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tim |
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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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atoms = info->atoms; |
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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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//save the reference coordinate |
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RealIntegrator::preMove(); |
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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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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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if (nConstrained){ |
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shakeR(); |
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} |
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calcForce(1, 1); |
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if (nConstrained){ |
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shakeF(); |
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} |
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x = getCoor(); |
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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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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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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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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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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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DirectionalAtom* dAtom; |
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dim = 0; |
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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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} |
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//remove constraint force along the bond direction |
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void OOPSEMinimizerBase::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, ax, ay, az, bx, 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; |
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} |
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done = 0; |
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iteration = 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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atoms[a]->getPos(posA); |
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atoms[b]->getPos(posB); |
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for (j = 0; j < 3; j++) |
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rab[j] = posA[j] - posB[j]; |
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info->wrapVector(rab); |
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atoms[a]->getFrc(frcA); |
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atoms[b]->getFrc(frcB); |
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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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fpab[0] = frcA[0] * rma - frcB[0] * rmb; |
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fpab[1] = frcA[1] * rma - frcB[1] * rmb; |
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fpab[2] = frcA[2] * rma - frcB[2] * rmb; |
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gab=fpab[0] * fpab[0] + fpab[1] * fpab[1] + fpab[2] * fpab[2]; |
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if (gab < 1.0) |
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gab = 1.0; |
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rabsq = rab[0] * rab[0] + rab[1] * rab[1] + rab[2] * rab[2]; |
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rfab = rab[0] * fpab[0] + rab[1] * fpab[1] + rab[2] * fpab[2]; |
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if (fabs(rfab) > sqrt(rabsq*gab) * 0.00001){ |
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gab = -rfab /(rabsq*(rma + rmb)); |
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frcA[0] = rab[0] * gab; |
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frcA[1] = rab[1] * gab; |
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frcA[2] = rab[2] * gab; |
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atoms[a]->addFrc(frcA); |
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frcB[0] = -rab[0] * gab; |
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frcB[1] = -rab[1] * gab; |
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frcB[2] = -rab[2] * gab; |
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atoms[b]->addFrc(frcB); |
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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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} |
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void OOPSEMinimizerBase::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, ax, ay, az, bx, by, bz; |
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double rma, rmb; |
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double dx, dy, dz; |
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double rpab; |
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double rabsq, pabsq, 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 < 2*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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atoms[a]->getPos(posA); |
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atoms[b]->getPos(posB); |
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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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//cerr << "Waring: constraint failure" << endl; |
| 353 |
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gab = sqrt(rabsq/pabsq); |
| 354 |
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rab[0] = (posA[0] - posB[0])*gab; |
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rab[1]= (posA[1] - posB[1])*gab; |
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rab[2] = (posA[2] - posB[2])*gab; |
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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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} |
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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] * gab; |
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dy = rab[1] * gab; |
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dz = rab[2] * 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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| 381 |
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posB[0] -= rmb * dx; |
| 382 |
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posB[1] -= rmb * dy; |
| 383 |
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posB[2] -= rmb * dz; |
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| 385 |
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atoms[b]->setPos(posB); |
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| 387 |
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moving[a] = 1; |
| 388 |
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moving[b] = 1; |
| 389 |
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done = 0; |
| 390 |
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} |
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} |
| 392 |
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} |
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for (i = 0; i < nAtoms; i++){ |
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|
|
moved[i] = moving[i]; |
| 396 |
|
|
moving[i] = 0; |
| 397 |
|
|
} |
| 398 |
|
|
|
| 399 |
|
|
iteration++; |
| 400 |
|
|
} |
| 401 |
|
|
|
| 402 |
|
|
if (!done) |
| 403 |
|
|
cerr << "Waring: can not constraint within maxIteration" << endl; |
| 404 |
|
|
} |
