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Lj/albedo #634

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a03d77d
added albedo updating agni
Nov 25, 2025
c8e0cf3
fixed line indentation proteus.py
Nov 25, 2025
ff98eb2
add outgassing with lavatmos
Jan 13, 2026
5585252
remove unnecessary print statement
Jan 15, 2026
cd66078
chnaged plotting routines
Jan 23, 2026
3cb7203
added the option to th einput file that the included refractory vapou…
Jan 26, 2026
d40c26b
fixed bug geerated by plotting routine when running models with atomi…
Jan 27, 2026
0d723fb
added a plotting routine where the temperature structures of two diff…
Jan 28, 2026
f58aba7
implemented lavatmos feed back of fO2 to calliope
Feb 10, 2026
a54c7e1
updated the feedback between lavatmos and calliope: fO2 is now passed…
Feb 10, 2026
2ce4c1e
removed unnecessary printing statements
Feb 12, 2026
dcd7477
add key of fO2 shift to helpfile
Feb 13, 2026
6660d06
added new plotting routine to plot selected timesteps and added a 150…
Feb 13, 2026
01be5b0
resolve merging issues
Feb 16, 2026
dbefba6
Merging the newest changes of mass conservation into the branch which…
Feb 16, 2026
a5a2353
added copilot sggestions
Feb 17, 2026
03a650e
Merge branch 'main' into lj/albedo
Feb 17, 2026
304a839
made required changes by copilot
Feb 17, 2026
e5a968d
lavatmos-calliope loop with removing oxygen each iteration
Feb 19, 2026
129d970
made an option to run calliope and lavatmos without coupling for fO2,…
Feb 20, 2026
9b195cb
removed the fO2 loop
Feb 25, 2026
2e5c03c
added wrapperfunctions from lavatmos_goot_runner and the path setting…
Feb 27, 2026
fe67caf
added bash script to run a grid of proteus runs
Mar 4, 2026
c3cb41b
added code to convert vmrs from ncdf files as well as TPs to datafram…
Mar 5, 2026
66c8e7a
fixed choice of pressure and temeprature values to layer centers
Mar 5, 2026
074588f
added python routine to edit ARCiS config file and bash file to run A…
Mar 6, 2026
c9bf2bf
corrected the updating of volatile species mass after outgassing happ…
Mar 12, 2026
5816652
changed back to the old abuundance conversion by changing the 0 conve…
Mar 12, 2026
511fb9e
updated the bash script and python routines how to run the proteus gr…
Mar 17, 2026
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20 changes: 20 additions & 0 deletions elementfiles/element_abundances_0.0.dat
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# Abundances determined using atmosphere_builder
C 30.534470505135875
H 30.152318522695243
He 0
N 31.275553280903257
O 31.764930257913814
P 0
S 31.254614270091718
Si 28.86375863776548
Ti 25.144501233229494
V 0
Cl 0
K 27.28102676306397
Na 28.493327798969585
Mg 27.790669254764097
F 0
Ca 24.168711262144342
Fe 27.992707036090664
Al 25.537168719930825
e- 0
20 changes: 20 additions & 0 deletions elementfiles/element_abundances_1.0.dat
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# Abundances determined using atmosphere_builder
C 30.55207127508565
H 30.10592597507962
He 0
N 31.309815173469723
O 31.75352135931247
P 0
S 31.25401796329841
Si 28.816638163129266
Ti 25.102494667878368
V 0
Cl 0
K 27.23761215338637
Na 28.44995400962075
Mg 27.745748667645316
F 0
Ca 24.123871122685916
Fe 27.94859375199561
Al 25.491913446355376
e- 0
20 changes: 20 additions & 0 deletions elementfiles/element_abundances_10092.0000092.dat
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# Abundances determined using atmosphere_builder
C 30.59935280409514
H 29.94496228311196
He 0
N 31.412273866847766
O 31.714166291727178
P 0
S 31.241749056401503
Si 28.654635163100092
Ti 24.95740050229667
V 0
Cl 0
K 27.0849832715104
Na 28.2971431632935
Mg 27.590844831668335
F 0
Ca 23.971513845409113
Fe 27.794833579494927
Al 25.339480583291582
e- 0
20 changes: 20 additions & 0 deletions elementfiles/element_abundances_101248.85193439838.dat
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# Abundances determined using atmosphere_builder
