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halomet.py
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halomet.py
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# -*- coding: utf-8 -*-
# vim: set fileencoding=utf-8
"""Module for creating the DLA hydrogen density plots. Can find integrated HI grids around halos (or across the whole box).
column density functions, cross-sections, etc.
Classes:
HaloMet - Creates a grid around the halo center with the metal density fraction calculated at each grid cell
"""
import numpy as np
import hdfsim
import convert_cloudy
import cold_gas
import os.path as path
import hsml
import h5py
import numexpr as ne
import halohi as hi
import boxhi as bi
import fieldize
class HaloMet(hi.HaloHI):
"""Class to find the integrated metal density around a halo.
Inherits from HaloMet, and finds grids of metal density in amu / cm^3."""
def __init__(self,snap_dir,snapnum,elem,ion,minpart=400,reload_file=False,savefile=None):
self.elem=elem
self.ion=ion
self.species = ['H', 'He', 'C', 'N', 'O', 'Ne', 'Mg', 'Si', 'Fe']
self.minpart=minpart
self.snapnum=snapnum
self.snap_dir=snap_dir
self.set_units()
if savefile==None:
self.savefile=path.join(snap_dir,"snapdir_"+str(snapnum).rjust(3,'0'),"halomet_grid.hdf5")
else:
self.savefile = savefile
try:
if reload_file:
raise KeyError("reloading")
#First try to load from a file
self.load_savefile(self.savefile)
except (IOError,KeyError):
self.load_header()
self.load_halos(minpart)
#Generate cloudy tables
self.cloudy_table = convert_cloudy.CloudyTable(self.redshift)
# Conversion factors from internal units
rscale = self.UnitLength_in_cm/(1+self.redshift)/self.hubble # convert length to cm
mscale = self.UnitMass_in_g/self.hubble # convert mass to g
self.dscale = mscale / rscale **3 # Convert density to g / cm^3
escale = 1.0e6 # convert energy/unit mass to J kg^-1
#convert U (J/kg) to T (K) : U = N k T / (γ - 1)
#T = U (γ-1) μ m_P / k_B
#where k_B is the Boltzmann constant
#γ is 5/3, the perfect gas constant
#m_P is the proton mass
#μ is 1 / (mean no. molecules per unit atomic weight) calculated in loop.
boltzmann = 1.3806504e-23
self.tscale = ((5./3.-1.0) * 1e-3*self.protonmass * escale ) / boltzmann
#Otherwise regenerate from the raw data
self.sub_nHI_grid=np.array([np.zeros([self.ngrid[i],self.ngrid[i]]) for i in xrange(0,self.nhalo)])
self.set_nHI_grid()
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 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
class BoxMet(bi.BoxHI):
"""
Class to find the mass-weighted metallicity for a box.
Inherits from BoxHI
"""
def __init__(self,snap_dir,snapnum,nslice=1,savefile=None, start=0, end=3000, ngrid=16384):
bi.BoxHI.__init__(self, snap_dir, snapnum, nslice, False, savefile, False,start=start, end=end,ngrid=ngrid)
self.sub_ZZ_grid=np.zeros([nslice, ngrid,ngrid])
try:
thisstart = self.load_met_tmp(self.start)
except (IOError,KeyError):
print "Could not load file"
thisstart = self.start
self.set_ZZ_grid(thisstart)
#Find the metallicity
for ii in xrange(0, self.nhalo):
self.sub_ZZ_grid[ii] -= self.sub_nHI_grid[ii]
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 save_file(self):
"""This does something a little perverse: open up self.savefile
and save the metallicity values only for the indices found in the abslists group"""
f=h5py.File(self.savefile,'r+')
grp = f["abslists"]
#This is needed to make the dimensions right
dlaind = (grp["DLA"][0,:],grp["DLA"][1,:],grp["DLA"][2,:])
llsind = (grp["LLS"][0,:],grp["LLS"][1,:],grp["LLS"][2,:])
mgrp = f.create_group("Metallicities")
mgrp.create_dataset("DLA",data=self.sub_ZZ_grid[dlaind])
mgrp.create_dataset("LLS",data=self.sub_ZZ_grid[llsind])
f.close()
def save_met_tmp(self, location):
"""Save a partially completed file"""
f = h5py.File(self.savefile+"."+str(self.start)+".met.tmp",'w')
grp_grid = f.create_group("GridZZData")
for i in xrange(0,self.nhalo):
grp_grid.create_dataset(str(i),data=self.sub_ZZ_grid[i])
f.attrs["met_file"]=location
f.close()
def load_met_tmp(self, start):
"""
Load a partially completed file
"""
print self.savefile+"."+str(start)+".met.tmp"
f = h5py.File(self.savefile+"."+str(start)+".met.tmp",'r')
grp = f["GridZZData"]
[ grp[str(i)].read_direct(self.sub_ZZ_grid[i]) for i in xrange(0,self.nhalo)]
location = f.attrs["met_file"]
f.close()
print "Successfully loaded metals from tmp file. Next to do is:",location+1
return location+1
class FastBoxMet(bi.BoxHI):
"""
Class to find the mass-weighted metallicity for a box.
