mirror of
https://github.com/Richard-Sti/csiborgtools.git
synced 2024-12-22 17:48:01 +00:00
c14be720b5
* Add paths * Add dumping script * Remove snap from density fields * Add progress statement * Update import ordering * Update nb
75 lines
2.5 KiB
Python
75 lines
2.5 KiB
Python
# This program is free software; you can redistribute it and/or modify it
|
|
# under the terms of the GNU General Public License as published by the
|
|
# Free Software Foundation; either version 3 of the License, or (at your
|
|
# option) any later version.
|
|
#
|
|
# This program is distributed in the hope that it will be useful, but
|
|
# WITHOUT ANY WARRANTY; without even the implied warranty of
|
|
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
|
|
# Public License for more details.
|
|
#
|
|
# 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 load in the simulation particles and dump them to a HDF5 file for the
|
|
SPH density field calculation.
|
|
"""
|
|
|
|
from datetime import datetime
|
|
from gc import collect
|
|
|
|
import h5py
|
|
import numpy
|
|
from mpi4py import MPI
|
|
|
|
try:
|
|
import csiborgtools
|
|
except ModuleNotFoundError:
|
|
import sys
|
|
|
|
sys.path.append("../")
|
|
import csiborgtools
|
|
|
|
from argparse import ArgumentParser
|
|
|
|
# We set up the MPI
|
|
comm = MPI.COMM_WORLD
|
|
rank = comm.Get_rank()
|
|
nproc = comm.Get_size()
|
|
|
|
# And next parse all the arguments and set up CSiBORG objects
|
|
parser = ArgumentParser()
|
|
parser.add_argument("--ics", type=int, nargs="+", default=None,
|
|
help="IC realisatiosn. If `-1` processes all simulations.")
|
|
args = parser.parse_args()
|
|
paths = csiborgtools.read.CSiBORGPaths(**csiborgtools.paths_glamdring)
|
|
partreader = csiborgtools.read.ParticleReader(paths)
|
|
pars_extract = ['x', 'y', 'z', 'vx', 'vy', 'vz', 'M']
|
|
if args.ics is None or args.ics == -1:
|
|
ics = paths.get_ics(tonew=False)
|
|
else:
|
|
ics = args.ics
|
|
|
|
# We MPI loop over individual simulations.
|
|
jobs = csiborgtools.fits.split_jobs(len(ics), nproc)[rank]
|
|
for i in jobs:
|
|
nsim = ics[i]
|
|
nsnap = max(paths.get_snapshots(nsim))
|
|
print(f"{datetime.now()}: Rank {rank} completing simulation {nsim}.",
|
|
flush=True)
|
|
|
|
# We read in the particles from RASMSES files, switch from a
|
|
# structured array to 2-dimensional array and dump it.
|
|
parts = partreader.read_particle(nsnap, nsim, pars_extract,
|
|
verbose=nproc == 1)
|
|
out = numpy.full((parts.size, len(pars_extract)), numpy.nan,
|
|
dtype=numpy.float32)
|
|
for j, par in enumerate(pars_extract):
|
|
out[:, j] = parts[par]
|
|
|
|
with h5py.File(paths.particle_h5py_path(nsim), "w") as f:
|
|
dset = f.create_dataset("particles", data=out)
|
|
|
|
del parts, out
|
|
collect()
|