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Add invariant species and add entries for the status of parameterized and advected #3

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Add invariant species and add entries for the status of parameterized and advected #3

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9a46c05
add invariant species
boulderdaze Nov 20, 2024
df29247
fix parameterized status
boulderdaze Nov 20, 2024
907473f
remove H2O because MICM error (species not found)
boulderdaze Nov 27, 2024
dbf95e8
add molecular weight
boulderdaze Nov 27, 2024
de74ff5
remove N2, M from terminator because of unknown species issue in atmos
boulderdaze Nov 28, 2024
908f0b7
remove o2, o3, air profile
boulderdaze Dec 4, 2024
9e84370
correct config file
boulderdaze Dec 4, 2024
61efe58
add gas species profile entry
boulderdaze Dec 11, 2024
cdd4b51
trace is constant
boulderdaze Dec 11, 2024
8bedfdc
modify as dry air
boulderdaze Dec 12, 2024
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36 changes: 30 additions & 6 deletions mechanisms/chapman/micm/species.json
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Original file line number Diff line number Diff line change
Expand Up @@ -5,40 +5,64 @@
"type": "CHEM_SPEC",
"absolute tolerance": 1e-12,
"molecular weight [kg mol-1]": 0.0280134,
"__is advected": true
"__is advected": false,
"__is parameterized": true
},
{
"name": "M",
"type": "CHEM_SPEC",
"tracer type": "THIRD_BODY"
"tracer type": "THIRD_BODY",
"__is advected": false,
"__is parameterized": true
},
{
"name": "O",
"type": "CHEM_SPEC",
"absolute tolerance": 1e-12,
"molecular weight [kg mol-1]": 0.0159994,
"__is advected": false
"__is advected": false,
"__is parameterized": false
},
{
"name": "O1D",
"type": "CHEM_SPEC",
"absolute tolerance": 1e-12,
"molecular weight [kg mol-1]": 0.0159994,
"__is advected": false
"__is advected": false,
"__is parameterized": false
},
{
"name": "O2",
"type": "CHEM_SPEC",
"absolute tolerance": 1e-12,
"molecular weight [kg mol-1]": 0.0319988,
"__is advected": true
"__is advected": false,
"__is parameterized": false,
"__is added to profile": true,
"__unit" : "molecule cm-3",
"__scale height [km]": 7.0
},
{
"name": "O3",
"type": "CHEM_SPEC",
"absolute tolerance": 1e-12,
"molecular weight [kg mol-1]": 0.0479982,
"__is advected": true
"__is advected": true,
"__is parameterized": false,
"__is added to profile": true,
"__unit" : "molecule cm-3",
"__scale height [km]": 7.0
},
{
"name": "air",
"type": "CHEM_SPEC",
"absolute tolerance": 1e-12,
"molecular weight [kg mol-1]": 0.0289644,
"__is advected": false,
"__is parameterized": false,
"__is added to profile": true,
"__unit" : "molecule cm-3",
"__scale height [km]": 8.01
}
]
}
18 changes: 0 additions & 18 deletions mechanisms/chapman/tuvx/config.json
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Original file line number Diff line number Diff line change
Expand Up @@ -12,24 +12,6 @@
}
],
"profiles": [
{
"name": "O3",
"type": "O3",
"units": "molecule cm-3",
"file path": "musica_configurations/chapman/tuvx/data/profiles/atmosphere/ussa.ozone"
},
{
"name": "air",
"type": "air",
"units": "molecule cm-3",
"file path": "musica_configurations/chapman/tuvx/data/profiles/atmosphere/ussa.dens"
},
{
"name": "O2",
"type": "O2",
"units": "molecule cm-3",
"file path": "musica_configurations/chapman/tuvx/data/profiles/atmosphere/ussa.dens"
},
{
"name": "solar zenith angle",
"type": "solar zenith angle",
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39 changes: 37 additions & 2 deletions mechanisms/terminator/micm/species.json
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Original file line number Diff line number Diff line change
Expand Up @@ -5,14 +5,49 @@
"type": "CHEM_SPEC",
"absolute tolerance": 1e-12,
"molecular weight [kg mol-1]": 0.035453,
"__is advected": true
"__is advected": true,
"__is parameterized": false
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},
{
"name": "Cl2",
"type": "CHEM_SPEC",
"absolute tolerance": 1e-12,
"molecular weight [kg mol-1]": 0.070906,
"__is advected": true
"__is advected": true,
"__is parameterized": false
},
{
"name": "O2",
"type": "CHEM_SPEC",
"tracer type": "CONSTANT",
"molecular weight [kg mol-1]": 0.0319988,
"__is advected": false,
"__is parameterized": true,
"__is added to profile": true,
"__unit" : "molecule cm-3",
"__scale height [km]": 7.0
},
{
"name": "O3",
"type": "CHEM_SPEC",
"tracer type": "CONSTANT",
"molecular weight [kg mol-1]": 0.0479982,
"__is advected": false,
"__is parameterized": true,
"__is added to profile": true,
"__unit" : "molecule cm-3",
"__scale height [km]": 7.0
},
{
"name": "air",
"type": "CHEM_SPEC",
"absolute tolerance": 1e-12,
"molecular weight [kg mol-1]": 0.0289644,
"__is advected": false,
"__is parameterized": false,
"__is added to profile": true,
"__unit" : "molecule cm-3",
"__scale height [km]": 8.01
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@boulderdaze boulderdaze Dec 11, 2024 •
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Hi @mattldawson, Is it okay to include air in the species.json? The goal is to avoid hardcoding the gas species in atmospheric physics configuration

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I think that's fine, if CAM-SIMA expects air to be in the constituents array. I would just add a "tracer type": "CONSTANT" so that the solver doesn't treat it as a variable to be solved for.

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Okay, thank you! I will fix that. Hi @nusbaume, @peverwhee and @jimmielin, is it acceptable to add air into the constituent array?

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Hi @boulderdaze, I also believe that should be fine, but it might be good to call it dry_air or something like that ( assuming it is not including H2O as part of the mixture, which CAM-SIMA might complain about). Of course if that doesn't work for you please let me know!

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Yeah, I'll use dry_air. Thank you for your suggestion!

}
]
}
18 changes: 0 additions & 18 deletions mechanisms/terminator/tuvx/config.json
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,24 +12,6 @@
}
],
"profiles": [
{
"name": "O3",
"type": "O3",
"units": "molecule cm-3",
"file path": "musica_configurations/chapman/tuvx/data/profiles/atmosphere/ussa.ozone"
},
{
"name": "air",
"type": "air",
"units": "molecule cm-3",
"file path": "musica_configurations/chapman/tuvx/data/profiles/atmosphere/ussa.dens"
},
{
"name": "O2",
"type": "O2",
"units": "molecule cm-3",
"file path": "musica_configurations/chapman/tuvx/data/profiles/atmosphere/ussa.dens"
},
{
"name": "solar zenith angle",
"type": "solar zenith angle",
Expand Down