def mNuICs(nreal, sim='paco', overwrite=False, verbose=False):
''' Read in initial condition of Paco's simulations. According to
Paco, each of the realizations (regardless of neutrino mass) should
have the same initial conditions.
parameters
----------
nreal : int,
realization number
sim : str
option kwarg to specify which simulation. At this moment
this doesn't really do much since we only have paco's
simulatin
'''
if sim not in ['paco']: raise NotImplementedError('%s simulation not supported yet')
ics_dir = ''.join([UT.hades_dir(), 'ics/'])
f = ''.join([ics_dir, 'ics.', str(nreal), '.hdf5']) # snapshot
particle_data = {}
if os.path.isfile(f) and not overwrite: # read in the file
f_ics = h5py.File(f, 'r') # read in hdf5 file
particle_data['meta'] = {}
for k in f_ics.attrs.keys():
particle_data['meta'][k] = f_ics.attrs[k]
# read in datasets
for k in f_ics.keys():
particle_data[k] = f_ics[k].value
f_ics.close()
else: # write file
hades_dir = ''.join([UT.mNuDir(0.0, sim=sim), str(nreal), '/ICs/'])
if not os.path.isdir(hades_dir): raise ValueError("directory %s not found" % hades_dir)
f_gadget = ''.join([hades_dir, 'ics']) # read in Gadget header
header = ReadSnap.read_gadget_header(f_gadget)
# read in CDM particles (parttype = 1) and create catalogue
read_keys = ['POS ', 'VEL ', 'ID ', 'MASS'] # currently only reading POS, VEL, ID, and MASS
save_keys = ['Position', 'Velocity', 'ID', 'Mass']
particle_data['meta'] = header # store meta data
for k_s, k_r in zip(save_keys, read_keys):
particle_data[k_s] = ReadSnap.read_block(f_gadget, k_r, parttype=1, verbose=verbose)
if k_s == 'Position':
particle_data[k_s] /= 1000. # convert ot Mpc/h
f_ics = h5py.File(f, 'w') # save ID's to hdf5 file
for k in particle_data.keys():
if k == 'meta': continue
f_ics.create_dataset(k, data=particle_data[k])
for k in particle_data['meta'].keys(): # store meta data
f_ics.attrs.create(k, particle_data['meta'][k])
f_ics.close()
return particle_data
from mnucosmomap import catalogs as mNuCat
if __name__ == "__main__":
tt = sys.argv[1]
if tt == 'ics':
nreal = int(sys.argv[2])
nside = int(sys.argv[3])
nsubbox = range(int(sys.argv[4]), int(sys.argv[5]) + 1)
n_cpu = int(sys.argv[6])
sim = 'paco'
#mNuICs_subboxes(range(nsubbox0, nsubbox1+1), nreal, sim='paco', nside=nside, n_cpu=n_cpu)
t00 = time.time()
assert np.array(nsubbox).max() <= nside**3
_dir = ''.join([UT.hades_dir(), 'subbox/ics/'])
if not os.path.isdir(_dir):
raise ValueError("directory %s not found" % _dir)
F = lambda isub: ''.join([
_dir, 'ics.',
str(nreal), '.nside',
str(nside), '.',
str(isub), '.hdf5'
])
# read in full IC box.
print('Reading in full IC box...')
t0 = time.time()
fullbox = mNuCat.mNuICs(nreal, sim=sim, verbose=True)
print('full box read in takes: %f mins' % ((time.time() - t0) / 60.))
