def sub_gridize_single_halo(self,
pos,
hsml,
ion_mass,
grid,
weights=None,
kernel_type='SPH'):
coords = fieldize.convert_centered(pos, self.ngrid,
2 * self.grid_radius)
#Convert smoothing lengths to grid coordinates.
hsml_grid = hsml * (self.ngrid / (2 * self.grid_radius))
#interpolate the density
ts = time.time()
if self.verbose:
print "Starting to fieldize"
if kernel_type == 'SPH':
fieldize.sph_str(coords,
ion_mass,
grid,
hsml_grid,
weights=weights)
elif kernel_type == 'TOPHAT':
fieldize.tophat_str(coords,
ion_mass,
grid,
hsml_grid,
weights=weights)
if self.verbose:
print "Time to fieldize: ", time.time() - ts
return
def sub_gridize_single_file(self,ipos,ismooth,mHI,sub_nHI_grid,weights=None):
"""Helper function for sub_nHI_grid
that puts data arrays loaded from a particular file onto the grid.
Arguments:
pos - Position array
rho - Density array to be interpolated
smooth - Smoothing lengths
sub_grid - Grid to add the interpolated data to
"""
#Find particles near each halo
sub_pos=self.sub_pos
grid_radius = self.sub_radius
#Need a local for numexpr
box = self.box
#Gather all nearby cells, paying attention to periodic box conditions
for dim in np.arange(3):
jpos = sub_pos[dim]
jjpos = ipos[:,dim]
indj = np.where(ne.evaluate("(abs(jjpos-jpos) < grid_radius+ismooth) | (abs(jjpos-jpos+box) < grid_radius+ismooth) | (abs(jjpos-jpos-box) < grid_radius+ismooth)"))
if np.size(indj) == 0:
return
ipos = ipos[indj]
# Update smooth and rho arrays as well:
ismooth = ismooth[indj]
mHI = mHI[indj]
jjpos = ipos[:,dim]
# BC 1:
ind_bc1 = np.where(ne.evaluate("(abs(jjpos-jpos+box) < grid_radius+ismooth)"))
ipos[ind_bc1,dim] = ipos[ind_bc1,dim] + box
# BC 2:
ind_bc2 = np.where(ne.evaluate("(abs(jjpos-jpos-box) < grid_radius+ismooth)"))
ipos[ind_bc2,dim] = ipos[ind_bc2,dim] - box
#if np.size(ind_bc1)>0 or np.size(ind_bc2)>0:
# print "Fixed some periodic cells!"
if np.size(ipos) == 0:
return
#coords in grid units
coords=fieldize.convert_centered(ipos-sub_pos,self.ngrid,2*self.sub_radius)
#NH0
cellspkpc=(self.ngrid/(2*self.sub_radius))
#Convert smoothing lengths to grid coordinates.
ismooth*=cellspkpc
if self.once:
avgsmth=np.mean(ismooth)
print " Av. smoothing length is ",avgsmth/cellspkpc," kpc/h ",avgsmth, "grid cells min: ",np.min(ismooth)
self.once=False
#interpolate the density
fieldize.sph_str(coords,mHI,sub_nHI_grid,ismooth,weights=weights)
return
def _convert_interp_units(self, ii, ipos, ismooth):
"""Convert smoothing lengths and positions to grid units"""
#coords in grid units
coords=fieldize.convert_centered(ipos-self.sub_cofm[ii].astype('float32'),int(self.ngrid[ii]),2*self.sub_radii[ii])
#To Convert smoothing lengths to grid coordinates.
cellspkpc=(self.ngrid[ii]/(2*self.sub_radii[ii]))
if self.once:
avgsmth=np.mean(ismooth)
print ii," Av. smoothing length is ",avgsmth," kpc/h ",avgsmth*cellspkpc, "grid cells min: ",np.min(ismooth)*cellspkpc
self.once=False
return (coords, ismooth*cellspkpc)
def _convert_interp_units(self, ii, ipos, ismooth):
"""Convert smoothing lengths and positions to grid units"""
#coords in grid units
coords=fieldize.convert_centered(ipos-self.sub_cofm[ii].astype('float32'),int(self.ngrid[ii]),2*self.sub_radii[ii])
#To Convert smoothing lengths to grid coordinates.
cellspkpc=(self.ngrid[ii]/(2*self.sub_radii[ii]))
if self.once:
avgsmth=np.mean(ismooth)
print ii," Av. smoothing length is ",avgsmth," kpc/h ",avgsmth*cellspkpc, "grid cells min: ",np.min(ismooth)*cellspkpc
self.once=False
return (coords, ismooth*cellspkpc)
def sub_gridize_single_halo(self,i,pos,hsml,ion_mass,grid,weights=None):
coords=fieldize.convert_centered(pos,self.ngrid[i],2*self.grid_radii[i])
#Convert smoothing lengths to grid coordinates.
