LevelPopsGasServer.py
# -*- coding: utf-8 -*-
"""
Created on Mon Apr 24 14:13:47 2017
@author: ishort
"""
import math
import Useful
import ToolBox
#import numpy
#JB#
#from matplotlib.pyplot import plot, title, show, scatter
#storage for fits (not all may be used)
uw = []
uwa = []
uwb = []
uwStage = []
uwbStage = []
uwu = []
uwl = []
uua=[]
uub=[]
"""
#a function to create a cubic function fit extrapolation
def cubicFit(x,y):
coeffs = numpy.polyfit(x,y,3)
#returns an array of coefficents for the cubic fit of the form
#Ax^3 + Bx^2 + Cx + D as [A,B,C,D]
return coeffs
#this will work for any number of data points!
def valueFromFit(fit,x):
#return the value y for a given fit, at point x
return (fit[0]*(x**3)+fit[1]*(x**2)+fit[2]*x+fit[3])
#holds the five temperature at which we have partition function data
"""
masterTemp = [130, 500, 3000, 8000, 10000]
#JB#
#def levelPops(lam0In, logNStage, chiL, log10UwStage, gwL, numDeps, temp):
def levelPops(lam0In, logNStage, chiL, logUw, gwL, numDeps, temp):
""" Returns depth distribution of occupation numbers in lower level of b-b transition,
// Input parameters:
// lam0 - line centre wavelength in nm
// logNStage - log_e density of absorbers in relevent ion stage (cm^-3)
// logFlu - log_10 oscillator strength (unitless)
// chiL - energy of lower atomic E-level of b-b transition in eV
// Also needs atsmopheric structure information:
// numDeps
// temp structure """
c = Useful.c()
logC = Useful.logC()
k = Useful.k()
logK = Useful.logK()
logH = Useful.logH()
logEe = Useful.logEe()
logMe = Useful.logMe()
ln10 = math.log(10.0)
logE = math.log10(math.e); #// for debug output
log2pi = math.log(2.0 * math.pi)
log2 = math.log(2.0)
#//double logNl = logNlIn * ln10; // Convert to base e
#// Parition functions passed in are 2-element vectore with remperature-dependent base 10 log Us
#// Convert to natural logs:
#double thisLogUw, Ttheta;
thisLogUw = 0.0 # //default initialization
#logUw = [ 0.0 for i in range(5) ]
logE10 = math.log(10.0)
#print("log10UwStage ", log10UwStage)
#for kk in range(len(logUw)):
# logUw[kk] = logE10*log10UwStage[kk] #// lburns new loop
logGwL = math.log(gwL)
#//System.out.println("chiL before: " + chiL);
#// If we need to subtract chiI from chiL, do so *before* converting to tiny numbers in ergs!
#////For testing with Ca II lines using gS3 internal line list only:
#//boolean ionized = true;
#//if (ionized) {
#// //System.out.println("ionized, doing chiL - chiI: " + ionized);
#// // chiL = chiL - chiI;
#// chiL = chiL - 6.113;
#// }
#// //
#//Log of line-center wavelength in cm
logLam0 = math.log(lam0In) #// * 1.0e-7);
#// energy of b-b transition
logTransE = logH + logC - logLam0 #//ergs
if (chiL <= 0.0):
chiL = 1.0e-49
logChiL = math.log(chiL) + Useful.logEv() #// Convert lower E-level from eV to ergs
logBoltzFacL = logChiL - Useful.logK() #// Pre-factor for exponent of excitation Boltzmann factor
boltzFacL = math.exp(logBoltzFacL)
boltzFacGround = 0.0 / k #//I know - its zero, but let's do it this way anyway'
#// return a 1D numDeps array of logarithmic number densities
#// level population of lower level of bb transition (could be in either stage I or II!)
logNums = [ 0.0 for i in range(numDeps)]
#double num, logNum, expFac;
#JB#
#print("thisLogUw:",numpy.shape(logUw))
logUwFit = ToolBox.cubicFit(masterTemp,logUw)#u(T) fit
uw.append(logUwFit)
#JB#
for id in range(numDeps):
#//Determine temperature dependenet partition functions Uw:
#Ttheta = 5040.0 / temp[0][id]
#//NEW Determine temperature dependent partition functions Uw: lburns
thisTemp = temp[0][id]
"""
if (Ttheta >= 1.0):
thisLogUw = logUw[0]
if (Ttheta <= 0.5):
thisLogUw = logUw[1]
if (Ttheta > 0.5 and Ttheta < 1.0):
thisLogUw = ( logUw[1] * (Ttheta - 0.5)/(1.0 - 0.5) ) \
+ ( logUw[0] * (1.0 - Ttheta)/(1.0 - 0.5) )
"""
#JB#
thisLogUw = ToolBox.valueFromFit(logUwFit,thisTemp)#u(T) value extrapolated
#JB#
if (thisTemp >= 10000.0):
thisLogUw = logUw[4]
if (thisTemp <= 130.0):
thisLogUw = logUw[0]
"""
if (thisTemp > 130 and thisTemp <= 500):
thisLogUw = logUw[1] * (thisTemp - 130)/(500 - 130) \
+ logUw[0] * (500 - thisTemp)/(500 - 130)
if (thisTemp > 500 and thisTemp <= 3000):
thisLogUw = logUw[2] * (thisTemp - 500)/(3000 - 500) \
+ logUw[1] * (3000 - thisTemp)/(3000 - 500)
if (thisTemp > 3000 and thisTemp <= 8000):
thisLogUw = logUw[3] * (thisTemp - 3000)/(8000 - 3000) \
+ logUw[2] * (8000 - thisTemp)/(8000 - 3000)
if (thisTemp > 8000 and thisTemp < 10000):
thisLogUw = logUw[4] * (thisTemp - 8000)/(10000 - 8000) \
+ logUw[3] * (10000 - thisTemp)/(10000 - 8000)
"""
#print("logUw ", logUw, " thisLogUw ", thisLogUw)
#//System.out.println("LevPops: ionized branch taken, ionized = " + ionized);
#// Take stat weight of ground state as partition function:
logNums[id] = logNStage[id] - boltzFacL / temp[0][id] + logGwL - thisLogUw #// lower level of b-b transition
#print("LevelPopsServer.stagePops id ", id, " logNStage[id] ", logNStage[id], " boltzFacL ", boltzFacL, " temp[0][id] ", temp[0][id], " logGwL ", logGwL, " thisLogUw ", thisLogUw, " logNums[id] ", logNums[id]);
#// System.out.println("LevelPops: id, logNums[0][id], logNums[1][id], logNums[2][id], logNums[3][id]: " + id + " "
#// + Math.exp(logNums[0][id]) + " "
#// + Math.exp(logNums[1][id]) + " "
#// + Math.exp(logNums[2][id]) + " "
#// + Math.exp(logNums[3][id]));
#//System.out.println("LevelPops: id, logNums[0][id], logNums[1][id], logNums[2][id], logNums[3][id], logNums[4][id]: " + id + " "
#// + logE * (logNums[0][id]) + " "
#// + logE * (logNums[1][id]) + " "
#// + logE * (logNums[2][id]) + " "
# // + logE * (logNums[3][id]) + " "
#// + logE * (logNums[4][id]) );
#//System.out.println("LevelPops: id, logIonFracI, logIonFracII: " + id + " " + logE*logIonFracI + " " + logE*logIonFracII
#// + "logNum, logNumI, logNums[0][id], logNums[1][id] "
#// + logE*logNum + " " + logE*logNumI + " " + logE*logNums[0][id] + " " + logE*logNums[1][id]);
#//System.out.println("LevelPops: id, logIonFracI: " + id + " " + logE*logIonFracI
#// + "logNums[0][id], boltzFacL/temp[0][id], logNums[2][id]: "
#// + logNums[0][id] + " " + boltzFacL/temp[0][id] + " " + logNums[2][id]);
#//id loop
#stop
#print (uw)
return logNums
#//This version - ionization equilibrium *WITHOUT* molecules - logNum is TOTAL element population
#def stagePops2(logNum, Ne, chiIArr, log10UwAArr, \
# numMols, logNumB, dissEArr, log10UwBArr, logQwABArr, logMuABArr, \
# numDeps, temp):
def stagePops(logNum, Ne, chiIArr, logUw, \
numDeps, temp):
#line 1: //species A data - ionization equilibrium of A
#line 2: //data for set of species "B" - molecular equlibrium for set {AB}
"""Ionization equilibrium routine WITHOUT molecule formation:
