@@ -23,14 +23,17 @@ along with this program. If not, see <https://www.gnu.org/licenses/>.
# How to compile and run GYACOMO
1. Be sure to have correct library paths in local/dirs.inc for the different libraries, see INSTALATION.txt for a tutorial to install the required libraries.
2. Compile from /gyacomo using make, the binary will be located in /gyacomo/bin (you can also compile a debug version using make dbg)
4. The fort.90 file should contain the parameters for a typical CBC to test the compilation. One can run it by calling the executable /bin/gyacomo in the directory where the fort.90 is located.
5. It is possible to run GYACOMO in parallel using MPI: mpirun -np N ./bin/gyacomo Np Ny Nz where N=Np x Ny x Nz is the number of processes and Np Ny Nz are the parallel dimensions in Hermite polynomials, binormal direction and parallel direction, respectively
6. You can stop your simulation without corrupting the output file by creating a blank file call "mystop", using e.g. "touch mystop" in the directory where the simulation is running. (the file will be removed once read)
7. It is also possible to put simulations ID in order to chain them. The parameter Job2load allows you to tell which output file should be read in order to restart a simulation. E.g. I run a first simulation with job2load = -1, it creates a outputs_00.h5 then I create a new fort.90 which I call fort_01.90 where job2load = 0. I run then GYACOMO, indicating that I want it to read the fort_00.90 using 0 as a last argument, i.e. "./gyacomo 0" or "mpirun -np N ./gyacomo Np Ny Nz 0", which will start from the latest 5D state saved in outputs_00.h5. A new output file has also been created, output_01.h5.
8. You can obtain various plots and gifs using gyacomo/wk/gyacomo_analysis.m once the simulation is done. The directory where the results are located must be given in the scripts. It is not a function (yet...)
// Comment : For some collision operators (Sugama and Full Coulomb) you have to run COSOlver from B.J.Frei first in order to generate the required matrices in gyacomo/iCa folder. //
To compile and run GYACOMO, follow these steps:
1. Make sure the correct library paths are set in local/dirs.inc. Refer to INSTALATION.txt for instructions on installing the required libraries.
2. Go to the /gyacomo directory and run make to compile the code. The resulting binary will be located in /gyacomo/bin. You can also compile a debug version by running make dbg.
3. The file fort.90 should contain the parameters for a typical CBC. To test the compilation, navigate to the directory where fort.90 is located and run the executable /bin/gyacomo.
4. GYACOMO can be run in parallel using MPI by running mpirun -np N ./bin/gyacomo Np Ny Nz, where N = Np x Ny x Nz is the number of processes and Np Ny Nz are the parallel dimensions in Hermite polynomials, binormal direction, and parallel direction, respectively.
5. To stop the simulation without corrupting the output file, create a blank file called "mystop" using touch mystop in the directory where the simulation is running. The file will be removed once it is read.
6. It is possible to chain simulations by using the parameter "Job2load" in the fort.90 file. For example, to restart a simulation from the latest 5D state saved in outputs_00.h5, create a new fort.90 file called fort_01.90 and set "Job2load" to 0. Then run GYACOMO with the command ./gyacomo 0 or mpirun -np N ./gyacomo Np Ny Nz 0. This will create a new output file called output_01.h5.
7. To generate plots and gifs using the simulation results, use the script gyacomo/wk/gyacomo_analysis.m and specify the directory where the results are located. Note that this script is not currently a function.
Note: For some collision operators (Sugama and Full Coulomb), you will need to run COSOlver from B.J.Frei to generate the required matrices in the gyacomo/iCa folder before running GYACOMO.
