Minimal Simulation

The following tutorial pertains to a single component Lennard-Jones, NVE molecular dynamics simulation.

• Verified 10-4-07; code revision 390
• Created 5-8-07; code revision 173

Linking to the simulation builder library/header

First we must include the Simulation Builder header file:

#include <glotzilla++.h>

This tells the compiler about all of the pre-defined Glotzilla classes. We will now be able to access the MdSimulation class within the Simulation Builder library and can create an instance of it:

#include <glotzilla++.h>

int main(int argc, char ** argv) 
{       
   MdSimulation my_simulation;
   return 0;
}

Setting up the simulation

Now that we have declared an instance of the MdSimulation called my_simulation, we can now set up the simulation. An MD simulation needs a few aspects of it defined 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
• integration routine - defines how the equations of motion are integrated

In the following code excerpt, we will:

• add 2 particles at <0,0,0> and <1,1,1>
• set the interaction between particles to Lennard-Jones
• set the code to use a brute force routine for calculating pair interactions
• set the boundaries of the box to be periodic where Lx = Ly = Lz = 10
• set the integration routine to VelocityVerletIntegrator

#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.SetIntegrationRoutine(new VelocityVerletIntegrator);

   return 0;
}

Integrating the equations of motion

To advance the simulation through time, i.e. integrate the equations of motion, we need only use the "++" operator declared in MdSimulation. The following excerpt of code will advance the simulation through 10000 timesteps and then exit.

#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.SetIntegrationRoutine(new VelocityVerletIntegrator);
        
   for(int i=0; i<10000; i++)
      my_simulation ++;

   return 0;
}

Getting information from the simulation

The MdSimulation class provides a variety of methods to query the simulation.

• Temperature
• Pressure
• Potential Energy
• Kinetic Energy
• Virial
• Positions
• Velocities
• Forces
• Visualization data

Temperature

The following code excerpt will print temperature to the screen (std::cout) every 5 timesteps.

for(int i=0; i<10000; i++)
{
        my_simulation ++;
                
        if(i%5 == 0)
                my_simulation.PrintTemperature(std::cout);
}

Visualization

The following code excerpt will print visualization data to a pipe for the "vis3d" application every 5 timesteps. The topic of pipes will be covered in depth in the the pipes tutorial?.

opstream vis_pipe("vis3d");

for(int timesteps=0; timesteps<10000; timesteps++)
{
        my_simulation ++;
                
        if(timesteps%5 == 0)
                my_simulation.PrintVisual(vis_pipe);
}

Compiling the code

To compile the code you will need to use the "glotzcc" command. The glotzcc command calls the mpic++ compiler and gives it the appropriate library and header search paths. Within your shell, execute the following command:

glotzcc MDMinimalSimulation.cpp

where MDMinimalSimulation.cpp is the name of the file where the code resides.

Problems

Refer to the FAQ? page.