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Update prior in VF (#135)
* Update priors * Update submit * Update README * Relax width of calibration priors * Relax width of calibration priors * Update smooth scales * Update settings * Update README * Update submit * Add names * Update nb * Fix bug * Update script * Move files * Small bug fix * Add script * Add script * Add script * Add more power * Update script * Quick fix * Rm blank line * Update nb * Update nb * Update nb
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Richard Stiskalek
GitHub
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18 changed files with 999 additions and 179 deletions
39
scripts/output/csiborg_halocatalogue.py
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scripts/output/csiborg_halocatalogue.py
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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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"""Quick script to write halo catalogues as a HDF5 file."""
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import csiborgtools
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from h5py import File
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from tqdm import tqdm
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if __name__ == "__main__":
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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simname = "csiborg1"
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nsims = paths.get_ics(simname)
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print(f"Number of simulations: {nsims}.")
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fname_out = f"/mnt/users/rstiskalek/csiborgtools/data/halos_{simname}.hdf5"
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print(f"Writing to `{fname_out}`.")
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with File(fname_out, 'w') as f:
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for nsim in tqdm(nsims, desc="Simulations"):
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grp = f.create_group(f"sim_{nsim}")
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cat = csiborgtools.read.CSiBORG1Catalogue(nsim, paths)
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grp["pos"] = cat["cartesian_pos"]
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grp["totmass"] = cat["totmass"]
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173
scripts/output/quijote_catalogue_from_field.py
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scripts/output/quijote_catalogue_from_field.py
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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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"""Quick script to write halo catalogues as a HDF5 file."""
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from os import remove
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from os.path import exists, join
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import numpy as np
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from h5py import File
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import csiborgtools
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from csiborgtools import fprint
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###############################################################################
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# Evaluating fields at a fixed radius. #
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###############################################################################
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def load_fields(nsim, MAS, grid, paths):
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# reader = csiborgtools.read.QuijoteField(nsim, paths)
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# velocity_field = reader.velocity_field(MAS, grid)
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# reader = csiborgtools.read.CSiBORG2Field(nsim, "random", paths)
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# velocity_field = reader.velocity_field(MAS, grid)
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folder = "/mnt/extraspace/rstiskalek/catalogs"
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fpath = join(folder, "twompp_velocity_carrick2015.npy")
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field = np.load(fpath).astype(np.float32)
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field[0] -= 89
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field[1] -= -131
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field[2] -= 17
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# field /= 0.43
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return field
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# return velocity_field
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def uniform_points_at_radius(R, npoints, seed):
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gen = np.random.RandomState(seed)
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phi = gen.uniform(0, 2*np.pi, npoints)
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theta = np.arccos(gen.uniform(-1, 1, npoints))
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return R * np.vstack([
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np.sin(theta) * np.cos(phi),
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np.sin(theta) * np.sin(phi),
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np.cos(theta)]).T
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def main_field(velocity_field, radius, observers, npoints, fname, boxsize):
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if exists(fname):
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print(f"Removing existing file `{fname}`.", flush=True)
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remove(fname)
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points = uniform_points_at_radius(radius, npoints, 42)
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for i, observer in enumerate(observers):
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current_points = (points + observer)
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current_points_box_units = current_points / boxsize
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vel = np.vstack([csiborgtools.field.evaluate_cartesian_cic(
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velocity_field[i], pos=current_points_box_units,
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smooth_scales=None,) for i in range(3)]).T
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vel_observer = np.vstack([csiborgtools.field.evaluate_cartesian_cic(
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velocity_field[i],
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pos=np.asarray(observer).reshape(1, 3) / boxsize,
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smooth_scales=None) for i in range(3)]).T[0]
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with File(fname, 'a') as f:
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grp = f.create_group(f"obs_{i}")
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grp.create_dataset("pos", data=current_points)
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grp.create_dataset("vel", data=vel)
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grp.create_dataset("observer", data=observer)
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grp.create_dataset("vel_observer", data=vel_observer)
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print(f"Written to `{fname}`.", flush=True)
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###############################################################################
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# Selecting particles in a thin radial shell. #
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###############################################################################
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def load_particles(nsim, paths):
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reader = csiborgtools.read.QuijoteSnapshot(nsim, 4, paths)
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fprint("reading particles positions...")
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pos = reader.coordinates()
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fprint("reading particles velocities...")
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vel = reader.velocities()
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fprint("finished reading the snapshot.")
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return pos, vel
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def main_particles(pos, vel, rmin, rmax, observers, fname):
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if exists(fname):
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print(f"Removing existing file `{fname}`.", flush=True)
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remove(fname)
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for i, observer in enumerate(observers):
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r = np.linalg.norm(pos - observer, axis=1)
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mask = (r > rmin) & (r < rmax)
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print(f"Observer {i}: {mask.sum()} particles in the shell.")
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with File(fname, 'a') as f:
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grp = f.create_group(f"obs_{i}")
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grp.create_dataset("pos", data=pos[mask])
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grp.create_dataset("vel", data=vel[mask])
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grp.create_dataset("observer", data=observer)
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print(f"Written to `{fname}`.", flush=True)
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###############################################################################
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# Interface #
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###############################################################################
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if __name__ == "__main__":
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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fdir = "/mnt/extraspace/rstiskalek/BBF/Quijote_field_points"
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# grid = 512
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# MAS = "PCS"
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# boxsize = csiborgtools.simname2boxsize("quijote")
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# rmax = 200
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# radius_evaluate = 150
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# npoints = 1000
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# fiducial_observers = csiborgtools.read.fiducial_observers(boxsize, rmax)
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# print(f"There are {len(fiducial_observers)} observers.")
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# # fiducial_observers = [[boxsize/2, boxsize/2, boxsize/2]]
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# nsims = [0]
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# for nsim in nsims:
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# fname = join(fdir, f"field_points_{nsim}.h5")
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# velocity_field = load_fields(nsim, MAS, grid, paths)
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# main_field(velocity_field, radius_evaluate, fiducial_observers,
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# npoints, fname, boxsize)
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rmin = 100
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rmax = 100.5
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boxsize = csiborgtools.simname2boxsize("quijote")
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fiducial_observers = csiborgtools.read.fiducial_observers(boxsize, 200)
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print(f"There are {len(fiducial_observers)} observers.")
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nsims = [0]
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for nsim in nsims:
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fname = join(fdir, f"particles_points_{nsim}.h5")
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pos, vel = load_particles(nsim, paths)
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main_particles(pos, vel, rmin, rmax, fiducial_observers, fname)
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# grid = None
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# MAS = None
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# boxsize = csiborgtools.simname2boxsize("Carrick2015")
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# radius_evaluate = 75
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# npoints = 1000
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# fiducial_observers = [[boxsize/2, boxsize/2, boxsize/2]]
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# nsims = [0]
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# for nsim in nsims:
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# fname = join(fdir, f"Carrick2015_field_points_{nsim}.h5")
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# velocity_field = load_fields(nsim, MAS, grid, paths)
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# main_field(velocity_field, radius_evaluate, fiducial_observers,
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# npoints, fname, boxsize)
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