def createmesh_catalog(self,
bs,
nc,
halocat,
cencat,
satcat,
mode='halos',
position='RSDpos',
weight='HImass',
tofield=False):
'''use this to create mesh of HI
'''
comm = halocat.comm
if mode == 'halos': catalogs = [halocat]
else: print('Mode not recognized')
rankweight = sum([cat[weight].sum().compute() for cat in catalogs])
totweight = comm.allreduce(rankweight)
for cat in catalogs:
cat[weight] /= totweight / float(nc)**3
allcat = MultipleSpeciesCatalog(
['%d' % i for i in range(len(catalogs))], *catalogs)
mesh = allcat.to_mesh(BoxSize=bs,Nmesh=[nc,nc,nc],\
position=position,weight=weight)
if tofield: mesh = mesh.to_field()
return mesh
def calc_pk1d(aa, suff):
'''Compute the 1D redshift-space P(k) for the HI'''
if rank == 0: print('Read in central/satellite catalogs')
cencat = BigFileCatalog(scratch2 + sim +
'/fastpm_%0.4f/cencat-16node' % aa)
satcat = BigFileCatalog(scratch2 + sim + '/fastpm_%0.4f/satcat' % aa +
suff)
rsdfac = read_conversions(scratch1 + sim + '/fastpm_%0.4f/' % aa)
# Compute the power spectrum
los = [0, 0, 1]
cencat['RSDpos'] = cencat['Position'] + cencat['Velocity'] * los * rsdfac
satcat['RSDpos'] = satcat['Position'] + satcat['Velocity'] * los * rsdfac
cencat['HImass'] = HI_hod(cencat['Mass'], aa)
satcat['HImass'] = HI_hod(satcat['Mass'], aa)
rankHImass = cencat['HImass'].sum().compute() +\
satcat['HImass'].sum().compute()
totHImass = comm.allreduce(rankHImass)
cencat['HImass'] /= totHImass / float(nc)**3
satcat['HImass'] /= totHImass / float(nc)**3
allcat = MultipleSpeciesCatalog(['cen', 'sat'], cencat, satcat)
h1mesh = allcat.to_mesh(BoxSize=bs,Nmesh=[nc,nc,nc],\
position='RSDpos',weight='HImass')
pkh1h1 = FFTPower(h1mesh, mode='1d', kmin=0.025, dk=0.0125).power
# Extract the quantities we want and write the file.
kk = pkh1h1['k']
sn = pkh1h1.attrs['shotnoise']
pk = np.abs(pkh1h1['power'])
if rank == 0:
fout = open("HI_pks_1d_{:6.4f}.txt".format(aa), "w")
fout.write("# Subtracting SN={:15.5e}.\n".format(sn))
fout.write("# {:>8s} {:>15s}\n".format("k", "Pk_0_HI"))
for i in range(kk.size):
fout.write("{:10.5f} {:15.5e}\n".format(kk[i], pk[i] - sn))
fout.close()
def calc_bias(aa,mcut,suff):
'''Compute the bias(es) for the HI'''
print('Read in DM mesh')
dm = BigFileMesh(project+sim+'/fastpm_%0.4f/'%aa+\
'/dmesh_N%04d'%nc,'1').paint()
dm /= dm.cmean()
pkmm = FFTPower(dm,mode='1d').power
k,pkmm= pkmm['k'],pkmm['power'] # Ignore shotnoise.
#
print('Read in central/satellite catalogs')
cencat = BigFileCatalog(project+sim+'/fastpm_%0.4f/cencat'%aa)
satcat = BigFileCatalog(project+sim+'/fastpm_%0.4f/satcat'%aa+suff)
#
cencat['HImass'] = HI_hod(cencat['Mass'],aa,mcut)
satcat['HImass'] = HI_hod(satcat['Mass'],aa,mcut)
totHImass = cencat['HImass'].sum().compute() +\
satcat['HImass'].sum().compute()
cencat['HImass']/= totHImass/float(nc)**3
satcat['HImass']/= totHImass/float(nc)**3
#
allcat = MultipleSpeciesCatalog(['cen','sat'],cencat,satcat)
#
h1mesh = allcat.to_mesh(BoxSize=bs,Nmesh=[nc,nc,nc],weight='HImass')
pkh1h1 = FFTPower(h1mesh,mode='1d').power
pkh1h1 = pkh1h1['power']-pkh1h1.attrs['shotnoise']
pkh1mm = FFTPower(h1mesh,second=dm,mode='1d').power['power']
