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Velocity observer (#86)

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* 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 2023-08-30 23:27:20 +01:00 • committed by GitHub
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108
scripts/field_obs_vp.py Normal file
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@ -0,0 +1,108 @@
# Copyright (C) 2022 Richard Stiskalek
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option) any later version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
# Public License for more details.
#
# You should have received a copy of the GNU General Public License along
# with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
"""
Script to calculate the peculiar velocity of an observer in the centre of the
CSiBORG box.
"""
from argparse import ArgumentParser
from distutils.util import strtobool
import numpy
from mpi4py import MPI
from taskmaster import work_delegation
from tqdm import tqdm
from utils import get_nsims
try:
import csiborgtools
except ModuleNotFoundError:
import sys
sys.path.append("../")
import csiborgtools
def observer_peculiar_velocity(nsim, parser_args):
"""
Calculate the peculiar velocity of an observer in the centre of the box
for several smoothing scales.
"""
pos = numpy.array([0.5, 0.5, 0.5]).reshape(-1, 3)
boxsize = 677.7
smooth_scales = [0, 0.5, 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0]
observer_vp = numpy.full((len(smooth_scales), 3), numpy.nan,
dtype=numpy.float32)
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
field_path = paths.field("velocity", parser_args.MAS, parser_args.grid,
nsim, in_rsp=False)
field0 = numpy.load(field_path)
for j, smooth_scale in enumerate(tqdm(smooth_scales,
desc="Smoothing the fields",
disable=not parser_args.verbose)):
if smooth_scale > 0:
field = [None, None, None]
for k in range(3):
field[k] = csiborgtools.field.smoothen_field(
field0[k], smooth_scale, boxsize)
else:
field = field0
v = csiborgtools.field.evaluate_cartesian(
field[0], field[1], field[2], pos=pos)
observer_vp[j, 0] = v[0][0]
observer_vp[j, 1] = v[1][0]
observer_vp[j, 2] = v[2][0]
fout = paths.observer_peculiar_velocity(parser_args.MAS, parser_args.grid,
nsim)
if parser_args.verbose:
print(f"Saving to ... `{fout}`")
numpy.savez(fout, smooth_scales=smooth_scales, observer_vp=observer_vp)
return observer_vp
###############################################################################
# Command line interface #
###############################################################################
if __name__ == "__main__":
parser = ArgumentParser()
parser.add_argument("--nsims", type=int, nargs="+", default=None,
help="IC realisations. `-1` for all simulations.")
parser.add_argument("--kind", type=str,
choices=["density", "rspdensity", "velocity", "radvel",
"potential", "environment"],
help="What derived field to calculate?")
parser.add_argument("--MAS", type=str,
choices=["NGP", "CIC", "TSC", "PCS"])
parser.add_argument("--grid", type=int, help="Grid resolution.")
parser.add_argument("--verbose", type=lambda x: bool(strtobool(x)),
help="Verbosity flag for reading in particles.")
parser.add_argument("--simname", type=str, default="csiborg",
help="Verbosity flag for reading in particles.")
parser_args = parser.parse_args()
comm = MPI.COMM_WORLD
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
nsims = get_nsims(parser_args, paths)
def main(nsim):
return observer_peculiar_velocity(nsim, parser_args)
work_delegation(main, nsims, comm, master_verbose=True)

