Introduce aerosol chemistry validation and parser support by boulderdaze · Pull Request #282 · NCAR/MechanismConfiguration

boulderdaze · 2026-06-26T01:16:47Z

This PR:

Adds aerosol representations and processes functions
Adds check schema, validation function for aerosol
Adds an integration test for the CAM cloud chemistry
Makes reactions an optional key, since an aerosol configuration does not always require reactions. See the code and comments for details.
Part of Add MIAM types to canonical Mechanism #271

Notes:

I noticed that the emissions PR creates its own directory, which I think is a good approach for keeping things clean and organized. I considered doing the same for the aerosol model, but decided against it. Gas-phase chemistry and aerosol processes can be used together within a single chemistry system, and their configurations are often closely related.
More unit tests will be added in a follow up PR.
I restructured the Validate function into ValidateGasModel and introduced a separate ValidateAerosolModel.

Errors ValidateGasModel(const Mechanism& mechanism);
Errors ValidateAerosolModel(const Mechanism& mechanism);

During aerosol validation, the relationship between phases and species(eg. condensed phase and species, gas phase and species, solvent, molecular weight, density ) cannot be expressed in the current semantics::Input because the required relationship information is lost during flattening. It does not preserve which species belongs to which phase.

The intermediate type that I tried to introduced AerosolProcessRef also loses the structure by dropping the association between a specific species and its phase context.

The current aerosol validation cannot preserve the error locations for the reasons above. This will be addressed in #284

Co-authored-by: Kyle Shores <kyle.shores44@gmail.com>

codecov-commenter · 2026-06-26T01:21:17Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 31.57%. Comparing base (04d2f08) to head (534eabb).

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K20shores

We need to divorce the validation and parsing so that in-code mechanism can be validated. That means we need to update Validate to include aerosol validation

K20shores · 2026-06-26T14:16:49Z

+  {
+    namespace
+    {
+      Errors CheckArrheniusReferenceTemperatureSchema(const YAML::Node& object)


in the gas-phase parsing, we include this stuff directly in the parse function. Any reason we are doing it here?

The one in the gas-phase parser for arrhenius includes A,B,C,D,E as well as the phase, reactants and products.

The aerosol model defines rate constant to calculate equilibrium rate constant in the form of arrhenius expression, but it only takes A, C values. This configuration calls micm::CalculateArrhenius in miam implementation, which is why it remains as arrhneinus struct in aerosol types.

On the other hand, henrys law constant uses a reference temperature, which uses van't hoff equation to calculate the rate constant. It depends on temperature difference. That's why the ArrheniusReferenceTemperature type was crated.

The direct answer to your question is that the required and optional keys should be different.

Errors CheckArrheniusSchema(const YAML::Node& object) { const std::vector<std::string_view> required_keys = { keys::A, keys::C }; const std::vector<std::string_view> optional_keys = { keys::type }; return CheckSchema(object, required_keys, optional_keys); }

Ah, that wasn't my question. My question is why the schema checks are here and not in src/v1/aerosol_type_parsers.cpp. All of the gas phase checks have their schema checks include in the parsers.

…s separtely

K20shores

A couple of comments, but nothing that should hold up a merge. There's only one comment that wouldn't be addressed by a future issue anyway. If you like the way things look now, I'm happy to accept it

K20shores · 2026-07-01T20:59:28Z

  {
    std::string name;
    std::optional<double> diffusion_coefficient;
+    std::optional<double> density;


do we know what this is? Is this just the molecular weight? If so, it's duplicated in the species

It is the density of a species in a given phase, so it's expected to be different for solids, liquids, etc.

"name": "AQUEOUS", "species": [ "SO2", "H2O2", "O3", "Hp", "OHm", "HSO3m", "SO3mm", "SO4mm", "SO2OOHm", { "name": "H2O", "density [kg m-3]": 997.0 } ]

K20shores · 2026-07-01T21:16:14Z

+  // Aerosol cross-references are validated separately by ValidateAerosolModel, which works on the
+  // domain structs directly because it needs phase membership and optional-property values that
+  // this name-only view cannot carry.