hsml_grid = hsml*(self.ngrid[i]/(2*self.grid_radii[i]))
#interpolate the density
ts = time.time()
print "starting to fieldize"
fieldize.sph_str(coords,ion_mass,grid[i],hsml_grid,weights=weights)
print "time to fieldize: ",time.time()-ts
return
def sub_gridize_single_halo(self,pos,hsml,ion_mass,grid,weights=None,kernel_type='SPH'):
coords=fieldize.convert_centered(pos,self.ngrid,2*self.grid_radius)
#Convert smoothing lengths to grid coordinates.
hsml_grid = hsml*(self.ngrid/(2*self.grid_radius))
#interpolate the density
ts = time.time()
if self.verbose:
print "Starting to fieldize"
if kernel_type == 'SPH':
fieldize.sph_str(coords,ion_mass,grid,hsml_grid,weights=weights)
elif kernel_type == 'TOPHAT':
fieldize.tophat_str(coords,ion_mass,grid,hsml_grid,weights=weights)
if self.verbose:
print "Time to fieldize: ",time.time()-ts
return
def sub_gridize_single_file(self,ii,ipos,ismooth,bar,sub_nHI_grid,weights=None):
"""Helper function for sub_nHI_grid
that puts data arrays loaded from a particular file onto the grid.
Arguments:
pos - Position array
rho - Density array to be interpolated
smooth - Smoothing lengths
sub_grid - Grid to add the interpolated data to
"""
#Find particles near each halo
sub_pos=self.sub_cofm[ii]
grid_radius = self.sub_radii[ii]
#Need a local for numexpr
box = self.box
#Get gas mass in internal units
mass=np.array(bar["Masses"])
#Density in this species
nelem = self.species.index(self.elem)
mass_frac=np.array(bar["GFM_Metals"][:,nelem])
#In g/cm^3
den = np.array(bar["Density"])*self.dscale
#In (hydrogen) atoms / cm^3
den /= self.protonmass
#Mean molecular weight:
# \mu = 1 / molecules per unit atomic weight
# = 1 / (X + Y /4 + E)
# where E = Ne * X, and Y = (1-X).
# Can neglect metals as they are heavy.
# Leading contribution is from electrons, which is already included
# [+ Z / (12->16)] from metal species
# [+ Z/16*4 ] for OIV from electrons.
mu = 1.0/(0.76*(0.75+np.array(bar["ElectronAbundance"])) + 0.25)
temp = np.array(bar["InternalEnergy"])*self.tscale*mu
#Gather all nearby cells, paying attention to periodic box conditions
for dim in np.arange(3):
jpos = sub_pos[dim]
jjpos = ipos[:,dim]
indj = np.where(ne.evaluate("(abs(jjpos-jpos) < grid_radius+ismooth) | (abs(jjpos-jpos+box) < grid_radius+ismooth) | (abs(jjpos-jpos-box) < grid_radius+ismooth)"))
if np.size(indj) == 0:
return
ipos = ipos[indj]
# Update smooth and rho arrays as well:
ismooth = ismooth[indj]
mass = mass[indj]
mass_frac = mass_frac[indj]
den = den[indj]
jjpos = ipos[:,dim]
# BC 1:
ind_bc1 = np.where(ne.evaluate("(abs(jjpos-jpos+box) < grid_radius+ismooth)"))
ipos[ind_bc1,dim] = ipos[ind_bc1,dim] + box
# BC 2:
ind_bc2 = np.where(ne.evaluate("(abs(jjpos-jpos-box) < grid_radius+ismooth)"))
ipos[ind_bc2,dim] = ipos[ind_bc2,dim] - box
#if np.size(ind_bc1)>0 or np.size(ind_bc2)>0:
# print "Fixed some periodic cells!"
if np.size(ipos) == 0:
return
mass_frac *= self.cloudy_table.ion(self.elem, self.ion, den, temp)
#coords in grid units
coords=fieldize.convert_centered(ipos-sub_pos,self.ngrid[ii],2*self.sub_radii[ii])
#NH0
cellspkpc=(self.ngrid[ii]/(2*self.sub_radii[ii]))
#Convert smoothing lengths to grid coordinates.
ismooth*=cellspkpc
if self.once:
avgsmth=np.mean(ismooth)
print ii," Av. smoothing length is ",avgsmth/cellspkpc," kpc/h ",avgsmth, "grid cells min: ",np.min(ismooth)
self.once=False
#interpolate the density
fieldize.sph_str(coords,mass*mass_frac,sub_nHI_grid[ii],ismooth,weights=weights)
return
