Simple toy model

This run generates an artificial (i.e.) unphysical set of halos and evolves them following perfect exponential growth. The distribution of halos is used to paint a grid and compute the corresponding signal and their evolution over a few redshift snapshots. The remaining parameters are unphysical as well and chosen for illustration purposes.

NOTE:

• running this notebook will store output files in the current working directory:

• cache files (intermediate computations) are stored under ./cache

• final files (the resulting grid data) are stored under ./output

Make sure to change these paths below.

import numpy as np
from pathlib import Path
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec
%matplotlib inline

import logging
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger(__name__)

# Change the output of the computatiojs
FILE_ROOT = Path(".")
CACHE_ROOT = FILE_ROOT / "cache"
OUTPUT_ROOT = FILE_ROOT / "output"

import beorn

parameters = beorn.structs.Parameters()

# Halo Mass bins
parameters.simulation.halo_mass_bin_min = 1e7
parameters.simulation.halo_mass_bin_max = 1e15
parameters.simulation.halo_mass_bin_n = 200

parameters.simulation.Lbox = 100
parameters.simulation.Ncell = 128

# Nbr of cores to use
parameters.simulation.cores = 5


# cosmo
parameters.cosmology.Om = 0.31
parameters.cosmology.Ob = 0.045
parameters.cosmology.Ol = 0.69
parameters.cosmology.h = 0.68

# Source parameters
# lyman-alpha
parameters.simulation.halo_mass_accretion_alpha = np.array([0.785, 0.795])
parameters.source.n_lyman_alpha_photons = 9690*10  # 1500
parameters.source.lyman_alpha_power_law = 0.0
# ion
parameters.source.Nion = 5000 * 3
# xray
parameters.source.energy_cutoff_min_xray = 500
parameters.source.energy_cutoff_max_xray = 2000
parameters.source.energy_min_sed_xray = 500
parameters.source.energy_max_sed_xray = 2000
parameters.source.alS_xray = 1.5
parameters.source.xray_normalisation = 3.4e40 * 3

# fesc
parameters.source.f0_esc = 0.2
parameters.source.pl_esc = 0

# fstar
parameters.source.f_st = 1
parameters.source.g1 = 0
parameters.source.g2 = 0

parameters.source.g3 = 4
parameters.source.g4 = -1
parameters.source.Mp = 1.6e11 * parameters.cosmology.h
parameters.source.Mt = 1e7

# Minimum star forming halo
parameters.source.halo_mass_min = 1e5


parameters.simulation.store_grids = ['Tk','bubbles','lyal', 'Grid_dTb']

cache_handler = beorn.io.Handler(CACHE_ROOT)
loader = beorn.load_input_data.ArtificialHaloLoader(
    parameters,
    halo_count = 100,
)

17:44:43 - INFO - handler.py - Using persistence directory at .plotting and kwargs None

try:
    profiles = cache_handler.load_file(parameters, beorn.structs.RadiationProfiles)
except FileNotFoundError:
    s = beorn.radiation_profiles.ProfileSolver(parameters, cache_handler, loader.redshifts)
    profiles = s.solve()

    # since we want to skip recalculating the profiles, we save them
    cache_handler.write_file(parameters, profiles)

17:44:43 - INFO - solver.py - param.solver.fXh is set to constant. We will assume f_X,h = 2e-4**0.225
17:44:43 - INFO - solver.py - Computing profiles for 38 redshifts, 199 halo mass bins and 1 alpha bins.
17:44:49 - WARNING - base_struct.py - Field Tk not found in RadiationProfiles. It will not be written to the HDF5 file.
17:44:49 - WARNING - base_struct.py - Field bubbles not found in RadiationProfiles. It will not be written to the HDF5 file.
17:44:49 - WARNING - base_struct.py - Field lyal not found in RadiationProfiles. It will not be written to the HDF5 file.
17:44:49 - WARNING - base_struct.py - Field Grid_dTb not found in RadiationProfiles. It will not be written to the HDF5 file.
17:44:49 - INFO - base_struct.py - Data written to .plotting/RadiationProfiles_db7a2ba19daaf0b9cb026ba418579de5_.h5 (80.98 MB)

halo_catalog = loader.load_halo_catalog(9)

mesh = halo_catalog.to_mesh()
stacked_mesh = np.sum(mesh, axis=0)

plt.figure()
plt.imshow(stacked_mesh, origin='lower', cmap='viridis')
plt.show()

17:44:49 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.

output_handler = beorn.io.Handler(OUTPUT_ROOT)

p = beorn.painting.Painter(
    parameters,
    loader = loader,
    cache_handler = cache_handler,
    output_handler = output_handler
)

multi_z_quantities = p.paint_full(profiles)

17:44:49 - INFO - handler.py - Using persistence directory at .plotting/output and kwargs None
17:44:49 - INFO - painter.py - Painting profiles onto grid for 38 redshift snapshots. Using 5 processes.

