mirror of
https://github.com/Richard-Sti/csiborgtools.git
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Calculate upglade redshifts (#128)
* Update redshift reading * Add helio to CMB redshift * Update imports * Update nb * Run for Quijote * Add script * Update * Update .gitignore * Update imports * Add Peery estimator * Add bulk flow scripts * Update typs * Add comment * Add blank space * Update submission script * Update description * Add barriers * Update nb * Update nb * Rename script * Move to old * Update imports * Add nb * Update script * Fix catalogue key * Update script * Update submit * Update comment * Update .gitignore * Update nb * Update for stationary obsrevers * Update submission * Add nb * Add better verbose control * Update nb * Update submit * Update nb * Add SN errors * Add draft of the script * Update verbosity flags * Add submission script * Debug script * Quickfix * Remove comment * Update nb * Update submission * Update nb * Processed UPGLADE
This commit is contained in:
Richard Stiskalek
GitHub
parent
c447d2e7b0
commit
779f2e76ac
24 changed files with 2066 additions and 300 deletions
5
.gitignore
vendored
5
.gitignore
vendored
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@ -36,4 +36,9 @@ scripts_independent/clear.sh
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# Generated plots
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plots/*
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# Data files
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data/*
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notebooks/test.ipynb
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data/BulkFlowPlot.npy
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data/upglade_z_0p05_all.h5
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@ -20,7 +20,8 @@ from .utils import (center_of_mass, delta2ncells, number_counts,
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binned_statistic, cosine_similarity, fprint, # noqa
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hms_to_degrees, dms_to_degrees, great_circle_distance, # noqa
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radec_to_cartesian, cartesian_to_radec, # noqa
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thin_samples_by_acl, numpyro_gof, radec_to_galactic) # noqa
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thin_samples_by_acl, numpyro_gof, radec_to_galactic, # noqa
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heliocentric_to_cmb, calculate_acl) # noqa
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from .params import (paths_glamdring, simname2boxsize, simname2Omega_m, # noqa
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snap2redshift) # noqa
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@ -16,8 +16,9 @@ from .density import (DensityField, PotentialField, TidalTensorField,
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VelocityField, radial_velocity, power_spectrum, # noqa
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overdensity_field) # noqa
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from .enclosed_mass import (particles_enclosed_mass, # noqa
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particles_enclosed_momentum, field_enclosed_mass) # noqa
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from .interp import (evaluate_cartesian_cic, evaluate_sky, evaluate_los, # noqa
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particles_enclosed_momentum, field_enclosed_mass, # noqa
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bulkflow_peery2018) # noqa
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from .interp import (evaluate_cartesian_cic, evaluate_sky, evaluate_los, # noqa
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field2rsp, fill_outside, make_sky, # noqa
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observer_peculiar_velocity, smoothen_field, # noqa
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field_at_distance) # noqa
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@ -12,10 +12,13 @@
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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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import numpy
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"""
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Code to calculate the enclosed mass, momentum or bulk flow from various
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radial-velocity based estimators (that may be flawed, be careful).
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"""
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import numpy as np
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from numba import jit
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from tqdm import tqdm
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###############################################################################
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@ -55,7 +58,7 @@ def particles_enclosed_mass(rdist, mass, distances):
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enclosed_mass : 1-dimensional array
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Enclosed mass at each distance.
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"""
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enclosed_mass = numpy.full_like(distances, 0.)
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enclosed_mass = np.full_like(distances, 0.)
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start_index = 0
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for i, dist in enumerate(distances):
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if i > 0:
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@ -121,9 +124,10 @@ def field_enclosed_mass(field, distances, boxsize):
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enclosed_volume : 1-dimensional array
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Enclosed grid-like volume at each distance.
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"""
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enclosed_mass = numpy.zeros_like(distances)
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enclosed_volume = numpy.zeros_like(distances)
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for i, dist in enumerate(distances):
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enclosed_mass = np.zeros_like(distances)
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enclosed_volume = np.zeros_like(distances)
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for i, dist in enumerate(tqdm(distances)):
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enclosed_mass[i], enclosed_volume[i] = _field_enclosed_mass(
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field, dist, boxsize)
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@ -137,7 +141,7 @@ def field_enclosed_mass(field, distances, boxsize):
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@jit(nopython=True, boundscheck=False)
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def _enclosed_momentum(rdist, mass, vel, rmax, start_index):
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bulk_momentum = numpy.zeros(3, dtype=rdist.dtype)
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bulk_momentum = np.zeros(3, dtype=rdist.dtype)
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for i in range(start_index, len(rdist)):
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if rdist[i] <= rmax:
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@ -169,7 +173,7 @@ def particles_enclosed_momentum(rdist, mass, vel, distances):
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bulk_momentum : 2-dimensional array
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Enclosed momentum at each distance.
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"""
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bulk_momentum = numpy.zeros((len(distances), 3))
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bulk_momentum = np.zeros((len(distances), 3))
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start_index = 0
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for i, dist in enumerate(distances):
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if i > 0:
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@ -179,4 +183,68 @@ def particles_enclosed_momentum(rdist, mass, vel, distances):
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start_index)
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bulk_momentum[i] += v
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return bulk_momentum
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return bulk_momentum
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###############################################################################
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# Bulk flow estimators #
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###############################################################################
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def bulkflow_peery2018(rdist, mass, pos, vel, distances, weights,
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verbose=True):
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"""
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Calculate the bulk flow from a set of particles using the estimator from
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Peery+2018. Supports either `1/r^2` or `constant` weights. Particles
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are assumed to be sorted by distance from the center of the box.
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Parameters
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----------
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rdist : 1-dimensional array
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Sorted distance of particles from the center of the box.
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mass : 1-dimensional array
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Sorted mass of particles.
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pos : 2-dimensional array
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Sorted position of particles.
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vel : 2-dimensional array
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Sorted velocity of particles.
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distances : 1-dimensional array
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Distances at which to calculate the bulk flow.
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weights : str
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Weights to use in the estimator, either `1/r^2` or `constant`.
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verbose : bool
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Verbosity flag.
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Returns
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-------
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bulk_flow : 2-dimensional array
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"""
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# Select only the particles within the maximum distance to speed up the
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# calculation.
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if verbose:
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print("Selecting particles within the maximum distance...")
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kmax = np.searchsorted(rdist, np.max(distances))
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rdist = rdist[:kmax]
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mass = mass[:kmax]
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pos = pos[:kmax]
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vel = vel[:kmax]
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if verbose:
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print("Computing the cumulative quantities...")
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if weights == "1/r^2":
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cumulative_x = np.cumsum(mass[:, np.newaxis] * np.sum(vel * pos, axis=1)[:, np.newaxis] * pos / rdist[:, np.newaxis]**4, axis=0) # noqa
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norm = lambda R: R**2 # noqa
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elif weights == "constant":
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cumulative_x = np.cumsum(mass[:, np.newaxis] * np.sum(vel * pos, axis=1)[:, np.newaxis] * pos / rdist[:, np.newaxis]**2, axis=0) # noqa
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norm = lambda R: 3. # noqa
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else:
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raise ValueError("Invalid weights.")
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cumulative_x /= np.cumsum(mass)[:, np.newaxis]
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B = np.zeros((len(distances), 3))
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for i in range(3):
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for j, R in enumerate(distances):
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k = np.searchsorted(rdist, R)
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B[j, i] = norm(R) * cumulative_x[k - 1, i]
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return B
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@ -48,7 +48,6 @@ H0 = 100 # km / s / Mpc
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def t():
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"""Shortcut to get the current time."""
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return datetime.now().strftime("%H:%M:%S")
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@ -79,21 +78,26 @@ class DataLoader:
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store_full_velocity : bool, optional
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Whether to store the full 3D velocity field. Otherwise stores only
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the radial velocity.
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verbose : bool, optional
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Verbose flag.
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"""
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def __init__(self, simname, ksim, catalogue, catalogue_fpath, paths,
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ksmooth=None, store_full_velocity=False):
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print(f"{t()}: reading the catalogue.")
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ksmooth=None, store_full_velocity=False, verbose=True):
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if verbose:
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print(f"{t()}: reading the catalogue.", flush=True)
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self._cat = self._read_catalogue(catalogue, catalogue_fpath)
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self._catname = catalogue
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print(f"{t()}: reading the interpolated field.")
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if verbose:
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print(f"{t()}: reading the interpolated field.", flush=True)
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self._field_rdist, self._los_density, self._los_velocity = self._read_field( # noqa
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simname, ksim, catalogue, ksmooth, paths)
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if len(self._field_rdist) % 2 == 0:
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warn(f"The number of radial steps is even. Skipping the first "
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f"step at {self._field_rdist[0]} because Simpson's rule "
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"requires an odd number of steps.")
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if verbose:
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warn(f"The number of radial steps is even. Skipping the first "
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f"step at {self._field_rdist[0]} because Simpson's rule "
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"requires an odd number of steps.")
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self._field_rdist = self._field_rdist[1:]
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self._los_density = self._los_density[..., 1:]
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self._los_velocity = self._los_velocity[..., 1:]
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@ -102,7 +106,8 @@ class DataLoader:
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raise ValueError("The number of objects in the catalogue does not "
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"match the number of objects in the field.")
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print(f"{t()}: calculating the radial velocity.")
