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/* |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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#include "minimizers/Minimizer.hpp" |
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#include "primitives/Molecule.hpp" |
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namespace oopse { |
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double dotProduct(const std::vector<double>& v1, const std::vector<double>& v2) { |
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double dotProduct(const std::vector<double>& v1, const std::vector<double>& v2) { |
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if (v1.size() != v2.size()) { |
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|
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} |
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|
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double result = 0.0; |
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for (unsigned int i = 0; i < v1.size(); ++i) { |
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result += v1[i] * v2[i]; |
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result += v1[i] * v2[i]; |
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} |
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return result; |
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} |
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} |
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|
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Minimizer::Minimizer(SimInfo* rhs) : |
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Minimizer::Minimizer(SimInfo* rhs) : |
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info(rhs), usingShake(false) { |
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|
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forceMan = new ForceManager(info); |
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paramSet= new MinimizerParameterSet(info), |
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calcDim(); |
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curX = getCoor(); |
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curG.resize(ndim); |
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forceMan = new ForceManager(info); |
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paramSet= new MinimizerParameterSet(info), |
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calcDim(); |
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curX = getCoor(); |
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curG.resize(ndim); |
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|
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} |
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} |
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Minimizer::~Minimizer() { |
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Minimizer::~Minimizer() { |
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delete forceMan; |
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delete paramSet; |
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} |
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} |
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|
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void Minimizer::calcEnergyGradient(std::vector<double> &x, |
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std::vector<double> &grad, double&energy, int&status) { |
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void Minimizer::calcEnergyGradient(std::vector<double> &x, |
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std::vector<double> &grad, double&energy, int&status) { |
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SimInfo::MoleculeIterator i; |
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Molecule::IntegrableObjectIterator j; |
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setCoor(x); |
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if (usingShake) { |
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shakeStatus = shakeR(); |
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shakeStatus = shakeR(); |
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} |
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energy = calcPotential(); |
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if (usingShake) { |
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shakeStatus = shakeF(); |
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shakeStatus = shakeF(); |
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} |
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x = getCoor(); |
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int index = 0; |
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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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for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(j)) { |
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|
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myGrad = integrableObject->getGrad(); |
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for (unsigned int k = 0; k < myGrad.size(); ++k) { |
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//gradient is equal to -f |