250
scripts/field_prop.py
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@ -43,44 +43,29 @@ from utils import get_nsims
def density_field(nsim, parser_args, to_save=True):
"""
Calculate the density field in the CSiBORG simulation.
Parameters
----------
nsim : int
Simulation index.
parser_args : argparse.Namespace
Parsed arguments.
to_save : bool, optional
Whether to save the output to disk.
Returns
-------
field : 3-dimensional array
"""
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
nsnap = max(paths.get_snapshots(nsim, "csiborg"))
box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
parts = csiborgtools.read.read_h5(paths.particles(nsim, "csiborg"))
parts = parts["particles"]
gen = csiborgtools.field.DensityField(box, parser_args.MAS)
if parser_args.kind == "density":
field = gen(parts, parser_args.grid, in_rsp=False,
verbose=parser_args.verbose)
if parser_args.in_rsp:
field = csiborgtools.field.field2rsp(*field, parts=parts, box=box,
verbose=parser_args.verbose)
if not parser_args.in_rsp:
parts = csiborgtools.read.read_h5(paths.particles(nsim, "csiborg"))
parts = parts["particles"]
gen = csiborgtools.field.DensityField(box, parser_args.MAS)
field = gen(parts, parser_args.grid, verbose=parser_args.verbose)
else:
field = gen(parts, parser_args.grid, in_rsp=parser_args.in_rsp,
verbose=parser_args.verbose)
field = numpy.load(paths.field(
"density", parser_args.MAS, parser_args.grid, nsim, False))
radvel_field = numpy.load(paths.field(
"radvel", parser_args.MAS, parser_args.grid, nsim, False))
if parser_args.smooth_scale > 0:
field = csiborgtools.field.smoothen_field(
field, parser_args.smooth_scale, box.boxsize * box.h, threads=1)
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, parser_args.smooth_scale)
nsim, parser_args.in_rsp)
print(f"{datetime.now()}: saving output to `{fout}`.")
numpy.save(fout, field)
return field
@ -93,35 +78,20 @@ def density_field(nsim, parser_args, to_save=True):
def velocity_field(nsim, parser_args, to_save=True):
"""
Calculate the velocity field in the CSiBORG simulation.
Parameters
----------
nsim : int
Simulation index.
parser_args : argparse.Namespace
Parsed arguments.
to_save : bool, optional
Whether to save the output to disk.
Returns
-------
velfield : 4-dimensional array
Calculate the velocity field in a CSiBORG simulation.
"""
if parser_args.in_rsp:
raise NotImplementedError("Velocity field in RSP is not implemented.")
if parser_args.smooth_scale > 0:
raise NotImplementedError(
"Smoothed velocity field is not implemented.")
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
mpart = 1.1641532e-10 # Particle mass in CSiBORG simulations.
nsnap = max(paths.get_snapshots(nsim, "csiborg"))
box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
parts = csiborgtools.read.read_h5(paths.particles(nsim, "csiborg"))
parts = parts["particles"]
gen = csiborgtools.field.VelocityField(box, parser_args.MAS)
field = gen(parts, parser_args.grid, mpart, verbose=parser_args.verbose)
field = gen(parts, parser_args.grid, verbose=parser_args.verbose)
if to_save:
fout = paths.field("velocity", parser_args.MAS, parser_args.grid,
@ -131,57 +101,6 @@ def velocity_field(nsim, parser_args, to_save=True):
return field
###############################################################################
# Potential field #
###############################################################################
def potential_field(nsim, parser_args, to_save=True):
"""
Calculate the potential field in the CSiBORG simulation.
Parameters
----------
nsim : int
Simulation index.
parser_args : argparse.Namespace
Parsed arguments.
to_save : bool, optional
Whether to save the output to disk.
Returns
-------
potential : 3-dimensional array
"""
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
nsnap = max(paths.get_snapshots(nsim, "csiborg"))
box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
# Load the real space overdensity field
density_gen = csiborgtools.field.DensityField(box, parser_args.MAS)
rho = numpy.load(paths.field("density", parser_args.MAS, parser_args.grid,
nsim, in_rsp=False))
if parser_args.smooth_scale > 0:
rho = csiborgtools.field.smoothen_field(rho, parser_args.smooth_scale,
box.boxsize * box.h, threads=1)
rho = density_gen.overdensity_field(rho)
# Calculate the real space potentiel field
gen = csiborgtools.field.PotentialField(box, parser_args.MAS)
field = gen(rho)
if parser_args.in_rsp:
parts = csiborgtools.read.read_h5(paths.particles(nsim, "csiborg"))
parts = parts["particles"]
field = csiborgtools.field.field2rsp(*field, parts=parts, box=box,
verbose=parser_args.verbose)
if to_save:
fout = paths.field(parser_args.kind, 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, field)
return field
###############################################################################
# Radial velocity field #
###############################################################################
@ -190,33 +109,21 @@ def potential_field(nsim, parser_args, to_save=True):
def radvel_field(nsim, parser_args, to_save=True):
"""
Calculate the radial velocity field in the CSiBORG simulation.
