mirror of
https://github.com/Richard-Sti/csiborgtools.git
synced 2024-10-18 20:15:05 +02:00
aaa14fc880
* Add RAMSES2HDF5 conversion * Upload changes * Clean up * More clean up * updates * Little change * pep9 * Add basic SPH calculation for a snapshot * Add submit script * Remove echo * Little changes * Send off changes * Little formatting * Little updates * Add nthreads argument * Upload chagnes * Add nthreads arguemnts * Some local changes.. * Update scripts * Add submission script * Update script * Update params * Rename CSiBORGBox to CSiBORG1box * Rename CSiBORG1 reader * Move files * Rename folder again * Add basic plotting here * Add new skeletons * Move def * Update nbs * Edit directories * Rename files * Add units to converted snapshots * Fix empty dataset bug * Delete file * Edits to submission scripts * Edit paths * Update .gitignore * Fix attrs * Update weighting * Fix RA/dec bug * Add FORNAX cluster * Little edit * Remove boxes since will no longer need * Move func back * Edit to include sort by membership * Edit paths * Purge basic things * Start removing * Bring file back * Scratch * Update the rest * Improve the entire file * Remove old things * Remove old * Delete old things * Fully updates * Rename file * Edit submit script * Little things * Add print statement * Add here cols_to_structured * Edit halo cat * Remove old import * Add comment * Update paths manager * Move file * Remove file * Add chains
77 lines
2.9 KiB
Python
77 lines
2.9 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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def add_initial_snapshot(nsim, simname, halo_finder, verbose):
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"""
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Sort the initial snapshot particles according to their final snapshot and
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add them to the final snapshot's HDF5 file.
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"""
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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fname = paths.processed_output(nsim, simname, halo_finder)
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if simname == "csiborg":
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partreader = csiborgtools.read.CSiBORGReader(paths)
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else:
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partreader = csiborgtools.read.QuijoteReader(paths)
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fprint(f"processing simulation `{nsim}`.", verbose)
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if simname == "csiborg":
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nsnap0 = 1
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elif simname == "quijote":
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nsnap0 = -1
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else:
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raise ValueError(f"Unknown simulation `{simname}`.")
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fprint("loading and sorting the initial PID.", verbose)
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sort_indxs = numpy.argsort(partreader.read_snapshot(nsnap0, nsim, "pid"))
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fprint("loading the final particles.", verbose)
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with h5py.File(fname, "r") as f:
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sort_indxs_final = f["snapshot_final/pid"][:]
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f.close()
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fprint("sorting the particles according to the final snapshot.", verbose)
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sort_indxs_final = numpy.argsort(numpy.argsort(sort_indxs_final))
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sort_indxs = sort_indxs[sort_indxs_final]
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del sort_indxs_final
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collect()
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fprint("loading and sorting the initial particle position.", verbose)
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pos = partreader.read_snapshot(nsnap0, nsim, "pos")[sort_indxs]
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del sort_indxs
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collect()
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# In Quijote some particles are position precisely at the edge of the
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# box. Move them to be just inside.
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if simname == "quijote":
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mask = pos >= 1
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if numpy.any(mask):
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spacing = numpy.spacing(pos[mask])
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assert numpy.max(spacing) <= 1e-5
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pos[mask] -= spacing
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fprint(f"dumping particles for `{nsim}` to `{fname}`.", verbose)
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with h5py.File(fname, "r+") as f:
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if "snapshot_initial" in f.keys():
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del f["snapshot_initial"]
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group = f.create_group("snapshot_initial")
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group.attrs["header"] = "Initial snapshot data."
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dset = group.create_dataset("pos", data=pos)
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dset.attrs["header"] = "DM particle positions in box units."
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f.close() |