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#include "integrators/LDForceManager.hpp" |
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#include "math/CholeskyDecomposition.hpp" |
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#include "utils/OOPSEConstant.hpp" |
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#include "hydrodynamics/Sphere.hpp" |
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#include "hydrodynamics/Ellipsoid.hpp" |
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#include "openbabel/mol.hpp" |
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|
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using namespace OpenBabel; |
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namespace oopse { |
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|
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LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info){ |
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Globals* simParams = info->getSimParams(); |
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std::map<std::string, HydroProp> hydroPropMap; |
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if (simParams->haveHydroPropFile()) { |
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hydroPropMap = parseFrictionFile(simParams->getHydroPropFile()); |
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} else { |
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//error |
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|
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sphericalBoundaryConditions_ = false; |
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if (simParams->getUseSphericalBoundaryConditions()) { |
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sphericalBoundaryConditions_ = true; |
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if (simParams->haveLangevinBufferRadius()) { |
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langevinBufferRadius_ = simParams->getLangevinBufferRadius(); |
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} else { |
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sprintf( painCave.errMsg, |
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"langevinBufferRadius must be specified " |
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"when useSphericalBoundaryConditions is turned on.\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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if (simParams->haveFrozenBufferRadius()) { |
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frozenBufferRadius_ = simParams->getFrozenBufferRadius(); |
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} else { |
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sprintf( painCave.errMsg, |
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"frozenBufferRadius must be specified " |
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"when useSphericalBoundaryConditions is turned on.\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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if (frozenBufferRadius_ < langevinBufferRadius_) { |
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sprintf( painCave.errMsg, |
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"frozenBufferRadius has been set smaller than the " |
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"langevinBufferRadius. This is probably an error.\n"); |
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painCave.severity = OOPSE_WARNING; |
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painCave.isFatal = 0; |
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simError(); |
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} |
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} |
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|
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SimInfo::MoleculeIterator i; |
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Molecule::IntegrableObjectIterator j; |
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// Build the hydroProp map: |
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std::map<std::string, HydroProp> hydroPropMap; |
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|
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Molecule* mol; |
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StuntDouble* integrableObject; |
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for (mol = info->beginMolecule(i); mol != NULL; mol = info->nextMolecule(i)) { |
