long NormalModeRelax::run(const long numTimesteps) {
if( numTimesteps < 1 ) return 0;
//check valid eigenvectors
if(*Q == NULL)
report << error << "No Eigenvectors for NormalMode integrator."<<endr;
//
//do minimization with local forces, max loop 100, set subSpace minimization true
itrs = minimizer(minLim, 100, simpleMin, reDiag, true, &forceCalc, &lastLambda, &app->energies, &app->positions, app->topology);
Real minPotEnergy = app->energies.potentialEnergy(); //save potential energy before random
//constraints?
app->energies.clear();
//run brownian if any remaining modes
if(testRemainingModes()) myNextIntegrator->run(myCycleLength); //cyclelength
(app->energies)[ScalarStructure::OTHER] = minPotEnergy; //store minimum potential energy
if(*Q == NULL){ //rediagonalize?
if(myPreviousIntegrator == NULL)
report << error << "[NormalModeRelax::Run] Re-diagonalization forced with NormalModeRelax as outermost Integrator. Aborting."<<endr;
return numTimesteps;
}
//
postStepModify();
return numTimesteps;
}
void NormalModeLangLf::run(int numTimesteps) {
//Real h = getTimestep() * Constant::INV_TIMEFACTOR;
Real actTime;
if( numTimesteps < 1 )
return;
//check valid eigenvectors
if(*Q == NULL)
report << error << "No Eigenvectors for NormalMode integrator."<<endr;
//
//time calculated in forces! so fix here
actTime = app->topology->time + numTimesteps * getTimestep();
//
//main loop
for( int i = 0; i < numTimesteps; i++ ) {
//****main loop*************************************
preStepModify();
genProjGauss(&gaussRandCoord1, app->topology);
doHalfKick();
//
//nmlDrift(&app->positions, &app->velocities, h, app->topology);
doDrift();
//constraints?
app->energies.clear();
//run minimizer if any remaining modes
if(testRemainingModes()) myNextIntegrator->run(myCycleLength); //cyclelength
if(app->eigenInfo.reDiagonalize){ //rediagonalize?
app->topology->time = actTime + (i - numTimesteps) * getTimestep();
if(myPreviousIntegrator == NULL)
report << error << "[NormalModeLangLf::Run] Re-diagonalization forced with NormalModeLangLf as outermost Integrator. Aborting."<<endr;
return;
}
//calculate sub space forces
app->energies.clear();
calculateForces();
//
genProjGauss(&gaussRandCoord1, app->topology);
doHalfKick();
//
postStepModify();
}
//fix time
app->topology->time = actTime;
//
}
void NormalModeMinimizer::run(int numTimesteps) {
if( numTimesteps < 1 )
return;
//check valid eigenvectors
if(*Q == NULL)
report << error << "No Eigenvectors for NormalMode integrator."<<endr;
//
preStepModify();
//remove last random pertubation
if(randforce) app->positions.intoSubtract(gaussRandCoord1);
//(*myPositions).intoWeightedAdd(-randStp,gaussRandCoord1);
//do minimization with local forces, max loop rediagOnMaxMinSteps, set subSpace minimization true
itrs = minimizer(minLim, rediagOnMaxMinSteps>0 ? rediagOnMaxMinSteps : 100 , simpleMin, reDiag, true, &forceCalc, &lastLambda, &app->energies, &app->positions, app->topology);
//flag excessive minimizations
if(itrs > 10) report << debug(1) << "[NormalModeMinimizer::run] iterations = " << itrs << "." << endr;
else report << debug(3) << "[NormalModeMinimizer::run] iterations = " << itrs << "." << endr;
avItrs += itrs;
//rediagonalize if minimization steps exceeds 'rediagOnMaxMinSteps'
if(reDiag && rediagOnMaxMinSteps > 0 && itrs >= rediagOnMaxMinSteps){
report << debug(1) << "[NormalModeMinimizer::run] Minimization steps ("
<< itrs << ") exceeded maximum (" << rediagOnMaxMinSteps << "), forcing re-diagonalize." << endr;
itrs = -1; //force re-diag
}
numSteps++;
avMinForceCalc += forceCalc;
report <<debug(5)<<"[NormalModeMinimizer::run] iterations = "<<itrs<<" average = "<<
(float)avItrs/(float)numSteps<<" force calcs = "<<forceCalc<<" average = "<<(float)avMinForceCalc/(float)numSteps<<endl;
if(randforce && itrs != -1 && lastLambda > 0){ //add random force, but not if rediagonalizing
//add random force
if(myPreviousNormalMode->genCompNoise) gaussRandCoord1 = myPreviousNormalMode->tempV3DBlk;
else genProjGauss(&gaussRandCoord1, app->topology);
//lambda = eUFactor / *eigValP; //user factor
randStp = sqrt(2 * Constant::BOLTZMANN * myTemp * lastLambda); //step length
//(*myPositions).intoWeightedAdd(randStp,gaussRandCoord1);
gaussRandCoord1.intoWeighted(randStp,gaussRandCoord1);
app->positions.intoAdd(gaussRandCoord1);
//additional random steps?
