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Add Quijote (#61)

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* Rename paths object

* Remove redshift calculation

* Explicit keywrod arg

* Rename box units

* Basic renaming

* Little docs

* Rename paths

* add imports

* Sort imports

* Add Quijote cat

* Split boxes

* add Quijote path

* Add origin argument

* Update nbs
This commit is contained in:
Richard Stiskalek 2023-05-13 17:37:34 +01:00 • committed by GitHub
parent b3fd14b81f
commit 1d847cbd06
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GPG key ID: 4AEE18F83AFDEB23
34 changed files with 1401 additions and 292 deletions
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4
scripts/cluster_crosspk.py
View file

@ -48,8 +48,8 @@ rank = comm.Get_rank()
nproc = comm.Get_size()
MAS = "CIC" # mass asignment scheme
paths = csiborgtools.read.CSiBORGPaths(**csiborgtools.paths_glamdring)
box = csiborgtools.read.BoxUnits(paths)
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
box = csiborgtools.read.CSiBORGBox(paths)
reader = csiborgtools.read.ParticleReader(paths)
ics = paths.get_ics()
nsims = len(ics)

2
scripts/cluster_knn_auto.py
View file

@ -49,7 +49,7 @@ with open("../scripts/knn_auto.yml", "r") as file:
Rmax = 155 / 0.705 # Mpc (h = 0.705) high resolution region radius
totvol = 4 * numpy.pi * Rmax**3 / 3
paths = csiborgtools.read.CSiBORGPaths(**csiborgtools.paths_glamdring)
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
ics = paths.get_ics()
knncdf = csiborgtools.clustering.kNN_CDF()

2
scripts/cluster_knn_cross.py
View file

@ -48,7 +48,7 @@ with open("../scripts/knn_cross.yml", "r") as file:
config = yaml.safe_load(file)
Rmax = 155 / 0.705 # Mpc (h = 0.705) high resolution region radius
paths = csiborgtools.read.CSiBORGPaths(**csiborgtools.paths_glamdring)
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
ics = paths.get_ics()
knncdf = csiborgtools.clustering.kNN_CDF()

2
scripts/cluster_tcpf_auto.py
View file

@ -47,7 +47,7 @@ with open("../scripts/tpcf_auto.yml", "r") as file:
config = yaml.safe_load(file)
Rmax = 155 / 0.705 # Mpc (h = 0.705) high resolution region radius
paths = csiborgtools.read.CSiBORGPaths()
paths = csiborgtools.read.Paths()
ics = paths.get_ics()
tpcf = csiborgtools.clustering.Mock2PCF()

4
scripts/field_derived.py
View file

@ -45,7 +45,7 @@ parser.add_argument("--grid", type=int, help="Grid resolution.")
parser.add_argument("--in_rsp", type=lambda x: bool(strtobool(x)),
help="Calculate from the RSP density field?")
args = parser.parse_args()
paths = csiborgtools.read.CSiBORGPaths(**csiborgtools.paths_glamdring)
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
if args.ics is None or args.ics[0] == -1:
ics = paths.get_ics()
@ -59,7 +59,7 @@ for i in csiborgtools.fits.split_jobs(len(ics), nproc)[rank]:
print(f"{datetime.now()}: rank {rank} working on simulation {nsim}.",
flush=True)
nsnap = max(paths.get_snapshots(nsim))
box = csiborgtools.read.BoxUnits(nsnap, nsim, paths)
box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
density_gen = csiborgtools.field.DensityField(box, args.MAS)
rho = numpy.load(paths.field_path("density", args.MAS, args.grid, nsim,

4
scripts/field_fromparts.py
View file

@ -46,7 +46,7 @@ parser.add_argument("--grid", type=int, help="Grid resolution.")
parser.add_argument("--in_rsp", type=lambda x: bool(strtobool(x)),
help="Calculate the density field in redshift space?")
args = parser.parse_args()
paths = csiborgtools.read.CSiBORGPaths(**csiborgtools.paths_glamdring)
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
mpart = 1.1641532e-10 # Particle mass in CSiBORG simulations.
if args.ics is None or args.ics[0] == -1:
@ -61,7 +61,7 @@ for i in csiborgtools.fits.split_jobs(len(ics), nproc)[rank]:
flush=True)
nsnap = max(paths.get_snapshots(nsim))
box = csiborgtools.read.BoxUnits(nsnap, nsim, paths)
box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
parts = csiborgtools.read.read_h5(paths.particles_path(nsim))["particles"]
if args.kind == "density":

