The current installation of the MOpS Particle Simulator uses cmake to compile the program. The installation procedure below refers to installation on Linux systems, but can easily be modified for other operating systems. Additional resources to install and develop the MOpS Particle Simulator under a Windows subsystem for Linux can be found on the Installation on WSL page.
- Boost C++ Libraries v1.47 or later.
- CMake v2.6 or later.
- PkgConfig
- OpenBabel v2.3.1 or later (only for PAH and carbonaceous particle simulations)
Download the latest version of the code from the MOpS Github Repository.
Alternatively use git to set up your download:
git clone https://github.com/ucam-ceb-como/MOpS
Set the following variables (substitute for your name/email):
git config --global user.name "John Doe"
git config --global user.email "[email protected]"
The PAH layer of the carbonaceous particle model requires OpenBabel to be built as a statically linked library. Folders to locate and install OpenBabel have been added to the MOpS Particle Simulator. IMPORTANT: If you do not plan to use the MOpS Particle Simulator to resolve carbonaceous structures skip this section.
Before installing OpenBabel make sure you have PkgConfig on your system. This is used with cmake/modules/FindOpenBabel2.cmake for MOpS to use the OpenBabel API.
Installation procedure:
Download OpenBabel 2.3.1 from the download website (https://github.com/openbabel/openbabel/releases/tag/openbabel-2-3-1). Note that newer versions have not been tested. Place the unzipped source files inside the openbabel_location folder like MOpS/openbabel_location/openbabel-2-3-1 and then use the following commands:
cd openbabel_location
bash build.sh
You should now set up the OpenBabel environmental variables in your bashrc. A reminder of these variables is shown by the build.sh script. Remember to source the updated bashrc before continuing.
The following commands should be called from the MOpS Particle Simulator main folder to complete the DEBUG build of the MOpS Particle Simulator:
mkdir debug
cd debug
cmake -D CMAKE_BUILD_TYPE=Debug ..
make -j 4 #for 4 threads of compilation (more if you can!)
ctest -j 4 #for 4 threads of testing
The following commands should be called from the MOpS Particle Simulator main folder to complete the RELEASE build of the MOpS Particle Simulator:
mkdir release
cd release
cmake -D CMAKE_BUILD_TYPE=Release ..
make -j 4 #for 4 threads of compilation (more if you can!)
ctest -j 4 #for 4 threads of testing
Examples of different simulations are found in the folder /test/mopsc/
Use the MOpS Particle Simulator help to see the different options for running the program.
mops-app --help
Generic options:
-h [ --help ] print usage message
-v [ --version ] print version number
-w [ --new ] use new network interface
Input file options:
-r [ --mops ] arg (=mops.inx) path to main input file
-c [ --chem ] arg (=chem.inp) path to chemical mechanism
-t [ --therm ] arg (=therm.dat) path to thermochemical data
-n [ --trans ] arg (=tran.dat) path to transport data
-g [ --gasphase ] arg (=gasphase.inp) path to gas phase profile
-s [ --sweep ] arg (=sweep.xml) path to particle mechanism
-q [ --sensi ] arg (=sensi.xml) path to sensitivity analysis
--schem arg (=surfchem.inp) path to surface chemical mechanism
--stherm arg (=surftherm.dat) path to surface thermochemical data
Solver options:
-e [ --rand ] arg (=456) adjust random seed value
--surf turn-on surface chemistry
--opsplit use (simple) opsplit solver
--strang use strang solver
--predcor use predcor solver
--flamepp use flamepp solver
Output options:
-p [ --postproc ] postprocess files
-o [ --only ] postprocess files only (don't solve)
--diag arg (=0) set diagnostics level (0-4)
--ensemble write full ensembles to binary files
--ppah write full PAHPP data
--ppri write full primary particle data
--jumps write stochastic jumps data
--wdotA4 postprocess based on the molar rate of production
by chemical reaction of the inception species
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Computational Modelling Group, University of Cambridge.
10 September 2020
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