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Kurucz4.py
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Kurucz4.py
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import numpy as np
import math
import struct
import os
import argparse
# This script produces the binary and *.param files for HELIOS-K
# It also calculates the natural broadening coefficients
# Date: June 2020
# Author: Simon Grimm
filename="gfallwn08oct17.dat"
elt0=[
[ 100, "H" , 1.00794],
[ 200, "He" , 4.002602],
[ 300, "Li" , 6.941],
[ 400, "Be" , 9.012182],
[ 500, "B" , 10.811],
[ 600, "C" , 12.011],
[ 700, "N" , 14.00674],
[ 800, "O" , 15.9994],
[ 900, "F" , 18.9984032],
[ 1000, "Ne" , 20.1797],
[ 1100, "Na" , 22.989768],
[ 1200, "Mg" , 24.3050],
[ 1300, "Al" , 26.981539],
[ 1400, "Si" , 28.0855],
[ 1500, "P" , 30.973762],
[ 1600, "S" , 32.066],
[ 1700, "Cl" , 35.4527],
[ 1800, "Ar" , 39.948],
[ 1900, "K" , 39.0983],
[ 2000, "Ca" , 40.078],
[ 2100, "Sc" , 44.955910],
[ 2200, "Ti" , 47.88],
[ 2300, "V" , 50.9415],
[ 2400, "Cr" , 51.9961],
[ 2500, "Mn" , 54.93805],
[ 2600, "Fe" , 55.847],
[ 2700, "Co" , 58.93320],
[ 2800, "Ni" , 58.6934],
[ 2900, "Cu" , 63.546],
[ 3000, "Zn" , 65.39],
[ 3100, "Ga" , 69.723],
[ 3200, "Ge" , 72.61],
[ 3300, "As" , 74.92159],
[ 3400, "Se" , 78.96],
[ 3500, "Br" , 79.904],
[ 3600, "Kr" , 83.80],
[ 3700, "Rb" , 85.4678],
[ 3800, "Sr" , 87.62],
[ 3900, "Y" , 88.90585],
[ 4000, "Zr" , 91.224],
[ 4100, "Nb" , 92.90638],
[ 4200, "Mo" , 95.94],
[ 4300, "Tc" , 97.9072],
[ 4400, "Ru" ,101.07],
[ 4500, "Rh" ,102.90550],
[ 4600, "Pd" ,106.42],
[ 4700, "Ag" ,107.8682],
[ 4800, "Cd" ,112.411],
[ 4900, "In" ,114.818],
[ 5000, "Sn" ,118.710],
[ 5100, "Sb" ,121.757],
[ 5200, "Te" ,127.60],
[ 5300, "I" ,126.90447],
[ 5400, "Xe" ,131.29],
[ 5500, "Cs" ,132.90543],
[ 5600, "Ba" ,137.327],
[ 5700, "La" ,138.9055],
[ 5800, "Ce" ,140.115],
[ 5900, "Pr" ,140.90765],
[ 6000, "Nd" ,144.24],
[ 6100, "Pm" ,144.9127],
[ 6200, "Sm" ,150.36],
[ 6300, "Eu" ,151.965],
[ 6400, "Gd" ,157.25],
[ 6500, "Tb" ,158.92534],
[ 6600, "Dy" ,162.50],
[ 6700, "Ho" ,164.93032],
[ 6800, "Er" ,167.26],
[ 6900, "Tm" ,168.93421],
[ 7000, "Yb" ,173.04],
[ 7100, "Lu" ,174.967],
[ 7200, "Hf" ,178.49],
[ 7300, "Ta" ,180.9479],
[ 7400, "W" ,183.84],
[ 7500, "Re" ,186.207],
[ 7600, "Os" ,190.23],
[ 7700, "Ir" ,192.22],
[ 7800, "Pt" ,195.08],
[ 7900, "Au" ,196.96654],
[ 8000, "Hg" ,200.59],
[ 8100, "Tl" ,204.3833],
[ 8200, "Pb" ,207.2],
[ 8300, "Bi" ,208.98037],
[ 8400, "Po" ,208.9824],
[ 8500, "At" ,209.9871],
[ 8600, "Rn" ,222.0176],
[ 8700, "Fr" ,223.0197],
[ 8800, "Ra" ,226.0254],
[ 8900, "Ac" ,227.0278],
[ 9000, "Th" ,232.0381],
[ 9100, "Pa" ,231.03588],
[ 9200, "U" ,238.0289],
[ 9300, "Np" ,237.0482],
[ 9400, "Pu" ,244.0642],
[ 9500, "Am" ,243.0614],
[ 9600, "Cu" ,247.0703],
[ 9700, "Bk" ,247.0703],
[ 9800, "Cf" ,251.0796],
[ 9900, "Es" ,252.0830],
[10000, "Fm" ,257.0951],
[10100, "Md" ,258.0984],
[10200, "No" ,259.1011],
[10300, "Lr" ,262.1098],
[10400, "Rf" ,261.1089],
[10500, "Db" ,262.1144],
[10600, "Sg" ,263.1186],
[10700, "Bh" ,264.12],
[10800, "Hs" ,265.1306],
[10900, "Mt" ,268.00],
[11000, "Ds" ,268.00],
[11100, "Rg" ,272.00],
[11200, "Cn" ,277.00],
[11300, "Uut" ,0.00],
[11400, "Fl" ,289.00],
[11500, "Uup" ,0.00],
[11600, "Lv" ,289.00],
[11700, "Uus" ,294.00],
[11800, "Uuo" ,293.00]
]
def main(Z, I, printA):
if(Z == -1 and I == -1):
# all species in Z and I
for i in range(0,100):
for j in range(0,3):
processLineList(i, j, printA)
if(Z == -1 and I > -1):
# all species in Z
for i in range(0,100):
processLineList(i, I, printA)
if(Z > -1 and I == -1):
# all species in I
for j in range(0,3):
processLineList(Z - 1, j, printA)
if(Z > -1 and I > -1):
processLineList(Z - 1, I, printA)
def processLineList(i, j, printA):
