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#include "Integrator.hpp" |
| 2 |
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|
| 3 |
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OOPSEMinimizerBase::OOPSEMinimizerBase(SimInfo* theInfo, ForceFields* the_ff) |
| 4 |
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: RealIntegrator( theInfo, the_ff ){ |
| 5 |
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tStats = new Thermo(info); |
| 6 |
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dumpOut = new DumpWriter(info); |
| 7 |
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calcDim(); |
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} |
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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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} |
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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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double OOPSEMinimizerBase::calcGradient(vector<double>& x, vector<double>& grad){ |
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Atom** atoms; |
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DirectionalAtom* dAtom; |
| 23 |
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int index; |
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double force[3]; |
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double dAtomGrad[6]; |
| 26 |
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|
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setOptCoor(x); |
| 28 |
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|
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atoms = this->atoms; |
| 30 |
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index = 0; |
| 31 |
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|
| 32 |
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for(int i = 0; i < nAtoms; i++){ |
| 33 |
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|
| 34 |
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if(atoms[i]->isDirectional()){ |
| 35 |
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dAtom = (DirectionalAtom*) atoms[i]; |
| 36 |
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dAtom->getGrad(dAtomGrad); |
| 37 |
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|
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grad[index++] = dAtomGrad[0]; |
| 39 |
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grad[index++] = dAtomGrad[1]; |
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grad[index++] = dAtomGrad[2]; |
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grad[index++] = dAtomGrad[3]; |
| 42 |
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grad[index++] = dAtomGrad[4]; |
| 43 |
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grad[index++] = dAtomGrad[5]; |
| 44 |
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|
| 45 |
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} |
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else{ |
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atoms[i]->getFrc(force); |
| 48 |
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|
| 49 |
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grad[index++] = force[0]; |
| 50 |
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grad[index++] = force[1]; |
| 51 |
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grad[index++] = force[2]; |
| 52 |
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|
| 53 |
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} |
| 54 |
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|
| 55 |
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} |
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|
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return tStats->getPotential(); |
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|
| 59 |
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} |
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|
