diff --git a/ChangeLog b/ChangeLog
index c87113ead4fe21f54f286d60fde3072b74478fc9..0c11b6356fc6a7a298deeb40a991cd127e6e1d95 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,18 @@
+2013-08-17 Jana Mendrok <jana.mendrok@ltu.se>
+
+ * ARTS-XML-DATA-2-1-57
+
+ * planets/[Venus,Mars,Jupiter]/isotopratio_[Venus,Mars,Jupiter].xml:
+ Adapted for isotopologues recently added/adapted to newest HITRAn data
+ in species_data.cc.
+
+ * planets/aux/isotopologue_ratios/isotopratios.txt:
+ Some additions to documention of calculation method. Adapted molecule
+ list. Spellfixes.
+
+ * planets/aux/isotopologue_ratios/isotopratios.py:
+ Bugfixes. More documentation. More support/suggested setups.
+
2013-08-17 Jana Mendrok <jana.mendrok@ltu.se>
* ARTS-XML-DATA-2-1-56
diff --git a/planets/Jupiter/isotopratio_Jupiter.xml b/planets/Jupiter/isotopratio_Jupiter.xml
index f6c0aa8cd80581c9b4395ea70cb7ddd3ef60cd3b..51fa81a34d7948feeffe806fca11f47c1eb8b018 100644
--- a/planets/Jupiter/isotopratio_Jupiter.xml
+++ b/planets/Jupiter/isotopratio_Jupiter.xml
@@ -1,6 +1,6 @@
<?xml version="1.0"?>
<arts format="ascii" version="1">
-<SpeciesAuxData version="1" nelem="194" nparam="1">
+<SpeciesAuxData version="1" nelem="204" nparam="1">
@ H2O-161 0.997572947934
@ H2O-181 0.00200034318924
@ H2O-171 0.000372095461312
@@ -88,19 +88,23 @@
@ NH3-4111 9.976597e-01
@ NH3-5111 2.244734e-03
@ NH3-4112 7.781746e-05
-@ HNO3-146 9.906273e-01
+@ HNO3-146 9.906402e-01
+@ HNO3-156 2.228940e-03
@ OH-61 0.997602433337
@ OH-81 0.00200039954065
@ OH-62 2.59376632668e-05
-@ HF-19 0.999968195957
-@ HF-29 2.59991730949e-05
-@ HCl-15 0.757681348634
-@ HCl-17 0.242287170287
-@ HCl-25 1.95600947671e-05
-@ HCl-27 6.3441134375e-06
-@ HBr-19 5.068438e-01
-@ HBr-11 4.931241e-01
-@ HI-17 9.999682e-01
+@ HF-19 9.999740e-01
+@ HF-29 2.599932e-05
+@ HCl-15 7.576853e-01
+@ HCl-17 2.422884e-01
+@ HCl-25 1.969809e-05
+@ HCl-27 6.300051e-06
+@ HBr-19 5.068468e-01
+@ HBr-11 4.931270e-01
+@ HBr-29 1.317829e-05
+@ HBr-21 1.282104e-05
+@ HI-17 9.999740e-01
+@ HI-27 2.599932e-05
@ ClO-56 0.755908
@ ClO-76 0.24172
@ OCS-622 0.937395
@@ -115,7 +119,8 @@
@ H2CO-2226 6.669066e-10
@ HOCl-165 7.558837e-01
@ HOCl-167 2.417130e-01
-@ N2-44 0.99548843
+@ N2-44 9.955459e-01
+@ N2-45 4.479957e-03
@ N2-SelfContMPM93 nan
@ N2-SelfContPWR93 nan
@ N2-SelfContStandardType nan
@@ -137,6 +142,7 @@
@ C2H6-1231 2.196894e-02
@ PH3-1111 9.999047e-01
@ COF2-269 0.986544
+@ COF2-369 0.01108
@ SF6-29 0.95018
@ H2S-121 9.501345e-01
@ H2S-141 4.214801e-02
@@ -189,9 +195,13 @@
@ SO-46 0.0420727
@ SO-28 0.00194089
@ C3H8-21 9.672486e-01
