Table 1
A summary of the functionality provided by the Fortran modules of RMPCDMD found in the src/ directory.
| Module name | Functionality |
|---|---|
| common | Routines of general use: histogramming, parsing of command-line arguments, timing and minimum-image convention function. |
| hilbert | Computation of the compact Hilbert index of a lattice cell and vice-versa. |
| cell_system | Cell data structure. |
| particle_system | Particles data structure and sorting routine. |
| particle_system_io | Data structures to facilitate the storage of thermodynamic and particle data. |
| interaction | Computation of Lennard-Jones force and energy. |
| neighbor_list | Data structure and routines to update the neighbor list. |
| mpcd | Algorithms for MPCD streaming and collision, and for bulk reactions. |
| md | Algorithms for velocity-Verlet and rigid body MD. |
Figure 1
Output of the program plot_velocity.py with options --directed and --histogram for the single dimer simulation.
Figure 2
Output of the program plot_histogram.py for the single dimer simulation. The region close to z = 0 is the catalytic sphere and displays the highest values for the concentration of B product.
Figure 3
Output of the program view_last_simulation_frame.py for the single dimer simulation with option --show-B. The product of reaction B is mostly found around the catalytic sphere (red) and the periodic character of the simulation box is visible.