| 61 |
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/** |
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* |
| 63 |
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*/ |
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|
| 65 |
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void OOPSEMinimizerBase::setOptCoor(vector<double>& x){ |
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Atom** atoms; |
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DirectionalAtom* dAtom; |
| 68 |
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int index; |
| 69 |
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double position[3]; |
| 70 |
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double eulerAngle[3]; |
| 71 |
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|
| 72 |
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atoms = this->atoms; |
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index = 0; |
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|
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for(int i = 0; i < nAtoms; i++){ |
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|
| 77 |
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position[0] = x[index++]; |
| 78 |
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position[1] = x[index++]; |
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position[2] = x[index++]; |
| 80 |
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|
| 81 |
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atoms[i]->setPos(position); |
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|
| 83 |
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if (atoms[i]->isDirectional()){ |
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dAtom = (DirectionalAtom*) atoms[i]; |
| 85 |
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|
| 86 |
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eulerAngle[0] = x[index++]; |
| 87 |
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eulerAngle[1] = x[index++]; |
| 88 |
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eulerAngle[2] = x[index++]; |
| 89 |
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|
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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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|
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/** |
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* |
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*/ |
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vector<double> OOPSEMinimizerBase::getOptCoor(){ |
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Atom** atoms; |
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DirectionalAtom* dAtom; |
| 104 |
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int index; |
| 105 |
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double position[3]; |
| 106 |
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double eulerAngle[3]; |
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vector<double> x; |
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|
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x.resize(getDim()); |
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atoms = this->atoms; |
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index = 0; |
| 112 |
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|
| 113 |
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for(int i = 0; i < nAtoms; i++){ |
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atoms[i]->getPos(position); |
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|
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x[index++] = position[0]; |
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x[index++] = position[1]; |
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x[index++] = position[2]; |
| 119 |
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|
| 120 |
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if (atoms[i]->isDirectional()){ |
