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gezelter |
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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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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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#include <cmath> |
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#include "integrators/Integrator.cpp" |
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#include "io/StatWriter.hpp" |
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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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if (v1.size() != v2.size()) { |
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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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} |
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return result; |
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} |
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Minimizer::Minimizer(SimInfo* rhs) : |
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info(rhs), usingShake(false) { |
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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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Minimizer::~Minimizer() { |
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delete forceMan; |
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delete paramSet; |
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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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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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std::vector<double> myGrad; |
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int shakeStatus; |
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status = 1; |
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setCoor(x); |
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if (usingShake) { |
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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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} |
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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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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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} |
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} |
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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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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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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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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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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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} |
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} |
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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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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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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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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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int Minimizer::shakeR() { |
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int i, j; |
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int done; |
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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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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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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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double rabsq, pabsq, |
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rpabsq; |
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double diffsq; |
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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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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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for(i = 0; i < nConstrained; i++) { |
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a = constrainedA[i]; |
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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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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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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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//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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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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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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info->wrapVector(rab); |
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rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
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rpabsq = rpab * rpab; |
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if (rpabsq < (rabsq * -diffsq)) { |
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#ifdef IS_MPI |
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a = atoms[a]->getGlobalIndex(); |
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b = atoms[b]->getGlobalIndex(); |
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#endif //is_mpi |
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//std::cerr << "Waring: constraint failure" << std::endl; |
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gab = sqrt(rabsq / pabsq); |
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rab[0] = (posA[0] - posB[0]) |
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* gab; |
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rab[1] = (posA[1] - posB[1]) |
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* gab; |
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rab[2] = (posA[2] - posB[2]) |
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* gab; |
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info->wrapVector(rab); |
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rpab = |
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rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
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} |
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//rma = 1.0 / atoms[a]->getMass(); |
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//rmb = 1.0 / atoms[b]->getMass(); |
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rma = 1.0; |
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rmb = 1.0; |
