Particle dumping (#49)

* Add paths

* Add dumping script

* Remove snap from density fields

* Add progress statement

* Update import ordering

* Update nb

scripts/pre_dumppath5.py

@@ -0,0 +1,75 @@
+# 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()