The semantic input for an aerosol model doesn't yet exist. I suggest we do that as part of this PR, and then we can operate on the semantic inputs and share structural validation between in-code mechanisms and parsed mechanisms.

This work requires to restructure *Def classes. Right now, they only store values in flat arrays without any information about relationships (which species belong to which phases or where the solvent is). I think the restrucuting work is outside the scope of this PR. As mentioned in the comments, we can track it separately in the issue:

Make aerosol validation location-aware #284

K20shores · 2026-07-01T21:18:24Z

+  {
+    namespace
+    {
+      Errors CheckArrheniusReferenceTemperatureSchema(const YAML::Node& object)


Ah, that wasn't my question. My question is why the schema checks are here and not in src/v1/aerosol_type_parsers.cpp. All of the gas phase checks have their schema checks include in the parsers.

K20shores · 2026-07-01T21:20:46Z

+      return errors;
+    }
+
+    Errors CheckAerosolProcessesSchema(const YAML::Node& processes_list)


To me this reads like each of the types could be their own functions that we dispatch, similar to how we do for each different reaction type. Do you prefer this apporach?

K20shores · 2026-07-01T21:22:27Z

+        // Uses the same ValidateSemantics engine as ValidateGasModel, but with
+        // YAML-derived input so errors include source locations.


ValidateGasModel also includes line information because we have the semantic reference inputs, which I feel we should also add for aerosols

The gas model can store them in a flat array without relationship information unlike aerosol.

K20shores · 2026-07-01T21:26:11Z

+    // pair 'aerosol representations' + 'aerosol processes'. The two modes may also coexist.
+    const bool has_reactions = static_cast<bool>(object[keys::reactions]);
+    const bool has_aerosol_representations = static_cast<bool>(object[keys::aerosol_representations]);
+    const bool has_aerosol_processes = static_cast<bool>(object[keys::aerosol_processes]);


We need to replicate these checks in src/validate.cpp so that in-code mechanisms also have this checked

boulderdaze and others added 14 commits June 23, 2026 13:24

clean up the config file for cloud chemistry

54d39e6

distinguish between micm arrhenius and miam arrhneius

d8a9d51

add miam struct and keys

e6a6f30

code cleanup

5bee7cb

Update test/integration/integration_configs/cam_clound_chemistry.json

d2e6a89

Co-authored-by: Kyle Shores <kyle.shores44@gmail.com>

add headers

8f57804

Merge branch '271-add-miam-config' into 271-add-miam-parser

65cd40e

merge main

8ad3b8c

Add parsers

557d8b2

replace species with name to reuse the general parser

0fb6d3d

remove duplicate functions

01629df

gas diffusion coefficient

b3b4b01

support reading diffusion coefficieint form phases species

cd913cc

support reading solvent molecular weight and density

f4033f5

boulderdaze changed the title ~~Add aerosol parser~~ Add aerosol chemistry parser Jun 26, 2026

boulderdaze added 2 commits June 25, 2026 19:46

add integration test

4f27093

remove unit

8d72d0f

boulderdaze self-assigned this Jun 26, 2026

boulderdaze added this to the Cloud Chemistry milestone Jun 26, 2026

boulderdaze requested a review from K20shores June 26, 2026 04:45

boulderdaze marked this pull request as ready for review June 26, 2026 04:45

K20shores requested changes Jun 26, 2026

View reviewed changes

boulderdaze added 7 commits June 26, 2026 14:40

add validation for aerosol

a904c87

flattening aerosol into semantics input

26edebd

density should be onwed by species, not phase species

c334c5a

differentiate validate gas/aerosol

15180e9

code clean up after adding validation for aerosol

9336659

construct aerosol instead of constructing representation and processe…

09287c7

…s separtely

code clean up

170833b

add unit tests

534eabb

boulderdaze requested a review from K20shores June 27, 2026 02:25

boulderdaze changed the title ~~Add aerosol chemistry parser~~ Introduce aerosol chemistry validation and parser support Jun 27, 2026

cleanup comments

238ca18

K20shores approved these changes Jul 1, 2026

View reviewed changes

		// Uses the same ValidateSemantics engine as ValidateGasModel, but with
		// YAML-derived input so errors include source locations.

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