src and include -> contains the C++ source and headers of the gen.parRep software.
build -> directory where dependencies will be downloaded, and the program built.
external -> contains source and headers of dependencies used by the gen.parRep software.
cmake -> contains files required for locating external packages (e.g. OpenMM and a MPI implementation).
docs -> contains files required for building the documentation using Doxygen.
mol -> contains ready to use test systems, i.e. input files and OpenMM configurations of various molecular systems.
run -> contains bash scripts demonstrating how to run the software using either mpirun or the SLURM scheduler; also contains bash files for running the software under the following debuggers/profilers: GDB, Valgrind and Scalasca.
ci -> contains a molecular system, an input script and reference data for performing continuous integration and non regression tests.