def getStatic(self):
''' calculate the static matrix for the specified temperature'''
temperature = self.Temperature
z = self.Z
ionList = []
chIons = []
evolver = np.zeros((z + 1, z + 1), 'float64')
for ion in range(1, z + 2):
ions = util.zion2name(z, ion)
ionList.append(ions)
# print z, ion, ions
atom = ch.ion(ions, temperature=temperature)
atom.ionizRate()
atom.recombRate()
chIons.append(atom)
for stage in range(0, z):
atom = chIons[stage]
# if type(atom.IonizRate) != types.NoneType:
evolver[stage, stage] -= atom.IonizRate['rate']
atom = chIons[stage + 1]
evolver[stage, stage + 1] += atom.RecombRate['rate']
# evolver[stage-2,stage] += atom.IonizRate['rate']
for stage in range(1, z + 1):
atom = chIons[stage]
# if type(atom.RecombRate) != types.NoneType:
evolver[stage, stage] -= atom.RecombRate['rate']
atom = chIons[stage - 1]
evolver[stage, stage - 1] += atom.IonizRate['rate']
# evolver[stage-1,stage-2] += atom.RecombRate['rate']
# include normalization of ionization stages
for stage in range(0, z + 1):
evolver[0, stage] = 1.
self.Static = evolver
def getStatic(self):
''' calculate the static matrix for the specified temperature'''
temperature = self.Temperature
z = self.Z
ionList=[]
chIons=[]
evolver = np.zeros((z+1,z+1),'float64')
for ion in range(1, z+2):
ions=util.zion2name(z, ion)
ionList.append(ions)
# print z, ion, ions
atom=ch.ion(ions, temperature=temperature)
atom.ionizRate()
atom.recombRate()
chIons.append(atom)
for stage in range(0,z):
atom = chIons[stage]
# if type(atom.IonizRate) != types.NoneType:
evolver[stage,stage] -= atom.IonizRate['rate']
atom = chIons[stage+1]
evolver[stage,stage+1] += atom.RecombRate['rate']
# evolver[stage-2,stage] += atom.IonizRate['rate']
for stage in range(1,z+1):
atom = chIons[stage]
# if type(atom.RecombRate) != types.NoneType:
evolver[stage,stage] -= atom.RecombRate['rate']
atom = chIons[stage-1]
evolver[stage,stage-1] += atom.IonizRate['rate']
# evolver[stage-1,stage-2] += atom.RecombRate['rate']
# include normalization of ionization stages
for stage in range(0,z+1):
evolver[0,stage] = 1.
self.Static = evolver
def match_line(ion_name, wvls, s_flux, tmax, density):
# t = 10**((tmax - 0.3) + 0.001*np.arange(600))
lowtemp = 4.0
hightemp = 8.0
npoints = 1000
t = 10**(np.linspace(lowtemp, hightemp, npoints))
ion_n = ch.ion(ion_name, temperature=t, eDensity=density)
ion_n.gofnt(wvlRange=[min(wvls) - 1, max(wvls) + 1])
return ion_n.Gofnt
def sum_match_lines(ion_name,wvls,t,density,search_width = 1.0):
ion_n = ch.ion(ion_name, temperature=t, eDensity=density)
intensity = t.copy()*0.0
print(wvls)
for wvl in wvls:
ion_n.intensity(wvlRange=[min(wvls)-search_width,max(wvls)+search_width])
if wvl in(ion_n.Intensity['wvl']):
intensity_s = ion_n.Intensity['intensity'][:,(ion_n.Intensity['wvl'] == wvl)]
intensity += np.array(intensity_s.T[0])
print('match')
else:
print('Something is wrong - cannot find matching line! for {} {}'.format(ion_name,wvl))
intensity += 0
return intensity
def getIoneq(self):
''' get the ionization equilibrium for this ion at the specified temperature
getIoneqFromEvolver does the same but is a bit less accurate'''
z = self.Z
temperature = self.Temperature
ionList = []
chIons = []
for ion in range(1, z + 2):
ions = util.zion2name(z, ion)
ionList.append(ions)
# print z, ion, ions
atom = ch.ion(ions, temperature=temperature, setup=0)
atom.ionizRate()
atom.recombRate()
chIons.append(atom)
ioneq = np.zeros((z + 1), 'float64')
factor = []
for anIon in chIons:
if type(anIon.IonizRate) != type(None) and type(
anIon.RecombRate) != type(None):
rat = anIon.IonizRate['rate'] / anIon.RecombRate['rate']
factor.append(rat**2 + rat**(-2))
else:
factor.append(0.)
factor[0] = max(factor)
factor[-1] = max(factor)
ionmax = factor.index(min(factor))
ioneq[ionmax] = 1.
