A First Example

We will start by running a simple Molecular Dynamics simulation with two particles interacting via the Lennard-Jones potential. The sample code is given below.

#include <glotzilla++.h>

int main(int argc, char ** argv) 
{       
   MdSimulation my_simulation;

   my_simulation.AddParticle(new MdPointParticle(0,0,0));
   my_simulation.AddParticle(new MdPointParticle(1,1,1));
   my_simulation.SetInteraction(new LennardJones);
   my_simulation.SetForceRoutine(new BruteForce);
   my_simulation.SetBoundaryConditions(new PeriodicBoundary(10));
   my_simulation.SetMoveRoutine(new VerletMove);                
        
   for(int i=0; i<1000; i++)
      my_simulation ++;

   return 0;
}

Compile the code using

glotzcc md.c

where md.c is the name of the file where the code resides.

Let's take a look at the code step by step. The first thing that we do is include the Glotzilla header files. This is accomplished with the line

#include <glotzilla++.h>

The compiler now knows about all of the pre-defined Glotzilla classes. The next thing that we do is declare a simulation

MdSimulation my_simulation;

Here, MdSimulation is a class from <glotzilla++.h>. An MD simulation needs a few classes in order to work:

• particles - objects that exist in the simulation
• interactions - defines how particles interact
• force routine - calculates force particles exert on one another
• boundary conditions - the space accessable to the particles
• move routine - defines how the particles move

We define these classes using the following lines:

   my_simulation.AddParticle(new MdPointParticle(0,0,0));
   my_simulation.AddParticle(new MdPointParticle(1,1,1));
   my_simulation.SetInteraction(new LennardJones);
   my_simulation.SetForceRoutine(new BruteForce);
   my_simulation.SetBoundaryConditions(new PeriodicBoundary(10));
   my_simulation.SetMoveRoutine(new VerletMove);                

Here, we declare two point particles, one at <0,0,0> and another at <1, 1, 1>. They interact via the 12-6 Lennard-Jones potential. The force routine calculates forces between all particles, interacting or not (brute force). The boundary is periodic with a period of length 10 in x, y, and z. The equations of motion are integrated using the Verlet integration scheme.

To run the simulation for 1000 timesteps, we write:

   for(int i=0; i<1000; i++)
      my_simulation ++;

Here, the ++ operator in my_simulation integrates the equations of motion forward by 1 timestep. We do this 1000 times in all, and then the code exits.

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