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Add density field plot and start preparing CSiBORG2 (#94)
* 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
This commit is contained in:
Richard Stiskalek
GitHub
parent
6042a87111
commit
aaa14fc880
30 changed files with 1682 additions and 1728 deletions
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@ -1,116 +0,0 @@
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# 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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"""Convert the HDF5 CSiBORG particle file to an ASCII file."""
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from argparse import ArgumentParser
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import h5py
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import numpy
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from mpi4py import MPI
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from taskmaster import work_delegation
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from tqdm import trange
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import csiborgtools
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from utils import get_nsims
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def positions_to_ascii(positions, output_filename, boxsize=None,
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chunk_size=50_000, verbose=True):
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"""
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Convert array of positions to an ASCII file. If `boxsize` is given,
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multiples the positions by it.
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"""
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total_size = len(positions)
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if verbose:
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print(f"Number of rows to write: {total_size}")
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with open(output_filename, 'w') as out_file:
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# Write the header
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out_file.write("#px py pz\n")
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# Loop through data in chunks
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for i in trange(0, total_size, chunk_size,
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desc=f"Writing to ... `{output_filename}`",
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disable=not verbose):
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end = i + chunk_size
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if end > total_size:
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end = total_size
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data_chunk = positions[i:end]
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# Convert to positions Mpc / h
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data_chunk = data_chunk[:, :3]
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if boxsize is not None:
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data_chunk *= boxsize
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chunk_str = "\n".join([f"{x:.4f} {y:.4f} {z:.4f}"
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for x, y, z in data_chunk])
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out_file.write(chunk_str + "\n")
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def extract_positions(nsim, simname, paths, kind):
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"""
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Extract either the particle or halo positions.
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"""
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if kind == "particles":
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fname = paths.processed_output(nsim, simname, "FOF")
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return h5py.File(fname, 'r')["snapshot_final/pos"][:]
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if kind == "particles_rsp":
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raise NotImplementedError("RSP of particles is not implemented yet.")
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fpath = paths.observer_peculiar_velocity("PCS", 512, nsim)
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vpec_observer = numpy.load(fpath)["observer_vp"][0, :]
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cat = csiborgtools.read.CSiBORGHaloCatalogue(
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nsim, paths, "halo_catalogue", "FOF", bounds={"dist": (0, 155.5)},
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observer_velocity=vpec_observer)
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if kind == "halos":
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return cat["cartesian_pos"]
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if kind == "halos_rsp":
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return cat["cartesian_redshift_pos"]
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raise ValueError(f"Unknown kind `{kind}`. Allowed values are: "
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"`particles`, `particles_rsp`, `halos`, `halos_rsp`.")
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def main(args, paths):
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boxsize = 677.7 if "particles" in args.kind else None
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pos = extract_positions(args.nsim, args.simname, paths, args.kind)
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output_filename = paths.ascii_positions(args.nsim, args.kind)
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positions_to_ascii(pos, output_filename, boxsize=boxsize)
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if __name__ == "__main__":
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parser = ArgumentParser()
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parser.add_argument("--kind", type=str, required=True,
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choices=["particles", "particles_rsp", "halos", "halos_rsp"], # noqa
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help="Kind of data to extract.")
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parser.add_argument("--nsims", type=int, nargs="+", default=None,
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help="IC realisations. If `-1` processes all.")
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parser.add_argument("--simname", type=str, default="csiborg",
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choices=["csiborg"],
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help="Simulation name")
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args = parser.parse_args()
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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nsims = get_nsims(args, paths)
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def _main(nsim):
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main(nsim, paths, args.kind)
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work_delegation(_main, nsims, MPI.COMM_WORLD)
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@ -1,108 +0,0 @@
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# Copyright (C) 2022 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 calculate the peculiar velocity of an observer in the centre of the
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CSiBORG box.
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"""
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from argparse import ArgumentParser
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from distutils.util import strtobool
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import numpy
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from mpi4py import MPI
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from taskmaster import work_delegation
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from tqdm import tqdm
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from utils import get_nsims
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try:
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import csiborgtools
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except ModuleNotFoundError:
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import sys
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sys.path.append("../")
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import csiborgtools
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def observer_peculiar_velocity(nsim, parser_args):
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"""
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Calculate the peculiar velocity of an observer in the centre of the box
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for several smoothing scales.
