mirror of
https://github.com/Richard-Sti/csiborgtools_public.git
synced 2025-06-30 19:41:12 +00:00
Clean density calculation (#97)
* Get rid of utils * Clean up imports * Move some utils here * Rename file * Add simname to boxsize * Add imports * Delete old files * Update README * Update imports * Add a new draft of the density calculator * Update fields * Draft of new density field calculatiosn * Add snapshot * Add boxsizes * Little updates * Bring back utils * Edit docstrings * Edits imports * Add progress on snapshots * edit improts * add basic snapshot catalogue * Add support for CSiBORG2 snapshot reader * add paths to fofcat for csiborg2 * Add more imports * Add more boxsize * Add more imports * Add field readers * Simplify field paths * Fix typo * Add observer vp * Clean up density field calculation * Add a short note * Edit args * Remove old comments * Edit docs * Remove blank line * Stop flipping RAMSES * Remove comment * Edit desc * Remove normalization * Remove old dist array * Remove non-volume weighting * Remove non-volume weight * Add ignore of flake8 notebooks * Fix path typo * Fix units * Edit paths docs * Update nb
This commit is contained in:
Richard Stiskalek
GitHub
parent
eeff8f0ab9
commit
eb1797e8a9
19 changed files with 1260 additions and 1139 deletions
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@ -12,14 +12,9 @@
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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 density field-derived fields in the CSiBORG
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simulations' final snapshot.
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"""
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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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from distutils.util import strtobool
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from gc import collect
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import numpy
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from mpi4py import MPI
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@ -29,55 +24,43 @@ import csiborgtools
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from utils import get_nsims
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###############################################################################
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# Cosmotool SPH density & velocity field #
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###############################################################################
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def cosmotool_sph(nsim, parser_args):
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pass
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###############################################################################
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# Density field #
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###############################################################################
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def density_field(nsim, parser_args, to_save=True):
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"""
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Calculate the density field in the CSiBORG simulation.
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"""
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def density_field(nsim, parser_args):
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"""Calculate the density field."""
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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, "csiborg"))
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box = csiborgtools.read.CSiBORG1Box(nsnap, nsim, paths)
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fname = paths.processed_output(nsim, "csiborg", "halo_catalogue")
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nsnap = max(paths.get_snapshots(nsim, parser_args.simname))
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if not parser_args.in_rsp:
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# TODO I removed this function
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snap = csiborgtools.read.read_h5(fname)["snapshot_final"]
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pos = snap["pos"]
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mass = snap["mass"]
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gen = csiborgtools.field.DensityField(box, parser_args.MAS)
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field = gen(pos, mass, parser_args.grid, verbose=parser_args.verbose)
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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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field = numpy.load(paths.field(
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"density", 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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raise RuntimeError(f"Unknown simulation name `{parser_args.simname}`.")
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if parser_args.verbose:
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print(f"{datetime.now()}: converting density field to RSP.",
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flush=True)
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pos = snapshot.coordinates()
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mass = snapshot.masses()
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field = csiborgtools.field.field2rsp(field, radvel_field, box,
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parser_args.MAS)
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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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if to_save:
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fout = paths.field(parser_args.kind, parser_args.MAS, 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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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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@ -86,31 +69,36 @@ def density_field(nsim, parser_args, to_save=True):
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###############################################################################
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def velocity_field(nsim, parser_args, to_save=True):
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"""
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Calculate the velocity field in a CSiBORG simulation.
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"""
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if parser_args.in_rsp:
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raise NotImplementedError("Velocity field in RSP is not implemented.")
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def velocity_field(nsim, parser_args):
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"""Calculate the velocity field."""