Inherits from BoxHI
"""
def __init__(self,snap_dir,snapnum,nslice=1,savefile=None, start=0, end=3000, ngrid=16384, cdir=None):
bi.BoxHI.__init__(self, snap_dir, snapnum, nslice, False, savefile, False,start=start, end=end,ngrid=ngrid)
if cdir != None:
self.cloudy_table = convert_cloudy.CloudyTable(self.redshift, cdir)
else:
self.cloudy_table = convert_cloudy.CloudyTable(self.redshift)
def set_ZZ_fast_dla(self, dla=True):
"""Faster metallicity computation for only those cells with a DLA"""
dlaind = self._load_dla_index(dla)
#Computing z distances
xhmass = self.set_zdir_grid(dlaind,gas=True, key="met")
hmass = self.set_zdir_grid(dlaind,gas=True,key="")
met = xhmass/hmass
f=h5py.File(self.savefile,'r+')
mgrp = f.create_group("Metallicities")
if dla:
mgrp.create_dataset("DLA",data=met)
else:
mgrp.create_dataset("LLS",data=met)
f.close()
def set_metal_species_fast_dla(self, elem, ion, dla=True):
"""Faster metallicity computation for only those cells with a DLA"""
dlaind = self._load_dla_index(dla)
#Computing z distances
species = self.set_zdir_grid(dlaind,gas=True, key=elem, ion=ion)
f=h5py.File(self.savefile,'r+')
try:
mgrp = f.create_group(elem)
mmgrp = mgrp.create_group(str(ion))
except ValueError:
mmgrp = f[elem][str(ion)]
if dla:
datas="DLA"
else:
datas="LLS"
try:
del mmgrp[datas]
except KeyError:
pass
mmgrp.create_dataset(datas,data=species)
f.close()
def _get_secondary_array(self, ind, bar, elem="", ion=-1):
"""Get the array whose HI weighted amount we want to compute. Throws ValueError
if key is not a desired species. Note this saves the total projected mass of each species in
atoms of that species / cm ^2. If you want the total mass in the species, multiply by its atomic mass."""
if elem == "met":
met = np.array(bar["GFM_Metallicity"])[ind]
else:
nelem = self.species.index(elem)
met = np.array(bar["GFM_Metals"][:,nelem])[ind]
#What is saved is the column density in amu, we want the column density,
#which is in atoms. So there is a factor of mass.
met /= self.amasses[elem]
if ion != -1:
star=cold_gas.RahmatiRT(self.redshift, self.hubble)
den=star.get_code_rhoH(bar)
temp = star.get_temp(bar)
temp = temp[ind]
den = den[ind]
met *= self.cloudy_table.ion(elem, ion, den, temp)
met[np.where(met <=0)] = 1e-50
return met
class BoxCIV(bi.BoxHI):
"""
Class to find omega_CIV for a box.
Inherits from BoxHI
"""
def __init__(self,snap_dir,snapnum,nslice=1,reload_file=True, savefile=None, start=0, end=3000, ngrid=16384):
bi.BoxHI.__init__(self, snap_dir, snapnum, nslice, reload_file=reload_file, savefile=savefile, start=start, end=end,ngrid=ngrid)
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", 4, 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 _rho_DLA(self, thresh=14, upthresh=50.):
"""Find the average density in DLAs in g/cm^3 (comoving). Helper for omega_DLA and rho_DLA."""
#Average column density of HI in atoms cm^-2 (physical)
try:
self.sub_nHI_grid
except AttributeError:
self.load_hi_grid()
if thresh > 0:
grids=self.sub_nHI_grid
HImass = np.sum(10**grids[np.where((grids < upthresh)*(grids > thresh))])/np.size(grids)
else:
HImass = np.mean(10**self.sub_nHI_grid)
#Avg. Column density of HI in g cm^-2 (comoving)
HImass = 12.011*self.protonmass * HImass/(1+self.redshift)**2
#Length of column in comoving cm
length = (self.box*self.UnitLength_in_cm/self.hubble/self.nhalo)
#Avg density in g/cm^3 (comoving)
return HImass/length
class HaloCIV(hi.HaloHI, BoxCIV):
"""Plots of the CIV around a single halo"""
def __init__(self,snap_dir,snapnum,reload_file=True, savefile=None, start=0, end=3000):
hi.HaloHI.__init__(self,snap_dir,snapnum,minpart=400,reload_file=reload_file,savefile=savefile, gas=False, molec=True, start=start, end = end)
def set_nHI_grid(self, gas=False, start=0):
return BoxCIV.set_nHI_grid(self,gas,start)