# append extra metadata
def mNuParticles_subbox(nsubbox, mneut, nreal, nzbin, sim='paco', nside=8,
overwrite=False, verbose=False):
''' Read in (and write out if it doesn't exist) subbox of snapshots generated from
Paco's neutrino simulations. The positions and velocity of the CDM particles
have dimensions 3xNxNxN
'''
try:
Nsub = len(nsubbox)
except TypeError:
Nsub = 1
nsubbox = [nsubbox]
for isubbox in nsubbox:
if verbose: print('reading in %i of %i^3 subboxes' % (isubbox, nside))
if isubbox > nside**3: raise ValueError('%i exceeds number of subboxes specifed' % isubbox)
if sim not in ['paco']: raise NotImplementedError('%s simulation not supported yet')
_dir = ''.join([UT.hades_dir(), 'subbox/zbin', str(nzbin), '/'])
if not os.path.isdir(_dir): raise ValueError("directory %s not found" % _dir)
# snapshot subbox file
F = lambda isub: ''.join([_dir,
'part.', str(mneut), 'eV.', str(nreal), '.z', str(nzbin), '.nside', str(nside), '.', str(isub), '.hdf5'])
iread = 0
subboxes = []
for isubbox in nsubbox:
subbox = {}
if os.path.isfile(F(isubbox)) and not overwrite: # read in the file
fsub = h5py.File(F(isubbox), 'r') # read in hdf5 file
subbox['meta'] = {}
for k in fsub.attrs.keys():
subbox['meta'][k] = fsub.attrs[k]
for k in fsub.keys(): # read in datasets
subbox[k] = fsub[k].value
fsub.close()
else: # write file
print('Constructing %s ......' % F(isubbox))
if iread == 0:
# read in full box of Particles
fullbox = mNuParticles(mneut, nreal, nzbin, sim=sim, verbose=verbose)
isort_box = np.argsort(fullbox['ID'])
iread += 0
# read in subbox indicies
subb = mNuICs_subbox(isubbox, nreal, sim=sim, nside=nside, verbose=verbose)
N_partside, N_partside, N_partside = subb['ID'].shape
sub_id = subb['ID'].flatten()
subbox['meta'] = fullbox['meta'].copy()
subbox['meta']['n_side'] = nside # append extra metadata
subbox['meta']['n_subbox'] = nside**3
subbox['meta']['i_subbox'] = isubbox
subbox['meta']['subbox_ijk'] = subb['meta']['subbox_ijk']
subbox['ID'] = subb['ID'].copy()
for k in ['Position', 'Velocity']:
subbox[k] = np.zeros((3, N_partside, N_partside, N_partside))
for i in range(3):
subbox[k][i,:,:,:] = \
fullbox[k][:,i][isort_box][(sub_id - 1).astype('int')].reshape((N_partside, N_partside, N_partside))
fsub = h5py.File(F(isubbox), 'w') # save to hdf5 file
for k in ['ID', 'Position', 'Velocity']:
fsub.create_dataset(k, data=subbox[k])
for k in subbox['meta'].keys(): # store meta data
fsub.attrs.create(k, subbox['meta'][k])
fsub.close()
subboxes.append(subbox)
if Nsub == 1:
return subboxes[0]
else:
return subboxes
def mNuParticles(mneut, nreal, nzbin, sim='paco', overwrite=False, verbose=False):
''' Read in snapshot generated from Paco's code
parameters
----------
mneut : float,
total neutrino mass
nreal : int,
realization number
nzbin : int,
integer specifying the redshift of the snapshot.
