Particle dumping (#49)

* Add paths

* Add dumping script

* Remove snap from density fields

* Add progress statement

* Update import ordering

* Update nb

csiborgtools/read/paths.py

@@ -326,6 +326,49 @@ class CSiBORGPaths:
         fname = f"radpos_{str(nsim).zfill(5)}_{str(nsnap).zfill(5)}.npz"
         return join(fdir, fname)
 
+    def particle_h5py_path(self, nsim):
+        """
+        Path to the files containing all particles in a `.hdf5` file. Used for
+        the SPH calculation.
+
+        Parameters
+        ----------
+        nsim : int
+            IC realisation index.
+
+        Returns
+        -------
+        path : str
+        """
+        fdir = join(self.postdir, "environment")
+        if not isdir(fdir):
+            makedirs(fdir)
+            warn(f"Created directory `{fdir}`.", UserWarning, stacklevel=1)
+        fname = f"particles_{str(nsim).zfill(5)}.h5"
+        return join(fdir, fname)
+
+    def density_field_path(self, mas, nsim):
+        """
+        Path to the files containing the calculated density fields.
+
+        Parameters
+        ----------
+        mas : str
+           Mass-assignment scheme. Currently only SPH is supported.
+        nsim : int
+            IC realisation index.
+
+        Returns
+        -------
+        path : str
+        """
+        fdir = join(self.postdir, "environment")
+        if not isdir(fdir):
+            makedirs(fdir)
+            warn(f"Created directory `{fdir}`.", UserWarning, stacklevel=1)
+        fname = f"density_{mas}_{str(nsim).zfill(5)}.npy"
+        return join(fdir, fname)
+
     def knnauto_path(self, run, nsim=None):
         """
         Path to the `knn` auto-correlation files. If `nsim` is not specified

notebooks/fits.ipynb

@@ -74,18 +74,72 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "id": "f2986dd2",
    "metadata": {},
    "outputs": [],
+   "source": [
+    "import h5py"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "1d8ad8fe",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "f = h5py.File(\"../data/particles_7444.h5\", \"r\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "id": "020ac8e4",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "array([ 4.42346358e-01,  7.09757663e-03,  4.64053304e-01, -1.96926287e-03,\n",
+       "       -2.67177823e-03, -6.45721859e-04,  1.16415322e-10])"
+      ]
+     },
+     "execution_count": 8,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "f[\"particles\"][0, :]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1eb74f46",
+   "metadata": {},
+   "outputs": [],
    "source": []
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "venv_galomatch",
+   "display_name": "venv_csiborg",
    "language": "python",
-   "name": "venv_galomatch"
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.7"
   }
  },
  "nbformat": 4,

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()