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if verbose:
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print(f"{t()}: calculating the radial velocity.", flush=True)
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nobject = len(self._los_density)
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dtype = self._los_density.dtype
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@ -231,9 +236,7 @@ class DataLoader:
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return rdist, los_density, los_velocity
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def _read_catalogue(self, catalogue, catalogue_fpath):
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"""
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Read in the distance indicator catalogue.
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"""
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"""Read in the distance indicator catalogue."""
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if catalogue == "A2":
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with File(catalogue_fpath, 'r') as f:
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dtype = [(key, np.float32) for key in f.keys()]
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@ -256,10 +259,18 @@ class DataLoader:
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arr[key] = grp[key][:]
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elif "CB2_" in catalogue:
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with File(catalogue_fpath, 'r') as f:
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dtype = [(key, np.float32) for key in f.keys()]
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arr = np.empty(len(f["RA"]), dtype=dtype)
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for key in f.keys():
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arr[key] = f[key][:]
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elif "UPGLADE" in catalogue:
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with File(catalogue_fpath, 'r') as f:
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dtype = [(key, np.float32) for key in f.keys()]
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arr = np.empty(len(f["RA"]), dtype=dtype)
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for key in f.keys():
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if key == "mask":
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continue
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arr[key] = f[key][:]
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else:
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raise ValueError(f"Unknown catalogue: `{catalogue}`.")
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@ -916,6 +927,8 @@ class SN_PV_validation_model(BaseFlowValidationModel):
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Right ascension and declination in degrees.
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z_obs : 1-dimensional array of shape (n_objects)
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Observed redshifts.
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e_zobs : 1-dimensional array of shape (n_objects)
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Errors on the observed redshifts.
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mB, x1, c : 1-dimensional arrays of shape (n_objects)
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SALT2 light curve parameters.
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e_mB, e_x1, e_c : 1-dimensional arrays of shape (n_objects)
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@ -927,7 +940,7 @@ class SN_PV_validation_model(BaseFlowValidationModel):
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"""
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def __init__(self, los_density, los_velocity, RA, dec, z_obs,
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mB, x1, c, e_mB, e_x1, e_c, r_xrange, Omega_m):
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e_zobs, mB, x1, c, e_mB, e_x1, e_c, r_xrange, Omega_m):
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dt = jnp.float32
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# Convert everything to JAX arrays.
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self._los_density = jnp.asarray(los_density, dtype=dt)
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@ -936,6 +949,11 @@ class SN_PV_validation_model(BaseFlowValidationModel):
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self._RA = jnp.asarray(np.deg2rad(RA), dtype=dt)
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self._dec = jnp.asarray(np.deg2rad(dec), dtype=dt)
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self._z_obs = jnp.asarray(z_obs, dtype=dt)
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if e_zobs is not None:
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self._e2_cz_obs = jnp.asarray(
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(SPEED_OF_LIGHT * e_zobs)**2, dtype=dt)
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else:
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self._e2_cz_obs = jnp.zeros_like(self._z_obs)
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self._mB = jnp.asarray(mB, dtype=dt)
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self._x1 = jnp.asarray(x1, dtype=dt)
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@ -1121,6 +1139,7 @@ class SN_PV_validation_model(BaseFlowValidationModel):
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alpha_cal = numpyro.sample("alpha_cal", self._alpha_cal)
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beta_cal = numpyro.sample("beta_cal", self._beta_cal)
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cz_err = jnp.sqrt(sigma_v**2 + self._e2_cz_obs)
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Vext_rad = project_Vext(Vx, Vy, Vz, self._RA, self._dec)
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mu = self.mu(mag_cal, alpha_cal, beta_cal)
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@ -1137,7 +1156,7 @@ class SN_PV_validation_model(BaseFlowValidationModel):
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# Calculate p(z_obs) and multiply it by p(r)
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zobs_pred = self._f_zobs(beta, Vext_rad[i], self._los_velocity[i])
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ptilde *= calculate_likelihood_zobs(
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self._z_obs[i], zobs_pred, sigma_v)
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self._z_obs[i], zobs_pred, cz_err[i])
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return ll + jnp.log(self._f_simps(ptilde) / pnorm), None
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@ -1385,17 +1404,19 @@ def get_model(loader, zcmb_max=None, verbose=True):
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if kind in ["LOSS", "Foundation"]:
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keys = ["RA", "DEC", "z_CMB", "mB", "x1", "c", "e_mB", "e_x1", "e_c"]
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RA, dec, zCMB, mB, x1, c, e_mB, e_x1, e_c = (loader.cat[k] for k in keys) # noqa
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e_zCMB = None
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mask = (zCMB < zcmb_max)
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model = SN_PV_validation_model(
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los_overdensity[mask], los_velocity[mask], RA[mask], dec[mask],
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zCMB[mask], mB[mask], x1[mask], c[mask], e_mB[mask], e_x1[mask],
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e_c[mask], loader.rdist, loader._Omega_m)
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zCMB[mask], e_zCMB, mB[mask], x1[mask], c[mask], e_mB[mask],
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e_x1[mask], e_c[mask], loader.rdist, loader._Omega_m)
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elif "Pantheon+" in kind:
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keys = ["RA", "DEC", "zCMB", "mB", "x1", "c", "biasCor_m_b", "mBERR",
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"x1ERR", "cERR", "biasCorErr_m_b", "zCMB_SN", "zCMB_Group"]
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"x1ERR", "cERR", "biasCorErr_m_b", "zCMB_SN", "zCMB_Group",
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"zCMBERR"]
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RA, dec, zCMB, mB, x1, c, bias_corr_mB, e_mB, e_x1, e_c, e_bias_corr_mB, zCMB_SN, zCMB_Group = (loader.cat[k] for k in keys) # noqa
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RA, dec, zCMB, mB, x1, c, bias_corr_mB, e_mB, e_x1, e_c, e_bias_corr_mB, zCMB_SN, zCMB_Group, e_zCMB = (loader.cat[k] for k in keys) # noqa
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mB -= bias_corr_mB
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e_mB = np.sqrt(e_mB**2 + e_bias_corr_mB**2)
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@ -1413,8 +1434,8 @@ def get_model(loader, zcmb_max=None, verbose=True):
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model = SN_PV_validation_model(
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los_overdensity[mask], los_velocity[mask], RA[mask], dec[mask],
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zCMB[mask], mB[mask], x1[mask], c[mask], e_mB[mask], e_x1[mask],
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e_c[mask], loader.rdist, loader._Omega_m)
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zCMB[mask], e_zCMB[mask], mB[mask], x1[mask], c[mask], e_mB[mask],
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e_x1[mask], e_c[mask], loader.rdist, loader._Omega_m)
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elif kind in ["SFI_gals", "2MTF", "SFI_gals_masked"]:
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keys = ["RA", "DEC", "z_CMB", "mag", "eta", "e_mag", "e_eta"]
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RA, dec, zCMB, mag, eta, e_mag, e_eta = (loader.cat[k] for k in keys)
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@ -15,7 +15,7 @@
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from .catalogue import (CSiBORG1Catalogue, CSiBORG2Catalogue, # noqa
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CSiBORG2SUBFINDCatalogue, # noqa
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CSiBORG2MergerTreeReader, QuijoteCatalogue, # noqa
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MDPL2Catalogue) # noqa
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MDPL2Catalogue, fiducial_observers) # noqa
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from .snapshot import (CSiBORG1Snapshot, CSiBORG2Snapshot, QuijoteSnapshot, # noqa
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CSiBORG1Field, CSiBORG2Field, QuijoteField, BORG2Field, # noqa
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BORG1Field, TNG300_1Field) # noqa
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@ -1372,7 +1372,7 @@ class QuijoteCatalogue(BaseCatalogue):
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@property
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def totmass(self):
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return self._read_fof_catalogue("group_mass")
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return self._read_fof_catalogue("GroupMass")
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@property
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def index(self):
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@ -413,6 +413,47 @@ def real2redshift(pos, vel, observer_location, observer_velocity, boxsize,
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return pos
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def heliocentric_to_cmb(z_helio, RA, dec, e_z_helio=None):
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"""
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Convert heliocentric redshift to CMB redshift using the Planck 2018 CMB
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dipole.