17:44:49 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:44:49 - INFO - painter.py - Painting 100 halos at zgrid=24.50 (z_index=0).
17:44:52 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:44:52 - INFO - painter.py - Profile painting took 0:00:02.621396.
17:44:52 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.0.
17:44:52 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:00.149064.
17:44:52 - INFO - painter.py - Postprocessing of the grids took 0:00:00.092145.
17:44:52 - INFO - painter.py - Current snapshot took 0:00:02.873108.
17:44:52 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:44:52 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:44:52 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:44:53 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=0.h5 (80.02 MB)
17:44:53 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:44:53 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:44:53 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:44:53 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:44:53 - INFO - painter.py - Painting 100 halos at zgrid=24.00 (z_index=1).
17:44:55 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:44:55 - INFO - painter.py - Profile painting took 0:00:02.619044.
17:44:56 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.0.
17:44:56 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:00.167218.
17:44:56 - INFO - painter.py - Postprocessing of the grids took 0:00:00.091559.
17:44:56 - INFO - painter.py - Current snapshot took 0:00:02.885424.
17:44:56 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:44:56 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:44:56 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:44:56 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=1.h5 (80.02 MB)
17:44:56 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:44:56 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:44:56 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:44:57 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:44:57 - INFO - painter.py - Painting 100 halos at zgrid=23.50 (z_index=2).
17:44:59 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:44:59 - INFO - painter.py - Profile painting took 0:00:02.546494.
17:44:59 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.0.
17:44:59 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:00.149441.
17:44:59 - INFO - painter.py - Postprocessing of the grids took 0:00:00.091451.
17:44:59 - INFO - painter.py - Current snapshot took 0:00:02.794777.
17:44:59 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:44:59 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:44:59 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:45:00 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=2.h5 (80.02 MB)
17:45:00 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:45:00 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:45:00 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:45:00 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:45:00 - INFO - painter.py - Painting 100 halos at zgrid=23.00 (z_index=3).
17:45:03 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:45:03 - INFO - painter.py - Profile painting took 0:00:02.556822.
17:45:03 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.0.
17:45:03 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:00.151746.
17:45:03 - INFO - painter.py - Postprocessing of the grids took 0:00:00.094143.
17:45:03 - INFO - painter.py - Current snapshot took 0:00:02.810905.
17:45:03 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:45:03 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:45:03 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:45:04 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=3.h5 (80.02 MB)
17:45:04 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:45:04 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:45:04 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:45:04 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:45:04 - INFO - painter.py - Painting 100 halos at zgrid=22.50 (z_index=4).
17:45:07 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:45:07 - INFO - painter.py - Profile painting took 0:00:02.709349.
17:45:07 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.0.
17:45:07 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:00.211461.
17:45:07 - INFO - painter.py - Postprocessing of the grids took 0:00:00.107734.
17:45:07 - INFO - painter.py - Current snapshot took 0:00:03.037188.
17:45:07 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:45:07 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:45:07 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:45:08 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=4.h5 (80.02 MB)
17:45:08 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:45:08 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:45:08 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:45:08 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:45:08 - INFO - painter.py - Painting 100 halos at zgrid=22.00 (z_index=5).
17:45:11 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:45:11 - INFO - painter.py - Profile painting took 0:00:02.989268.
17:45:11 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.0.
17:45:11 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:00.198648.
17:45:11 - INFO - painter.py - Postprocessing of the grids took 0:00:00.113694.
17:45:12 - INFO - painter.py - Current snapshot took 0:00:03.310685.
17:45:12 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:45:12 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:45:12 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:45:12 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=5.h5 (80.02 MB)
17:45:12 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:45:12 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:45:12 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:45:13 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:45:13 - INFO - painter.py - Painting 100 halos at zgrid=21.50 (z_index=6).
17:45:15 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:45:15 - INFO - painter.py - Profile painting took 0:00:02.725827.
17:45:15 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.0.
17:45:15 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:00.150039.
17:45:16 - INFO - painter.py - Postprocessing of the grids took 0:00:00.093026.
17:45:16 - INFO - painter.py - Current snapshot took 0:00:02.977129.
17:45:16 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:45:16 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:45:16 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:45:16 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=6.h5 (80.02 MB)
17:45:16 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:45:16 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:45:16 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:45:16 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:45:16 - INFO - painter.py - Painting 100 halos at zgrid=21.00 (z_index=7).
17:45:19 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:45:19 - INFO - painter.py - Profile painting took 0:00:02.947038.
17:45:20 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.0.
17:45:20 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:00.185234.
17:45:20 - INFO - painter.py - Postprocessing of the grids took 0:00:00.101561.
17:45:20 - INFO - painter.py - Current snapshot took 0:00:03.242813.