nzbin = 0 --> z=3
nzbin = 1 --> z=2
nzbin = 2 --> z=1
nzbin = 3 --> z=0.5
nzbin = 4 --> z=0
sim : str
option kwarg to specify which simulation. At this moment
this doesn't really do much since we only have paco's
simulatin
'''
if sim not in ['paco']: raise NotImplementedError('%s simulation not supported yet')
part_dir = ''.join([UT.hades_dir(), 'particles/zbin', str(nzbin), '/'])
f = ''.join([part_dir, 'part.', str(mneut), 'eV.', str(nreal), '.z', str(nzbin), '.hdf5']) # snapshot
particle_data = {}
if os.path.isfile(f) and not overwrite: # read in the file
f_par = h5py.File(f, 'r') # read in hdf5 file
particle_data['meta'] = {}
for k in f_par.attrs.keys():
particle_data['meta'][k] = f_par.attrs[k]
# read in datasets
for k in f_par.keys():
particle_data[k] = f_par[k].value
f_par.close()
else: # write file
_dir = ''.join([UT.mNuDir(mneut, sim=sim), str(nreal), '/snapdir_', str(nzbin).zfill(3), '/'])
if not os.path.isdir(_dir): raise ValueError("directory %s not found" % _dir)
f_gadget = ''.join([_dir, 'snap_', str(nzbin).zfill(3)]) # snapshot
# read in Gadget header
header = ReadSnap.read_gadget_header(f_gadget)
# read in CDM particles (parttype = 1) and create catalogue
read_keys = ['POS ', 'VEL ', 'ID ', 'MASS'] # currently only reading POS, VEL, ID, and MASS
save_keys = ['Position', 'Velocity', 'ID', 'Mass']
particle_data['meta'] = header # store meta data
for k_s, k_r in zip(save_keys, read_keys):
particle_data[k_s] = ReadSnap.read_block(f_gadget, k_r, parttype=1, verbose=verbose)
if k_s == 'Position':
particle_data[k_s] /= 1000. # convert ot Mpc/h
f_par = h5py.File(f, 'w') # save ID's to hdf5 file
for k in particle_data.keys():
if k == 'meta': continue
f_par.create_dataset(k, data=particle_data[k])
for k in particle_data['meta'].keys(): # store meta data
f_par.attrs.create(k, particle_data['meta'][k])
f_par.close()
return particle_data
def mNuICs_subbox(nsubbox, nreal, sim='paco', nside=8, overwrite=False, verbose=False):
''' Read in (and write out if it doesn't exist) particle ID, Positions and Velocities
of initial condition particles within subbox.
'''
assert 512 % nside == 0
try:
Nsub = len(nsubbox)
except TypeError:
Nsub = 1
nsubbox = [nsubbox]
for isubbox in nsubbox:
if isubbox > nside**3: raise ValueError('%i exceeds number of subboxes specifed' % isubbox)
if sim not in ['paco']: raise NotImplementedError('%s simulation not supported yet')
_dir = ''.join([UT.hades_dir(), 'subbox/ics/'])
if not os.path.isdir(_dir): raise ValueError("directory %s not found" % _dir)
F = lambda isub: ''.join([_dir, 'ics.', str(nreal), '.nside', str(nside), '.', str(isub), '.hdf5'])
iread = 0
subboxes = []
for isubbox in nsubbox:
subbox = {}
if os.path.isfile(F(isubbox)) and not overwrite: # read in the file
if verbose: print('reading in %i of %i^3 subboxes' % (isubbox, nside))
try:
fsub = h5py.File(F(isubbox), 'r') # read in hdf5 file
except IOError:
print("IOError while reading %s" % F(isubbox))
raise ValueError
subbox['meta'] = {}
for k in fsub.attrs.keys():
subbox['meta'][k] = fsub.attrs[k]
# read in datasets
for k in fsub.keys():
subbox[k] = fsub[k].value
fsub.close()
else: # write file
if verbose: print('Constructing %s ......' % F(isubbox))
if iread == 0: # read in full IC
if verbose: print('Reading in full IC box...')
if verbose: t_start = time.time()
fullbox = mNuICs(nreal, sim=sim, verbose=verbose)
# append extra metadata
fullbox['meta']['n_side'] = nside
fullbox['meta']['n_subbox'] = nside**3
x, y, z = fullbox['Position'].T
vx, vy, vz = fullbox['Velocity'].T
L_subbox = 1000./float(nside) # L_subbox
L_res = 1000./512.
L_halfres = 0.5 * L_res
N_partside = 512/nside
N_subbox = (N_partside)**3
iread += 1
if verbose: print('full box read in takes: %f mins' % ((time.time() - t_start)/60.))
if verbose: t_start = time.time()
i_x = ((isubbox % nside**2) % nside)
i_y = ((isubbox % nside**2) // nside)
i_z = (isubbox // nside**2)
if verbose: print('%i, %i, %i' % (i_x, i_y, i_z))
xmin = L_subbox * float(i_x) + L_halfres
xmax = (L_subbox * float(i_x+1) + L_halfres) % 1000.
ymin = L_subbox * float(i_y) + L_halfres
ymax = (L_subbox * float(i_y+1) + L_halfres) % 1000.