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"""
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# CMB dipole Planck 2018 values
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vsun_mag = 369 # km/s
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RA_sun = 167.942
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dec_sun = -6.944
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SPEED_OF_LIGHT = 299792.458 # km / s
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theta_sun = np.pi / 2 - np.deg2rad(dec_sun)
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phi_sun = np.deg2rad(RA_sun)
|
||||
|
||||
# Convert to theat/phi in radians
|
||||
theta = np.pi / 2 - np.deg2rad(dec)
|
||||
phi = np.deg2rad(RA)
|
||||
|
||||
# Unit vector in the direction of each galaxy
|
||||
n = np.asarray([np.sin(theta) * np.cos(phi),
|
||||
np.sin(theta) * np.sin(phi),
|
||||
np.cos(theta)]).T
|
||||
# CMB dipole unit vector
|
||||
vsun_normvect = np.asarray([np.sin(theta_sun) * np.cos(phi_sun),
|
||||
np.sin(theta_sun) * np.sin(phi_sun),
|
||||
np.cos(theta_sun)])
|
||||
|
||||
# Project the CMB dipole onto the line of sight and normalize
|
||||
vsun_projected = vsun_mag * np.dot(n, vsun_normvect) / SPEED_OF_LIGHT
|
||||
|
||||
zsun_tilde = np.sqrt((1 - vsun_projected) / (1 + vsun_projected))
|
||||
zcmb = (1 + z_helio) / zsun_tilde - 1
|
||||
|
||||
# Optional linear error propagation
|
||||
if e_z_helio is not None:
|
||||
e_zcmb = np.abs(e_z_helio / zsun_tilde)
|
||||
return zcmb, e_zcmb
|
||||
|
||||
return zcmb
|
||||
|
||||
|
||||
###############################################################################
|
||||
# Statistics #
|
||||
###############################################################################
|
||||
|
|
|
|||
257
notebooks/flow/estimator_bulk_flow.ipynb
Normal file
257
notebooks/flow/estimator_bulk_flow.ipynb
Normal file
File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
|
|
@ -9,7 +9,7 @@
|
|||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 1,
|
||||
"execution_count": 2,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
|
|
@ -38,7 +38,7 @@
|
|||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 2,
|
||||
"execution_count": 3,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
|
|
@ -63,7 +63,7 @@
|
|||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 3,
|
||||
"execution_count": 4,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
|
|
@ -86,9 +86,17 @@
|
|||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 138,
|
||||
"execution_count": 5,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"outputs": [
|
||||
{
|
||||
"name": "stdout",
|
||||
"output_type": "stream",
|
||||
"text": [
|
||||
"<KeysViewHDF5 ['DEGdeg', 'DEHdeg', 'DEJ2000', 'Host', 'IAUC', 'RAGdeg', 'RAHdeg', 'RAJ2000', 'SNID', 'SimbadName', 'e_vpec', 'e_zHD', 'e_zhel', 'recno', 'vpec', 'vpecG', 'zGHD', 'zGcmb', 'zGhel', 'zHD', 'zcmb', 'zhel']>\n"
|
||||
]
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"fpath_full = \"/mnt/extraspace/rstiskalek/catalogs/PV/Pantheon+SH0ES.dat\"\n",
|
||||
"fpath_group = \"/mnt/extraspace/rstiskalek/catalogs/PV/pantheon+_groups.hdf5\"\n",
|
||||
|
|
@ -96,22 +104,28 @@
|
|||
"data_full = np.genfromtxt(fpath_full, names=True, dtype=None, encoding=None)\n",
|
||||
"data_group = {}\n",
|
||||
"\n",
|
||||
"# Read in the groups\n",
|
||||
"with File(fpath_group, \"r\") as f:\n",
|
||||
" print(f.keys())\n",
|
||||
" for key in f.keys():\n",
|
||||
" data_group[key] = f[key][:]\n",
|
||||
" try:\n",
|
||||
" data_group[key] = f[key][...]\n",
|
||||
" except IndexError:\n",
|
||||
" print(f\"Failed to read {key}\")\n",
|
||||
" # data[key] = f[key][...]\n",
|
||||
"\n",
|
||||
"# data = data[data[\"zCMB\"] < 0.1]\n",
|
||||
"\n",
|
||||
"keys = [\"zCMB\", \"mB\", \"mBERR\", \"x1\", \"x1ERR\", \"c\", \"cERR\", \"RA\", \"DEC\",\n",
|
||||
" \"VPEC\", \"VPECERR\", \"biasCor_m_b\", \"biasCorErr_m_b\"]\n",
|
||||
"keys = [\"zCMB\", \"zCMBERR\", \"mB\", \"mBERR\", \"x1\", \"x1ERR\", \"c\", \"cERR\", \"RA\",\n",
|
||||
" \"DEC\", \"VPEC\", \"VPECERR\", \"biasCor_m_b\", \"biasCorErr_m_b\"]\n",
|
||||
"pantheon_data = {}\n",
|
||||
"for key in keys:\n",
|
||||
" pantheon_data[key] = data[key]\n"
|
||||
" pantheon_data[key] = data_full[key]\n"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 139,
|
||||
"execution_count": 25,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
|
|
@ -133,7 +147,7 @@
|
|||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 142,
|
||||
"execution_count": 26,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
|
|
@ -150,7 +164,7 @@
|
|||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 145,
|
||||
"execution_count": 27,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
|
|
@ -186,7 +200,7 @@
|
|||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 4,
|
||||
"execution_count": 28,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
|
|
@ -212,7 +226,7 @@
|
|||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 5,
|
||||
"execution_count": 29,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
|
|
@ -236,7 +250,7 @@
|
|||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 6,
|
||||
"execution_count": 30,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
|
|
@ -260,7 +274,7 @@
|
|||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 14,
|
||||
"execution_count": 31,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
|
|
@ -278,7 +292,7 @@
|
|||
" 2.0177503] deg>"
|
||||
]
|
||||
},
|
||||
"execution_count": 14,
|
||||
"execution_count": 31,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
}
|
||||
|
|
@ -294,7 +308,7 @@
|
|||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 26,
|
||||
"execution_count": 32,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
|
|
@ -320,13 +334,6 @@
|
|||
"plt.show()"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": []
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
|
|
@ -336,7 +343,7 @@
|
|||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 149,
|
||||
"execution_count": 33,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
|
|
@ -360,7 +367,7 @@
|
|||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 151,
|
||||
"execution_count": 34,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
|
|
@ -428,7 +435,7 @@
|
|||
"name": "python",
|
||||
"nbconvert_exporter": "python",
|
||||
"pygments_lexer": "ipython3",
|
||||
"version": "3.11.7"
|
||||
"version": "3.11.4"
|
||||
}
|
||||
},
|
||||
"nbformat": 4,
|
||||
|
|
|
|||
475
notebooks/flow/process_upglade.ipynb
Normal file
475
notebooks/flow/process_upglade.ipynb
Normal file
File diff suppressed because one or more lines are too long
|
|
@ -160,7 +160,7 @@
|
|||
"name": "python",
|
||||
"nbconvert_exporter": "python",
|
||||
"pygments_lexer": "ipython3",
|
||||
"version": "3.11.7"
|
||||
"version": "3.11.4"
|
||||
}
|
||||
},
|
||||
"nbformat": 4,
|
||||
|
|
|
|||
404
notebooks/match_observation/harry_clusters.ipynb
Normal file
404
notebooks/match_observation/harry_clusters.ipynb
Normal file
|
|
@ -0,0 +1,404 @@
|
|||
{
|
||||
"cells": [
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"# Matching of haloes to clusters"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 144,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"name": "stdout",
|
||||
"output_type": "stream",
|
||||
"text": [
|
||||
"The autoreload extension is already loaded. To reload it, use:\n",
