
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Calculate the peculiar velocity of an observer in the centre of the box
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for several hard-coded smoothing scales.
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Parameters
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----------
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nsim : int
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Simulation index.
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parser_args : argparse.Namespace
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Command line arguments.
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Returns
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-------
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observer_vp : 4-dimensional array
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"""
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boxsize = csiborgtools.simname2boxsize(parser_args.simname)
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# NOTE these values are hard-coded.
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smooth_scales = numpy.array([0., 2.0, 4.0, 8.0, 16.])
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smooth_scales /= boxsize
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if parser_args.simname == "csiborg1":
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field = csiborgtools.read.CSiBORG1Field(nsim, paths)
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elif "csiborg2" in parser_args.simname:
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kind = parser_args.simname.split("_")[-1]
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field = csiborgtools.read.CSiBORG2Field(nsim, paths, kind)
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elif parser_args.simname == "quijote":
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field = csiborgtools.read.QuijoteField(nsim, paths)
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else:
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raise RuntimeError(f"Unknown simulation name `{parser_args.simname}`.")
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vel = field.velocity_field(parser_args.MAS, parser_args.grid)
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observer_vp = csiborgtools.field.observer_peculiar_velocity(
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vel, smooth_scales)
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fout = paths.observer_peculiar_velocity(parser_args.MAS, parser_args.grid,
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nsim, parser_args.simname)
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print(f"Saving to ... `{fout}`")
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numpy.savez(fout, smooth_scales=smooth_scales, observer_vp=observer_vp)
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return observer_vp
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###############################################################################
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# Command line interface #
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###############################################################################
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if __name__ == "__main__":
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parser = ArgumentParser()
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parser.add_argument("--nsims", type=int, nargs="+", default=None,
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help="IC realisations. `-1` for all simulations.")
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parser.add_argument("--simname", type=str, help="Simulation name.")
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parser.add_argument("--kind", type=str,
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choices=["density", "velocity", "radvel", "observer_vp"], # noqa
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help="What derived field to calculate?")
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parser.add_argument("--MAS", type=str,
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choices=["NGP", "CIC", "TSC", "PCS", "SPH"],
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help="Mass assignment scheme.")
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parser.add_argument("--grid", type=int, help="Grid resolution.")
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parser_args = parser.parse_args()
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comm = MPI.COMM_WORLD
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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nsims = get_nsims(parser_args, paths)
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def main(nsim):
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if parser_args.kind == "density":
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density_field(nsim, parser_args)
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elif parser_args.kind == "velocity":
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velocity_field(nsim, parser_args)
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elif parser_args.kind == "radvel":
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radvel_field(nsim, parser_args)
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elif parser_args.kind == "observer_vp":
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observer_peculiar_velocity(nsim, parser_args)
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else:
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raise RuntimeError(f"Field {parser_args.kind} is not implemented.")
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work_delegation(main, nsims, comm, master_verbose=True)
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# def potential_field(nsim, parser_args, to_save=True):
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# """
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# Calculate the potential field in the CSiBORG simulation.
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# """
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# paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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# nsnap = max(paths.get_snapshots(nsim, "csiborg"))
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# box = csiborgtools.read.CSiBORG1Box(nsnap, nsim, paths)
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#
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# if not parser_args.in_rsp:
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# rho = numpy.load(paths.field(
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# "density", parser_args.MAS, parser_args.grid, nsim,
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# in_rsp=False))
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# density_gen = csiborgtools.field.DensityField(box, parser_args.MAS)
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# rho = density_gen.overdensity_field(rho)
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#
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# gen = csiborgtools.field.PotentialField(box, parser_args.MAS)
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# field = gen(rho)
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# else:
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# field = numpy.load(paths.field(
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# "potential", parser_args.MAS, parser_args.grid, nsim, False))
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# radvel_field = numpy.load(paths.field(
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# "radvel", parser_args.MAS, parser_args.grid, nsim, False))
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#
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# field = csiborgtools.field.field2rsp(field, radvel_field, box,
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# parser_args.MAS)
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#
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# if to_save:
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# fout = paths.field(parser_args.kind, parser_args.MAS,
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# parser_args.grid,
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# nsim, parser_args.in_rsp)
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# print(f"{datetime.now()}: saving output to `{fout}`.")
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# numpy.save(fout, field)
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# return field
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#
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#
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# #############################################################################
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# # Environment classification #
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# #############################################################################
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#
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#
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# def environment_field(nsim, parser_args, to_save=True):
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# """
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# Calculate the environmental classification in the CSiBORG simulation.
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# """
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# paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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# nsnap = max(paths.get_snapshots(nsim, "csiborg"))
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# box = csiborgtools.read.CSiBORG1Box(nsnap, nsim, paths)
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#
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# rho = numpy.load(paths.field(
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# "density", parser_args.MAS, parser_args.grid, nsim, in_rsp=False))
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# density_gen = csiborgtools.field.DensityField(box, parser_args.MAS)
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# rho = density_gen.overdensity_field(rho)
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#
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# if parser_args.smooth_scale > 0.0:
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# rho = csiborgtools.field.smoothen_field(
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# rho, parser_args.smooth_scale, box.box2mpc(1.))
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#
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# gen = csiborgtools.field.TidalTensorField(box, parser_args.MAS)
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# field = gen(rho)
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#
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# del rho
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# collect()
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#
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# if parser_args.in_rsp:
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# radvel_field = numpy.load(paths.field(
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# "radvel", parser_args.MAS, parser_args.grid, nsim, False))
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# args = (radvel_field, box, parser_args.MAS)
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#
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# field.T00 = csiborgtools.field.field2rsp(field.T00, *args)
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# field.T11 = csiborgtools.field.field2rsp(field.T11, *args)
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# field.T22 = csiborgtools.field.field2rsp(field.T22, *args)
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# field.T01 = csiborgtools.field.field2rsp(field.T01, *args)
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# field.T02 = csiborgtools.field.field2rsp(field.T02, *args)
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# field.T12 = csiborgtools.field.field2rsp(field.T12, *args)
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#
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# del radvel_field
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# collect()
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#
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# eigvals = gen.tensor_field_eigvals(field)
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#
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# del field
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# collect()
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#
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# env = gen.eigvals_to_environment(eigvals)
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#
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# if to_save:
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# fout = paths.field("environment", parser_args.MAS, parser_args.grid,
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# nsim, parser_args.in_rsp,
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# parser_args.smooth_scale)
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# print(f"{datetime.now()}: saving output to `{fout}`.")
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# numpy.save(fout, env)
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# return env
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