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Velocity observer (#86)
* Continue if r200c not defined * Remove smooth scale * Remove smooth scale * Edit Max Matching plot * Add peculiar velocity * Add Vobs calculation * Edit docs * Add Vobs plot * Improve plotting * Edit naming convention * Make a note * Add new cat options * Update density field RSP calculation * Update field 2 rsp * Move functions and shorten documentation * Improve transforms and comments * Update docs * Update imports * Edit calculation * Add docs * Remove imports * Add Quijote flags * Edit documentation * Shorten documentation * Edit func calls * Shorten * Docs edits * Edit docs * Shorten docs * Short docs edits * Simplify docs a little bit * Save plotting * Update env
This commit is contained in:
Richard Stiskalek
GitHub
parent
8e3127f4d9
commit
ae92fd9b72
18 changed files with 761 additions and 788 deletions
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@ -43,44 +43,29 @@ from utils import get_nsims
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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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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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Parsed arguments.
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to_save : bool, optional
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Whether to save the output to disk.
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Returns
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-------
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field : 3-dimensional array
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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.CSiBORGBox(nsnap, nsim, paths)
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parts = csiborgtools.read.read_h5(paths.particles(nsim, "csiborg"))
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parts = parts["particles"]
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gen = csiborgtools.field.DensityField(box, parser_args.MAS)
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if parser_args.kind == "density":
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field = gen(parts, parser_args.grid, in_rsp=False,
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verbose=parser_args.verbose)
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if parser_args.in_rsp:
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field = csiborgtools.field.field2rsp(*field, parts=parts, box=box,
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verbose=parser_args.verbose)
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if not parser_args.in_rsp:
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parts = csiborgtools.read.read_h5(paths.particles(nsim, "csiborg"))
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parts = parts["particles"]
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gen = csiborgtools.field.DensityField(box, parser_args.MAS)
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field = gen(parts, parser_args.grid, verbose=parser_args.verbose)
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else:
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field = gen(parts, parser_args.grid, in_rsp=parser_args.in_rsp,
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verbose=parser_args.verbose)
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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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if parser_args.smooth_scale > 0:
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field = csiborgtools.field.smoothen_field(
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field, parser_args.smooth_scale, box.boxsize * box.h, threads=1)
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field = csiborgtools.field.field2rsp(field, radvel_field, box,
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parser_args.MAS)
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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, parser_args.smooth_scale)
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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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@ -93,35 +78,20 @@ def density_field(nsim, parser_args, to_save=True):
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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 the CSiBORG simulation.
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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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Parsed arguments.
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to_save : bool, optional
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Whether to save the output to disk.
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Returns
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-------
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velfield : 4-dimensional array
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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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if parser_args.smooth_scale > 0:
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raise NotImplementedError(
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"Smoothed velocity field is not implemented.")
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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mpart = 1.1641532e-10 # Particle mass in CSiBORG simulations.
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nsnap = max(paths.get_snapshots(nsim, "csiborg"))
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box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
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parts = csiborgtools.read.read_h5(paths.particles(nsim, "csiborg"))
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parts = parts["particles"]
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gen = csiborgtools.field.VelocityField(box, parser_args.MAS)
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field = gen(parts, parser_args.grid, mpart, verbose=parser_args.verbose)
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field = gen(parts, parser_args.grid, verbose=parser_args.verbose)
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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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@ -131,57 +101,6 @@ def velocity_field(nsim, parser_args, to_save=True):
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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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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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Parsed arguments.
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to_save : bool, optional
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Whether to save the output to disk.