# Compute the biases.
b1x = np.abs(pkh1mm/(pkmm+1e-10))
b1a = np.abs(pkh1h1/(pkmm+1e-10))**0.5
return(k,b1x,b1a,np.abs(pkmm))
def calc_pkmu(aa,suff):
'''Compute the redshift-space P(k) for the HI in mu bins'''
if rank ==0 : print('Read in central/satellite catalogs')
cencat = BigFileCatalog(scratch2+sim+'/fastpm_%0.4f/cencat-16node'%aa)
satcat = BigFileCatalog(scratch2+sim+'/fastpm_%0.4f/satcat'%aa+suff)
rsdfac = read_conversions(scratch1+sim+'/fastpm_%0.4f/'%aa)
# Compute P(k,mu).
los = [0,0,1]
cencat['RSDpos'] = cencat['Position']+cencat['Velocity']*los * rsdfac
satcat['RSDpos'] = satcat['Position']+satcat['Velocity']*los * rsdfac
cencat['HImass'] = HI_hod(cencat['Mass'],aa)
satcat['HImass'] = HI_hod(satcat['Mass'],aa)
totHImass = cencat['HImass'].sum().compute() +\
satcat['HImass'].sum().compute()
cencat['HImass']/= totHImass/float(nc)**3
satcat['HImass']/= totHImass/float(nc)**3
allcat = MultipleSpeciesCatalog(['cen','sat'],cencat,satcat)
h1mesh = allcat.to_mesh(BoxSize=bs,Nmesh=[nc,nc,nc],\
position='RSDpos',weight='HImass')
#pkh1h1 = FFTPower(h1mesh,mode='2d',Nmu=4,los=los).power
cenmesh = pm.paint(cencat['RSDpos'], mass=cencat['HImass'])
satmesh = pm.paint(satcat['RSDpos'], mass=satcat['HImass'])
h1mesh = cenmesh + satmesh
pkh1h1 = FFTPower(h1mesh,mode='2d',Nmu=4,los=los).power
# Extract what we want.
kk = pkh1h1.coords['k']
sn = pkh1h1.attrs['shotnoise']
pk = pkh1h1['power']
# Write the results to a file.
if rank ==0 :
fout = open("../data/HI_pks_mu_{:06.4f}.txt".format(aa),"w")
fout.write("# Redshift space power spectrum in mu bins.\n")
fout.write("# Subtracting SN={:15.5e}.\n".format(sn))
ss = "# {:>8s}".format(r'k\mu')
for i in range(pkh1h1.shape[1]):
ss += " {:15.5f}".format(pkh1h1.coords['mu'][i])
fout.write(ss+"\n")
for i in range(1,pk.shape[0]):
ss = "{:10.5f}".format(kk[i])
for j in range(pk.shape[1]):
ss += " {:15.5e}".format(np.abs(pk[i,j]-sn))
fout.write(ss+"\n")
fout.close()
def calc_bias(aa, mcut, suff):
'''Compute the bias(es) for the HI'''
if rank == 0:
print("Processing a={:.4f}...".format(aa))
print('Reading DM mesh...')
dm = BigFileMesh(scratch1+sim+'/fastpm_%0.4f/'%aa+\
'/1-mesh/N%04d'%nc,'').paint()
dm /= dm.cmean()
if rank == 0: print('Computing DM P(k)...')
pkmm = FFTPower(dm, mode='1d').power
k, pkmm = pkmm['k'], pkmm['power'] # Ignore shotnoise.
if rank == 0: print('Done.')
#
if rank == 0: print('Reading central/satellite catalogs...')
cencat = BigFileCatalog(scratch2 + sim +
'/fastpm_%0.4f/cencat-16node' % aa)
satcat = BigFileCatalog(scratch2 + sim + '/fastpm_%0.4f/satcat' % aa +
suff)
if rank == 0: print('Catalogs read.')
