| 58 |
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/** Register different hydrodynamics models */ |
| 59 |
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void registerHydrodynamicsModels(); |
| 60 |
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|
| 61 |
< |
bool calcHydrodynamicsProp(const std::string& modelType, Molecule* mol, const DynamicProperty& param, const std::string& prefix,double viscosity); |
| 61 |
> |
bool calcHydrodynamicsProp(const std::string& modelType, StuntDouble* sd, const DynamicProperty& param, std::ostream& os, const std::string& prefix); |
| 62 |
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|
| 63 |
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int main(int argc, char* argv[]){ |
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//register force fields |
| 91 |
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} else { |
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prefix = "hydro"; |
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} |
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+ |
std::string outputFilename = prefix + ".diff"; |
| 95 |
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|
| 96 |
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DynamicProperty param; |
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+ |
param.insert(DynamicProperty::value_type("Viscosity", args_info.viscosity_arg)); |
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+ |
param.insert(DynamicProperty::value_type("Temperature", args_info.temperature_arg)); |
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+ |
|
| 100 |
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if (args_info.sigma_given) { |
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param.insert(DynamicProperty::value_type("Sigma", args_info.sigma_arg)); |
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} |
| 108 |
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|
| 109 |
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SimInfo::MoleculeIterator mi; |
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Molecule* mol; |
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< |
Molecule::RigidBodyIterator ri; |
| 112 |
< |
RigidBody* rb; |
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< |
//update atoms of rigidbody |
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> |
Molecule::IntegrableObjectIterator ii; |
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> |
StuntDouble* integrableObject; |
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> |
Mat3x3d identMat; |
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> |
identMat(0,0) = 1.0; |
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> |
identMat(1,1) = 1.0; |
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> |
identMat(2,2) = 1.0; |
| 117 |
> |
|
| 118 |
> |
|
| 119 |
> |
std::map<std::string, StuntDouble*> uniqueStuntDoubles; |
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> |
|
| 121 |
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for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 122 |
< |
|
| 123 |
< |
//change the positions of atoms which belong to the rigidbodies |
| 124 |
< |
for (rb = mol->beginRigidBody(ri); rb != NULL; rb = mol->nextRigidBody(ri)) { |
| 125 |
< |
rb->updateAtoms(); |
| 126 |
< |
} |
| 122 |
> |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
| 123 |
> |
integrableObject = mol->nextIntegrableObject(ii)) { |
| 124 |
> |
if (uniqueStuntDoubles.find(integrableObject->getType()) == uniqueStuntDoubles.end()) { |
| 125 |
> |
uniqueStuntDoubles.insert(std::map<std::string, StuntDouble*>::value_type(integrableObject->getType(), integrableObject)); |
| 126 |
> |
integrableObject->setPos(V3Zero); |
| 127 |
> |
integrableObject->setA(identMat); |
| 128 |
> |
if (integrableObject->isRigidBody()) { |
| 129 |
> |
RigidBody* rb = static_cast<RigidBody*>(integrableObject); |
| 130 |
> |
rb->updateAtoms(); |
| 131 |
> |
} |
| 132 |
> |
} |
| 133 |
> |
} |
| 134 |
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} |
| 135 |
< |
|
| 136 |
< |
for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 137 |
< |
calcHydrodynamicsProp(args_info.model_arg, mol, param, prefix, args_info.viscosity_arg); |
| 135 |
> |
|
| 136 |
> |
std::map<std::string, StuntDouble*>::iterator iter; |
| 137 |
> |
std::ofstream outputDiff(outputFilename.c_str()); |
| 138 |
> |
for (iter = uniqueStuntDoubles.begin(); iter != uniqueStuntDoubles.end(); ++iter) { |
| 139 |
> |
calcHydrodynamicsProp(args_info.model_arg, iter->second, param, outputDiff, prefix); |
| 140 |
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} |
| 141 |
|
|
| 142 |
|
delete info; |
| 149 |
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|
| 150 |
|
} |
| 151 |
|
|
| 152 |
< |
bool calcHydrodynamicsProp(const std::string& modelType, Molecule* mol, const DynamicProperty& param, const std::string& prefix,double viscosity) { |
| 153 |
< |
HydrodynamicsModel* hydroModel = HydrodynamicsModelFactory::getInstance()->createHydrodynamicsModel(modelType, mol, param); |
| 152 |
> |
bool calcHydrodynamicsProp(const std::string& modelType, StuntDouble* sd, const DynamicProperty& param, std::ostream& os, const std::string& prefix) { |
| 153 |
> |
HydrodynamicsModel* hydroModel = HydrodynamicsModelFactory::getInstance()->createHydrodynamicsModel(modelType, sd, param); |
| 154 |
|
bool ret = false; |
| 155 |
|
if (hydroModel == NULL) { |
| 156 |
|
std::cout << "Integrator Factory can not create " << modelType <<std::endl; |
| 157 |
|
} |
| 158 |
|
|
| 159 |
< |
if (hydroModel->calcHydrodyanmicsProps(viscosity)) { |
| 160 |
< |
ret = true; |
| 161 |
< |
std::stringstream outputDiffTensor; |
| 162 |
< |
outputDiffTensor << prefix << "_" << mol->getType() << ".diff"; |
| 159 |
> |
if (hydroModel->calcHydrodyanmicsProps()) { |
| 160 |
> |
ret = true; |
| 161 |
> |
hydroModel->writeDiffCenterAndDiffTensor(os); |
| 162 |
> |
|
| 163 |
|
std::ofstream ofs; |
| 144 |
– |
ofs.open(outputDiffTensor.str().c_str()); |
| 145 |
– |
hydroModel->writeDiffCenterAndDiffTensor(ofs); |
| 146 |
– |
ofs.close(); |
| 147 |
– |
|
| 164 |
|
std::stringstream outputBeads; |
| 165 |
< |
outputBeads << prefix << "_" << mol->getType() << ".xyz"; |
| 165 |
> |
outputBeads << prefix << "_" << sd->getType() << ".xyz"; |
| 166 |
|
ofs.open(outputBeads.str().c_str()); |
| 167 |
|
hydroModel->writeBeads(ofs); |
| 168 |
|
ofs.close(); |
