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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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LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info){ |
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Globals* simParams = info->getSimParams(); |
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|
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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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sprintf( painCave.errMsg, |
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"HydroPropFile must be set if Langevin Dynamics is specified.\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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sphericalBoundaryConditions_ = false; |
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if (simParams->getUseSphericalBoundaryConditions()) { |
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sphericalBoundaryConditions_ = true; |
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simError(); |
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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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|
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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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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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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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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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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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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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} 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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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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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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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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} |
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} |
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if (doLangevinForces) { |
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for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(j)) { |
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for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(j)) { |
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|
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if (freezeMolecule) |
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fdf += integrableObject->freeze(); |
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|
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if (doLangevinForces) { |
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vel =integrableObject->getVel(); |
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if (integrableObject->isDirectional()){ |
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//calculate angular velocity in lab frame |
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integrableObject->addFrc(frictionForce+randomForce); |
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} |
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} |
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++index; |
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++index; |
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} |
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} |
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if (freezeMolecule) |
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for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(j)) { |
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fdf += integrableObject->freeze(); |
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} |
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} |
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|
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} |
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info_->setFdf(fdf); |
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ForceManager::postCalculation(); |