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for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(j)) { |
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std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType()); |
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if (iter != hydroPropMap.end()) { |
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hydroProps_.push_back(iter->second); |
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SimInfo::MoleculeIterator i; |
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Molecule::IntegrableObjectIterator j; |
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bool needHydroPropFile = false; |
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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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|
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if (integrableObject->isRigidBody()) { |
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RigidBody* rb = static_cast<RigidBody*>(integrableObject); |
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if (rb->getNumAtoms() > 1) needHydroPropFile = true; |
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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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if (needHydroPropFile) { |
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if (simParams->haveHydroPropFile()) { |
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hydroPropMap = parseFrictionFile(simParams->getHydroPropFile()); |
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} else { |
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sprintf( painCave.errMsg, |
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"HydroPropFile must be set to a file name if Langevin\n" |
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"\tDynamics is specified for rigidBodies which contain more\n" |
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"\tthan one atom. To create a HydroPropFile, run \"Hydro\".\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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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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|
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std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType()); |
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if (iter != hydroPropMap.end()) { |
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hydroProps_.push_back(iter->second); |
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} else { |
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sprintf( painCave.errMsg, |
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"Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str()); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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} |
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} else { |
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|
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std::map<std::string, HydroProp> hydroPropMap; |
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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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Shape* currShape = NULL; |
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if (integrableObject->isDirectionalAtom()) { |
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DirectionalAtom* dAtom = static_cast<DirectionalAtom*>(integrableObject); |
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AtomType* atomType = dAtom->getAtomType(); |
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if (atomType->isGayBerne()) { |
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DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType); |
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|
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GenericData* data = dAtomType->getPropertyByName("GayBerne"); |
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if (data != NULL) { |
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GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data); |
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|
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if (gayBerneData != NULL) { |
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GayBerneParam gayBerneParam = gayBerneData->getData(); |
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currShape = new Ellipsoid(V3Zero, |