// Returns depth distribution of ionization stage populations
// Input parameters:
// logNum - array with depth-dependent total element number densities (cm^-3)
// chiI1 - ground state ionization energy of neutral stage
// chiI2 - ground state ionization energy of singly ionized stage
// Also needs atsmopheric structure information:
// numDeps
// temp structure
// rho structure
// Atomic element A is the one whose ionization fractions are being computed
//
"""
ln10 = math.log(10.0)
logE = math.log10(math.e) #// for debug output
log2pi = math.log(2.0 * math.pi)
log2 = math.log(2.0)
numStages = len(chiIArr) #// + 1; //need one more stage above the highest stage to be populated
#// var numMols = dissEArr.length;
#// Parition functions passed in are 2-element vectore with remperature-dependent base 10 log Us
#// Convert to natural logs:
#double Ttheta, thisTemp;
#//Default initializations:
#//We need one more stage in size of saha factor than number of stages we're actualy populating
thisLogUw = [ 0.0 for i in range(numStages+1) ]
for i in range(numStages+1):
thisLogUw[i] = 0.0
logE10 = math.log(10.0)
#//atomic ionization stage Boltzmann factors:
#double logChiI, logBoltzFacI;
boltzFacI = [ 0.0 for i in range(numStages) ]
#print("numStages ", numStages, " Useful.logEv ", Useful.logEv())
for i in range(numStages):
#print("i ", i, " chiIArr ", chiIArr[i])
logChiI = math.log(chiIArr[i]) + Useful.logEv()
logBoltzFacI = logChiI - Useful.logK()
boltzFacI[i] = math.exp(logBoltzFacI)
logSahaFac = log2 + (3.0 / 2.0) * (log2pi + Useful.logMe() + Useful.logK() - 2.0 * Useful.logH())
#// return a 2D 5 x numDeps array of logarithmic number densities
#// Row 0: neutral stage ground state population
#// Row 1: singly ionized stage ground state population
#// Row 2: doubly ionized stage ground state population
#// Row 3: triply ionized stage ground state population
#// Row 4: quadruply ionized stage ground state population
#double[][] logNums = new double[numStages][numDeps];
logNums = [ [ 0.0 for i in range(numDeps)] for j in range(numStages) ]
#//We need one more stage in size of saha factor than number of stages we're actualy populating
#// for index accounting pirposes
#// For atomic ionization stages:
logSaha = [ [ 0.0 for i in range(numStages+1)] for j in range(numStages+1) ]
saha = [ [ 0.0 for i in range(numStages+1)] for j in range(numStages+1) ]
#//
logIonFrac = [ 0.0 for i in range(numStages) ]
#double expFac, logNe;
#// Now - molecular variables:
thisLogUwA = 0.0 #// element A
#thisLogQwAB = math.log(300.0)
#//For clarity: neutral stage of atom whose ionization equilibrium is being computed is element A
#// for molecule formation:
logUwA = [ 0.0 for i in range(5) ]
#JB#
uua=[]
#uub=[]
#qwab=[]
for iStg in range(numStages):
currentUwArr=list(logUw[iStg])#u(T) determined values
UwFit = ToolBox.cubicFit(masterTemp,currentUwArr)#u(T) fit
uua.append(UwFit)
#print(logUw[iStg])
for id in range(numDeps):
#//// reduce or enhance number density by over-all Rosseland opcity scale parameter
#//
#//Row 1 of Ne is log_e Ne in cm^-3
logNe = Ne[1][id]
#//Determine temperature dependent partition functions Uw:
thisTemp = temp[0][id]
#Ttheta = 5040.0 / thisTemp
#JB#
#use temps and partition values to create a function
#then use said function to extrapolate values for all points
thisLogUw[numStages] = 0.0
for iStg in range(numStages):
thisLogUw[iStg] = ToolBox.valueFromFit(uua[iStg],thisTemp)#u(T) value extrapolated
#JB#
#// NEW Determine temperature dependent partition functions Uw: lburns
if (thisTemp <= 130.0):
for iStg in range(numStages):
thisLogUw[iStg] = logUw[iStg][0]
#for iMol in range(numMols):
# thisLogUwB[iMol] = logUwB[iMol][0]
if (thisTemp >= 10000.0):
for iStg in range(numStages):
thisLogUw[iStg] = logUw[iStg][4]
#for iMol in range(numMols):
# thisLogUwB[iMol] = logUwB[iMol][4]
#//For clarity: neutral stage of atom whose ionization equilibrium is being computed is element A
#// for molecule formation:
thisLogUwA = thisLogUw[0];
#//Ionization stage Saha factors:
for iStg in range(numStages):
#print("iStg ", iStg)
logSaha[iStg+1][iStg] = logSahaFac - logNe - (boltzFacI[iStg] /temp[0][id]) + (3.0 * temp[1][id] / 2.0) + thisLogUw[iStg+1] - thisLogUw[iStg]
saha[iStg+1][iStg] = math.exp(logSaha[iStg+1][iStg])
#//Compute log of denominator is ionization fraction, f_stage
denominator = 1.0 #//default initialization - leading term is always unity
#//ion stage contributions:
for jStg in range(1, numStages+1):
addend = 1.0 #//default initialization for product series
for iStg in range(jStg):
#//console.log("jStg " + jStg + " saha[][] indices " + (iStg+1) + " " + iStg);
addend = addend * saha[iStg+1][iStg]
denominator = denominator + addend
#//
logDenominator = math.log(denominator)
logIonFrac[0] = -1.0 * logDenominator #// log ionization fraction in stage I
for jStg in range(1, numStages):
addend = 0.0 #//default initialization for product series
for iStg in range(jStg):
#//console.log("jStg " + jStg + " saha[][] indices " + (iStg+1) + " " + iStg);
addend = addend + logSaha[iStg+1][iStg]
logIonFrac[jStg] = addend - logDenominator
for iStg in range(numStages):
logNums[iStg][id] = logNum[id] + logIonFrac[iStg]
#//id loop
return logNums;
#//end method stagePops
#end method levelPops
#def stagePops2(logNum, Ne, chiIArr, log10UwAArr, \
# numMols, logNumB, dissEArr, log10UwBArr, logQwABArr, logMuABArr, \
# numDeps, temp):
def stagePops2(logNum, Ne, chiIArr, logUw, \
numMols, logNumB, dissEArr, logUwB, logQwABArr, logMuABArr, \
numDeps, temp):
#line 1: //species A data - ionization equilibrium of A
#line 2: //data for set of species "B" - molecular equlibrium for set {AB}
"""Ionization equilibrium routine that accounts for molecule formation:
// Returns depth distribution of ionization stage populations
// Input parameters:
// logNum - array with depth-dependent total element number densities (cm^-3)
// chiI1 - ground state ionization energy of neutral stage
// chiI2 - ground state ionization energy of singly ionized stage
// Also needs atsmopheric structure information:
// numDeps
// temp structure
// rho structure
// Atomic element A is the one whose ionization fractions are being computed
// Element B refers to array of other species with which A forms molecules AB """
ln10 = math.log(10.0)
logE = math.log10(math.e) #// for debug output
log2pi = math.log(2.0 * math.pi)
log2 = math.log(2.0)
numStages = len(chiIArr) #// + 1; //need one more stage above the highest stage to be populated
#// var numMols = dissEArr.length;
#// Parition functions passed in are 2-element vectore with remperature-dependent base 10 log Us
#// Convert to natural logs:
#double Ttheta, thisTemp;
#//Default initializations:
