This code needs the following libraries to run:
- futils for writing and reading to .h5 files https://c4science.ch/diffusion/FUTILS/
- bsplines for 2D b-splines interpolation, solving and evaluating the Poisson equation https://c4science.ch/source/spclibs/
- SINTEF SISL a C library for NURBS curves interrogation and calculating the distance to a NURBS curve https://github.com/SINTEF-Geometry/SISL
- forSISL a library layer to use SINTEF SISL in Fortran https://github.com/rweed/forSISL/blob/main/LICENSE.txt
- xgrafix optional library to display a graphical interface during a run and show simulation variables https://ptsg.egr.msu.edu/
Each of these libraries must be compiled according to their respective instructions.
To compile the program, the dependencies must first be compiled according to their respective instructions. A Makefile is found in the src folder and prior to the compilation the environment variable $PLATFORM must be defined to use the correct *.mk file, which includes options specific to gcc or intel compilers and specifies the paths to the different libraries. An example can be found and adapted in intel.mk and gcc.mk.
To compile in linux:
- modify the intel.mk or gcc.mk to point to the correct libraries path
- $> export PLATFORM=intel
- $> make release
The code can also be compiled using cmake
- $> mkdir build
- $> cd build
- $> cmake .. -DFUTILS=<path to futils> -DBSPLINES=<path to bsplines> -DSISL=<path to SISL> -DforSISL=<path to forSISL>
- $> make
Running the code
An example of a simulation configuration can be found in wk/T-REX. The code can be run on a cluster using slurm, by calling the run.sh in command line. The code can be stopped using the stop.sh which will create a file called "mystop" containing the remaining number of time-steps to run.
A number of post-processing routines using matlab have been written and can be found in the matlab folder. To open a hdf5 result file, use the class fennecshdf5 with "result=fennecshdf5(filename);". The object result can then be interrogated to access variables stored in the hdf5 file.