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#include <math.h> |
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#include <cmath> |
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#include "minimizers/OOPSEMinimizer.hpp" |
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#include "integrators/Integrator.cpp" |
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namespace oopse { |
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OOPSEMinimizer::OOPSEMinimizer(SimInfo* theInfo, MinimizerParameterSet *param) : |
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info(theInfo), paramSet(param), bShake(true), bVerbose(false) { |
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OOPSEMinimizer::OOPSEMinimizer( SimInfo *theInfo, ForceFields* the_ff , |
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calcDim(); |
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curX = getCoor(); |
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curG.resize(ndim); |
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MinimizerParameterSet * param) : |
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} |
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RealIntegrator(theInfo, the_ff), bShake(true), bVerbose(false) { |
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OOPSEMinimizer::~OOPSEMinimizer() { |
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delete paramSet; |
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} |
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dumpOut = NULL; |
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void OOPSEMinimizer::calcEnergyGradient(std::vector < double > &x, |
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std::vector < double > &grad, double&energy, int&status) { |
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statOut = NULL; |
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DirectionalAtom *dAtom; |
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int index; |
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double force[3]; |
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double dAtomGrad[6]; |
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int shakeStatus; |
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status = 1; |
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tStats = new Thermo(info); |
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setCoor(x); |
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if (nConstrained && bShake) { |
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shakeStatus = shakeR(); |
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} |
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calcForce(1, 1); |
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if (nConstrained && bShake) { |
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shakeStatus = shakeF(); |
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} |
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paramSet = param; |
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x = getCoor(); |
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index = 0; |
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for(int i = 0; i < integrableObjects.size(); i++) { |
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if (integrableObjects[i]->isDirectional()) { |
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integrableObjects[i]->getGrad(dAtomGrad); |
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calcDim(); |
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//gradient is equal to -f |
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grad[index++] = -dAtomGrad[0]; |
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curX = getCoor(); |
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grad[index++] = -dAtomGrad[1]; |
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curG.resize(ndim); |
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grad[index++] = -dAtomGrad[2]; |
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grad[index++] = -dAtomGrad[3]; |
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grad[index++] = -dAtomGrad[4]; |
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preMove(); |
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grad[index++] = -dAtomGrad[5]; |
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} else { |
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integrableObjects[i]->getFrc(force); |
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} |
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grad[index++] = -force[0]; |
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grad[index++] = -force[1]; |
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grad[index++] = -force[2]; |
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} |
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} |
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OOPSEMinimizer::~OOPSEMinimizer(){ |
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energy = tStats->getPotential(); |
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} |
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delete tStats; |
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void OOPSEMinimizer::setCoor(std::vector<double> &x) { |
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Vector3d position; |
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Vector3d eulerAngle; |
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SimInfo::MoleculeIterator i; |
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Molecule::IntegrableObjectIterator j; |
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Molecule* mol; |
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StuntDouble* integrableObject; |
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int index = 0; |
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if(dumpOut) |
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for (mol = info->beginMolecule(i); mol != NULL; mol = info->nextMolecule(i)) { |
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for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(j)) { |
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delete dumpOut; |
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position[0] = x[index++]; |
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if(statOut) |
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position[1] = x[index++]; |
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delete statOut; |
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position[2] = x[index++]; |
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delete paramSet; |
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integrableObject->setPos(position); |
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} |
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if (integrableObject->isDirectional()) { |
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eulerAngle[0] = x[index++]; |
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eulerAngle[1] = x[index++]; |
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eulerAngle[2] = x[index++]; |
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void OOPSEMinimizer::calcEnergyGradient(vector<double>& x, std::vector<double>& grad, |
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integrableObject->setEuler(eulerAngle); |
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} |
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} |
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} |
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|