17:45:20 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:45:20 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:45:20 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:45:21 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=7.h5 (80.02 MB)
17:45:21 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:45:21 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:45:21 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:45:21 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:45:21 - INFO - painter.py - Painting 100 halos at zgrid=20.50 (z_index=8).
17:45:24 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:45:24 - INFO - painter.py - Profile painting took 0:00:03.114474.
17:45:24 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.0.
17:45:24 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:00.155210.
17:45:24 - INFO - painter.py - Postprocessing of the grids took 0:00:00.094838.
17:45:24 - INFO - painter.py - Current snapshot took 0:00:03.373085.
17:45:24 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:45:24 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:45:24 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:45:25 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=8.h5 (80.02 MB)
17:45:25 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:45:25 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:45:25 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:45:25 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:45:25 - INFO - painter.py - Painting 100 halos at zgrid=20.00 (z_index=9).
17:45:28 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:45:28 - INFO - painter.py - Profile painting took 0:00:02.792052.
17:45:28 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.0.
17:45:28 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:00.153152.
17:45:28 - INFO - painter.py - Postprocessing of the grids took 0:00:00.092770.
17:45:28 - INFO - painter.py - Current snapshot took 0:00:03.047881.
17:45:28 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:45:28 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:45:28 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:45:29 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=9.h5 (80.02 MB)
17:45:29 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:45:29 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:45:29 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:45:29 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:45:29 - INFO - painter.py - Painting 100 halos at zgrid=19.50 (z_index=10).
17:45:32 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:45:32 - INFO - painter.py - Profile painting took 0:00:02.722835.
17:45:32 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.0.
17:45:32 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:00.171027.
17:45:32 - INFO - painter.py - Postprocessing of the grids took 0:00:00.130702.
17:45:32 - INFO - painter.py - Current snapshot took 0:00:03.035465.
17:45:32 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:45:32 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:45:32 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:45:33 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=10.h5 (80.02 MB)
17:45:33 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:45:33 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:45:33 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:45:33 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:45:33 - INFO - painter.py - Painting 100 halos at zgrid=19.00 (z_index=11).
17:45:36 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:45:36 - INFO - painter.py - Profile painting took 0:00:02.929493.
17:45:36 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.0001.
17:45:37 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:01.317198.
17:45:37 - INFO - painter.py - Postprocessing of the grids took 0:00:00.094228.
17:45:37 - INFO - painter.py - Current snapshot took 0:00:04.350272.
17:45:37 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:45:37 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:45:37 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:45:38 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=11.h5 (80.02 MB)
17:45:38 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:45:38 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:45:38 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:45:38 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:45:38 - INFO - painter.py - Painting 100 halos at zgrid=18.50 (z_index=12).
17:45:41 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:45:41 - INFO - painter.py - Profile painting took 0:00:03.028838.
17:45:41 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.0001.
17:45:43 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:01.296057.
17:45:43 - INFO - painter.py - Postprocessing of the grids took 0:00:00.095458.
17:45:43 - INFO - painter.py - Current snapshot took 0:00:04.429410.
17:45:43 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:45:43 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:45:43 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:45:44 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=12.h5 (80.02 MB)
17:45:44 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:45:44 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:45:44 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:45:44 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:45:44 - INFO - painter.py - Painting 100 halos at zgrid=18.00 (z_index=13).
17:45:47 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:45:48 - INFO - painter.py - Profile painting took 0:00:03.789968.
17:45:48 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.0002.
17:45:48 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:00.164567.
17:45:48 - INFO - painter.py - Postprocessing of the grids took 0:00:00.150793.
17:45:48 - INFO - painter.py - Current snapshot took 0:00:04.114117.
17:45:48 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:45:48 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:45:48 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:45:49 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=13.h5 (80.02 MB)
17:45:49 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:45:49 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:45:49 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:45:49 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:45:49 - INFO - painter.py - Painting 100 halos at zgrid=17.50 (z_index=14).
17:45:52 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:45:53 - INFO - painter.py - Profile painting took 0:00:03.793716.
17:45:53 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.0003.
17:45:53 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:00.393661.
17:45:53 - INFO - painter.py - Postprocessing of the grids took 0:00:00.130712.
17:45:53 - INFO - painter.py - Current snapshot took 0:00:04.328410.
17:45:53 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:45:53 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:45:53 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:45:54 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=14.h5 (80.02 MB)
17:45:54 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:45:54 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:45:54 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:45:54 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:45:54 - INFO - painter.py - Painting 100 halos at zgrid=17.00 (z_index=15).
17:45:58 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:45:58 - INFO - painter.py - Profile painting took 0:00:03.720108.
17:45:58 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.0004.