#
for iz in range(ionmax + 1, z + 1):
ionrate = chIons[iz - 1].IonizRate['rate']
recrate = chIons[iz].RecombRate['rate']
ioneq[iz] = ionrate * ioneq[iz - 1] / recrate
# print ' iz, ioneq = ',iz,ioneq[iz]
#
for iz in range(ionmax - 1, -1, -1):
ionrate = chIons[iz].IonizRate['rate']
recrate = chIons[iz + 1].RecombRate['rate']
ioneq[iz] = recrate * ioneq[iz + 1] / ionrate
# print ' iz, ioneq = ',iz,ioneq[iz]
ionsum = ioneq.sum()
# print ' ionsum = ', ionsum
ioneq = ioneq / ionsum
self.Ioneq = ioneq
def getIoneq(self):
''' get the ionization equilibrium for this ion at the specified temperature
getIoneqFromEvolver does the same but is a bit less accurate'''
z = self.Z
temperature = self.Temperature
ionList=[]
chIons=[]
for ion in range(1, z+2):
ions=util.zion2name(z, ion)
ionList.append(ions)
# print z, ion, ions
atom=ch.ion(ions, temperature=temperature, setup=0)
atom.ionizRate()
atom.recombRate()
chIons.append(atom)
ioneq=np.zeros((z+1), 'float64')
factor=[]
for anIon in chIons:
if type(anIon.IonizRate) != type(None) and type(anIon.RecombRate) != type(None):
rat=anIon.IonizRate['rate']/anIon.RecombRate['rate']
factor.append(rat**2 + rat**(-2))
else:
factor.append(0.)
factor[0]=max(factor)
factor[-1]=max(factor)
ionmax=factor.index(min(factor))
ioneq[ionmax]=1.
#
for iz in range(ionmax+1, z+1):
ionrate=chIons[iz-1].IonizRate['rate']
recrate=chIons[iz].RecombRate['rate']
ioneq[iz]=ionrate*ioneq[iz-1]/recrate
# print ' iz, ioneq = ',iz,ioneq[iz]
#
for iz in range(ionmax-1, -1, -1):
ionrate=chIons[iz].IonizRate['rate']
recrate=chIons[iz+1].RecombRate['rate']
ioneq[iz]=recrate*ioneq[iz+1]/ionrate
# print ' iz, ioneq = ',iz,ioneq[iz]
ionsum=ioneq.sum()
# print ' ionsum = ', ionsum
ioneq=ioneq/ionsum
self.Ioneq=ioneq
def old_find_tm(ion_name):
h = 6.626068e-34
c = 299792458
k = 1.3806503e-23
ion_state = int(ion_name.rsplit('_')[1])
t = 10**(3.8 + 0.01 * np.arange(400))
ion = ch.ion(ion_name, temperature=t)
ioneq = ion.IoneqOne
W = h * c * ion.Elvlc['ecm'][ion_state - 1] * 100
gt = ioneq * (t**-0.5) * np.exp(-W / (k * t))
tm = t[np.argmax(gt)]
return np.log10(tm)
def old_e_measure(ion_name, wvls, s_flux, tmax, star_dist, star_radius,
density):
rs = 6.96e10
pc = 3.08567758e18
t = 10**((tmax - 0.3) + 0.001 * np.arange(600))
ion_n = ch.ion(ion_name, temperature=t, eDensity=density)
ion_n.gofnt(wvlRange=[min(wvls) - 1, max(wvls) + 1])
star_dist = star_dist * pc
star_radius = star_radius * rs
flux = s_flux * (star_dist / star_radius)**2.0
print('ANYONE THERE?!')