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} |
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double& energy, int& status){ |
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std::vector<double> OOPSEMinimizer::getCoor() { |
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Vector3d position; |
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Vector3d eulerAngle; |
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SimInfo::MoleculeIterator i; |
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Molecule::IntegrableObjectIterator j; |
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Molecule* mol; |
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StuntDouble* integrableObject; |
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int index = 0; |
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std::vector<double> x(getDim()); |
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for (mol = info->beginMolecule(i); mol != NULL; mol = info->nextMolecule(i)) { |
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for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(j)) { |
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|
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position = integrableObject->getPos(); |
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x[index++] = position[0]; |
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x[index++] = position[1]; |
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x[index++] = position[2]; |
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DirectionalAtom* dAtom; |
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if (integrableObject->isDirectional()) { |
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eulerAngle = integrableObject->getEuler(); |
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x[index++] = eulerAngle[0]; |
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x[index++] = eulerAngle[1]; |
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x[index++] = eulerAngle[2]; |
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} |
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} |
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} |
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return x; |
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} |
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int index; |
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double force[3]; |
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/* |
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int OOPSEMinimizer::shakeR() { |
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int i, j; |
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double dAtomGrad[6]; |
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int done; |
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int shakeStatus; |
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double posA[3], posB[3]; |
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double velA[3], velB[3]; |
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double pab[3]; |
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status = 1; |
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double rab[3]; |
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|
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int a, b, |
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ax, ay, |
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az, bx, |
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by, bz; |
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setCoor(x); |
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double rma, rmb; |
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double dx, dy, |
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dz; |
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double rpab; |
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if (nConstrained && bShake){ |
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double rabsq, pabsq, |
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rpabsq; |
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shakeStatus = shakeR(); |
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double diffsq; |
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} |
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double gab; |
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int iteration; |
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for(i = 0; i < nAtoms; i++) { |
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moving[i] = 0; |
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calcForce(1, 1); |
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moved[i] = 1; |
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} |
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iteration = 0; |
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done = 0; |
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if (nConstrained && bShake){ |
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while (!done && (iteration < maxIteration)) { |
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done = 1; |
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shakeStatus = shakeF(); |
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for(i = 0; i < nConstrained; i++) { |
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a = constrainedA[i]; |
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} |
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b = constrainedB[i]; |
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ax = (a * 3) + 0; |
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ay = (a * 3) + 1; |
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x = getCoor(); |
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az = (a * 3) + 2; |
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bx = (b * 3) + 0; |
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by = (b * 3) + 1; |
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bz = (b * 3) + 2; |
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index = 0; |
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if (moved[a] || moved[b]) { |
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posA = atoms[a]->getPos(); |
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posB = atoms[b]->getPos(); |
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for(j = 0; j < 3; j++) |
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pab[j] = posA[j] - posB[j]; |
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for(int i = 0; i < integrableObjects.size(); i++){ |
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//periodic boundary condition |
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info->wrapVector(pab); |
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pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
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if (integrableObjects[i]->isDirectional()) { |
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rabsq = constrainedDsqr[i]; |
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diffsq = rabsq - pabsq; |
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// the original rattle code from alan tidesley |
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integrableObjects[i]->getGrad(dAtomGrad); |
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if (fabs(diffsq) > (tol * rabsq * 2)) { |
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rab[0] = oldPos[ax] - oldPos[bx]; |
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rab[1] = oldPos[ay] - oldPos[by]; |