-@ H2-11 9.999479e-01
-@ H2-12 5.199729e-05
+@ H2-11 9.999594e-01
+@ H2-12 5.199789e-05
+@ H-1 1
@ He-4 1
+@ Ar-8 1
+@ C4H2-2211 9.562372e-01
+@ SO3-26 0.9434
@ liquidcloud-MPM93 nan
@ icecloud-MPM93 nan
@ rain-MPM93 nan
diff --git a/planets/Mars/isotopratio_Mars.xml b/planets/Mars/isotopratio_Mars.xml
index eba04ba65ddd5a022647c5314b8a183fef104660..a7edebe65b885507a041b7dfdb68b3d2acd882db 100644
--- a/planets/Mars/isotopratio_Mars.xml
+++ b/planets/Mars/isotopratio_Mars.xml
@@ -1,6 +1,6 @@
<?xml version="1.0"?>
<arts format="ascii" version="1">
-<SpeciesAuxData version="1" nelem="194" nparam="1">
+<SpeciesAuxData version="1" nelem="204" nparam="1">
@ H2O-161 0.996010631696
@ H2O-181 0.00199721041719
@ H2O-171 0.000371512716178
@@ -88,19 +88,23 @@
@ NH3-4111 9.919026e-01
@ NH3-5111 5.653845e-03
@ NH3-4112 2.410323e-03
-@ HNO3-146 9.864557e-01
+@ HNO3-146 9.864685e-01
+@ HNO3-156 5.622870e-03
@ OH-61 0.996820946034
@ OH-81 0.00199883249672
@ OH-62 0.000807424966287
-@ HF-19 0.999184855397
-@ HF-29 0.000809339732872
-@ HCl-15 0.757087807226
-@ HCl-17 0.242097370883
-@ HCl-25 0.000608894821999
-@ HCl-27 0.000197488706894
-@ HBr-19 5.064468e-01
-@ HBr-11 4.927378e-01
-@ HI-17 9.991849e-01
+@ HF-19 9.991906e-01
+@ HF-29 8.093444e-04
+@ HCl-15 7.570918e-01
+@ HCl-17 2.420986e-01
+@ HCl-25 6.131906e-04
+@ HCl-27 1.961171e-04
+@ HBr-19 5.064497e-01
+@ HBr-11 4.927407e-01
+@ HBr-29 4.102328e-04
+@ HBr-21 3.991117e-04
+@ HI-17 9.991906e-01
+@ HI-27 8.093444e-04
@ ClO-56 0.755908
@ ClO-76 0.24172
@ OCS-622 0.937395
@@ -115,7 +119,8 @@
@ H2CO-2226 6.462605e-07
@ HOCl-165 7.552916e-01
@ HOCl-167 2.415236e-01
-@ N2-44 0.9886702
+@ N2-44 9.887273e-01
+@ N2-45 1.127149e-02
@ N2-SelfContMPM93 nan
@ N2-SelfContPWR93 nan
@ N2-SelfContStandardType nan
@@ -137,6 +142,7 @@
@ C2H6-1231 2.186588e-02
@ PH3-1111 9.975567e-01
@ COF2-269 0.986544
+@ COF2-369 0.01108
@ SF6-29 0.95018
@ H2S-121 9.486465e-01
@ H2S-141 4.208200e-02
@@ -189,9 +195,13 @@
@ SO-46 0.0420727
@ SO-28 0.00194089
@ C3H8-21 9.612035e-01
-@ H2-11 9.983818e-01
-@ H2-12 1.617379e-03
+@ H2-11 9.983934e-01
+@ H2-12 1.617397e-03
+@ H-1 1
@ He-4 1
+@ Ar-8 1
+@ C4H2-2211 9.547396e-01
+@ SO3-26 0.9434
@ liquidcloud-MPM93 nan
@ icecloud-MPM93 nan
@ rain-MPM93 nan
diff --git a/planets/Venus/isotopratio_Venus.xml b/planets/Venus/isotopratio_Venus.xml
index b2d6a2635884981ca62c6ef0bc688385fab0cb6e..54af041ee38f7c30b6ddd383be246f3e3a4f42ff 100644
--- a/planets/Venus/isotopratio_Venus.xml
+++ b/planets/Venus/isotopratio_Venus.xml
@@ -1,6 +1,6 @@
<?xml version="1.0"?>
<arts format="ascii" version="1">
