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JianghuiDu committed Jul 26, 2023
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Expand Up @@ -8,10 +8,10 @@ The workflow is shown in the following figure. We will discuss each step in the


## Excel input
To generate code for the model user supplies an Excel file `model_config.xlsx` to SedTrace, including the following spreadsheets. The `substances` sheet lists the modelled substances, their types (e.g., solid or dissolved), chemical formula and boundary conditions. The `reactions` sheet lists the reactions, their chemical equations and rate expressions. The `speciation` sheet lists aqueous speciation reactions. The `adsorption` sheet lists the adsorbed species. The `diffusion` sheet lists information to compute the diffusion coefficients of dissolved substances. The `parameters` sheet lists the parameters required by the model. The `output` sheet is used to formulate output and plotting. The `data` sheet includes observational data that will be plotted together with model outputs. The `speciation`, `adsorption` and `data` sheets are optional and can be left empty if not needed (but their column headers must be preserved).
To generate code for the model user supplies an Excel file `model_config.xlsx` to SedTrace, including the following spreadsheets. The `substances` sheet lists the modelled substances, their types (e.g., solid or dissolved), chemical formula and boundary conditions. The `reactions` sheet lists the reactions, their chemical equations and rate expressions. The `speciation` sheet lists aqueous speciation reactions. The `adsorption` sheet lists the adsorbed species. The `diffusion` sheet lists information to compute the diffusion coefficients of dissolved substances. The `parameters` sheet lists the parameters required by the model. The `output` sheet is used to formulate output and plotting. The `data` sheet includes observational data that will be plotted together with model outputs. The `speciation`, `adsorption` and `data` sheets are optional and can be left empty if not needed (but their column headers must be preserved). Go to an example in `/SedTrace/examples` directory to see how to set up the configuration file.

## Main.jl
This is the Julia script that you can used to generate code and run model simulations.
This is the Julia script that you can use to generate code and run model simulations.

## Code generation
First, configure the model input using `modelconfig = ModelConfig(modeldirectory, modelfile, modelname)`, supplying information of the directory of the Excel input file, the name of the Excel file (e.g., `model_config.SimpleFe.xlsx`) and the model name (e.g., `SimpleFe`). Code generation is done by calling `generate_code(modelconfig; ParamDict::Dictionary, EnableList::Dictionary)`.
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