zmin = L_subbox * float(i_z) + L_halfres
zmax = (L_subbox * float(i_z+1) + L_halfres) % 1000.
if xmin <= xmax: xlim = ((x >= xmin) & (x < xmax))
else: xlim = ((x >= xmin) | (x < xmax))
if ymin <= ymax: ylim = ((y >= ymin) & (y < ymax))
else: ylim = ((y >= ymin) | (y < ymax))
if zmin <= zmax: zlim = ((z >= zmin) & (z < zmax))
else: zlim = ((z >= zmin) | (z < zmax))
in_subbox = (xlim & ylim & zlim)
assert np.sum(in_subbox) == N_subbox
ID_sub = fullbox['ID'][in_subbox]
x_subbox = x[in_subbox]
y_subbox = y[in_subbox]
z_subbox = z[in_subbox]
x_sub = (x_subbox - i_x * L_subbox) % 1000.
y_sub = (y_subbox - i_y * L_subbox) % 1000.
z_sub = (z_subbox - i_z * L_subbox) % 1000.
vx_subbox = vx[in_subbox]
vy_subbox = vy[in_subbox]
vz_subbox = vz[in_subbox]
if verbose:
print('%f < x_sub < %f' % (x_sub.min(), x_sub.max()))
print('%f < y_sub < %f' % (y_sub.min(), y_sub.max()))
print('%f < z_sub < %f' % (z_sub.min(), z_sub.max()))
subbox_ID = np.zeros((N_partside, N_partside, N_partside))
subbox_pos = np.zeros((3, N_partside, N_partside, N_partside))
subbox_vel = np.zeros((3, N_partside, N_partside, N_partside))
j_x = ((x_sub - L_halfres) // L_res).astype(int)
j_y = ((y_sub - L_halfres) // L_res).astype(int)
j_z = ((z_sub - L_halfres) // L_res).astype(int)
subbox_ID[j_x,j_y,j_z] = ID_sub
subbox_pos[0,j_x,j_y,j_z] = x_subbox
subbox_pos[1,j_x,j_y,j_z] = y_subbox
subbox_pos[2,j_x,j_y,j_z] = z_subbox
subbox_vel[0,j_x,j_y,j_z] = vx_subbox
subbox_vel[1,j_x,j_y,j_z] = vy_subbox
subbox_vel[2,j_x,j_y,j_z] = vz_subbox
if verbose: print('subbox construction takes: %f mins' % ((time.time() - t_start)/60.))
#for ii in range(N_subbox):
# j_x = int((x_sub[ii] - L_halfres) // L_res)
# j_y = int((y_sub[ii] - L_halfres) // L_res)
# j_z = int((z_sub[ii] - L_halfres) // L_res)
# subbox_ID[j_x,j_y,j_z] = ID_sub[ii]
# subbox_pos[0,j_x,j_y,j_z] = x_subbox[ii]
# subbox_pos[1,j_x,j_y,j_z] = y_subbox[ii]
# subbox_pos[2,j_x,j_y,j_z] = z_subbox[ii]
# subbox_vel[0,j_x,j_y,j_z] = vx_subbox[ii]
# subbox_vel[1,j_x,j_y,j_z] = vy_subbox[ii]
# subbox_vel[2,j_x,j_y,j_z] = vz_subbox[ii]
subbox['meta'] = fullbox['meta'].copy()
subbox['meta']['i_subbox'] = isubbox
subbox['meta']['subbox_ijk'] = [i_x, i_y, i_z]
subbox['ID'] = subbox_ID
subbox['Position'] = subbox_pos
subbox['Velocity'] = subbox_vel
fsub = h5py.File(F(isubbox), 'w') # save ID's to hdf5 file
for k in subbox['meta'].keys(): # store meta data
fsub.attrs.create(k, subbox['meta'][k])
fsub.create_dataset('ID', data=subbox['ID'])
fsub.create_dataset('Position', data=subbox['Position'])
fsub.create_dataset('Velocity', data=subbox['Velocity'])
fsub.close()
subboxes.append(subbox)
if Nsub == 1:
return subboxes[0]
else:
return subboxes