def set_nHI_grid(self, gas=False):
"""Set up the grid around each halo where the HI is calculated.
"""
self.once=True
#Now grid the HI for each halo
files = hdfsim.get_all_files(self.snapnum, self.snap_dir)
#Larger numbers seem to be towards the beginning
files.reverse()
for ff in files:
f = h5py.File(ff,"r")
print "Starting file ",ff
bar=f["PartType0"]
ipos=np.array(bar["Coordinates"])
smooth = hsml.get_smooth_length(bar)
[self.sub_gridize_single_file(ii,ipos,smooth,bar,self.sub_nHI_grid) for ii in xrange(0,self.nhalo)]
f.close()
#Explicitly delete some things.
del ipos
del smooth
#Deal with zeros: 0.1 will not even register for things at 1e17.
#Also fix the units:
#we calculated things in internal gadget /cell and we want atoms/cm^2
#So the conversion is mass/(cm/cell)^2
for ii in xrange(0,self.nhalo):
massg=self.UnitMass_in_g/self.hubble*self.hy_mass/self.protonmass
epsilon=2.*self.sub_radii[ii]/(self.ngrid[ii])*self.UnitLength_in_cm/self.hubble/(1+self.redshift)
self.sub_nHI_grid[ii]*=(massg/epsilon**2)
self.sub_nHI_grid[ii]+=0.1
[np.log10(grid,grid) for grid in self.sub_nHI_grid]
return
def omega_gas(self):
"""Compute Omega_gas, the sum of the hydrogen mass, divided by the critical density.
"""
mass = 0.
kpchincm = 1. / (1 + self.redshift)
self.protonmass = 1.67262178e-24
for files in np.arange(0, 500):
try:
ff = hdfsim.get_file(self.num, self.base, files)
except IOError:
break
bar = ff["PartType0"]
nH = self.gas.get_code_rhoH(bar)
pvol = 4. / 3. * math.pi * (hsml.get_smooth_length(bar) *
kpchincm)**3
#Total mass of H in g
ind = np.where(nH < 0.1)
mass += np.sum(nH[ind] * pvol[ind]) * protonmass
#mass += np.sum(nH*pvol)*protonmass
#Total volume of the box in comoving cm^3
volume = (self.box)**3
#Total mass of HI * m_p / r_c
omega_g = mass / volume / self.rho_crit()
return omega_g
def set_zdir_grid(self, dlaind, gas=False, key="zpos", ion=-1):
"""Set up the grid around each halo where the HI is calculated.
"""
star=cold_gas.RahmatiRT(self.redshift, self.hubble, molec=self.molec)
self.once=True
#Now grid the HI for each halo
files = hdfsim.get_all_files(self.snapnum, self.snap_dir)
#Larger numbers seem to be towards the beginning
files.reverse()
self.xslab = np.zeros_like(dlaind[0], dtype=np.float64)
try:
start = self.load_fast_tmp(self.start, key)
except IOError:
start = self.start
end = np.min([np.size(files),self.end])
for xx in xrange(start,end):
ff = files[xx]
f = h5py.File(ff,"r")
print "Starting file ",ff
bar=f["PartType0"]
ipos=np.array(bar["Coordinates"])
#Get HI mass in internal units
mass=np.array(bar["Masses"])
if not gas:
#Hydrogen mass fraction
try:
mass *= np.array(bar["GFM_Metals"][:,0])
except KeyError:
mass *= self.hy_mass
nhi = star.get_reproc_HI(bar)
ind = np.where(nhi > 1.e-3)
ipos = ipos[ind,:][0]
mass = mass[ind]
#Get x * m for the weighted z direction
if not gas:
mass *= nhi[ind]
if key == "zpos":
mass*=ipos[:,0]
elif key != "":
mass *= self._get_secondary_array(ind,bar,key, ion)
smooth = hsml.get_smooth_length(bar)[ind]
for slab in xrange(self.nhalo):
ind = np.where(dlaind[0] == slab)
self.xslab[ind] += self.sub_list_grid_file(slab,ipos,smooth,mass,dlaind[1][ind], dlaind[2][ind])
f.close()
#Explicitly delete some things.
