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;
//
}
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;
}