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gayBerneParam.GB_sigma/2.0, |
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gayBerneParam.GB_l2b_ratio*gayBerneParam.GB_sigma/2.0, |
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Mat3x3d::identity()); |
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} else { |
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sprintf( painCave.errMsg, |
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"Can not cast GenericData to GayBerneParam\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} else { |
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sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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} else { |
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Atom* atom = static_cast<Atom*>(integrableObject); |
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AtomType* atomType = atom->getAtomType(); |
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if (atomType->isLennardJones()){ |
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GenericData* data = atomType->getPropertyByName("LennardJones"); |
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if (data != NULL) { |
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LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data); |
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|
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if (ljData != NULL) { |
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LJParam ljParam = ljData->getData(); |
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currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0); |
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} else { |
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sprintf( painCave.errMsg, |
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"Can not cast GenericData to LJParam\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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} else { |
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//error |
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int obanum = etab.GetAtomicNum((atom->getType()).c_str()); |
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if (obanum != 0) { |
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currShape = new Sphere(atom->getPos(), etab.GetVdwRad(obanum)); |
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} else { |
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sprintf( painCave.errMsg, |
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"Could not find atom type in default element.txt\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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|
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} |
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} |
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HydroProps currHydroProp = currShape->getHydroProps(simParams->getViscosity(),simParams->getTargetTemp()); |
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std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType()); |
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if (iter != hydroPropMap.end()) |
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hydroProps_.push_back(iter->second); |
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else { |
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HydroProp myProp; |
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myProp.cor = V3Zero; |
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for (int i1 = 0; i1 < 3; i1++) { |
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for (int j1 = 0; j1 < 3; j1++) { |
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myProp.Xirtt(i1,j1) = currHydroProp.Xi(i1,j1); |
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myProp.Xirrt(i1,j1) = currHydroProp.Xi(i1,j1+3); |
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myProp.Xirtr(i1,j1) = currHydroProp.Xi(i1+3,j1); |
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myProp.Xirrr(i1,j1) = currHydroProp.Xi(i1+3,j1+3); |
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} |
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} |
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CholeskyDecomposition(currHydroProp.Xi, myProp.S); |
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hydroPropMap.insert(std::map<std::string, HydroProp>::value_type(integrableObject->getType(), myProp)); |