#//We need one more stage in size of saha factor than number of stages we're actualy populating
thisLogUw = [ 0.0 for i in range(numStages+1) ]
for i in range(numStages+1):
thisLogUw[i] = 0.0
logE10 = math.log(10.0)
#//atomic ionization stage Boltzmann factors:
#double logChiI, logBoltzFacI;
boltzFacI = [ 0.0 for i in range(numStages) ]
#print("numStages ", numStages, " Useful.logEv ", Useful.logEv())
for i in range(numStages):
#print("i ", i, " chiIArr ", chiIArr[i])
logChiI = math.log(chiIArr[i]) + Useful.logEv()
logBoltzFacI = logChiI - Useful.logK()
boltzFacI[i] = math.exp(logBoltzFacI)
logSahaFac = log2 + (3.0 / 2.0) * (log2pi + Useful.logMe() + Useful.logK() - 2.0 * Useful.logH())
#// return a 2D 5 x numDeps array of logarithmic number densities
#// Row 0: neutral stage ground state population
#// Row 1: singly ionized stage ground state population
#// Row 2: doubly ionized stage ground state population
#// Row 3: triply ionized stage ground state population
#// Row 4: quadruply ionized stage ground state population
#double[][] logNums = new double[numStages][numDeps];
logNums = [ [ 0.0 for i in range(numDeps)] for j in range(numStages) ]
#//We need one more stage in size of saha factor than number of stages we're actualy populating
#// for index accounting pirposes
#// For atomic ionization stages:
logSaha = [ [ 0.0 for i in range(numStages+1)] for j in range(numStages+1) ]
saha = [ [ 0.0 for i in range(numStages+1)] for j in range(numStages+1) ]
#//
logIonFrac = [ 0.0 for i in range(numStages) ]
#double expFac, logNe;
#// Now - molecular variables:
#//Treat at least one molecule - if there are really no molecules for an atomic species,
#//there will be one phantom molecule in the denominator of the ionization fraction
#//with an impossibly high dissociation energy
ifMols = True
if (numMols == 0):
ifMols = False
numMols = 1
#//This should be inherited, but let's make sure:
dissEArr[0] = 19.0 #//eV
#//Molecular partition functions - default initialization:
#double[] thisLogUwB = new double[numMols];
thisLogUwB = [ 0.0 for i in range(numMols) ]
for iMol in range(numMols):
thisLogUwB[iMol] = 0.0 #// variable for temp-dependent computed partn fn of array element B
thisLogUwA = 0.0 #// element A
thisLogQwAB = math.log(300.0)
#//For clarity: neutral stage of atom whose ionization equilibrium is being computed is element A
#// for molecule formation:
logUwA = [ 0.0 for i in range(5) ]
if (numMols > 0):
for kk in range(len(logUwA)):
logUwA[kk] = logUw[0][kk]
#// lburns
#//}
#//// Molecular partition functions:
#//Molecular dissociation Boltzmann factors:
boltzFacIAB = [ 0.0 for i in range(numMols) ]
logMolSahaFac = [ 0.0 for i in range(numMols) ]
#//if (numMols > 0){
#double logDissE, logBoltzFacIAB;
for iMol in range(numMols):
logDissE = math.log(dissEArr[iMol]) + Useful.logEv()
logBoltzFacIAB = logDissE - Useful.logK()
boltzFacIAB[iMol] = math.exp(logBoltzFacIAB)
logMolSahaFac[iMol] = (3.0 / 2.0) * (log2pi + logMuABArr[iMol] + Useful.logK() - 2.0 * Useful.logH())
#//console.log("iMol " + iMol + " dissEArr[iMol] " + dissEArr[iMol] + " logDissE " + logE*logDissE + " logBoltzFacIAB " + logE*logBoltzFacIAB + " boltzFacIAB[iMol] " + boltzFacIAB[iMol] + " logMuABArr " + logE*logMuABArr[iMol] + " logMolSahaFac " + logE*logMolSahaFac[iMol]);
#//}
#// For molecular species:
logSahaMol = [ 0.0 for i in range(numMols) ]
invSahaMol = [ 0.0 for i in range(numMols) ]
#JB#
uua=[]
uub=[]
qwab=[]
for iStg in range(numStages):
currentUwArr=list(logUw[iStg])#u(T) determined values
UwFit = ToolBox.cubicFit(masterTemp,currentUwArr)#u(T) fit
uua.append(UwFit)
#print(logUw[iStg])
for iMol in range(numMols):
currentUwBArr=list(logUwB[iMol])#u(T) determined values
UwBFit = ToolBox.cubicFit(masterTemp,currentUwBArr)#u(T) fit
uub.append(UwBFit)
for id in range(numDeps):
#//// reduce or enhance number density by over-all Rosseland opcity scale parameter
#//
#//Row 1 of Ne is log_e Ne in cm^-3
logNe = Ne[1][id]
#//Determine temperature dependent partition functions Uw:
thisTemp = temp[0][id]
#Ttheta = 5040.0 / thisTemp
#JB#
#use temps and partition values to create a function
#then use said function to extrapolate values for all points
thisLogUw[numStages] = 0.0
for iStg in range(numStages):
thisLogUw[iStg] = ToolBox.valueFromFit(uua[iStg],thisTemp)#u(T) value extrapolated
for iMol in range(numMols):
thisLogUwB[iMol] = ToolBox.valueFromFit(uub[iMol],thisTemp)#u(T) value extrapolated
#JB#
#// NEW Determine temperature dependent partition functions Uw: lburns
if (thisTemp <= 130.0):
for iStg in range(numStages):
thisLogUw[iStg] = logUw[iStg][0]
for iMol in range(numMols):
thisLogUwB[iMol] = logUwB[iMol][0]
if (thisTemp >= 10000.0):
for iStg in range(numStages):
thisLogUw[iStg] = logUw[iStg][4]
for iMol in range(numMols):
thisLogUwB[iMol] = logUwB[iMol][4]
for iMol in range(numMols):
if (thisTemp < 3000.0):
thisLogQwAB = ( logQwABArr[iMol][1] * (3000.0 - thisTemp)/(3000.0 - 500.0) ) \
+ ( logQwABArr[iMol][2] * (thisTemp - 500.0)/(3000.0 - 500.0) )
if ( (thisTemp >= 3000.0) and (thisTemp <= 8000.0) ):
thisLogQwAB = ( logQwABArr[iMol][2] * (8000.0 - thisTemp)/(8000.0 - 3000.0) ) \
+ ( logQwABArr[iMol][3] * (thisTemp - 3000.0)/(8000.0 - 3000.0) )
if ( thisTemp > 8000.0 ):
thisLogQwAB = ( logQwABArr[iMol][3] * (10000.0 - thisTemp)/(10000.0 - 8000.0) ) \
+ ( logQwABArr[iMol][4] * (thisTemp - 8000.0)/(10000.0 - 8000.0) )
#// iMol loop
#//For clarity: neutral stage of atom whose ionization equilibrium is being computed is element A
#// for molecule formation:
thisLogUwA = thisLogUw[0];
#//Ionization stage Saha factors:
for iStg in range(numStages):
#print("iStg ", iStg)
logSaha[iStg+1][iStg] = logSahaFac - logNe - (boltzFacI[iStg] /temp[0][id]) + (3.0 * temp[1][id] / 2.0) + thisLogUw[iStg+1] - thisLogUw[iStg]
saha[iStg+1][iStg] = math.exp(logSaha[iStg+1][iStg])
#//Molecular Saha factors:
for iMol in range(numMols):
logSahaMol[iMol] = logMolSahaFac[iMol] - logNumB[iMol][id] - (boltzFacIAB[iMol] / temp[0][id]) + (3.0 * temp[1][id] / 2.0) + thisLogUwB[iMol] + thisLogUwA - thisLogQwAB
#//For denominator of ionization fraction, we need *inverse* molecular Saha factors (N_AB/NI):
logSahaMol[iMol] = -1.0 * logSahaMol[iMol]
invSahaMol[iMol] = math.exp(logSahaMol[iMol])
#//Compute log of denominator is ionization fraction, f_stage
denominator = 1.0 #//default initialization - leading term is always unity
#//ion stage contributions:
for jStg in range(1, numStages+1):
addend = 1.0 #//default initialization for product series
for iStg in range(jStg):
#//console.log("jStg " + jStg + " saha[][] indices " + (iStg+1) + " " + iStg);
addend = addend * saha[iStg+1][iStg]
denominator = denominator + addend
#//molecular contribution