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gab = diffsq / (2.0 * (rma + rmb) * rpab); |
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dx = rab[0]* |
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gab; |
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dy = rab[1]* |
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gab; |
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dz = rab[2]* |
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gab; |
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posA[0] += rma *dx; |
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posA[1] += rma *dy; |
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posA[2] += rma *dz; |
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atoms[a]->setPos(posA); |
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posB[0] -= rmb *dx; |
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posB[1] -= rmb *dy; |
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posB[2] -= rmb *dz; |
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atoms[b]->setPos(posB); |
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moving[a] = 1; |
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moving[b] = 1; |
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done = 0; |
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} |
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} |
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} |
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for(i = 0; i < nAtoms; i++) { |
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moved[i] = moving[i]; |
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moving[i] = 0; |
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} |
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iteration++; |
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} |
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if (!done) { |
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std::cerr << "Waring: can not constraint within maxIteration" |
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<< std::endl; |
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return -1; |
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} else |
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return 1; |
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} |
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//remove constraint force along the bond direction |
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int Minimizer::shakeF() { |
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int i, j; |
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int done; |
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double posA[3], posB[3]; |
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double frcA[3], frcB[3]; |
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double rab[3], fpab[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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double rma, rmb; |
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double rvab; |
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double gab; |
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double rabsq; |
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double rfab; |
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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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|
moved[i] = 1; |
| 408 |
|
|
} |
| 409 |
|
|
|
| 410 |
|
|
done = 0; |
| 411 |
|
|
|
| 412 |
|
|
iteration = 0; |
| 413 |
|
|
|
| 414 |
|
|
while (!done && (iteration < maxIteration)) { |
| 415 |
|
|
done = 1; |