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grad[index++] = -myGrad[k]; |
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} |
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} |
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myGrad = integrableObject->getGrad(); |
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for (unsigned int k = 0; k < myGrad.size(); ++k) { |
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|
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grad[index++] = myGrad[k]; |
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} |
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} |
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} |
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|
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} |
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} |
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void Minimizer::setCoor(std::vector<double> &x) { |
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void Minimizer::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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int index = 0; |
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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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for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(j)) { |
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position[0] = x[index++]; |
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position[1] = x[index++]; |
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position[2] = x[index++]; |
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position[0] = x[index++]; |
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position[1] = x[index++]; |
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position[2] = x[index++]; |
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integrableObject->setPos(position); |
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integrableObject->setPos(position); |
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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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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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integrableObject->setEuler(eulerAngle); |
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} |
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} |
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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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std::vector<double> Minimizer::getCoor() { |
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std::vector<double> Minimizer::getCoor() { |
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Vector3d position; |
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Vector3d eulerAngle; |
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SimInfo::MoleculeIterator i; |
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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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for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(j)) { |
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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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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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|
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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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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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} |
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|
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/* |
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int Minimizer::shakeR() { |
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/* |
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int Minimizer::shakeR() { |
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int i, j; |
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int done; |
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double rab[3]; |
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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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ax, ay, |
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az, bx, |
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by, bz; |
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double rma, rmb; |
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double dx, dy, |
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dz; |
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dz; |
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double rpab; |
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double rabsq, pabsq, |
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rpabsq; |
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rpabsq; |
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double diffsq; |
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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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moving[i] = 0; |
