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Correct fitting script for both clumps and halos (#46)

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* Minor typos

* fix minor bugs

* pep8

* formatting

* pep8

* Fix minor bugs

* New path & pep8

* add splitt

* Updates

* Improve calculation within radius

* pep8

* pep8

* get the script working

* Add matter overdensity

* Add m200m to the script

* Fix looping bug

* add parents support

* add import

* Optionally concatenate velocities

* Make optional masking

* Ignore the error message

* Start reading in raw data

* Fix cat reading

* Additional units conversions

* Add clump reading

* Fix indexing

* Remove old comment

* Remove old comment

* set npart to 0 instead of overflow from NaN

* fix docs

* rm boring stuff

* Remove old stuff

* Remove old stuff

* Remove old comment

* Update nb
This commit is contained in:
Richard Stiskalek 2023-04-19 16:39:35 +02:00 • committed by GitHub
parent c2fde1566b
commit 39b3498621
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17 changed files with 709 additions and 357 deletions
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17
scripts/pre_splithalos.py
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@ -12,7 +12,10 @@
# 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 split particles to indivudual files according to their clump."""
"""
Script to split particles to individual files according to their clump. This is
useful for calculating the halo properties directly from the particles.
"""
from datetime import datetime
from gc import collect
from glob import glob
@ -28,6 +31,7 @@ try:
import csiborgtools
except ModuleNotFoundError:
import sys
sys.path.append("../")
import csiborgtools
@ -38,7 +42,7 @@ nproc = comm.Get_size()
paths = csiborgtools.read.CSiBORGPaths(**csiborgtools.paths_glamdring)
verbose = nproc == 1
partcols = ['x', 'y', 'z', "vx", "vy", "vz", 'M']
partcols = ["x", "y", "z", "vx", "vy", "vz", "M"]
def do_split(nsim):
@ -46,8 +50,8 @@ def do_split(nsim):
reader = csiborgtools.read.ParticleReader(paths)
ftemp_base = join(
paths.temp_dumpdir,
"split_{}_{}".format(str(nsim).zfill(5), str(nsnap).zfill(5))
)
"split_{}_{}".format(str(nsim).zfill(5), str(nsnap).zfill(5)),
)
ftemp = ftemp_base + "_{}.npz"
# Load the particles and their clump IDs
@ -85,7 +89,7 @@ def do_split(nsim):
# Now load back in every temporary file, combine them into a single
# dictionary and save as a single .npz file.
out = {}
for file in glob(ftemp_base + '*'):
for file in glob(ftemp_base + "*"):
inp = numpy.load(file)
for key in inp.files:
out.update({key: inp[key]})
@ -107,9 +111,8 @@ if nproc > 1:
worker_process(do_split, comm, verbose=False)
else:
tasks = paths.get_ics(tonew=False)
tasks = [tasks[0]] # REMOVE
for task in tasks:
print("{}: completing task `{}`.".format(datetime.now(), task))
do_split(task)
comm.Barrier()
comm.Barrier()