| 416 |
|
|
|
| 417 |
|
|
for(i = 0; i < nConstrained; i++) { |
| 418 |
|
|
a = constrainedA[i]; |
| 419 |
|
|
|
| 420 |
|
|
b = constrainedB[i]; |
| 421 |
|
|
|
| 422 |
|
|
ax = (a * 3) + 0; |
| 423 |
|
|
|
| 424 |
|
|
ay = (a * 3) + 1; |
| 425 |
|
|
|
| 426 |
|
|
az = (a * 3) + 2; |
| 427 |
|
|
|
| 428 |
|
|
bx = (b * 3) + 0; |
| 429 |
|
|
|
| 430 |
|
|
by = (b * 3) + 1; |
| 431 |
|
|
|
| 432 |
|
|
bz = (b * 3) + 2; |
| 433 |
|
|
|
| 434 |
|
|
if (moved[a] || moved[b]) { |
| 435 |
|
|
posA = atoms[a]->getPos(); |
| 436 |
|
|
|
| 437 |
|
|
posB = atoms[b]->getPos(); |
| 438 |
|
|
|
| 439 |
|
|
for(j = 0; j < 3; j++) |
| 440 |
|
|
rab[j] = posA[j] - posB[j]; |
| 441 |
|
|
|
| 442 |
|
|
info->wrapVector(rab); |
| 443 |
|
|
|
| 444 |
|
|
atoms[a]->getFrc(frcA); |
| 445 |
|
|
|
| 446 |
|
|
atoms[b]->getFrc(frcB); |
| 447 |
|
|
|
| 448 |
|
|
//rma = 1.0 / atoms[a]->getMass(); |
| 449 |
|
|
|
| 450 |
|
|
//rmb = 1.0 / atoms[b]->getMass(); |
| 451 |
|
|
|
| 452 |
|
|
rma = 1.0; |
| 453 |
|
|
|
| 454 |
|
|
rmb = 1.0; |
| 455 |
|
|
|
| 456 |
|
|
fpab[0] = frcA[0] * rma - frcB[0] * rmb; |
| 457 |
|
|
|
| 458 |
|
|
fpab[1] = frcA[1] * rma - frcB[1] * rmb; |
| 459 |
|
|
|
| 460 |
|
|
fpab[2] = frcA[2] * rma - frcB[2] * rmb; |
| 461 |
|
|
|
| 462 |
|
|
gab = fpab[0] * fpab[0] + fpab[1] * fpab[1] + fpab[2] * fpab[2]; |
| 463 |
|
|
|
| 464 |
|
|
if (gab < 1.0) |
| 465 |
|
|
gab = 1.0; |
| 466 |
|
|
|
| 467 |
|
|
rabsq = rab[0] * rab[0] + rab[1] * rab[1] + rab[2] * rab[2]; |
| 468 |
|
|
|
| 469 |
|
|
rfab = rab[0] * fpab[0] + rab[1] * fpab[1] + rab[2] * fpab[2]; |
| 470 |
|
|
|
| 471 |
|
|
if (fabs(rfab) > sqrt(rabsq*gab) * 0.00001) { |
| 472 |
|
|
gab = -rfab / (rabsq * (rma + rmb)); |
| 473 |
|
|
|
| 474 |
|
|
frcA[0] = rab[0]* |
| 475 |
|
|
gab; |
| 476 |
|
|
|
| 477 |
|
|
frcA[1] = rab[1]* |
| 478 |
|
|
gab; |
| 479 |
|
|
|
| 480 |
|
|
frcA[2] = rab[2]* |
| 481 |
|
|
gab; |
| 482 |
|
|
|
| 483 |
|
|
atoms[a]->addFrc(frcA); |
| 484 |
|
|
|
| 485 |
|
|
frcB[0] = -rab[0]*gab; |
| 486 |
|
|
|
| 487 |
|
|
frcB[1] = -rab[1]*gab; |
| 488 |
|
|
|
| 489 |
|
|
frcB[2] = -rab[2]*gab; |
| 490 |
|
|
|
| 491 |
|
|
atoms[b]->addFrc(frcB); |
| 492 |
|
|
|
| 493 |
|
|
moving[a] = 1; |
| 494 |
|
|
|
| 495 |
|
|
moving[b] = 1; |
| 496 |
|
|
|
| 497 |
|
|
done = 0; |
| 498 |
|
|
} |
| 499 |
|
|
} |
| 500 |
|
|
} |
| 501 |
|
|
|
| 502 |
|
|
for(i = 0; i < nAtoms; i++) { |
| 503 |
|
|
moved[i] = moving[i]; |
| 504 |
|
|
|
| 505 |
|
|
moving[i] = 0; |
| 506 |
|
|
} |
| 507 |
|
|
|
| 508 |
|
|
iteration++; |
| 509 |
|
|
} |
| 510 |
|
|
|
| 511 |
|
|
if (!done) { |
| 512 |
|
|
std::cerr << "Waring: can not constraint within maxIteration" |
| 513 |
|
|
<< std::endl; |
| 514 |
|
|
|
| 515 |
|
|
return -1; |
| 516 |
|
|
} else |
| 517 |
|
|
return 1; |
| 518 |
|
|
} |
| 519 |
|
|
|
| 520 |
|
|
*/ |
| 521 |
|
|
|
| 522 |
|
|
//calculate the value of object function |
| 523 |
|
|
|
| 524 |
|
|
void Minimizer::calcF() { |
| 525 |
|
|
calcEnergyGradient(curX, curG, curF, egEvalStatus); |
| 526 |
|
|
} |
| 527 |
|
|
|
| 528 |
|
|
void Minimizer::calcF(std::vector < double > &x, double&f, int&status) { |
| 529 |
|
|
std::vector < double > tempG; |
| 530 |
|
|
|
| 531 |
|
|
tempG.resize(x.size()); |
| 532 |
|
|
|
| 533 |
|
|
calcEnergyGradient(x, tempG, f, status); |
| 534 |
|
|
} |
| 535 |
|
|
|
| 536 |
|
|
//calculate the gradient |
| 537 |
|
|
|
| 538 |
|
|
void Minimizer::calcG() { |
| 539 |
|
|
calcEnergyGradient(curX, curG, curF, egEvalStatus); |
| 540 |
|
|
} |
| 541 |
|
|
|
| 542 |
|
|
void Minimizer::calcG(std::vector<double>& x, std::vector<double>& g, double&f, int&status) { |
| 543 |
|
|
calcEnergyGradient(x, g, f, status); |
| 544 |
|