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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, "csiborg"))
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box = csiborgtools.read.CSiBORG1Box(nsnap, nsim, paths)
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fname = paths.processed_output(nsim, "csiborg", "halo_catalogue")
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nsnap = max(paths.get_snapshots(nsim, parser_args.simname))
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snap = csiborgtools.read.read_h5(fname)["snapshot_final"]
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pos = snap["pos"]
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vel = snap["vel"]
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mass = snap["mass"]
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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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gen = csiborgtools.field.VelocityField(box, parser_args.MAS)
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field = gen(pos, vel, mass, parser_args.grid, verbose=parser_args.verbose)
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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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if to_save:
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fout = paths.field("velocity", parser_args.MAS, parser_args.grid,
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nsim, in_rsp=False)
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print(f"{datetime.now()}: saving output to `{fout}`.")
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numpy.save(fout, field)
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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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@ -119,125 +107,62 @@ def velocity_field(nsim, parser_args, to_save=True):
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###############################################################################
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def radvel_field(nsim, parser_args, to_save=True):
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"""
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Calculate the radial velocity field in the CSiBORG simulation.
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"""
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if parser_args.in_rsp:
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raise NotImplementedError("Radial vel. field in RSP not implemented.")
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def radvel_field(nsim, parser_args):
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"""Calculate the radial velocity field."""
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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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vel = numpy.load(paths.field("velocity", parser_args.MAS, parser_args.grid,
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nsim, parser_args.in_rsp))
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observer_velocity = csiborgtools.field.observer_vobs(vel)
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gen = csiborgtools.field.VelocityField(box, parser_args.MAS)
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field = gen.radial_velocity(vel, observer_velocity)
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if to_save:
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fout = paths.field("radvel", parser_args.MAS, 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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# Potential field #
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###############################################################################
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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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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, 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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gen = csiborgtools.field.PotentialField(box, parser_args.MAS)
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field = gen(rho)
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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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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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raise RuntimeError(f"Unknown simulation name `{parser_args.simname}`.")
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field = csiborgtools.field.field2rsp(field, radvel_field, box,
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parser_args.MAS)
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vel = field.velocity_field(parser_args.MAS, parser_args.grid)
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if to_save:
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fout = paths.field(parser_args.kind, parser_args.MAS, 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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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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###############################################################################
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# Environment classification #
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###############################################################################
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def environment_field(nsim, parser_args, to_save=True):
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def observer_peculiar_velocity(nsim, parser_args):
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"""
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Calculate the environmental classification in the CSiBORG simulation.
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Calculate the peculiar velocity of an observer in the centre of the box
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for several smoothing scales.
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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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boxsize = csiborgtools.simname2boxsize(parser_args.simname)
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# NOTE thevse values are hard-coded.
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smooth_scales = numpy.array([0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0])
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smooth_scales /= boxsize
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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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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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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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vel = field.velocity_field(parser_args.MAS, parser_args.grid)
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gen = csiborgtools.field.TidalTensorField(box, parser_args.MAS)
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field = gen(rho)
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observer_vp = csiborgtools.field.observer_peculiar_velocity(
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vel, smooth_scales)
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del rho
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collect()
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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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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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del radvel_field
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collect()
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eigvals = gen.tensor_field_eigvals(field)
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del field
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collect()
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env = gen.eigvals_to_environment(eigvals)
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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, 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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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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@ -249,39 +174,124 @@ 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", "rspdensity", "velocity", "radvel",
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"potential", "environment"],
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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"])
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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.add_argument("--in_rsp", type=lambda x: bool(strtobool(x)),
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help="Calculate in RSP?")
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parser.add_argument("--smooth_scale", type=float, default=0.0,
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help="Smoothing scale in Mpc / h. Only used for the environment field.") # noqa
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parser.add_argument("--verbose", type=lambda x: bool(strtobool(x)),
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help="Verbosity flag for reading in particles.")
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parser.add_argument("--simname", type=str, default="csiborg",
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choices=["csiborg", "csiborg2"],
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help="Verbosity flag for reading in particles.")