Parameters
----------
nsim : int
Simulation index.
parser_args : argparse.Namespace
Parsed arguments.
to_save : bool, optional
Whether to save the output to disk.
Returns
-------
radvel : 3-dimensional array
"""
if parser_args.in_rsp:
raise NotImplementedError("Radial vel. field in RSP not implemented.")
if parser_args.smooth_scale > 0:
raise NotImplementedError(
"Smoothed radial vel. field not implemented.")
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
nsnap = max(paths.get_snapshots(nsim, "csiborg"))
box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
vel = numpy.load(paths.field("velocity", parser_args.MAS, parser_args.grid,
nsim, parser_args.in_rsp))
observer_velocity = csiborgtools.field.observer_vobs(vel)
gen = csiborgtools.field.VelocityField(box, parser_args.MAS)
field = gen.radial_velocity(vel)
field = gen.radial_velocity(vel, observer_velocity)
if to_save:
fout = paths.field("radvel", parser_args.MAS, parser_args.grid,
nsim, parser_args.in_rsp)
@ -224,6 +131,43 @@ def radvel_field(nsim, parser_args, to_save=True):
numpy.save(fout, field)
return field
###############################################################################
# Potential field #
###############################################################################
def potential_field(nsim, parser_args, to_save=True):
"""
Calculate the potential field in the CSiBORG simulation.
"""
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
nsnap = max(paths.get_snapshots(nsim, "csiborg"))
box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
if not parser_args.in_rsp:
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)
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 #
@ -233,77 +177,47 @@ def radvel_field(nsim, parser_args, to_save=True):
def environment_field(nsim, parser_args, to_save=True):
"""
Calculate the environmental classification in the CSiBORG simulation.
Parameters
----------
nsim : int
Simulation index.
parser_args : argparse.Namespace
Parsed arguments.
to_save : bool, optional
Whether to save the output to disk.
Returns
-------
env : 3-dimensional array
"""
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
nsnap = max(paths.get_snapshots(nsim, "csiborg"))
box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
density_gen = csiborgtools.field.DensityField(box, parser_args.MAS)
gen = csiborgtools.field.TidalTensorField(box, parser_args.MAS)
# Load the real space overdensity field
if parser_args.verbose:
print(f"{datetime.now()}: loading density field.")
rho = numpy.load(paths.field("density", parser_args.MAS, parser_args.grid,
nsim, in_rsp=False))
if parser_args.smooth_scale > 0:
rho = csiborgtools.field.smoothen_field(rho, parser_args.smooth_scale,
box.boxsize * box.h, threads=1)
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)
# Calculate the real space tidal tensor field, delete overdensity.
if parser_args.verbose:
print(f"{datetime.now()}: calculating tidal tensor field.")
tensor_field = gen(rho)
gen = csiborgtools.field.TidalTensorField(box, parser_args.MAS)
field = gen(rho)
del rho
collect()
# Optionally drag the field to RSP.
if parser_args.in_rsp:
parts = csiborgtools.read.read_h5(paths.particles(nsim, "csiborg"))
parts = parts["particles"]
fields = (tensor_field.T00, tensor_field.T11, tensor_field.T22,
tensor_field.T01, tensor_field.T02, tensor_field.T12)
radvel_field = numpy.load(paths.field(
"radvel", parser_args.MAS, parser_args.grid, nsim, False))
args = (radvel_field, box, parser_args.MAS)
T00, T11, T22, T01, T02, T12 = csiborgtools.field.field2rsp(
*fields, parts=parts, box=box, verbose=parser_args.verbose)
tensor_field.T00[...] = T00
tensor_field.T11[...] = T11
tensor_field.T22[...] = T22
tensor_field.T01[...] = T01
tensor_field.T02[...] = T02
tensor_field.T12[...] = T12
del T00, T11, T22, T01, T02, T12
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()
# Calculate the eigenvalues of the tidal tensor field, delete tensor field.
if parser_args.verbose:
print(f"{datetime.now()}: calculating eigenvalues.")
eigvals = gen.tensor_field_eigvals(tensor_field)
del tensor_field
eigvals = gen.tensor_field_eigvals(field)
del field
collect()
# Classify the environment based on the eigenvalues.
if parser_args.verbose:
print(f"{datetime.now()}: classifying environment.")
env = gen.eigvals_to_environment(eigvals)
del eigvals
collect()
if to_save:
fout = paths.field("environment", parser_args.MAS, parser_args.grid,
nsim, parser_args.in_rsp, parser_args.smooth_scale)
nsim, parser_args.in_rsp)
print(f"{datetime.now()}: saving output to `{fout}`.")
numpy.save(fout, env)
return env
@ -327,8 +241,6 @@ if __name__ == "__main__":
parser.add_argument("--grid", type=int, help="Grid resolution.")
parser.add_argument("--in_rsp", type=lambda x: bool(strtobool(x)),
help="Calculate in RSP?")
parser.add_argument("--smooth_scale", type=float, default=0,
help="Smoothing scale in Mpc/h.")
parser.add_argument("--verbose", type=lambda x: bool(strtobool(x)),
help="Verbosity flag for reading in particles.")
parser.add_argument("--simname", type=str, default="csiborg",