| 121 |
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dAtom = (DirectionalAtom*) atoms[i]; |
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dAtom->getEulerAngles(eulerAngle); |
| 123 |
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|
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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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} |
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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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void OOPSEMinimizerBase::calcDim(){ |
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Atom** atoms; |
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DirectionalAtom* dAtom; |
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int dim; |
| 140 |
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|
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dim = 0; |
| 142 |
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|
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atoms = this->atoms; |
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|
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for(int i = 0; i < nAtoms; i++){ |
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dim += 3; |
| 147 |
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if (atoms[i]->isDirectional()) |
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dim += 3; |
| 149 |
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} |
| 150 |
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|
| 151 |
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} |
| 152 |
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|
| 153 |
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void OOPSEMinimizerBase::output(vector<double>& x, int iteration){ |
| 154 |
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setOptCoor(x); |
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dumpOut->writeDump(iteration); |
| 156 |
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} |
| 1 |
> |
#include "Integrator.hpp" |
| 2 |
> |
|
| 3 |
> |
OOPSEMinimizerBase::OOPSEMinimizerBase(SimInfo* theInfo, ForceFields* the_ff) |
| 4 |
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: RealIntegrator( theInfo, the_ff ){ |
| 5 |
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atoms = info->atoms; |
| 6 |
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tStats = new Thermo(info); |
| 7 |
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dumpOut = new DumpWriter(info); |
| 8 |
> |
statOut = new StatWriter(info); |
| 9 |
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calcDim(); |
| 10 |
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|
| 11 |
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//save the reference coordinate |
| 12 |
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RealIntegrator::preMove(); |
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|
| 14 |
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} |
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|
| 16 |
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OOPSEMinimizerBase::~OOPSEMinimizerBase(){ |
| 17 |
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delete tStats; |
| 18 |
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delete dumpOut; |
| 19 |
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delete statOut; |
| 20 |
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} |
| 21 |
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|
| 22 |
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/** |
| 23 |
> |
* |
| 24 |
> |
*/ |
| 25 |
> |
|
| 26 |
> |
|
| 27 |
> |
double OOPSEMinimizerBase::calcGradient(vector<double>& x, vector<double>& grad){ |
| 28 |
> |
|
| 29 |
> |
DirectionalAtom* dAtom; |
| 30 |
> |
int index; |
| 31 |
> |
double force[3]; |
| 32 |
> |
double dAtomGrad[6]; |
| 33 |
> |
|
| 34 |
> |
setCoor(x); |
| 35 |
> |
|
| 36 |
> |
if (nConstrained){ |
| 37 |
> |
shakeR(); |
| 38 |