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moved[i] = 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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while (!done && (iteration < maxIteration)) { |
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done = 1; |
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done = 1; |
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|
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for(i = 0; i < nConstrained; i++) { |
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a = constrainedA[i]; |
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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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b = constrainedB[i]; |
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ax = (a * 3) + 0; |
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ax = (a * 3) + 0; |
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ay = (a * 3) + 1; |
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ay = (a * 3) + 1; |
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|
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< |
az = (a * 3) + 2; |
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az = (a * 3) + 2; |
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|
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bx = (b * 3) + 0; |
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bx = (b * 3) + 0; |
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|
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by = (b * 3) + 1; |
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> |
by = (b * 3) + 1; |
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|
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bz = (b * 3) + 2; |
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> |
bz = (b * 3) + 2; |
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|
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< |
if (moved[a] || moved[b]) { |
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< |
posA = atoms[a]->getPos(); |
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> |
if (moved[a] || moved[b]) { |
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> |
posA = atoms[a]->getPos(); |
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|
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< |
posB = atoms[b]->getPos(); |
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> |
posB = atoms[b]->getPos(); |
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|
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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(j = 0; j < 3; j++) |
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> |
pab[j] = posA[j] - posB[j]; |
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|
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//periodic boundary condition |
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> |
//periodic boundary condition |
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|
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info->wrapVector(pab); |
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> |
info->wrapVector(pab); |
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|
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< |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
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> |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
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|
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< |
rabsq = constrainedDsqr[i]; |
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> |
rabsq = constrainedDsqr[i]; |
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|
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< |
diffsq = rabsq - pabsq; |
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> |
diffsq = rabsq - pabsq; |
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|
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// the original rattle code from alan tidesley |
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> |
// the original rattle code from alan tidesley |
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|
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< |
if (fabs(diffsq) > (tol * rabsq * 2)) { |
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< |
rab[0] = oldPos[ax] - oldPos[bx]; |
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< |
|
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< |
rab[1] = oldPos[ay] - oldPos[by]; |
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> |
if (fabs(diffsq) > (tol * rabsq * 2)) { |
| 269 |
> |
rab[0] = oldPos[ax] - oldPos[bx]; |
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|
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< |
rab[2] = oldPos[az] - oldPos[bz]; |
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> |
rab[1] = oldPos[ay] - oldPos[by]; |
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|
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< |
info->wrapVector(rab); |
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> |
rab[2] = oldPos[az] - oldPos[bz]; |
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|
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< |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
| 275 |
> |
info->wrapVector(rab); |
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|
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< |
rpabsq = rpab * rpab; |
| 277 |
> |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
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|
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< |
if (rpabsq < (rabsq * -diffsq)) { |
| 279 |
> |
rpabsq = rpab * rpab; |
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|
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< |
#ifdef IS_MPI |
| 281 |
> |
if (rpabsq < (rabsq * -diffsq)) { |
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|
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< |
a = atoms[a]->getGlobalIndex(); |
| 283 |
> |
#ifdef IS_MPI |
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|
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< |
b = atoms[b]->getGlobalIndex(); |
| 285 |
> |
a = atoms[a]->getGlobalIndex(); |
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|
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< |
#endif //is_mpi |
| 287 |
> |
b = atoms[b]->getGlobalIndex(); |
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|
| 289 |
< |
//std::cerr << "Waring: constraint failure" << std::endl; |
| 289 |
> |
#endif //is_mpi |
| 290 |
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|
| 291 |
< |
gab = sqrt(rabsq / pabsq); |
| 291 |
> |
//std::cerr << "Waring: constraint failure" << std::endl; |
| 292 |
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|
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< |
rab[0] = (posA[0] - posB[0]) |
| 296 |
< |
* gab; |
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> |
gab = sqrt(rabsq / pabsq); |
| 294 |
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|
| 295 |
< |
rab[1] = (posA[1] - posB[1]) |
| 296 |
< |
* gab; |
| 295 |
> |
rab[0] = (posA[0] - posB[0]) |
| 296 |
> |
* gab; |
| 297 |
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|
| 298 |
< |
rab[2] = (posA[2] - posB[2]) |
| 299 |
< |
* gab; |
| 298 |
> |
rab[1] = (posA[1] - posB[1]) |
| 299 |
> |
* gab; |
| 300 |
|
|
| 301 |
< |
info->wrapVector(rab); |
| 301 |
> |
rab[2] = (posA[2] - posB[2]) |
| 302 |
> |
* gab; |
| 303 |
|
|
| 304 |
< |
rpab = |
| 307 |
< |
rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
| 308 |
< |
} |
| 304 |
> |
info->wrapVector(rab); |
| 305 |
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|
| 306 |
< |
//rma = 1.0 / atoms[a]->getMass(); |
| 306 |
> |
rpab = |
| 307 |
> |
rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
| 308 |
> |
} |
| 309 |
|
|
| 310 |
< |
//rmb = 1.0 / atoms[b]->getMass(); |
| 310 |
> |
//rma = 1.0 / atoms[a]->getMass(); |
| 311 |
|
|
| 312 |
< |
rma = 1.0; |
| 312 |
> |
//rmb = 1.0 / atoms[b]->getMass(); |
| 313 |
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|
| 314 |
< |
rmb = 1.0; |
| 314 |
> |
rma = 1.0; |
| 315 |
|
|
| 316 |
< |
gab = diffsq / (2.0 * (rma + rmb) * rpab); |
| 316 |
> |
rmb = 1.0; |
| 317 |
|
|
| 318 |
< |
dx = rab[0]* |
| 321 |
< |
gab; |
| 318 |
> |
gab = diffsq / (2.0 * (rma + rmb) * rpab); |
| 319 |
|
|
| 320 |
< |
dy = rab[1]* |
| 321 |
< |
gab; |
| 320 |
> |
dx = rab[0]* |
| 321 |
> |
gab; |
| 322 |
|
|
| 323 |
< |
dz = rab[2]* |
| 324 |
< |
gab; |
| 323 |
> |
dy = rab[1]* |
| 324 |
> |
gab; |
| 325 |
|
|
| 326 |
< |
posA[0] += rma *dx; |
| 326 |
> |
dz = rab[2]* |
| 327 |
> |
gab; |
| 328 |
|
|
| 329 |
< |
posA[1] += rma *dy; |
| 329 |
> |
posA[0] += rma *dx; |
| 330 |
|
|
| 331 |
< |
posA[2] += rma *dz; |
| 331 |
> |
posA[1] += rma *dy; |
| 332 |
|
|
| 333 |
< |
atoms[a]->setPos(posA); |
| 333 |
> |
posA[2] += rma *dz; |
| 334 |
|
|
| 335 |
< |
posB[0] -= rmb *dx; |
| 335 |
> |
atoms[a]->setPos(posA); |
| 336 |
|
|
| 337 |
< |
posB[1] -= rmb *dy; |
| 337 |
> |
posB[0] -= rmb *dx; |
| 338 |
|
|
| 339 |
< |
posB[2] -= rmb *dz; |
| 339 |
> |
posB[1] -= rmb *dy; |
| 340 |
|
|
| 341 |
< |
atoms[b]->setPos(posB); |
| 341 |
> |
posB[2] -= rmb *dz; |
| 342 |
|
|
| 343 |
< |
moving[a] = 1; |
| 343 |
> |
atoms[b]->setPos(posB); |
| 344 |
|
|
| 345 |
< |
moving[b] = 1; |
| 345 |
> |
moving[a] = 1; |
| 346 |
|
|
| 347 |
< |
done = 0; |
| 350 |
< |
} |
| 351 |
< |
} |
| 352 |
< |
} |
| 347 |
> |
moving[b] = 1; |
| 348 |
|
|
| 349 |
< |
for(i = 0; i < nAtoms; i++) { |
| 350 |
< |
moved[i] = moving[i]; |
| 349 |
> |
done = 0; |
| 350 |
> |
} |
| 351 |
> |
} |
| 352 |
> |
} |
| 353 |
|
|
| 354 |
< |
moving[i] = 0; |
| 355 |
< |
} |
| 354 |
> |
for(i = 0; i < nAtoms; i++) { |
| 355 |
> |
moved[i] = moving[i]; |
| 356 |
|
|
| 357 |
< |
iteration++; |
| 357 |
> |
moving[i] = 0; |
| 358 |
|
} |
| 359 |
|
|
| 360 |
+ |
iteration++; |
| 361 |
+ |
} |
| 362 |
+ |
|
| 363 |
|
if (!done) { |
| 364 |
< |
std::cerr << "Waring: can not constraint within maxIteration" |
| 365 |
< |
<< std::endl; |
| 364 |
> |
std::cerr << "Waring: can not constraint within maxIteration" |
| 365 |
> |
<< std::endl; |
| 366 |
|
|
| 367 |
< |
return -1; |
| 367 |
> |
return -1; |
| 368 |
|
} else |
| 369 |
< |
return 1; |
| 370 |
< |
} |
| 369 |
> |
return 1; |
| 370 |
> |
} |
| 371 |
|
|
| 372 |
< |
//remove constraint force along the bond direction |
| 372 |
> |
//remove constraint force along the bond direction |
| 373 |
|
|
| 374 |
|
|
| 375 |
< |
int Minimizer::shakeF() { |
| 375 |
> |
int Minimizer::shakeF() { |
| 376 |
|
int i, j; |
| 377 |
|
|
| 378 |
|
int done; |
| 384 |
|
double rab[3], fpab[3]; |
| 385 |
|
|
| 386 |
|
int a, b, |
| 387 |
< |
ax, ay, |
| 388 |
< |
az, bx, |
| 389 |
< |
by, bz; |
| 387 |
> |
ax, ay, |
| 388 |
> |
az, bx, |
| 389 |
> |
by, bz; |
| 390 |
|
|
| 391 |
|
double rma, rmb; |
| 392 |
|
|
| 401 |
|
int iteration; |
| 402 |
|
|
| 403 |
|
for(i = 0; i < nAtoms; i++) { |
| 404 |
< |
moving[i] = 0; |
| 404 |
> |
moving[i] = 0; |
| 405 |
|
|
| 406 |
< |
moved[i] = 1; |
| 406 |
> |
moved[i] = 1; |
| 407 |
|
} |
| 408 |
|
|
| 409 |
|
done = 0; |
| 411 |
|
iteration = 0; |
| 412 |
|
|
| 413 |
|
while (!done && (iteration < maxIteration)) { |
| 414 |
< |
done = 1; |
| 414 |
> |
done = 1; |
| 415 |
|
|
| 416 |
< |
for(i = 0; i < nConstrained; i++) { |
| 417 |
< |
a = constrainedA[i]; |
| 416 |
> |
for(i = 0; i < nConstrained; i++) { |
| 417 |
> |
a = constrainedA[i]; |
| 418 |
|
|
| 419 |
< |
b = constrainedB[i]; |
| 419 |
> |
b = constrainedB[i]; |
| 420 |
|
|
| 421 |
< |
ax = (a * 3) + 0; |
| 421 |
> |
ax = (a * 3) + 0; |
| 422 |
|
|
| 423 |
< |
ay = (a * 3) + 1; |
| 423 |
> |
ay = (a * 3) + 1; |
| 424 |
|
|
| 425 |
< |
az = (a * 3) + 2; |
| 425 |
> |
az = (a * 3) + 2; |
| 426 |
|
|
| 427 |
< |
bx = (b * 3) + 0; |
| 427 |
> |
bx = (b * 3) + 0; |
| 428 |
|
|
| 429 |
< |
by = (b * 3) + 1; |
| 429 |
> |
by = (b * 3) + 1; |
| 430 |
|
|
| 431 |
< |
bz = (b * 3) + 2; |
| 431 |
> |
bz = (b * 3) + 2; |
| 432 |
|
|
| 433 |
< |
if (moved[a] || moved[b]) { |
| 434 |
< |
posA = atoms[a]->getPos(); |
| 433 |
> |
if (moved[a] || moved[b]) { |
| 434 |
> |
posA = atoms[a]->getPos(); |
| 435 |
|
|
| 436 |
< |
posB = atoms[b]->getPos(); |
| 436 |
> |
posB = atoms[b]->getPos(); |
| 437 |
|
|
| 438 |
< |
for(j = 0; j < 3; j++) |
| 439 |
< |
rab[j] = posA[j] - posB[j]; |
| 438 |
> |
for(j = 0; j < 3; j++) |
| 439 |
> |
rab[j] = posA[j] - posB[j]; |
| 440 |
|
|
| 441 |
< |
info->wrapVector(rab); |
| 441 |
> |
info->wrapVector(rab); |
| 442 |
|
|
| 443 |
< |
atoms[a]->getFrc(frcA); |
| 443 |
> |
atoms[a]->getFrc(frcA); |
| 444 |
|
|
| 445 |
< |
atoms[b]->getFrc(frcB); |
| 445 |
> |
atoms[b]->getFrc(frcB); |
| 446 |
|
|
| 447 |
< |
//rma = 1.0 / atoms[a]->getMass(); |
| 447 |
> |
//rma = 1.0 / atoms[a]->getMass(); |
| 448 |
|
|
| 449 |
< |
//rmb = 1.0 / atoms[b]->getMass(); |
| 449 |
> |
//rmb = 1.0 / atoms[b]->getMass(); |
| 450 |
|
|
| 451 |
< |
rma = 1.0; |
| 451 |
> |
rma = 1.0; |
| 452 |
|
|
| 453 |
< |
rmb = 1.0; |
| 453 |
> |
rmb = 1.0; |
| 454 |
|
|
| 455 |
< |
fpab[0] = frcA[0] * rma - frcB[0] * rmb; |
| 455 |
> |
fpab[0] = frcA[0] * rma - frcB[0] * rmb; |
| 456 |
|
|
| 457 |
< |
fpab[1] = frcA[1] * rma - frcB[1] * rmb; |
| 457 |
> |
fpab[1] = frcA[1] * rma - frcB[1] * rmb; |
| 458 |
|
|
| 459 |
< |
fpab[2] = frcA[2] * rma - frcB[2] * rmb; |
| 459 |
> |
fpab[2] = frcA[2] * rma - frcB[2] * rmb; |
| 460 |
|
|
| 461 |
< |
gab = fpab[0] * fpab[0] + fpab[1] * fpab[1] + fpab[2] * fpab[2]; |
| 461 |
> |
gab = fpab[0] * fpab[0] + fpab[1] * fpab[1] + fpab[2] * fpab[2]; |
| 462 |
|
|
| 463 |
< |
if (gab < 1.0) |
| 464 |
< |
gab = 1.0; |
| 463 |
> |
if (gab < 1.0) |
| 464 |
> |
gab = 1.0; |
| 465 |
|
|
| 466 |
< |
rabsq = rab[0] * rab[0] + rab[1] * rab[1] + rab[2] * rab[2]; |
| 466 |
> |
rabsq = rab[0] * rab[0] + rab[1] * rab[1] + rab[2] * rab[2]; |
| 467 |
|
|
| 468 |
< |
rfab = rab[0] * fpab[0] + rab[1] * fpab[1] + rab[2] * fpab[2]; |
| 468 |
> |
rfab = rab[0] * fpab[0] + rab[1] * fpab[1] + rab[2] * fpab[2]; |
| 469 |
|
|
| 470 |
< |
if (fabs(rfab) > sqrt(rabsq*gab) * 0.00001) { |
| 471 |
< |
gab = -rfab / (rabsq * (rma + rmb)); |
| 470 |
> |
if (fabs(rfab) > sqrt(rabsq*gab) * 0.00001) { |
| 471 |
> |
gab = -rfab / (rabsq * (rma + rmb)); |
| 472 |
|
|
| 473 |
< |
frcA[0] = rab[0]* |
| 474 |
< |
gab; |
| 473 |
> |
frcA[0] = rab[0]* |
| 474 |
> |
gab; |
| 475 |
|
|
| 476 |
< |
frcA[1] = rab[1]* |
| 477 |
< |
gab; |
| 476 |
> |
frcA[1] = rab[1]* |
| 477 |
> |
gab; |
| 478 |
|
|
| 479 |
< |
frcA[2] = rab[2]* |
| 480 |
< |
gab; |
| 479 |
> |
frcA[2] = rab[2]* |
| 480 |
> |
gab; |
| 481 |
|
|
| 482 |
< |
atoms[a]->addFrc(frcA); |
| 482 |
> |
atoms[a]->addFrc(frcA); |
| 483 |
|
|
| 484 |
< |
frcB[0] = -rab[0]*gab; |
| 484 |
> |
frcB[0] = -rab[0]*gab; |
| 485 |
|
|
| 486 |
< |
frcB[1] = -rab[1]*gab; |
| 486 |
> |
frcB[1] = -rab[1]*gab; |
| 487 |
|
|
| 488 |
< |
frcB[2] = -rab[2]*gab; |
| 488 |
> |
frcB[2] = -rab[2]*gab; |
| 489 |
|
|
| 490 |
< |
atoms[b]->addFrc(frcB); |
| 490 |
> |
atoms[b]->addFrc(frcB); |
| 491 |
|
|
| 492 |
< |
moving[a] = 1; |
| 492 |
> |
moving[a] = 1; |
| 493 |
|
|
| 494 |
< |
moving[b] = 1; |
| 494 |
> |
moving[b] = 1; |
| 495 |
|
|
| 496 |
< |
done = 0; |
| 497 |
< |
} |
| 498 |
< |
} |
| 499 |
< |
} |
| 496 |
> |
done = 0; |
| 497 |
> |
} |
| 498 |
> |
} |
| 499 |
> |
} |
| 500 |
|
|
| 501 |
< |
for(i = 0; i < nAtoms; i++) { |
| 502 |
< |
moved[i] = moving[i]; |
| 501 |
> |
for(i = 0; i < nAtoms; i++) { |
| 502 |
> |
moved[i] = moving[i]; |
| 503 |
|
|
| 504 |
< |
moving[i] = 0; |
| 505 |
< |
} |
| 504 |
> |
moving[i] = 0; |
| 505 |
> |
} |
| 506 |
|
|
| 507 |
< |
iteration++; |
| 507 |
> |
iteration++; |
| 508 |
|
} |
| 509 |
|
|
| 510 |
|
if (!done) { |
| 511 |
< |
std::cerr << "Waring: can not constraint within maxIteration" |
| 512 |
< |
<< std::endl; |
| 511 |
> |
std::cerr << "Waring: can not constraint within maxIteration" |
| 512 |
> |
<< std::endl; |
| 513 |
|
|
| 514 |
< |
return -1; |
| 514 |
> |
return -1; |
| 515 |
|
} else |
| 516 |
< |
return 1; |
| 517 |
< |
} |
| 516 |
> |
return 1; |
| 517 |
> |
} |
| 518 |
|
|
| 519 |
< |
*/ |
| 519 |
> |
*/ |
| 520 |
|
|
| 521 |
< |
//calculate the value of object function |
| 521 |
> |
//calculate the value of object function |
| 522 |
|
|
| 523 |
< |
void Minimizer::calcF() { |
| 523 |
> |
void Minimizer::calcF() { |
| 524 |
|
calcEnergyGradient(curX, curG, curF, egEvalStatus); |
| 525 |
< |
} |
| 525 |
> |
} |
| 526 |
|
|
| 527 |
< |
void Minimizer::calcF(std::vector < double > &x, double&f, int&status) { |
| 527 |
> |
void Minimizer::calcF(std::vector < double > &x, double&f, int&status) { |
| 528 |
|
std::vector < double > tempG; |
| 529 |
|
|
| 530 |
|
tempG.resize(x.size()); |
| 531 |
|
|
| 532 |
|
calcEnergyGradient(x, tempG, f, status); |
| 533 |
< |
} |
| 533 |
> |
} |
| 534 |
|
|
| 535 |
< |
//calculate the gradient |
| 535 |
> |
//calculate the gradient |
| 536 |
|
|
| 537 |
< |
void Minimizer::calcG() { |
| 537 |
> |
void Minimizer::calcG() { |
| 538 |
|
calcEnergyGradient(curX, curG, curF, egEvalStatus); |
| 539 |
< |
} |
| 539 |
> |
} |
| 540 |
|
|
| 541 |
< |
void Minimizer::calcG(std::vector<double>& x, std::vector<double>& g, double&f, int&status) { |
| 541 |
> |
void Minimizer::calcG(std::vector<double>& x, std::vector<double>& g, double&f, int&status) { |
| 542 |
|
calcEnergyGradient(x, g, f, status); |
| 543 |
< |
} |
| 543 |
> |
} |
| 544 |
|
|
| 545 |
< |
void Minimizer::calcDim() { |
| 545 |
> |
void Minimizer::calcDim() { |
| 546 |
|
|
| 547 |
|
SimInfo::MoleculeIterator i; |
| 548 |
|
Molecule::IntegrableObjectIterator j; |
| 551 |
|
ndim = 0; |
| 552 |
|
|
| 553 |
|
for (mol = info->beginMolecule(i); mol != NULL; mol = info->nextMolecule(i)) { |
| 554 |
< |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 555 |
< |
integrableObject = mol->nextIntegrableObject(j)) { |
| 554 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 555 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
| 556 |
|
|
| 557 |
< |
ndim += 3; |
| 557 |
> |
ndim += 3; |
| 558 |
|
|
| 559 |
< |
if (integrableObject->isDirectional()) { |
| 560 |
< |
ndim += 3; |
| 561 |
< |
} |
| 562 |
< |
} |
| 559 |
> |
if (integrableObject->isDirectional()) { |
| 560 |
> |
ndim += 3; |
| 561 |
> |
} |
| 562 |
> |
} |
| 563 |
|
|
| 564 |
|
} |
| 565 |
< |
} |
| 565 |
> |
} |
| 566 |
|
|
| 567 |
< |
void Minimizer::setX(std::vector < double > &x) { |
| 567 |
> |
void Minimizer::setX(std::vector < double > &x) { |
| 568 |
|
if (x.size() != ndim) { |
| 569 |
< |
sprintf(painCave.errMsg, "Minimizer Error: dimesion of x and curX does not match\n"); |
| 570 |
< |
painCave.isFatal = 1; |
| 571 |
< |
simError(); |
| 569 |
> |
sprintf(painCave.errMsg, "Minimizer Error: dimesion of x and curX does not match\n"); |
| 570 |
> |
painCave.isFatal = 1; |
| 571 |
> |
simError(); |
| 572 |
|
} |
| 573 |
|
|
| 574 |
|
curX = x; |
| 575 |
< |
} |
| 575 |
> |
} |
| 576 |
|
|
| 577 |
< |
void Minimizer::setG(std::vector < double > &g) { |
| 577 |
> |
void Minimizer::setG(std::vector < double > &g) { |
| 578 |
|
if (g.size() != ndim) { |
| 579 |
< |
sprintf(painCave.errMsg, "Minimizer Error: dimesion of g and curG does not match\n"); |
| 580 |
< |
painCave.isFatal = 1; |
| 581 |
< |
simError(); |
| 579 |
> |
sprintf(painCave.errMsg, "Minimizer Error: dimesion of g and curG does not match\n"); |
| 580 |
> |
painCave.isFatal = 1; |
| 581 |
> |
simError(); |
| 582 |
|
} |
| 583 |
|
|
| 584 |
|
curG = g; |
| 585 |
< |
} |
| 585 |
> |
} |
| 586 |
|
|
| 587 |
|
|
| 588 |
< |
/** |
| 588 |
> |
/** |
| 589 |
|
|
| 590 |
< |
* In thoery, we need to find the minimum along the search direction |
| 591 |
< |
* However, function evaluation is too expensive. |
| 592 |
< |
* At the very begining of the problem, we check the search direction and make sure |
| 593 |
< |
* it is a descent direction |
| 594 |
< |
* we will compare the energy of two end points, |
| 595 |
< |
* if the right end point has lower energy, we just take it |
| 596 |
< |
* @todo optimize this line search algorithm |
| 597 |
< |
*/ |
| 590 |
> |
* In thoery, we need to find the minimum along the search direction |
| 591 |
> |
* However, function evaluation is too expensive. |
| 592 |
> |
* At the very begining of the problem, we check the search direction and make sure |
| 593 |
> |
* it is a descent direction |
| 594 |
> |
* we will compare the energy of two end points, |
| 595 |
> |
* if the right end point has lower energy, we just take it |
| 596 |
> |
* @todo optimize this line search algorithm |
| 597 |
> |
*/ |
| 598 |
|
|
| 599 |
< |
int Minimizer::doLineSearch(std::vector<double> &direction, |
| 600 |
< |
double stepSize) { |
| 599 |
> |
int Minimizer::doLineSearch(std::vector<double> &direction, |
| 600 |
> |
double stepSize) { |
| 601 |
|
|
| 602 |
|
std::vector<double> xa; |
| 603 |
|
std::vector<double> xb; |
| 650 |
|
slopeA = 0; |
| 651 |
|
|
| 652 |
|
for(size_t i = 0; i < ndim; i++) { |
| 653 |
< |
slopeA += curG[i] * direction[i]; |
| 653 |
> |
slopeA += curG[i] * direction[i]; |
| 654 |
|
} |
| 655 |
|
|
| 656 |
|
initSlope = slopeA; |
| 659 |
|
|
| 660 |
|
if (slopeA > 0) { |
| 661 |
|
|
| 662 |
< |
for(size_t i = 0; i < ndim; i++) { |
| 663 |
< |
direction[i] = -curG[i]; |
| 664 |
< |
} |
| 662 |
> |
for(size_t i = 0; i < ndim; i++) { |
| 663 |
> |
direction[i] = -curG[i]; |
| 664 |
> |
} |
| 665 |
|
|
| 666 |
< |
for(size_t i = 0; i < ndim; i++) { |
| 667 |
< |
slopeA += curG[i] * direction[i]; |
| 668 |
< |
} |
| 666 |
> |
for(size_t i = 0; i < ndim; i++) { |
| 667 |
> |
slopeA += curG[i] * direction[i]; |
| 668 |
> |
} |
| 669 |
|
|
| 670 |
< |
initSlope = slopeA; |
| 670 |
> |
initSlope = slopeA; |
| 671 |
|
} |
| 672 |
|
|
| 673 |
|
// Take a trial step |
| 674 |
|
|
| 675 |
|
for(size_t i = 0; i < ndim; i++) { |
| 676 |
< |
xc[i] = curX[i] + direction[i]* c; |
| 676 |
> |
xc[i] = curX[i] + direction[i]* c; |
| 677 |
|
} |
| 678 |
|
|
| 679 |
|
calcG(xc, gc, fc, status); |
| 680 |
|
|
| 681 |
|
if (status < 0) { |
| 682 |
< |
if (bVerbose) |
| 683 |
< |
std::cerr << "Function Evaluation Error" << std::endl; |
| 682 |
> |
if (bVerbose) |
| 683 |
> |
std::cerr << "Function Evaluation Error" << std::endl; |
| 684 |
|
} |
| 685 |
|
|
| 686 |
|
//calculate the derivative at c |
| 688 |
|
slopeC = 0; |
| 689 |
|
|
| 690 |
|
for(size_t i = 0; i < ndim; i++) { |
| 691 |
< |
slopeC += gc[i] * direction[i]; |
| 691 |
> |
slopeC += gc[i] * direction[i]; |
| 692 |
|
} |
| 693 |
|
// found a lower point |
| 694 |
|
|
| 695 |
|
if (fc < fa) { |
| 696 |
< |
curX = xc; |
| 696 |
> |
curX = xc; |
| 697 |
|
|
| 698 |
< |
curG = gc; |
| 698 |
> |
curG = gc; |
| 699 |
|
|
| 700 |
< |
curF = fc; |
| 700 |
> |
curF = fc; |
| 701 |
|
|
| 702 |
< |
return LS_SUCCEED; |
| 702 |
> |
return LS_SUCCEED; |
| 703 |
|
} else { |
| 704 |
< |
if (slopeC > 0) |
| 705 |
< |
stepSize *= 0.618034; |
| 704 |
> |
if (slopeC > 0) |
| 705 |
> |
stepSize *= 0.618034; |
| 706 |
|
} |
| 707 |
|
|
| 708 |
|
maxLSIter = paramSet->getLineSearchMaxIteration(); |
| 711 |
|
|
| 712 |
|
do { |
| 713 |
|
|
| 714 |
< |
// Select a new trial point. |
| 714 |
> |
// Select a new trial point. |
| 715 |
|
|
| 716 |
< |
// If the derivatives at points a & c have different sign we use cubic interpolate |
| 716 |
> |
// If the derivatives at points a & c have different sign we use cubic interpolate |
| 717 |
|
|
| 718 |
< |
//if (slopeC > 0){ |
| 718 |
> |
//if (slopeC > 0){ |
| 719 |
|
|
| 720 |
< |
eta = 3 * (fa - fc) / (c - a) + slopeA + slopeC; |
| 720 |
> |
eta = 3 * (fa - fc) / (c - a) + slopeA + slopeC; |
| 721 |
|
|
| 722 |
< |
mu = sqrt(eta * eta - slopeA * slopeC); |
| 722 |
> |
mu = sqrt(eta * eta - slopeA * slopeC); |
| 723 |
|
|
| 724 |
< |
b = a + (c - a) |
| 725 |
< |
* (1 - (slopeC + mu - eta) / (slopeC - slopeA + 2 * mu)); |
| 724 |
> |
b = a + (c - a) |
| 725 |
> |
* (1 - (slopeC + mu - eta) / (slopeC - slopeA + 2 * mu)); |
| 726 |
|
|
| 727 |
< |
if (b < lsTol) { |
| 728 |
< |
break; |
| 729 |
< |
} |
| 727 |
> |
if (b < lsTol) { |
| 728 |
> |
break; |
| 729 |
> |
} |
| 730 |
|
|
| 731 |
< |
//} |
| 731 |
> |
//} |
| 732 |
|
|
| 733 |
< |
// Take a trial step to this new point - new coords in xb |
| 733 |
> |
// Take a trial step to this new point - new coords in xb |
| 734 |
|
|
| 735 |
< |
for(size_t i = 0; i < ndim; i++) { |
| 736 |
< |
xb[i] = curX[i] + direction[i]* b; |
| 737 |
< |
} |
| 735 |
> |
for(size_t i = 0; i < ndim; i++) { |
| 736 |
> |
xb[i] = curX[i] + direction[i]* b; |
| 737 |
> |
} |
| 738 |
|
|
| 739 |
< |
//function evaluation |
| 739 |
> |
//function evaluation |
| 740 |
|
|
| 741 |
< |
calcG(xb, gb, fb, status); |
| 741 |
> |
calcG(xb, gb, fb, status); |
| 742 |
|
|
| 743 |
< |
if (status < 0) { |
| 744 |
< |
if (bVerbose) |
| 745 |
< |
std::cerr << "Function Evaluation Error" << std::endl; |
| 746 |
< |
} |
| 743 |
> |
if (status < 0) { |
| 744 |
> |
if (bVerbose) |
| 745 |
> |
std::cerr << "Function Evaluation Error" << std::endl; |
| 746 |
> |
} |
| 747 |
|
|
| 748 |
< |
//calculate the derivative at c |
| 748 |
> |
//calculate the derivative at c |
| 749 |
|
|
| 750 |
< |
slopeB = 0; |
| 750 |
> |
slopeB = 0; |
| 751 |
|
|
| 752 |
< |
for(size_t i = 0; i < ndim; i++) { |
| 753 |
< |
slopeB += gb[i] * direction[i]; |
| 754 |
< |
} |
| 752 |
> |
for(size_t i = 0; i < ndim; i++) { |
| 753 |
> |
slopeB += gb[i] * direction[i]; |
| 754 |
> |
} |
| 755 |
|
|
| 756 |
< |
//Amijo Rule to stop the line search |
| 756 |
> |
//Amijo Rule to stop the line search |
| 757 |
|
|
| 758 |
< |
if (fb <= curF + initSlope * ftol * b) { |
| 759 |
< |
curF = fb; |
| 758 |
> |
if (fb <= curF + initSlope * ftol * b) { |
| 759 |
> |
curF = fb; |
| 760 |
|
|
| 761 |
< |
curX = xb; |
| 761 |
> |
curX = xb; |
| 762 |
|
|
| 763 |
< |
curG = gb; |
| 763 |
> |
curG = gb; |
| 764 |
|
|
| 765 |
< |
return LS_SUCCEED; |
| 766 |
< |
} |
| 765 |
> |
return LS_SUCCEED; |
| 766 |
> |
} |
| 767 |
|
|
| 768 |
< |
if (slopeB < 0 && fb < fa) { |
| 768 |
> |
if (slopeB < 0 && fb < fa) { |
| 769 |
|
|
| 770 |
< |
//replace a by b |
| 770 |
> |
//replace a by b |
| 771 |
|
|
| 772 |
< |
fa = fb; |
| 772 |
> |
fa = fb; |
| 773 |
|
|
| 774 |
< |
a = b; |
| 774 |
> |
a = b; |
| 775 |
|
|
| 776 |
< |
slopeA = slopeB; |
| 777 |
< |
|
| 778 |
< |
// swap coord a/b |
| 776 |
> |
slopeA = slopeB; |
| 777 |
|
|
| 778 |
< |
std::swap(xa, xb); |
| 778 |
> |
// swap coord a/b |
| 779 |
|
|
| 780 |
< |
std::swap(ga, gb); |
| 783 |
< |
} else { |
| 780 |
> |
std::swap(xa, xb); |
| 781 |
|
|
| 782 |
< |
//replace c by b |
| 782 |
> |
std::swap(ga, gb); |
| 783 |
> |
} else { |
| 784 |
|
|
| 785 |
< |
fc = fb; |
| 785 |
> |
//replace c by b |
| 786 |
|
|
| 787 |
< |
c = b; |
| 787 |
> |
fc = fb; |
| 788 |
|
|
| 789 |
< |
slopeC = slopeB; |
| 789 |
> |
c = b; |
| 790 |
|
|
| 791 |
< |
// swap coord b/c |
| 791 |
> |
slopeC = slopeB; |
| 792 |
|
|
| 793 |
< |
std::swap(gb, gc); |
| 793 |
> |
// swap coord b/c |
| 794 |
|
|
| 795 |
< |
std::swap(xb, xc); |
| 798 |
< |
} |
| 795 |
> |
std::swap(gb, gc); |
| 796 |
|
|
| 797 |
< |
iter++; |
| 797 |
> |
std::swap(xb, xc); |
| 798 |
> |
} |
| 799 |
> |
|
| 800 |
> |
iter++; |
| 801 |
|
} while ((fb > fa || fb > fc) && (iter < maxLSIter)); |
| 802 |
|
|
| 803 |
|
if (fb < curF || iter >= maxLSIter) { |
| 804 |
|
|
| 805 |
< |
//could not find a lower value, we might just go uphill. |
| 805 |
> |
//could not find a lower value, we might just go uphill. |
| 806 |
|
|
| 807 |
< |
return LS_ERROR; |
| 807 |
> |
return LS_ERROR; |
| 808 |
|
} |
| 809 |
|
|
| 810 |
|
//select the end point |
| 811 |
|
|
| 812 |
|
if (fa <= fc) { |
| 813 |
< |
curX = xa; |
| 813 |
> |
curX = xa; |
| 814 |
|
|
| 815 |
< |
curG = ga; |
| 815 |
> |
curG = ga; |
| 816 |
|
|
| 817 |
< |
curF = fa; |
| 817 |
> |
curF = fa; |
| 818 |
|
} else { |
| 819 |
< |
curX = xc; |
| 819 |
> |
curX = xc; |
| 820 |
|
|
| 821 |
< |
curG = gc; |
| 821 |
> |
curG = gc; |
| 822 |
|
|
| 823 |
< |
curF = fc; |
| 823 |
> |
curF = fc; |
| 824 |
|
} |
| 825 |
|
|
| 826 |
|
return LS_SUCCEED; |
| 827 |
< |
} |
| 827 |
> |
} |
| 828 |
|
|
| 829 |
< |
void Minimizer::minimize() { |
| 829 |
> |
void Minimizer::minimize() { |
| 830 |
|
int convgStatus; |
| 831 |
|
int stepStatus; |
| 832 |
|
int maxIter; |
| 833 |
|
int writeFrq; |
| 834 |
|
int nextWriteIter; |
| 835 |
|
Snapshot* curSnapshot =info->getSnapshotManager()->getCurrentSnapshot(); |
| 836 |
< |
DumpWriter dumpWriter(info, info->getDumpFileName()); |
| 836 |
> |
DumpWriter dumpWriter(info); |
| 837 |
|
StatsBitSet mask; |
| 838 |
|
mask.set(Stats::TIME); |
| 839 |
|
mask.set(Stats::POTENTIAL_ENERGY); |
| 848 |
|
maxIter = paramSet->getMaxIteration(); |
| 849 |
|
|
| 850 |
|
for(curIter = 1; curIter <= maxIter; curIter++) { |
| 851 |
< |
stepStatus = step(); |
| 851 |
> |
stepStatus = step(); |
| 852 |
|
|
| 853 |
< |
//if (usingShake) |
| 854 |
< |
// preMove(); |
| 853 |
> |
//if (usingShake) |
| 854 |
> |
// preMove(); |
| 855 |
|
|
| 856 |
< |
if (stepStatus < 0) { |
| 857 |
< |
saveResult(); |
| 856 |
> |
if (stepStatus < 0) { |
| 857 |
> |
saveResult(); |
| 858 |
|
|
| 859 |
< |
minStatus = MIN_LSERROR; |
| 859 |
> |
minStatus = MIN_LSERROR; |
| 860 |
|
|
| 861 |
< |
std::cerr |
| 862 |
< |
<< "Minimizer Error: line search error, please try a small stepsize" |
| 863 |
< |
<< std::endl; |
| 861 |
> |
std::cerr |
| 862 |
> |
<< "Minimizer Error: line search error, please try a small stepsize" |
| 863 |
> |
<< std::endl; |
| 864 |
|
|
| 865 |
< |
return; |
| 866 |
< |
} |
| 865 |
> |
return; |
| 866 |
> |
} |
| 867 |
|
|
| 868 |
< |
//save snapshot |
| 869 |
< |
info->getSnapshotManager()->advance(); |
| 870 |
< |
//increase time |
| 871 |
< |
curSnapshot->increaseTime(1); |
| 868 |
> |
//save snapshot |
| 869 |
> |
info->getSnapshotManager()->advance(); |
| 870 |
> |
//increase time |
| 871 |
> |
curSnapshot->increaseTime(1); |
| 872 |
|
|
| 873 |
< |
if (curIter == nextWriteIter) { |
| 874 |
< |
nextWriteIter += writeFrq; |
| 875 |
< |
calcF(); |
| 876 |
< |
dumpWriter.writeDump(); |
| 877 |
< |
statWriter.writeStat(curSnapshot->statData); |
| 878 |
< |
} |
| 873 |
> |
if (curIter == nextWriteIter) { |
| 874 |
> |
nextWriteIter += writeFrq; |
| 875 |
> |
calcF(); |
| 876 |
> |
dumpWriter.writeDump(); |
| 877 |
> |
statWriter.writeStat(curSnapshot->statData); |
| 878 |
> |
} |
| 879 |
|
|
| 880 |
< |
convgStatus = checkConvg(); |
| 880 |
> |
convgStatus = checkConvg(); |
| 881 |
|
|
| 882 |
< |
if (convgStatus > 0) { |
| 883 |
< |
saveResult(); |
| 882 |
> |
if (convgStatus > 0) { |
| 883 |
> |
saveResult(); |
| 884 |
|
|
| 885 |
< |
minStatus = MIN_CONVERGE; |
| 885 |
> |
minStatus = MIN_CONVERGE; |
| 886 |
|
|
| 887 |
< |
return; |
| 888 |
< |
} |
| 887 |
> |
return; |
| 888 |
> |
} |
| 889 |
|
|
| 890 |
< |
prepareStep(); |
| 890 |
> |
prepareStep(); |
| 891 |
|
} |
| 892 |
|
|
| 893 |
|
if (bVerbose) { |
| 894 |
< |
std::cout << "Minimizer Warning: " << minimizerName |
| 895 |
< |
<< " algorithm did not converge within " << maxIter << " iteration" |
| 896 |
< |
<< std::endl; |
| 894 |
> |
std::cout << "Minimizer Warning: " << minimizerName |
| 895 |
> |
<< " algorithm did not converge within " << maxIter << " iteration" |
| 896 |
> |
<< std::endl; |
| 897 |
|
} |
| 898 |
|
|
| 899 |
|
minStatus = MIN_MAXITER; |
| 900 |
|
|
| 901 |
|
saveResult(); |
| 902 |
< |
} |
| 902 |
> |
} |
| 903 |
|
|
| 904 |
|
|
| 905 |
< |
double Minimizer::calcPotential() { |
| 905 |
> |
double Minimizer::calcPotential() { |
| 906 |
|
forceMan->calcForces(true, false); |
| 907 |
|
|
| 908 |
|
Snapshot* curSnapshot = info->getSnapshotManager()->getCurrentSnapshot(); |
| 909 |
|
double potential_local = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] + |
| 910 |
< |
curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ; |
| 910 |
> |
curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ; |
| 911 |
|
double potential; |
| 912 |
|
|
| 913 |
|
#ifdef IS_MPI |
| 920 |
|
//save total potential |
| 921 |
|
curSnapshot->statData[Stats::POTENTIAL_ENERGY] = potential; |
| 922 |
|
return potential; |
| 923 |
< |
} |
| 923 |
> |
} |
| 924 |
|
|
| 925 |
|
} |
