void NormalModeMori::initialize(ProtoMolApp* app){
MTSIntegrator::initialize(app);
//
//point to bottom integrator, for average force
myBottomNormalMode = dynamic_cast<NormalModeUtilities*>(bottom());
//check valid eigenvectors
//NM initialization if OK
NormalModeUtilities::initialize((int)app->positions.size(), app, myForces, NO_NM_FLAGS); //last for non-complimentary forces
//
//do first force calculation, and remove non sub-space part
app->energies.clear(); //Need this or initial error, due to inner integrator energy?
initializeForces();
//
//take initial C velocites from system and remove non-subspace part
if(*Q != NULL) subspaceVelocity(&app->velocities, &app->velocities);
//
//####diagnostics
if(modeOutput != ""){
//save initial positions
ex0 = new Vector3DBlock;
*ex0 = app->positions;
ofstream myFile;
myFile.open(modeOutput.c_str(),ofstream::out);
//close file
myFile.close();
}
}
void NormalModeLangLf::doHalfKick() {
const Real dt = getTimestep() * Constant::INV_TIMEFACTOR; // in fs
const Real fdt = ( 1.0 - exp( -0.5 * myGamma * dt ) ) / myGamma;
const Real vdt = exp(-0.5*myGamma*dt);
const Real ndt = sqrt( ( 1.0 - exp( -myGamma * dt ) ) / (2.0 * myGamma) ); //was sqrt( fdt );
const Real sqrtFCoverM = sqrt( 2.0 * Constant::BOLTZMANN * myTemp * myGamma );
for( int i = 0; i < _N; i++ ) {
// semi-update velocities
app->velocities[i] = app->velocities[i]*vdt
+(*myForces)[i] * fdt / app->topology->atoms[i].scaledMass
+gaussRandCoord1[i]*sqrtFCoverM*ndt;
}
subspaceVelocity(&app->velocities, &app->velocities);
buildMolecularMomentum(&app->velocities, app->topology);
}
void NormalModeLangLf::initialize(ProtoMolApp *app){
MTSIntegrator::initialize(app);
//check valid eigenvectors
//NM initialization if OK
int nm_flags = NO_NM_FLAGS;
if(genCompNoise) nm_flags |= GEN_COMP_NOISE;
NormalModeUtilities::initialize((int)app->positions.size(), app, myForces, nm_flags); //last int for no complimentary forces or gen noise: GEN_COMP_NOISE
//
//do first force calculation, and remove non sub-space part
app->energies.clear(); //Need this or initial error, due to inner integrator energy?
initializeForces();
//
//take initial C velocites from system and remove non-subspace part
if(*Q != NULL) subspaceVelocity(&app->velocities, &app->velocities);
//
}