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Quijote snapshots support (#77)

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* Renaming

* Edit docs

* Delete old function

* Add a blank space

* Rename particle reader

* Add comments

* Rename

* Rename

* edit get_snapshots

* More renaming

* Remove old correction

* Add import

* Add basics of the Quijote reader

* Add a blank space

* Fix paths

* Rename function

* Fix HID and path

* Add more FoF reading

* Move definition

* Adding arguments

* Renaming

* Add kwargs for backward comp

* FoF Quijote return only hids

* Add sorting of quijote

* Add path to CSiBORG ICs snapshot

* Add support for Quijote

* initmatch paths for quijote

* Add kwargs

* Fix blank lines

* Rename kwarg

* Remove unused import

* Remove hardcoded numbers

* Update for Quijote

* Do not store velocities in QUijote ICs

* Box units mass Quijote

* Fix typo

* Ensure particles are not right at the edge

* Add structfit paths for QUuijote

* Basic CSiBORG units

* Add more quijote halo reading

* Add Quijote fitting

* Docs changes

* Docs changes
This commit is contained in:
Richard Stiskalek 2023-07-27 18:41:00 +02:00 • committed by GitHub
parent e08c741fc8
commit fb4b4edf19
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18 changed files with 800 additions and 300 deletions
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43
scripts/pre_sortinit.py
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@ -50,34 +50,55 @@ def _main(nsim, simname, verbose):
verbose : bool
Verbosity flag.
"""
if simname == "quijote":
raise NotImplementedError("Quijote not implemented yet.")
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
partreader = csiborgtools.read.ParticleReader(paths)
if simname == "csiborg":
partreader = csiborgtools.read.CSiBORGReader(paths)
else:
partreader = csiborgtools.read.QuijoteReader(paths)
if verbose:
print(f"{datetime.now()}: reading and processing simulation {nsim}.",
print(f"{datetime.now()}: reading and processing simulation `{nsim}`.",
flush=True)
# We first load the particle IDs in the final snapshot.
pidf = csiborgtools.read.read_h5(paths.particles(nsim))
pidf = csiborgtools.read.read_h5(paths.particles(nsim, simname))
pidf = pidf["particle_ids"]
# Then we load the particles in the initil snapshot and make sure that
# their particle IDs are sorted as in the final snapshot. Again, because of
# precision this must be read as structured.
# NOTE: ID has to be the last column.
pars_extract = ["x", "y", "z", "M", "ID"]
if simname == "csiborg":
pars_extract = ["x", "y", "z", "M", "ID"]
# CSiBORG's initial snapshot ID
nsnap = 1
else:
pars_extract = None
# Use this to point the reader to the ICs snapshot
nsnap = -1
part0, pid0 = partreader.read_particle(
1, nsim, pars_extract, return_structured=False, verbose=verbose)
nsnap, nsim, pars_extract, return_structured=False, verbose=verbose)
# Quijote's initial snapshot information also contains velocities but we
# don't need those.
if simname == "quijote":
part0 = part0[:, [0, 1, 2, 6]]
# In Quijote some particles are position precisely at the edge of the
# box. Move them to be just inside.
pos = part0[:, :3]
mask = pos >= 1
if numpy.any(mask):
spacing = numpy.spacing(pos[mask])
assert numpy.max(spacing) <= 1e-5
pos[mask] -= spacing
# First enforce them to already be sorted and then apply reverse
# sorting from the final snapshot.
part0 = part0[numpy.argsort(pid0)]
del pid0
collect()
part0 = part0[numpy.argsort(numpy.argsort(pidf))]
fout = paths.initmatch(nsim, simname, "particles")
if verbose:
print(f"{datetime.now()}: dumping particles for {nsim}.", flush=True)
with h5py.File(paths.initmatch(nsim, "particles"), "w") as f:
print(f"{datetime.now()}: dumping particles for `{nsim}` to `{fout}`",
flush=True)
with h5py.File(fout, "w") as f:
f.create_dataset("particles", data=part0)