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Introduction

The main program in this package, pmd, is an acronym of parallel molecular dynamics, that is, molecular dynamics (MD) using spatial decomposition technique on parallel (ditributed-memory) computers.

The main features of pmd are the following:

  • several interatomic potentials for solid state systems are available;
  • Deep neural-network (DNN) interatomic potential;
  • QEq or variable charge Coulombic potential;
  • MPI parallel computation using spatial decomposition technique and hybrid parallelization using OpenMP;
  • efficient searching of neighbor atoms using linked-cell list method;
  • structure relaxation using simple velocity damping or FIRE algorithm;
  • thermostats: Berendsen and Langevin;
  • barostat: Berendsen;
  • variable-timestep MD for high-energy ion-bombardment simulation;
  • non-equilibrium MD (NEMD) for heat flux and/or ion flux simulation;
  • two-temperature model MD (TTM-MD) for laser-ablation simulation.

Since this program has been developed for the purpose of personal research tool, there are not so many functionalities. And there are some (open source) MD programs that can do almost the same thing that pmd can do. But there are some features only pmd or the parent packange nap can do. Please feel free to contact me to ask anything if you want to use pmd or nap for your specific purpose.

Bug reports and questions about pmd and nap are welcome, but I am afraid that I might not be able to respond all the reports or questions.