-<SpeciesAuxData version="1" nelem="194" nparam="1">
+<SpeciesAuxData version="1" nelem="204" nparam="1">
@ H2O-161 0.960768771556
@ H2O-181 0.001926543089
@ H2O-171 0.000358367475789
@@ -88,19 +88,23 @@
@ NH3-4111 9.416209e-01
@ NH3-5111 3.461839e-03
@ NH3-4112 5.367239e-02
-@ HNO3-146 9.708129e-01
+@ HNO3-146 9.708130e-01
+@ HNO3-156 3.568739e-03
@ OH-61 0.979026860648
@ OH-81 0.00196315166932
@ OH-62 0.0186015103523
-@ HF-19 0.981348572257
-@ HF-29 0.0186456228729
-@ HCl-15 0.743573158341
-@ HCl-17 0.237775730867
-@ HCl-25 0.0140277596158
-@ HCl-27 0.00454975803218
-@ HBr-19 4.974063e-01
-@ HBr-11 4.839421e-01
-@ HI-17 9.813486e-01
+@ HF-19 9.813542e-01
+@ HF-29 1.864573e-02
+@ HCl-15 7.435770e-01
+@ HCl-17 2.377770e-01
+@ HCl-25 1.412673e-02
+@ HCl-27 4.518158e-03
+@ HBr-19 4.974092e-01
+@ HBr-11 4.839448e-01
+@ HBr-29 9.450970e-03
+@ HBr-21 9.194762e-03
+@ HI-17 9.813542e-01
+@ HI-27 1.864573e-02
@ ClO-56 0.755908
@ ClO-76 0.24172
@ OCS-622 0.937395
@@ -115,7 +119,8 @@
@ H2CO-2226 3.430044e-04
@ HOCl-165 7.418090e-01
@ HOCl-167 2.372122e-01
-@ N2-44 0.992687
+@ N2-44 0.9926874
+@ N2-45 0.00733
@ N2-SelfContMPM93 nan
@ N2-SelfContPWR93 nan
@ N2-SelfContStandardType nan
@@ -137,6 +142,7 @@
@ C2H6-1231 1.962600e-02
@ PH3-1111 9.450830e-01
@ COF2-269 0.986544
+@ COF2-369 0.01108
@ SF6-29 0.95018
@ H2S-121 9.150805e-01
@ H2S-141 4.059302e-02
@@ -189,9 +195,13 @@
@ SO-46 0.0420727
@ SO-28 0.00194089
@ C3H8-21 8.322139e-01
-@ H2-11 9.630561e-01
-@ H2-12 3.659613e-02
+@ H2-11 9.630672e-01
+@ H2-12 3.659655e-02
+@ H-1 1
@ He-4 1
+@ Ar-8 1
+@ C4H2-2211 9.209580e-01
+@ SO3-26 0.9434
@ liquidcloud-MPM93 nan
@ icecloud-MPM93 nan
@ rain-MPM93 nan
diff --git a/planets/aux/isotopologue_ratios/isotopratios.py b/planets/aux/isotopologue_ratios/isotopratios.py
index f216ffc3a5009c0d1ae1090d6c6dc4f3517b7823..925c29d8e3110fdc6e107944cb91c9787b5a2f95 100644
--- a/planets/aux/isotopologue_ratios/isotopratios.py
+++ b/planets/aux/isotopologue_ratios/isotopratios.py
@@ -15,13 +15,14 @@
import numpy as N
+import pdb
#--------------------
#this to be done once
#--------------------
''' copy to commandline:
import isotopratios as iso
-tags,dhv,dhm,dhj,dnm,dnj,dheh2,dnen2 = iso.InitIR()
+tags,d = iso.InitIR()
'''
#-------------------------------------------
@@ -43,58 +44,84 @@ ir,st,en = iso.getMolInfo(name,tags)
##### (B)-(E)
''' adapt (B)-(E) in IRSingSpec, then copy to commandline:
reload(iso)
-iso.IRSingSpec(ir,st,en)
+iso.IRSingSpec(ir,st,en,tags,d)
'''
-def IRSingSpec(ir,st,en):
+def IRSingSpec(ir,st,en,tags,d):
'''
'''
+ #pdb.set_trace()