|
} |
| 545 |
|
|
|
| 546 |
|
|
void Minimizer::calcDim() { |
| 547 |
|
|
|
| 548 |
|
|
SimInfo::MoleculeIterator i; |
| 549 |
|
|
Molecule::IntegrableObjectIterator j; |
| 550 |
|
|
Molecule* mol; |
| 551 |
|
|
StuntDouble* integrableObject; |
| 552 |
|
|
ndim = 0; |
| 553 |
|
|
|
| 554 |
|
|
for (mol = info->beginMolecule(i); mol != NULL; mol = info->nextMolecule(i)) { |
| 555 |
|
|
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 556 |
|
|
integrableObject = mol->nextIntegrableObject(j)) { |
| 557 |
|
|
|
| 558 |
|
|
ndim += 3; |
| 559 |
|
|
|
| 560 |
|
|
if (integrableObject->isDirectional()) { |
| 561 |
|
|
ndim += 3; |
| 562 |
|
|
} |
| 563 |
|
|
} |
| 564 |
|
|
|
| 565 |
|
|
} |
| 566 |
|
|
} |
| 567 |
|
|
|
| 568 |
|
|
void Minimizer::setX(std::vector < double > &x) { |
| 569 |
|
|
if (x.size() != ndim) { |
| 570 |
|
|
sprintf(painCave.errMsg, "Minimizer Error: dimesion of x and curX does not match\n"); |
| 571 |
|
|
painCave.isFatal = 1; |
| 572 |
|
|
simError(); |
| 573 |
|
|
} |
| 574 |
|
|
|
| 575 |
|
|
curX = x; |
| 576 |
|
|
} |
| 577 |
|
|
|
| 578 |
|
|
void Minimizer::setG(std::vector < double > &g) { |
| 579 |
|
|
if (g.size() != ndim) { |
| 580 |
|
|
sprintf(painCave.errMsg, "Minimizer Error: dimesion of g and curG does not match\n"); |
| 581 |
|
|
painCave.isFatal = 1; |
| 582 |
|
|
simError(); |
| 583 |
|
|
} |
| 584 |
|
|
|
| 585 |
|
|
curG = g; |
| 586 |
|
|
} |
| 587 |
|
|
|
| 588 |
|
|
|
| 589 |
|
|
/** |
| 590 |
|
|
|
| 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 |
|
|
* @todo optimize this line search algorithm |
| 598 |
|
|
*/ |
| 599 |
|
|
|
| 600 |
|
|
int Minimizer::doLineSearch(std::vector<double> &direction, |
| 601 |
|
|
double stepSize) { |
| 602 |
|
|
|
| 603 |
|
|
std::vector<double> xa; |
| 604 |
|
|
std::vector<double> xb; |
| 605 |
|
|
std::vector<double> xc; |
| 606 |
|
|
std::vector<double> ga; |
| 607 |
|
|
std::vector<double> gb; |
| 608 |
|
|
std::vector<double> gc; |
| 609 |
|
|
double fa; |
| 610 |
|
|
double fb; |
| 611 |
|
|
double fc; |
| 612 |
|
|
double a; |
| 613 |
|
|
double b; |
| 614 |
|
|
double c; |
| 615 |
|
|
int status; |
| 616 |
|
|
double initSlope; |
| 617 |
|
|
double slopeA; |
| 618 |
|
|
double slopeB; |
| 619 |
|
|
double slopeC; |
| 620 |
|
|
bool foundLower; |
| 621 |
|
|
int iter; |
| 622 |
|
|
int maxLSIter; |
| 623 |
|
|
double mu; |
| 624 |
|
|
double eta; |
| 625 |
|
|
double ftol; |
| 626 |
|
|
double lsTol; |
| 627 |
|
|
|
| 628 |
|
|
xa.resize(ndim); |
| 629 |
|
|
xb.resize(ndim); |
| 630 |
|
|
xc.resize(ndim); |
| 631 |
|
|
ga.resize(ndim); |
| 632 |
|
|
gb.resize(ndim); |
| 633 |
|
|
gc.resize(ndim); |
| 634 |
|
|
|
| 635 |
|
|
a = 0.0; |
| 636 |
|
|
|
| 637 |
|
|
fa = curF; |
| 638 |
|
|
|
| 639 |
|
|
xa = curX; |
| 640 |
|
|
|
| 641 |
|
|
ga = curG; |
| 642 |
|
|
|
| 643 |
|
|
c = a + stepSize; |
| 644 |
|
|
|
| 645 |
|
|
ftol = paramSet->getFTol(); |
| 646 |
|
|
|
| 647 |
|
|
lsTol = paramSet->getLineSearchTol(); |
| 648 |
|
|
|
| 649 |
|
|
//calculate the derivative at a = 0 |
| 650 |
|
|
|
| 651 |
|
|
slopeA = 0; |
| 652 |
|
|
|
| 653 |
|
|
for(size_t i = 0; i < ndim; i++) { |
| 654 |
|
|
slopeA += curG[i] * direction[i]; |
| 655 |
|
|
} |
| 656 |
|
|
|
| 657 |
|
|
initSlope = slopeA; |
| 658 |
|
|
|
| 659 |
|
|
// if going uphill, use negative gradient as searching direction |
| 660 |
|
|
|
| 661 |
|
|
if (slopeA > 0) { |
| 662 |
|
|
|
| 663 |
|
|
for(size_t i = 0; i < ndim; i++) { |
| 664 |
|
|
direction[i] = -curG[i]; |
| 665 |
|
|
} |
| 666 |
|
|
|
| 667 |
|
|
for(size_t i = 0; i < ndim; i++) { |
| 668 |
|
|
slopeA += curG[i] * direction[i]; |
| 669 |
|
|
} |
| 670 |
|
|
|
| 671 |
|
|
initSlope = slopeA; |