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} |
| 39 |
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|
| 40 |
> |
calcForce(1, 1); |
| 41 |
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|
| 42 |
> |
if (nConstrained){ |
| 43 |
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shakeF(); |
| 44 |
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} |
| 45 |
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|
| 46 |
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x = getCoor(); |
| 47 |
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|
| 48 |
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|
| 49 |
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index = 0; |
| 50 |
> |
|
| 51 |
> |
for(int i = 0; i < nAtoms; i++){ |
| 52 |
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|
| 53 |
> |
if(atoms[i]->isDirectional()){ |
| 54 |
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dAtom = (DirectionalAtom*) atoms[i]; |
| 55 |
> |
dAtom->getGrad(dAtomGrad); |
| 56 |
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|
| 57 |
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//gradient = du/dx = -f |
| 58 |
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grad[index++] = -dAtomGrad[0]; |
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grad[index++] = -dAtomGrad[1]; |
| 60 |
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grad[index++] = -dAtomGrad[2]; |
| 61 |
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grad[index++] = -dAtomGrad[3]; |
| 62 |
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grad[index++] = -dAtomGrad[4]; |
| 63 |
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grad[index++] = -dAtomGrad[5]; |
| 64 |
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|
| 65 |
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} |
| 66 |
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else{ |
| 67 |
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atoms[i]->getFrc(force); |
| 68 |
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|
| 69 |
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grad[index++] = -force[0]; |
| 70 |
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grad[index++] = -force[1]; |
| 71 |
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grad[index++] = -force[2]; |
| 72 |
> |
|
| 73 |
> |
} |
| 74 |
> |
|
| 75 |
> |
} |
| 76 |
> |
|
| 77 |
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return tStats->getPotential(); |
| 78 |
> |
|
| 79 |
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} |
| 80 |
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|
| 81 |
> |
/** |
| 82 |
> |
* |
| 83 |
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*/ |
| 84 |
> |
|
| 85 |
> |
void OOPSEMinimizerBase::setCoor(vector<double>& x){ |
| 86 |
> |
|
| 87 |
> |
DirectionalAtom* dAtom; |
| 88 |
> |
int index; |
| 89 |
> |
double position[3]; |
| 90 |
> |
double eulerAngle[3]; |
| 91 |
> |
|
| 92 |
> |
|
| 93 |
> |
index = 0; |
| 94 |
> |
|
| 95 |
> |
for(int i = 0; i < nAtoms; i++){ |
| 96 |
> |
|
| 97 |
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position[0] = x[index++]; |
| 98 |
> |
position[1] = x[index++]; |
| 99 |
> |
position[2] = x[index++]; |
| 100 |
> |
|
| 101 |
> |
atoms[i]->setPos(position); |
| 102 |
> |
|
| 103 |
> |
if (atoms[i]->isDirectional()){ |
| 104 |
> |
dAtom = (DirectionalAtom*) atoms[i]; |
| 105 |
> |
|
| 106 |
> |
eulerAngle[0] = x[index++]; |
| 107 |
> |
eulerAngle[1] = x[index++]; |
| 108 |
> |
eulerAngle[2] = x[index++]; |
| 109 |
> |
|
| 110 |
> |
dAtom->setEuler(eulerAngle[0], eulerAngle[1], eulerAngle[2]); |
| 111 |
> |
|
| 112 |
> |
} |
| 113 |
> |
|
| 114 |
> |
} |
| 115 |
> |
|
| 116 |
> |
} |
| 117 |
> |
|
| 118 |
> |
/** |
| 119 |
> |
* |
| 120 |
> |
*/ |
| 121 |
> |
vector<double> OOPSEMinimizerBase::getCoor(){ |
| 122 |
> |
|
| 123 |
> |
DirectionalAtom* dAtom; |
| 124 |
> |
int index; |
| 125 |
> |
double position[3]; |
| 126 |
> |
double eulerAngle[3]; |
| 127 |
> |
vector<double> x; |
| 128 |
> |
|
| 129 |
> |
x.resize(getDim()); |