if (ifMols == True):
for iMol in range(numMols):
denominator = denominator + invSahaMol[iMol]
#//
logDenominator = math.log(denominator)
logIonFrac[0] = -1.0 * logDenominator #// log ionization fraction in stage I
for jStg in range(1, numStages):
addend = 0.0 #//default initialization for product series
for iStg in range(jStg):
#//console.log("jStg " + jStg + " saha[][] indices " + (iStg+1) + " " + iStg);
addend = addend + logSaha[iStg+1][iStg]
logIonFrac[jStg] = addend - logDenominator
for iStg in range(numStages):
logNums[iStg][id] = logNum[id] + logIonFrac[iStg]
#//id loop
return logNums;
#//end method stagePops
def stagePops3(logNum, Ne, chiIArr, logUw, numDeps, temp):
#Version for ChromaStarPyGas: logNum is now *neutral stage* population from Phil
# Bennett's GAS package
#line 1: //species A data - ionization equilibrium of A
#line 2: //data for set of species "B" - molecular equlibrium for set {AB}
"""Ionization equilibrium routine that accounts for molecule formation:
// Returns depth distribution of ionization stage populations
// Input parameters:
// logNum - array with depth-dependent neutral stage number densities (cm^-3)
// chiI1 - ground state ionization energy of neutral stage
// chiI2 - ground state ionization energy of singly ionized stage
// Also needs atsmopheric structure information:
// numDeps
// temp structure
// rho structure
// Atomic element A is the one whose ionization fractions are being computed
// Element B refers to array of other species with which A forms molecules AB """
ln10 = math.log(10.0)
logE = math.log10(math.e) #// for debug output
log2pi = math.log(2.0 * math.pi)
log2 = math.log(2.0)
numStages = len(chiIArr) #// + 1; //need one more stage above the highest stage to be populated
#// var numMols = dissEArr.length;
#// Parition functions passed in are 2-element vectore with remperature-dependent base 10 log Us
#// Convert to natural logs:
#double Ttheta, thisTemp;
#//Default initializations:
#//We need one more stage in size of saha factor than number of stages we're actualy populating
thisLogUw = [ 0.0 for i in range(numStages+1) ]
for i in range(numStages+1):
thisLogUw[i] = 0.0
logE10 = math.log(10.0)
#//atomic ionization stage Boltzmann factors:
#double logChiI, logBoltzFacI;
boltzFacI = [ 0.0 for i in range(numStages) ]
#print("numStages ", numStages, " Useful.logEv ", Useful.logEv())
for i in range(numStages):
#print("i ", i, " chiIArr ", chiIArr[i])
logChiI = math.log(chiIArr[i]) + Useful.logEv()
logBoltzFacI = logChiI - Useful.logK()
boltzFacI[i] = math.exp(logBoltzFacI)
logSahaFac = log2 + (3.0 / 2.0) * (log2pi + Useful.logMe() + Useful.logK() - 2.0 * Useful.logH())
#// return a 2D 5 x numDeps array of logarithmic number densities
#// Row 0: neutral stage ground state population
#// Row 1: singly ionized stage ground state population
#// Row 2: doubly ionized stage ground state population
#// Row 3: triply ionized stage ground state population
#// Row 4: quadruply ionized stage ground state population
#double[][] logNums = new double[numStages][numDeps];
logNums = [ [ 0.0 for i in range(numDeps)] for j in range(numStages) ]
#//We need one more stage in size of saha factor than number of stages we're actualy populating
#// for index accounting pirposes
#// For atomic ionization stages:
#logSaha = [ [ 0.0 for i in range(numStages+1)] for j in range(numStages+1) ]
#saha = [ [ 0.0 for i in range(numStages+1)] for j in range(numStages+1) ]
#//
#logIonFrac = [ 0.0 for i in range(numStages) ]
#double expFac, logNe;
#JB#
uua=[]
uub=[]
qwab=[]
for iStg in range(numStages):
currentUwArr=list(logUw[iStg])#u(T) determined values
UwFit = ToolBox.cubicFit(masterTemp,currentUwArr)#u(T) fit
uua.append(UwFit)
#print(logUw[iStg])
for id in range(numDeps):
#//// reduce or enhance number density by over-all Rosseland opcity scale parameter
#//
#//Row 1 of Ne is log_e Ne in cm^-3
logNe = Ne[1][id]
#//Determine temperature dependent partition functions Uw:
thisTemp = temp[0][id]
#Ttheta = 5040.0 / thisTemp
#JB#
#use temps and partition values to create a function
#then use said function to extrapolate values for all points
thisLogUw[numStages] = 0.0
for iStg in range(numStages):
thisLogUw[iStg] = ToolBox.valueFromFit(uua[iStg],thisTemp)#u(T) value extrapolated
#JB#
#// NEW Determine temperature dependent partition functions Uw: lburns
if (thisTemp <= 130.0):
for iStg in range(numStages):
thisLogUw[iStg] = logUw[iStg][0]
if (thisTemp >= 10000.0):
for iStg in range(numStages):
thisLogUw[iStg] = logUw[iStg][4]
#//For clarity: neutral stage of atom whose ionization equilibrium is being computed is element A
#// for molecule formation:
#thisLogUwA = thisLogUw[0];
#//Ionization stage Saha factors:
logNums[0][id] = logNum[id]
for iStg in range(1, numStages):
#print("iStg ", iStg)
thisLogSaha = logSahaFac - logNe - (boltzFacI[iStg-1] /temp[0][id]) + (3.0 * temp[1][id] / 2.0) + thisLogUw[iStg] - thisLogUw[iStg-1]
#saha[iStg+1][iStg] = math.exp(logSaha[iStg+1][iStg])
logNums[iStg][id] = logNums[iStg-1][id] + thisLogSaha
#//id loop
return logNums;
#//end method stagePops
#def sahaRHS(chiI, log10UwUArr, log10UwLArr, temp):
def sahaRHS(chiI, logUwU, logUwL, temp):
"""RHS of partial pressure formulation of Saha equation in standard form (N_U*P_e/N_L on LHS)
// Returns depth distribution of LHS: Phi(T) === N_U*P_e/N_L (David Gray notation)
// Input parameters:
// chiI - ground state ionization energy of lower stage
// log10UwUArr, log10UwLArr - array of temperature-dependent partition function for upper and lower ionization stage
// Also needs atsmopheric structure information:
// numDeps
// temp structure
//
// Atomic element "A" is the one whose ionization fractions are being computed
// Element "B" refers to array of other species with which A forms molecules "AB" """
ln10 = math.log(10.0)
logE = math.log10(math.e) #// for debug output
log2pi = math.log(2.0 * math.pi)
log2 = math.log(2.0)
#// var numMols = dissEArr.length;
#// Parition functions passed in are 2-element vectore with remperature-dependent base 10 log Us
#// Convert to natural logs:
#double Ttheta, thisTemp;
#//Default initializations:
#//We need one more stage in size of saha factor than number of stages we're actualy populating
thisLogUwU = 0.0
thisLogUwL = 0.0
logE10 = math.log(10.0)
#//We need one more stage in size of saha factor than number of stages we're actualy populating
#logUwU = [0.0 for i in range(5)]
#logUwL = [0.0 for i in range(5)]
for kk in range(len(logUwL)):
logUwU[kk] = logUwL[kk]
# logUwL[kk] = logE10*log10UwLArr[kk]
#//System.out.println("chiL before: " + chiL);
#// If we need to subtract chiI from chiL, do so *before* converting to tiny numbers in ergs!