4
scripts/fit_halos.py
View file

@ -42,7 +42,7 @@ parser.add_argument("--kind", type=str, choices=["halos", "clumps"])
parser.add_argument("--ics", type=int, nargs="+", default=None,
help="IC realisations. If `-1` processes all simulations.")
args = parser.parse_args()
paths = csiborgtools.read.CSiBORGPaths(**csiborgtools.paths_glamdring)
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
partreader = csiborgtools.read.ParticleReader(paths)
nfwpost = csiborgtools.fits.NFWPosterior()
@ -105,7 +105,7 @@ for nsim in [ics[i] for i in jobs]:
print(f"{datetime.now()}: rank {rank} calculating simulation `{nsim}`.",
flush=True)
nsnap = max(paths.get_snapshots(nsim))
box = csiborgtools.read.BoxUnits(nsnap, nsim, paths)
box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
# Particle archive
f = csiborgtools.read.read_h5(paths.particles_path(nsim))

3
scripts/fit_init.py
View file

@ -22,7 +22,6 @@ from datetime import datetime
import numpy
from mpi4py import MPI
from tqdm import tqdm
try:
@ -45,7 +44,7 @@ parser = ArgumentParser()
parser.add_argument("--ics", type=int, nargs="+", default=None,
help="IC realisations. If `-1` processes all simulations.")
args = parser.parse_args()
paths = csiborgtools.read.CSiBORGPaths(**csiborgtools.paths_glamdring)
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
partreader = csiborgtools.read.ParticleReader(paths)
if args.ics is None or args.ics[0] == -1:

4
scripts/fit_profiles.py
View file

@ -45,7 +45,7 @@ nproc = comm.Get_size()
if nproc > 1:
raise NotImplementedError("MPI is not implemented implemented yet.")
paths = csiborgtools.read.CSiBORGPaths(**csiborgtools.paths_glamdring)
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
cols_collect = [("r", numpy.float32), ("M", numpy.float32)]
if args.ics is None or args.ics == -1:
nsims = paths.get_ics()
@ -59,7 +59,7 @@ for i, nsim in enumerate(nsims):
now = datetime.now()
print(f"{now}: calculating {i}th simulation `{nsim}`.", flush=True)
nsnap = max(paths.get_snapshots(nsim))
box = csiborgtools.read.BoxUnits(nsnap, nsim, paths)
box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
f = csiborgtools.read.read_h5(paths.particles_path(nsim))
particles = f["particles"]

2
scripts/match_all.py
View file

@ -54,7 +54,7 @@ def get_combs():
Get the list of all pairs of simulations, then permute them with a known
seed to minimise loading the same files simultaneously.
"""
paths = csiborgtools.read.CSiBORGPaths(**csiborgtools.paths_glamdring)
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
ics = paths.get_ics()
combs = list(combinations(ics, 2))
Random(42).shuffle(combs)

2
scripts/match_singlematch.py
View file

@ -32,7 +32,7 @@ except ModuleNotFoundError:
def pair_match(nsim0, nsimx, sigma, smoothen, verbose):
from csiborgtools.read import HaloCatalogue, read_h5
paths = csiborgtools.read.CSiBORGPaths(**csiborgtools.paths_glamdring)
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
smooth_kwargs = {"sigma": sigma, "mode": "constant", "cval": 0.0}
overlapper = csiborgtools.match.ParticleOverlap()
matcher = csiborgtools.match.RealisationsMatcher()

2
scripts/pre_dumppart.py
View file

@ -49,7 +49,7 @@ parser.add_argument("--ics", type=int, nargs="+", default=None,
args = parser.parse_args()
verbose = nproc == 1
paths = csiborgtools.read.CSiBORGPaths(**csiborgtools.paths_glamdring)
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
partreader = csiborgtools.read.ParticleReader(paths)
# Keep "ID" as the last column!
pars_extract = ['x', 'y', 'z', 'vx', 'vy', 'vz', 'M', "ID"]

2
scripts/pre_mmain.py
View file

@ -33,7 +33,7 @@ comm = MPI.COMM_WORLD
rank = comm.Get_rank()
nproc = comm.Get_size()
paths = csiborgtools.read.CSiBORGPaths(**csiborgtools.paths_glamdring)
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
mmain_reader = csiborgtools.read.MmainReader(paths)

4
scripts/pre_sortinit.py
View file

@ -18,9 +18,9 @@ snapshot ordering, which is sorted by the clump IDs.
"""
from argparse import ArgumentParser
from datetime import datetime
from gc import collect
import h5py
from gc import collect
import numpy
from mpi4py import MPI
@ -44,7 +44,7 @@ parser = ArgumentParser()
parser.add_argument("--ics", type=int, nargs="+", default=None,
help="IC realisations. If `-1` processes all simulations.")
args = parser.parse_args()
paths = csiborgtools.read.CSiBORGPaths(**csiborgtools.paths_glamdring)
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
partreader = csiborgtools.read.ParticleReader(paths)
# NOTE: ID has to be the last column.
pars_extract = ["x", "y", "z", "M", "ID"]