def set_stellar_grid(self):
"""Set up a grid around each halo containing the stellar column density
"""
self.sub_star_grid=np.zeros([self.nhalo, self.ngrid[0],self.ngrid[0]])
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["PartType4"]
ipos=np.array(bar["Coordinates"])
#Get HI mass in internal units
mass=np.array(bar["Masses"])
smooth = np.array(bar["SubfindHsml"])
[self.sub_gridize_single_file(ii,ipos,smooth,mass,self.sub_star_grid) for ii in xrange(0,self.nhalo)]
f.close()
#Explicitly delete some things.
del ipos
del mass
del smooth
#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_star_grid[ii]*=(massg/epsilon**2)
return
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 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 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, 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 set_stellar_grid(self):
"""Set up a grid around each halo containing the stellar column density
"""
self.sub_star_grid = np.zeros(
[self.nhalo, self.ngrid[0], self.ngrid[0]])
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["PartType4"]
ipos = np.array(bar["Coordinates"])
#Get HI mass in internal units
mass = np.array(bar["Masses"])
smooth = np.array(bar["SubfindHsml"])
[
self.sub_gridize_single_file(ii, ipos, smooth, mass,
self.sub_star_grid)
for ii in xrange(0, self.nhalo)
]
f.close()
#Explicitly delete some things.
del ipos
del mass
del smooth
#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_star_grid[ii] *= (massg / epsilon**2)
return
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