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hydroProps_.push_back(myProp); |
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} |
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} |
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} |
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} |
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variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt(); |
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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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std::map<std::string, HydroProp> LDForceManager::parseFrictionFile(const std::string& filename) { |
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std::map<std::string, HydroProp> props; |
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std::ifstream ifs(filename.c_str()); |
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if (ifs.is_open()) { |
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|
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|
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} |
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|
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|
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const unsigned int BufferSize = 65535; |
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char buffer[BufferSize]; |
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while (ifs.getline(buffer, BufferSize)) { |
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StringTokenizer tokenizer(buffer); |
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HydroProp currProp; |
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if (tokenizer.countTokens() >= 67) { |
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std::string atomName = tokenizer.nextToken(); |
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currProp.cod[0] = tokenizer.nextTokenAsDouble(); |
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currProp.cod[1] = tokenizer.nextTokenAsDouble(); |
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currProp.cod[2] = tokenizer.nextTokenAsDouble(); |
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|
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currProp.Ddtt(0,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddtt(0,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddtt(0,2) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddtt(1,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddtt(1,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddtt(1,2) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddtt(2,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddtt(2,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddtt(2,2) = tokenizer.nextTokenAsDouble(); |
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|
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currProp.Ddtr(0,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddtr(0,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddtr(0,2) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddtr(1,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddtr(1,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddtr(1,2) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddtr(2,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddtr(2,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddtr(2,2) = tokenizer.nextTokenAsDouble(); |
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|
283 |
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currProp.Ddrr(0,0) = tokenizer.nextTokenAsDouble(); |
284 |
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currProp.Ddrr(0,1) = tokenizer.nextTokenAsDouble(); |
285 |
< |
currProp.Ddrr(0,2) = tokenizer.nextTokenAsDouble(); |
286 |
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currProp.Ddrr(1,0) = tokenizer.nextTokenAsDouble(); |
287 |
< |
currProp.Ddrr(1,1) = tokenizer.nextTokenAsDouble(); |
288 |
< |
currProp.Ddrr(1,2) = tokenizer.nextTokenAsDouble(); |
289 |
< |
currProp.Ddrr(2,0) = tokenizer.nextTokenAsDouble(); |
290 |
< |
currProp.Ddrr(2,1) = tokenizer.nextTokenAsDouble(); |
291 |
< |
currProp.Ddrr(2,2) = tokenizer.nextTokenAsDouble(); |
292 |
< |
|
293 |
< |
currProp.Xidtt(0,0) = tokenizer.nextTokenAsDouble(); |
294 |
< |
currProp.Xidtt(0,1) = tokenizer.nextTokenAsDouble(); |
295 |
< |
currProp.Xidtt(0,2) = tokenizer.nextTokenAsDouble(); |
296 |
< |
currProp.Xidtt(1,0) = tokenizer.nextTokenAsDouble(); |
297 |
< |
currProp.Xidtt(1,1) = tokenizer.nextTokenAsDouble(); |
298 |
< |