17:45:59 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:01.380507.
17:45:59 - INFO - painter.py - Postprocessing of the grids took 0:00:00.139338.
17:45:59 - INFO - painter.py - Current snapshot took 0:00:05.248452.
17:45:59 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:45:59 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:45:59 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:46:00 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=15.h5 (80.02 MB)
17:46:00 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:46:00 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:46:00 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:46:00 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:46:00 - INFO - painter.py - Painting 100 halos at zgrid=16.50 (z_index=16).
17:46:04 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:46:04 - INFO - painter.py - Profile painting took 0:00:03.695125.
17:46:04 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.0006.
17:46:05 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:01.384303.
17:46:05 - INFO - painter.py - Postprocessing of the grids took 0:00:00.151858.
17:46:05 - INFO - painter.py - Current snapshot took 0:00:05.240312.
17:46:05 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:46:05 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:46:05 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:46:06 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=16.h5 (80.02 MB)
17:46:06 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:46:06 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:46:06 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:46:06 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:46:06 - INFO - painter.py - Painting 100 halos at zgrid=16.00 (z_index=17).
17:46:10 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:46:10 - INFO - painter.py - Profile painting took 0:00:03.427137.
17:46:10 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.001.
17:46:10 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:00.195154.
17:46:10 - INFO - painter.py - Postprocessing of the grids took 0:00:00.128926.
17:46:10 - INFO - painter.py - Current snapshot took 0:00:03.759521.
17:46:10 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:46:10 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:46:10 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:46:11 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=17.h5 (80.02 MB)
17:46:11 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:46:11 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:46:11 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:46:11 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:46:11 - INFO - painter.py - Painting 100 halos at zgrid=15.50 (z_index=18).
17:46:15 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:46:15 - INFO - painter.py - Profile painting took 0:00:03.929310.
17:46:15 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.0014.
17:46:15 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:00.199903.
17:46:15 - INFO - painter.py - Postprocessing of the grids took 0:00:00.129144.
17:46:15 - INFO - painter.py - Current snapshot took 0:00:04.266155.
17:46:15 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:46:15 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:46:15 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:46:16 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=18.h5 (80.02 MB)
17:46:16 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:46:16 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:46:16 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:46:16 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:46:16 - INFO - painter.py - Painting 100 halos at zgrid=15.00 (z_index=19).
17:46:20 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:46:20 - INFO - painter.py - Profile painting took 0:00:03.741651.
17:46:20 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.0023.
17:46:20 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:00.193064.
17:46:20 - INFO - painter.py - Postprocessing of the grids took 0:00:00.128156.
17:46:20 - INFO - painter.py - Current snapshot took 0:00:04.070485.
17:46:20 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:46:20 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:46:20 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:46:21 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=19.h5 (80.02 MB)
17:46:21 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:46:21 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:46:21 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:46:21 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:46:21 - INFO - painter.py - Painting 100 halos at zgrid=14.50 (z_index=20).
17:46:25 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:46:25 - INFO - painter.py - Profile painting took 0:00:03.703592.
17:46:25 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.0032.
17:46:27 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:02.092572.
17:46:27 - INFO - painter.py - Postprocessing of the grids took 0:00:00.128018.
17:46:27 - INFO - painter.py - Current snapshot took 0:00:05.932910.
17:46:27 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:46:27 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:46:27 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:46:28 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=20.h5 (80.02 MB)
17:46:28 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:46:28 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:46:28 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:46:28 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:46:28 - INFO - painter.py - Painting 100 halos at zgrid=14.00 (z_index=21).
17:46:32 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:46:32 - INFO - painter.py - Profile painting took 0:00:03.645973.
17:46:32 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.0044.
17:46:35 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:03.075817.
17:46:35 - INFO - painter.py - Postprocessing of the grids took 0:00:00.128815.
17:46:35 - INFO - painter.py - Current snapshot took 0:00:06.860382.
17:46:35 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:46:35 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:46:35 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:46:36 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=21.h5 (80.02 MB)
17:46:36 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:46:36 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:46:36 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:46:36 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:46:36 - INFO - painter.py - Painting 100 halos at zgrid=13.50 (z_index=22).
17:46:40 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:46:40 - INFO - painter.py - Profile painting took 0:00:03.746450.
17:46:40 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.0073.
17:46:42 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:02.194220.
17:46:42 - INFO - painter.py - Postprocessing of the grids took 0:00:00.126613.
17:46:42 - INFO - painter.py - Current snapshot took 0:00:06.075639.
17:46:42 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:46:42 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:46:42 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:46:43 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=22.h5 (80.02 MB)