quit()
ion_n.Gofnt['emeasure'] = (flux / density) / (2 * np.pi *
ion_n.Gofnt['gofnt'])
return ion_n.Gofnt
def getEvolver(self, temperature, density, time):
''' calculate the evolver matrix for the new temperature'''
self.NewTemperature = temperature
z = self.Z
ionList = []
chIons = []
evolver = np.zeros((z + 1, z + 1), 'float64')
for ion in range(1, z + 2):
ions = util.zion2name(z, ion)
ionList.append(ions)
# print z, ion, ions
atom = ch.ion(ions, temperature=temperature, setup=0)
atom.ionizRate()
atom.recombRate()
chIons.append(atom)
for stage in range(0, z):
# atom = chIons[stage]
# if type(atom.IonizRate) != types.NoneType:
evolver[stage, stage] -= chIons[stage].IonizRate['rate']
# atom = chIons[stage+1]
evolver[stage, stage + 1] += chIons[stage + 1].RecombRate['rate']
# evolver[stage-2,stage] += atom.IonizRate['rate']
for stage in range(1, z + 1):
# atom = chIons[stage]
# if type(atom.RecombRate) != types.NoneType:
evolver[stage, stage] -= chIons[stage].RecombRate['rate']
# atom = chIons[stage-1]
evolver[stage, stage - 1] += chIons[stage - 1].IonizRate['rate']
# evolver[stage-1,stage-2] += atom.RecombRate['rate']
# include normalization of ionization stages
# for stage in range(0,z+1):
# evolver[0,stage] = 1.
# this is the first order Euler solution
# implicitEvolver = np.invert(np.identity(z+1,'float64') - evolver)
implicitEvolver = np.dual.inv(
np.identity(z + 1, 'float64') - density * time * evolver)
self.Evolver = implicitEvolver
def getEvolver(self,temperature,density,time):
''' calculate the evolver matrix for the new temperature'''
self.NewTemperature = temperature
z = self.Z
ionList=[]
chIons=[]
evolver = np.zeros((z+1,z+1),'float64')
for ion in range(1, z+2):
ions=util.zion2name(z, ion)
ionList.append(ions)
# print z, ion, ions
atom=ch.ion(ions, temperature=temperature, setup=0)
atom.ionizRate()
atom.recombRate()
chIons.append(atom)
for stage in range(0,z):
# atom = chIons[stage]
# if type(atom.IonizRate) != types.NoneType:
evolver[stage,stage] -= chIons[stage].IonizRate['rate']
# atom = chIons[stage+1]
evolver[stage,stage+1] += chIons[stage+1].RecombRate['rate']
# evolver[stage-2,stage] += atom.IonizRate['rate']
for stage in range(1,z+1):
# atom = chIons[stage]
# if type(atom.RecombRate) != types.NoneType:
evolver[stage,stage] -= chIons[stage].RecombRate['rate']
# atom = chIons[stage-1]
evolver[stage,stage-1] += chIons[stage-1].IonizRate['rate']
# evolver[stage-1,stage-2] += atom.RecombRate['rate']
# include normalization of ionization stages
# for stage in range(0,z+1):
# evolver[0,stage] = 1.
# this is the first order Euler solution
# implicitEvolver = np.invert(np.identity(z+1,'float64') - evolver)
implicitEvolver = np.dual.inv(np.identity(z+1,'float64') - density*time*evolver)
self.Evolver = implicitEvolver
def read_chianti(symbol, ion_number, level_observed=True, temperatures = np.linspace(2000, 50000, 20)):
ion_data = ch.ion('{0}_{1:d}'.format(symbol.lower(), ion_number+1))
levels_data = {}
levels_data['level_number'] = ion_data.Elvlc['lvl']
temperatures = np.array(temperatures)
if level_observed:
levels_data['energy'] = units.Unit('cm').to('eV', 1 / np.array(ion_data.Elvlc['ecm']), units.spectral())
else:
levels_data['energy'] = units.Unit('cm').to('eV', 1 / np.array(ion_data.Elvlc['ecmth']), units.spectral())
levels_data['g'] = 2*np.array(ion_data.Elvlc['j']) + 1
if levels_data['energy'][0] != 0.0:
raise ValueError('Level 0 energy is not 0.0')
levels_data = pd.DataFrame(levels_data)
levels_data.set_index('level_number', inplace=True)
last_bound_level = levels_data[levels_data['energy'] < ion_data.Ip].index[-1]
levels_data = levels_data.ix[:last_bound_level]
lines_data = {}
lines_data['wavelength'] = ion_data.Wgfa['wvl']
lines_data['level_number_lower'] = ion_data.Wgfa['lvl1']
lines_data['level_number_upper'] = ion_data.Wgfa['lvl2']