currProp.Xidtt(1,2) = tokenizer.nextTokenAsDouble(); |
299 |
< |
currProp.Xidtt(2,0) = tokenizer.nextTokenAsDouble(); |
300 |
< |
currProp.Xidtt(2,1) = tokenizer.nextTokenAsDouble(); |
301 |
< |
currProp.Xidtt(2,2) = tokenizer.nextTokenAsDouble(); |
302 |
< |
|
303 |
< |
currProp.Xidrt(0,0) = tokenizer.nextTokenAsDouble(); |
304 |
< |
currProp.Xidrt(0,1) = tokenizer.nextTokenAsDouble(); |
305 |
< |
currProp.Xidrt(0,2) = tokenizer.nextTokenAsDouble(); |
306 |
< |
currProp.Xidrt(1,0) = tokenizer.nextTokenAsDouble(); |
307 |
< |
currProp.Xidrt(1,1) = tokenizer.nextTokenAsDouble(); |
308 |
< |
currProp.Xidrt(1,2) = tokenizer.nextTokenAsDouble(); |
309 |
< |
currProp.Xidrt(2,0) = tokenizer.nextTokenAsDouble(); |
310 |
< |
currProp.Xidrt(2,1) = tokenizer.nextTokenAsDouble(); |
311 |
< |
currProp.Xidrt(2,2) = tokenizer.nextTokenAsDouble(); |
141 |
< |
|
142 |
< |
currProp.Xidtr(0,0) = tokenizer.nextTokenAsDouble(); |
143 |
< |
currProp.Xidtr(0,1) = tokenizer.nextTokenAsDouble(); |
144 |
< |
currProp.Xidtr(0,2) = tokenizer.nextTokenAsDouble(); |
145 |
< |
currProp.Xidtr(1,0) = tokenizer.nextTokenAsDouble(); |
146 |
< |
currProp.Xidtr(1,1) = tokenizer.nextTokenAsDouble(); |
147 |
< |
currProp.Xidtr(1,2) = tokenizer.nextTokenAsDouble(); |
148 |
< |
currProp.Xidtr(2,0) = tokenizer.nextTokenAsDouble(); |
149 |
< |
currProp.Xidtr(2,1) = tokenizer.nextTokenAsDouble(); |
150 |
< |
currProp.Xidtr(2,2) = tokenizer.nextTokenAsDouble(); |
151 |
< |
|
152 |
< |
currProp.Xidrr(0,0) = tokenizer.nextTokenAsDouble(); |
153 |
< |
currProp.Xidrr(0,1) = tokenizer.nextTokenAsDouble(); |
154 |
< |
currProp.Xidrr(0,2) = tokenizer.nextTokenAsDouble(); |
155 |
< |
currProp.Xidrr(1,0) = tokenizer.nextTokenAsDouble(); |
156 |
< |
currProp.Xidrr(1,1) = tokenizer.nextTokenAsDouble(); |
157 |
< |
currProp.Xidrr(1,2) = tokenizer.nextTokenAsDouble(); |
158 |
< |
currProp.Xidrr(2,0) = tokenizer.nextTokenAsDouble(); |
159 |
< |
currProp.Xidrr(2,1) = tokenizer.nextTokenAsDouble(); |
160 |
< |
currProp.Xidrr(2,2) = tokenizer.nextTokenAsDouble(); |
161 |
< |
props.insert(std::map<std::string, HydroProp>::value_type(atomName, currProp)); |
162 |
< |
} |
255 |
> |
StringTokenizer tokenizer(buffer); |
256 |
> |
HydroProp currProp; |
257 |
> |
if (tokenizer.countTokens() >= 40) { |
258 |
> |
std::string atomName = tokenizer.nextToken(); |
259 |
> |
currProp.cor[0] = tokenizer.nextTokenAsDouble(); |
260 |
> |
currProp.cor[1] = tokenizer.nextTokenAsDouble(); |
261 |
> |
currProp.cor[2] = tokenizer.nextTokenAsDouble(); |
262 |
> |
|
263 |
> |
currProp.Xirtt(0,0) = tokenizer.nextTokenAsDouble(); |
264 |
> |
currProp.Xirtt(0,1) = tokenizer.nextTokenAsDouble(); |
265 |
> |
currProp.Xirtt(0,2) = tokenizer.nextTokenAsDouble(); |
266 |
> |
currProp.Xirtt(1,0) = tokenizer.nextTokenAsDouble(); |
267 |
> |
currProp.Xirtt(1,1) = tokenizer.nextTokenAsDouble(); |
268 |
> |
currProp.Xirtt(1,2) = tokenizer.nextTokenAsDouble(); |
269 |
> |
currProp.Xirtt(2,0) = tokenizer.nextTokenAsDouble(); |
270 |
> |
currProp.Xirtt(2,1) = tokenizer.nextTokenAsDouble(); |
271 |
> |
currProp.Xirtt(2,2) = tokenizer.nextTokenAsDouble(); |
272 |
> |
|
273 |
> |
currProp.Xirrt(0,0) = tokenizer.nextTokenAsDouble(); |
274 |
> |
currProp.Xirrt(0,1) = tokenizer.nextTokenAsDouble(); |
275 |
> |
currProp.Xirrt(0,2) = tokenizer.nextTokenAsDouble(); |
276 |
> |
currProp.Xirrt(1,0) = tokenizer.nextTokenAsDouble(); |
277 |
> |
currProp.Xirrt(1,1) = tokenizer.nextTokenAsDouble(); |
278 |
> |
currProp.Xirrt(1,2) = tokenizer.nextTokenAsDouble(); |
279 |
> |
currProp.Xirrt(2,0) = tokenizer.nextTokenAsDouble(); |
280 |
> |
currProp.Xirrt(2,1) = tokenizer.nextTokenAsDouble(); |
281 |
> |
currProp.Xirrt(2,2) = tokenizer.nextTokenAsDouble(); |
282 |
> |
|
283 |
> |
currProp.Xirtr(0,0) = tokenizer.nextTokenAsDouble(); |
284 |
> |
currProp.Xirtr(0,1) = tokenizer.nextTokenAsDouble(); |
285 |
> |
currProp.Xirtr(0,2) = tokenizer.nextTokenAsDouble(); |
286 |
> |
currProp.Xirtr(1,0) = tokenizer.nextTokenAsDouble(); |
287 |
> |
currProp.Xirtr(1,1) = tokenizer.nextTokenAsDouble(); |
288 |
> |
currProp.Xirtr(1,2) = tokenizer.nextTokenAsDouble(); |
289 |
> |
currProp.Xirtr(2,0) = tokenizer.nextTokenAsDouble(); |
290 |
> |
currProp.Xirtr(2,1) = tokenizer.nextTokenAsDouble(); |
291 |
> |
currProp.Xirtr(2,2) = tokenizer.nextTokenAsDouble(); |
292 |
> |
|
293 |
> |
currProp.Xirrr(0,0) = tokenizer.nextTokenAsDouble(); |
294 |
> |
currProp.Xirrr(0,1) = tokenizer.nextTokenAsDouble(); |
295 |
> |
currProp.Xirrr(0,2) = tokenizer.nextTokenAsDouble(); |
296 |
> |
currProp.Xirrr(1,0) = tokenizer.nextTokenAsDouble(); |
297 |
> |
currProp.Xirrr(1,1) = tokenizer.nextTokenAsDouble(); |
298 |
> |
currProp.Xirrr(1,2) = tokenizer.nextTokenAsDouble(); |
299 |
> |
currProp.Xirrr(2,0) = tokenizer.nextTokenAsDouble(); |
300 |
> |
currProp.Xirrr(2,1) = tokenizer.nextTokenAsDouble(); |
301 |
> |
currProp.Xirrr(2,2) = tokenizer.nextTokenAsDouble(); |
302 |
> |
|
303 |
> |
SquareMatrix<RealType, 6> Xir; |
304 |
> |
Xir.setSubMatrix(0, 0, currProp.Xirtt); |
305 |
> |
Xir.setSubMatrix(0, 3, currProp.Xirrt); |
306 |
> |
Xir.setSubMatrix(3, 0, currProp.Xirtr); |
307 |
> |
Xir.setSubMatrix(3, 3, currProp.Xirrr); |
308 |
> |
CholeskyDecomposition(Xir, currProp.S); |
309 |
> |
|
310 |
> |
props.insert(std::map<std::string, HydroProp>::value_type(atomName, currProp)); |
311 |
> |
} |
312 |
|
} |
313 |
< |
|
313 |
> |
|
314 |
|
return props; |
315 |
|
} |
316 |
|
|
326 |
|
Mat3x3d Atrans; |
327 |
|
Vector3d Tb; |
328 |
|
Vector3d ji; |
329 |
< |
double mass; |
329 |
> |
RealType mass; |
330 |
|
unsigned int index = 0; |
331 |
+ |
bool doLangevinForces; |
332 |
+ |
bool freezeMolecule; |
333 |
+ |
int fdf; |
334 |
+ |
|
335 |
+ |
fdf = 0; |
336 |
|
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
183 |
– |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
184 |
– |
integrableObject = mol->nextIntegrableObject(j)) { |
337 |
|
|
338 |
+ |
doLangevinForces = true; |
339 |
+ |
freezeMolecule = false; |
340 |
+ |
|
341 |
+ |
if (sphericalBoundaryConditions_) { |
342 |
+ |
|
343 |
+ |
Vector3d molPos = mol->getCom(); |
344 |
+ |
RealType molRad = molPos.length(); |
345 |
+ |
|
346 |
+ |
doLangevinForces = false; |
347 |
+ |
|
348 |
+ |
if (molRad > langevinBufferRadius_) { |
349 |
+ |
doLangevinForces = true; |
350 |
+ |
freezeMolecule = false; |
351 |
+ |
} |
352 |
+ |
if (molRad > frozenBufferRadius_) { |
353 |
+ |
doLangevinForces = false; |
354 |
+ |
freezeMolecule = true; |
355 |
+ |
} |
356 |
+ |
} |
357 |
+ |
|
358 |
+ |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
359 |
+ |
integrableObject = mol->nextIntegrableObject(j)) { |
360 |
+ |
|
361 |
+ |
if (freezeMolecule) |
362 |
+ |
fdf += integrableObject->freeze(); |
363 |
+ |
|
364 |
+ |
if (doLangevinForces) { |
365 |
|
vel =integrableObject->getVel(); |
366 |
|
if (integrableObject->isDirectional()){ |
367 |
< |
//calculate angular velocity in lab frame |
368 |
< |
Mat3x3d I = integrableObject->getI(); |
369 |
< |
Vector3d angMom = integrableObject->getJ(); |
370 |
< |
Vector3d omega; |
371 |
< |
|
372 |
< |
if (integrableObject->isLinear()) { |
373 |
< |
int linearAxis = integrableObject->linearAxis(); |
374 |
< |
int l = (linearAxis +1 )%3; |
375 |
< |
int m = (linearAxis +2 )%3; |
376 |
< |
omega[l] = angMom[l] /I(l, l); |
377 |
< |
omega[m] = angMom[m] /I(m, m); |
378 |
< |
|
379 |
< |
} else { |
380 |
< |
omega[0] = angMom[0] /I(0, 0); |
381 |
< |
omega[1] = angMom[1] /I(1, 1); |
382 |
< |
omega[2] = angMom[2] /I(2, 2); |
383 |
< |
} |
384 |
< |
|
385 |
< |
//apply friction force and torque at center of diffusion |
386 |
< |
A = integrableObject->getA(); |
387 |
< |
Atrans = A.transpose(); |
388 |
< |
Vector3d rcd = Atrans * hydroProps_[index].cod; |
389 |
< |
Vector3d vcd = vel + cross(omega, rcd); |
390 |
< |
vcd = A* vcd; |
391 |
< |
Vector3d frictionForce = -(hydroProps_[index].Xidtt * vcd + hydroProps_[index].Xidrt * omega); |
392 |
< |
frictionForce = Atrans*frictionForce; |
393 |
< |
integrableObject->addFrc(frictionForce); |
394 |
< |
Vector3d frictionTorque = - (hydroProps_[index].Xidtr * vcd + hydroProps_[index].Xidrr * omega); |
395 |
< |
frictionTorque = Atrans*frictionTorque; |
396 |
< |
integrableObject->addTrq(frictionTorque+ cross(rcd, frictionForce)); |
397 |
< |
|
398 |
< |
//apply random force and torque at center of diffustion |
399 |
< |
Vector3d randomForce; |
400 |
< |
Vector3d randomTorque; |
401 |
< |
genRandomForceAndTorque(randomForce, randomTorque, index, variance_); |
402 |
< |
randomForce = Atrans*randomForce; |
403 |
< |
randomTorque = Atrans* randomTorque; |
404 |
< |
integrableObject->addFrc(randomForce); |
405 |
< |
integrableObject->addTrq(randomTorque + cross(rcd, randomForce )); |
406 |
< |
|
367 |
> |
//calculate angular velocity in lab frame |
368 |
> |
Mat3x3d I = integrableObject->getI(); |
369 |
> |
Vector3d angMom = integrableObject->getJ(); |
370 |
> |
Vector3d omega; |
371 |
> |
|
372 |
> |
if (integrableObject->isLinear()) { |
373 |
> |
int linearAxis = integrableObject->linearAxis(); |
374 |
> |
int l = (linearAxis +1 )%3; |
375 |
> |
int m = (linearAxis +2 )%3; |
376 |
> |
omega[l] = angMom[l] /I(l, l); |