del ipos
del mass
del smooth
self.save_fast_tmp(start,key)
#Fix the units:
#we calculated things in internal gadget /cell and we want atoms/cm^2
#So the conversion is mass/(cm/cell)^2
massg=self.UnitMass_in_g/self.hubble/self.protonmass
epsilon=2.*self.sub_radii[0]/(self.ngrid[0])*self.UnitLength_in_cm/self.hubble/(1+self.redshift)
self.xslab*=(massg/epsilon**2)
return self.xslab
def _age_single_file(self,fn, elem, ion):
"""Get the density weighted interpolated temperature field for a single file"""
(pos, vel, age, temp, hh, amumass) = self._read_particle_data(fn, elem, ion,True)
if amumass == False:
return np.zeros([np.shape(self.cofm)[0],self.nbins],dtype=np.float32)
else:
ff = h5py.File(fn, "r")
data = ff["PartType0"]
hh2 = hsml.get_smooth_length(data)
pos2 = np.array(data["Coordinates"],dtype=np.float32)
ind = self.particles_near_lines(pos2, hh2,self.axis,self.cofm)
ind2 = self._filter_particles(age, None, None, None)
part_ids = np.array(data["ParticleIDs"])[ind][ind2]
assert np.size(part_ids) == np.size(age)
tracer = ff["PartType3"]
#Last star time is {a, -a, a+1, a+2} depending on from a star/wind to a gas, or from a gas to a star/wind.
laststar = np.array(tracer["FluidQuantities"][:,8])
#Only interested in moving from star or wind to gas.
#Assume that something from a wind came out of a star reasonably soon before
#Zero value means was never in a star
t_ind = np.where(np.logical_and(laststar < 1, laststar != 0))
laststar = laststar[t_ind]
#Associate each tracer particle with a gas particle
tracerparents = np.array(tracer["ParentID"])[t_ind]
ff.close()
#Now we have tracers we look through our gas cells to find
#attached tracers. If we don't find a tracer, set this gas particle to zero time.
#It was never in a star or wind.
#Find all particles that don't have attached tracers
withtracers = np.in1d(part_ids, tracerparents)
withouttracers = np.where(np.logical_not(withtracers))
withtracers = np.where(withtracers)
#Metal density of stuff that has been in a star should be much higher than stuff which hasn't been in a star
#Otherwise we have problems.
if np.any(withouttracers):
print("Metal density in a star ",np.mean(age[withouttracers]))
#It is not allowed to set individual elements of arrays selected in this complex way, so we must create a new array of
#the multiplication factor.
if np.size(withtracers) > 0:
print("metal density not in star ",np.mean(age[withtracers]))
lastfactor = np.array([np.max(np.abs(laststar[np.where(tracerparents == pid)])) for pid in part_ids[withtracers]])
age = age[withtracers] * lastfactor
pos = pos[withtracers]
vel = vel[withtracers]
temp = temp[withtracers]
hh = hh[withtracers]
line = self.lines[("H",1)][1215]
stuff = self._do_interpolation_work(pos, vel, age, temp, hh, amumass, line, False)
return stuff
else:
return np.zeros([np.shape(self.cofm)[0],self.nbins],dtype=np.float32)
def set_nHI_grid(self, gas=False, start=0):
"""Set up the grid around each halo where the HI is calculated.
"""
star=cold_gas.RahmatiRT(self.redshift, self.hubble, molec=self.molec)
self.cloudy_table = convert_cloudy.CloudyTable(self.redshift)
self.once=True
#Now grid the HI for each halo
files = hdfsim.get_all_files(self.snapnum, self.snap_dir)
#Larger numbers seem to be towards the beginning
files.reverse()
end = np.min([np.size(files),self.end])
for xx in xrange(start, end):
ff = files[xx]
f = h5py.File(ff,"r")
print "Starting file ",ff
bar=f["PartType0"]
ipos=np.array(bar["Coordinates"])
#Get HI mass in internal units
mass=np.array(bar["Masses"])
#Carbon mass fraction
den = star.get_code_rhoH(bar)
temp = star.get_temp(bar)
mass_frac = np.array(bar["GFM_Metals"][:,2])
#Floor on the mass fraction of the metal
ind = np.where(mass_frac > 1e-10)
mass = mass[ind]*mass_frac[ind]
#High densities will have no CIV anyway.
den[np.where(den > 1e4)] = 9999.
den[np.where(den < 1e-7)] = 1.01e-7
temp[np.where(temp > 3e8)] = 3e8
temp[np.where(temp < 1e3)] = 1e3
mass *= self.cloudy_table.ion("C", self.ion, den[ind], temp[ind])
smooth = hsml.get_smooth_length(bar)[ind]
ipos = ipos[ind,:][0]
[self.sub_gridize_single_file(ii,ipos,smooth,mass,self.sub_nHI_grid) for ii in xrange(0,self.nhalo)]
f.close()
#Explicitly delete some things.
del ipos
del mass
del smooth
#Deal with zeros: 0.1 will not even register for things at 1e17.
#Also fix the units:
#we calculated things in internal gadget /cell and we want atoms/cm^2
#So the conversion is mass/(cm/cell)^2
for ii in xrange(0,self.nhalo):
massg=self.UnitMass_in_g/self.hubble/(self.protonmass*12.011)
epsilon=2.*self.sub_radii[ii]/(self.ngrid[ii])*self.UnitLength_in_cm/self.hubble/(1+self.redshift)
self.sub_nHI_grid[ii]*=(massg/epsilon**2)
self.sub_nHI_grid[ii]+=0.1
np.log10(self.sub_nHI_grid[ii],self.sub_nHI_grid[ii])
return
def set_nHI_grid(self):
"""Set up the grid around each halo where the velocity HI is calculated.
