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#include "Integrator.hpp"
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OOPSEMinimizerBase::OOPSEMinimizerBase(SimInfo* theInfo, ForceFields* the_ff)
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: RealIntegrator( theInfo, the_ff ){
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tStats = new Thermo(info);
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dumpOut = new DumpWriter(info);
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statOut = new StatWriter(info);
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calcDim();
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}
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OOPSEMinimizerBase::~OOPSEMinimizerBase(){
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delete tStats;
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delete dumpOut;
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delete statOut;
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}
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/**
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*
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*/
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double OOPSEMinimizerBase::calcGradient(vector<double>& x, vector<double>& grad){
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Atom** atoms;
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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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setCoor(x);
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calcForce(1, 1);
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atoms = info->atoms;
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index = 0;
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for(int i = 0; i < nAtoms; i++){
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if(atoms[i]->isDirectional()){
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dAtom = (DirectionalAtom*) atoms[i];
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dAtom->getGrad(dAtomGrad);
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//gradient = du/dx = -f
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grad[index++] = -dAtomGrad[0];
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grad[index++] = -dAtomGrad[1];
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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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grad[index++] = dAtomGrad[5];
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}
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else{
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atoms[i]->getFrc(force);
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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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return tStats->getPotential();
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}
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/**
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*
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*/
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void OOPSEMinimizerBase::setCoor(vector<double>& x){
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Atom** atoms;
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DirectionalAtom* dAtom;
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int index;
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double position[3];
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double eulerAngle[3];
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atoms = info->atoms;
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index = 0;
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for(int i = 0; i < nAtoms; i++){
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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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atoms[i]->setPos(position);
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if (atoms[i]->isDirectional()){
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dAtom = (DirectionalAtom*) atoms[i];
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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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dAtom->setEuler(eulerAngle[0], eulerAngle[1], eulerAngle[2]);
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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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vector<double> OOPSEMinimizerBase::getCoor(){
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Atom** atoms;
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DirectionalAtom* dAtom;
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int index;
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double position[3];
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double eulerAngle[3];
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vector<double> x;
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x.resize(getDim());
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atoms = info->atoms;
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index = 0;
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for(int i = 0; i < nAtoms; i++){
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atoms[i]->getPos(position);
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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 (atoms[i]->isDirectional()){
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dAtom = (DirectionalAtom*) atoms[i];
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dAtom->getEulerAngles(eulerAngle);
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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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return x;
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}
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void OOPSEMinimizerBase::calcDim(){
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Atom** atoms;
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DirectionalAtom* dAtom;
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dim = 0;
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atoms = info->atoms;
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for(int i = 0; i < nAtoms; i++){
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dim += 3;
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if (atoms[i]->isDirectional())
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dim += 3;
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}
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}
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void OOPSEMinimizerBase::output(vector<double>& x, int iteration){
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setCoor(x);
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calcForce(1, 1);
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dumpOut->writeDump(iteration);
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statOut->writeStat(iteration);
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} |