377 |
> |
omega[m] = angMom[m] /I(m, m); |
378 |
> |
|
379 |
> |
} else { |
380 |
> |
omega[0] = angMom[0] /I(0, 0); |
381 |
> |
omega[1] = angMom[1] /I(1, 1); |
382 |
> |
omega[2] = angMom[2] /I(2, 2); |
383 |
> |
} |
384 |
> |
|
385 |
> |
//apply friction force and torque at center of resistance |
386 |
> |
A = integrableObject->getA(); |
387 |
> |
Atrans = A.transpose(); |
388 |
> |
Vector3d rcr = Atrans * hydroProps_[index].cor; |
389 |
> |
Vector3d vcdLab = vel + cross(omega, rcr); |
390 |
> |
Vector3d vcdBody = A* vcdLab; |
391 |
> |
Vector3d frictionForceBody = -(hydroProps_[index].Xirtt * vcdBody + hydroProps_[index].Xirrt * omega); |
392 |
> |
Vector3d frictionForceLab = Atrans*frictionForceBody; |
393 |
> |
integrableObject->addFrc(frictionForceLab); |
394 |
> |
Vector3d frictionTorqueBody = - (hydroProps_[index].Xirtr * vcdBody + hydroProps_[index].Xirrr * omega); |
395 |
> |
Vector3d frictionTorqueLab = Atrans*frictionTorqueBody; |
396 |
> |
integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab)); |
397 |
> |
|
398 |
> |
//apply random force and torque at center of resistance |
399 |
> |
Vector3d randomForceBody; |
400 |
> |
Vector3d randomTorqueBody; |
401 |
> |
genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_); |
402 |
> |
Vector3d randomForceLab = Atrans*randomForceBody; |
403 |
> |
Vector3d randomTorqueLab = Atrans* randomTorqueBody; |
404 |
> |
integrableObject->addFrc(randomForceLab); |
405 |
> |
integrableObject->addTrq(randomTorqueLab + cross(rcr, randomForceLab )); |
406 |
> |
|
407 |
|
} else { |
408 |
< |
//spheric atom |
409 |
< |
Vector3d frictionForce = -(hydroProps_[index].Xidtt *vel); |
410 |
< |
Vector3d randomForce; |
411 |
< |
Vector3d randomTorque; |
412 |
< |
genRandomForceAndTorque(randomForce, randomTorque, index, variance_); |
413 |
< |
|
414 |
< |
//randomForce /= OOPSEConstant::energyConvert; |
236 |
< |
//randomTorque /= OOPSEConstant::energyConvert; |
237 |
< |
integrableObject->addFrc(frictionForce+randomForce); |
408 |
> |
//spherical atom |
409 |
> |
Vector3d frictionForce = -(hydroProps_[index].Xirtt *vel); |
410 |
> |
Vector3d randomForce; |
411 |
> |
Vector3d randomTorque; |
412 |
> |
genRandomForceAndTorque(randomForce, randomTorque, index, variance_); |
413 |
> |
|
414 |
> |
integrableObject->addFrc(frictionForce+randomForce); |
415 |
|
} |
416 |
< |
|
416 |
> |
} |
417 |
> |
|
418 |
|
++index; |
419 |
|
|
420 |
|
} |
421 |
|
} |
422 |
< |
|
423 |
< |
ForceManager::postCalculation(); |
424 |
< |
|
247 |
< |
|
248 |
< |
|
422 |
> |
info_->setFdf(fdf); |
423 |
> |
|
424 |
> |
ForceManager::postCalculation(); |
425 |
|
} |
426 |
|
|
427 |
< |
void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, double variance) { |
252 |
< |
/* |
253 |
< |
SquareMatrix<double, 6> Dd; |
254 |
< |
SquareMatrix<double, 6> S; |
255 |
< |
Vector<double, 6> Z; |
256 |
< |
Vector<double, 6> generalForce; |
257 |
< |
Dd.setSubMatrix(0, 0, hydroProps_[index].Ddtt); |
258 |
< |
Dd.setSubMatrix(0, 3, hydroProps_[index].Ddtr.transpose()); |
259 |
< |
Dd.setSubMatrix(3, 0, hydroProps_[index].Ddtr); |
260 |
< |
Dd.setSubMatrix(3, 3, hydroProps_[index].Ddrr); |
261 |
< |
CholeskyDecomposition(Dd, S); |
262 |
< |
*/ |
427 |
> |
void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) { |
428 |
|
|
264 |
– |
SquareMatrix<double, 6> Xid; |
265 |
– |
SquareMatrix<double, 6> S; |
266 |
– |
Vector<double, 6> Z; |
267 |
– |
Vector<double, 6> generalForce; |
268 |
– |
Xid.setSubMatrix(0, 0, hydroProps_[index].Xidtt); |
269 |
– |
Xid.setSubMatrix(0, 3, hydroProps_[index].Xidrt); |
270 |
– |
Xid.setSubMatrix(3, 0, hydroProps_[index].Xidtr); |
271 |
– |
Xid.setSubMatrix(3, 3, hydroProps_[index].Xidrr); |
272 |
– |
CholeskyDecomposition(Xid, S); |
429 |
|
|
430 |
< |
/* |
431 |
< |
Xid *= variance; |
432 |
< |
Z[0] = randNumGen_.randNorm(0, 1.0); |
277 |
< |
Z[1] = randNumGen_.randNorm(0, 1.0); |
278 |
< |
Z[2] = randNumGen_.randNorm(0, 1.0); |
279 |
< |
Z[3] = randNumGen_.randNorm(0, 1.0); |
280 |
< |
Z[4] = randNumGen_.randNorm(0, 1.0); |
281 |
< |
Z[5] = randNumGen_.randNorm(0, 1.0); |
282 |
< |
*/ |
430 |
> |
Vector<RealType, 6> Z; |
431 |
> |
Vector<RealType, 6> generalForce; |
432 |
> |
|
433 |
|
|
434 |
|
Z[0] = randNumGen_.randNorm(0, variance); |
435 |
|
Z[1] = randNumGen_.randNorm(0, variance); |
439 |
|
Z[5] = randNumGen_.randNorm(0, variance); |
440 |
|
|
441 |
|
|
442 |
< |
generalForce = S*Z; |
442 |
> |
generalForce = hydroProps_[index].S*Z; |
443 |
|
|
444 |
|
force[0] = generalForce[0]; |
445 |
|
force[1] = generalForce[1]; |