| 672 |
|
|
} |
| 673 |
|
|
|
| 674 |
|
|
// Take a trial step |
| 675 |
|
|
|
| 676 |
|
|
for(size_t i = 0; i < ndim; i++) { |
| 677 |
|
|
xc[i] = curX[i] + direction[i]* c; |
| 678 |
|
|
} |
| 679 |
|
|
|
| 680 |
|
|
calcG(xc, gc, fc, status); |
| 681 |
|
|
|
| 682 |
|
|
if (status < 0) { |
| 683 |
|
|
if (bVerbose) |
| 684 |
|
|
std::cerr << "Function Evaluation Error" << std::endl; |
| 685 |
|
|
} |
| 686 |
|
|
|
| 687 |
|
|
//calculate the derivative at c |
| 688 |
|
|
|
| 689 |
|
|
slopeC = 0; |
| 690 |
|
|
|
| 691 |
|
|
for(size_t i = 0; i < ndim; i++) { |
| 692 |
|
|
slopeC += gc[i] * direction[i]; |
| 693 |
|
|
} |
| 694 |
|
|
// found a lower point |
| 695 |
|
|
|
| 696 |
|
|
if (fc < fa) { |
| 697 |
|
|
curX = xc; |
| 698 |
|
|
|
| 699 |
|
|
curG = gc; |
| 700 |
|
|
|
| 701 |
|
|
curF = fc; |
| 702 |
|
|
|
| 703 |
|
|
return LS_SUCCEED; |
| 704 |
|
|
} else { |
| 705 |
|
|
if (slopeC > 0) |
| 706 |
|
|
stepSize *= 0.618034; |
| 707 |
|
|
} |
| 708 |
|
|
|
| 709 |
|
|
maxLSIter = paramSet->getLineSearchMaxIteration(); |
| 710 |
|
|
|
| 711 |
|
|
iter = 0; |
| 712 |
|
|
|
| 713 |
|
|
do { |
| 714 |
|
|
|
| 715 |
|
|
// Select a new trial point. |
| 716 |
|
|
|
| 717 |
|
|
// If the derivatives at points a & c have different sign we use cubic interpolate |
| 718 |
|
|
|
| 719 |
|
|
//if (slopeC > 0){ |
| 720 |
|
|
|
| 721 |
|
|
eta = 3 * (fa - fc) / (c - a) + slopeA + slopeC; |
| 722 |
|
|
|
| 723 |
|
|
mu = sqrt(eta * eta - slopeA * slopeC); |
| 724 |
|
|
|
| 725 |
|
|
b = a + (c - a) |
| 726 |
|
|
* (1 - (slopeC + mu - eta) / (slopeC - slopeA + 2 * mu)); |
| 727 |
|
|
|
| 728 |
|
|
if (b < lsTol) { |
| 729 |
|
|
break; |
| 730 |
|
|
} |
| 731 |
|
|
|
| 732 |
|
|
//} |
| 733 |
|
|
|
| 734 |
|
|
// Take a trial step to this new point - new coords in xb |
| 735 |
|
|
|
| 736 |
|
|
for(size_t i = 0; i < ndim; i++) { |
| 737 |
|
|
xb[i] = curX[i] + direction[i]* b; |
| 738 |
|
|
} |
| 739 |
|
|
|
| 740 |
|
|
//function evaluation |
| 741 |
|
|
|
| 742 |
|
|
calcG(xb, gb, fb, status); |
| 743 |
|
|
|
| 744 |
|
|
if (status < 0) { |
| 745 |
|
|
if (bVerbose) |
| 746 |
|
|
std::cerr << "Function Evaluation Error" << std::endl; |
| 747 |
|
|
} |
| 748 |
|
|
|
| 749 |
|
|
//calculate the derivative at c |
| 750 |
|
|
|
| 751 |
|
|
slopeB = 0; |
| 752 |
|
|
|
| 753 |
|
|
for(size_t i = 0; i < ndim; i++) { |
| 754 |
|
|
slopeB += gb[i] * direction[i]; |
| 755 |
|
|
} |
| 756 |
|
|
|
| 757 |
|
|
//Amijo Rule to stop the line search |
| 758 |
|
|
|
| 759 |
|
|
if (fb <= curF + initSlope * ftol * b) { |
| 760 |
|
|
curF = fb; |
| 761 |
|
|
|
| 762 |
|
|
curX = xb; |
| 763 |
|
|
|
| 764 |
|
|
curG = gb; |
| 765 |
|
|
|
| 766 |
|
|
return LS_SUCCEED; |
| 767 |
|
|
} |
| 768 |
|
|
|
| 769 |
|
|
if (slopeB < 0 && fb < fa) { |
| 770 |
|
|
|
| 771 |
|
|
//replace a by b |
| 772 |
|
|
|
| 773 |
|
|
fa = fb; |
| 774 |
|
|
|
| 775 |
|
|
a = b; |
| 776 |
|
|
|
| 777 |
|
|
slopeA = slopeB; |
| 778 |
|
|
|
| 779 |
|
|
// swap coord a/b |
| 780 |
|
|
|
| 781 |
|
|
std::swap(xa, xb); |
| 782 |
|
|
|
| 783 |
|
|
std::swap(ga, gb); |
| 784 |
|
|
} else { |
| 785 |
|
|
|
| 786 |
|
|
//replace c by b |
| 787 |
|
|
|
| 788 |
|
|
fc = fb; |
| 789 |
|
|
|
| 790 |
|
|
c = b; |
| 791 |
|
|
|
| 792 |
|
|
slopeC = slopeB; |
| 793 |
|
|
|
| 794 |
|
|
// swap coord b/c |
| 795 |
|
|
|
| 796 |
|
|
std::swap(gb, gc); |
| 797 |
|
|
|
| 798 |
|
|
std::swap(xb, xc); |
| 799 |
|
|
} |
| 800 |
|
|
|
| 801 |
|
|
iter++; |
| 802 |
|
|
} while ((fb > fa || fb > fc) && (iter < maxLSIter)); |
| 803 |
|
|
|
| 804 |
|
|
if (fb < curF || iter >= maxLSIter) { |
| 805 |
|
|
|
| 806 |
|
|
//could not find a lower value, we might just go uphill. |