#//atomic ionization stage Boltzmann factors:
#double logChiI, logBoltzFacI;
#double boltzFacI;
logChiI = math.log(chiI) + Useful.logEv()
logBoltzFacI = logChiI - Useful.logK()
boltzFacI = math.exp(logBoltzFacI)
#//Extra factor of k to get k^5/2 in the P_e formulation of Saha Eq.
logSahaFac = log2 + (3.0 / 2.0) * (log2pi + Useful.logMe() + Useful.logK() - 2.0 * Useful.logH()) + Useful.logK()
#//double[] logLHS = new double[numDeps];
#double logLHS;
#// For atomic ionization stages:
#double logSaha, saha, expFac;
#// for (int id = 0; id < numDeps; id++) {
#//
#//Determine temperature dependent partition functions Uw:
thisTemp = temp[0]
#Ttheta = 5040.0 / thisTemp
"""
if (Ttheta >= 1.0):
thisLogUwU = logUwU[0]
thisLogUwL = logUwL[0]
if (Ttheta <= 0.5):
thisLogUwU = logUwU[1]
thisLogUwL = logUwL[1]
if (Ttheta > 0.5 and Ttheta < 1.0):
thisLogUwU = ( logUwU[1] * (Ttheta - 0.5)/(1.0 - 0.5) )
+ ( logUwU[0] * (1.0 - Ttheta)/(1.0 - 0.5) )
thisLogUwL = ( logUwL[1] * (Ttheta - 0.5)/(1.0 - 0.5) )
+ ( logUwL[0] * (1.0 - Ttheta)/(1.0 - 0.5) )
"""
#JB#
currentUwUArr=list(logUwU)#u(T) determined values
UwUFit = ToolBox.cubicFit(masterTemp,currentUwUArr)#u(T) fit
thisLogUwU = ToolBox.valueFromFit(UwUFit,thisTemp)#u(T) value extrapolated
currentUwLArr=list(logUwL)#u(T) determined values
UwLFit = ToolBox.cubicFit(masterTemp,currentUwLArr)#u(T) fit
thisLogUwL = ToolBox.valueFromFit(UwLFit,thisTemp)#u(T) value extrapolated
#JB#
#will need to do this one in Main as it goes through its own loop of temp
#if thisTemp == superTemp[0][len(superTemp[0])]:
# uwu.append(UwUFit)
# uwl.append(UwLFit)
#
#JB#
if (thisTemp <= 130.0):
thisLogUwU = logUwU[0]
thisLogUwL = logUwL[0]
if (thisTemp >= 10000.0):
thisLogUwU = logUwU[4]
thisLogUwL = logUwL[4]
"""
if (thisTemp > 130 and thisTemp <= 500):
thisLogUwU = logUwU[1] * (thisTemp - 130)/(500 - 130) \
+ logUwU[0] * (500 - thisTemp)/(500 - 130)
thisLogUwL = logUwL[1] * (thisTemp - 130)/(500 - 130) \
+ logUwL[0] * (500 - thisTemp)/(500 - 130)
if (thisTemp > 500 and thisTemp <= 3000):
thisLogUwU = logUwU[2] * (thisTemp - 500)/(3000 - 500) \
+ logUwU[1] * (3000 - thisTemp)/(3000 - 500)
thisLogUwL = logUwL[2] * (thisTemp - 500)/(3000 - 500) \
+ logUwL[1] * (3000 - thisTemp)/(3000 - 500)
if (thisTemp > 3000 and thisTemp <= 8000):
thisLogUwU = logUwU[3] * (thisTemp - 3000)/(8000 - 3000) \
+ logUwU[2] * (8000 - thisTemp)/(8000 - 3000)
thisLogUwL = logUwL[3] * (thisTemp - 3000)/(8000 - 3000) \
+ logUwL[2] * (8000 - thisTemp)/(8000 - 3000)
if (thisTemp > 8000 and thisTemp < 10000):
thisLogUwU = logUwU[4] * (thisTemp - 8000)/(10000 - 8000) \
+ logUwU[3] * (10000 - thisTemp)/(10000 - 8000)
thisLogUwL = logUwL[4] * (thisTemp - 8000)/(10000 - 8000) \
+ logUwL[3] * (10000 - thisTemp)/(10000 - 8000)
if (thisTemp >= 10000):
thisLogUwU = logUwU[4]
thisLogUwL = logUwL[4]
"""
#//Ionization stage Saha factors:
#//Need T_kin^5/2 in the P_e formulation of Saha Eq.