|
||||
" %reload_ext autoreload\n"
|
||||
]
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"import numpy as np\n",
|
||||
"import matplotlib.pyplot as plt\n",
|
||||
"from astropy.cosmology import FlatLambdaCDM\n",
|
||||
"\n",
|
||||
"import pandas as pd\n",
|
||||
"\n",
|
||||
"%load_ext autoreload\n",
|
||||
"%autoreload 2\n",
|
||||
"%matplotlib inline"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"### Load in the data\n",
|
||||
"Harry: the exact routine may not work, I had to edit the raw .txt file a little"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 124,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"name": "stdout",
|
||||
"output_type": "stream",
|
||||
"text": [
|
||||
"[34.14606699 9.28692846 11.11279198 16.85641068 3.71636485 33.43032196\n",
|
||||
" 24.65595192 29.91007806 40.31604335 9.346801 ]\n"
|
||||
]
|
||||
},
|
||||
{
|
||||
"data": {
|
||||
"text/html": [
|
||||
"<div>\n",
|
||||
"<style scoped>\n",
|
||||
" .dataframe tbody tr th:only-of-type {\n",
|
||||
" vertical-align: middle;\n",
|
||||
" }\n",
|
||||
"\n",
|
||||
" .dataframe tbody tr th {\n",
|
||||
" vertical-align: top;\n",
|
||||
" }\n",
|
||||
"\n",
|
||||
" .dataframe thead th {\n",
|
||||
" text-align: right;\n",
|
||||
" }\n",
|
||||
"</style>\n",
|
||||
"<table border=\"1\" class=\"dataframe\">\n",
|
||||
" <thead>\n",
|
||||
" <tr style=\"text-align: right;\">\n",
|
||||
" <th></th>\n",
|
||||
" <th>halo_ID</th>\n",
|
||||
" <th>KIND</th>\n",
|
||||
" <th>l[deg]</th>\n",
|
||||
" <th>b[deg]</th>\n",
|
||||
" <th>d[kpc]</th>\n",
|
||||
" <th>z</th>\n",
|
||||
" <th>Rdelta[kpc]</th>\n",
|
||||
" <th>rhos[Msol/kpc^3]</th>\n",
|
||||
" <th>rs[kpc]</th>\n",
|
||||
" <th>prof[keywrd]</th>\n",
|
||||
" <th>#1</th>\n",
|
||||
" <th>#2</th>\n",
|
||||
" <th>#3</th>\n",
|
||||
" <th>FOVDiam[deg]</th>\n",
|
||||
" </tr>\n",
|
||||
" </thead>\n",
|
||||
" <tbody>\n",
|
||||
" <tr>\n",
|
||||
" <th>0</th>\n",
|
||||
" <td>halo_647110</td>\n",
|
||||
" <td>CLUSTER</td>\n",
|
||||
" <td>-47.66</td>\n",
|
||||
" <td>29.96</td>\n",
|
||||
" <td>-1</td>\n",
|
||||
" <td>0.01142</td>\n",
|
||||
" <td>4523.71</td>\n",
|
||||
" <td>643822.01573</td>\n",
|
||||
" <td>663.92743</td>\n",
|
||||
" <td>kZHAO</td>\n",
|
||||
" <td>1.0</td>\n",
|
||||
" <td>3.0</td>\n",
|
||||
" <td>1.0</td>\n",
|
||||
" <td>37.74875</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>1</th>\n",
|
||||
" <td>halo_10128802</td>\n",
|
||||
" <td>CLUSTER</td>\n",
|
||||
" <td>-90.76</td>\n",
|
||||
" <td>25.97</td>\n",
|
||||
" <td>-1</td>\n",
|
||||
" <td>0.00310</td>\n",
|
||||
" <td>1975.98</td>\n",
|
||||
" <td>611499.11522</td>\n",
|
||||
" <td>294.56973</td>\n",
|
||||
" <td>kZHAO</td>\n",
|
||||
" <td>1.0</td>\n",
|
||||
" <td>3.0</td>\n",
|
||||
" <td>1.0</td>\n",
|
||||
" <td>60.00762</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>2</th>\n",
|
||||
" <td>halo_1338057</td>\n",
|
||||
" <td>CLUSTER</td>\n",
|
||||
" <td>-35.42</td>\n",
|
||||
" <td>-6.15</td>\n",
|
||||
" <td>-1</td>\n",
|
||||
" <td>0.00371</td>\n",
|
||||
" <td>2738.50</td>\n",
|
||||
" <td>593219.40743</td>\n",
|
||||
" <td>413.73423</td>\n",
|
||||
" <td>kZHAO</td>\n",
|
||||
" <td>1.0</td>\n",
|
||||
" <td>3.0</td>\n",
|
||||
" <td>1.0</td>\n",
|
||||
" <td>69.19885</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>3</th>\n",
|
||||
" <td>halo_20419495</td>\n",
|
||||
" <td>CLUSTER</td>\n",
|
||||
" <td>87.42</td>\n",
|
||||
" <td>88.09</td>\n",
|
||||
" <td>-1</td>\n",
|
||||
" <td>0.00563</td>\n",
|
||||
" <td>3082.73</td>\n",
|
||||
" <td>596355.51967</td>\n",
|
||||
" <td>465.36921</td>\n",
|
||||
" <td>kZHAO</td>\n",
|
||||
" <td>1.0</td>\n",
|
||||
" <td>3.0</td>\n",
|
||||
" <td>1.0</td>\n",
|
||||
" <td>51.83070</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>4</th>\n",
|
||||
" <td>halo_20355327</td>\n",
|
||||
" <td>CLUSTER</td>\n",
|
||||
" <td>-94.48</td>\n",
|
||||
" <td>75.29</td>\n",
|
||||
" <td>-1</td>\n",
|
||||
" <td>0.00124</td>\n",
|
||||
" <td>1644.94</td>\n",
|
||||
" <td>635981.23866</td>\n",
|
||||
" <td>240.83028</td>\n",
|
||||
" <td>kZHAO</td>\n",
|
||||
" <td>1.0</td>\n",
|
||||
" <td>3.0</td>\n",
|
||||
" <td>1.0</td>\n",
|
||||
" <td>119.66328</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>5</th>\n",
|
||||
" <td>halo_2503990</td>\n",
|
||||
" <td>CLUSTER</td>\n",
|
||||
" <td>-35.24</td>\n",
|
||||
" <td>-12.06</td>\n",
|
||||
" <td>-1</td>\n",
|
||||
" <td>0.01118</td>\n",
|
||||
" <td>3164.45</td>\n",
|
||||
" <td>600754.77263</td>\n",
|
||||
" <td>478.21044</td>\n",
|
||||
" <td>kZHAO</td>\n",
|
||||
" <td>1.0</td>\n",
|
||||
" <td>3.0</td>\n",
|
||||
" <td>1.0</td>\n",
|
||||
" <td>27.04669</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>6</th>\n",
|
||||
" <td>halo_21251859</td>\n",
|
||||
" <td>CLUSTER</td>\n",
|
||||
" <td>31.15</td>\n",
|
||||
" <td>44.45</td>\n",
|
||||
" <td>-1</td>\n",
|
||||
" <td>0.00824</td>\n",
|
||||
" <td>2731.34</td>\n",
|
||||
" <td>595715.63380</td>\n",
|
||||
" <td>413.32640</td>\n",
|
||||
" <td>kZHAO</td>\n",
|
||||
" <td>1.0</td>\n",
|
||||
" <td>3.0</td>\n",
|
||||
" <td>1.0</td>\n",
|
||||
" <td>31.59913</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>7</th>\n",
|
||||
" <td>halo_745775</td>\n",
|
||||
" <td>CLUSTER</td>\n",
|
||||
" <td>-47.49</td>\n",
|
||||
" <td>36.08</td>\n",
|
||||
" <td>-1</td>\n",
|
||||
" <td>0.01000</td>\n",
|
||||
" <td>2878.14</td>\n",
|
||||
" <td>597011.32933</td>\n",
|
||||
" <td>435.71418</td>\n",
|
||||
" <td>kZHAO</td>\n",
|
||||
" <td>1.0</td>\n",
|
||||
" <td>3.0</td>\n",
|
||||
" <td>1.0</td>\n",
|
||||
" <td>27.49495</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>8</th>\n",
|
||||
" <td>halo_3003328</td>\n",
|
||||
" <td>CLUSTER</td>\n",
|
||||
" <td>39.76</td>\n",
|
||||
" <td>-46.41</td>\n",
|
||||
" <td>-1</td>\n",
|
||||
" <td>0.01349</td>\n",
|
||||
" <td>3172.97</td>\n",
|
||||
" <td>602266.09230</td>\n",
|
||||
" <td>479.82208</td>\n",
|
||||
" <td>kZHAO</td>\n",
|
||||
" <td>1.0</td>\n",
|
||||
" <td>3.0</td>\n",
|
||||
" <td>1.0</td>\n",
|
||||
" <td>22.50342</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>9</th>\n",
|
||||
" <td>halo_4200359</td>\n",
|
||||
" <td>CLUSTER</td>\n",
|
||||
" <td>-28.67</td>\n",
|
||||
" <td>-22.77</td>\n",
|
||||
" <td>-1</td>\n",
|
||||
" <td>0.00312</td>\n",
|
||||
" <td>1826.88</td>\n",
|
||||
" <td>621061.51007</td>\n",
|
||||
" <td>270.55674</td>\n",
|
||||
" <td>kZHAO</td>\n",
|
||||
" <td>1.0</td>\n",
|
||||
" <td>3.0</td>\n",
|
||||
" <td>1.0</td>\n",
|
||||
" <td>55.35257</td>\n",
|
||||
" </tr>\n",
|
||||
" </tbody>\n",
|
||||
"</table>\n",
|
||||
"</div>"
|
||||
],
|
||||
"text/plain": [
|
||||
" halo_ID KIND l[deg] b[deg] d[kpc] z Rdelta[kpc] \\\n",
|
||||
"0 halo_647110 CLUSTER -47.66 29.96 -1 0.01142 4523.71 \n",
|
||||
"1 halo_10128802 CLUSTER -90.76 25.97 -1 0.00310 1975.98 \n",
|
||||
"2 halo_1338057 CLUSTER -35.42 -6.15 -1 0.00371 2738.50 \n",
|
||||
"3 halo_20419495 CLUSTER 87.42 88.09 -1 0.00563 3082.73 \n",
|
||||
"4 halo_20355327 CLUSTER -94.48 75.29 -1 0.00124 1644.94 \n",
|
||||
"5 halo_2503990 CLUSTER -35.24 -12.06 -1 0.01118 3164.45 \n",
|
||||
"6 halo_21251859 CLUSTER 31.15 44.45 -1 0.00824 2731.34 \n",
|
||||
"7 halo_745775 CLUSTER -47.49 36.08 -1 0.01000 2878.14 \n",
|
||||
"8 halo_3003328 CLUSTER 39.76 -46.41 -1 0.01349 3172.97 \n",
|
||||