| 807 |
|
|
|
| 808 |
|
|
return LS_ERROR; |
| 809 |
|
|
} |
| 810 |
|
|
|
| 811 |
|
|
//select the end point |
| 812 |
|
|
|
| 813 |
|
|
if (fa <= fc) { |
| 814 |
|
|
curX = xa; |
| 815 |
|
|
|
| 816 |
|
|
curG = ga; |
| 817 |
|
|
|
| 818 |
|
|
curF = fa; |
| 819 |
|
|
} else { |
| 820 |
|
|
curX = xc; |
| 821 |
|
|
|
| 822 |
|
|
curG = gc; |
| 823 |
|
|
|
| 824 |
|
|
curF = fc; |
| 825 |
|
|
} |
| 826 |
|
|
|
| 827 |
|
|
return LS_SUCCEED; |
| 828 |
|
|
} |
| 829 |
|
|
|
| 830 |
|
|
void Minimizer::minimize() { |
| 831 |
|
|
int convgStatus; |
| 832 |
|
|
int stepStatus; |
| 833 |
|
|
int maxIter; |
| 834 |
|
|
int writeFrq; |
| 835 |
|
|
int nextWriteIter; |
| 836 |
|
|
Snapshot* curSnapshot =info->getSnapshotManager()->getCurrentSnapshot(); |
| 837 |
|
|
DumpWriter dumpWriter(info, info->getDumpFileName()); |
| 838 |
|
|
StatsBitSet mask; |
| 839 |
|
|
mask.set(Stats::TIME); |
| 840 |
|
|
mask.set(Stats::POTENTIAL_ENERGY); |
| 841 |
|
|
StatWriter statWriter(info->getStatFileName(), mask); |
| 842 |
|
|
|
| 843 |
|
|
init(); |
| 844 |
|
|
|
| 845 |
|
|
writeFrq = paramSet->getWriteFrq(); |
| 846 |
|
|
|
| 847 |
|
|
nextWriteIter = writeFrq; |
| 848 |
|
|
|
| 849 |
|
|
maxIter = paramSet->getMaxIteration(); |
| 850 |
|
|
|
| 851 |
|
|
for(curIter = 1; curIter <= maxIter; curIter++) { |
| 852 |
|
|
stepStatus = step(); |
| 853 |
|
|
|
| 854 |
|
|
//if (usingShake) |
| 855 |
|
|
// preMove(); |
| 856 |
|
|
|
| 857 |
|
|
if (stepStatus < 0) { |
| 858 |
|
|
saveResult(); |
| 859 |
|
|
|
| 860 |
|
|
minStatus = MIN_LSERROR; |
| 861 |
|
|
|
| 862 |
|
|
std::cerr |
| 863 |
|
|
<< "Minimizer Error: line search error, please try a small stepsize" |
| 864 |
|
|
<< std::endl; |
| 865 |
|
|
|
| 866 |
|
|
return; |
| 867 |
|
|
} |
| 868 |
|
|
|
| 869 |
|
|
//save snapshot |
| 870 |
|
|
info->getSnapshotManager()->advance(); |
| 871 |
|
|
//increase time |
| 872 |
|
|
curSnapshot->increaseTime(1); |
| 873 |
|
|
|
| 874 |
|
|
if (curIter == nextWriteIter) { |
| 875 |
|
|
nextWriteIter += writeFrq; |
| 876 |
|
|
calcF(); |
| 877 |
|
|
dumpWriter.writeDump(); |
| 878 |
|
|
statWriter.writeStat(curSnapshot->statData); |
| 879 |
|
|
} |
| 880 |
|
|
|
| 881 |
|
|
convgStatus = checkConvg(); |
| 882 |
|
|
|
| 883 |
|
|
if (convgStatus > 0) { |
| 884 |
|
|
saveResult(); |
| 885 |
|
|
|
| 886 |
|
|
minStatus = MIN_CONVERGE; |
| 887 |
|
|
|
| 888 |
|
|
return; |
| 889 |
|
|
} |
| 890 |
|
|
|
| 891 |
|
|
prepareStep(); |
| 892 |
|
|
} |
| 893 |
|
|
|
| 894 |
|
|
if (bVerbose) { |
| 895 |
|
|
std::cout << "Minimizer Warning: " << minimizerName |
| 896 |
|
|
<< " algorithm did not converge within " << maxIter << " iteration" |
| 897 |
|
|
<< std::endl; |
| 898 |
|
|
} |
| 899 |
|
|
|
| 900 |
|
|
minStatus = MIN_MAXITER; |
| 901 |
|
|
|
| 902 |
|
|
saveResult(); |
| 903 |
|
|
} |
| 904 |
|
|
|
| 905 |
|
|
|
| 906 |
|
|
double Minimizer::calcPotential() { |
| 907 |
|
|
forceMan->calcForces(true, false); |
| 908 |
|
|
|
| 909 |
|
|
Snapshot* curSnapshot = info->getSnapshotManager()->getCurrentSnapshot(); |
| 910 |
|
|
double potential_local = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] + |
| 911 |
|
|
curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ; |
| 912 |
|
|
double potential; |
| 913 |
|
|
|
| 914 |
|
|
#ifdef IS_MPI |
| 915 |
|
|
MPI_Allreduce(&potential_local, &potential, 1, MPI_DOUBLE, MPI_SUM, |
| 916 |
|
|
MPI_COMM_WORLD); |
| 917 |
|
|
#else |
| 918 |
|
|
potential = potential_local; |
| 919 |
|
|
#endif |
| 920 |
|
|
|
| 921 |
|
|
//save total potential |
| 922 |
|
|
curSnapshot->statData[Stats::POTENTIAL_ENERGY] = potential; |
| 923 |
|
|
return potential; |
| 924 |
|
|
} |
| 925 |
|
|
|
| 926 |
|
|
} |