lines_data['A_ul'] = ion_data.Wgfa['avalue']
nu = units.Unit('angstrom').to('Hz', lines_data['wavelength'], units.spectral())
lines_data = pd.DataFrame(lines_data)
g_lower = levels_data['g'].ix[lines_data['level_number_lower'].values].values
g_upper = levels_data['g'].ix[lines_data['level_number_upper'].values].values
A_coeff = (8 * np.pi**2 * constants.e.gauss.value**2 * nu**2)/ (constants.m_e.cgs.value * constants.c.cgs.value**3)
lines_data['f_ul'] = lines_data['A_ul'] / A_coeff
lines_data['f_lu'] = (lines_data['A_ul'] * g_upper) / (A_coeff * g_lower)
lines_data['loggf'] = np.log10(lines_data['f_lu'] * g_lower)
lines_data['wavelength'] = lines_data['wavelength']# / (1.0 + 2.735182E-4 + 131.4182 / lines_data['wavelength']**2
# + 2.76249E8 / lines_data['wavelength']**4)
lines_data = lines_data[lines_data['level_number_upper'] <= last_bound_level]
collision_data_index = pd.MultiIndex.from_arrays((ion_data.Splups['lvl1'], ion_data.Splups['lvl2']))
c_lvl1 = []
c_lvl2 = []
c_upper_lowers = []
g_ratios = []
delta_es = []
for i, (lvl1, lvl2) in enumerate(zip(ion_data.Splups['lvl1'], ion_data.Splups['lvl2'])):
if lvl2 > last_bound_level:
continue
c_lvl1.append(lvl1)
c_lvl2.append(lvl2)
c_upper_lower, g_ratio, delta_e = calculate_collisional_strength(ion_data.Splups, i, temperatures, levels_data)
c_upper_lowers.append(c_upper_lower)
g_ratios.append(g_ratio)
delta_es.append(delta_e)
c_upper_lowers = np.array(c_upper_lowers)
g_ratios = np.array(g_ratios)
delta_es = np.array(delta_es)
collision_data = pd.DataFrame(c_upper_lowers, index=collision_data_index)
collision_data['g_ratio'] = g_ratios
#CAREFUL!!! delta_e has already been divided by k!!
collision_data['delta_e'] = delta_es
collision_data['level_number_lower'] = c_lvl1
collision_data['level_number_upper'] = c_lvl2
lines_data = lines_data[lines_data.wavelength>0]
return levels_data, lines_data, collision_data
init_values['de'][:] = 1e-30
init_values = ion_by_ion.convert_to_mass_density(init_values)
else:
# start CIE
import chianti.core as ch
import chianti.util as chu
for s in sorted(ion_by_ion.required_species):
if s.name != 'ge':
if s.name == 'de':
continue
else:
print s.name, s.free_electrons + 1
ion_name = chu.zion2name(np.int(s.number),
np.int(s.free_electrons + 1))
ion = ch.ion(ion_name, temperature=init_values['T'])
ion.ioneqOne()
ion_frac = ion.IoneqOne
init_values[s.name] = ion_frac * init_array * ion.Abundance
# in case something is negative or super small:
init_values[s.name][init_values[s.name] < tiny] = tiny
init_values['de'] = init_array * 0.0
# total_density = combined.calculate_total_density(init_values, ("OI",))
# init_values["OI"] = init_array.copy() - total_density
init_values = ion_by_ion.convert_to_mass_density(init_values)
init_values['de'] = ion_by_ion.calculate_free_electrons(init_values)
init_values['density'] = ion_by_ion.calculate_total_density(init_values)
number_density = ion_by_ion.calculate_number_density(init_values)
def rec_rate(network):
ion = ch.ion(ion_name, temperature = network.T)
ion.recombRate()
vals = ion.RecombRate['rate']
return vals
def ion_rate(network):
ion = ch.ion(ion_name, temperature = network.T)
ion.ionizRate()
vals = ion.IonizRate['rate']
return vals
def __init__(self, ion_name):
self.ion = ch.ion(ion_name)
self._levels = None
self._lines = None
self._collisions = None
"""
import ares
import numpy as np
import matplotlib.pyplot as pl
import chianti.core as cc
pl.rcParams['legend.fontsize'] = 14
#
dims = 32
T = np.logspace(2, 7, dims)
#
# Chianti rates
h1 = cc.ion('h_1', T)
h2 = cc.ion('h_2', T)
he1 = cc.ion('he_1', T)
he2 = cc.ion('he_2', T)
he3 = cc.ion('he_3', T)
# Analytic fits
coeff = ares.physics.RateCoefficients()
"""
Plot collisional ionization rate coefficients.
"""
h1.diRate()
he1.diRate()
he2.diRate()