17:46:43 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:46:43 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:46:43 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:46:43 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:46:43 - INFO - painter.py - Painting 100 halos at zgrid=13.00 (z_index=23).
17:46:47 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:46:47 - INFO - painter.py - Profile painting took 0:00:03.680354.
17:46:47 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.0101.
17:46:50 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:03.208861.
17:46:50 - INFO - painter.py - Postprocessing of the grids took 0:00:00.132745.
17:46:50 - INFO - painter.py - Current snapshot took 0:00:07.030831.
17:46:50 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:46:50 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:46:50 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:46:51 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=23.h5 (80.02 MB)
17:46:51 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:46:51 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:46:51 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:46:51 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:46:51 - INFO - painter.py - Painting 100 halos at zgrid=12.50 (z_index=24).
17:46:55 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:46:55 - INFO - painter.py - Profile painting took 0:00:03.735740.
17:46:55 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.0166.
17:46:57 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:02.240705.
17:46:57 - INFO - painter.py - Postprocessing of the grids took 0:00:00.125489.
17:46:57 - INFO - painter.py - Current snapshot took 0:00:06.115974.
17:46:57 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:46:57 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:46:57 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:46:58 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=24.h5 (80.02 MB)
17:46:58 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:46:58 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:46:58 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:46:58 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:46:58 - INFO - painter.py - Painting 100 halos at zgrid=12.00 (z_index=25).
17:47:02 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:47:02 - INFO - painter.py - Profile painting took 0:00:03.588076.
17:47:02 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.0232.
17:47:05 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:03.383949.
17:47:05 - INFO - painter.py - Postprocessing of the grids took 0:00:00.128451.
17:47:05 - INFO - painter.py - Current snapshot took 0:00:07.111845.
17:47:05 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:47:05 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:47:05 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:47:06 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=25.h5 (80.02 MB)
17:47:06 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:47:06 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:47:06 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:47:06 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:47:06 - INFO - painter.py - Painting 100 halos at zgrid=11.50 (z_index=26).
17:47:10 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:47:10 - INFO - painter.py - Profile painting took 0:00:03.595604.
17:47:10 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.0381.
17:47:14 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:03.761156.
17:47:14 - INFO - painter.py - Postprocessing of the grids took 0:00:00.132746.
17:47:14 - INFO - painter.py - Current snapshot took 0:00:07.497632.
17:47:14 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:47:14 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:47:14 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:47:14 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=26.h5 (80.02 MB)
17:47:14 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:47:14 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:47:14 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:47:15 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:47:15 - INFO - painter.py - Painting 100 halos at zgrid=11.00 (z_index=27).
17:47:18 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:47:19 - INFO - painter.py - Profile painting took 0:00:03.934346.
17:47:19 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.0531.
17:47:21 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:02.919672.
17:47:22 - INFO - painter.py - Postprocessing of the grids took 0:00:00.128355.
17:47:22 - INFO - painter.py - Current snapshot took 0:00:06.991058.
17:47:22 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:47:22 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:47:22 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:47:22 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=27.h5 (80.02 MB)
17:47:22 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:47:22 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:47:22 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:47:23 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:47:23 - INFO - painter.py - Painting 100 halos at zgrid=10.50 (z_index=28).
17:47:26 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:47:26 - INFO - painter.py - Profile painting took 0:00:03.629965.
17:47:26 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.0874.
17:47:31 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:04.476950.
17:47:31 - INFO - painter.py - Postprocessing of the grids took 0:00:00.130495.
17:47:31 - INFO - painter.py - Current snapshot took 0:00:08.246552.
17:47:31 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:47:31 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:47:31 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:47:32 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=28.h5 (80.02 MB)
17:47:32 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:47:32 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:47:32 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:47:32 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:47:32 - INFO - painter.py - Painting 100 halos at zgrid=10.00 (z_index=29).
17:47:35 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:47:35 - INFO - painter.py - Profile painting took 0:00:03.799711.
17:47:36 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.1218.
17:47:42 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:06.545997.
17:47:42 - INFO - painter.py - Postprocessing of the grids took 0:00:00.143571.
17:47:42 - INFO - painter.py - Current snapshot took 0:00:10.499135.
17:47:42 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:47:42 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:47:42 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:47:43 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=29.h5 (80.02 MB)
17:47:43 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:47:43 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:47:43 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:47:43 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:47:43 - INFO - painter.py - Painting 100 halos at zgrid=9.50 (z_index=30).
17:47:47 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:47:47 - INFO - painter.py - Profile painting took 0:00:03.487577.
17:47:47 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.1697.
17:47:56 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:08.868893.
17:47:56 - INFO - painter.py - Postprocessing of the grids took 0:00:00.136416.
17:47:56 - INFO - painter.py - Current snapshot took 0:00:12.502402.
