Chapter 2

An MICM Box Model Example in Fortran

In this next MUSICA Fortran example, we will setup a MICM solver, starting with a set of MICM configuration files, and run the solver for a single integration time step.

The following three configuration files (config.json, species.json, and reactions.json) should be saved in a subdirectory named configs/analytical relative directory from which you plan to call the box model executable.

(You can find a copy of these files in the MUSICA repository at configs/analytical.)

The top-level MICM configuration config.json file simply lists the configuration files to parse. In this case, these are the chemical species configuration file species.json and the reactions configuration file reactions.json.

The contents of the config.json file for this example are:

{
  "camp-files": [
    "species.json",
    "reactions.json"
  ]
}

For this example, we will have a system of three chemical species A, B, and C, defined in the JSON file species.json as follows:

{
  "camp-data": [
    {
      "name": "A",
      "type": "CHEM_SPEC"
    },
    {
      "name": "B",
      "type": "CHEM_SPEC"
    },
    {
      "name": "C",
      "type": "CHEM_SPEC"
    },
    {
      "name": "D",
      "type": "CHEM_SPEC"
    },
    {
      "name": "E",
      "type": "CHEM_SPEC"
    },
    {
      "name": "F",
      "type": "CHEM_SPEC"
    }
  ]
}

The reactions.json specifies a mechanism, or a set of reactions for the system. Here, we will introduce two Arrhenius type reactions, the first with B evolving to C, and specifying all five reaction parameters, and the second reaction with A evolving to B and using only two reaction parameters.

We also include two reactions with rate constants that are provided by the host application at runtime. These types of reactions are useful when outside calculations are needed to determine the rate constants, such as in the case of photolysis reactions.

The reactions.json file for this example should look like this:

{
  "camp-data": [
    {
      "type": "MECHANISM",
      "name": "analytical test",
      "reactions": [
        {
          "type": "ARRHENIUS",
          "A": 0.004,
          "C": 50,
          "reactants": {
            "A": {
              "qty": 1
            }
          },
          "products": {
            "B": {
              "yield": 1
            }
          }
        },
        {
          "type": "ARRHENIUS",
          "A": 0.012,
          "B": -2,
          "C": 75,
          "D": 50,
          "E": 1.0e-6,
          "reactants": {
            "B": {
              "qty": 1
            }
          },
          "products": {
            "C": {
              "yield": 1
            }
          }
        },
        {
          "type": "USER_DEFINED",
          "MUSICA name": "reaction 1",
          "reactants": {
            "D": {
              "qty": 1
            }
          },
          "products": {
            "E": {
              "yield": 1
            }
          }
        },
        {
          "type": "USER_DEFINED",
          "MUSICA name": "reaction 2",
          "reactants": {
            "E": {
              "qty": 1
            }
          },
          "products": {
            "F": {
              "yield": 1
            }
          }
        }
      ]
    }
  ]
}

More information on MICM configurations and reactions can be found in the MICM documentation

To create a simple box model, save the following Fortran code to a file named micm_box_model.F90:

From the musica_util module we need the Fortran types error_t, string_t, and mapping_t. A pointer to a musica_micm::micm_t will serve as the interface to the MICM solver (in the example the pointer name is micm). Note that the config_path in the code sample has been set to configs/analytical, so that subdirectory should be created relative to the main program and contain the MICM JSON configuration files, otherwise the config_path should be modified appropriately. The initial species concentrations are initialized in the concentrations array, which is an argument to the MICM solver.

Finally, a single time step solution is obtained through a call to micm%solve, after which the updated concentrations may be displayed.

To build the example, follow the instructions in Chapter 1.

Assuming you name the executable micm_box_model, you can run the program as follows:

 $ ./micm_box_model
Creating MICM solver...
Species Name:A, Index:           1
Species Name:B, Index:           2
Species Name:C, Index:           5
Species Name:D, Index:           3
Species Name:E, Index:           4
Species Name:F, Index:           6
Solving starts...
After solving, concentrations  0.38236272259073301        1.4676807523204496       0.67030703490468713        1.1155750798779909        1.1499565250888166        1.2141178852173222
 $