def produce_perturb_field_data(redshift, **kwargs):
options = get_all_options(redshift, **kwargs)
options_ics = get_all_options_ics(**kwargs)
out = {
key: kwargs[key]
for key in kwargs
if key.upper() in (k.upper() for k in global_params.keys())
}
velocity_normalisation = 1e16
with config.use(regenerate=True, write=False):
init_box = initial_conditions(**options_ics)
pt_box = perturb_field(redshift=redshift, init_boxes=init_box, **out)
p_dens, k_dens = get_power(
pt_box.density,
boxlength=options["user_params"]["BOX_LEN"],
)
p_vel, k_vel = get_power(
pt_box.velocity * velocity_normalisation,
boxlength=options["user_params"]["BOX_LEN"],
)
def hist(kind, xmin, xmax, nbins):
data = getattr(pt_box, kind)
if kind == "velocity":
data = velocity_normalisation * data
bins, edges = np.histogram(
data,
bins=np.linspace(xmin, xmax, nbins),
range=[xmin, xmax],
density=True,
)
left, right = edges[:-1], edges[1:]
X = np.array([left, right]).T.flatten()
Y = np.array([bins, bins]).T.flatten()
return X, Y
X_dens, Y_dens = hist("density", -0.8, 2.0, 50)
X_vel, Y_vel = hist("velocity", -2, 2, 50)
return k_dens, p_dens, k_vel, p_vel, X_dens, Y_dens, X_vel, Y_vel, init_box
def test_first_box(default_user_params):
"""Tests whether the first_box idea works for spin_temp.
This test was breaking before we set the z_heat_max box to actually get
the correct dimensions (before it was treated as a dummy).
"""
initial_conditions = p21c.initial_conditions(
user_params=default_user_params.clone(
HII_DIM=default_user_params.HII_DIM + 1),
random_seed=1,
)
perturbed_field = p21c.perturb_field(redshift=29.0,
init_boxes=initial_conditions)
spin_temp = p21c.spin_temperature(perturbed_field=perturbed_field,
z_heat_max=30.0)
assert spin_temp.redshift == 29.0
zeta = 39.204 #65.204
Rmfp = 12.861 #11.861
Tvir = 4.539 #4.539
params = {'HII_DIM': 128, 'DIM': 384, 'BOX_LEN': 256}
my_ext = [0, params['BOX_LEN'], 0, params['BOX_LEN']]
c_params = {'OMm': 0.27, 'OMb': 0.046, 'SIGMA_8': 0.82, 'POWER_INDEX': 0.96}
a_params = {'HII_EFF_FACTOR': zeta, 'R_BUBBLE_MAX': Rmfp, 'ION_Tvir_MIN': Tvir}
# late, middle and early stage of reionization
bins = np.array([[0.18, 0.22], [0.48, 0.52], [0.78, 0.82]])
compare_tobs_mean = np.zeros((bins.shape[0], tobs.size))
compare_tobs_std = np.zeros((bins.shape[0], tobs.size))
ic = p21c.initial_conditions(user_params=params,
cosmo_params=c_params,
random_seed=2021)
compare_tobs = np.zeros((redshift.size, tobs.size))
for i in tqdm(range(len(redshift))):
z = redshift[i]
cube = p21c.run_coeval(redshift=z,
init_box=ic,
astro_params=a_params,
zprime_step_factor=1.05)
dT = cube.brightness_temp
xH = cube.xH_box
uv = uvs['%.3f' % z]
eff_fact = random.gauss(52.5, 20.) # eff_fact = [5, 100]
Rmfp = random.gauss(12.5, 5.) # Rmfp = [5, 20]
Tvir = random.gauss(4.65, 0.5) # Tvir = [log10(1e4), log10(2e5)]
# Define astronomical parameters
a_params = {'HII_EFF_FACTOR':eff_fact, 'R_BUBBLE_MAX':Rmfp, 'ION_Tvir_MIN':Tvir}
# Create 21cmFast cube
if(i%1 == 0):
try:
os.system('rm %s*h5' %path_chache)
except:
pass
comm.Barrier()
ic = p21.initial_conditions(user_params=params, cosmo_params=c_params, random_seed=GenerateSeed())
cube = p21.run_coeval(redshift=z, init_box=ic, astro_params=a_params, zprime_step_factor=1.05)
# Mean neutral fraction
xn = np.mean(cube.xH_box)
if(xn > 0.1 and xn <= 0.8):
print('processor: %d/%d idx=%d\n z=%.3f, xn=%.3f, eff_fact=%.3f, Rmfp=%.3f, Tvir=%.3f' %(rank, nprocs, i, z, xn, eff_fact, Rmfp, Tvir))
"""
dT = cube.brightness_temp
dT1 = t2c.subtract_mean_signal(signal=dT, los_axis=2)
# calculate uv-coverage
file_uv, file_Nant = 'uv_coverage_%d/uvmap_z%.3f.npy' %(params['HII_DIM'], z), 'uv_coverage_%d/Nantmap_z%.3f.npy' %(params['HII_DIM'], z)
"===================== Begin Trace (TOTAL MEM={:1.4e} MB... [{:+1.4e} MB]):"
.format(thismem, diff))
top_stats = snapshot2.compare_to(snapshot, "lineno", cumulative=True)
for stat in top_stats[:4]:
print(stat)
print("End Trace ===========================================")
oldmem = thismem
snapshot = snapshot2
NITER = 50
init = initial_conditions(user_params={
"HII_DIM": 50,
"BOX_LEN": 125.0
},
regenerate=True)
perturb = (
perturb_field(redshift=7, init_boxes=init),
perturb_field(redshift=8, init_boxes=init),
perturb_field(redshift=9, init_boxes=init),
)
astro_params = {"HII_EFF_FACTOR": np.random.normal(30, 0.1)}
for i in range(NITER):
trace_print()
coeval = run_coeval(
redshift=[7, 8, 9],
ALPHA_ESC=-0.5,
ALPHA_STAR=0.5,
F_ESC10=-1.30102999566,
F_STAR10=-1.0,
L_X=40.5,
M_TURN=8.7,
NU_X_THRESH=500.0,
X_RAY_SPEC_INDEX=1.0,
t_STAR=0.5,
R_BUBBLE_MAX=15.0,
)
init_box = initial_conditions(
user_params=user_params,
cosmo_params=cosmo_params,
random_seed=random_seed,
regenerate=True,
write=False,
)
redshift = 9.0
pt_box = perturb_field(
redshift=redshift,
init_boxes=init_box,
user_params=user_params,
cosmo_params=cosmo_params,
)
halos = determine_halo_list(
redshift=redshift,