#STEP (1): derive the Earth isotopic ratio that we are going to replace
##### (B)
#(1b) - D/H
- dhe = dheh2 #D/H from H2 (if no molecule-specific available)
+ dhe = d['dheh2'] #D/H from H2 (if no molecule-specific available)
+ print('D/H from H2: %.3e' %dhe)
#(1a) - D/H
- n = 3. #replace permutational factor properly
- # in case only one pair we can derive internal isotopic ratio from (that's the common case)
- dhe = (1./n)*ir[-1]/ir[0] #replace indices properly
- # in case there's more than one we are taking the mean (e.g. for H2O, HCl)
+ n = 2. #REPLACE permutational factor of H properly (equal the number of
+ # H-atoms that can be interchanged in position, e.g. 4 for CH4)
+
+ #in case of only one pair of main-isotope-minor-isotope isotopologue (e.g.
+ # HF and DF) we can derive internal isotopic ratio from
+ dhe = (1./n)*ir[-1]/ir[0] #REPLACE indices properly
+
+ #in case there's more than one main-isotope-minor-isotope pair (e.g. for H2O
+ # (which has H2O-16/HDO-16, H2O-18/HDO-18, H2O-17/HDO-17), HCl, ...) we take
+ # the mean
#dhe = N.mean(ir[1:3]/ir[0])
#n=2; dhe = N.mean(N.append((1./n)*ir[3:6]/ir[0:3],N.sqrt(ir[6]/ir[0]))) #D/H from H2O
#n=4; dhe = N.mean((1./n)*ir[2:]/ir[0:2]) #D/H from CH4
#n=2; dhe = N.mean(N.append((1./n)*ir[3]/ir[0],N.sqrt(ir[-1]/ir[0]))) #D/H from H2CO
+ #n=1; dhe = N.mean((1./n)*ir[-2:]/ir[0:2]) #HBr,HCl
+ print('D/H from internal: %.3e' %dhe)
##### (C)
#(1b) - 15N/14N
- #dne = dnen2 #15N/14N from N2 (if no molecule-specific available)
+ # REPLACE dne calc properly
+ dne = d['dnen2'] #15N/14N from N2 (if no molecule-specific available)
+ print('N4/N5 from N2: %.3e' %dne)
#(1a) - 15N/14N
- # in case only one pair we can derive internal isotopic ratio from (that's the common case)
- dne = ir[-2]/ir[0]
- # in case there's more than one we are taking the mean
+ n = 2. #REPLACE permutational factor of N properly (equal the number of
+ # N-atoms that can be interchanged in position, e.g. 2 for N2)
+
+ # in case of only one pair of main-isotope-minor-isotope isotopologue we can
+ # derive internal isotopic ratio from
+
+ #miniso=-2 #common (if both H and N can be calculated)
+ #miniso=1 #if only N can be calculated, e.g. HNO3, N2
+ #dne = (1./n)*ir[miniso]/ir[0] #REPLACE indices properly
+
+ # in case there's more than one pair we take the mean
#dne=N.mean(ir[1:3]/ir[0]) #N2O
+ print('N4/N5 from internal: %.3e' %dne)
#STEP (2): derive the rescaling factors
##### (D)
- #if no H/N atom in molecule, then set the respective m to 0
- mh=3; mn=1
+ #REPLACE numbers properly. if no H/N atom in molecule, then set the
+ # respective m to 0.