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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" or parser_args.kind == "rspdensity":
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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 == "potential":
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potential_field(nsim, parser_args)
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elif parser_args.kind == "environment":
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environment_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,
|
||||
# in_rsp=False))
|
||||
# density_gen = csiborgtools.field.DensityField(box, parser_args.MAS)
|
||||
# rho = density_gen.overdensity_field(rho)
|
||||
#
|
||||
# gen = csiborgtools.field.PotentialField(box, parser_args.MAS)
|
||||
# field = gen(rho)
|
||||
# else:
|
||||
# field = numpy.load(paths.field(
|
||||
# "potential", parser_args.MAS, parser_args.grid, nsim, False))
|
||||
# radvel_field = numpy.load(paths.field(
|
||||
# "radvel", parser_args.MAS, parser_args.grid, nsim, False))
|
||||
#
|
||||
# field = csiborgtools.field.field2rsp(field, radvel_field, box,
|
||||
# parser_args.MAS)
|
||||
#
|
||||
# if to_save:
|
||||
# fout = paths.field(parser_args.kind, parser_args.MAS,
|
||||
# parser_args.grid,
|
||||
# nsim, parser_args.in_rsp)
|
||||
# print(f"{datetime.now()}: saving output to `{fout}`.")
|
||||
# numpy.save(fout, field)
|
||||
# return field
|
||||
#
|
||||
#
|
||||
# #############################################################################
|
||||
# # Environment classification #
|
||||
# #############################################################################
|
||||
#
|
||||
#
|
||||
# def environment_field(nsim, parser_args, to_save=True):
|
||||
# """
|
||||
# Calculate the environmental classification in the CSiBORG simulation.
|
||||
# """
|
||||
# paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
|
||||
# nsnap = max(paths.get_snapshots(nsim, "csiborg"))
|
||||
# box = csiborgtools.read.CSiBORG1Box(nsnap, nsim, paths)
|
||||
#
|
||||
# rho = numpy.load(paths.field(
|
||||
# "density", parser_args.MAS, parser_args.grid, nsim, in_rsp=False))
|
||||
# density_gen = csiborgtools.field.DensityField(box, parser_args.MAS)
|
||||
# rho = density_gen.overdensity_field(rho)
|
||||
#
|
||||
# if parser_args.smooth_scale > 0.0:
|
||||
# rho = csiborgtools.field.smoothen_field(
|
||||
# rho, parser_args.smooth_scale, box.box2mpc(1.))
|
||||
#
|
||||
# gen = csiborgtools.field.TidalTensorField(box, parser_args.MAS)
|
||||
# field = gen(rho)
|
||||
#
|
||||
# del rho
|
||||
# collect()
|
||||
#
|
||||
# if parser_args.in_rsp:
|
||||
# radvel_field = numpy.load(paths.field(
|
||||
# "radvel", parser_args.MAS, parser_args.grid, nsim, False))
|
||||
# args = (radvel_field, box, parser_args.MAS)
|
||||
#
|
||||
# field.T00 = csiborgtools.field.field2rsp(field.T00, *args)
|
||||
# field.T11 = csiborgtools.field.field2rsp(field.T11, *args)
|
||||
# field.T22 = csiborgtools.field.field2rsp(field.T22, *args)
|
||||
# field.T01 = csiborgtools.field.field2rsp(field.T01, *args)
|
||||
# field.T02 = csiborgtools.field.field2rsp(field.T02, *args)
|
||||
# field.T12 = csiborgtools.field.field2rsp(field.T12, *args)
|
||||
#
|
||||
# del radvel_field
|
||||
# collect()
|
||||
#
|
||||
# eigvals = gen.tensor_field_eigvals(field)
|
||||
#
|
||||
# del field
|
||||
# collect()
|
||||
#
|
||||
# env = gen.eigvals_to_environment(eigvals)
|
||||
#
|
||||
# if to_save:
|
||||
# fout = paths.field("environment", parser_args.MAS, parser_args.grid,
|
||||
# nsim, parser_args.in_rsp,
|
||||
# parser_args.smooth_scale)
|
||||
# print(f"{datetime.now()}: saving output to `{fout}`.")
|
||||
# numpy.save(fout, env)
|
||||
# return env
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue