no effect on velocity scaling

From: Philipp Schön (phschoen_at_web.de)
Date: Fri Aug 03 2007 - 02:36:19 CDT

Dear Users
I changed the source code in order to apply a constant temperature gradient across a surface. In doing so I add an additional part (=> see /* THIS PART IS NEW */ below) to the subroutine langevinVelocities for all atoms with i < 1000.
However, there is no effect on the simulation, i.e. on the temperature profile! At least something should change to all atoms between 0 and 1000 when running these lines? Do the atom counter ( int i = 0; i < numAtoms; ++i ) coincide with the integer given in the pdb file or can it change during run time? If it changes how can I assign a certain temperature to certain atoms?
Thanks for any help.
Regards
Philipp

void Sequencer::langevinVelocities(BigReal dt_fs)
{
  if ( simParams->langevinOn )
  {
    FullAtom *a = patch->atom.begin();
    int numAtoms = patch->numAtoms;
    Molecule *molecule = Node::Object()->molecule;
    BigReal dt = dt_fs * 0.001; // convert to ps
    BigReal kbT = BOLTZMAN*(simParams->langevinTemp);
    int lesReduceTemp = simParams->lesOn && simParams->lesReduceTemp;
    BigReal tempFactor = lesReduceTemp ? 1.0 / simParams->lesFactor : 1.0;

    for ( int i = 0; i < numAtoms; ++i )
    {
        int aid = a[i].id;
        BigReal f1 = exp( -1. * dt * molecule->langevin_param(aid) );
        BigReal f2 = sqrt( ( 1. - f1*f1 ) * kbT *
                           ( a[i].partition ? tempFactor : 1.0 ) / a[i].mass );
        
        a[i].velocity *= f1;
        a[i].velocity += f2 * random->gaussian_vector();
        
/* THIS PART IS NEW */
        if (i < 1000)
        {
            int aid = a[i].id;
            BigReal f1 = exp( -1. * dt * molecule->langevin_param(aid) );
            BigReal f2 = sqrt( ( 1. - f1*f1 ) * (BOLTZMAN * 1000.0) *
                               ( a[i].partition ? tempFactor : 1.0 ) / a[i].mass );
            a[i].velocity *= f1;
            a[i].velocity += f2 * random->gaussian_vector();
        }
/* IBLATH_2 => END */
    }
  }
}

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