logSaha = logSahaFac - (boltzFacI /temp[0]) + (5.0 * temp[1] / 2.0) + thisLogUwU - thisLogUwL
#// saha = Math.exp(logSaha);
#//logLHS[id] = logSaha;
logLHS = logSaha;
#// } //id loop
return logLHS;
#JB
#return [logLHS,[[UwUFit,thisLogUwU],[UwLFit,thisLogUwL]]]
#//
# } //end method sahaRHS
#def molPops(nmrtrLogNumB, nmrtrDissE, log10UwA, nmrtrLog10UwB, nmrtrLogQwAB, nmrtrLogMuAB, \
# numMolsB, logNumB, dissEArr, log10UwBArr, logQwABArr, logMuABArr, \
# logGroundRatio, numDeps, temp):
def molPops(nmrtrLogNumB, nmrtrDissE, logUwA, nmrtrLogUwB, nmrtrLogQwAB, nmrtrLogMuAB, \
numMolsB, logNumB, dissEArr, logUwB, logQwABArr, logMuABArr, \
logGroundRatio, numDeps, temp):
# line 1: //species A data - ionization equilibrium of A
# //data for set of species "B" - molecular equlibrium for set {AB}
"""Diatomic molecular equilibrium routine that accounts for molecule formation:
// Returns depth distribution of molecular population
// Input parameters:
// logNum - array with depth-dependent total element number densities (cm^-3)
// chiI1 - ground state ionization energy of neutral stage
// chiI2 - ground state ionization energy of singly ionized stage
// Also needs atsmopheric structure information:
// numDeps
// temp structure
// rho structure
//
// Atomic element "A" is the one kept on the LHS of the master fraction, whose ionization fractions are included
// in the denominator of the master fraction
// Element "B" refers to array of other sintpecies with which A forms molecules "AB" """
logE = math.log10(math.e) #// for debug output
#//System.out.println("molPops: nmrtrDissE " + nmrtrDissE + " log10UwA " + log10UwA[0] + " " + log10UwA[1] + " nmrtrLog10UwB " +
#// nmrtrLog10UwB[0] + " " + nmrtrLog10UwB[1] + " nmrtrLog10QwAB " + logE*nmrtrLogQwAB[2] + " nmrtrLogMuAB " + logE*nmrtrLogMuAB
#// + " numMolsB " + numMolsB + " dissEArr " + dissEArr[0] + " log10UwBArr " + log10UwBArr[0][0] + " " + log10UwBArr[0][1] + " log10QwABArr " +
#// logE*logQwABArr[0][2] + " logMuABArr " + logE*logMuABArr[0]);
#//System.out.println("Line: nmrtrLog10UwB[0] " + logE*nmrtrLog10UwB[0] + " nmrtrLog10UwB[1] " + logE*nmrtrLog10UwB[1]);
ln10 = math.log(10.0)
log2pi = math.log(2.0 * math.pi)
log2 = math.log(2.0)
logE10 = math.log(10.0)
#// Convert to natural logs:
#double Ttheta, thisTemp;
#//Treat at least one molecule - if there are really no molecules for an atomic species,
#//there will be one phantom molecule in the denominator of the ionization fraction
#//with an impossibly high dissociation energy
if (numMolsB == 0):
numMolsB = 1
#//This should be inherited, but let's make sure:
dissEArr[0] = 29.0 #//eV
#//var molPops = function(logNum, numeratorLogNumB, numeratorDissE, numeratorLog10UwA, numeratorLog10QwAB, numeratorLogMuAB, //species A data - ionization equilibrium of A
#//Molecular partition functions - default initialization:
thisLogUwB = [0.0 for i in range(numMolsB)]
for iMol in range(numMolsB):
thisLogUwB[iMol] = 0.0 #// variable for temp-dependent computed partn fn of array element B
thisLogUwA = 0.0 #// element A
nmrtrThisLogUwB = 0.0 #// element A
thisLogQwAB = math.log(300.0)
nmrtrThisLogQwAB = math.log(300.0)
#//For clarity: neutral stage of atom whose ionization equilibrium is being computed is element A
#// for molecule formation:
#logUwA = [0.0 for i in range(5)]
#nmrtrLogUwB = [0.0 for i in range(5)]
#for kk in range(len(logUwA)):
#logUwA[kk] = logE10*log10UwA[kk]
#nmrtrLogUwB[kk] = logE10*nmrtrLog10UwB[kk]
#// lburns
#// Array of elements B for all molecular species AB:
#double[][] logUwB = new double[numMolsB][2];
#logUwB = [ [ 0.0 for i in range(5) ] for j in range(numMolsB) ]
#//if (numMolsB > 0){
#for iMol in range(numMolsB):
# for kk in range(5):
# logUwB[iMol][kk] = logE10*log10UwBArr[iMol][kk]
# // lburns new loop
#//}
#// Molecular partition functions:
#// double nmrtrLogQwAB = logE10*nmrtrLog10QwAB;
#// double[] logQwAB = new double[numMolsB];
#// //if (numMolsB > 0){
#// for (int iMol = 0; iMol < numMolsB; iMol++){
#// logQwAB[iMol] = logE10*log10QwABArr[iMol];
#// }
# //}
#//Molecular dissociation Boltzmann factors:
nmrtrBoltzFacIAB = 0.0
nmrtrLogMolSahaFac = 0.0
logDissE = math.log(nmrtrDissE) + Useful.logEv()
#//System.out.println("logDissE " + logE*logDissE)
logBoltzFacIAB = logDissE - Useful.logK()
#//System.out.println("logBoltzFacIAB " + logE*logBoltzFacIAB);
nmrtrBoltzFacIAB = math.exp(logBoltzFacIAB)
nmrtrLogMolSahaFac = (3.0 / 2.0) * (log2pi + nmrtrLogMuAB + Useful.logK() - 2.0 * Useful.logH())
#//System.out.println("nmrtrLogMolSahaFac " + logE*nmrtrLogMolSahaFac);
#//System.out.println("nmrtrDissE " + nmrtrDissE + " logDissE " + logE*logDissE + " logBoltzFacIAB " + logE*logBoltzFacIAB + " nmrtrBoltzFacIAB " + nmrtrBoltzFacIAB + " nmrtrLogMuAB " + logE*nmrtrLogMuAB + " nmrtrLogMolSahaFac " + logE*nmrtrLogMolSahaFac);
boltzFacIAB = [0.0 for i in range(numMolsB)]
logMolSahaFac = [0.0 for i in range(numMolsB)]
#//if (numMolsB > 0){
for iMol in range(numMolsB):
logDissE = math.log(dissEArr[iMol]) + Useful.logEv()
logBoltzFacIAB = logDissE - Useful.logK()
boltzFacIAB[iMol] = math.exp(logBoltzFacIAB)
logMolSahaFac[iMol] = (3.0 / 2.0) * (log2pi + logMuABArr[iMol] + Useful.logK() - 2.0 * Useful.logH())
#//System.out.println("logMolSahaFac[iMol] " + logE*logMolSahaFac[iMol]);
#//System.out.println("iMol " + iMol + " dissEArr[iMol] " + dissEArr[iMol] + " logDissE " + logE*logDissE + " logBoltzFacIAB " + logE*logBoltzFacIAB + " boltzFacIAB[iMol] " + boltzFacIAB[iMol] + " logMuABArr " + logE*logMuABArr[iMol] + " logMolSahaFac " + logE*logMolSahaFac[iMol]);