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Returns
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-------
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potential : 3-dimensional array
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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.CSiBORGBox(nsnap, nsim, paths)
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# Load the real space overdensity field
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density_gen = csiborgtools.field.DensityField(box, parser_args.MAS)
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rho = numpy.load(paths.field("density", parser_args.MAS, parser_args.grid,
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nsim, in_rsp=False))
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if parser_args.smooth_scale > 0:
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rho = csiborgtools.field.smoothen_field(rho, parser_args.smooth_scale,
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box.boxsize * box.h, threads=1)
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rho = density_gen.overdensity_field(rho)
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# Calculate the real space potentiel field
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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.in_rsp:
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parts = csiborgtools.read.read_h5(paths.particles(nsim, "csiborg"))
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parts = parts["particles"]
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field = csiborgtools.field.field2rsp(*field, parts=parts, box=box,
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verbose=parser_args.verbose)
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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, parser_args.smooth_scale)
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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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@ -190,33 +109,21 @@ def potential_field(nsim, parser_args, to_save=True):
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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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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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Parsed arguments.
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to_save : bool, optional
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Whether to save the output to disk.
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Returns
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-------
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radvel : 3-dimensional array
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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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if parser_args.smooth_scale > 0:
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raise NotImplementedError(
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"Smoothed radial vel. field not implemented.")
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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.CSiBORGBox(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)
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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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@ -224,6 +131,43 @@ def radvel_field(nsim, parser_args, to_save=True):
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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.CSiBORGBox(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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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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field = csiborgtools.field.field2rsp(field, radvel_field, box,
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parser_args.MAS)
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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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return field
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###############################################################################
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# Environment classification #
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@ -233,77 +177,47 @@ def radvel_field(nsim, parser_args, to_save=True):
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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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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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Parsed arguments.
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to_save : bool, optional
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Whether to save the output to disk.
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Returns
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-------
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env : 3-dimensional array
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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.CSiBORGBox(nsnap, nsim, paths)
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density_gen = csiborgtools.field.DensityField(box, parser_args.MAS)
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gen = csiborgtools.field.TidalTensorField(box, parser_args.MAS)
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# Load the real space overdensity field
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if parser_args.verbose:
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print(f"{datetime.now()}: loading density field.")
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rho = numpy.load(paths.field("density", parser_args.MAS, parser_args.grid,
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nsim, in_rsp=False))
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if parser_args.smooth_scale > 0:
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rho = csiborgtools.field.smoothen_field(rho, parser_args.smooth_scale,
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box.boxsize * box.h, threads=1)
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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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# Calculate the real space tidal tensor field, delete overdensity.
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if parser_args.verbose:
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print(f"{datetime.now()}: calculating tidal tensor field.")
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tensor_field = gen(rho)
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gen = csiborgtools.field.TidalTensorField(box, parser_args.MAS)
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field = gen(rho)
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del rho
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collect()
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# Optionally drag the field to RSP.
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if parser_args.in_rsp:
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parts = csiborgtools.read.read_h5(paths.particles(nsim, "csiborg"))
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parts = parts["particles"]
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fields = (tensor_field.T00, tensor_field.T11, tensor_field.T22,
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tensor_field.T01, tensor_field.T02, tensor_field.T12)
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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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T00, T11, T22, T01, T02, T12 = csiborgtools.field.field2rsp(
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*fields, parts=parts, box=box, verbose=parser_args.verbose)
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tensor_field.T00[...] = T00
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tensor_field.T11[...] = T11
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tensor_field.T22[...] = T22
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tensor_field.T01[...] = T01
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tensor_field.T02[...] = T02
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tensor_field.T12[...] = T12
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del T00, T11, T22, T01, T02, T12
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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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# Calculate the eigenvalues of the tidal tensor field, delete tensor field.
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if parser_args.verbose:
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print(f"{datetime.now()}: calculating eigenvalues.")
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eigvals = gen.tensor_field_eigvals(tensor_field)
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del tensor_field
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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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# Classify the environment based on the eigenvalues.
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if parser_args.verbose:
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print(f"{datetime.now()}: classifying environment.")
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env = gen.eigvals_to_environment(eigvals)
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del eigvals
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collect()
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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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nsim, parser_args.in_rsp)
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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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@ -327,8 +241,6 @@ if __name__ == "__main__":
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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,
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help="Smoothing scale in Mpc/h.")
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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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