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#include "applications/hydrodynamics/HydrodynamicsModel.hpp" |
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#include "applications/hydrodynamics/HydrodynamicsModelCreator.hpp" |
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#include "applications/hydrodynamics/HydrodynamicsModelFactory.hpp" |
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#include "applications/hydrodynamics/AnalyticalModel.hpp" |
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#include "applications/hydrodynamics/BeadModel.hpp" |
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#include "applications/hydrodynamics/RoughShell.hpp" |
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#include "applications/hydrodynamics/ShapeBuilder.hpp" |
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#include "brains/Register.hpp" |
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#include "brains/SimCreator.hpp" |
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#include "brains/SimInfo.hpp" |
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#include "utils/StringUtils.hpp" |
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#include "utils/simError.h" |
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#include "utils/MemoryUtils.hpp" |
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using namespace oopse; |
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/** Register different hydrodynamics models */ |
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struct SDShape{ |
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StuntDouble* sd; |
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Shape* shape; |
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}; |
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void registerHydrodynamicsModels(); |
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void writeHydroProps(std::ostream& os); |
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bool calcHydrodynamicsProp(const std::string& modelType, Molecule* mol, const DynamicProperty& param, const std::string& prefix,double viscosity); |
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int main(int argc, char* argv[]){ |
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//register force fields |
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registerForceFields(); |
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exit(1); |
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} |
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mdFileName = dumpFileName; |
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mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md"; |
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if (args_info.output_given){ |
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prefix = args_info.output_arg; |
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} else { |
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prefix = "hydro"; |
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prefix = getPrefix(dumpFileName); |
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} |
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DynamicProperty param; |
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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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} |
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std::string outputFilename = prefix + ".diff"; |
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//parse md file and set up the system |
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SimCreator creator; |
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SimInfo* info = creator.createSim(mdFileName, true); |
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SimInfo* info = creator.createSim(dumpFileName, true); |
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SimInfo::MoleculeIterator mi; |
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Molecule* mol; |
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Molecule::RigidBodyIterator ri; |
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RigidBody* rb; |
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//update atoms of rigidbody |
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for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
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//change the positions of atoms which belong to the rigidbodies |
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for (rb = mol->beginRigidBody(ri); rb != NULL; rb = mol->nextRigidBody(ri)) { |
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rb->updateAtoms(); |
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} |
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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; |
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Globals* simParams = info->getSimParams(); |
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RealType temperature; |
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RealType viscosity; |
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if (simParams->haveViscosity()) { |
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viscosity = simParams->getViscosity(); |
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} else { |
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sprintf(painCave.errMsg, "viscosity must be set\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
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calcHydrodynamicsProp(args_info.model_arg, mol, param, prefix, args_info.viscosity_arg); |
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if (simParams->haveTargetTemp()) { |
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temperature = simParams->getTargetTemp(); |
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} else { |
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sprintf(painCave.errMsg, "target temperature must be set\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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std::map<std::string, SDShape> uniqueStuntDoubles; |
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delete info; |
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} |
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for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
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for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(ii)) { |
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if (uniqueStuntDoubles.find(integrableObject->getType()) == uniqueStuntDoubles.end()) { |
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void registerHydrodynamicsModels() { |
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HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<RoughShell>("RoughShell")); |
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HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<BeadModel>("BeadModel")); |
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integrableObject->setPos(V3Zero); |
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integrableObject->setA(identMat); |
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if (integrableObject->isRigidBody()) { |
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RigidBody* rb = static_cast<RigidBody*>(integrableObject); |
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rb->updateAtoms(); |
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} |
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} |
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SDShape tmp; |
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tmp.shape = ShapeBuilder::createShape(integrableObject); |
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tmp.sd = integrableObject; |
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uniqueStuntDoubles.insert(std::map<std::string, SDShape>::value_type(integrableObject->getType(), tmp)); |
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bool calcHydrodynamicsProp(const std::string& modelType, Molecule* mol, const DynamicProperty& param, const std::string& prefix,double viscosity) { |
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HydrodynamicsModel* hydroModel = HydrodynamicsModelFactory::getInstance()->createHydrodynamicsModel(modelType, mol, param); |
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bool ret = false; |
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if (hydroModel == NULL) { |
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std::cout << "Integrator Factory can not create " << modelType <<std::endl; |
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} |
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} |
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} |
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} |
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if (hydroModel->calcHydrodyanmicsProps(viscosity)) { |
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ret = true; |
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std::stringstream outputDiffTensor; |
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outputDiffTensor << prefix << "_" << mol->getType() << ".diff"; |
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std::ofstream ofs; |
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ofs.open(outputDiffTensor.str().c_str()); |
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hydroModel->writeDiffCenterAndDiffTensor(ofs); |
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ofs.close(); |
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std::ofstream outputDiff(outputFilename.c_str()); |
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std::map<std::string, SDShape>::iterator si; |
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for (si = uniqueStuntDoubles.begin(); si != uniqueStuntDoubles.end(); ++si) { |
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HydrodynamicsModel* model; |
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Shape* shape = si->second.shape; |
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StuntDouble* sd = si->second.sd;; |
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if (args_info.model_given) { |
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model = HydrodynamicsModelFactory::getInstance()->createHydrodynamicsModel(args_info.model_arg, sd, info); |
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} else if (shape->hasAnalyticalSolution()) { |
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model = new AnalyticalModel(sd, info); |
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} else { |
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model = new BeadModel(sd, info); |
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} |
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|
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model->init(); |
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std::ofstream ofs; |
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std::stringstream outputBeads; |
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outputBeads << prefix << "_" << mol->getType() << ".xyz"; |
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ofs.open(outputBeads.str().c_str()); |
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hydroModel->writeBeads(ofs); |
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outputBeads << prefix << "_" << model->getStuntDoubleName() << ".xyz"; |
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ofs.open(outputBeads.str().c_str()); |
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model->writeBeads(ofs); |
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ofs.close(); |
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} |
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delete hydroModel; |
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//if beads option is turned on, skip the calculation |
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if (!args_info.beads_flag) { |
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model->calcHydroProps(shape, viscosity, temperature); |
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model->writeHydroProps(outputDiff); |
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} |
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|
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delete model; |
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} |
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return ret; |
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|
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//MemoryUtils::deletePointers(shapes); |
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delete info; |
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|
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} |
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|
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void registerHydrodynamicsModels() { |
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HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<RoughShell>("RoughShell")); |
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HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<BeadModel>("BeadModel")); |
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HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<AnalyticalModel>("AnalyticalModel")); |
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|
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} |