#
if rank == 0: print('Computing HI masses...')
cencat['HImass'] = HI_hod(cencat['Mass'], aa, mcut)
satcat['HImass'] = HI_hod(satcat['Mass'], aa, mcut)
rankHImass = cencat['HImass'].sum().compute() +\
satcat['HImass'].sum().compute()
rankHImass = np.array([rankHImass])
totHImass = np.zeros(1, dtype='float')
comm.Allreduce(rankHImass, totHImass, MPI.SUM)
totHImass = totHImass[0]
cencat['HImass'] /= totHImass / float(nc)**3
satcat['HImass'] /= totHImass / float(nc)**3
if rank == 0: print('HI masses done.')
#
if rank == 0: print('Combining catalogs and computing P(k)...')
allcat = MultipleSpeciesCatalog(['cen', 'sat'], cencat, satcat)
h1mesh = allcat.to_mesh(BoxSize=bs, Nmesh=[nc, nc, nc], weight='HImass')
pkh1h1 = FFTPower(h1mesh, mode='1d').power
pkh1h1 = pkh1h1['power'] - pkh1h1.attrs['shotnoise']
pkh1mm = FFTPower(h1mesh, second=dm, mode='1d').power['power']
if rank == 0: print('Done.')
# Compute the biases.
b1x = np.abs(pkh1mm / (pkmm + 1e-10))
b1a = np.abs(pkh1h1 / (pkmm + 1e-10))**0.5
if rank == 0: print("Finishing processing a={:.4f}.".format(aa))
return (k, b1x, b1a, np.abs(pkmm))
def calc_pkll(aa,suff):
'''Compute the redshift-space P_ell(k) for the HI'''
if rank ==0 : print('Read in central/satellite catalogs')
cencat = BigFileCatalog(scratch2+sim+'/fastpm_%0.4f/cencat-16node'%aa)
satcat = BigFileCatalog(scratch2+sim+'/fastpm_%0.4f/satcat'%aa+suff)
rsdfac = read_conversions(scratch1+sim+'/fastpm_%0.4f/'%aa)
#
los = [0,0,1]
cencat['RSDpos'] = cencat['Position']+cencat['Velocity']*los * rsdfac
satcat['RSDpos'] = satcat['Position']+satcat['Velocity']*los * rsdfac
cencat['HImass'] = HI_hod(cencat['Mass'],aa)
satcat['HImass'] = HI_hod(satcat['Mass'],aa)
totHImass = cencat['HImass'].sum().compute() +\
satcat['HImass'].sum().compute()
cencat['HImass']/= totHImass/float(nc)**3
satcat['HImass']/= totHImass/float(nc)**3
allcat = MultipleSpeciesCatalog(['cen','sat'],cencat,satcat)
h1mesh = allcat.to_mesh(BoxSize=bs,Nmesh=[nc,nc,nc],\
position='RSDpos',weight='HImass')
#pkh1h1 = FFTPower(h1mesh,mode='2d',Nmu=8,los=los,poles=[0,2,4]).poles
cenmesh = pm.paint(cencat['RSDpos'], mass=cencat['HImass'])
satmesh = pm.paint(satcat['RSDpos'], mass=satcat['HImass'])
h1mesh = cenmesh + satmesh
pkh1h1 = FFTPower(h1mesh,mode='2d',Nmu=8,los=los,poles=[0,2,4]).poles
# Extract the quantities of interest.
kk = pkh1h1.coords['k']
sn = pkh1h1.attrs['shotnoise']