# i molecule id 0 to 100
# j ion id 0 to 3
name ="gfnew%02d%02d" % (i + 1, j)
NISTname ="NIST%02d%02d" % (i + 1, j)
if(printA == 1):
Afile = open("gfnew_A%02d%02d.dat" % (i + 1, j), "w")
inname = "gfnewCorr%02d%02d.dat" % (i + 1, j)
outname = "gfnew%02d%02d.bin" % (i + 1, j)
pfname = "gfnew%02d%02d.pf" % (i + 1, j)
el=elt0[i]
mass = el[2]
output_file = open(outname,"wb")
pf_filename = "partfn%.4d.dat" % el[0]
numax = 0.0
filesize = os.path.getsize(inname)
if(filesize != 0):
wn, S, A, ELow, EUP, ELowAverage, EUPAverage, gLow, gUP, GammaR, isotope, hyperFineFraction, ISOFraction, sameLabel = np.loadtxt(inname, unpack=True)
else:
exit()
for i in range(len(wn)):
GammaRad = 0.0
numax = max(numax, wn[i])
#print(" ", ELowAverage[i], EUPAverage[i], gLow[i], gUP[i], isotope[i], hyperFineFraction[i], ISOFraction[i])
for j in range(len(wn)):
if(EUPAverage[i] == EUPAverage[j] and gUP[i] == gUP[j]):
#if(EUPAverage[i] == EUPAverage[j]):
#print("-", ELowAverage[j], EUPAverage[j], gLow[j], gUP[j], A[j], isotope[j], hyperFineFraction[j], ISOFraction[j])
GammaRad += A[j] * hyperFineFraction[j] * ISOFraction[j]
for j in range(len(wn)):
if(ELowAverage[i] == EUPAverage[j] and gLow[i] == gUP[j]):
#if(ELowAverage[i] == EUPAverage[j]):
#print("+", ELowAverage[j], EUPAverage[j], gLow[j], gUP[j], A[j], isotope[j], hyperFineFraction[j], ISOFraction[j])
GammaRad += A[j] * hyperFineFraction[j] * ISOFraction[j]
#print(A[i], GammaRad, GammaR[i], wn[i])
if(printA == 1):
print(i, wn[i], A[i], ELow[i], ELowAverage[i], gUP[i], GammaRad, GammaR[i], Z, mass, file = Afile)
if(i % 10000 == 0):
print("reached line %d from %d" % (i, len(wn)))
G = GammaR[i]
if(G == 1.0):
G = GammaRad
s = struct.pack('d', wn[i])
output_file.write(s)
s = struct.pack('d', S[i])
output_file.write(s)
s = struct.pack('d', ELow[i])
output_file.write(s)
s = struct.pack('d', 0.0)
output_file.write(s)
s = struct.pack('d', G)
output_file.write(s)
output_file.close()
if(printA == 1):
Afile.close()
pfile = 0
if(os.path.isfile(pf_filename)):
#print(" ", pf_filename)
pf_file = open(pfname,"w")
T, Q = np.loadtxt(pf_filename, unpack=True, usecols = (2,3), skiprows=3)
for ii in range(len(T)):
pf_file.write("%g %g\n" % (T[ii], Q[ii]))
pf_file.close()
pfile = 1
else:
print(" No partition function file, use NIST")
printCode = 1
if(len(wn) > 0 and printCode == 1):
f = open("%s.param" % name,'w')
print("Database = 30", file = f)
print("Molecule number = %d" % el[0], file = f)
print("Name = %s" % name, file = f)
print("Number of Isotopes = 1", file = f)
print("#Id Abundance Q(296K) g Molar Mass(g) partition file :", file = f)
if(pfile == 1):
print("0 1.0 0.0 0 %s %s.pf" % (mass, name), file = f)
else:
print("0 1.0 0.0 0 %s %s.pf" % (mass, NISTname), file = f)
print("Number of columns in partition File = 2", file = f)
print("Number of line/transition files = 1", file = f)
print("Number of lines per file :", file = f)
print("%d" % len(wn), file = f)
print("Line file limits :", file = f)
print("0", file = f)
print("%d" % (int(numax)+1), file = f)
print("#ExoMol :", file = f)
print("Number of states = 0", file = f)
print("Number of columns in transition files = 0", file = f)
print("Default value of Lorentzian half-width for all lines = 0.0", file = f)
print("Default value of temperature exponent for all lines = 0.0", file = f)
print("Version = %s" % filename, file = f)
f.close()
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('-Z', '--Z', type=int,
help='Z', default = -1)
parser.add_argument('-I', '--I', type=int,
help='I', default = -1)
parser.add_argument('-printA', '--printA', type=int,
help='print A to file', default = 0)
args = parser.parse_args()
Z = args.Z
I = args.I
printA = args.printA
print("Z:%d, I: %d, printA: %d" % (Z, I, printA))
main(Z, I, printA)