"9 halo_4200359 CLUSTER -28.67 -22.77 -1 0.00312 1826.88 \n",
|
||||
"\n",
|
||||
" rhos[Msol/kpc^3] rs[kpc] prof[keywrd] #1 #2 #3 FOVDiam[deg] \n",
|
||||
"0 643822.01573 663.92743 kZHAO 1.0 3.0 1.0 37.74875 \n",
|
||||
"1 611499.11522 294.56973 kZHAO 1.0 3.0 1.0 60.00762 \n",
|
||||
"2 593219.40743 413.73423 kZHAO 1.0 3.0 1.0 69.19885 \n",
|
||||
"3 596355.51967 465.36921 kZHAO 1.0 3.0 1.0 51.83070 \n",
|
||||
"4 635981.23866 240.83028 kZHAO 1.0 3.0 1.0 119.66328 \n",
|
||||
"5 600754.77263 478.21044 kZHAO 1.0 3.0 1.0 27.04669 \n",
|
||||
"6 595715.63380 413.32640 kZHAO 1.0 3.0 1.0 31.59913 \n",
|
||||
"7 597011.32933 435.71418 kZHAO 1.0 3.0 1.0 27.49495 \n",
|
||||
"8 602266.09230 479.82208 kZHAO 1.0 3.0 1.0 22.50342 \n",
|
||||
"9 621061.51007 270.55674 kZHAO 1.0 3.0 1.0 55.35257 "
|
||||
]
|
||||
},
|
||||
"execution_count": 124,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"\n",
|
||||
"cosmo = FlatLambdaCDM(H0=100, Om0=0.307)\n",
|
||||
"\n",
|
||||
"data0 = pd.read_csv(\"/mnt/users/rstiskalek/csiborgtools/data/top10_pwave_coords.txt\", sep='\\s+')\n",
|
||||
"data = {}\n",
|
||||
"\n",
|
||||
"data[\"id\"] = np.array([int(x.split(\"_\")[-1]) for x in data0[\"halo_ID\"].values])\n",
|
||||
"data[\"l\"] = data0[\"l[deg]\"].values\n",
|
||||
"data[\"b\"] = data0[\"b[deg]\"].values\n",
|
||||
"data[\"dist\"] = cosmo.comoving_distance(data0[\"z\"].values).value\n",
|
||||
"\n",
|
||||
"print(data[\"dist\"])\n",
|
||||
"data0"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"### Load in the halo catalogue"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 126,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"boxsize = 677.7\n",
|
||||
"\n",
|
||||
"halos = np.load(\"/users/hdesmond/Mmain/Mmain_9844.npy\")\n",
|
||||
"names = [\"id\", \"x\", \"y\", \"z\", \"M\"]\n",
|
||||
"halos = {k: halos[:, i] for i, k in enumerate(names)}\n",
|
||||
"halos[\"id\"] = halos[\"id\"].astype(int)\n",
|
||||
"# Coordinates are in box units. Convert to Mpc/h\n",
|
||||
"for p in (\"x\", \"y\", \"z\"):\n",
|
||||
" halos[p] = halos[p] * boxsize\n",
|
||||
"\n",
|
||||
"halos[\"dist\"] = np.sqrt((halos[\"x\"] - boxsize/2)**2 + (halos[\"y\"] - boxsize/2)**2 + (halos[\"z\"] - boxsize/2)**2)\n"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 142,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"name": "stdout",
|
||||
"output_type": "stream",
|
||||
"text": [
|
||||
"5791\n"
|
||||
]
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"# Find which item in the catalogue matches the nth halo in the .txt file\n",
|
||||
"n = 0\n",
|
||||
"k = np.where(data[\"id\"][n] == halos[\"id\"])[0][0]\n",
|
||||
"print(k)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 143,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"data": {
|
||||
"text/plain": [
|
||||
"(34.14606698507264, 149.24046381654668)"
|
||||
]
|
||||
},
|
||||
"execution_count": 143,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"data[\"dist\"][n], halos[\"dist\"][k]"
|
||||
]
|
||||
}
|
||||
],
|
||||
"metadata": {
|
||||
"kernelspec": {
|
||||
"display_name": "venv_csiborg",
|
||||
"language": "python",
|
||||
"name": "python3"
|
||||
},
|
||||
"language_info": {
|
||||
"codemirror_mode": {
|
||||
"name": "ipython",
|
||||
"version": 3
|
||||
},
|
||||
"file_extension": ".py",
|
||||
"mimetype": "text/x-python",
|
||||
"name": "python",
|
||||
"nbconvert_exporter": "python",
|
||||
"pygments_lexer": "ipython3",
|
||||
"version": "3.11.7"
|
||||
}
|
||||
},
|
||||
"nbformat": 4,
|
||||
"nbformat_minor": 2
|
||||
}
|
||||
|
|
@ -77,9 +77,17 @@ def get_los(catalogue_name, simname, comm):
|
|||
with File(fname, 'r') as f:
|
||||
RA = f["RA"][:]
|
||||
dec = f["DEC"][:]
|
||||
elif catalogue_name == "UPGLADE":
|
||||
fname = "/mnt/users/rstiskalek/csiborgtools/data/upglade_z_0p05_all_PROCESSED.h5" # noqa
|
||||
with File(fname, 'r') as f:
|
||||
RA = f["RA"][:]
|
||||
dec = f["DEC"][:]
|
||||
else:
|
||||
raise ValueError(f"Unknown field name: `{catalogue_name}`.")
|
||||
|
||||
if comm.Get_rank() == 0:
|
||||
print(f"The dataset contains {len(RA)} objects.")
|
||||
|
||||
# The Carrick+2015 is in galactic coordinates, so we need to convert
|
||||
# the RA/dec to galactic coordinates.
|
||||
if simname == "Carrick2015":
|
||||
|
|
@ -210,7 +218,7 @@ def combine_from_simulations(catalogue_name, simname, nsims, outfolder,
|
|||
|
||||
|
||||
def interpolate_field(pos, simname, nsim, MAS, grid, dump_folder, rmax,
|
||||
dr, smooth_scales):
|
||||
dr, smooth_scales, verbose=False):
|
||||
"""
|
||||
Interpolate the density and velocity fields along the line of sight.
|
||||
|
||||
|
|
@ -243,11 +251,13 @@ def interpolate_field(pos, simname, nsim, MAS, grid, dump_folder, rmax,
|
|||
fname_out = join(dump_folder, f"los_{simname}_{nsim}.hdf5")
|
||||
|
||||
# First do the density field.
|
||||
if verbose:
|
||||
print(f"Interpolating density field for IC realisation `{nsim}`.",
|
||||
flush=True)
|
||||
density = get_field(simname, nsim, "density", MAS, grid)
|
||||
|
||||
rdist, finterp = csiborgtools.field.evaluate_los(
|
||||
density, sky_pos=pos, boxsize=boxsize, rmax=rmax, dr=dr,
|
||||
smooth_scales=smooth_scales, verbose=False)
|
||||
smooth_scales=smooth_scales, verbose=verbose)
|
||||
|
||||
print(f"Writing temporary file `{fname_out}`.")
|
||||
with File(fname_out, 'w') as f:
|
||||
|
|
@ -257,11 +267,14 @@ def interpolate_field(pos, simname, nsim, MAS, grid, dump_folder, rmax,
|
|||
del density, rdist, finterp
|
||||
collect()
|
||||
|
||||
if verbose:
|
||||
print(f"Interpolating velocity field for IC realisation `{nsim}`.",
|
||||
flush=True)
|
||||
velocity = get_field(simname, nsim, "velocity", MAS, grid)
|
||||
rdist, finterp = csiborgtools.field.evaluate_los(
|
||||
velocity[0], velocity[1], velocity[2],
|
||||
sky_pos=pos, boxsize=boxsize, rmax=rmax, dr=dr,
|
||||
smooth_scales=smooth_scales, verbose=False)
|
||||
smooth_scales=smooth_scales, verbose=verbose)
|
||||
|
||||
with File(fname_out, 'a') as f:
|
||||
f.create_dataset("velocity", data=finterp)
|
||||
|
|
@ -308,7 +321,8 @@ if __name__ == "__main__":
|
|||
|
||||
def main(nsim):
|
||||
interpolate_field(pos, args.simname, nsim, args.MAS, args.grid,
|
||||
dump_folder, rmax, dr, smooth_scales)
|
||||
dump_folder, rmax, dr, smooth_scales,
|
||||
verbose=comm.Get_size() == 1)
|
||||
|
||||
work_delegation(main, nsims, comm, master_verbose=True)
|
||||
comm.Barrier()
|
||||
|
|
|
|||
|
|
@ -1,5 +1,5 @@
|
|||
nthreads=6
|
||||
memory=42
|
||||
nthreads=1
|
||||
memory=32
|
||||
on_login=0
|
||||
queue="berg"
|
||||
env="/mnt/users/rstiskalek/csiborgtools/venv_csiborg/bin/python"
|
||||
|
|
|
|||
|
|
@ -7,8 +7,9 @@ queue="berg"
|
|||
env="/mnt/users/rstiskalek/csiborgtools/venv_csiborg/bin/python"
|
||||
file="flow_validation.py"
|
||||
|
||||
#"Pantheon+_zSN"
|
||||
catalogue="Pantheon+_groups"
|
||||
simname="csiborg2_varysmall"
|
||||
simname="Carrick2015"
|
||||
|
||||
|
||||
pythoncm="$env $file --catalogue $catalogue --simname $simname --ksmooth $ksmooth"
|
||||
|
|
|
|||
165
scripts/old/field_bulk_estimator.py
Normal file
165
scripts/old/field_bulk_estimator.py
Normal file
|
|
@ -0,0 +1,165 @@
|
|||
# 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.
|
||||
"""
|
||||
A script to calculate the bulk flow in Quijote to compare the volume average
|
||||
definition to various estimators that rely on radial velocities (e.g. Nusser
|
||||
2014 and Peery+2018).