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rab[2] = oldPos[az] - oldPos[bz]; |
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//gradient is equal to -f |
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info->wrapVector(rab); |
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|
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grad[index++] = -dAtomGrad[0]; |
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rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
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|
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grad[index++] = -dAtomGrad[1]; |
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rpabsq = rpab * rpab; |
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< |
grad[index++] = -dAtomGrad[2]; |
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|
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< |
grad[index++] = -dAtomGrad[3]; |
142 |
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|
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< |
grad[index++] = -dAtomGrad[4]; |
144 |
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|
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< |
grad[index++] = -dAtomGrad[5]; |
244 |
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if (rpabsq < (rabsq * -diffsq)) { |
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|
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+ |
#ifdef IS_MPI |
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248 |
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a = atoms[a]->getGlobalIndex(); |
249 |
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< |
} |
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b = atoms[b]->getGlobalIndex(); |
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else{ |
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#endif //is_mpi |
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254 |
< |
integrableObjects[i]->getFrc(force); |
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> |
//std::cerr << "Waring: constraint failure" << std::endl; |
255 |
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|
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+ |
gab = sqrt(rabsq / pabsq); |
257 |
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258 |
+ |
rab[0] = (posA[0] - posB[0]) |
259 |
+ |
* gab; |
260 |
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261 |
< |
grad[index++] = -force[0]; |
261 |
> |
rab[1] = (posA[1] - posB[1]) |
262 |
> |
* gab; |
263 |
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|
264 |
< |
grad[index++] = -force[1]; |
264 |
> |
rab[2] = (posA[2] - posB[2]) |
265 |
> |
* gab; |
266 |
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|
267 |
< |
grad[index++] = -force[2]; |
267 |
> |
info->wrapVector(rab); |
268 |
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|
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+ |
rpab = |
270 |
+ |
rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
271 |
+ |
} |
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|
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+ |
//rma = 1.0 / atoms[a]->getMass(); |
274 |
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|
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< |
} |
275 |
> |
//rmb = 1.0 / atoms[b]->getMass(); |
276 |
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|
277 |
< |
|
277 |
> |
rma = 1.0; |
278 |
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|
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< |
} |
279 |
> |
rmb = 1.0; |
280 |
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|
281 |
< |
|
281 |
> |
gab = diffsq / (2.0 * (rma + rmb) * rpab); |
282 |
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|
283 |
< |
energy = tStats->getPotential(); |
283 |
> |
dx = rab[0]* |
284 |
> |
gab; |
285 |
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|
286 |
+ |
dy = rab[1]* |
287 |
+ |
gab; |
288 |
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|
289 |
+ |
dz = rab[2]* |
290 |
+ |
gab; |
291 |
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|
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< |
} |
292 |
> |
posA[0] += rma *dx; |
293 |
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|
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+ |
posA[1] += rma *dy; |
295 |
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|
296 |
+ |
posA[2] += rma *dz; |
297 |
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|
298 |
< |
void OOPSEMinimizer::setCoor(vector<double>& x){ |
298 |
> |
atoms[a]->setPos(posA); |
299 |
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|
300 |
+ |
posB[0] -= rmb *dx; |
301 |
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|
302 |
+ |
posB[1] -= rmb *dy; |
303 |
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|
304 |
< |
DirectionalAtom* dAtom; |
304 |
> |
posB[2] -= rmb *dz; |
305 |
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|
306 |
< |
int index; |
306 |
> |
atoms[b]->setPos(posB); |
307 |
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|
308 |
< |
double position[3]; |
308 |
> |
moving[a] = 1; |
309 |
|
|
310 |
< |
double eulerAngle[3]; |
310 |
> |
moving[b] = 1; |
311 |
|
|
312 |
+ |
done = 0; |
313 |
+ |
} |
314 |
+ |
} |
315 |
+ |
} |
316 |
|
|
317 |
+ |
for(i = 0; i < nAtoms; i++) { |
318 |
+ |
moved[i] = moving[i]; |
319 |
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|
320 |
+ |
moving[i] = 0; |
321 |
+ |
} |
322 |
|
|
323 |
+ |
iteration++; |
324 |
+ |
} |
325 |
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|
326 |
< |
index = 0; |
326 |
> |
if (!done) { |
327 |
> |
std::cerr << "Waring: can not constraint within maxIteration" |
328 |
> |
<< std::endl; |
329 |
|
|
330 |
< |
|
330 |
> |
return -1; |
331 |
> |
} else |
332 |
> |
return 1; |
333 |
> |
} |
334 |
|
|
335 |
< |
for(int i = 0; i < integrableObjects.size(); i++){ |
335 |
> |
//remove constraint force along the bond direction |
336 |
|
|
203 |
– |
|
337 |
|
|
338 |
< |
position[0] = x[index++]; |
338 |
> |
int OOPSEMinimizer::shakeF() { |
339 |
> |
int i, j; |
340 |
|
|
341 |
< |
position[1] = x[index++]; |
341 |
> |
int done; |
342 |
|
|
343 |
< |
position[2] = x[index++]; |
343 |
> |
double posA[3], posB[3]; |
344 |
|
|
345 |
+ |
double frcA[3], frcB[3]; |
346 |
|
|
347 |
+ |
double rab[3], fpab[3]; |
348 |
|
|
349 |
< |
integrableObjects[i]->setPos(position); |
349 |
> |
int a, b, |
350 |
> |
ax, ay, |
351 |
> |
az, bx, |
352 |
> |
by, bz; |
353 |
|
|
354 |
+ |
double rma, rmb; |
355 |
|
|
356 |
+ |
double rvab; |
357 |
|
|
358 |
< |
if (integrableObjects[i]->isDirectional()){ |
358 |
> |
double gab; |
359 |
|
|
360 |
< |
|
360 |
> |
double rabsq; |
361 |
|
|
362 |
< |
eulerAngle[0] = x[index++]; |
362 |
> |
double rfab; |
363 |
|
|
364 |
< |
eulerAngle[1] = x[index++]; |
364 |
> |
int iteration; |
365 |
|
|
366 |
< |
eulerAngle[2] = x[index++]; |
366 |
> |
for(i = 0; i < nAtoms; i++) { |
367 |
> |
moving[i] = 0; |
368 |
|
|
369 |
+ |
moved[i] = 1; |
370 |
+ |
} |
371 |
|
|
372 |
+ |
done = 0; |
373 |
|
|
374 |
< |
integrableObjects[i]->setEuler(eulerAngle[0], |
374 |
> |
iteration = 0; |
375 |
|
|
376 |
< |
eulerAngle[1], |
376 |
> |
while (!done && (iteration < maxIteration)) { |
377 |
> |
done = 1; |
378 |
|
|
379 |
< |
eulerAngle[2]); |
379 |
> |
for(i = 0; i < nConstrained; i++) { |
380 |
> |
a = constrainedA[i]; |
381 |
> |
|
382 |
> |
b = constrainedB[i]; |
383 |
|
|
384 |
+ |
ax = (a * 3) + 0; |
385 |
|
|
386 |
+ |
ay = (a * 3) + 1; |
387 |
|
|
388 |
< |
} |
388 |
> |
az = (a * 3) + 2; |
389 |
|
|
390 |
< |
|
390 |
> |
bx = (b * 3) + 0; |
391 |
|
|
392 |
< |
} |
392 |
> |
by = (b * 3) + 1; |
393 |
|
|
394 |
< |
|
394 |
> |
bz = (b * 3) + 2; |
395 |
|
|
396 |
< |
} |
396 |
> |
if (moved[a] || moved[b]) { |
397 |
> |
posA = atoms[a]->getPos(); |
398 |
|
|
399 |
+ |
posB = atoms[b]->getPos(); |
400 |
|
|
401 |
+ |
for(j = 0; j < 3; j++) |
402 |
+ |
rab[j] = posA[j] - posB[j]; |
403 |
|
|
404 |
< |
std::vector<double> OOPSEMinimizer::getCoor(){ |
404 |
> |
info->wrapVector(rab); |
405 |
|
|
406 |
< |
|
406 |
> |
atoms[a]->getFrc(frcA); |
407 |
|
|
408 |
< |
DirectionalAtom* dAtom; |
408 |
> |
atoms[b]->getFrc(frcB); |
409 |
|
|
410 |
< |
int index; |
410 |
> |
//rma = 1.0 / atoms[a]->getMass(); |
411 |
|
|
412 |
< |
double position[3]; |
412 |
> |
//rmb = 1.0 / atoms[b]->getMass(); |
413 |
|
|
414 |
< |
double eulerAngle[3]; |
414 |
> |
rma = 1.0; |
415 |
|
|
416 |
< |
std::vector<double> x; |
416 |
> |
rmb = 1.0; |
417 |
|
|
418 |
+ |
fpab[0] = frcA[0] * rma - frcB[0] * rmb; |
419 |
|
|
420 |
+ |
fpab[1] = frcA[1] * rma - frcB[1] * rmb; |
421 |
|
|
422 |
< |
x.resize(getDim()); |
422 |
> |
fpab[2] = frcA[2] * rma - frcB[2] * rmb; |
423 |
|
|
424 |
+ |
gab = fpab[0] * fpab[0] + fpab[1] * fpab[1] + fpab[2] * fpab[2]; |
425 |
|
|
426 |
+ |
if (gab < 1.0) |
427 |
+ |
gab = 1.0; |
428 |
|
|
429 |
< |
index = 0; |
429 |
> |
rabsq = rab[0] * rab[0] + rab[1] * rab[1] + rab[2] * rab[2]; |
430 |
|
|
431 |
< |
|
431 |
> |
rfab = rab[0] * fpab[0] + rab[1] * fpab[1] + rab[2] * fpab[2]; |
432 |
|
|
433 |
< |
for(int i = 0; i < integrableObjects.size(); i++){ |
433 |
> |
if (fabs(rfab) > sqrt(rabsq*gab) * 0.00001) { |
434 |
> |
gab = -rfab / (rabsq * (rma + rmb)); |
435 |
|
|
436 |
< |
position = integrableObjects[i]->getPos(); |
436 |
> |
frcA[0] = rab[0]* |
437 |
> |
gab; |
438 |
|
|
439 |
+ |
frcA[1] = rab[1]* |
440 |
+ |
gab; |
441 |
|
|
442 |
+ |
frcA[2] = rab[2]* |
443 |
+ |
gab; |
444 |
|
|
445 |
< |
x[index++] = position[0]; |
445 |
> |
atoms[a]->addFrc(frcA); |
446 |
|
|
447 |
< |
x[index++] = position[1]; |
447 |
> |
frcB[0] = -rab[0]*gab; |
448 |
|
|
449 |
< |
x[index++] = position[2]; |
449 |
> |
frcB[1] = -rab[1]*gab; |
450 |
|
|
451 |
+ |
frcB[2] = -rab[2]*gab; |
452 |
|
|
453 |
+ |
atoms[b]->addFrc(frcB); |
454 |
|
|
455 |
< |
if (integrableObjects[i]->isDirectional()){ |
455 |
> |
moving[a] = 1; |
456 |
|
|
457 |
+ |
moving[b] = 1; |
458 |
|
|
459 |
+ |
done = 0; |
460 |
+ |
} |
461 |
+ |
} |
462 |
+ |
} |
463 |
|
|
464 |
< |
integrableObjects[i]->getEulerAngles(eulerAngle); |
464 |
> |
for(i = 0; i < nAtoms; i++) { |
465 |
> |
moved[i] = moving[i]; |
466 |
|
|
467 |
< |
|
467 |
> |
moving[i] = 0; |
468 |
> |
} |
469 |
|
|
470 |
< |
x[index++] = eulerAngle[0]; |
470 |
> |
iteration++; |
471 |
> |
} |
472 |
|
|
473 |
< |
x[index++] = eulerAngle[1]; |
473 |
> |
if (!done) { |
474 |
> |
std::cerr << "Waring: can not constraint within maxIteration" |
475 |
> |
<< std::endl; |
476 |
|
|
477 |
< |
x[index++] = eulerAngle[2]; |
477 |
> |
return -1; |
478 |
> |
} else |
479 |
> |
return 1; |
480 |
> |
} |
481 |
|
|
482 |
< |
|
302 |
< |
|
303 |
< |
} |
304 |
< |
|
482 |
> |
*/ |
483 |
|
|
484 |
+ |
//calculate the value of object function |
485 |
|
|
486 |
< |
} |
486 |
> |
void OOPSEMinimizer::calcF() { |
487 |
> |
calcEnergyGradient(curX, curG, curF, egEvalStatus); |
488 |
> |
} |
489 |
|
|
490 |
+ |
void OOPSEMinimizer::calcF(std::vector < double > &x, double&f, int&status) { |
491 |
+ |
std::vector < double > tempG; |
492 |
|
|
493 |
+ |
tempG.resize(x.size()); |
494 |
|
|
495 |
< |
return x; |
495 |
> |
calcEnergyGradient(x, tempG, f, status); |
496 |
> |
} |
497 |
|
|
498 |
+ |
//calculate the gradient |
499 |
|
|
500 |
+ |
void OOPSEMinimizer::calcG() { |
501 |
+ |
calcEnergyGradient(curX, curG, curF, egEvalStatus); |
502 |
+ |
} |
503 |
|
|
504 |
+ |
void OOPSEMinimizer::calcG(std::vector<double>& x, std::vector<double>& g, double&f, int&status) { |
505 |
+ |
calcEnergyGradient(x, g, f, status); |
506 |
|
} |
507 |
|
|
508 |
+ |
void OOPSEMinimizer::calcDim() { |
509 |
|
|
510 |
+ |
SimInfo::MoleculeIterator i; |
511 |
+ |
Molecule::IntegrableObjectIterator j; |
512 |
+ |
Molecule* mol; |
513 |
+ |
StuntDouble* integrableObject; |
514 |
+ |
int ndim = 0; |
515 |
|
|
516 |
+ |
for (mol = info->beginMolecule(i); mol != NULL; mol = info->nextMolecule(i)) { |
517 |
+ |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
518 |
+ |
integrableObject = mol->nextIntegrableObject(j)) { |
519 |
|
|
520 |
+ |
ndim += 3; |
521 |
|
|
522 |
< |
int OOPSEMinimizer::shakeR(){ |
522 |
> |
if (integrableObject->isDirectional()) { |
523 |
> |
ndim += 3; |
524 |
> |
} |
525 |
> |
} |
526 |
|
|
323 |
– |
int i, j; |
527 |
|
|
528 |
< |
int done; |
528 |
> |
} |
529 |
|
|
530 |
< |
double posA[3], posB[3]; |
530 |
> |
void OOPSEMinimizer::setX(std::vector < double > &x) { |
531 |
> |
if (x.size() != ndim) { |
532 |
> |
sprintf(painCave.errMsg, "OOPSEMinimizer Error: dimesion of x and curX does not match\n"); |
533 |
> |
painCave.isFatal = 1; |
534 |
> |
simError(); |
535 |
> |
} |
536 |
|
|
537 |
< |
double velA[3], velB[3]; |
537 |
> |
curX = x; |
538 |
> |
} |
539 |
|
|
540 |
< |
double pab[3]; |
540 |
> |
void OOPSEMinimizer::setG(std::vector < double > &g) { |
541 |
> |
if (g.size() != ndim) { |
542 |
> |
sprintf(painCave.errMsg, "OOPSEMinimizer Error: dimesion of g and curG does not match\n"); |
543 |
> |
painCave.isFatal = 1; |
544 |
> |
simError(); |
545 |
> |
} |
546 |
|
|
547 |
< |
double rab[3]; |
547 |
> |
curG = g; |
548 |
> |
} |
549 |
|
|
550 |
< |
int a, b, ax, ay, az, bx, by, bz; |
550 |
> |
void OOPSEMinimizer::writeOut(std::vector < double > &x, double iter) { |
551 |
> |
setX(x); |
552 |
|
|
553 |
< |
double rma, rmb; |
553 |
> |
calcG(); |
554 |
|
|
555 |
< |
double dx, dy, dz; |
555 |
> |
dumpOut->writeDump(iter); |
556 |
|
|
557 |
< |
double rpab; |
557 |
> |
statOut->writeStat(iter); |
558 |
> |
} |
559 |
|
|
560 |
< |
double rabsq, pabsq, rpabsq; |
560 |
> |
void OOPSEMinimizer::printMinimizerInfo() { |
561 |
> |
cout |
562 |
> |
<< "--------------------------------------------------------------------" |
563 |
> |
<< std::endl; |
564 |
|
|
565 |
< |
double diffsq; |
565 |
> |
cout << minimizerName << std::endl; |
566 |
|
|
567 |
< |
double gab; |
567 |
> |
cout << "minimization parameter set" << std::endl; |
568 |
|
|
569 |
< |
int iteration; |
569 |
> |
cout << "function tolerance = " << paramSet->getFTol() << std::endl; |
570 |
|
|
571 |
+ |
cout << "gradient tolerance = " << paramSet->getGTol() << std::endl; |
572 |
|
|
573 |
+ |
cout << "step tolerance = " << paramSet->getFTol() << std::endl; |
574 |
|
|
575 |
< |
for (i = 0; i < nAtoms; i++){ |
575 |
> |
cout << "absolute gradient tolerance = " << std::endl; |
576 |
|
|
577 |
< |
moving[i] = 0; |
577 |
> |
cout << "max iteration = " << paramSet->getMaxIteration() << std::endl; |
578 |
|
|
579 |
< |
moved[i] = 1; |
579 |
> |
cout << "max line search iteration = " |
580 |
> |
<< paramSet->getLineSearchMaxIteration() << std::endl; |
581 |
|
|
582 |
< |
} |
582 |
> |
cout << "shake algorithm = " << bShake << std::endl; |
583 |
|
|
584 |
+ |
cout |
585 |
+ |
<< "--------------------------------------------------------------------" |
586 |
+ |
<< std::endl; |
587 |
+ |
} |
588 |
|
|
589 |
+ |
/** |
590 |
|
|
591 |
< |
iteration = 0; |
592 |
< |
|
593 |
< |
done = 0; |
594 |
< |
|
595 |
< |
while (!done && (iteration < maxIteration)){ |
596 |
< |
|
597 |
< |
done = 1; |
370 |
< |
|
371 |
< |
for (i = 0; i < nConstrained; i++){ |
372 |
< |
|
373 |
< |
a = constrainedA[i]; |
374 |
< |
|
375 |
< |
b = constrainedB[i]; |
591 |
> |
* In thoery, we need to find the minimum along the search direction |
592 |
> |
* However, function evaluation is too expensive. |
593 |
> |
* At the very begining of the problem, we check the search direction and make sure |
594 |
> |
* it is a descent direction |
595 |
> |
* we will compare the energy of two end points, |
596 |
> |
* if the right end point has lower energy, we just take it |
597 |
> |
*/ |
598 |
|
|
599 |
+ |
int OOPSEMinimizer::doLineSearch(std::vector<double> &direction, |
600 |
+ |
double stepSize) { |
601 |
|
|
602 |
+ |
std::vector<double> xa; |
603 |
+ |
std::vector<double> xb; |
604 |
+ |
std::vector<double> xc; |
605 |
+ |
std::vector<double> ga; |
606 |
+ |
std::vector<double> gb; |
607 |
+ |
std::vector<double> gc; |
608 |
+ |
double fa; |
609 |
+ |
double fb; |
610 |
+ |
double fc; |
611 |
+ |
double a; |
612 |
+ |
double b; |
613 |
+ |
double c; |
614 |
+ |
int status; |
615 |
+ |
double initSlope; |
616 |
+ |
double slopeA; |
617 |
+ |
double slopeB; |
618 |
+ |
double slopeC; |
619 |
+ |
bool foundLower; |
620 |
+ |
int iter; |
621 |
+ |
int maxLSIter; |
622 |
+ |
double mu; |
623 |
+ |
double eta; |
624 |
+ |
double ftol; |
625 |
+ |
double lsTol; |
626 |
|
|
627 |
< |
ax = (a * 3) + 0; |
627 |
> |
xa.resize(ndim); |
628 |
> |
xb.resize(ndim); |
629 |
> |
xc.resize(ndim); |
630 |
> |
ga.resize(ndim); |
631 |
> |
gb.resize(ndim); |
632 |
> |
gc.resize(ndim); |
633 |
|
|
634 |
< |
ay = (a * 3) + 1; |
634 |
> |
a = 0.0; |
635 |
|
|
636 |
< |
az = (a * 3) + 2; |
636 |
> |
fa = curF; |
637 |
|
|
638 |
+ |
xa = curX; |
639 |
|
|
640 |
+ |
ga = curG; |
641 |
|
|
642 |
< |
bx = (b * 3) + 0; |
642 |
> |
c = a + stepSize; |
643 |
|
|
644 |
< |
by = (b * 3) + 1; |
644 |
> |
ftol = paramSet->getFTol(); |
645 |
|
|
646 |
< |
bz = (b * 3) + 2; |
646 |
> |
lsTol = paramSet->getLineSearchTol(); |
647 |
|
|
648 |
+ |
//calculate the derivative at a = 0 |
649 |
|
|
650 |
+ |
slopeA = 0; |
651 |
|
|
652 |
< |
if (moved[a] || moved[b]){ |
652 |
> |
for(size_t i = 0; i < ndim; i++) { |
653 |
> |
slopeA += curG[i] * direction[i]; |
654 |
> |
} |
655 |
> |
|
656 |
> |
initSlope = slopeA; |
657 |
|
|
658 |
< |
posA = atoms[a]->getPos(); |
658 |
> |
// if going uphill, use negative gradient as searching direction |
659 |
|
|
660 |
< |
posB = atoms[b]->getPos(); |
660 |
> |
if (slopeA > 0) { |
661 |
> |
if (bVerbose) { |
662 |
> |
cout |
663 |
> |
<< "LineSearch Warning: initial searching direction is not a descent searching direction, " << " use negative gradient instead. Therefore, finding a smaller vaule of function " << " is guaranteed" |
664 |
> |
<< std::endl; |
665 |
> |
} |
666 |
|
|
667 |
+ |
for(size_t i = 0; i < ndim; i++) { |
668 |
+ |
direction[i] = -curG[i]; |
669 |
+ |
} |
670 |
+ |
|
671 |
+ |
for(size_t i = 0; i < ndim; i++) { |
672 |
+ |
slopeA += curG[i] * direction[i]; |
673 |
+ |
} |
674 |
+ |
|
675 |
+ |
initSlope = slopeA; |
676 |
+ |
} |
677 |
|
|
678 |
+ |
// Take a trial step |
679 |
|
|
680 |
< |
for (j = 0; j < 3; j++) |
680 |
> |
for(size_t i = 0; i < ndim; i++) { |
681 |
> |
xc[i] = curX[i] + direction[i]* c; |
682 |
> |
} |
683 |
> |
|
684 |
> |
calcG(xc, gc, fc, status); |
685 |
|
|
686 |
< |
pab[j] = posA[j] - posB[j]; |
686 |
> |
if (status < 0) { |
687 |
> |
if (bVerbose) |
688 |
> |
std::cerr << "Function Evaluation Error" << std::endl; |
689 |
> |
} |
690 |
|
|
691 |
+ |
//calculate the derivative at c |
692 |
|
|
693 |
+ |
slopeC = 0; |
694 |
|
|
695 |
< |
//periodic boundary condition |
695 |
> |
for(size_t i = 0; i < ndim; i++) { |
696 |
> |
slopeC += gc[i] * direction[i]; |
697 |
> |
} |
698 |
> |
// found a lower point |
699 |
|
|
700 |
+ |
if (fc < fa) { |
701 |
+ |
curX = xc; |
702 |
|
|
703 |
+ |
curG = gc; |
704 |
|
|
705 |
< |
info->wrapVector(pab); |
705 |
> |
curF = fc; |
706 |
|
|
707 |
+ |
return LS_SUCCEED; |
708 |
+ |
} else { |
709 |
+ |
if (slopeC > 0) |
710 |
+ |
stepSize *= 0.618034; |
711 |
+ |
} |
712 |
|
|
713 |
+ |
maxLSIter = paramSet->getLineSearchMaxIteration(); |
714 |
|
|
715 |
< |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
715 |
> |
iter = 0; |
716 |
|
|
717 |
+ |
do { |
718 |
|
|
719 |
+ |
// Select a new trial point. |
720 |
|
|
721 |
< |
rabsq = constrainedDsqr[i]; |
721 |
> |
// If the derivatives at points a & c have different sign we use cubic interpolate |
722 |
|
|
723 |
< |
diffsq = rabsq - pabsq; |
723 |
> |
//if (slopeC > 0){ |
724 |
|
|
725 |
+ |
eta = 3 * (fa - fc) / (c - a) + slopeA + slopeC; |
726 |
|
|
727 |
+ |
mu = sqrt(eta * eta - slopeA * slopeC); |
728 |
|
|
729 |
< |
// the original rattle code from alan tidesley |
729 |
> |
b = a + (c - a) |
730 |
> |
* (1 - (slopeC + mu - eta) / (slopeC - slopeA + 2 * mu)); |
731 |
|
|
732 |
< |
if (fabs(diffsq) > (tol * rabsq * 2)){ |
732 |
> |
if (b < lsTol) { |
733 |
> |
if (bVerbose) |
734 |
> |
cout << "stepSize is less than line search tolerance" |
735 |
> |
<< std::endl; |
736 |
|
|
737 |
< |
rab[0] = oldPos[ax] - oldPos[bx]; |
737 |
> |
break; |
738 |
> |
} |
739 |
|
|
740 |
< |
rab[1] = oldPos[ay] - oldPos[by]; |
740 |
> |
//} |
741 |
|
|
742 |
< |
rab[2] = oldPos[az] - oldPos[bz]; |
742 |
> |
// Take a trial step to this new point - new coords in xb |
743 |
|
|
744 |
+ |
for(size_t i = 0; i < ndim; i++) { |
745 |
+ |
xb[i] = curX[i] + direction[i]* b; |
746 |
+ |
} |
747 |
+ |
|
748 |
+ |
//function evaluation |
749 |
|
|
750 |
+ |
calcG(xb, gb, fb, status); |
751 |
|
|
752 |
< |
info->wrapVector(rab); |
752 |
> |
if (status < 0) { |
753 |
> |
if (bVerbose) |
754 |
> |
std::cerr << "Function Evaluation Error" << std::endl; |
755 |
> |
} |
756 |
|
|
757 |
< |
|
757 |
> |
//calculate the derivative at c |
758 |
|
|
759 |
< |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
759 |
> |
slopeB = 0; |
760 |
|
|
761 |
+ |
for(size_t i = 0; i < ndim; i++) { |
762 |
+ |
slopeB += gb[i] * direction[i]; |
763 |
+ |
} |
764 |
+ |
|
765 |
+ |
//Amijo Rule to stop the line search |
766 |
|
|
767 |
+ |
if (fb <= curF + initSlope * ftol * b) { |
768 |
+ |
curF = fb; |
769 |
|
|
770 |
< |
rpabsq = rpab * rpab; |
770 |
> |
curX = xb; |
771 |
|
|
772 |
+ |
curG = gb; |
773 |
|
|
774 |
+ |
return LS_SUCCEED; |
775 |
+ |
} |
776 |
|
|
777 |
+ |
if (slopeB < 0 && fb < fa) { |
778 |
|
|
779 |
+ |
//replace a by b |
780 |
|
|
781 |
< |
if (rpabsq < (rabsq * -diffsq)){ |
781 |
> |
fa = fb; |
782 |
|
|
783 |
< |
#ifdef IS_MPI |
783 |
> |
a = b; |
784 |
|
|
785 |
< |
a = atoms[a]->getGlobalIndex(); |
785 |
> |
slopeA = slopeB; |
786 |
|
|
787 |
< |
b = atoms[b]->getGlobalIndex(); |
787 |
> |
// swap coord a/b |
788 |
|
|
789 |
< |
#endif //is_mpi |
789 |
> |
std::swap(xa, xb); |
790 |
|
|
791 |
< |
//std::cerr << "Waring: constraint failure" << std::endl; |
791 |
> |
std::swap(ga, gb); |
792 |
> |
} else { |
793 |
|
|
794 |
< |
gab = sqrt(rabsq/pabsq); |
794 |
> |
//replace c by b |
795 |
|
|
796 |
< |
rab[0] = (posA[0] - posB[0])*gab; |
796 |
> |
fc = fb; |
797 |
|
|
798 |
< |
rab[1]= (posA[1] - posB[1])*gab; |
798 |
> |
c = b; |
799 |
|
|
800 |
< |
rab[2] = (posA[2] - posB[2])*gab; |
800 |
> |
slopeC = slopeB; |
801 |
|
|
802 |
< |
|
802 |
> |
// swap coord b/c |
803 |
|
|
804 |
< |
info->wrapVector(rab); |
804 |
> |
std::swap(gb, gc); |
805 |
|
|
806 |
< |
|
806 |
> |
std::swap(xb, xc); |
807 |
> |
} |
808 |
|
|
809 |
< |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
809 |
> |
iter++; |
810 |
> |
} while ((fb > fa || fb > fc) && (iter < maxLSIter)); |
811 |
|
|
812 |
< |
|
812 |
> |
if (fb < curF || iter >= maxLSIter) { |
813 |
|
|
814 |
< |
} |
814 |
> |
//could not find a lower value, we might just go uphill. |
815 |
|
|
816 |
+ |
return LS_ERROR; |
817 |
+ |
} |
818 |
|
|
819 |
< |
|
487 |
< |
//rma = 1.0 / atoms[a]->getMass(); |
819 |
> |
//select the end point |
820 |
|
|
821 |
< |
//rmb = 1.0 / atoms[b]->getMass(); |
821 |
> |
if (fa <= fc) { |
822 |
> |
curX = xa; |
823 |
|
|
824 |
< |
rma = 1.0; |
824 |
> |
curG = ga; |
825 |
|
|
826 |
< |
rmb =1.0; |
826 |
> |
curF = fa; |
827 |
> |
} else { |
828 |
> |
curX = xc; |
829 |
|
|
830 |
+ |
curG = gc; |
831 |
|
|
832 |
< |
|
497 |
< |
gab = diffsq / (2.0 * (rma + rmb) * rpab); |
498 |
< |
|
499 |
< |
|
500 |
< |
|
501 |
< |
dx = rab[0] * gab; |
502 |
< |
|
503 |
< |
dy = rab[1] * gab; |
504 |
< |
|
505 |
< |
dz = rab[2] * gab; |
506 |
< |
|
507 |
< |
|
508 |
< |
|
509 |
< |
posA[0] += rma * dx; |
510 |
< |
|
511 |
< |
posA[1] += rma * dy; |
512 |
< |
|
513 |
< |
posA[2] += rma * dz; |
514 |
< |
|
515 |
< |
|
516 |
< |
|
517 |
< |
atoms[a]->setPos(posA); |
518 |
< |
|
519 |
< |
|
520 |
< |
|
521 |
< |
posB[0] -= rmb * dx; |
522 |
< |
|
523 |
< |
posB[1] -= rmb * dy; |
524 |
< |
|
525 |
< |
posB[2] -= rmb * dz; |
526 |
< |
|
527 |
< |
|
528 |
< |
|
529 |
< |
atoms[b]->setPos(posB); |
530 |
< |
|
531 |
< |
|
532 |
< |
|
533 |
< |
moving[a] = 1; |
534 |
< |
|
535 |
< |
moving[b] = 1; |
536 |
< |
|
537 |
< |
done = 0; |
538 |
< |
|
539 |
< |
} |
540 |
< |
|
541 |
< |
} |
542 |
< |
|
832 |
> |
curF = fc; |
833 |
|
} |
834 |
|
|
835 |
< |
|
546 |
< |
|
547 |
< |
for (i = 0; i < nAtoms; i++){ |
548 |
< |
|
549 |
< |
moved[i] = moving[i]; |
550 |
< |
|
551 |
< |
moving[i] = 0; |
552 |
< |
|
553 |
< |
} |
554 |
< |
|
555 |
< |
|
556 |
< |
|
557 |
< |
iteration++; |
558 |
< |
|
559 |
< |
} |
560 |
< |
|
561 |
< |
|
562 |
< |
|
563 |
< |
if (!done){ |
564 |
< |
|
565 |
< |
std::cerr << "Waring: can not constraint within maxIteration" << std::endl; |
566 |
< |
|
567 |
< |
return -1; |
568 |
< |
|
569 |
< |
} |
570 |
< |
|
571 |
< |
else |
572 |
< |
|
573 |
< |
return 1; |
574 |
< |
|
835 |
> |
return LS_SUCCEED; |
836 |
|
} |
837 |
|
|
838 |
+ |
void OOPSEMinimizer::minimize() { |
839 |
+ |
int convgStatus; |
840 |
|
|
841 |
+ |
int stepStatus; |
842 |
|
|
843 |
+ |
int maxIter; |
844 |
|
|
845 |
+ |
int writeFrq; |
846 |
|
|
847 |
< |
//remove constraint force along the bond direction |
847 |
> |
int nextWriteIter; |
848 |
|
|
849 |
< |
int OOPSEMinimizer::shakeF(){ |
849 |
> |
if (bVerbose) |
850 |
> |
printMinimizerInfo(); |
851 |
|
|
852 |
< |
int i, j; |
852 |
> |
dumpOut = new DumpWriter(info); |
853 |
|
|
854 |
< |
int done; |
854 |
> |
statOut = new StatWriter(info); |
855 |
|
|
856 |
< |
double posA[3], posB[3]; |
856 |
> |
init(); |
857 |
|
|
858 |
< |
double frcA[3], frcB[3]; |
858 |
> |
writeFrq = paramSet->getWriteFrq(); |
859 |
|
|
860 |
< |
double rab[3], fpab[3]; |
860 |
> |
nextWriteIter = writeFrq; |
861 |
|
|
862 |
< |
int a, b, ax, ay, az, bx, by, bz; |
862 |
> |
maxIter = paramSet->getMaxIteration(); |
863 |
|
|
864 |
< |
double rma, rmb; |
864 |
> |
for(curIter = 1; curIter <= maxIter; curIter++) { |
865 |
> |
stepStatus = step(); |
866 |
|
|
867 |
< |
double rvab; |
867 |
> |
if (nConstrained && bShake) |
868 |
> |
preMove(); |
869 |
|
|
870 |
< |
double gab; |
870 |
> |
if (stepStatus < 0) { |
871 |
> |
saveResult(); |
872 |
|
|
873 |
< |
double rabsq; |
873 |
> |
minStatus = MIN_LSERROR; |
874 |
|
|
875 |
< |
double rfab; |
875 |
> |
std::cerr |
876 |
> |
<< "OOPSEMinimizer Error: line search error, please try a small stepsize" |
877 |
> |
<< std::endl; |
878 |
|
|
879 |
< |
int iteration; |
879 |
> |
return; |
880 |
> |
} |
881 |
|
|
882 |
+ |
if (curIter == nextWriteIter) { |
883 |
+ |
nextWriteIter += writeFrq; |
884 |
|
|
885 |
+ |
writeOut(curX, curIter); |
886 |
+ |
} |
887 |
|
|
888 |
< |
for (i = 0; i < nAtoms; i++){ |
888 |
> |
convgStatus = checkConvg(); |
889 |
|
|
890 |
< |
moving[i] = 0; |
890 |
> |
if (convgStatus > 0) { |
891 |
> |
saveResult(); |
892 |
|
|
893 |
< |
moved[i] = 1; |
893 |
> |
minStatus = MIN_CONVERGE; |
894 |
|
|
895 |
< |
} |
896 |
< |
|
619 |
< |
|
620 |
< |
|
621 |
< |
done = 0; |
622 |
< |
|
623 |
< |
iteration = 0; |
895 |
> |
return; |
896 |
> |
} |
897 |
|
|
898 |
< |
while (!done && (iteration < maxIteration)){ |
626 |
< |
|
627 |
< |
done = 1; |
628 |
< |
|
629 |
< |
|
630 |
< |
|
631 |
< |
for (i = 0; i < nConstrained; i++){ |
632 |
< |
|
633 |
< |
a = constrainedA[i]; |
634 |
< |
|
635 |
< |
b = constrainedB[i]; |
636 |
< |
|
637 |
< |
|
638 |
< |
|
639 |
< |
ax = (a * 3) + 0; |
640 |
< |
|
641 |
< |
ay = (a * 3) + 1; |
642 |
< |
|
643 |
< |
az = (a * 3) + 2; |
644 |
< |
|
645 |
< |
|
646 |
< |
|
647 |
< |
bx = (b * 3) + 0; |
648 |
< |
|
649 |
< |
by = (b * 3) + 1; |
650 |
< |
|
651 |
< |
bz = (b * 3) + 2; |
652 |
< |
|
653 |
< |
|
654 |
< |
|
655 |
< |
if (moved[a] || moved[b]){ |
656 |
< |
|
657 |
< |
|
658 |
< |
|
659 |
< |
posA = atoms[a]->getPos(); |
660 |
< |
|
661 |
< |
posB = atoms[b]->getPos(); |
662 |
< |
|
663 |
< |
|
664 |
< |
|
665 |
< |
for (j = 0; j < 3; j++) |
666 |
< |
|
667 |
< |
rab[j] = posA[j] - posB[j]; |
668 |
< |
|
669 |
< |
|
670 |
< |
|
671 |
< |
info->wrapVector(rab); |
672 |
< |
|
673 |
< |
|
674 |
< |
|
675 |
< |
atoms[a]->getFrc(frcA); |
676 |
< |
|
677 |
< |
atoms[b]->getFrc(frcB); |
678 |
< |
|
679 |
< |
|
680 |
< |
|
681 |
< |
//rma = 1.0 / atoms[a]->getMass(); |
682 |
< |
|
683 |
< |
//rmb = 1.0 / atoms[b]->getMass(); |
684 |
< |
|
685 |
< |
rma = 1.0; |
686 |
< |
|
687 |
< |
rmb = 1.0; |
688 |
< |
|
689 |
< |
|
690 |
< |
|
691 |
< |
|
692 |
< |
|
693 |
< |
fpab[0] = frcA[0] * rma - frcB[0] * rmb; |
694 |
< |
|
695 |
< |
fpab[1] = frcA[1] * rma - frcB[1] * rmb; |
696 |
< |
|
697 |
< |
fpab[2] = frcA[2] * rma - frcB[2] * rmb; |
698 |
< |
|
699 |
< |
|
700 |
< |
|
701 |
< |
|
702 |
< |
|
703 |
< |
gab=fpab[0] * fpab[0] + fpab[1] * fpab[1] + fpab[2] * fpab[2]; |
704 |
< |
|
705 |
< |
|
706 |
< |
|
707 |
< |
if (gab < 1.0) |
708 |
< |
|
709 |
< |
gab = 1.0; |
710 |
< |
|
711 |
< |
|
712 |
< |
|
713 |
< |
rabsq = rab[0] * rab[0] + rab[1] * rab[1] + rab[2] * rab[2]; |
714 |
< |
|
715 |
< |
rfab = rab[0] * fpab[0] + rab[1] * fpab[1] + rab[2] * fpab[2]; |
716 |
< |
|
717 |
< |
|
718 |
< |
|
719 |
< |
if (fabs(rfab) > sqrt(rabsq*gab) * 0.00001){ |
720 |
< |
|
721 |
< |
|
722 |
< |
|
723 |
< |
gab = -rfab /(rabsq*(rma + rmb)); |
724 |
< |
|
725 |
< |
|
726 |
< |
|
727 |
< |
frcA[0] = rab[0] * gab; |
728 |
< |
|
729 |
< |
frcA[1] = rab[1] * gab; |
730 |
< |
|
731 |
< |
frcA[2] = rab[2] * gab; |
732 |
< |
|
733 |
< |
|
734 |
< |
|
735 |
< |
atoms[a]->addFrc(frcA); |
736 |
< |
|
737 |
< |
|
738 |
< |
|
739 |
< |
|
740 |
< |
|
741 |
< |
frcB[0] = -rab[0] * gab; |
742 |
< |
|
743 |
< |
frcB[1] = -rab[1] * gab; |
744 |
< |
|
745 |
< |
frcB[2] = -rab[2] * gab; |
746 |
< |
|
747 |
< |
|
748 |
< |
|
749 |
< |
atoms[b]->addFrc(frcB); |
750 |
< |
|
751 |
< |
|
752 |
< |
|
753 |
< |
moving[a] = 1; |
754 |
< |
|
755 |
< |
moving[b] = 1; |
756 |
< |
|
757 |
< |
done = 0; |
758 |
< |
|
759 |
< |
} |
760 |
< |
|
761 |
< |
} |
762 |
< |
|
898 |
> |
prepareStep(); |
899 |
|
} |
900 |
|
|
901 |
< |
|
902 |
< |
|
903 |
< |
for (i = 0; i < nAtoms; i++){ |
904 |
< |
|
769 |
< |
moved[i] = moving[i]; |
770 |
< |
|
771 |
< |
moving[i] = 0; |
772 |
< |
|
901 |
> |
if (bVerbose) { |
902 |
> |
cout << "OOPSEMinimizer Warning: " << minimizerName |
903 |
> |
<< " algorithm did not converge within " << maxIter << " iteration" |
904 |
> |
<< std::endl; |
905 |
|
} |
906 |
|
|
907 |
+ |
minStatus = MIN_MAXITER; |
908 |
|
|
909 |
< |
|
777 |
< |
iteration++; |
778 |
< |
|
779 |
< |
} |
780 |
< |
|
781 |
< |
|
782 |
< |
|
783 |
< |
if (!done){ |
784 |
< |
|
785 |
< |
std::cerr << "Waring: can not constraint within maxIteration" << std::endl; |
786 |
< |
|
787 |
< |
return -1; |
788 |
< |
|
789 |
< |
} |
790 |
< |
|
791 |
< |
else |
792 |
< |
|
793 |
< |
return 1; |
794 |
< |
|
909 |
> |
saveResult(); |
910 |
|
} |
911 |
|
|
797 |
– |
|
798 |
– |
|
799 |
– |
|
800 |
– |
|
801 |
– |
|
802 |
– |
|
803 |
– |
//calculate the value of object function |
804 |
– |
|
805 |
– |
void OOPSEMinimizer::calcF(){ |
806 |
– |
|
807 |
– |
calcEnergyGradient(curX, curG, curF, egEvalStatus); |
808 |
– |
|
912 |
|
} |
810 |
– |
|
811 |
– |
|
812 |
– |
|
813 |
– |
void OOPSEMinimizer::calcF(vector<double>& x, double&f, int& status){ |
814 |
– |
|
815 |
– |
std::vector<double> tempG; |
816 |
– |
|
817 |
– |
tempG.resize(x.size()); |
818 |
– |
|
819 |
– |
|
820 |
– |
|
821 |
– |
calcEnergyGradient(x, tempG, f, status); |
822 |
– |
|
823 |
– |
} |
824 |
– |
|
825 |
– |
|
826 |
– |
|
827 |
– |
//calculate the gradient |
828 |
– |
|
829 |
– |
void OOPSEMinimizer::calcG(){ |
830 |
– |
|
831 |
– |
calcEnergyGradient(curX, curG, curF, egEvalStatus); |
832 |
– |
|
833 |
– |
} |
834 |
– |
|
835 |
– |
|
836 |
– |
|
837 |
– |
void OOPSEMinimizer::calcG(vector<double>& x, std::vector<double>& g, double& f, int& status){ |
838 |
– |
|
839 |
– |
calcEnergyGradient(x, g, f, status); |
840 |
– |
|
841 |
– |
} |
842 |
– |
|
843 |
– |
|
844 |
– |
|
845 |
– |
void OOPSEMinimizer::calcDim(){ |
846 |
– |
|
847 |
– |
DirectionalAtom* dAtom; |
848 |
– |
|
849 |
– |
|
850 |
– |
|
851 |
– |
ndim = 0; |
852 |
– |
|
853 |
– |
|
854 |
– |
|
855 |
– |
for(int i = 0; i < integrableObjects.size(); i++){ |
856 |
– |
|
857 |
– |
ndim += 3; |
858 |
– |
|
859 |
– |
if (integrableObjects[i]->isDirectional()) |
860 |
– |
|
861 |
– |
ndim += 3; |
862 |
– |
|
863 |
– |
} |
864 |
– |
|
865 |
– |
} |
866 |
– |
|
867 |
– |
|
868 |
– |
|
869 |
– |
void OOPSEMinimizer::setX(vector < double > & x){ |
870 |
– |
|
871 |
– |
|
872 |
– |
|
873 |
– |
if (x.size() != ndim && bVerbose){ |
874 |
– |
|
875 |
– |
//sprintf(painCave.errMsg, |
876 |
– |
|
877 |
– |
// "OOPSEMinimizer Error: dimesion of x and curX does not match\n"); |
878 |
– |
|
879 |
– |
// painCave.isFatal = 1; |
880 |
– |
|
881 |
– |
// simError(); |
882 |
– |
|
883 |
– |
} |
884 |
– |
|
885 |
– |
|
886 |
– |
|
887 |
– |
curX = x; |
888 |
– |
|
889 |
– |
} |
890 |
– |
|
891 |
– |
|
892 |
– |
|
893 |
– |
void OOPSEMinimizer::setG(vector < double > & g){ |
894 |
– |
|
895 |
– |
|
896 |
– |
|
897 |
– |
if (g.size() != ndim && bVerbose){ |
898 |
– |
|
899 |
– |
//sprintf(painCave.errMsg, |
900 |
– |
|
901 |
– |
// "OOPSEMinimizer Error: dimesion of g and curG does not match\n"); |
902 |
– |
|
903 |
– |
// painCave.isFatal = 1; |
904 |
– |
|
905 |
– |
//simError(); |
906 |
– |
|
907 |
– |
} |
908 |
– |
|
909 |
– |
|
910 |
– |
|
911 |
– |
curG = g; |
912 |
– |
|
913 |
– |
} |
914 |
– |
|
915 |
– |
|
916 |
– |
|
917 |
– |
void OOPSEMinimizer::writeOut(vector<double>& x, double iter){ |
918 |
– |
|
919 |
– |
|
920 |
– |
|
921 |
– |
setX(x); |
922 |
– |
|
923 |
– |
|
924 |
– |
|
925 |
– |
calcG(); |
926 |
– |
|
927 |
– |
|
928 |
– |
|
929 |
– |
dumpOut->writeDump(iter); |
930 |
– |
|
931 |
– |
statOut->writeStat(iter); |
932 |
– |
|
933 |
– |
} |
934 |
– |
|
935 |
– |
|
936 |
– |
|
937 |
– |
|
938 |
– |
|
939 |
– |
void OOPSEMinimizer::printMinimizerInfo(){ |
940 |
– |
|
941 |
– |
cout << "--------------------------------------------------------------------" << std::endl; |
942 |
– |
|
943 |
– |
cout << minimizerName << std::endl; |
944 |
– |
|
945 |
– |
cout << "minimization parameter set" << std::endl; |
946 |
– |
|
947 |
– |
cout << "function tolerance = " << paramSet->getFTol() << std::endl; |
948 |
– |
|
949 |
– |
cout << "gradient tolerance = " << paramSet->getGTol() << std::endl; |
950 |
– |
|
951 |
– |
cout << "step tolerance = "<< paramSet->getFTol() << std::endl; |
952 |
– |
|
953 |
– |
cout << "absolute gradient tolerance = " << std::endl; |
954 |
– |
|
955 |
– |
cout << "max iteration = " << paramSet->getMaxIteration() << std::endl; |
956 |
– |
|
957 |
– |
cout << "max line search iteration = " << paramSet->getLineSearchMaxIteration() <<std::endl; |
958 |
– |
|
959 |
– |
cout << "shake algorithm = " << bShake << std::endl; |
960 |
– |
|
961 |
– |
cout << "--------------------------------------------------------------------" << std::endl; |
962 |
– |
|
963 |
– |
|
964 |
– |
|
965 |
– |
} |
966 |
– |
|
967 |
– |
|
968 |
– |
|
969 |
– |
/** |
970 |
– |
|
971 |
– |
* In thoery, we need to find the minimum along the search direction |
972 |
– |
|
973 |
– |
* However, function evaluation is too expensive. |
974 |
– |
|
975 |
– |
* At the very begining of the problem, we check the search direction and make sure |
976 |
– |
|
977 |
– |
* it is a descent direction |
978 |
– |
|
979 |
– |
* we will compare the energy of two end points, |
980 |
– |
|
981 |
– |
* if the right end point has lower energy, we just take it |
982 |
– |
|
983 |
– |
* |
984 |
– |
|
985 |
– |
* |
986 |
– |
|
987 |
– |
* |
988 |
– |
|
989 |
– |
*/ |
990 |
– |
|
991 |
– |
|
992 |
– |
|
993 |
– |
int OOPSEMinimizer::doLineSearch(vector<double>& direction, double stepSize){ |
994 |
– |
|
995 |
– |
std::vector<double> xa; |
996 |
– |
|
997 |
– |
std::vector<double> xb; |
998 |
– |
|
999 |
– |
std::vector<double> xc; |
1000 |
– |
|
1001 |
– |
std::vector<double> ga; |
1002 |
– |
|
1003 |
– |
std::vector<double> gb; |
1004 |
– |
|
1005 |
– |
std::vector<double> gc; |
1006 |
– |
|
1007 |
– |
double fa; |
1008 |
– |
|
1009 |
– |
double fb; |
1010 |
– |
|
1011 |
– |
double fc; |
1012 |
– |
|
1013 |
– |
double a; |
1014 |
– |
|
1015 |
– |
double b; |
1016 |
– |
|
1017 |
– |
double c; |
1018 |
– |
|
1019 |
– |
int status; |
1020 |
– |
|
1021 |
– |
double initSlope; |
1022 |
– |
|
1023 |
– |
double slopeA; |
1024 |
– |
|
1025 |
– |
double slopeB; |
1026 |
– |
|
1027 |
– |
double slopeC; |
1028 |
– |
|
1029 |
– |
bool foundLower; |
1030 |
– |
|
1031 |
– |
int iter; |
1032 |
– |
|
1033 |
– |
int maxLSIter; |
1034 |
– |
|
1035 |
– |
double mu; |
1036 |
– |
|
1037 |
– |
double eta; |
1038 |
– |
|
1039 |
– |
double ftol; |
1040 |
– |
|
1041 |
– |
double lsTol; |
1042 |
– |
|
1043 |
– |
|
1044 |
– |
|
1045 |
– |
xa.resize(ndim); |
1046 |
– |
|
1047 |
– |
xb.resize(ndim); |
1048 |
– |
|
1049 |
– |
xc.resize(ndim); |
1050 |
– |
|
1051 |
– |
|
1052 |
– |
|
1053 |
– |
ga.resize(ndim); |
1054 |
– |
|
1055 |
– |
gb.resize(ndim); |
1056 |
– |
|
1057 |
– |
gc.resize(ndim); |
1058 |
– |
|
1059 |
– |
|
1060 |
– |
|
1061 |
– |
a = 0.0; |
1062 |
– |
|
1063 |
– |
fa = curF; |
1064 |
– |
|
1065 |
– |
xa = curX; |
1066 |
– |
|
1067 |
– |
ga = curG; |
1068 |
– |
|
1069 |
– |
c = a + stepSize; |
1070 |
– |
|
1071 |
– |
ftol = paramSet->getFTol(); |
1072 |
– |
|
1073 |
– |
lsTol = paramSet->getLineSearchTol(); |
1074 |
– |
|
1075 |
– |
|
1076 |
– |
|
1077 |
– |
//calculate the derivative at a = 0 |
1078 |
– |
|
1079 |
– |
slopeA = 0; |
1080 |
– |
|
1081 |
– |
for (size_t i = 0; i < ndim; i++) |
1082 |
– |
|
1083 |
– |
slopeA += curG[i]*direction[i]; |
1084 |
– |
|
1085 |
– |
|
1086 |
– |
|
1087 |
– |
initSlope = slopeA; |
1088 |
– |
|
1089 |
– |
|
1090 |
– |
|
1091 |
– |
// if going uphill, use negative gradient as searching direction |
1092 |
– |
|
1093 |
– |
if (slopeA > 0) { |
1094 |
– |
|
1095 |
– |
|
1096 |
– |
|
1097 |
– |
if (bVerbose){ |
1098 |
– |
|
1099 |
– |
cout << "LineSearch Warning: initial searching direction is not a descent searching direction, " |
1100 |
– |
|
1101 |
– |
<< " use negative gradient instead. Therefore, finding a smaller vaule of function " |
1102 |
– |
|
1103 |
– |
<< " is guaranteed" |
1104 |
– |
|
1105 |
– |
<< std::endl; |
1106 |
– |
|
1107 |
– |
} |
1108 |
– |
|
1109 |
– |
|
1110 |
– |
|
1111 |
– |
for (size_t i = 0; i < ndim; i++) |
1112 |
– |
|
1113 |
– |
direction[i] = -curG[i]; |
1114 |
– |
|
1115 |
– |
|
1116 |
– |
|
1117 |
– |
for (size_t i = 0; i < ndim; i++) |
1118 |
– |
|
1119 |
– |
slopeA += curG[i]*direction[i]; |
1120 |
– |
|
1121 |
– |
|
1122 |
– |
|
1123 |
– |
initSlope = slopeA; |
1124 |
– |
|
1125 |
– |
} |
1126 |
– |
|
1127 |
– |
|
1128 |
– |
|