"""
star=cold_gas.RahmatiRT(self.redshift, self.hubble)
self.once=True
#This is the real HI grid
nHI_grid=np.array([np.zeros([self.ngrid[i],self.ngrid[i]]) for i in xrange(0,self.nhalo)])
#Now grid the HI for each halo
for fnum in xrange(0,500):
try:
f=hdfsim.get_file(self.snapnum,self.snap_dir,fnum)
except IOError:
break
print "Starting file ",fnum
bar=f["PartType0"]
ipos=np.array(bar["Coordinates"],dtype=np.float64)
smooth = hsml.get_smooth_length(bar)
# Velocity in cm/s
vel = np.array(bar["Velocities"],dtype=np.float64)*self.UnitVelocity_in_cm_per_s
#We will weight by neutral mass per cell
irhoH0 = star.get_reproc_rhoHI(bar)
irho=np.array(bar["Density"],dtype=np.float64)*(self.UnitMass_in_g/self.UnitLength_in_cm**3)*self.hubble**2
#HI * Cell Mass, internal units
mass = np.array(bar["Masses"],dtype=np.float64)*irhoH0/irho
f.close()
#Perform the grid interpolation
#sub_gas_grid is x velocity
#sub_nHI_grid is y velocity
[self.sub_gridize_single_file(ii,ipos,smooth,vel[:,1]*mass,self.sub_gas_grid,vel[:,2]*mass,self.sub_nHI_grid,mass) for ii in xrange(0,self.nhalo)]
#Find the HI density also, so that we can discard
#velocities in cells that are not DLAs.
[self.sub_gridize_single_file(ii,ipos,smooth,irhoH0,nHI_grid,np.zeros(np.size(irhoH0)),nHI_grid) for ii in xrange(0,self.nhalo)]
#Explicitly delete some things.
del ipos
del irhoH0
del irho
del smooth
del mass
del vel
#No /= in list comprehensions... :|
#Average over z
for i in xrange(0,self.nhalo):
self.sub_gas_grid[i]/=self.sub_radii[i]
self.sub_nHI_grid[i]/=self.sub_radii[i]
ind = np.where(nHI_grid[i] < 10**20.3)
self.sub_nHI_grid[i][ind] = 0
self.sub_gas_grid[i][ind] = 0
return
def set_nHI_grid(self, gas=False, start=0):
"""Set up the grid around each halo where the HI is calculated.
"""
star=cold_gas.RahmatiRT(self.redshift, self.hubble, molec=self.molec)
self.once=True
#Now grid the HI for each halo
files = hdfsim.get_all_files(self.snapnum, self.snap_dir)
#Larger numbers seem to be towards the beginning
files.reverse()
restart = 10
end = np.min([np.size(files),self.end])
for xx in xrange(start, end):
ff = files[xx]
f = h5py.File(ff,"r")
print "Starting file ",ff
bar=f["PartType0"]
ipos=np.array(bar["Coordinates"])
#Get HI mass in internal units
mass=np.array(bar["Masses"])
if not gas:
#Hydrogen mass fraction
try:
mass *= np.array(bar["GFM_Metals"][:,0])
except KeyError:
mass *= self.hy_mass
mass *= star.get_reproc_HI(bar)
smooth = hsml.get_smooth_length(bar)
[self.sub_gridize_single_file(ii,ipos,smooth,mass,self.sub_nHI_grid) for ii in xrange(0,self.nhalo)]
f.close()
#Explicitly delete some things.
del ipos
del mass
del smooth
if xx % restart == 0 or xx == end-1:
self.save_tmp(xx)
#Deal with zeros: 0.1 will not even register for things at 1e17.
#Also fix the units:
#we calculated things in internal gadget /cell and we want atoms/cm^2
#So the conversion is mass/(cm/cell)^2
for ii in xrange(0,self.nhalo):
massg=self.UnitMass_in_g/self.hubble/self.protonmass
epsilon=2.*self.sub_radii[ii]/(self.ngrid[ii])*self.UnitLength_in_cm/self.hubble/(1+self.redshift)
self.sub_nHI_grid[ii]*=(massg/epsilon**2)
np.log10(self.sub_nHI_grid[ii],self.sub_nHI_grid[ii])
return
def set_ZZ_grid(self, start=0):
"""Set up the mass * metallicity grid for the box
Same as set_nHI_grid except mass is multiplied by GFM_Metallicity.