#//double[] logNums = new double[numDeps]
#//}
#// For molecular species:
#double nmrtrSaha, nmrtrLogSahaMol, nmrtrLogInvSahaMol; //, nmrtrInvSahaMol;
logMolFrac = [0.0 for i in range(numDeps)]
logSahaMol = [0.0 for i in range(numMolsB)]
invSahaMol = [0.0 for i in range(numMolsB)]
#JB#
currentUwAArr=list(logUwA)#u(T) determined values
UwAFit = ToolBox.cubicFit(masterTemp, currentUwAArr)#u(T) fit
nmrtrLogUwBArr=list(nmrtrLogUwB)#u(T) determined values
nmrtrLogUwBFit = ToolBox.cubicFit(masterTemp, nmrtrLogUwBArr)#u(T) fit
#uwa.append(UwAFit)
#uwb.append(nmrtrLogUwBFit)
uwbFits=[]
qwabFit = []
for iMol in range(numMolsB):
currentUwBArr=list(logUwB[iMol])
UwBFit = ToolBox.cubicFit(masterTemp, currentUwBArr)
uwbFits.append(UwBFit)
currentLogQwABArr=list(logQwABArr[iMol])#u(T) determined values
QwABFit = ToolBox.cubicFit(masterTemp, currentLogQwABArr)#u(T) fit
qwabFit.append(QwABFit)
#nmrtrQwABArr=list(nmrtrLogQwAB)#u(T) determined values
#nmrtrQwABFit = ToolBox.cubicFit(masterTemp, nmrtrQwABArr)#u(T) fit
#for Mols in range(numMolsB):
# currentLogUwBArr=list(logUwB[Mols])#u(T) determined values
# UwBFit=cubicFit(masterTemp,currentLogUwBArr)#u(T) fit
#JB#
#//
temps=[]
#valb=[]
#vala=[]
#valnb=[]
#valqab=[]
#valnmrtrqwb=[]
#// System.out.println("molPops: id nmrtrLogNumB logNumBArr[0] logGroundRatio");
for id in range(numDeps):
#//System.out.format("%03d, %21.15f, %21.15f, %21.15f, %n", id, logE*nmrtrLogNumB[id], logE*logNumB[0][id], logE*logGroundRatio[id]);
#//// reduce or enhance number density by over-all Rosseland opcity scale parameter
#//Determine temparature dependent partition functions Uw:
thisTemp = temp[0][id]
temps.append(thisTemp)
#Ttheta = 5040.0 / thisTemp
"""
if (Ttheta >= 1.0):
thisLogUwA = logUwA[0]
nmrtrThisLogUwB = nmrtrLogUwB[0]
for iMol in range(numMolsB):
thisLogUwB[iMol] = logUwB[iMol][0]
if (Ttheta <= 0.5):
thisLogUwA = logUwA[1]
nmrtrThisLogUwB = nmrtrLogUwB[1]
for iMol in range(numMolsB):
thisLogUwB[iMol] = logUwB[iMol][1]
if (Ttheta > 0.5 and Ttheta < 1.0):
thisLogUwA = ( logUwA[1] * ((Ttheta - 0.5)/(1.0 - 0.5)) ) \
+ ( logUwA[0] * ((1.0 - Ttheta)/(1.0 - 0.5)) )
nmrtrThisLogUwB = ( nmrtrLogUwB[1] * ((Ttheta - 0.5)/(1.0 - 0.5)) ) \
+ ( nmrtrLogUwB[0] * ((1.0 - Ttheta)/(1.0 - 0.5)) )
for iMol in range(numMolsB):
thisLogUwB[iMol] = ( logUwB[iMol][1] * ((Ttheta - 0.5)/(1.0 - 0.5)) ) \
+ ( logUwB[iMol][0] * ((1.0 - Ttheta)/(1.0 - 0.5)) )
"""
#JB#
thisLogUwA = float(ToolBox.valueFromFit(UwAFit,thisTemp))#u(T) value extrapolated
#vala.append(thisLogUwA)
nmrtrThisLogUwB = float(ToolBox.valueFromFit(nmrtrLogUwBFit,thisTemp))#u(T) value extrapolated
#valnb.append(nmrtrThisLogUwB)
#for iMol in range(numMolsB):
# thisLogUwB[iMol]=logUwB[iMol]
for iMol in range(numMolsB):
thisLogUwB[iMol] = ToolBox.valueFromFit(uwbFits[iMol],thisTemp)#u(T) value extrapolated
#valb.append(thisLogUwB[iMol])
#// NEW Determine temperature dependent partition functions Uw: lburns
thisTemp = temp[0][id]
if (thisTemp <= 130.0):
thisLogUwA = logUwA[0]
nmrtrThisLogUwB = nmrtrLogUwB[0]
for iMol in range(numMolsB):
thisLogUwB[iMol] = logUwB[iMol][0]
if (thisTemp >= 10000.0):
thisLogUwA = logUwA[4]
nmrtrThisLogUwB = nmrtrLogUwB[4]
for iMol in range(numMolsB):
thisLogUwB[iMol] = logUwB[iMol][4]
"""
if (thisTemp > 130 and thisTemp <= 500):
thisLogUwA = logUwA[1] * (thisTemp - 130)/(500 - 130) \
+ logUwA[0] * (500 - thisTemp)/(500 - 130)
nmrtrThisLogUwB = nmrtrLogUwB[1] * (thisTemp - 130)/(500 - 130) \
+ nmrtrLogUwB[0] * (500 - thisTemp)/(500 - 130)
for iMol in range(numMolsB):
thisLogUwB[iMol] = logUwB[iMol][1] * (thisTemp - 130)/(500 - 130) \
+ logUwB[iMol][0] * (500 - thisTemp)/(500 - 130)
if (thisTemp > 500 and thisTemp <= 3000):
thisLogUwA = logUwA[2] * (thisTemp - 500)/(3000 - 500) \
+ logUwA[1] * (3000 - thisTemp)/(3000 - 500)
nmrtrThisLogUwB = nmrtrLogUwB[2] * (thisTemp - 500)/(3000 - 500) \
+ nmrtrLogUwB[1] * (3000 - thisTemp)/(3000 - 500)
for iMol in range(numMolsB):
thisLogUwB[iMol] = logUwB[iMol][2] * (thisTemp - 500)/(3000 - 500) \
+ logUwB[iMol][1] * (3000 - thisTemp)/(3000 - 500)
if (thisTemp > 3000 and thisTemp <= 8000):
thisLogUwA = logUwA[3] * (thisTemp - 3000)/(8000 - 3000) \
+ logUwA[2] * (8000 - thisTemp)/(8000 - 3000)
nmrtrThisLogUwB = nmrtrLogUwB[3] * (thisTemp - 3000)/(8000 - 3000) \
+ nmrtrLogUwB[2] * (8000 - thisTemp)/(8000 - 3000)
for iMol in range(numMolsB):
thisLogUwB[iMol] = logUwB[iMol][3] * (thisTemp - 3000)/(8000 - 3000) \
+ logUwB[iMol][2] * (8000 - thisTemp)/(8000 - 3000)
if (thisTemp > 8000 and thisTemp < 10000):
thisLogUwA = logUwA[4] * (thisTemp - 8000)/(10000 - 8000) \
+ logUwA[3] * (10000 - thisTemp)/(10000 - 8000)
nmrtrThisLogUwB = nmrtrLogUwB[4] * (thisTemp - 8000)/(10000 - 8000) \
+ nmrtrLogUwB[3] * (10000 - thisTemp)/(10000 - 8000)
for iMol in range(numMolsB):
thisLogUwB[iMol] = logUwB[iMol][4] * (thisTemp - 8000)/(10000 - 8000) \
+ logUwB[iMol][3] * (10000 - thisTemp)/(10000 - 8000)
if (thisTemp >= 10000):
thisLogUwA = logUwA[4]
nmrtrThisLogUwB = nmrtrLogUwB[4]
for iMol in range(numMolsB):
thisLogUwB[iMol] = logUwB[iMol][4]
"""
#iMol loops for Q's
for iMol in range(numMolsB):
if (thisTemp < 3000.0):
thisLogQwAB = ( logQwABArr[iMol][1] * (3000.0 - thisTemp)/(3000.0 - 500.0) ) \
+ ( logQwABArr[iMol][2] * (thisTemp - 500.0)/(3000.0 - 500.0) )
if ( (thisTemp >= 3000.0) and (thisTemp <= 8000.0) ):
thisLogQwAB = ( logQwABArr[iMol][2] * (8000.0 - thisTemp)/(8000.0 - 3000.0) ) \
