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Periodic neighbours (#84)

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* Edit the HMF plot

* Add periodic dist 2 points

* Add boxsize to RVSSphere

* Add periodic distance

* Adding periodic distance

* Add imports

* Change arguments

* Update bounds

* Lower min number of particles

* Change kwargs

* Add paths overlap quijote

* Add some comments
This commit is contained in:
Richard Stiskalek 2023-08-08 12:19:40 +02:00 • committed by GitHub
parent c7e447df01
commit c7b600d0ad
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14 changed files with 196 additions and 61 deletions
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12
scripts/cluster_knn_auto.py
View file

@ -59,10 +59,10 @@ def do_auto(args, config, cats, nsim, paths):
-------
None
"""
rvs_gen = csiborgtools.clustering.RVSinsphere(args.Rmax)
knncdf = csiborgtools.clustering.kNN_1DCDF()
cat = cats[nsim]
knn = cat.knn(in_initial=False)
rvs_gen = csiborgtools.clustering.RVSinsphere(args.Rmax, cat.boxsize)
knncdf = csiborgtools.clustering.kNN_1DCDF()
knn = cat.knn(in_initial=False, subtract_observer=False, periodic=True)
rs, cdf = knncdf(
knn, rvs_gen=rvs_gen, nneighbours=config["nneighbours"],
rmin=config["rmin"], rmax=config["rmax"],
@ -97,9 +97,9 @@ def do_cross_rand(args, config, cats, nsim, paths):
-------
None
"""
rvs_gen = csiborgtools.clustering.RVSinsphere(args.Rmax)
cat = cats[nsim]
knn1 = cat.knn(in_initial=False)
rvs_gen = csiborgtools.clustering.RVSinsphere(args.Rmax, cat.boxsize)
knn1 = cat.knn(in_initial=False, subtract_observer=False, periodic=True)
knn2 = NearestNeighbors()
pos2 = rvs_gen(len(cat).shape[0])
@ -126,7 +126,7 @@ if __name__ == "__main__":
help="Simulation name")
parser.add_argument("--nsims", type=int, nargs="+", default=None,
help="Indices of simulations to cross. If `-1` processes all simulations.") # noqa
parser.add_argument("--Rmax", type=float, default=155/0.705,
parser.add_argument("--Rmax", type=float, default=155,
help="High-resolution region radius") # noqa
parser.add_argument("--verbose", type=lambda x: bool(strtobool(x)),
default=False)

6
scripts/cluster_tpcf_auto.py
View file

@ -37,12 +37,12 @@ except ModuleNotFoundError:
def do_auto(args, config, cats, nsim, paths):
cat = cats[nsim]
tpcf = csiborgtools.clustering.Mock2PCF()
rvs_gen = csiborgtools.clustering.RVSinsphere(args.Rmax)
rvs_gen = csiborgtools.clustering.RVSinsphere(args.Rmax, cat.boxsize)
bins = numpy.logspace(
numpy.log10(config["rpmin"]), numpy.log10(config["rpmax"]),
config["nrpbins"] + 1,)
cat = cats[nsim]
pos = cat.position(in_initial=False, cartesian=True)
nrandom = int(config["randmult"] * pos.shape[0])
@ -59,7 +59,7 @@ if __name__ == "__main__":
help="Simulation name")
parser.add_argument("--nsims", type=int, nargs="+", default=None,
help="Indices of simulations to cross. If `-1` processes all simulations.") # noqa
parser.add_argument("--Rmax", type=float, default=155/0.705,
parser.add_argument("--Rmax", type=float, default=155,
help="High-resolution region radius.")
parser.add_argument("--verbose", type=lambda x: bool(strtobool(x)),
default=False, help="Verbosity flag.")

9
scripts/fit_init.py
View file

@ -14,8 +14,9 @@
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
"""
Script to calculate the particle centre of mass, Lagrangian patch size in the
initial snapshot. The initial snapshot particles are read from the sorted
files.
initial snapshot.
The initial snapshot particles are read from the sorted files.
"""
from argparse import ArgumentParser
from datetime import datetime
@ -74,7 +75,7 @@ def _main(nsim, simname, verbose):
# Initialise the overlapper.
if simname == "csiborg":
kwargs = {"box_size": 2048, "bckg_halfsize": 475}
kwargs = {"box_size": 2048, "bckg_halfsize": 512}
else:
kwargs = {"box_size": 512, "bckg_halfsize": 256}
overlapper = csiborgtools.match.ParticleOverlap(**kwargs)
@ -86,7 +87,7 @@ def _main(nsim, simname, verbose):
hid2map)
# Skip if the halo has no particles or is too small.
if part is None or part.size < 100:
if part is None or part.size < 40:
continue
pos, mass = part[:, :3], part[:, 3]

20
scripts/match_singlematch.py
View file

@ -57,12 +57,13 @@ def pair_match(nsim0, nsimx, simname, sigma, verbose):
None
"""
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
smooth_kwargs = {"sigma": sigma, "mode": "wrap"}
smooth_kwargs = {"sigma": sigma, "mode": "constant", "cval": 0}
if simname == "csiborg":
overlapper_kwargs = {"box_size": 2048, "bckg_halfsize": 475}
overlapper_kwargs = {"box_size": 2048, "bckg_halfsize": 512}
mass_kind = "fof_totpartmass"
bounds = {mass_kind: (1e13, None)}
bounds = {"dist": (0, 155), mass_kind: (10**13.25, None)}
cat0 = csiborgtools.read.CSiBORGHaloCatalogue(
nsim0, paths, bounds=bounds, load_fitted=False,
with_lagpatch=True)
@ -72,11 +73,14 @@ def pair_match(nsim0, nsimx, simname, sigma, verbose):
elif simname == "quijote":
overlapper_kwargs = {"box_size": 512, "bckg_halfsize": 256}
mass_kind = "group_mass"
bounds = {mass_kind: (1e14, None)}
bounds = {mass_kind: (10**13.25, None)}
cat0 = csiborgtools.read.QuijoteHaloCatalogue(
nsim0, paths, 4, load_fitted=False, with_lagpatch=True)
nsim0, paths, 4, bounds=bounds, load_fitted=False,
with_lagpatch=True)
catx = csiborgtools.read.QuijoteHaloCatalogue(
nsimx, paths, 4, load_fitted=False, with_lagpatch=True)
nsimx, paths, 4, bounds=bounds, load_fitted=False,
with_lagpatch=True)
else:
raise ValueError(f"Unknown simulation name: `{simname}`.")
@ -116,7 +120,7 @@ def pair_match(nsim0, nsimx, simname, sigma, verbose):
for j, match in enumerate(matches):
match_hids[i][j] = catx["index"][match]
fout = paths.overlap(nsim0, nsimx, smoothed=False)
fout = paths.overlap(simname, nsim0, nsimx, smoothed=False)
if verbose:
print(f"{datetime.now()}: saving to ... `{fout}`.", flush=True)
numpy.savez(fout, ref_hids=cat0["index"], match_hids=match_hids,
@ -135,7 +139,7 @@ def pair_match(nsim0, nsimx, simname, sigma, verbose):
match_indxs, smooth_kwargs,
verbose=verbose)
fout = paths.overlap(nsim0, nsimx, smoothed=True)
fout = paths.overlap(simname, nsim0, nsimx, smoothed=True)
if verbose:
print(f"{datetime.now()}: saving to ... `{fout}`.", flush=True)
numpy.savez(fout, smoothed_overlap=smoothed_overlap, sigma=sigma)