17:47:56 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:47:56 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:47:56 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:47:56 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=30.h5 (80.02 MB)
17:47:56 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:47:56 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:47:56 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:47:57 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:47:57 - INFO - painter.py - Painting 100 halos at zgrid=9.00 (z_index=31).
17:48:00 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:48:00 - INFO - painter.py - Profile painting took 0:00:03.555975.
17:48:01 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.2791.
17:48:16 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:15.776641.
17:48:16 - INFO - painter.py - Postprocessing of the grids took 0:00:00.134669.
17:48:16 - INFO - painter.py - Current snapshot took 0:00:19.478287.
17:48:16 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:48:16 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:48:16 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:48:17 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=31.h5 (80.02 MB)
17:48:17 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:48:17 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:48:17 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:48:17 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:48:17 - INFO - painter.py - Painting 100 halos at zgrid=8.50 (z_index=32).
17:48:21 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:48:21 - INFO - painter.py - Profile painting took 0:00:03.583298.
17:48:21 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.3889.
17:48:33 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:12.641136.
17:48:33 - INFO - painter.py - Postprocessing of the grids took 0:00:00.149429.
17:48:33 - INFO - painter.py - Current snapshot took 0:00:16.383140.
17:48:33 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:48:33 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:48:33 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:48:34 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=32.h5 (80.02 MB)
17:48:34 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:48:34 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:48:34 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:48:34 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:48:34 - INFO - painter.py - Painting 100 halos at zgrid=8.00 (z_index=33).
17:48:38 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:48:38 - INFO - painter.py - Profile painting took 0:00:03.715269.
17:48:39 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.6397.
17:48:42 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:03.470978.
17:48:42 - INFO - painter.py - Postprocessing of the grids took 0:00:00.139976.
17:48:42 - INFO - painter.py - Current snapshot took 0:00:07.338906.
17:48:42 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:48:42 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:48:42 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:48:43 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=33.h5 (80.02 MB)
17:48:43 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:48:43 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:48:43 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:48:43 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:48:43 - INFO - painter.py - Painting 100 halos at zgrid=7.50 (z_index=34).
17:48:46 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:48:46 - INFO - painter.py - Profile painting took 0:00:03.414091.
17:48:46 - INFO - spread_old.py - Universe not fully ionized : xHII is 0.8913.
17:48:51 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:04.825353.
17:48:51 - INFO - painter.py - Postprocessing of the grids took 0:00:00.144148.
17:48:51 - INFO - painter.py - Current snapshot took 0:00:08.392919.
17:48:51 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:48:51 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:48:51 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:48:52 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=34.h5 (80.02 MB)
17:48:52 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:48:52 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:48:52 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:48:52 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:48:52 - INFO - painter.py - Painting 100 halos at zgrid=7.00 (z_index=35).
17:48:55 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:48:56 - INFO - painter.py - Profile painting took 0:00:03.514022.
17:48:56 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:00.422761.
17:48:56 - INFO - painter.py - Postprocessing of the grids took 0:00:00.062578.
17:48:56 - INFO - painter.py - Current snapshot took 0:00:04.008426.
17:48:56 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:48:56 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:48:56 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:48:57 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=35.h5 (64.02 MB)
17:48:57 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:48:57 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:48:57 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:50:21 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:50:21 - INFO - painter.py - Painting 100 halos at zgrid=6.50 (z_index=36).
17:50:24 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:50:24 - INFO - painter.py - Profile painting took 0:00:03.530383.
17:50:25 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:00.518745.
17:50:25 - INFO - painter.py - Postprocessing of the grids took 0:00:00.062307.
17:50:25 - INFO - painter.py - Current snapshot took 0:00:04.120498.
17:50:25 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:50:25 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:50:25 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:50:26 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=36.h5 (64.02 MB)
17:50:26 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:50:26 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:50:26 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:51:49 - INFO - halo_catalog.py - No alpha values provided, using default value of 0.79 for all halos.
17:51:49 - INFO - painter.py - Painting 100 halos at zgrid=6.00 (z_index=37).
17:51:53 - INFO - painter.py - painted total_halos=100 with initially halo_catalog.size=100 halos.
17:51:53 - INFO - painter.py - Profile painting took 0:00:03.567008.
17:51:54 - INFO - painter.py - Redistributing excess photons from the overlapping regions took 0:00:00.526156.
17:51:54 - INFO - painter.py - Postprocessing of the grids took 0:00:00.062740.
17:51:54 - INFO - painter.py - Current snapshot took 0:00:04.164299.
17:51:54 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:51:54 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:51:54 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:51:54 - INFO - base_struct.py - Data written to .plotting/GridData_db7a2ba19daaf0b9cb026ba418579de5_z_index=37.h5 (64.02 MB)
17:51:54 - WARNING - base_struct.py - Field Tk not found in GridData. It will not be written to the HDF5 file.
17:51:54 - WARNING - base_struct.py - Field bubbles not found in GridData. It will not be written to the HDF5 file.
17:51:54 - WARNING - base_struct.py - Field lyal not found in GridData. It will not be written to the HDF5 file.
17:53:18 - INFO - painter.py - Painting of 38 snapshots done.
Did not find field file_root in group simulation.

