Design¶
General principles¶
General purpose routines and computational algorithms are implemented as Fortran modules in src/. Parts of the code is tested with programs in test/.
Actual simulations are found in programs/, where every program corresponds to a given setup. The programs read parameters from a text file and store trajectories in H5MD files.
The aim of the code organization is that one can write a program that call trusted routines from the modules, giving a high-level view on the simulation. There is no global variable in the code so that a routine may only act on variables that are passed to it.
Storage of cell and particle data¶
The storage of particle and cell data is defined in the module particle_system and cell_system, respectively.
The derived type particle_system_t defines arrays for the position, velocity, etc of every particle.
The derived type cell_system_t defines a cell list with a one-dimensional index that is mapped to a three-dimensional compact Hilbert index [Ham06]. Particles are sorted according to this cell system, as in the nano-dimer software [Col15].
Operations on particles can proceed in two different ways:
Particle-wise: The loop goes over every particle, following the particle index of the particle data in memory.
Cell-wise: The loop runs over successive cells, where an inner loop runs over all particles. Thanks to the sorting of particles, the indices of the particles in a given cell are contiguous.
Programming language¶
RMPCDMD is written in Fortran 2008 and uses derived types objects to store simulation data.
RMPCDMD is built using CMake, which facilitates the inclusion of external libraries (fortran_h5md, random_module, ParseText and fortran_tester). The HDF5 library, with the Fortran 2003 interface, is also necessary to build RMPCDMD.
Random numbers¶
A C library implements the Threefry Random Number Generator (RNG) [SMDS11]. This RNG can be used in separate independent threads, provided that the thread’s numerical ID is part of the key of the RNG. The other part of the key, that is made of two 64-bit integers, is the seed that is provided by the user.
The RNG is implemented in random_module, that
is fetched as a git submodule in RMPCDMD. A Fortran wrapper, using the bind(c)
attribute, manages the Fortran/C interface.