README for the APCEMM source code repository

APCEMM is the Aircraft Plume Chemistry, Emissions, and Microphysics Model. It simulates the aerosol microphysics and chemistry in an aircraft exhaust plume in 2D for up to 24 hours, with a focus on accurate simulation of the ice - providing an intermediate-fidelity representation of an aircraft contrail. Originally described in Fritz et al. (2020), the model has since been heavily modified and the focus shifted from chemistry towards a flexible and efficient contrail simulation. APCEMM is a community-developed code and we strongly encourage users to contribute to the code base, whether through new features, improvements, or bug fixes. We use semantic versioning, and (as of v1.1.0) users can expect that the API will only change with new major versions.

The latest stable release of APCEMM is v1.2.1.

APCEMM development

The development of APCEMM in C++ started in September 2018. The most recent version of the code can be found in the main branch. Although usually functional, this code is not necessarily stable and new features are added to this branch relatively frequently.

For users of APCEMM who do not intend to do any development, we recommend downloading a recent stable version. To acquire (for example) version 1.2.1, use git checkout v1.2.1 after cloning the repository.
For developers of APCEMM, we ask that you create a fork of this repository. Any user can contribute to APCEMM - see "contributing to APCEMM".

For VSCode users, a Docker Dev Container is defined in .devcontainer. See the tutorial to develop inside a containerized environment.

Contributing to APCEMM

Users can contribute to the code base in two key ways:

• Raising issues. If you find a bug, have a request for a new feature, or find that you cannot compile APCEMM with a specific compiler, please raise an issue.
• Submitting pull requests. Any user can contribute code for consideration by the APCEMM development team by submitting a pull request.

Every pull request should refer in its commit message to an existing issue (whether that's a bug, a compatibility issue, or a feature request); if no issue yet exists, for example if you have developed code to allow a new feature to be implemented which nobody has previously requested, then we ask that you first raise an issue and then tag that issue in the pull request.

Dependencies

These are all managed using the vcpkg tool (see below) so do not need to be installed explicitly.

• netcdf-c (requires HDF5 and zlib)
• netcdf-cxx4
• Catch2
• FFTW3
• OpenMP
• Boost libraries
• yaml-cpp
• Eigen3

APCEMM: Installation instructions

APCEMM can be built using CMake and requires GCC >= 11.2. Previously, the dependency structure and compile instructions were specified using manually generated Makefiles. CMake generates these Makefiles automatically, and should lead to a more pleasant software build experience. Dependencies on external libraries are managed using the vcpkg tool, which is installed as a Git submodule. (This means that you just need to run the git submodule update command below to set it up.)

CMake will generate a single executable APCEMM that can receive an input file input.yaml. To compile this executable, you can call CMake as follows:

git submodule update --init --recursive
mkdir build
cd build
cmake ../Code.v05-00
cmake --build .

The git submodule update command installs the vcpkg dependency management tool, and the first time that you run CMake, all of the C++ dependencies will be installed. This will take some time, but subsequent runs of CMake will use cached binary builds of the dependencies, so will be much quicker.

The above commands will generate the APCEMM executable in the build directory (an "out-of-source" build). It is also possible to perform a build directly in the Code.v05-00 directory, but this is not preferred. You can perform an "out-of-source" build anywhere that it's convenient, simply by calling CMake from within a different directory. For example,

cd APCEMM/rundirs/SampleRunDir/
cmake ../../Code.v05-00
cmake --build .

will generate the executable in the rundirs/SampleRunDir/ directory.

Getting started

To start a run from the aforementioned rundirs/SampleRunDir, simply call:

./../../Code.v05-00 input.yaml

Three examples and their accompanying jupyter notebooks for postprocessing tutorials are provided in the examples folder. The first example is one where the contrail doesn't persists, and only focuses on analyzing the output of the early plume model (EPM) module of APCEMM. The second example is a persistent contrail simulation where the ice supersaturated layer depth is specified. The third example features using a meteorological input file.

The input file options are explained via comments in the file rundirs/SampleRunDir/input.yaml

Advanced simulation parameters hidden in the input files (e.g. Aerosol bin size ratios, minimum/max bin aerosol sizes, etc) can be modified in Code.v05-00/src/include/Parameters.hpp.

Debugging

APCEMM can be compiled in debug mode to ensure reproducible results during testing. This fixes the seed of the random number generator and enforces single threaded computation. It can be enabled by passing the -DDEBUG=ON flag to CMake:

cmake ../Code.v05-00 -DDEBUG=ON

To debug APCEMM using gdb and the VSCode debugger the binary can be compiled with debug instructions by adding the -DCMAKE_BUILD_TYPE="Debug" flag. This comes at a significant cost in performance.

cmake ../Code.v05-00 -DCMAKE_BUILD_TYPE="Debug"

Here's an example configuration of the VSCode debugger in APCEMM/.vscode/launch.json:

{
    "version": "0.2.0",
    "configurations": [
        {
            "name": "(gdb) Launch APCEMM debug",
            "type": "cppdbg",
            "request": "launch",
            "program": "${workspaceFolder}/rundirs/debug/APCEMM",
            "cwd": "${workspaceFolder}/rundirs/debug/test_rundir/",
            "args": ["${workspaceFolder}/examples/issl_rhi140/input.yaml"],
            "environment": [
                {
                    "name": "LD_LIBRARY_PATH",
                    "value": "${workspaceFolder}/build/lib"
                },
            ],
            "externalConsole": false,
            "MIMode": "gdb",
            "setupCommands": [
                {
                    "description": "Enable pretty-printing for gdb",
                    "text": "-enable-pretty-printing",
                    "ignoreFailures": true
                }
            ]
        },
    ]
}

This configuration runs the APCEMM binary located in "${workspaceFolder}/rundirs/debug/ using the input file located in ${workspaceFolder}/examples/issl_rhi140/input.yaml and the working directory ${workspaceFolder}/rundirs/debug/test_rundir/. Paths can be changed to suit the case to debug.