|
||||
"""
|
||||
from argparse import ArgumentParser
|
||||
from datetime import datetime
|
||||
from os import remove
|
||||
from os.path import join
|
||||
|
||||
import csiborgtools
|
||||
import numpy as np
|
||||
from mpi4py import MPI
|
||||
from taskmaster import work_delegation # noqa
|
||||
|
||||
|
||||
###############################################################################
|
||||
# Read in information about the simulation #
|
||||
###############################################################################
|
||||
|
||||
|
||||
def t():
|
||||
return datetime.now()
|
||||
|
||||
|
||||
def get_reader(simname, paths, nsim):
|
||||
"""Get the appropriate snaspshot reader for the simulation."""
|
||||
# We only want Quijote because it has all particles of the same mass.
|
||||
if simname == "quijote":
|
||||
# We want the z = 0 snapshots
|
||||
reader = csiborgtools.read.QuijoteSnapshot(nsim, 4, paths)
|
||||
else:
|
||||
raise ValueError(f"Unknown simname: `{simname}`.")
|
||||
|
||||
return reader
|
||||
|
||||
|
||||
def get_particles(reader, verbose=True):
|
||||
"""
|
||||
Get the distance of particles from the center of the box and their masses.
|
||||
"""
|
||||
if verbose:
|
||||
print(f"{t()},: reading coordinates and calculating radial distance.")
|
||||
pos = reader.coordinates().astype(np.float64)
|
||||
vel = reader.velocities().astype(np.float64)
|
||||
return pos, vel
|
||||
|
||||
|
||||
###############################################################################
|
||||
# Main & command line interface #
|
||||
###############################################################################
|
||||
|
||||
|
||||
def main(simname, nsim, folder, Rmax):
|
||||
observers = csiborgtools.read.fiducial_observers(boxsize, Rmax)
|
||||
distances = np.linspace(0, Rmax, 101)[1:]
|
||||
|
||||
reader = get_reader(simname, paths, nsim)
|
||||
pos, vel = get_particles(reader, verbose=False)
|
||||
mass = np.ones(len(pos)) # Quijote has equal masses
|
||||
|
||||
bf_volume = np.full((len(observers), len(distances), 3), np.nan)
|
||||
bf_peery = np.full_like(bf_volume, np.nan)
|
||||
bf_const = np.full_like(bf_volume, np.nan)
|
||||
|
||||
for i in range(len(observers)):
|
||||
print(f"{t()}: Calculating bulk flow for observer {i + 1} of simulation {nsim}.") # noqa
|
||||
|
||||
# Subtract the observer position.
|
||||
pos_current = pos - observers[i]
|
||||
# Get the distance of each particle from the observer and sort it.
|
||||
rdist = np.linalg.norm(pos_current, axis=1)
|
||||
indxs = np.argsort(rdist)
|
||||
|
||||
pos_current = pos_current[indxs]
|
||||
vel_current = vel[indxs]
|
||||
rdist = rdist[indxs]
|
||||
|
||||
# Volume average
|
||||
bf_volume[i, ...] = csiborgtools.field.particles_enclosed_momentum(
|
||||
rdist, mass, vel_current, distances)
|
||||
bf_volume[i, ...] /= csiborgtools.field.particles_enclosed_mass(
|
||||
rdist, mass, distances)[:, np.newaxis]
|
||||
|
||||
# Peery 2018 1 / r^2 weighted
|
||||
bf_peery[i, ...] = csiborgtools.field.bulkflow_peery2018(
|
||||
rdist, mass, pos_current, vel_current, distances, "1/r^2",
|
||||
verbose=False)
|
||||
|
||||
# Constant weight
|
||||
bf_const[i, ...] = csiborgtools.field.bulkflow_peery2018(
|
||||
rdist, mass, pos_current, vel_current, distances, "constant",
|
||||
verbose=False)
|
||||
|
||||
# Finally save the output
|
||||
fname = join(folder, f"bf_estimators_addconstant_{simname}_{nsim}.npz")
|
||||
print(f"Saving to `{fname}`.")
|
||||
np.savez(fname, bf_volume=bf_volume, bf_peery=bf_peery, bf_const=bf_const,
|
||||
distances=distances)
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
parser = ArgumentParser()
|
||||
parser.add_argument("--simname", type=str, help="Simulation name.",
|
||||
choices=["quijote"]) # noqa
|
||||
args = parser.parse_args()
|
||||
Rmax = 150
|
||||
folder = "/mnt/extraspace/rstiskalek/csiborg_postprocessing/field_shells"
|
||||
|
||||
comm = MPI.COMM_WORLD
|
||||
rank = comm.Get_rank()
|
||||
|
||||
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
|
||||
boxsize = csiborgtools.simname2boxsize(args.simname)
|
||||
|
||||
def main_wrapper(nsim):
|
||||
main(args.simname, nsim, folder, Rmax)
|
||||
|
||||
nsims = list(paths.get_ics(args.simname))
|
||||
if rank == 0:
|
||||
print(f"Running with {len(nsims)} Quijote simulations.")
|
||||
|
||||
comm.Barrier()
|
||||
work_delegation(main_wrapper, nsims, comm, master_verbose=True)
|
||||
comm.Barrier()
|
||||
|
||||
# Collect the results
|
||||
if rank == 0:
|
||||
for i, nsim in enumerate(nsims):
|
||||
fname = join(folder, f"bf_estimators_{args.simname}_{nsim}.npz")
|
||||
data = np.load(fname)
|
||||
|
||||
if i == 0:
|
||||
bf_volume = np.empty((len(nsims), *data["bf_volume"].shape))
|
||||
bf_peery = np.empty_like(bf_volume)
|
||||
bf_const = np.empty_like(bf_volume)
|
||||
|
||||
distances = data["distances"]
|
||||
|
||||
bf_volume[i, ...] = data["bf_volume"]
|
||||
bf_peery[i, ...] = data["bf_peery"]
|
||||
bf_const[i, ...] = data["bf_const"]
|
||||
|
||||
# Remove file from this rank
|
||||
remove(fname)
|
||||
|
||||
# Save the results
|
||||
fname = join(folder, f"bf_estimators_{args.simname}.npz")
|
||||
print(f"Saving final results to `{fname}`.")
|
||||
np.savez(fname, bf_volume=bf_volume, bf_peery=bf_peery,
|
||||
bf_const=bf_const, distances=distances)
|
||||
21
scripts/old/field_bulk_estimator.sh
Executable file
21
scripts/old/field_bulk_estimator.sh
Executable file
|
|
@ -0,0 +1,21 @@
|
|||
nthreads=20
|
||||
memory=24
|
||||
on_login=0
|
||||
queue="berg"
|
||||
env="/mnt/zfsusers/rstiskalek/csiborgtools/venv_csiborg/bin/python"
|
||||
file="field_bulk_estimator.py"
|
||||
|
||||
simname="quijote"
|
||||
|
||||
|
||||
pythoncm="$env $file --simname $simname"
|
||||
if [ $on_login -eq 1 ]; then
|
||||
echo $pythoncm
|
||||
$pythoncm
|
||||
else
|
||||
cm="addqueue -q $queue -n $nthreads -m $memory $pythoncm"
|
||||
echo "Submitting:"
|
||||
echo $cm
|
||||
echo
|
||||
eval $cm
|
||||
fi
|
||||
162
scripts/post_upglade.py
Normal file
162
scripts/post_upglade.py
Normal file
|
|
@ -0,0 +1,162 @@
|
|||
# Copyright (C) 2024 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 calculate cosmological redshifts from observed redshifts assuming
|
||||
the Carrick+2015 peculiar velocity model. In the future this may be extended
|
||||
to include other peculiar velocity models.
|
||||
"""
|
||||
from datetime import datetime
|
||||
from os import remove
|
||||
from os.path import join
|
||||
|
||||
import csiborgtools
|
||||
import numpy as np
|
||||
from h5py import File
|
||||
from mpi4py import MPI
|
||||
from taskmaster import work_delegation # noqa
|
||||
from tqdm import tqdm
|
||||
|
||||
SPEED_OF_LIGHT = 299792.458 # km / s
|
||||
|
||||
|
||||
def t():
|
||||
return datetime.now().strftime("%H:%M:%S")
|
||||
|
||||
|
||||
def load_calibration(catalogue, simname, nsim, ksmooth, verbose=False):
|
||||
"""Load the pre-computed calibration samples."""
