SEC

A Fortran-based pmicrobial-explicit soil carbon cycle model.

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1. Overview

The SEC model is a process-oriented soil carbon model that explicitly represents microbial decomposition processes (using Michaelis-Menten kinetics) implemented in Fortran, designed to simulate soil and ecosystem carbon dynamics and their controlling mechanisms.

The model adopts a modular architecture, clearly separating core process representation, input/output handling, and model control logic.
It is compiled using inetl compiler(ifort) and linked against netCDF (C + Fortran), enabling efficient handling of structured scientific data and deployment on high-performance computing (HPC) systems.

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2. Code Structure and Design

SEC/
├── src/                   # Core Fortran source code
│   ├── main.f90           # main program or test program
│   ├── mod_calcost.f90    # compute cost for 14C, POC/MAOC fractions, HWSD SOC profile ...
│   ├── mod_constants.f90  # all constants
│   ├── mod_functions.f90  # different functions for 14C, POC/MAOC fractions, HWSD SOC profile ...
│   ├── mod_inout.f90      # input or output (netcdf files)
│   ├── mod_interface.f90  # 
│   ├── mod_model_core.f90 # the core routines for the mesc model
│   └── mod_variables.f90  # all variables
│
├── cmake/                 # CMake helper modules
│   └── FindNetCDFFortran.cmake
│
├── test/                  # Test and example runs
│   ├── input              # input data
│   ├── output             # ouput
│   ├── run_main.sh        # One-command run test script
│   └── readme      
│
├── CMakeLists.txt         # Build configuration
├── build.sh               # One-command build script
├── README.md
└── LICENSE

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3. Software Requirements

The SEC model has been developed and tested in the following software environment:

• Fortran compiler: Intel (ifort) version 2021.9.0
• netCDF-Fortran: version 4.6.1
• netCDF-C: version 4.9.2

On HPC systems, the required environment is typically provided via modules, for example:

module load oneapi23u1
module load netcdf_intel

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4. Building the Model

Recommended: One-command build

chmod +x build.sh
./build.sh

This script automatically: 1. Loads the required compiler and libraries 2. Creates an out-of-source build directory 3. Configures and builds the model 4. Copies the executable to SEC/build/ or SEC/test/

The final executable is located at: SEC/build/main or SEC/test/main

Manual build (for development)

module load oneapi23u1 
module load netcdf_intel
mkdir build
cd build
cmake .. -DCMAKE_Fortran_COMPILER=ifort
cmake --build . -j

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5. Running the Model

Input files (e.g., parameter files or netCDF datasets) should be placed in the same directory to ensure consistent input–output management.

cd /SEC/test
chmod +x run_main.sh
./run_main.sh