Re: [Protomol-users] Adding a new integration algorithm to Protomol

[Nava W. <nwh...@tc...>]

On Mon, 28 May 2007, Paul R Brenner wrote:

> Looks like there are Gravitation and ExternalGravitation forces.

Thanks again, I've worked up a very simple Gravitation system, in case  
anybody else might find it useful it's online at:  
http://moloch.tchpc.tcd.ie/~new299/gravitation.tar.gz

I have implemented my integrator basically as for Leapfrog but with the 
following run method (and overriding addModifierAfterInitialize, because 
I am performing two force calculations per timestep). It this the correct 
setup for Protomol?:

void MyIntegrator::run(int numTimesteps) {
   if( numTimesteps < 1 )
      return;

    preStepModify();
    for( int i = 0; i < numTimesteps; i++ ) {

      * perform a single integration step *      

      myTopo->time += getTimestep();

      buildMolecularCenterOfMass(myPositions,myTopo);
      buildMolecularMomentum(myVelocities,myTopo);
      postDriftOrNextModify();
    }
    postStepModify();
}

The trajectory for my system appears to be more or less correct, but I 
have currently omitted the following code which is present in 
LeapfrogIntegrator::doKickdoDrift(). Could you give me some idea of what 
these methods do, and where I should include them?:

    if(anyPreDriftOrNextModify() || anyPreStepModify() || anyPostStepModify()){
      if(anyPreStepModify() || anyPostStepModify()){
        doHalfKick();
        postStepModify();
        preStepModify();
        doHalfKick();
      }
      else {
        doKick();
      }
      doDriftOrNextIntegrator();
    }
    else {
      ... integration step
    }

Many Thanks,

Dr Nava Whiteford
Trinity Centre for High Performance Computing
Room 203, Second Floor,
Lloyd Building,
Trinity College
Dublin 2
Ireland
Tel: +353 1 896 8458