C 0
H 31.725426479611563
He 0
N 0
O 31.546075596867706
P 0
S 29.35784847388061
Si 30.88891280833268
Ti 26.86689414209222
V 0
Cl 0
K 29.141958815435245
Na 30.35661099210795
Mg 29.715207962673954
F 0
Ca 26.049073407282094
Fe 29.898764672266104
Al 27.401968127806587
e- 0
20 changes: 20 additions & 0 deletions elementfiles/element_abundances_104641.08200679332.dat
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# Abundances determined using atmosphere_builder
C 31.002151106372715
H 31.891650464053015
He 0
N 30.359667258799917
O 30.833806641365666
P 0
S 25.71048730271462
Si 30.408718604016457
Ti 25.09758147497292
V 0
Cl 0
K 27.405718863483145
Na 28.624198610905047
Mg 29.1103897897378
F 0
Ca 25.364703489681744
Fe 29.261809887632694
Al 27.143890498255132
e- 0
20 changes: 20 additions & 0 deletions elementfiles/element_abundances_105900.41858576344.dat
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# Abundances determined using atmosphere_builder
C 0
H 31.883148777095066
He 0
N 0
O 31.348267968813747
P 0
S 28.548363109100755
Si 29.98127498507016
Ti 25.5037858999289
V 0
Cl 0
K 27.98199379466712
Na 29.19813334410201
Mg 28.727589725424224
F 0
Ca 25.01429626046638
Fe 28.89180293185923
Al 26.294859121428622
e- 0
20 changes: 20 additions & 0 deletions elementfiles/element_abundances_105913.58789933729.dat
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# Abundances determined using atmosphere_builder
C 0
H 31.883078611792026
He 0
N 0
O 31.348406856486474
P 0
S 28.548190853179996
Si 29.983057239836977
Ti 25.505788138850157
V 0
Cl 0
K 27.983903204819683
Na 29.200042318317006
Mg 28.729395983739128
F 0
Ca 25.01611888522649
Fe 28.893615689925138
Al 26.29672263631523
e- 0
20 changes: 20 additions & 0 deletions elementfiles/element_abundances_106247.24942115354.dat
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# Abundances determined using atmosphere_builder
C 31.419618832238587
H 30.437062499546233
He 0
N 31.11276056212032
O 31.747605758790588
P 0
S 30.320704544709763
Si 26.55000363330405
Ti 20.617955143129993
V 0
Cl 0
K 25.762423043123142
Na 27.137486681427944
Mg 25.98696673851628
F 0
Ca 20.94818674890654
Fe 26.739862330216262
Al 20.94387903628982
e- 0
20 changes: 20 additions & 0 deletions elementfiles/element_abundances_1066380.091816709.dat
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# Abundances determined using atmosphere_builder
C 31.42468762077317
H 30.395426450776814
He 0
N 31.124568603319965
O 31.746874410341597
P 0
S 30.24842531498385
Si 26.33568168426939
Ti 20.352126529731144
V 0
Cl 0
K 25.588731370674306
Na 26.969066697042436
Mg 25.791926954960818
F 0
Ca 20.71138349909603
Fe 26.56761673102817
Al 20.679686881617442
e- 0
20 changes: 20 additions & 0 deletions elementfiles/element_abundances_1066885.2583350732.dat
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# Abundances determined using atmosphere_builder
C 0
H 31.136773280833648
He 0
N 0
O 31.811143427825836
P 0
S 0
Si 31.007808085554124
Ti 27.395166650097828
V 0
Cl 0
K 29.668161281381742
Na 30.898826020547457
Mg 29.994763937933254
F 0
Ca 26.24574037490334
Fe 30.30094748999452
Al 27.530409757063136
e- 0
20 changes: 20 additions & 0 deletions elementfiles/element_abundances_108246.60067925722.dat
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Original file line number Diff line number Diff line change
@@ -0,0 +1,20 @@
# Abundances determined using atmosphere_builder
C 0
H 31.96010762841182
He 0
N 0
O 30.795525000521284
P 0
S 27.85892059784538
Si 30.333018117870616
Ti 25.14841778540412
V 0
Cl 0
K 27.78171484372296
Na 28.99893846309008
Mg 29.039287088845303
F 0
Ca 25.296464664055264
Fe 29.191989159132763
Al 26.62402487505056
e- 0
20 changes: 20 additions & 0 deletions elementfiles/element_abundances_112295.11169366694.dat
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Original file line number Diff line number Diff line change