|
||||
fname = f"/mnt/extraspace/rstiskalek/csiborg_postprocessing/peculiar_velocity/flow_samples_{catalogue}_{simname}_smooth_{ksmooth}.hdf5" # noqa
|
||||
keys = ["Vext_x", "Vext_y", "Vext_z", "alpha", "beta", "sigma_v"]
|
||||
|
||||
calibration_samples = {}
|
||||
with File(fname, 'r') as f:
|
||||
for key in keys:
|
||||
# NOTE: here the posterior samples are down-sampled
|
||||
calibration_samples[key] = f[f"sim_{nsim}/{key}"][:][::10]
|
||||
|
||||
if verbose:
|
||||
k = list(calibration_samples.keys())[0]
|
||||
nsamples = len(calibration_samples[k])
|
||||
print(f"{t()}: found {nsamples} calibration posterior samples.",
|
||||
flush=True)
|
||||
|
||||
return calibration_samples
|
||||
|
||||
|
||||
def main(loader, model, indxs, fdir, fname, num_split, verbose):
|
||||
out = np.full(
|
||||
len(indxs), np.nan,
|
||||
dtype=[("mean_zcosmo", float), ("std_zcosmo", float)])
|
||||
|
||||
# Process each galaxy in this split
|
||||
for i, n in enumerate(tqdm(indxs, desc=f"Split {num_split}",
|
||||
disable=not verbose)):
|
||||
x, y = model.posterior_zcosmo(
|
||||
loader.cat["zcmb"][n], loader.cat["RA"][n], loader.cat["DEC"][n],
|
||||
loader.los_density[n], loader.los_radial_velocity[n],
|
||||
extra_sigma_v=loader.cat["e_zcmb"][n] * SPEED_OF_LIGHT,
|
||||
verbose=False)
|
||||
|
||||
mu, std = model.posterior_mean_std(x, y)
|
||||
out["mean_zcosmo"][i], out["std_zcosmo"][i] = mu, std
|
||||
|
||||
# Save the results of this rank
|
||||
fname = join(fdir, f"{fname}_{num_split}.hdf5")
|
||||
with File(fname, 'w') as f:
|
||||
f.create_dataset("mean_zcosmo", data=out["mean_zcosmo"])
|
||||
f.create_dataset("std_zcosmo", data=out["std_zcosmo"])
|
||||
f.create_dataset("indxs", data=indxs)
|
||||
|
||||
|
||||
###############################################################################
|
||||
# Command line interface #
|
||||
###############################################################################
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
comm = MPI.COMM_WORLD
|
||||
rank, size = comm.Get_rank(), comm.Get_size()
|
||||
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
|
||||
|
||||
# Calibration parameters
|
||||
simname = "Carrick2015"
|
||||
ksmooth = 0
|
||||
nsim = 0
|
||||
catalogue_calibration = "Pantheon+_zSN"
|
||||
|
||||
# Galaxy sample parameters
|
||||
catalogue = "UPGLADE"
|
||||
fpath_data = "/mnt/users/rstiskalek/csiborgtools/data/upglade_z_0p05_all_PROCESSED.h5" # noqa
|
||||
|
||||
# Number of splits for MPI
|
||||
nsplits = 1000
|
||||
|
||||
# Folder to save the results
|
||||
fdir = "/mnt/extraspace/rstiskalek/csiborg_postprocessing/peculiar_velocity/UPGLADE" # noqa
|
||||
fname = f"zcosmo_{catalogue}"
|
||||
|
||||
# Load in the data, calibration samples and the model
|
||||
loader = csiborgtools.flow.DataLoader(
|
||||
simname, nsim, catalogue, fpath_data, paths, ksmooth=ksmooth,
|
||||
verbose=rank == 0)
|
||||
calibration_samples = load_calibration(
|
||||
catalogue_calibration, simname, nsim, ksmooth, verbose=rank == 0)
|
||||
model = csiborgtools.flow.Observed2CosmologicalRedshift(
|
||||
calibration_samples, loader.rdist, loader._Omega_m)
|
||||
if rank == 0:
|
||||
print(f"{t()}: the catalogue size is {loader.cat['zcmb'].size}.")
|
||||
print(f"{t()}: loaded calibration samples and model.", flush=True)
|
||||
|
||||
# Decide how to split up the job
|
||||
if rank == 0:
|
||||
indxs = np.arange(loader.cat["zcmb"].size)
|
||||
split_indxs = np.array_split(indxs, nsplits)
|
||||
else:
|
||||
indxs = None
|
||||
split_indxs = None
|
||||
indxs = comm.bcast(indxs, root=0)
|
||||
split_indxs = comm.bcast(split_indxs, root=0)
|
||||
|
||||
# Process all splits with MPI, the rank 0 delegates the jobs.
|
||||
def main_wrapper(n):
|
||||
main(loader, model, split_indxs[n], fdir, fname, n, verbose=size == 1)
|
||||
|
||||
comm.Barrier()
|
||||
work_delegation(
|
||||
main_wrapper, list(range(nsplits)), comm, master_verbose=True)
|
||||
comm.Barrier()
|
||||
|
||||
# Combine the results to a single file
|
||||
if rank == 0:
|
||||
print("Combining results from all ranks.", flush=True)
|
||||
mean_zcosmo = np.full(loader.cat["zcmb"].size, np.nan)
|
||||
std_zcosmo = np.full_like(mean_zcosmo, np.nan)
|
||||
|
||||
for n in range(nsplits):
|
||||
fname_current = join(fdir, f"{fname}_{n}.hdf5")
|
||||
with File(fname_current, 'r') as f:
|
||||
mask = f["indxs"][:]
|
||||
mean_zcosmo[mask] = f["mean_zcosmo"][:]
|
||||
std_zcosmo[mask] = f["std_zcosmo"][:]
|
||||
|
||||
remove(fname_current)
|
||||
|
||||
# Save the results
|
||||
fname = join(fdir, f"{fname}.hdf5")
|
||||
print(f"Saving results to `{fname}`.")
|
||||
with File(fname, 'w') as f:
|
||||
f.create_dataset("mean_zcosmo", data=mean_zcosmo)
|
||||
f.create_dataset("std_zcosmo", data=std_zcosmo)
|
||||
f.create_dataset("indxs", data=indxs)
|
||||
31
scripts/post_upglade.sh
Executable file
31
scripts/post_upglade.sh
Executable file
|
|
@ -0,0 +1,31 @@
|
|||
nthreads=${1}
|
||||
on_login=${2}
|
||||
memory=4
|
||||
queue="redwood"
|
||||
env="/mnt/zfsusers/rstiskalek/csiborgtools/venv_csiborg/bin/python"
|
||||
file="post_upglade.py"
|
||||
|
||||
|
||||
if [[ "$on_login" != "0" && "$on_login" != "1" ]]
|
||||
then
|
||||
echo "Error: on_login must be either 0 or 1."
|
||||
exit 1
|
||||
fi
|
||||
|
||||
if ! [[ "$nthreads" =~ ^[0-9]+$ ]] || [ "$nthreads" -le 0 ]; then
|
||||
echo "Error: nthreads must be an integer larger than 0."
|
||||
exit 1
|
||||
fi
|
||||
|
||||
|
||||
pythoncm="$env $file"
|
||||
if [ $on_login -eq 1 ]; then
|
||||
echo $pythoncm
|
||||
$pythoncm
|
||||
else
|
||||
cm="addqueue -q $queue -n $nthreads -m $memory $pythoncm"
|
||||
echo "Submitting:"
|
||||
echo $cm
|
||||
echo
|
||||
eval $cm
|
||||
fi
|
||||
199
scripts/quijote_bulkflow.py
Normal file
199
scripts/quijote_bulkflow.py
Normal file
|
|
@ -0,0 +1,199 @@
|
|||
# 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.
|
||||
"""
|
||||
A script to calculate the bulk flow in Quijote simulations from either
|
||||
particles or FoF haloes and to also save the resulting smaller halo catalogues.
|
||||
"""
|
||||
from datetime import datetime
|
||||
from os.path import join
|
||||
|
||||
import csiborgtools
|
||||
import numpy as np
|
||||
from mpi4py import MPI
|
||||
from taskmaster import work_delegation # noqa
|
||||
from warnings import catch_warnings, simplefilter
|
||||
from h5py import File
|
||||
from sklearn.neighbors import NearestNeighbors
|
||||
|
||||
|
||||
###############################################################################
|
||||
# Read in information about the simulation #
|
||||
###############################################################################
|
||||
|
||||
|
||||
def t():
|
||||
return datetime.now()
|
||||
|
||||
|
||||
def get_data(nsim, verbose=True):
|
||||
if verbose:
|
||||
print(f"{t()}: reading particles of simulation `{nsim}`.")
|
||||
reader = csiborgtools.read.QuijoteSnapshot(nsim, 4, paths)
|
||||
part_pos = reader.coordinates().astype(np.float64)
|
||||
part_vel = reader.velocities().astype(np.float64)
|
||||
|
||||
if verbose:
|
||||
print(f"{t()}: reading haloes of simulation `{nsim}`.")