| 130 |
> |
|
| 131 |
> |
index = 0; |
| 132 |
> |
|
| 133 |
> |
for(int i = 0; i < nAtoms; i++){ |
| 134 |
> |
atoms[i]->getPos(position); |
| 135 |
> |
|
| 136 |
> |
x[index++] = position[0]; |
| 137 |
> |
x[index++] = position[1]; |
| 138 |
> |
x[index++] = position[2]; |
| 139 |
> |
|
| 140 |
> |
if (atoms[i]->isDirectional()){ |
| 141 |
> |
dAtom = (DirectionalAtom*) atoms[i]; |
| 142 |
> |
dAtom->getEulerAngles(eulerAngle); |
| 143 |
> |
|
| 144 |
> |
x[index++] = eulerAngle[0]; |
| 145 |
> |
x[index++] = eulerAngle[1]; |
| 146 |
> |
x[index++] = eulerAngle[2]; |
| 147 |
> |
|
| 148 |
> |
} |
| 149 |
> |
|
| 150 |
> |
} |
| 151 |
> |
|
| 152 |
> |
return x; |
| 153 |
> |
|
| 154 |
> |
} |
| 155 |
> |
|
| 156 |
> |
void OOPSEMinimizerBase::calcDim(){ |
| 157 |
> |
|
| 158 |
> |
DirectionalAtom* dAtom; |
| 159 |
> |
|
| 160 |
> |
dim = 0; |
| 161 |
> |
|
| 162 |
> |
for(int i = 0; i < nAtoms; i++){ |
| 163 |
> |
dim += 3; |
| 164 |
> |
if (atoms[i]->isDirectional()) |
| 165 |
> |
dim += 3; |
| 166 |
> |
} |
| 167 |
> |
|
| 168 |
> |
} |
| 169 |
> |
|
| 170 |
> |
void OOPSEMinimizerBase::output(vector<double>& x, int iteration){ |
| 171 |
> |
setCoor(x); |
| 172 |
> |
calcForce(1, 1); |
| 173 |
> |
dumpOut->writeDump(iteration); |
| 174 |
> |
statOut->writeStat(iteration); |
| 175 |
> |
} |
| 176 |
> |
|
| 177 |
> |
|
| 178 |
> |
//remove constraint force along the bond direction |
| 179 |
> |
void OOPSEMinimizerBase::shakeF(){ |
| 180 |
> |
int i, j; |
| 181 |
> |
int done; |
| 182 |
> |
double posA[3], posB[3]; |
| 183 |
> |
double frcA[3], frcB[3]; |
| 184 |
> |
double rab[3], fpab[3]; |
| 185 |
> |
int a, b, ax, ay, az, bx, by, bz; |
| 186 |
> |
double rma, rmb; |
| 187 |
> |
double rvab; |
| 188 |
> |
double gab; |
| 189 |
> |
double rabsq; |
| 190 |
> |
double rfab; |
| 191 |
> |
int iteration; |
| 192 |
> |
|
| 193 |
> |
for (i = 0; i < nAtoms; i++){ |
| 194 |
> |
moving[i] = 0; |
| 195 |
> |
moved[i] = 1; |
| 196 |
> |
} |
| 197 |
> |
|
| 198 |
> |
done = 0; |
| 199 |
> |
iteration = 0; |
| 200 |
> |
while (!done && (iteration < maxIteration)){ |
| 201 |
> |
done = 1; |
| 202 |
> |
|
| 203 |
> |
for (i = 0; i < nConstrained; i++){ |
| 204 |
> |
a = constrainedA[i]; |
| 205 |
> |
b = constrainedB[i]; |
| 206 |
> |
|
| 207 |
> |
ax = (a * 3) + 0; |
| 208 |
> |
ay = (a * 3) + 1; |
| 209 |
> |
az = (a * 3) + 2; |
| 210 |
> |
|
| 211 |
> |
bx = (b * 3) + 0; |
| 212 |
> |
by = (b * 3) + 1; |
| 213 |
> |
bz = (b * 3) + 2; |
| 214 |
> |
|
| 215 |
> |
if (moved[a] || moved[b]){ |
| 216 |
> |
|
| 217 |
> |
atoms[a]->getPos(posA); |
| 218 |
> |
atoms[b]->getPos(posB); |
| 219 |
> |
|
| 220 |
> |
for (j = 0; j < 3; j++) |
| 221 |
> |
rab[j] = posA[j] - posB[j]; |
| 222 |
> |
|
| 223 |
> |
info->wrapVector(rab); |
| 224 |
> |
|
| 225 |
> |
atoms[a]->getFrc(frcA); |
| 226 |
> |
atoms[b]->getFrc(frcB); |
| 227 |
> |
|
| 228 |
> |
//rma = 1.0 / atoms[a]->getMass(); |
| 229 |
> |
//rmb = 1.0 / atoms[b]->getMass(); |
| 230 |
> |
rma = 1.0; |
| 231 |
> |
rmb = 1.0; |
| 232 |
> |
|
| 233 |
> |
|
| 234 |
> |
fpab[0] = frcA[0] * rma - frcB[0] * rmb; |
| 235 |
> |
fpab[1] = frcA[1] * rma - frcB[1] * rmb; |
| 236 |
> |
fpab[2] = frcA[2] * rma - frcB[2] * rmb; |
| 237 |
> |
|
| 238 |
> |
|
| 239 |
> |
gab=fpab[0] * fpab[0] + fpab[1] * fpab[1] + fpab[2] * fpab[2]; |
| 240 |
> |
|
| 241 |
> |
if (gab < 1.0) |
| 242 |
> |
gab = 1.0; |
| 243 |
> |
|
| 244 |
> |
rabsq = rab[0] * rab[0] + rab[1] * rab[1] + rab[2] * rab[2]; |
| 245 |
> |
rfab = rab[0] * fpab[0] + rab[1] * fpab[1] + rab[2] * fpab[2]; |
| 246 |
> |
|
| 247 |
> |
if (fabs(rfab) > sqrt(rabsq*gab) * 0.00001){ |
| 248 |
> |
|
| 249 |
> |
gab = -rfab /(rabsq*(rma + rmb)); |
| 250 |
> |
|
| 251 |
> |
frcA[0] = rab[0] * gab; |
| 252 |
> |
frcA[1] = rab[1] * gab; |
| 253 |
> |
frcA[2] = rab[2] * gab; |
| 254 |
> |
|
| 255 |
> |
atoms[a]->addFrc(frcA); |
| 256 |
> |
|
| 257 |
> |
|
| 258 |
> |
frcB[0] = -rab[0] * gab; |
| 259 |
> |
frcB[1] = -rab[1] * gab; |
| 260 |
> |
frcB[2] = -rab[2] * gab; |
| 261 |
> |
|
| 262 |
> |
atoms[b]->addFrc(frcB); |