+ ( logQwABArr[iMol][3] * (thisTemp - 3000.0)/(8000.0 - 3000.0) )
if ( thisTemp > 8000.0 ):
thisLogQwAB = ( logQwABArr[iMol][3] * (10000.0 - thisTemp)/(10000.0 - 8000.0) ) \
+ ( logQwABArr[iMol][4] * (thisTemp - 8000.0)/(10000.0 - 8000.0) )
if (thisTemp < 3000.0):
nmrtrThisLogQwAB = ( nmrtrLogQwAB[1] * (3000.0 - thisTemp)/(3000.0 - 500.0) ) \
+ ( nmrtrLogQwAB[2] * (thisTemp - 500.0)/(3000.0 - 500.0) )
if ( (thisTemp >= 3000.0) and (thisTemp <= 8000.0) ):
nmrtrThisLogQwAB = ( nmrtrLogQwAB[2] * (8000.0 - thisTemp)/(8000.0 - 3000.0) ) \
+ ( nmrtrLogQwAB[3] * (thisTemp - 3000.0)/(8000.0 - 3000.0) )
if ( thisTemp > 8000.0 ):
nmrtrThisLogQwAB = ( nmrtrLogQwAB[3] * (10000.0 - thisTemp)/(10000.0 - 8000.0) ) \
+ ( nmrtrLogQwAB[4] * (thisTemp - 8000.0)/(10000.0 - 8000.0) )
#//For clarity: neutral stage of atom whose ionization equilibrium is being computed is element A
#// for molecule formation:
# //Ionization stage Saha factors:
#//System.out.println("id " + id + " nmrtrLogNumB[id] " + logE*nmrtrLogNumB[id]);
# // if (id == 16){
# // System.out.println("id " + id + " nmrtrLogNumB[id] " + logE*nmrtrLogNumB[id] + " pp nmrtB " + (logE*(nmrtrLogNumB[id]+temp[1][id]+Useful.logK())) + " nmrtrThisLogUwB " + logE*nmrtrThisLogUwB + " thisLogUwA " + logE*thisLogUwA + " nmrtrLogQwAB " + logE*nmrtrThisLogQwAB);
# //System.out.println("nmrtrThisLogUwB " + logE*nmrtrThisLogUwB + " thisLogUwA " + logE*thisLogUwA + " nmrtrThisLogQwAB " + logE*nmrtrThisLogQwAB);
# // }
nmrtrLogSahaMol = nmrtrLogMolSahaFac - nmrtrLogNumB[id] - (nmrtrBoltzFacIAB / temp[0][id]) + (3.0 * temp[1][id] / 2.0) + nmrtrThisLogUwB + thisLogUwA - nmrtrThisLogQwAB
nmrtrLogInvSahaMol = -1.0 * nmrtrLogSahaMol
#//System.out.println("nmrtrLogInvSahaMol " + logE*nmrtrLogInvSahaMol);
#//nmrtrInvSahaMol = Math.exp(nmrtrLogSahaMol);
#// if (id == 16){
#// System.out.println("nmrtrLogInvSahaMol " + logE*nmrtrLogInvSahaMol);
#// }
#// if (id == 16){
#// System.out.println("nmrtrBoltzFacIAB " + nmrtrBoltzFacIAB + " nmrtrThisLogUwB " + logE*nmrtrThisLogUwB + " thisLogUwA " + logE*thisLogUwA + " nmrtrThisLogQwAB " + nmrtrThisLogQwAB);
#// System.out.println("nmrtrLogSahaMol " + logE*nmrtrLogSahaMol); // + " nmrtrInvSahaMol " + nmrtrInvSahaMol);
#// }
#//Molecular Saha factors:
for iMol in range(numMolsB):
#//System.out.println("iMol " + iMol + " id " + id + " logNumB[iMol][id] " + logE*nmrtrLogNumB[id]);
#//System.out.println("iMol " + iMol + " thisLogUwB[iMol] " + logE*thisLogUwB[iMol] + " thisLogUwA " + logE*thisLogUwA + " thisLogQwAB " + logE*thisLogQwAB);
logSahaMol[iMol] = logMolSahaFac[iMol] - logNumB[iMol][id] - (boltzFacIAB[iMol] / temp[0][id]) + (3.0 * temp[1][id] / 2.0) + float(thisLogUwB[iMol]) + thisLogUwA - thisLogQwAB
#//For denominator of ionization fraction, we need *inverse* molecular Saha factors (N_AB/NI):
logSahaMol[iMol] = -1.0 * logSahaMol[iMol]
invSahaMol[iMol] = math.exp(logSahaMol[iMol])
#//TEST invSahaMol[iMol] = 1.0e-99; //test
#// if (id == 16){
#// System.out.println("iMol " + iMol + " boltzFacIAB[iMol] " + boltzFacIAB[iMol] + " thisLogUwB[iMol] " + logE*thisLogUwB[iMol] + " logQwAB[iMol] " + logE*thisLogQwAB + " logNumB[iMol][id] " + logE*logNumB[iMol][id] + " logMolSahaFac[iMol] " + logE*logMolSahaFac[iMol]);
#// System.out.println("iMol " + iMol + " logSahaMol " + logE*logSahaMol[iMol] + " invSahaMol[iMol] " + invSahaMol[iMol]);
#// }
#//Compute log of denominator is ionization fraction, f_stage
# //default initialization
# // - ratio of total atomic particles in all ionization stages to number in ground state:
denominator = math.exp(logGroundRatio[id]) #//default initialization - ratio of total atomic particles in all ionization stages to number in ground state
#//molecular contribution
for iMol in range(numMolsB):
#// if (id == 16){
#// System.out.println("invSahaMol[iMol] " + invSahaMol[iMol] + " denominator " + denominator);
#// }
denominator = denominator + invSahaMol[iMol]
#//
logDenominator = math.log(denominator)
#//System.out.println("logGroundRatio[id] " + logE*logGroundRatio[id] + " logDenominator " + logE*logDenominator);
#// if (id == 16){
#// System.out.println("id " + id + " logGroundRatio " + logGroundRatio[id] + " logDenominator " + logDenominator);
#// }
#//if (id == 36){
#// System.out.println("logDenominator " + logE*logDenominator);
#// }
#//var logDenominator = Math.log( 1.0 + saha21 + (saha32 * saha21) + (saha43 * saha32 * saha21) + (saha54 * saha43 * saha32 * saha21) );
logMolFrac[id] = nmrtrLogInvSahaMol - logDenominator
#// if (id == 16){
#// System.out.println("id " + id + " logMolFrac[id] " + logE*logMolFrac[id]);
#// }
#//logNums[id] = logNum[id] + logMolFrac;
#} //id loop
#JB - check (never used)#
#print(uwa)
#print(uwb)
#title("logUwA")
"""
plot(temps,vala)
tempT=[]
for t in masterTemp:
tempT.append(valueFromFit(UwAFit,t))
scatter(masterTemp,(tempT))
show()
#title("nmrtrlogUwB")
plot(temps,valnb)
tempT=[]
for t in masterTemp:
tempT.append(valueFromFit(nmrtrLogUwBFit,t))
scatter(masterTemp,(tempT))
show()
#title("logUwB")
plot(temps,valb)
tempT=[]
for t in masterTemp:
tempT.append(valueFromFit(UwBFit,t))
scatter(masterTemp,(tempT))
show()
#title("logQwAB")
plot(temps,valqab)
tempT=[]
for t in masterTemp:
tempT.append(valueFromFit(QwABFit,t))
scatter(masterTemp,(tempT))
show()
#title("nmrtrlogQwAB")
plot(temps,valnmrtrqwb)
tempT=[]
for t in masterTemp:
tempT.append(valueFromFit(nmrtrQwABFit,t))
scatter(masterTemp,(tempT))
show()
"""
#JB#
return logMolFrac
#//end method stagePops 