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Add pynbody and other support (#92)

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* Simplify box units

* Move old scripts

* Add printing

* Update readers

* Disable boundscheck

* Add new ordering

* Clean up imports

* Enforce dtype and add mass to quijote

* Simplify print statements

* Fix little typos

* Fix key bug

* Bug fixing

* Delete boring comments

* Improve ultimate clumps for PHEW

* Delete boring comments

* Add basic reading

* Remove 0th index HID

* Add flipping of X and Z

* Updates to halo catalogues

* Add ordered caching

* Fix flipping

* Add new flags

* Fix PHEW empty clumps

* Stop over-wrriting

* Little improvements to angular neighbours

* Add catalogue masking

* Change if-else statements

* Cache only filtered data

* Add PHEW cats

* Add comments

* Sort imports

* Get Quijote workign

* Docs

* Add HMF calculation

* Move to old

* Fix angular

* Add great circle distance

* Update imports

* Update impotrts

* Update docs

* Remove unused import

* Fix a quick bug

* Update compatibility

* Rename files

* Renaming

* Improve compatiblity

* Rename snapsht

* Fix snapshot bug

* Update interface

* Finish updating interface

* Update all paths

* Add old scripts

* Add basic halo

* Update imports

* Improve snapshot processing

* Update ordering

* Fix how CM positions accessed

* Add merger paths

* Add imports

* Add merger reading

* Add making a merger tree

* Add a basic merger tree reader

* Add imports

* Add main branch walking + comments + debuggin

* Get tree running

* Add working merger tree walking along main branch

* Add units conversion for merger data

* Add hid_to_array_index

* Update merger tree

* Add mergertree mass to PHEWcat

* Edit comments

* Add this to track changes...

* Fix a little bug

* Add mergertree mass

* Add cache clearing

* Improve summing substructure code

* Littbe bug

* Little updates to the merger tree reader

* Update .giignore

* Add box selection

* Add optional deletingf of a group

* add to keep track of changes

* Update changes

* Remove

* Add manual tracker

* Fix bug

* Add m200c_to_r200c

* Add manual halo tracking

* Remove skipped snapshots

* update cosmo params to match csiborg

* remove old comments

* Add SDSSxALFALFA

* Fix bugs

* Rename

* Edit paths

* Updates

* Add comments

* Add comment

* Add hour conversion

* Add imports

* Add new observation class

* Add selection

* Add imports

* Fix small bug

* Add field copying for safety

* Add matching to survey without masking

* Add P(k) calculation

* Add nb

* Edit comment

* Move files

* Remove merger import

* Edit setup.yp

* Fix typo

* Edit import warnigns

* update nb

* Update README

* Update README

* Update README

* Add skeleton

* Add skeleton
This commit is contained in:
Richard Stiskalek 2023-12-07 14:23:32 +00:00 • committed by GitHub
parent 5500fbd2b9
commit e972f8e3f2
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GPG key ID: 4AEE18F83AFDEB23
53 changed files with 4627 additions and 1774 deletions
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28
scripts/field_prop.py
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@ -28,6 +28,16 @@ from taskmaster import work_delegation
import csiborgtools
from utils import get_nsims
###############################################################################
# Cosmotool SPH density & velocity field #
###############################################################################
def cosmotool_sph(nsim, parser_args):
pass
###############################################################################
# Density field #
###############################################################################
@ -40,13 +50,15 @@ def density_field(nsim, parser_args, to_save=True):
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
nsnap = max(paths.get_snapshots(nsim, "csiborg"))
box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
fname = paths.processed_output(nsim, "csiborg", "halo_catalogue")
if not parser_args.in_rsp:
parts = csiborgtools.read.read_h5(paths.particles(nsim, "csiborg"))
parts = parts["particles"]
snap = csiborgtools.read.read_h5(fname)["snapshot_final"]
pos = snap["pos"]
mass = snap["mass"]
gen = csiborgtools.field.DensityField(box, parser_args.MAS)
field = gen(parts, parser_args.grid, verbose=parser_args.verbose)
field = gen(pos, mass, parser_args.grid, verbose=parser_args.verbose)
else:
field = numpy.load(paths.field(
"density", parser_args.MAS, parser_args.grid, nsim, False))
@ -83,12 +95,15 @@ def velocity_field(nsim, parser_args, to_save=True):
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
nsnap = max(paths.get_snapshots(nsim, "csiborg"))
box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
fname = paths.processed_output(nsim, "csiborg", "halo_catalogue")
parts = csiborgtools.read.read_h5(paths.particles(nsim, "csiborg"))
parts = parts["particles"]
snap = csiborgtools.read.read_h5(fname)["snapshot_final"]
pos = snap["pos"]
vel = snap["vel"]
mass = snap["mass"]
gen = csiborgtools.field.VelocityField(box, parser_args.MAS)
field = gen(parts, parser_args.grid, verbose=parser_args.verbose)
field = gen(pos, vel, mass, parser_args.grid, verbose=parser_args.verbose)
if to_save:
fout = paths.field("velocity", parser_args.MAS, parser_args.grid,
@ -247,6 +262,7 @@ if __name__ == "__main__":
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",
choices=["csiborg", "csiborg2"],
help="Verbosity flag for reading in particles.")
parser_args = parser.parse_args()
comm = MPI.COMM_WORLD