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1dfc11e462
* Rename files * Delet efile * Add new submission script * Update README * Add submit script * Renaming file * Correct typos * Update README * Add all nsims
201 lines
7.5 KiB
Python
201 lines
7.5 KiB
Python
# Copyright (C) 2023 Richard Stiskalek
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# This program is free software; you can redistribute it and/or modify it
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# under the terms of the GNU General Public License as published by the
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# Free Software Foundation; either version 3 of the License, or (at your
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# option) any later version.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
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# Public License for more details.
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#
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# You should have received a copy of the GNU General Public License along
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# with this program; if not, write to the Free Software Foundation, Inc.,
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# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
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"""
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Script to construct the density and velocity fields for a simulation snapshot.
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The SPH filter is implemented in the cosmotool package.
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"""
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from argparse import ArgumentParser
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from os import remove
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from os.path import join, exists
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import subprocess
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from datetime import datetime
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import hdf5plugin # noqa
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import numpy as np
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from h5py import File
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def now():
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return datetime.now()
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def generate_unique_id(file_path):
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"""
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Generate a unique ID for a file path.
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"""
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return file_path.replace('/', '_').replace(':', '_')
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def prepare_random(temporary_output_path, npart=100, dtype=np.float32):
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"""
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Prepare a random dataset for the SPH filter.
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"""
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print("Preparing random dataset.", flush=True)
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arr = np.full((npart, 7), np.nan, dtype=dtype)
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arr[:, :3] = np.random.uniform(0, 1, (npart, 3))
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arr[:, 3:6] = np.random.normal(0, 1, (npart, 3))
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arr[:, 6] = np.ones(npart, dtype=dtype)
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dset = np.random.random((npart, 7)).astype(dtype)
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dset[:, 6] = np.ones(npart, dtype=dtype)
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with File(temporary_output_path, 'w') as target:
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target.create_dataset("particles", data=dset, dtype=dtype)
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return 1.
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def prepare_gadget(snapshot_path, temporary_output_path):
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"""
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Prepare a GADGET snapshot for the SPH filter. Assumes there is only a
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single file per snapshot.
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"""
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with File(snapshot_path, 'r') as source, File(temporary_output_path, 'w') as target: # noqa
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boxsize = source["Header"].attrs["BoxSize"]
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npart = sum(source["Header"].attrs["NumPart_Total"])
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nhighres = source["Header"].attrs["NumPart_Total"][1]
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dset = target.create_dataset("particles", (npart, 7), dtype=np.float32)
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# Copy to this dataset the high-resolution particles.
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dset[:nhighres, :3] = source["PartType1/Coordinates"][:]
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dset[:nhighres, 3:6] = source["PartType1/Velocities"][:]
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dset[:nhighres, 6] = np.ones(nhighres, dtype=np.float32) * source["Header"].attrs["MassTable"][1] # noqa
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# Now copy the low-resolution particles.
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dset[nhighres:, :3] = source["PartType5/Coordinates"][:]
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dset[nhighres:, 3:6] = source["PartType5/Velocities"][:]
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dset[nhighres:, 6] = source["PartType5/Masses"][:]
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return boxsize
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def run_sph_filter(particles_path, output_path, boxsize, resolution,
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SPH_executable):
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"""
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Run the SPH filter on a snapshot.
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"""
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if not exists(particles_path):
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raise RuntimeError(f"Particles file `{particles_path}` does not exist.") # noqa
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if not isinstance(boxsize, (int, float)):
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raise TypeError("`boxsize` must be a number.")
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if not isinstance(resolution, int):
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raise TypeError("`resolution` must be an integer.")
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if not exists(SPH_executable):
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raise RuntimeError(f"SPH executable `{SPH_executable}` does not exist.") # noqa
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command = [SPH_executable, particles_path, str(1e14), str(boxsize),
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str(resolution), str(0), str(0), str(0), output_path, "1"]
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print(f"{now()}: executing `simple3DFilter`.", flush=True)
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start_time = now()
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process = subprocess.Popen(
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command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT,
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universal_newlines=True)
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for line in iter(process.stdout.readline, ""):
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print(line, end="", flush=True)
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process.wait()
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if process.returncode != 0:
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raise RuntimeError("`simple3DFilter`failed.")
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else:
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dt = now() - start_time
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print(f"{now()}: `simple3DFilter`completed successfully in {dt}.",
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flush=True)
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def main(snapshot_path, output_path, resolution, scratch_space, SPH_executable,
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snapshot_kind):
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"""
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Construct the density and velocity fields for a simulation snapshot using
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`cosmotool` [1].
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Parameters
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----------
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snapshot_path : str
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Path to the simulation snapshot.
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output_path : str
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Path to the output HDF5 file.
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resolution : int
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Resolution of the density field.
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scratch_space : str
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Path to a folder where temporary files can be stored.
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SPH_executable : str
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Path to the `simple3DFilter` executable [1].
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snapshot_kind : str
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Kind of the simulation snapshot. Currently only `gadget4` is supported.
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Returns
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-------
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None
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References
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----------
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[1] https://bitbucket.org/glavaux/cosmotool/src/master/sample/simple3DFilter.cpp # noqa
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"""
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if snapshot_kind != "gadget4":
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raise NotImplementedError("Only GADGET HDF5 snapshots are supported.")
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print("---------- SPH Density & Velocity Field Job Information ----------")
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print(f"Snapshot path: {snapshot_path}")
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print(f"Output path: {output_path}")
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print(f"Resolution: {resolution}")
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print(f"Scratch space: {scratch_space}")
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print(f"SPH executable: {SPH_executable}")
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print(f"Snapshot kind: {snapshot_kind}")
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print("------------------------------------------------------------------")
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print(flush=True)
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temporary_output_path = join(
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scratch_space, generate_unique_id(snapshot_path))
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if not temporary_output_path.endswith(".hdf5"):
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raise RuntimeError("Temporary output path must end with `.hdf5`.")
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print(f"{now()}: preparing snapshot...", flush=True)
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boxsize = prepare_gadget(snapshot_path, temporary_output_path)
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print(f"{now()}: wrote temporary data to {temporary_output_path}.",
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flush=True)
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run_sph_filter(temporary_output_path, output_path, boxsize, resolution,
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SPH_executable)
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print(f"{now()}: removing the temporary snapshot file.", flush=True)
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try:
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remove(temporary_output_path)
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except FileNotFoundError:
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pass
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if __name__ == "__main__":
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parser = ArgumentParser(description="Generate SPH density and velocity field.") # noqa
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parser.add_argument("--snapshot_path", type=str, required=True,
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help="Path to the simulation snapshot.")
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parser.add_argument("--output_path", type=str, required=True,
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help="Path to the output HDF5 file.")
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parser.add_argument("--resolution", type=int, required=True,
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help="Resolution of the density and velocity field.")
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parser.add_argument("--scratch_space", type=str, required=True,
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help="Path to a folder where temporary files can be stored.") # noqa
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parser.add_argument("--SPH_executable", type=str, required=True,
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help="Path to the `simple3DFilter` executable.")
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parser.add_argument("--snapshot_kind", type=str, required=True,
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choices=["gadget4"],
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help="Kind of the simulation snapshot.")
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args = parser.parse_args()
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main(args.snapshot_path, args.output_path, args.resolution,
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args.scratch_space, args.SPH_executable, args.snapshot_kind)
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