+ mh=2; mn=0
- rvh=((dhe+1)/(dhv+1))**mh; rvn=1.
- rmh=((dhe+1)/(dhm+1))**mh; rmn=((dne+1)/(dnm+1))**mn
- rjh=((dhe+1)/(dhj+1))**mh; rjn=((dne+1)/(dnj+1))**mn
+ rvh=((dhe+1)/(d['dhv']+1))**mh; rvn=1.
+ rmh=((dhe+1)/(d['dhm']+1))**mh; rmn=((dne+1)/(d['dnm']+1))**mn
+ rjh=((dhe+1)/(d['dhj']+1))**mh; rjn=((dne+1)/(d['dnj']+1))**mn
#now apply the rescaling (including minor-isotope refactoring)
- dp = N.array([[dhv,dhm,dhj],[dne,dnm,dnj]])
+ dp = N.array([[d['dhv'],d['dhm'],d['dhj']],[dne,d['dnm'],d['dnj']]])
rp = N.array([[rvh,rmh,rjh],[rvn,rmn,rjn]])
planet = ['Venus','Mars','Jupiter']
for i in N.arange(dp.shape[1]):
dhp = dp[0,i]; dnp=dp[1,i]; rph = rp[0,i]; rpn = rp[1,i]
##### (E)
- #fac = N.append(N.ones(3),N.append((dnp/dne),(dhp/dhe)))
- fac = N.append(N.ones(3),N.append(N.ones(3)*(dhp/dhe),(dhp/dhe)**2)) #H2O
- fac = N.append(1.,N.append(N.ones(2)*(dnp/dne),N.ones(2))) #N2O
- fac = N.append(N.ones(2),N.ones(2)*(dhp/dhe)) #CH4
- fac = N.append(1.,N.append((dnp/dne),(dhp/dhe))) #NH3
+ # REPLACE fac calc properly
+ #fac = N.ones(1) #when only the main isotopologue exists, e.g. C4H2
+ #fac = N.append(N.ones(3),N.append(N.ones(3)*(dhp/dhe),(dhp/dhe)**2)) #H2O
+ #fac = N.append(1.,N.append(N.ones(2)*(dnp/dne),N.ones(2))) #N2O
+ #fac = N.append(N.ones(2),N.ones(2)*(dhp/dhe)) #CH4
+ #fac = N.append(1.,N.append((dnp/dne),(dhp/dhe))) #NH3
+ #fac = N.append(1.,(dnp/dne)) #HNO3, N2
+ #fac = N.append(N.ones(2),N.ones(2)*(dhp/dhe)) #HBr,HCl
+ fac = N.append(1.,(dhp/dhe)) #HI,HF,H2
nir = fac.size
irp = ir[:nir]*rph*rpn*fac
print(planet[i])
@@ -120,27 +147,31 @@ def InitIR(infile='IRfromARTSBuiltin.xml'):
the ARTS built-in isotopologue records. the 3 second-dim elements are the
line-start symbol '@', the species&isotoplogue tag, and the
corresponding isotopologue ratio.
- dhv, dhm, dhj, dnm, dnj : float
+ d: dict
+ holds the isotopic ratios of H and N for different planets. entries as
+ below:
+ dhv, dhm, dhj, dnm, dnj : float
D/H (dh) and 15N/14N (dn) isotopic ratios for [V]enus, [M]ars, and
[J]upiter
- dheh2, dnen2 : float
+ dheh2, dnen2 : float
D/H and 15N/14N Earth (fixed) isotopic ratios from H2 and N2 isotopologue
abundances
'''
+ d = {}
#set the planetary isotopic ratios
- dhv = 1.9e-2; dhm = 8.1e-4; dhj = 2.6e-5 #D/H
- dnm = 5.7e-3; dnj = 2.25e-3
+ d['dhv'] = 1.9e-2; d['dhm'] = 8.1e-4; d['dhj'] = 2.6e-5 #D/H
+ d['dnm'] = 5.7e-3; d['dnj'] = 2.25e-3
#get ARTS built-in data
tags=N.loadtxt(infile,comments='<',dtype=N.str)
#inititialise D/H and 15N/14N from H2 and N2 (we don't want to do this over and over...
ir,st,en=getMolInfo('H2',tags,do_print=0)
- dheh2 = 1./N.sqrt(ir[0])-1.
