void Integrator::Minimize( const unsigned int max, unsigned int &simpleSteps, unsigned int &quadraticSteps ) {
const double eigStore = maxEigenvalue;
if( !mParameters.ShouldProtoMolDiagonalize && eigenvectors.size() == 0 ) {
computeProjectionVectors();
}
SaveStep();
double initialPE = context->calcForcesAndEnergy( true, true );
( ( StepKernel & )( kernel.getImpl() ) ).setOldPositions();
//context->getPositions(oldPos); // I need to get old positions here
simpleSteps = 0;
quadraticSteps = 0;
for( unsigned int i = 0; i < max; i++ ) {
SetProjectionChanged( false );
if( initialPE < mMetropolisPE ) {
break;
}
const double prob = exp(-( 1.0 / ( BOLTZ * temperature )) * ( initialPE - mMetropolisPE ));
if( SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber() < prob ) {
break;
}
simpleSteps++;
double currentPE = LinearMinimize( initialPE );
if( mParameters.isAlwaysQuadratic || currentPE > initialPE ) {
quadraticSteps++;
double lambda = 0.0;
currentPE = QuadraticMinimize( currentPE, lambda );
if( currentPE > initialPE ) {
std::cout << "Quadratic Minimization Failed Energy Test [" << currentPE << ", " << initialPE << "] - Forcing Rediagonalization" << std::endl;
if( !mParameters.ShouldProtoMolDiagonalize ) computeProjectionVectors();
break;
} else {
if( mParameters.ShouldForceRediagOnQuadraticLambda && lambda < 1.0 / maxEigenvalue ) {
std::cout << "Quadratic Minimization Failed Lambda Test [" << lambda << ", " << 1.0 / maxEigenvalue << "] - Forcing Rediagonalization" << std::endl;
if( !mParameters.ShouldProtoMolDiagonalize ) computeProjectionVectors();
break;
}
}
}
if( mParameters.ShouldUseMetropolisMinimization ) {
if( currentPE < mMetropolisPE ) {
break;
}
const double prob = exp(-( 1.0 / ( BOLTZ * temperature )) * ( currentPE - mMetropolisPE ));
if( SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber() < prob ) {
break;
}
} else {
const double diff = initialPE - currentPE;
if( diff < getMinimumLimit() && diff >= 0.0 ) {
break;
}
if( diff > 0.0 ) {
SaveStep();
initialPE = currentPE;
} else {
RevertStep();
context->calcForcesAndEnergy( true, false );
maxEigenvalue *= 2;
}
}
}
mSimpleMinimizations += simpleSteps;
mQuadraticMinimizations += quadraticSteps;
maxEigenvalue = eigStore;
}
void SeekPath(int stepleft)
{
DuplicatePos(stepleft, 'b');
int i = 0, j = 0, k = 0, l = 0, x = 0, y = 0, activeCount = 0;
//int o, p;//more spaces involved
for (x = 0;x <= y;x++)
{
DuplicatePos(stepleft + maxstep, 'b');
Compare(x, 0, stepleft, 1);
if (stepleft > 0)
{
DuplicatePos((stepleft + maxstep + maxstep), 'b');
for (i = 1;i <= maxlength;i++)
{
for (j = 1;j <= (int)pow(2, i);j++)
{
if (pos[0][i][j] == 0)
continue;
else
{
Detach(i, j);
DuplicatePos(stepleft + maxstep + maxstep + maxstep, 'b');
for (k = 1;k <= maxlength;k++)//k = 0 need to examine
{
for (l = 1;l <= (int)pow(2, k);l++)
{
if (pos[0][k][l] < 1 && pos[0][k - 1][(l + 1) / 2] >= 1)
{
if (l % 2 == 1 && pos[0][k][l] == 0)
{
Attach(k, l);
//printf("\n1step%d %d,%d ---> %d,%d:\n", maxstep + 1 - stepleft, i, j, k, l);
//Display();
if (stepleft > 1)
{
SaveStep(i, j, k, l, x, stepleft);
Compare(x, 0, stepleft, 0);
//printf("1");
SeekPath(stepleft - 1);
}
else
{
activeCount = Active(1);
SaveStep(i, j, k, l, x, stepleft);
Compare(x, activeCount, stepleft, 0);
//printf("1");
}
}
else if (l % 2 == 0 && pos[0][k][l - 1] >= 1 && pos[0][k][l - 1] != 2 && pos[1][0][1] != 2)
{
if (pos[0][k][l] == -1)//case 1 -1 ---> 1 1
{
SideSwitch(k, l - 1);
Attach(k, l - 1);
//printf("\n2step%d %d,%d ---> %d,%d:\n", maxstep + 1 - stepleft, i, j, k, l - 1);
//Display();
if (stepleft > 1)
{
SaveStep(i, j, k, l - 1, x, stepleft);
Compare(x, 0, stepleft, 0);
//printf("2");
SeekPath(stepleft - 1);
}
else
{
activeCount = Active(1);
SaveStep(i, j, k, l - 1, x, stepleft);
Compare(x, activeCount, stepleft, 0);
//printf("2");
}
}
else if (pos[0][k][l] == -2)//case 1 -2 ---> 1 1
{
Attach(k, l);
//printf("\n3step%d %d,%d ---> %d,%d:\n", maxstep + 1 - stepleft, i, j, k, l);
//Display();
if (stepleft > 1)
{
SaveStep(i, j, k, l, x, stepleft);
Compare(x, 0, stepleft, 0);
//printf("3");
SeekPath(stepleft - 1);
}
else
{
activeCount = Active(1);
SaveStep(i, j, k, l, x, stepleft);
Compare(x, activeCount, stepleft, 0);
//printf("3");
}
}
else if (pos[0][k][l] == 0)//case 1 0 ---> 1 1 ,two ways to attach, left and right
{
//attach left
SideSwitch(k, l - 1);
Attach(k, l - 1);
//printf("\n4step%d %d,%d ---> %d,%d:\n", maxstep + 1 - stepleft, i, j, k, l - 1);
//Display();
if (stepleft > 1)
{
SaveStep(i, j, k, l - 1, x, stepleft);
Compare(x, 0, stepleft, 0);
//printf("4");
SeekPath(stepleft - 1);
}
else
{
activeCount = Active(1);
SaveStep(i, j, k, l - 1, x, stepleft);
Compare(x, activeCount, stepleft, 0);
//printf("4");
}
DuplicatePos(stepleft + maxstep + maxstep + maxstep, 'r');
//attach right
Attach(k, l);
//printf("\n5step%d %d,%d ---> %d,%d:\n", maxstep + 1 - stepleft, i, j, k, l);
//Display();
if (stepleft > 1)
{
SaveStep(i, j, k, l, x, stepleft);
Compare(x, 0, stepleft, 0);
//printf("5");
SeekPath(stepleft - 1);
}
else
{
activeCount = Active(1);
SaveStep(i, j, k, l, x, stepleft);
Compare(x, activeCount, stepleft, 0);
//printf("5");
}
}
}
DuplicatePos(stepleft + maxstep + maxstep + maxstep, 'r');
}
}
}
DuplicatePos(stepleft + maxstep + maxstep, 'r');
}
}
}
}
DuplicatePos(stepleft + maxstep, 'r');
y += Active(0);
}
}