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"""
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pos = numpy.array([0.5, 0.5, 0.5]).reshape(-1, 3)
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boxsize = 677.7
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smooth_scales = [0, 0.5, 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0]
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observer_vp = numpy.full((len(smooth_scales), 3), numpy.nan,
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dtype=numpy.float32)
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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field_path = paths.field("velocity", parser_args.MAS, parser_args.grid,
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nsim, in_rsp=False)
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field0 = numpy.load(field_path)
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for j, smooth_scale in enumerate(tqdm(smooth_scales,
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desc="Smoothing the fields",
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disable=not parser_args.verbose)):
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if smooth_scale > 0:
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field = [None, None, None]
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for k in range(3):
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field[k] = csiborgtools.field.smoothen_field(
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field0[k], smooth_scale, boxsize)
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else:
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field = field0
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v = csiborgtools.field.evaluate_cartesian(
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field[0], field[1], field[2], pos=pos)
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observer_vp[j, 0] = v[0][0]
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observer_vp[j, 1] = v[1][0]
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observer_vp[j, 2] = v[2][0]
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fout = paths.observer_peculiar_velocity(parser_args.MAS, parser_args.grid,
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nsim)
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if parser_args.verbose:
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print(f"Saving to ... `{fout}`")
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numpy.savez(fout, smooth_scales=smooth_scales, observer_vp=observer_vp)
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return observer_vp
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###############################################################################
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# Command line interface #
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###############################################################################
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if __name__ == "__main__":
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parser = ArgumentParser()
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parser.add_argument("--nsims", type=int, nargs="+", default=None,
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help="IC realisations. `-1` for all simulations.")
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parser.add_argument("--kind", type=str,
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choices=["density", "rspdensity", "velocity", "radvel",
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"potential", "environment"],
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help="What derived field to calculate?")
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parser.add_argument("--MAS", type=str,
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choices=["NGP", "CIC", "TSC", "PCS"])
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parser.add_argument("--grid", type=int, help="Grid resolution.")
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parser.add_argument("--verbose", type=lambda x: bool(strtobool(x)),
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help="Verbosity flag for reading in particles.")
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parser.add_argument("--simname", type=str, default="csiborg",
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help="Verbosity flag for reading in particles.")
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parser_args = parser.parse_args()
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comm = MPI.COMM_WORLD
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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nsims = get_nsims(parser_args, paths)
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def main(nsim):
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return observer_peculiar_velocity(nsim, parser_args)
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work_delegation(main, nsims, comm, master_verbose=True)
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@ -49,10 +49,11 @@ def density_field(nsim, parser_args, to_save=True):
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"""
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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nsnap = max(paths.get_snapshots(nsim, "csiborg"))
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box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
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box = csiborgtools.read.CSiBORG1Box(nsnap, nsim, paths)
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fname = paths.processed_output(nsim, "csiborg", "halo_catalogue")
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if not parser_args.in_rsp:
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# TODO I removed this function
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snap = csiborgtools.read.read_h5(fname)["snapshot_final"]
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pos = snap["pos"]
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mass = snap["mass"]
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@ -94,7 +95,7 @@ def velocity_field(nsim, parser_args, to_save=True):
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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nsnap = max(paths.get_snapshots(nsim, "csiborg"))
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box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
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box = csiborgtools.read.CSiBORG1Box(nsnap, nsim, paths)
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fname = paths.processed_output(nsim, "csiborg", "halo_catalogue")
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snap = csiborgtools.read.read_h5(fname)["snapshot_final"]
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@ -127,7 +128,7 @@ def radvel_field(nsim, parser_args, to_save=True):
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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nsnap = max(paths.get_snapshots(nsim, "csiborg"))
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box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
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box = csiborgtools.read.CSiBORG1Box(nsnap, nsim, paths)
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vel = numpy.load(paths.field("velocity", parser_args.MAS, parser_args.grid,
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nsim, parser_args.in_rsp))
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@ -154,7 +155,7 @@ def potential_field(nsim, parser_args, to_save=True):
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"""
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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nsnap = max(paths.get_snapshots(nsim, "csiborg"))
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box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
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box = csiborgtools.read.CSiBORG1Box(nsnap, nsim, paths)
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if not parser_args.in_rsp:
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rho = numpy.load(paths.field(
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@ -192,7 +193,7 @@ def environment_field(nsim, parser_args, to_save=True):
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"""
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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nsnap = max(paths.get_snapshots(nsim, "csiborg"))
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box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
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box = csiborgtools.read.CSiBORG1Box(nsnap, nsim, paths)
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rho = numpy.load(paths.field(
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"density", parser_args.MAS, parser_args.grid, nsim, in_rsp=False))
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@ -371,4 +371,4 @@ if __name__ == "__main__":
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def _main(nsim):
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main(nsim, args)
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work_delegation(_main, nsims, MPI.COMM_WORLD)
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work_delegation(_main, nsims, MPI.COMM_WORLD)
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