+ d['dheh2'] = 1./N.sqrt(ir[0])-1.
ir,st,en=getMolInfo('N2',tags,do_print=0)
- dnen2 = 1./N.sqrt(ir[0])-1.
+ d['dnen2'] = 1./N.sqrt(ir[0])-1.
- return tags,dhv,dhm,dhj,dnm,dnj,dheh2,dnen2
+ return tags, d
def getMolInfo(name,tags,do_print=1):
diff --git a/planets/aux/isotopologue_ratios/isotopratios.txt b/planets/aux/isotopologue_ratios/isotopratios.txt
index 6c8b9e24f311f118d95414b0f6007716ba51d96b..de212437fea6397ef5b49d163569941caa4c7380 100644
--- a/planets/aux/isotopologue_ratios/isotopratios.txt
+++ b/planets/aux/isotopologue_ratios/isotopratios.txt
@@ -11,11 +11,11 @@ Files with adapted planetary isotopologue ratios have been created and can be
Isotopic ratios of planets (Mars, Venus, Jupiter) differ from Earth only for
D/H (all planets) and 15N/14N (Mars and Jupiter, not Venus), while 13C/12C as
- well as 18O/16O and 17O/16O are within 5% or Earths values.
+ well as 18O/16O and 17O/16O are within 5% of Earth's values.
That is, only species containing H (all 3 planets) and N (Mars, Jupiter) need
adaptation.
-Applied planetary isotopic ratios were provided by L.Rezac under ESA planetary
+Applied planetary isotopic ratios were provided by L. Rezac under ESA planetary
toolbox study (see TN1). Earth values were derived from ARTS built-in
isotopologue ratios separately per molecular species (hence only an approximate
value given here):
@@ -116,10 +116,11 @@ In the IR formula derived above we now replace (D/H)_earth by (D/H)_planet by
= IR(CH3D_e) * [(1+D/H_p) / (1+D/H_e)]**4 * [(D/H_p) / (D/H_e)]
That is, all IR_e get rescaled by [(1+D/H_p) / (1+D/H_e)]**N, where N is the
- number of atoms of the specific species in this molecul (here: H and N=4).
+ number of atoms of the specific species in this molecule (here: atom=H and
+ N=4). This is the planetary rescaling factor (rp).
Isotopologues with other than the main isotope furthermore get refactored by
[(D/H_p) / (D/H_e)]**M, where M is the number of atoms of the isotope
- replacing the main one (here: D and M=1; CD4 would have M=4).
+ replacing the main one (here: D and M=1; CD4 would have M=4). This is isotopologue rescaling factor (fac).
Note: using this refactoring method, we do not need to care about the
positional permutation factors. As they occur in both the Earth and the planet
IR, they factor out.
@@ -153,17 +154,17 @@ Below is a list of species implemented in ARTS including tags showing what
SO2
xx NO2
* NH3
-x HNO3
+*/x HNO3 (no internal calc of D/H, only of N14/15)
*** OH
*** HF
*** HCl
-xxx HBr
-xxx HI
+*** HBr
+*** HI
ClO
OCS
*** H2CO
xxx HOCl
-xx N2
+** N2
* HCN
xxx CH3Cl
xxx H2O2
@@ -189,11 +190,14 @@ xxx CH3Br
* CH3CN
CF4
* HC3N
- CS
+ CS
* HNC
- SO
+ SO
xxx C3H8
-*** H2
- He
+*** H2
+ He
+ Ar
+x C4H2
+ SO3
#############################