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# Abundances determined using atmosphere_builder
C 0
H 31.965137849617335
He 0
N 0
O 30.71620524976555
P 0
S 27.072159083249844
Si 30.333447875883284
Ti 25.10510368456176
V 0
Cl 0
K 27.71087738276313
Na 28.928234341731546
Mg 29.03864920951192
F 0
Ca 25.294999068098186
Fe 29.19102538347343
Al 26.67434677959401
e- 0
20 changes: 20 additions & 0 deletions elementfiles/element_abundances_112652.01961555614.dat
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# Abundances determined using atmosphere_builder
C 0
H 31.18249729819671
He 0
N 0
O 31.809845746800995
P 0
S 0
Si 31.069787598749095
Ti 27.410019923691607
V 0
Cl 0
K 29.52100864805236
Na 30.732738065802327
Mg 30.022302024654127
F 0
Ca 26.40861110330239
Fe 30.228836891470433
Al 27.77612693967572
e- 0
20 changes: 20 additions & 0 deletions elementfiles/element_abundances_1128749.9466383653.dat
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# Abundances determined using atmosphere_builder
C 0
H 0
He 0
N 0
O 31.78741971105431
P 0
S 23.35429317320456
Si 31.407220999052452
Ti 27.450497449069367
V 0
Cl 0
K 29.695662930395383
Na 30.909952694339005
Mg 30.251384727271873
F 0
Ca 26.594068789479724
Fe 30.438696514409017
Al 27.952925652313624
e- 0
20 changes: 20 additions & 0 deletions elementfiles/element_abundances_1133223.9695499486.dat
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# Abundances determined using atmosphere_builder
C 0
H 0
He 0
N 0
O 31.83990636156622
P 0
S 31.463356480526443
Si 30.016864357075097
Ti 26.3307620532104
V 0
Cl 0
K 28.453399097892053
Na 29.66543510414035
Mg 28.95783567834806
F 0
Ca 25.340181410022474
Fe 29.16257945999848
Al 26.708053970271113
e- 0
20 changes: 20 additions & 0 deletions elementfiles/element_abundances_113340.73409906306.dat
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# Abundances determined using atmosphere_builder
C 30.996127079428646
H 31.75881321443037
He 0
N 30.576427553656966
O 31.369521124567004
P 0
S 28.1123655587657
Si 30.65145878447131
Ti 25.79243301716186
V 0
Cl 0
K 28.410752702151623
Na 29.627470493769323
Mg 29.36913008484304
F 0
Ca 25.63517011751138
Fe 29.525250386924693
Al 26.865142633575573
e- 0
20 changes: 20 additions & 0 deletions elementfiles/element_abundances_113636.52311865713.dat
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@@ -0,0 +1,20 @@
# Abundances determined using atmosphere_builder
C 0
H 31.40493558205188
He 0
N 0
O 31.7102333016772
P 0
S 30.33470896224528
Si 31.04751758339553
Ti 27.23161258406702
V 0
Cl 0
K 29.60270794922211
Na 30.834555441333922
Mg 29.97254447337259
F 0
Ca 26.188515463812514
Fe 30.25203748367305
Al 27.460418593427008
e- 0
20 changes: 20 additions & 0 deletions elementfiles/element_abundances_1149734.6870918784.dat
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Original file line number Diff line number Diff line change
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# Abundances determined using atmosphere_builder
C 0
H 30.287603250509697
He 0
N 0
O 31.788231810527208
P 0
S 30.19606739356524
Si 31.2784505204759
Ti 27.413478586534193
V 0
Cl 0
K 29.808259882676648
Na 31.04031482579019
Mg 30.191396677634913
F 0
Ca 26.399560338355975
Fe 30.465007241758926
Al 27.66615444300688
e- 0
20 changes: 20 additions & 0 deletions elementfiles/element_abundances_115696.34587109213.dat
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Original file line number Diff line number Diff line change
@@ -0,0 +1,20 @@
# Abundances determined using atmosphere_builder
C 0
H 0
He 0
N 0
O 31.787430617406788
P 0
S 27.561773826275815
Si 31.40715368573197
Ti 27.450488043634493
V 0
Cl 0
K 29.695627016629587
Na 30.909916434560873
Mg 30.251334136413345
F 0
Ca 26.594026201254067
Fe 30.438649351055012
Al 27.952887695418305
e- 0
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