A flexible and modular MD code

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Las Palmeras Molecular Dynamics (LPMD) is a highly modular, extensible molecular dynamics (MD) free code. LPMD is able to perform equilibrium MD simulations of bulk crystalline solids, amorphous solids and liquids, as well as non-equilibrium MD (NEMD) simulations such as shock waves simulations, projectile impacts, cluster collisions, shearing, deformation under load, heat conduction, melting, among others. The program includes several tools to prepare the atomic systems, such as freezing atoms to act like walls, unstoppable group of atoms with constant-velocity, adding external forces such as electric fields, among others. The current 0.7 version of LPMD (unstable, not available yet) is being written in python and C, based in the same original idea, that connects code simplicity and efficiency. Its architecture is based on separate components or plug-ins, implemented as modules which are loaded on demand at runtime.

As an extra feature, the plug-in API (Application Programming Interface) allows to use LPMD to analyze data coming from other simulation packages, such structure identification and calculation of mean squared displacement; to convert between input file formats (XYZ, VASP, LAMMPS; PDB, DLPOLY, etc.); manipulate and modify saved MD atomic trajectories, and visualize dynamical processes either in real-time or as a post-processing step.

LPMD includes already several pair potential functions such as Lennard-Jones, Morse, Buckingham, MCY and the harmonic potential, as well as embedded-atom model (EAM) functions such as the Sutton–Chen and Gupta potentials. Integrators available include Euler (for demonstration purposes only), Verlet and Velocity Verlet, Leapfrog and Beeman, among others. Electrostatic forces are treated as another potential function, by default using the plug-in implementing the Ewald summation method.

Las Palmeras Molecular Dynamics: A flexible and modular molecular dynamics code
S Davis, C Loyola, F González, J Peralta – Computer Physics Communications, 2010.

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