1129 |
– |
// Take a trial step |
1130 |
– |
|
1131 |
– |
for(size_t i = 0; i < ndim; i++) |
1132 |
– |
|
1133 |
– |
xc[i] = curX[i] + direction[i] * c; |
1134 |
– |
|
1135 |
– |
|
1136 |
– |
|
1137 |
– |
calcG(xc, gc, fc, status); |
1138 |
– |
|
1139 |
– |
|
1140 |
– |
|
1141 |
– |
if (status < 0){ |
1142 |
– |
|
1143 |
– |
if (bVerbose) |
1144 |
– |
|
1145 |
– |
std::cerr << "Function Evaluation Error" << std::endl; |
1146 |
– |
|
1147 |
– |
} |
1148 |
– |
|
1149 |
– |
|
1150 |
– |
|
1151 |
– |
//calculate the derivative at c |
1152 |
– |
|
1153 |
– |
slopeC = 0; |
1154 |
– |
|
1155 |
– |
for (size_t i = 0; i < ndim; i++) |
1156 |
– |
|
1157 |
– |
slopeC += gc[i]*direction[i]; |
1158 |
– |
|
1159 |
– |
|
1160 |
– |
|
1161 |
– |
// found a lower point |
1162 |
– |
|
1163 |
– |
if (fc < fa) { |
1164 |
– |
|
1165 |
– |
curX = xc; |
1166 |
– |
|
1167 |
– |
curG = gc; |
1168 |
– |
|
1169 |
– |
curF = fc; |
1170 |
– |
|
1171 |
– |
return LS_SUCCEED; |
1172 |
– |
|
1173 |
– |
} |
1174 |
– |
|
1175 |
– |
else { |
1176 |
– |
|
1177 |
– |
|
1178 |
– |
|
1179 |
– |
if (slopeC > 0) |
1180 |
– |
|
1181 |
– |
stepSize *= 0.618034; |
1182 |
– |
|
1183 |
– |
} |
1184 |
– |
|
1185 |
– |
|
1186 |
– |
|
1187 |
– |
maxLSIter = paramSet->getLineSearchMaxIteration(); |
1188 |
– |
|
1189 |
– |
|
1190 |
– |
|
1191 |
– |
iter = 0; |
1192 |
– |
|
1193 |
– |
|
1194 |
– |
|
1195 |
– |
do { |
1196 |
– |
|
1197 |
– |
// Select a new trial point. |
1198 |
– |
|
1199 |
– |
// If the derivatives at points a & c have different sign we use cubic interpolate |
1200 |
– |
|
1201 |
– |
//if (slopeC > 0){ |
1202 |
– |
|
1203 |
– |
eta = 3 *(fa -fc) /(c - a) + slopeA + slopeC; |
1204 |
– |
|
1205 |
– |
mu = sqrt(eta * eta - slopeA * slopeC); |
1206 |
– |
|
1207 |
– |
b = a + (c - a) * (1 - (slopeC + mu - eta) /(slopeC - slopeA + 2 * mu)); |
1208 |
– |
|
1209 |
– |
|
1210 |
– |
|
1211 |
– |
if (b < lsTol){ |
1212 |
– |
|
1213 |
– |
if (bVerbose) |
1214 |
– |
|
1215 |
– |
cout << "stepSize is less than line search tolerance" << std::endl; |
1216 |
– |
|
1217 |
– |
break; |
1218 |
– |
|
1219 |
– |
} |
1220 |
– |
|
1221 |
– |
//} |
1222 |
– |
|
1223 |
– |
|
1224 |
– |
|
1225 |
– |
// Take a trial step to this new point - new coords in xb |
1226 |
– |
|
1227 |
– |
for(size_t i = 0; i < ndim; i++) |
1228 |
– |
|
1229 |
– |
xb[i] = curX[i] + direction[i] * b; |
1230 |
– |
|
1231 |
– |
|
1232 |
– |
|
1233 |
– |
//function evaluation |
1234 |
– |
|
1235 |
– |
calcG(xb, gb, fb, status); |
1236 |
– |
|
1237 |
– |
|
1238 |
– |
|
1239 |
– |
if (status < 0){ |
1240 |
– |
|
1241 |
– |
if (bVerbose) |
1242 |
– |
|
1243 |
– |
std::cerr << "Function Evaluation Error" << std::endl; |
1244 |
– |
|
1245 |
– |
} |
1246 |
– |
|
1247 |
– |
|
1248 |
– |
|
1249 |
– |
//calculate the derivative at c |
1250 |
– |
|
1251 |
– |
slopeB = 0; |
1252 |
– |
|
1253 |
– |
for (size_t i = 0; i < ndim; i++) |
1254 |
– |
|
1255 |
– |
slopeB += gb[i]*direction[i]; |
1256 |
– |
|
1257 |
– |
|
1258 |
– |
|
1259 |
– |
//Amijo Rule to stop the line search |
1260 |
– |
|
1261 |
– |
if (fb <= curF + initSlope * ftol * b) { |
1262 |
– |
|
1263 |
– |
curF = fb; |
1264 |
– |
|
1265 |
– |
curX = xb; |
1266 |
– |
|
1267 |
– |
curG = gb; |
1268 |
– |
|
1269 |
– |
return LS_SUCCEED; |
1270 |
– |
|
1271 |
– |
} |
1272 |
– |
|
1273 |
– |
|
1274 |
– |
|
1275 |
– |
if (slopeB <0 && fb < fa) { |
1276 |
– |
|
1277 |
– |
//replace a by b |
1278 |
– |
|
1279 |
– |
fa = fb; |
1280 |
– |
|
1281 |
– |
a = b; |
1282 |
– |
|
1283 |
– |
slopeA = slopeB; |
1284 |
– |
|
1285 |
– |
|
1286 |
– |
|
1287 |
– |
// swap coord a/b |
1288 |
– |
|
1289 |
– |
std::swap(xa, xb); |
1290 |
– |
|
1291 |
– |
std::swap(ga, gb); |
1292 |
– |
|
1293 |
– |
} |
1294 |
– |
|
1295 |
– |
else { |
1296 |
– |
|
1297 |
– |
//replace c by b |
1298 |
– |
|
1299 |
– |
fc = fb; |
1300 |
– |
|
1301 |
– |
c = b; |
1302 |
– |
|
1303 |
– |
slopeC = slopeB; |
1304 |
– |
|
1305 |
– |
|
1306 |
– |
|
1307 |
– |
// swap coord b/c |
1308 |
– |
|
1309 |
– |
std::swap(gb, gc); |
1310 |
– |
|
1311 |
– |
std::swap(xb, xc); |
1312 |
– |
|
1313 |
– |
} |
1314 |
– |
|
1315 |
– |
|
1316 |
– |
|
1317 |
– |
|
1318 |
– |
|
1319 |
– |
iter++; |
1320 |
– |
|
1321 |
– |
} while((fb > fa || fb > fc) && (iter < maxLSIter)); |
1322 |
– |
|
1323 |
– |
|
1324 |
– |
|
1325 |
– |
if(fb < curF || iter >= maxLSIter) { |
1326 |
– |
|
1327 |
– |
//could not find a lower value, we might just go uphill. |
1328 |
– |
|
1329 |
– |
return LS_ERROR; |
1330 |
– |
|
1331 |
– |
} |
1332 |
– |
|
1333 |
– |
|
1334 |
– |
|
1335 |
– |
//select the end point |
1336 |
– |
|
1337 |
– |
|
1338 |
– |
|
1339 |
– |
if (fa <= fc) { |
1340 |
– |
|
1341 |
– |
curX = xa; |
1342 |
– |
|
1343 |
– |
curG = ga; |
1344 |
– |
|
1345 |
– |
curF = fa; |
1346 |
– |
|
1347 |
– |
} |
1348 |
– |
|
1349 |
– |
else { |
1350 |
– |
|
1351 |
– |
curX = xc; |
1352 |
– |
|
1353 |
– |
curG = gc; |
1354 |
– |
|
1355 |
– |
curF = fc; |
1356 |
– |
|
1357 |
– |
} |
1358 |
– |
|
1359 |
– |
|
1360 |
– |
|
1361 |
– |
return LS_SUCCEED; |
1362 |
– |
|
1363 |
– |
|
1364 |
– |
|
1365 |
– |
} |
1366 |
– |
|
1367 |
– |
|
1368 |
– |
|
1369 |
– |
void OOPSEMinimizer::minimize(){ |
1370 |
– |
|
1371 |
– |
|
1372 |
– |
|
1373 |
– |
int convgStatus; |
1374 |
– |
|
1375 |
– |
int stepStatus; |
1376 |
– |
|
1377 |
– |
int maxIter; |
1378 |
– |
|
1379 |
– |
int writeFrq; |
1380 |
– |
|
1381 |
– |
int nextWriteIter; |
1382 |
– |
|
1383 |
– |
|
1384 |
– |
|
1385 |
– |
if (bVerbose) |
1386 |
– |
|
1387 |
– |
printMinimizerInfo(); |
1388 |
– |
|
1389 |
– |
|
1390 |
– |
|
1391 |
– |
dumpOut = new DumpWriter(info); |
1392 |
– |
|
1393 |
– |
statOut = new StatWriter(info); |
1394 |
– |
|
1395 |
– |
|
1396 |
– |
|
1397 |
– |
init(); |
1398 |
– |
|
1399 |
– |
|
1400 |
– |
|
1401 |
– |
writeFrq = paramSet->getWriteFrq(); |
1402 |
– |
|
1403 |
– |
nextWriteIter = writeFrq; |
1404 |
– |
|
1405 |
– |
|
1406 |
– |
|
1407 |
– |
maxIter = paramSet->getMaxIteration(); |
1408 |
– |
|
1409 |
– |
|
1410 |
– |
|
1411 |
– |
for (curIter = 1; curIter <= maxIter; curIter++){ |
1412 |
– |
|
1413 |
– |
|
1414 |
– |
|
1415 |
– |
stepStatus = step(); |
1416 |
– |
|
1417 |
– |
|
1418 |
– |
|
1419 |
– |
if (nConstrained && bShake) |
1420 |
– |
|
1421 |
– |
preMove(); |
1422 |
– |
|
1423 |
– |
|
1424 |
– |
|
1425 |
– |
if (stepStatus < 0){ |
1426 |
– |
|
1427 |
– |
saveResult(); |
1428 |
– |
|
1429 |
– |
minStatus = MIN_LSERROR; |
1430 |
– |
|
1431 |
– |
std::cerr << "OOPSEMinimizer Error: line search error, please try a small stepsize" << std::endl; |
1432 |
– |
|
1433 |
– |
return; |
1434 |
– |
|
1435 |
– |
} |
1436 |
– |
|
1437 |
– |
|
1438 |
– |
|
1439 |
– |
if (curIter == nextWriteIter){ |
1440 |
– |
|
1441 |
– |
nextWriteIter += writeFrq; |
1442 |
– |
|
1443 |
– |
writeOut(curX, curIter); |
1444 |
– |
|
1445 |
– |
} |
1446 |
– |
|
1447 |
– |
|
1448 |
– |
|
1449 |
– |
convgStatus = checkConvg(); |
1450 |
– |
|
1451 |
– |
|
1452 |
– |
|
1453 |
– |
if (convgStatus > 0){ |
1454 |
– |
|
1455 |
– |
saveResult(); |
1456 |
– |
|
1457 |
– |
minStatus = MIN_CONVERGE; |
1458 |
– |
|
1459 |
– |
return; |
1460 |
– |
|
1461 |
– |
} |
1462 |
– |
|
1463 |
– |
|
1464 |
– |
|
1465 |
– |
prepareStep(); |
1466 |
– |
|
1467 |
– |
|
1468 |
– |
|
1469 |
– |
} |
1470 |
– |
|
1471 |
– |
|
1472 |
– |
|
1473 |
– |
|
1474 |
– |
|
1475 |
– |
if (bVerbose) { |
1476 |
– |
|
1477 |
– |
cout << "OOPSEMinimizer Warning: " |
1478 |
– |
|
1479 |
– |
<< minimizerName << " algorithm did not converge within " |
1480 |
– |
|
1481 |
– |
<< maxIter << " iteration" << std::endl; |
1482 |
– |
|
1483 |
– |
} |
1484 |
– |
|
1485 |
– |
minStatus = MIN_MAXITER; |
1486 |
– |
|
1487 |
– |
saveResult(); |
1488 |
– |
|
1489 |
– |
|
1490 |
– |
|
1491 |
– |
} |
1492 |
– |
|