|
||||
reader = csiborgtools.read.QuijoteCatalogue(nsim)
|
||||
halo_pos = reader.coordinates
|
||||
halo_vel = reader.velocities
|
||||
halo_mass = reader.totmass
|
||||
|
||||
return part_pos, part_vel, halo_pos, halo_vel, halo_mass
|
||||
|
||||
|
||||
def volume_bulk_flow(rdist, mass, vel, distances):
|
||||
out = csiborgtools.field.particles_enclosed_momentum(
|
||||
rdist, mass, vel, distances)
|
||||
with catch_warnings():
|
||||
simplefilter("ignore", category=RuntimeWarning)
|
||||
out /= csiborgtools.field.particles_enclosed_mass(
|
||||
rdist, mass, distances)[:, np.newaxis]
|
||||
|
||||
return out
|
||||
|
||||
|
||||
###############################################################################
|
||||
# Main & command line interface #
|
||||
###############################################################################
|
||||
|
||||
|
||||
def main(nsim, folder, fname_basis, Rmax, subtract_observer_velocity,
|
||||
verbose=True):
|
||||
boxsize = csiborgtools.simname2boxsize("quijote")
|
||||
observers = csiborgtools.read.fiducial_observers(boxsize, Rmax)
|
||||
distances = np.linspace(0, Rmax, 101)[1:]
|
||||
part_pos, part_vel, halo_pos, halo_vel, halo_mass = get_data(nsim, verbose)
|
||||
|
||||
if verbose:
|
||||
print(f"{t()}: Fitting the particle and halo trees of simulation `{nsim}`.") # noqa
|
||||
part_tree = NearestNeighbors().fit(part_pos)
|
||||
halo_tree = NearestNeighbors().fit(halo_pos)
|
||||
|
||||
samples = {}
|
||||
bf_volume_part = np.full((len(observers), len(distances), 3), np.nan)
|
||||
bf_volume_halo = np.full_like(bf_volume_part, np.nan)
|
||||
bf_volume_halo_uniform = np.full_like(bf_volume_part, np.nan)
|
||||
bf_vrad_weighted_part = np.full_like(bf_volume_part, np.nan)
|
||||
bf_vrad_weighted_halo_uniform = np.full_like(bf_volume_part, np.nan)
|
||||
bf_vrad_weighted_halo = np.full_like(bf_volume_part, np.nan)
|
||||
|
||||
for i in range(len(observers)):
|
||||
print(f"{t()}: Calculating bulk flow for observer {i + 1} of simulation {nsim}.") # noqa
|
||||
|
||||
# Select particles within Rmax of the observer
|
||||
rdist_part, indxs = part_tree.radius_neighbors(
|
||||
np.asarray(observers[i]).reshape(1, -1), Rmax,
|
||||
return_distance=True, sort_results=True)
|
||||
rdist_part, indxs = rdist_part[0], indxs[0]
|
||||
|
||||
part_pos_current = part_pos[indxs] - observers[i]
|
||||
part_vel_current = part_vel[indxs]
|
||||
# Quijote particle masses are all equal
|
||||
part_mass = np.ones_like(rdist_part)
|
||||
|
||||
# Select haloes within Rmax of the observer
|
||||
rdist_halo, indxs = halo_tree.radius_neighbors(
|
||||
np.asarray(observers[i]).reshape(1, -1), Rmax,
|
||||
return_distance=True, sort_results=True)
|
||||
rdist_halo, indxs = rdist_halo[0], indxs[0]
|
||||
|
||||
halo_pos_current = halo_pos[indxs] - observers[i]
|
||||
halo_vel_current = halo_vel[indxs]
|
||||
halo_mass_current = halo_mass[indxs]
|
||||
|
||||
# Subtract the observer velocity
|
||||
if subtract_observer_velocity:
|
||||
rscale = 0.5 # Mpc / h
|
||||
weights = np.exp(-0.5 * (rdist_part / rscale)**2)
|
||||
obs_vel_x = np.average(part_vel_current[:, 0], weights=weights)
|
||||
obs_vel_y = np.average(part_vel_current[:, 1], weights=weights)
|
||||
obs_vel_z = np.average(part_vel_current[:, 2], weights=weights)
|
||||
|
||||
part_vel_current[:, 0] -= obs_vel_x
|
||||
part_vel_current[:, 1] -= obs_vel_y
|
||||
part_vel_current[:, 2] -= obs_vel_z
|
||||
|
||||
halo_vel_current[:, 0] -= obs_vel_x
|
||||
halo_vel_current[:, 1] -= obs_vel_y
|
||||
halo_vel_current[:, 2] -= obs_vel_z
|
||||
|
||||
# Calculate the volume average bulk flows
|
||||
bf_volume_part[i, ...] = volume_bulk_flow(
|
||||
rdist_part, part_mass, part_vel_current, distances)
|
||||
bf_volume_halo[i, ...] = volume_bulk_flow(
|
||||
rdist_halo, halo_mass_current, halo_vel_current, distances)
|
||||
bf_volume_halo_uniform[i, ...] = volume_bulk_flow(
|
||||
rdist_halo, np.ones_like(halo_mass_current), halo_vel_current,
|
||||
distances)
|
||||
bf_vrad_weighted_part[i, ...] = csiborgtools.field.bulkflow_peery2018(
|
||||
rdist_part, part_mass, part_pos_current, part_vel_current,
|
||||
distances, weights="1/r^2", verbose=False)
|
||||
|
||||
# Calculate the bulk flow from projected velocities w. 1/r^2 weights
|
||||
bf_vrad_weighted_halo_uniform[i, ...] = csiborgtools.field.bulkflow_peery2018( # noqa
|
||||
rdist_halo, np.ones_like(halo_mass_current), halo_pos_current,
|
||||
halo_vel_current, distances, weights="1/r^2", verbose=False)
|
||||
bf_vrad_weighted_halo[i, ...] = csiborgtools.field.bulkflow_peery2018(
|
||||
rdist_halo, halo_mass_current, halo_pos_current,
|
||||
halo_vel_current, distances, weights="1/r^2", verbose=False)
|
||||
|
||||
# Store the haloes around this observer
|
||||
samples[i] = {
|
||||
"halo_pos": halo_pos_current,
|
||||
"halo_vel": halo_vel_current,
|
||||
"halo_mass": halo_mass_current}
|
||||
|
||||
# Finally save the output
|
||||
fname = join(folder, f"{fname_basis}_{nsim}.hdf5")
|
||||
if verbose:
|
||||
print(f"Saving to `{fname}`.")
|
||||
with File(fname, 'w') as f:
|
||||
f["distances"] = distances
|
||||
f["bf_volume_part"] = bf_volume_part
|
||||
f["bf_volume_halo"] = bf_volume_halo
|
||||
f["bf_vrad_weighted_part"] = bf_vrad_weighted_part
|
||||
f["bf_volume_halo_uniform"] = bf_volume_halo_uniform
|
||||
f["bf_vrad_weighted_halo_uniform"] = bf_vrad_weighted_halo_uniform
|
||||
f["bf_vrad_weighted_halo"] = bf_vrad_weighted_halo
|
||||
|
||||
for i in range(len(observers)):
|
||||
g = f.create_group(f"obs_{str(i)}")
|
||||
g["halo_pos"] = samples[i]["halo_pos"]
|
||||
g["halo_vel"] = samples[i]["halo_vel"]
|
||||
g["halo_mass"] = samples[i]["halo_mass"]
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
Rmax = 150
|
||||
subtract_observer_velocity = True
|
||||
folder = "/mnt/extraspace/rstiskalek/quijote/BulkFlow_fiducial"
|
||||
fname_basis = "sBF_nsim" if subtract_observer_velocity else "BF_nsim"
|
||||
|
||||
comm = MPI.COMM_WORLD
|
||||
rank = comm.Get_rank()
|
||||
|
||||
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
|
||||
nsims = list(paths.get_ics("quijote"))
|
||||
|
||||
def main_wrapper(nsim):
|
||||
main(nsim, folder, fname_basis, Rmax, subtract_observer_velocity,
|
||||
verbose=rank == 0)
|
||||
|
||||
if rank == 0:
|
||||
print(f"Running with {len(nsims)} Quijote simulations.")
|
||||
|
||||
comm.Barrier()
|
||||
work_delegation(main_wrapper, nsims, comm, master_verbose=True)
|
||||
19
scripts/quijote_bulkflow.sh
Executable file
19
scripts/quijote_bulkflow.sh
Executable file
|
|
@ -0,0 +1,19 @@
|
|||
nthreads=20
|
||||
memory=24
|
||||
on_login=0
|
||||
queue="berg"
|
||||
env="/mnt/zfsusers/rstiskalek/csiborgtools/venv_csiborg/bin/python"
|
||||
file="quijote_bulkflow.py"
|
||||
|
||||
|
||||
pythoncm="$env $file"
|
||||
if [ $on_login -eq 1 ]; then
|
||||
echo $pythoncm
|
||||
$pythoncm
|
||||
else
|
||||
cm="addqueue -q $queue -n $nthreads -m $memory $pythoncm"
|
||||
echo "Submitting:"
|
||||
echo $cm
|
||||
echo
|
||||
eval $cm
|
||||
fi
|
||||
|
|
@ -14,6 +14,7 @@
|
|||
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
|
||||
from os import system
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
# chains = [15717, 15817, 15917, 16017, 16117, 16217, 16317, 16417, 16517,
|
||||
# 16617, 16717, 16817, 16917, 17017, 17117, 17217, 17317, 17417]
|
||||
|
|
@ -28,12 +29,15 @@ if __name__ == "__main__":
|
|||
# simname = "csiborg2_random"
|
||||
# mode = 1
|
||||
|
||||
chains = [7444 + n * 24 for n in range(101)]
|
||||
simname = "csiborg1"
|
||||
mode = 2
|
||||
# chains = [7444 + n * 24 for n in range(101)]
|
||||
# simname = "csiborg1"
|
||||
# mode = 2
|
||||
chains = [i for i in range(41, 50 + 1)]
|
||||
simname = "quijote"
|
||||
mode = 0
|
||||
|
||||
env = "/mnt/zfsusers/rstiskalek/csiborgtools/venv_csiborg/bin/python"
|
||||
memory = 64
|
||||
memory = 32
|
||||
|
||||
for chain in chains:
|
||||
out = f"output_{simname}_{chain}_%j.out"
|
||||
|
|
|
|||
Loading…
Reference in a new issue