"""
self.once=True
#Now grid the HI for each halo
files = hdfsim.get_all_files(self.snapnum, self.snap_dir)
#Larger numbers seem to be towards the beginning
files.reverse()
restart = 10
end = np.min([np.size(files),self.end])
for xx in xrange(start, end):
ff = files[xx]
f = h5py.File(ff,"r")
print "Starting file ",ff
bar=f["PartType0"]
ipos=np.array(bar["Coordinates"])
#Get HI mass in internal units
mass=np.array(bar["Masses"])
#Sometimes the metallicity is less than zero: fix that
met = np.array(bar["GFM_Metallicity"])
met[np.where(met <=0)] = 1e-50
mass *= met
smooth = hsml.get_smooth_length(bar)
[self.sub_gridize_single_file(ii,ipos,smooth,mass,self.sub_ZZ_grid) for ii in xrange(0,self.nhalo)]
f.close()
#Explicitly delete some things.
del ipos
del mass
del smooth
if xx % restart == 0 or xx == end-1:
self.save_met_tmp(xx)
#Deal with zeros: 0.1 will not even register for things at 1e17.
#Also fix the units:
#we calculated things in internal gadget /cell and we want atoms/cm^2
#So the conversion is mass/(cm/cell)^2
for ii in xrange(0,self.nhalo):
massg=self.UnitMass_in_g/self.hubble/self.protonmass
epsilon=2.*self.sub_radii[ii]/(self.ngrid[ii])*self.UnitLength_in_cm/self.hubble/(1+self.redshift)
self.sub_ZZ_grid[ii]*=(massg/epsilon**2)
self.sub_ZZ_grid[ii]+=0.1
np.log10(self.sub_ZZ_grid[ii],self.sub_ZZ_grid[ii])
return
def omega_gas(self):
"""Compute Omega_gas, the sum of the hydrogen mass, divided by the critical density.
"""
mass = 0.
kpchincm = 1./(1+self.redshift)
self.protonmass=1.67262178e-24
for files in np.arange(0,500):
try:
ff = hdfsim.get_file(self.num, self.base,files)
except IOError:
break
bar = ff["PartType0"]
nH = self.gas.get_code_rhoH(bar)
pvol = 4./3.*math.pi*(hsml.get_smooth_length(bar)*kpchincm)**3
#Total mass of H in g
ind = np.where(nH < 0.1)
mass += np.sum(nH[ind]*pvol[ind])*protonmass
#mass += np.sum(nH*pvol)*protonmass
#Total volume of the box in comoving cm^3
volume = (self.box)**3
#Total mass of HI * m_p / r_c
omega_g=mass/volume/self.rho_crit()
return omega_g
def set_zdir_grid(self, dlaind, gas=False, key="zpos", ion=-1):
"""Set up the grid around each halo where the HI is calculated.
"""
star = cold_gas.RahmatiRT(self.redshift, self.hubble, molec=self.molec)
self.once = True
#Now grid the HI for each halo
files = hdfsim.get_all_files(self.snapnum, self.snap_dir)
#Larger numbers seem to be towards the beginning
files.reverse()
self.xslab = np.zeros_like(dlaind[0], dtype=np.float64)
try:
start = self.load_fast_tmp(self.start, key)
except IOError:
start = self.start
end = np.min([np.size(files), self.end])
for xx in xrange(start, end):
ff = files[xx]
f = h5py.File(ff, "r")
print "Starting file ", ff
bar = f["PartType0"]
ipos = np.array(bar["Coordinates"])
#Get HI mass in internal units
mass = np.array(bar["Masses"])
if not gas:
#Hydrogen mass fraction
try:
mass *= np.array(bar["GFM_Metals"][:, 0])
except KeyError:
mass *= self.hy_mass
nhi = star.get_reproc_HI(bar)
ind = np.where(nhi > 1.e-3)
ipos = ipos[ind, :][0]
mass = mass[ind]
#Get x * m for the weighted z direction
if not gas:
mass *= nhi[ind]
if key == "zpos":
mass *= ipos[:, 0]
elif key != "":
mass *= self._get_secondary_array(ind, bar, key, ion)
smooth = hsml.get_smooth_length(bar)[ind]
for slab in xrange(self.nhalo):
ind = np.where(dlaind[0] == slab)
self.xslab[ind] += self.sub_list_grid_file(
slab, ipos, smooth, mass, dlaind[1][ind], dlaind[2][ind])
f.close()
#Explicitly delete some things.
del ipos
del mass
del smooth
self.save_fast_tmp(start, key)
#Fix the units:
#we calculated things in internal gadget /cell and we want atoms/cm^2
#So the conversion is mass/(cm/cell)^2
massg = self.UnitMass_in_g / self.hubble / self.protonmass
epsilon = 2. * self.sub_radii[0] / (
self.ngrid[0]) * self.UnitLength_in_cm / self.hubble / (
1 + self.redshift)
self.xslab *= (massg / epsilon**2)
return self.xslab