P0 = pkh1h1['power_0'].real - sn
P2 = pkh1h1['power_2'].real
P4 = pkh1h1['power_4'].real
# Write the results to a file.
if rank ==0 :
fout = open("../data/HI_pks_ll_{:06.4f}.txt".format(aa),"w")
fout.write("# Redshift space power spectrum multipoles.\n")
fout.write("# Subtracting SN={:15.5e} from monopole.\n".format(sn))
fout.write("# {:>8s} {:>15s} {:>15s} {:>15s}\n".format("k","P0","P2","P4"))
for i in range(1,kk.size):
fout.write("{:10.5f} {:15.5e} {:15.5e} {:15.5e}\n".\
format(kk[i],P0[i],P2[i],P4[i]))
fout.close()
def to_catalog(self, **kwargs):
from nbodykit.lab import MultipleSpeciesCatalog
names = []
sources = []
for spname, sp in self.species.items():
sources.append(sp.to_catalog())
names.append(spname)
cat = MultipleSpeciesCatalog(names, *sources, **kwargs)
return cat
def measurexi(N, edges):
'''plot the power spectrum of halos and H1 with subsampling'''
suff = '-m1_00p3mh-alpha-0p8-subvol'
outfolder = ofolder + suff[1:]
if bs == 1024: outfolder = outfolder + "-big"
outfolder += "/%s/" % modelname
for i, aa in enumerate(alist):
dm = BigFileCatalog(scratchyf + sim + '/fastpm_%0.4f/' % aa,
dataset='1')
rng = np.random.RandomState(dm.comm.rank)
rank = dm.comm.rank
halocat = BigFileCatalog(scratchyf + sim + '/fastpm_%0.4f//' % aa,
dataset='LL-0.200')
mp = halocat.attrs['MassTable'][1] * 1e10 ##
halocat['Mass'] = halocat['Length'].compute() * mp
cencat = BigFileCatalog(scratchcm + sim + '/fastpm_%0.4f/cencat' % aa +
suff)
satcat = BigFileCatalog(scratchcm + sim + '/fastpm_%0.4f/satcat' % aa +
suff)
#
HImodelz = HImodel(aa)
los = [0, 0, 1]
halocat['HImass'], cencat['HImass'], satcat[
'HImass'] = HImodelz.assignHI(halocat, cencat, satcat)
for cat in [halocat, cencat, satcat]:
cat['Weight'] = cat['HImass']
dm['Weight'] = np.ones(dm.size)
for cat in [dm, halocat, cencat,
satcat]: # nbodykit bug in SimBox2PCF that asserts boxsize
cat.attrs['BoxSize'] = np.broadcast_to(cat.attrs['BoxSize'], 3)
#
#Combine galaxies to halos
comm = halocat.comm
if mode == 'halos': catalogs = [halocat]
elif mode == 'galaxies': catalogs = [cencat, satcat]
elif mode == 'all': catalogs = [halocat, cencat, satcat]
else: print('Mode not recognized')
rankweight = sum([cat['Weight'].sum().compute() for cat in catalogs])
totweight = comm.allreduce(rankweight)
for cat in catalogs:
cat['Weight'] /= totweight / float(nc)**3
allcat = MultipleSpeciesCatalog(
['%d' % i for i in range(len(catalogs))], *catalogs)
#Subsample
if rank == 0:
print('redshift = ', 1 / aa - 1)
print('Number of dm particles = ', dm.csize)
print('Number of halos particles = ', halocat.csize)
def subsampler(cat, rng, N, rmax):
# subsample such that we have at most N particles to rmax
nbar = (cat.csize / cat.attrs['BoxSize'].prod())
ratio = (N / rmax**3) / nbar
mask = rng.uniform(size=cat.size) < ratio
cat1 = cat[mask]
if rank == 0:
print('truncating catalog from %d to %d' %
(cat.csize, cat1.csize))
return cat1
if rank == 0: print('Create weight array')
#halocat = subsampler(halocat, rng, N, edges.max())
dm = subsampler(dm, rng, N, edges.max())
if rank == 0: print("Correlation function for edges :\n", edges)
start = time()
#xim = SimulationBox2PCF('1d', data1=dm, edges=edges)
end = time()
if rank == 0: print('Time for matter = ', end - start)
#Others mass weighted
start = time()
xih1mass = SimulationBox2PCF('1d',
data1=halocat,
weight='Weight',
edges=edges)
end = time()
if rank == 0: print('Time for HI = ', end - start)
start = time()
ximxh1mass = SimulationBox2PCF('1d',
data1=halocat,
data2=dm,
weight='Weight',
edges=edges)
end = time()
if rank == 0: print('Time for Cross = ', end - start)
def savebinned(path, binstat, header):
r, xi = binstat.corr['r'].real, binstat.corr['corr'].real
if rank == 0:
try:
os.makedirs(os.path.dirname(path))
except IOError:
pass
np.savetxt(path, np.stack((r, xi), axis=1), header=header)
#savebinned(ofolder+'ximatter.txt', xim, header='r, xi(r)')
savebinned(outfolder + "xih1mass_{:6.4f}.txt".format(aa),
xih1mass,
header='r, xi(r)')
savebinned(outfolder + "ximxh1mass_{:6.4f}.txt".format(aa),
ximxh1mass,
header='r, xi(r)')