Takes 3D particle data and maps on to a density grid, using MPI. Can optionally apply convolution using serial R scripts.
Given a box size lbox, and grid size grid, the gridder finds the density using a Nearest Grid Point assignment scheme.
|---------lbox----------|
|-|-|-|-|-|-|-|-|-|-|-|-| <- grid=12
Center of each grid point in each dimension = lbox/grid/2
Configuration parameters are contained in config.txt, which now does not need to be set at compile time. The configurable parameters are as follows:
- INPUT_DIRECTORY: location of input particle files
- OUTPUT_DIRECTORY: location of output file, with name and extension
- GRID_DIMS: grid dimensions over which density calculated (
grid) - SIM_DIMS: size of simulation box along one side (
lbox/h)
To compile gridder.c execute the following in the top level directory.
make clean
make
To run gridder on a SLURM batch system:
sbatch grid_run.sh.
You may need to change the modules depending on your system availability / compiler requirements. To run on the login node you need to load the following modules.
module unload intel_comp
module load gsl
module load openmpi
module load hdf5
mpirun -np 4 gridder.x