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Overlap calculation (#18)

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* Move cosine similarity out

* Basic overlap calculation

* add overlap import

* Add clump0 dict path

* Update README

* fix path bug

* Save as dict instead

* Change format to array of arrays

* Update paths

* Take fewer ICs for now

* Change to structured array

* Add overlap calculation

* Start saving IDs

* Add a blank space

* Update TODO
This commit is contained in:
Richard Stiskalek 2022-12-19 11:58:22 +01:00 • committed by GitHub
parent 13a9d11afe
commit 18f09767f4
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6 changed files with 297 additions and 65 deletions
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55
scripts/run_initmatch.py
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@ -24,8 +24,7 @@ import numpy
from datetime import datetime
from mpi4py import MPI
from distutils.util import strtobool
from os.path import join, isdir
from os import mkdir
from os.path import join
from os import remove
from sys import stdout
from gc import collect
@ -51,21 +50,15 @@ fin_paths = csiborgtools.read.CSiBORGPaths(to_new=False)
nsims = init_paths.ic_ids
# Output files
dumpdir = "/mnt/extraspace/rstiskalek/csiborg/initmatch"
ftemp = join(dumpdir, "temp", "temp_{}_{}.npy")
fperm = join(dumpdir, "clump_cm_{}.npy")
dumpdir = "/mnt/extraspace/rstiskalek/csiborg/"
ftemp = join(dumpdir, "temp_initmatch", "temp_{}_{}_{}.npy")
fpermcm = join(dumpdir, "initmatch", "clump_{}_cm.npy")
fpermpart = join(dumpdir, "initmatch", "clump_{}_particles.npy")
for nsim in nsims:
if rank == 0:
print("{}: reading simulation {}.".format(datetime.now(), nsim))
stdout.flush()
# Check that the output folder for this sim exists
clumpdumpdir = join(dumpdir, "out_{}".format(nsim))
if args.dump_clumps and rank == 0 and not isdir(clumpdumpdir):
mkdir(clumpdumpdir)
# Barrier to make sure we created the directory with the rank 0
comm.Barrier()
# Set the snapshot numbers
init_paths.set_info(nsim, init_paths.get_minimum_snapshot(nsim))
@ -111,15 +104,16 @@ for nsim in nsims:
cm = numpy.asanyarray(
[numpy.average(x0[p], weights=x0["M"]) for p in ('x', 'y', 'z')])
# Dump the center of mass
with open(ftemp.format(nsim, n), 'wb') as f:
with open(ftemp.format(nsim, n, "cm"), 'wb') as f:
numpy.save(f, cm)
# Optionally dump the entire clump
if args.dump_clumps:
fout = join(clumpdumpdir, "clump_{}.npy".format(n))
stdout.flush()
with open(fout, "wb") as f:
with open(ftemp.format(nsim, n, "clump"), "wb") as f:
numpy.save(f, x0)
del part0, clump_ids
collect()
comm.Barrier()
if rank == 0:
print("Collecting CM files...")
@ -130,14 +124,33 @@ for nsim in nsims:
out = numpy.full(njobs, numpy.nan, dtype=dtype)
for i, n in enumerate(unique_clumpids):
with open(ftemp.format(nsim, n), 'rb') as f:
fpath = ftemp.format(nsim, n, "cm")
with open(fpath, 'rb') as f:
fin = numpy.load(f)
out['x'][i] = fin[0]
out['y'][i] = fin[1]
out['z'][i] = fin[2]
out["ID"][i] = n
remove(ftemp.format(nsim, n))
print("Dumping CM files to .. `{}`.".format(fperm.format(nsim)))
with open(fperm.format(nsim), 'wb') as f:
remove(fpath)
print("Dumping CM files to .. `{}`.".format(fpermcm.format(nsim)))
with open(fpermcm.format(nsim), 'wb') as f:
numpy.save(f, out)
print("Collecting clump files...")
stdout.flush()
out = [None] * unique_clumpids.size
dtype = {"names": ["clump", "ID"], "formats": [object, numpy.int32]}
out = numpy.full(unique_clumpids.size, numpy.nan, dtype=dtype)
for i, n in enumerate(unique_clumpids):
fpath = ftemp.format(nsim, n, "clump")
with open(fpath, 'rb') as f:
fin = numpy.load(f)
out["clump"][i] = fin
out["ID"][i] = n
remove(fpath)
print("Dumping clump files to .. `{}`.".format(fpermpart.format(nsim)))
with open(fpermpart.format(nsim), "wb") as f:
numpy.save(f, out)
del out
collect()