if(randforce > 1){
eUFactor = 0.5;
Real lambda;
for(int i=1;i<randforce;i++){
utilityCalculateForces();
nonSubspaceForce(myForces, myForces);
for(int j=0;j<_N;j++) (*myForces)[j] /= app->topology->atoms[j].scaledMass;
lambda = eUFactor / *eigValP; //user factor
//update positions
app->positions.intoWeightedAdd(lambda,*myForces);
gaussRandCoord1.intoWeightedAdd(lambda,*myForces); //add to grc1 so can be removed at the next step
//random force
genProjGauss(&gaussRandCoord2, app->topology);
randStp = sqrt(2 * Constant::BOLTZMANN * myTemp * lambda);
app->positions.intoWeightedAdd(randStp,gaussRandCoord2);
//add to grc1 so can be removed at the next step
gaussRandCoord1.intoWeightedAdd(randStp,gaussRandCoord2);
}
}
}else{
gaussRandCoord1.zero(-1);
//flag re-diagonalize if detected
if(itrs == -1) app->eigenInfo.reDiagonalize = true;
}
//
postStepModify();
}
long NormalModeMori::run(const long numTimesteps) {
Real h = getTimestep() * Constant::INV_TIMEFACTOR;
Real actTime;
if( numTimesteps < 1 ) return 0;
//check valid eigenvectors
if(*Q == NULL)
report << error << "No Eigenvectors for NormalMode integrator."<<endr;
//
//time calculated in forces! so fix here
actTime = app->topology->time + numTimesteps * getTimestep();
//
//main loop
for( int i = 0; i < numTimesteps; i++ ) {
//****main loop*************************************
preStepModify();
doHalfKick();
//
nmlDrift(&app->positions, &app->velocities, h, app->topology);
//constraints?
app->energies.clear();
//run minimizer if any remaining modes
if(testRemainingModes()) myNextIntegrator->run(myCycleLength); //cyclelength
if(*Q == NULL){ //rediagonalize?
app->topology->time = actTime - (i - numTimesteps) * getTimestep();
if(myPreviousIntegrator == NULL)
report << error << "[NormalModeMori::Run] Re-diagonalization forced with NormalModeMori as outermost Integrator. Aborting."<<endr;
return i;
}
//#################Put averaged force code here##############################
//calculate sub space forces, just do this for the energy
Real minPotEnergy = (app->energies)[ScalarStructure::OTHER]; //save minimum potential energy
app->energies.clear();
calculateForces();
//transfer the real average force, Note: force fields must be identical
if(!instForce){
for( unsigned int i=0;i < app->positions.size(); i++) (*myForces)[i] = myBottomNormalMode->tempV3DBlk[i];
}
(app->energies)[ScalarStructure::OTHER] = minPotEnergy; //restore minimum potential energy
//###########################################################################
//
doHalfKick();
//
postStepModify();
}
//####diagnostics
//output modes?
if(modeOutput != ""){
//get modes
modeSpaceProj(tmpC, &app->positions, ex0);
//Output modes for analysis
ofstream myFile;
myFile.open(modeOutput.c_str(),ofstream::app);
myFile.precision(10);
for(int ii=0;ii<_rfM-1;ii++) myFile << tmpC[ii] << ", ";
myFile << tmpC[_rfM-1] << endl; //last
//close file
myFile.close();
}
//####
//fix time
app->topology->time = actTime;
return numTimesteps;
}
void NormalModeQuadratic::run( int numTimesteps )
{
//check valid eigenvectors
if ( *Q == NULL ){
report << error << "No Eigenvectors for NormalMode integrator." << endr;
}
if ( app->eigenInfo.myEigenvalues.size() <
(unsigned)firstMode + numMode - 1 ){
report << error << "Insufficient Eigenvalues for Quadratic integrator (" << app->eigenInfo.myEigenvalues.size() << "." << endr;
}
if ( numTimesteps < 1 ){
return;
}
//timestep
Real h = getTimestep() * Constant::INV_TIMEFACTOR;
//time calculated in forces! so fix here
Real actTime = app->topology->time + numTimesteps * getTimestep();
Real tempFrq;
Real tempKt = sqrt( 2.0 * myTemp * Constant::BOLTZMANN );
//find ex0 if re-diag present
if ( myPreviousNormalMode && myPreviousNormalMode->newDiag ) {
//reset ex0 and restart time for \omega t if new diagonalization
*ex0 = myPreviousNormalMode->diagAt;
total_time = 0;
}
//main loop
for ( int i = 0; i < numTimesteps; i++ ) {
preStepModify();
numSteps++;
if ( stepModes ) {
//set mode
if ( !( numSteps % cycleSteps ) ) {
cPos[currMode++] = 0.0;
app->positions = *ex0;
if ( currMode >= firstMode + numMode - 1 ) {
currMode = firstMode - 1;
}
}
app->eigenInfo.currentMode = currMode + 1;
//****Analytical mode integrator loop*****
tempFrq = sqrt( fabs( app->eigenInfo.myEigenvalues[currMode] ) );
cPos[currMode] = tempKt * sin( ( double )( numSteps % cycleSteps ) / ( double )cycleSteps * 2.0 * M_PI );
cPos[currMode] /= fScale ? tempFrq : sqrt( tempFrq );
subspaceProj( cPos, &app->positions );
} else {
//full dynamics here
int startm = firstMode - 1;
if ( startm < 7 ) {
startm = 7;
}
for ( int i = startm; i < firstMode + numMode - 1;i++ ) {
//****Analytical mode integrator loop*****
tempFrq = sqrt( fabs( app->eigenInfo.myEigenvalues[i] ) );
cPos[i] = tempKt * sin( total_time * tempFrq );
cPos[i] /= fScale ? tempFrq : sqrt( tempFrq );
}
subspaceProj( cPos, &app->positions );
}
postStepModify();
total_time += h;
}
//fix time
app->topology->time = actTime;
}
