Scripts for CSiBORG1 SPH calculation (#106)

* Rename files

* Delet efile

* Add new submission script

* Update README

* Add submit script

* Renaming file

* Correct typos

* Update README

* Add all nsims

scripts_independent/field_sph_ramses.py

@@ -0,0 +1,113 @@
+# Copyright (C) 2023 Richard Stiskalek
+# 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 construct the density and velocity fields for a simulation snapshot.
+The SPH filter is implemented in the cosmotool package.
+"""
+from argparse import ArgumentParser
+from os.path import join
+
+import numpy as np
+from h5py import File
+
+from field_sph_gadget import now, run_sph_filter
+from process_snapshot import CSiBORG1Reader
+
+
+def prepare_csiborg1(nsim, output_path):
+    """
+    Prepare a RAMSES snapshot for the SPH filter.
+
+    Parameters
+    ----------
+    nsim : int
+        Simulation index.
+    output_path : str
+        Path to the output HDF5 file.
+
+    Returns
+    -------
+    None
+    """
+    reader = CSiBORG1Reader(nsim, "final")
+
+    with File(output_path, 'w') as target:
+        print(f"{now()}: loading positions.")
+        pos = reader.read_snapshot("pos")
+        print(f"{now()}: loading velocities.")
+        vel = reader.read_snapshot("vel")
+        print(f"{now()}: loading masses.")
+        mass = reader.read_snapshot("mass")
+
+        print(f"Writing {len(pos)} particles to {output_path}.")
+        dset = target.create_dataset("particles", (len(pos), 7),
+                                     dtype=np.float32)
+
+        dset[:, :3] = pos
+        print(f"{now()}: written positions.")
+        dset[:, 3:6] = vel
+        print(f"{now()}: written velocities.")
+        dset[:, 6] = mass
+        print(f"{now()}: written masses.")
+
+
+if __name__ == "__main__":
+    parser = ArgumentParser(description="Generate SPH density and velocity field.")  # noqa
+    parser.add_argument("--nsim", type=int, required=True,
+                        help="Simulation index")
+    parser.add_argument("--mode", type=str, required=True,
+                        choices=["prepare", "run"], help="Mode of operation.")
+    parser.add_argument("--output_folder", type=str, required=True,
+                        help="Path to the output HDF5 file.")
+    parser.add_argument("--resolution", type=int, required=True,
+                        help="Resolution of the density and velocity field.")
+    parser.add_argument("--scratch_space", type=str, required=True,
+                        help="Path to a folder where temporary files can be stored.")  # noqa
+    parser.add_argument("--SPH_executable", type=str, required=True,
+                        help="Path to the `simple3DFilter` executable.")
+    parser.add_argument("--snapshot_kind", type=str, required=True,
+                        choices=["ramses"],
+                        help="Kind of the simulation snapshot.")
+    args = parser.parse_args()
+
+    if args.snapshot_kind != "ramses":
+        raise NotImplementedError("Only RAMSES snapshots are supported.")
+
+    particles_path = join(args.scratch_space,
+                          f"ramses_{str(args.nsim).zfill(5)}.hdf5")
+    output_path = join(args.output_folder,
+                       f"sph_ramses_{str(args.nsim).zfill(5)}.hdf5")
+
+    print("---------- SPH Density & Velocity Field Job Information ----------")
+    print(f"Mode:              {args.mode}")
+    print(f"Simulation index:  {args.nsim}")
+    print(f"Paticles path:     {particles_path}")
+    print(f"Output path:       {output_path}")
+    print(f"Resolution:        {args.resolution}")
+    print(f"SPH executable:    {args.SPH_executable}")
+    print(f"Snapshot kind:     {args.snapshot_kind}")
+    print("------------------------------------------------------------------")
+    print(flush=True)
+
+    if args.mode == "prepare":
+        prepare_csiborg1(args.nsim, particles_path)
+    elif args.mode == "run":
+        output_path = join(args.output_folder,
+                           f"sph_ramses_{str(args.nsim).zfill(5)}.hdf5")
+        boxsize = 677.7
+        run_sph_filter(particles_path, output_path, boxsize, args.resolution,
+                       args.SPH_executable)
+    else:
+        raise NotImplementedError(f"Mode `{args.mode}` is not supported.")