C++ Monte Carlo photoionization and radiation hydrodynamics code.
First, clone the repository using
git clone https://github.com/bwvdnbro/CMacIonize.git
This creates a new folder named CMacIonize. Enter this folder and create a new
build folder:
cd CMacIonize
mkdir build
Enter the build folder and call CMake:
cd build
cmake ..
Now compile the program using make.
Documentation can be generated using make doc.
Unit tests can be run using make check.
A number of benchmark problems is provided in the folder
build/rundir/benchmark. Each benchmark problem consists of at least a
parameter file that can be used to run the benchmark, and a .txt file
containing some more information about the benchmark problem.
The only thing you need to compile and run CMacIonize is the CMake build system and a C++ compiler. However, some plugins for reading and writing files require the HDF5 library as well. The CMake build system automatically tries to locate a working HDF5 installation on your system. If this fails, the program will still compile, but the following functionality will not work:
- reading a density field from a Gadget snapshot file
- reading a density field from a FLASH snapshot file
- reading ionizing sources from a Gadget snapshot file
- writing Gadget output files. Since this is currently the only supported output format, this means output will not work, and the program is in fact useless.
To install the HDF5 (development) libraries on a Linux system, use
sudo apt-get install libhdf5-dev
On Mac OS X, the easiest way to install the HDF5 (development) libraries is a manual installation. Get the latest HDF5 release tarball from the HDF5 website (make sure to choose a distribution with UNIX line endings). Extract the tarball in a folder of choice, and configure and build the program:
./configure
make
make install
Depending on where the HDF5 library is installed, you might need to tell CMake
where to find HDF5: locate the folder containing libhdf5.so (or similar).
This folder should be named lib, and should be part of a parent folder that
also contains folders named include and bin. You should set the environment
variable HDF5_ROOT to the name of this folder:
export HDF5_ROOT=/name/of/the/folder
Check the messages generated when you run CMake, as it will tell you whether or not a working HDF5 development installation was found.
CMacIonize uses Doxygen to generate code documentation, but this is in no way
necessary to compile or run the program. CMake will automatically try to find
a Doxygen installation. If it finds one, you can generate documentation using
make doc. If not, make doc will not work.
Some scripts used for analyzing benchmark results, or for writing files used
by the unit tests, require Python, and the numpy, matplotlib and h5py
libraries. However, all files that are necessary for the unit tests are also
included in the repository (even if the scripts to generate them are), so
it is still possible to compile and run the code without Python.
The CMacIonize code contains a full inline documentation using Doxygen. A recent version of this documentation is available from an online mirror. A small number of online tutorials is available from the CMacIonize webpage. Other sources of documentation include:
- the journal article describing the original photoionization code on which CMacIonize was based, Wood, Mathis & Ercolano (2004)
- the journal article describing CMacIonize 1.0, Vandenbroucke & Wood (2018)
- the journal article describing the task-based algorithm underlying CMacIonize 2.0, Vandenbroucke & Camps (2020)
If you have any issues obtaining, compiling or running the code, please consult the wiki or the online tutorials, or let us know by email (bert.vandenbroucke@gmail.com). A Slack workspace is available for regular users and contributors upon invitation. Try to use github issue were applicable to