23
scripts/fit_hmf.py
View file

@ -37,21 +37,6 @@ except ModuleNotFoundError:
def get_counts(nsim, bins, paths, parser_args):
"""
Calculate and save the number of haloes in each mass bin.
Parameters
----------
nsim : int
Simulation index.
bins : 1-dimensional array
Array of bin edges (in log10 mass).
paths : csiborgtools.read.Paths
Paths object.
parser_args : argparse.Namespace
Parsed command-line arguments.
Returns
-------
None
"""
simname = parser_args.simname
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
@ -75,13 +60,14 @@ def get_counts(nsim, bins, paths, parser_args):
counts[nobs, :] = csiborgtools.number_counts(logmass, bins)
elif simname == "quijote_full":
cat = csiborgtools.read.QuijoteHaloCatalogue(
nsim, paths, nsnap=4, load_fitted=False, load_initial=False)
nsim, paths, nsnap=4, load_fitted=False, load_initial=False,
load_backup=parser_args.from_quijote_backup)
logmass = numpy.log10(cat["group_mass"])
counts = csiborgtools.number_counts(logmass, bins)
else:
raise ValueError(f"Unknown simulation name `{simname}`.")
fout = paths.halo_counts(simname, nsim)
fout = paths.halo_counts(simname, nsim, parser_args.from_quijote_backup)
if parser_args.verbose:
print(f"{datetime.now()}: saving halo counts to `{fout}`.")
numpy.savez(fout, counts=counts, bins=bins, rmax=parser_args.Rmax)
@ -97,6 +83,9 @@ if __name__ == "__main__":
parser.add_argument(
"--Rmax", type=float, default=155,
help="High-res region radius in Mpc / h. Ignored for `quijote_full`.")
parser.add_argument("--from_quijote_backup",
type=lambda x: bool(strtobool(x)), default=False,
help="Flag to indicate Quijote backup data.")
parser.add_argument("--lims", type=float, nargs="+", default=[11., 16.],
help="Mass limits in Msun / h.")
parser.add_argument("--bw", type=float, default=0.2,

9
scripts/fit_init.py
View file

@ -41,15 +41,6 @@ def _main(nsim, simname, verbose):
"""
Calculate the Lagrangian halo centre of mass and Lagrangian patch size in
the initial snapshot.
Parameters
----------
nsim : int
IC realisation index.
simname : str
Simulation name.
verbose : bool
Verbosity flag.
"""
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
cols = [("index", numpy.int32),

31
scripts/match_all.py
View file

@ -29,16 +29,6 @@ def get_combs(simname):
"""
Get the list of all pairs of IC indices and permute them with a fixed
seed.
Parameters
----------
simname : str
Simulation name.
Returns
-------
combs : list
List of pairs of simulations.
"""
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
combs = list(combinations(paths.get_ics(simname), 2))
@ -50,27 +40,6 @@ def get_combs(simname):
def main(comb, kind, simname, min_logmass, sigma, mult, verbose):
"""
Match a pair of simulations.
Parameters
----------
comb : tuple
Pair of simulation IC indices.
kind : str
Kind of matching.
simname : str
Simulation name.
min_logmass : float
Minimum log halo mass.
sigma : float
Smoothing scale in number of grid cells.
mult : float
Multiplicative factor for search radius.
verbose : bool
Verbosity flag.
Returns
-------
None
"""
nsim0, nsimx = comb
if kind == "overlap":

11
scripts/utils.py
View file

@ -52,7 +52,7 @@ def get_nsims(args, paths):
Simulation indices.
"""
if args.nsims is None or args.nsims[0] == -1:
nsims = paths.get_ics(args.simname)
nsims = paths.get_ics(args.simname, args.from_quijote_backup)
else:
nsims = args.nsims
return list(nsims)
@ -93,9 +93,14 @@ def read_single_catalogue(args, config, nsim, run, rmax, paths, nobs=None):
nsim, paths, load_fitted=True, load_inital=True,
with_lagpatch=False)
else:
if args.from_quijote_backup:
load_fitted = False
load_initial = False
cat = csiborgtools.read.QuijoteHaloCatalogue(
nsim, paths, nsnap=4, load_fitted=True, load_initial=True,
with_lagpatch=False)
nsim, paths, nsnap=4, load_fitted=load_fitted,
load_initial=load_initial, with_lagpatch=False,
load_backup=args.from_quijote_backup)
if nobs is not None:
# We may optionally already here pick a fiducial observer.
cat = cat.pick_fiducial_observer(nobs, args.Rmax)