z = 9
z_index = np.argmin(np.abs(loader.redshifts - z))

xHII_grid = multi_z_quantities.Grid_xHII[z_index, ...]
plt.figure()
plt.imshow(xHII_grid[:, 64, :], origin='lower', cmap='viridis')
plt.show()

dTb_grid = multi_z_quantities.Grid_dTb[z_index, ...]
plt.figure()
plt.imshow(dTb_grid[:, 64, :], origin='lower', cmap='viridis')
plt.show()

# Set up the figure and axes
fig = plt.figure(constrained_layout=True)
fig.set_figwidth(18)
fig.set_figheight(6)
gs = gridspec.GridSpec(2, 3, figure=fig)
ax1 = fig.add_subplot(gs[:,0])
ax2 = fig.add_subplot(gs[0,1])
ax3 = fig.add_subplot(gs[1,1], sharex=ax2)
ax4 = fig.add_subplot(gs[:,2])

# Plot for each grid data that is available

beorn.plotting.draw_dTb_signal(ax1, multi_z_quantities)
beorn.plotting.draw_Temp_signal(ax2, multi_z_quantities)
beorn.plotting.draw_xHII_signal(ax3, multi_z_quantities)
beorn.plotting.draw_dTb_power_spectrum_of_z(ax4, multi_z_quantities, parameters)

ax4.legend(loc='best')
ax2.axes.get_xaxis().set_visible(False)
plt.show()

lightcone = beorn.structs.Lightcone.build(
    parameters,
    multi_z_quantities,
    quantity = "Grid_dTb",
)

fig, ax = plt.subplots()
fig.set_figwidth(18)
fig.set_figheight(6)
beorn.plotting.plot_lightcone(lightcone, ax, "", slice_number=80)
fig.show()

Making lightcone between 0.039216 < z < 0.142703

100%|██████████| 547/547 [00:00<00:00, 766.91it/s]

...done