huanglangwen / reproduce_model

Guidance on reproducing atmospheric chemistry simulations descripted in GMD paper

PyBox

1. Build a docker image for PyBox using docker build . -t pybox under the pybox subfolder.
2. Run and enter the docker container using the built image docker run -it --rm pybox.
3. Inside the container, enter the directory /Code/Git_repos/PyBox/Aerosol/f2py.
4. Execute python Aerosol_simulation_f2py.py to run the mixed-phase simulation for Alpha-Pinene mechanism.
5. Enter the directory /Code/Git_repos/PyBox/f2py, and execute python Gas_simulation_f2py.py to run the gas phase only simulation for Alpha-Pinene mechanism.

JlBox

1. Build a docker image for JlBox using docker build . -t jlbox under the jlbox subfolder.
2. Run and enter the docker container using the built image docker run -it --rm jlbox.
3. Insider the container, where the julia console is activated automatically, run using Pkg;Pkg.activate(".");Pkg.instantiate() to retrieve environment for reproduce.
4. Run include("example/Simulation_aerosol.jl") to run the mixed-phase simuation for Alpha-Pinene mechanism.
5. Run include("Simulation_gas.jl") to run the gas phase only simulation for Alpha-Pinene mechanism.

KPP

1. Build a docker image for KPP generated model using docker build . -t kpp under the kpp subfolder.
2. Run gas phase only simulation for Alpha-Pinene mechanism using docker run --rm kpp