| 263 |
> |
|
| 264 |
> |
moving[a] = 1; |
| 265 |
> |
moving[b] = 1; |
| 266 |
> |
done = 0; |
| 267 |
> |
} |
| 268 |
> |
} |
| 269 |
> |
} |
| 270 |
> |
|
| 271 |
> |
for (i = 0; i < nAtoms; i++){ |
| 272 |
> |
moved[i] = moving[i]; |
| 273 |
> |
moving[i] = 0; |
| 274 |
> |
} |
| 275 |
> |
|
| 276 |
> |
iteration++; |
| 277 |
> |
} |
| 278 |
> |
|
| 279 |
> |
} |
| 280 |
> |
|
| 281 |
> |
void OOPSEMinimizerBase::shakeR(){ |
| 282 |
> |
int i, j; |
| 283 |
> |
int done; |
| 284 |
> |
double posA[3], posB[3]; |
| 285 |
> |
double velA[3], velB[3]; |
| 286 |
> |
double pab[3]; |
| 287 |
> |
double rab[3]; |
| 288 |
> |
int a, b, ax, ay, az, bx, by, bz; |
| 289 |
> |
double rma, rmb; |
| 290 |
> |
double dx, dy, dz; |
| 291 |
> |
double rpab; |
| 292 |
> |
double rabsq, pabsq, rpabsq; |
| 293 |
> |
double diffsq; |
| 294 |
> |
double gab; |
| 295 |
> |
int iteration; |
| 296 |
> |
|
| 297 |
> |
for (i = 0; i < nAtoms; i++){ |
| 298 |
> |
moving[i] = 0; |
| 299 |
> |
moved[i] = 1; |
| 300 |
> |
} |
| 301 |
> |
|
| 302 |
> |
iteration = 0; |
| 303 |
> |
done = 0; |
| 304 |
> |
while (!done && (iteration < 2*maxIteration)){ |
| 305 |
> |
done = 1; |
| 306 |
> |
for (i = 0; i < nConstrained; i++){ |
| 307 |
> |
a = constrainedA[i]; |
| 308 |
> |
b = constrainedB[i]; |
| 309 |
> |
|
| 310 |
> |
ax = (a * 3) + 0; |
| 311 |
> |
ay = (a * 3) + 1; |
| 312 |
> |
az = (a * 3) + 2; |
| 313 |
> |
|
| 314 |
> |
bx = (b * 3) + 0; |
| 315 |
> |
by = (b * 3) + 1; |
| 316 |
> |
bz = (b * 3) + 2; |
| 317 |
> |
|
| 318 |
> |
if (moved[a] || moved[b]){ |
| 319 |
> |
atoms[a]->getPos(posA); |
| 320 |
> |
atoms[b]->getPos(posB); |
| 321 |
> |
|
| 322 |
> |
for (j = 0; j < 3; j++) |
| 323 |
> |
pab[j] = posA[j] - posB[j]; |
| 324 |
> |
|
| 325 |
> |
//periodic boundary condition |
| 326 |
> |
|
| 327 |
> |
info->wrapVector(pab); |
| 328 |
> |
|
| 329 |
> |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
| 330 |
> |
|
| 331 |
> |
rabsq = constrainedDsqr[i]; |
| 332 |
> |
diffsq = rabsq - pabsq; |
| 333 |
> |
|
| 334 |
> |
// the original rattle code from alan tidesley |
| 335 |
> |
if (fabs(diffsq) > (tol * rabsq * 2)){ |
| 336 |
> |
rab[0] = oldPos[ax] - oldPos[bx]; |
| 337 |
> |
rab[1] = oldPos[ay] - oldPos[by]; |
| 338 |
> |
rab[2] = oldPos[az] - oldPos[bz]; |
| 339 |
> |
|
| 340 |
> |
info->wrapVector(rab); |
| 341 |
> |
|
| 342 |
> |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
| 343 |
> |
|
| 344 |
> |
rpabsq = rpab * rpab; |
| 345 |
> |
|
| 346 |
> |
|
| 347 |
> |
if (rpabsq < (rabsq * -diffsq)){ |
| 348 |
> |
#ifdef IS_MPI |
| 349 |
> |
a = atoms[a]->getGlobalIndex(); |
| 350 |
> |
b = atoms[b]->getGlobalIndex(); |
| 351 |
> |
#endif //is_mpi |
| 352 |
> |
//cerr << "Waring: constraint failure" << endl; |
| 353 |
> |
gab = sqrt(rabsq/pabsq); |
| 354 |
> |
rab[0] = (posA[0] - posB[0])*gab; |
| 355 |
> |
rab[1]= (posA[1] - posB[1])*gab; |
| 356 |
> |
rab[2] = (posA[2] - posB[2])*gab; |
| 357 |
> |
|
| 358 |
> |
info->wrapVector(rab); |
| 359 |
> |
|
| 360 |
> |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
| 361 |
> |
|
| 362 |
> |
} |
| 363 |
> |
|
| 364 |
> |
//rma = 1.0 / atoms[a]->getMass(); |
| 365 |
> |
//rmb = 1.0 / atoms[b]->getMass(); |
| 366 |
> |
rma = 1.0; |
| 367 |
> |
rmb =1.0; |
| 368 |
> |
|
| 369 |
> |
gab = diffsq / (2.0 * (rma + rmb) * rpab); |
| 370 |
> |
|
| 371 |
> |
dx = rab[0] * gab; |
| 372 |
> |
dy = rab[1] * gab; |
| 373 |
> |
dz = rab[2] * gab; |
| 374 |
> |
|
| 375 |
> |
posA[0] += rma * dx; |
| 376 |
> |
posA[1] += rma * dy; |
| 377 |
> |
posA[2] += rma * dz; |
| 378 |
> |
|
| 379 |
> |
atoms[a]->setPos(posA); |
| 380 |
> |
|
| 381 |
> |
posB[0] -= rmb * dx; |
| 382 |
> |
posB[1] -= rmb * dy; |
| 383 |
> |
posB[2] -= rmb * dz; |
| 384 |
> |
|
| 385 |
> |
atoms[b]->setPos(posB); |
| 386 |
> |
|
| 387 |
> |
moving[a] = 1; |
| 388 |
> |
moving[b] = 1; |
| 389 |
> |
done = 0; |
| 390 |
> |
} |
| 391 |
> |
} |
| 392 |
> |
} |
| 393 |
> |
|
| 394 |
> |
for (i = 0; i < nAtoms; i++){ |
| 395 |
> |
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 |
> |
} |
