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namespace OpenMD{ |
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PotentialEnergyObjectiveFunction::PotentialEnergyObjectiveFunction(SimInfo* info, ForceManager* forceMan) |
| 48 |
< |
: info_(info), forceMan_(forceMan), thermo(info) { |
| 48 |
> |
: info_(info), forceMan_(forceMan), thermo(info) { |
| 49 |
> |
shake_ = new Shake(info_); |
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} |
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RealType PotentialEnergyObjectiveFunction::value(const DynamicVector<RealType>& x) { |
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setCoor(x); |
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+ |
shake_->constraintR(); |
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forceMan_->calcForces(); |
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+ |
shake_->constraintF(); |
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return thermo.getPotential(); |
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} |
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void PotentialEnergyObjectiveFunction::gradient(DynamicVector<RealType>& grad, const DynamicVector<RealType>& x) { |
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| 64 |
< |
setCoor(x); |
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< |
forceMan_->calcForces(); |
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< |
getGrad(grad); |
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> |
setCoor(x); |
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> |
shake_->constraintR(); |
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> |
forceMan_->calcForces(); |
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> |
shake_->constraintF(); |
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> |
getGrad(grad); |
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} |
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RealType PotentialEnergyObjectiveFunction::valueAndGradient(DynamicVector<RealType>& grad, |
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const DynamicVector<RealType>& x) { |
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< |
|
| 74 |
< |
setCoor(x); |
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< |
forceMan_->calcForces(); |
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> |
setCoor(x); |
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> |
shake_->constraintR(); |
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> |
forceMan_->calcForces(); |
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> |
shake_->constraintF(); |
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getGrad(grad); |
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return thermo.getPotential(); |
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} |
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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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> |
StuntDouble* sd; |
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int index = 0; |
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|
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for (mol = info_->beginMolecule(i); mol != NULL; |
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mol = info_->nextMolecule(i)) { |
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< |
for (integrableObject = mol->beginIntegrableObject(j); |
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< |
integrableObject != NULL; |
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< |
integrableObject = mol->nextIntegrableObject(j)) { |
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> |
|
| 93 |
> |
for (sd = mol->beginIntegrableObject(j); sd != NULL; |
| 94 |
> |
sd = mol->nextIntegrableObject(j)) { |
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|
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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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|
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< |
integrableObject->setPos(position); |
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> |
sd->setPos(position); |
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| 102 |
< |
if (integrableObject->isDirectional()) { |
| 102 |
> |
if (sd->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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|
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< |
integrableObject->setEuler(eulerAngle); |
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< |
} |
| 107 |
> |
sd->setEuler(eulerAngle); |
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> |
|
| 109 |
> |
if (sd->isRigidBody()) { |
| 110 |
> |
RigidBody* rb = static_cast<RigidBody*>(sd); |
| 111 |
> |
rb->updateAtoms(); |
| 112 |
> |
} |
| 113 |
> |
|
| 114 |
> |
} |
| 115 |
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} |
| 116 |
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} |
| 117 |
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} |
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SimInfo::MoleculeIterator i; |
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Molecule::IntegrableObjectIterator j; |
| 122 |
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Molecule* mol; |
| 123 |
< |
StuntDouble* integrableObject; |
| 123 |
> |
StuntDouble* sd; |
| 124 |
|
std::vector<RealType> myGrad; |
| 125 |
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|
| 126 |
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int index = 0; |
| 127 |
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|
| 128 |
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for (mol = info_->beginMolecule(i); mol != NULL; |
| 129 |
|
mol = info_->nextMolecule(i)) { |
| 130 |
< |
for (integrableObject = mol->beginIntegrableObject(j); |
| 131 |
< |
integrableObject != NULL; |
| 132 |
< |
integrableObject = mol->nextIntegrableObject(j)) { |
| 133 |
< |
myGrad = integrableObject->getGrad(); |
| 134 |
< |
for (size_t k = 0; k < myGrad.size(); ++k) { |
| 130 |
> |
|
| 131 |
> |
for (sd = mol->beginIntegrableObject(j); sd != NULL; |
| 132 |
> |
sd = mol->nextIntegrableObject(j)) { |
| 133 |
> |
|
| 134 |
> |
myGrad = sd->getGrad(); |
| 135 |
> |
|
| 136 |
> |
for (size_t k = 0; k < myGrad.size(); ++k) { |
| 137 |
|
grad[index++] = myGrad[k]; |
| 138 |
|
} |
| 139 |
+ |
|
| 140 |
|
} |
| 141 |
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} |
| 142 |
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} |
| 145 |
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SimInfo::MoleculeIterator i; |
| 146 |
|
Molecule::IntegrableObjectIterator j; |
| 147 |
|
Molecule* mol; |
| 148 |
< |
StuntDouble* integrableObject; |
| 148 |
> |
StuntDouble* sd; |
| 149 |
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|
| 150 |
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Vector3d pos; |
| 151 |
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Vector3d eulerAngle; |
| 156 |
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|
| 157 |
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for (mol = info_->beginMolecule(i); mol != NULL; |
| 158 |
|
mol = info_->nextMolecule(i)) { |
| 144 |
– |
for (integrableObject = mol->beginIntegrableObject(j); |
| 145 |
– |
integrableObject != NULL; |
| 146 |
– |
integrableObject = mol->nextIntegrableObject(j)) { |
| 159 |
|
|
| 160 |
< |
pos = integrableObject->getPos(); |
| 160 |
> |
for (sd = mol->beginIntegrableObject(j); sd != NULL; |
| 161 |
> |
sd = mol->nextIntegrableObject(j)) { |
| 162 |
|
|
| 163 |
+ |
pos = sd->getPos(); |
| 164 |
+ |
|
| 165 |
|
xinit[index++] = pos[0]; |
| 166 |
|
xinit[index++] = pos[1]; |
| 167 |
|
xinit[index++] = pos[2]; |
| 168 |
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|
| 169 |
< |
if (integrableObject->isDirectional()) { |
| 170 |
< |
eulerAngle = integrableObject->getEuler(); |
| 169 |
> |
if (sd->isDirectional()) { |
| 170 |
> |
eulerAngle = sd->getEuler(); |
| 171 |
|
xinit[index++] = eulerAngle[0]; |
| 172 |
|
xinit[index++] = eulerAngle[1]; |
| 173 |
|
xinit[index++] = eulerAngle[2]; |
| 174 |
|
} |
| 175 |
+ |
|
| 176 |
|
} |
| 177 |
|
} |
| 178 |
|
return xinit; |
