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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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#include <fstream> |
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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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|
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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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// 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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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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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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|
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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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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() >= 40) { |
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std::string atomName = tokenizer.nextToken(); |
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currProp.cor[0] = tokenizer.nextTokenAsDouble(); |
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currProp.cor[1] = tokenizer.nextTokenAsDouble(); |
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currProp.cor[2] = tokenizer.nextTokenAsDouble(); |
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|
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currProp.Xirtt(0,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Xirtt(0,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Xirtt(0,2) = tokenizer.nextTokenAsDouble(); |
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currProp.Xirtt(1,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Xirtt(1,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Xirtt(1,2) = tokenizer.nextTokenAsDouble(); |
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currProp.Xirtt(2,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Xirtt(2,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Xirtt(2,2) = tokenizer.nextTokenAsDouble(); |
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|
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currProp.Xirrt(0,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Xirrt(0,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Xirrt(0,2) = tokenizer.nextTokenAsDouble(); |
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currProp.Xirrt(1,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Xirrt(1,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Xirrt(1,2) = tokenizer.nextTokenAsDouble(); |
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currProp.Xirrt(2,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Xirrt(2,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Xirrt(2,2) = tokenizer.nextTokenAsDouble(); |
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|
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currProp.Xirtr(0,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Xirtr(0,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Xirtr(0,2) = tokenizer.nextTokenAsDouble(); |
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currProp.Xirtr(1,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Xirtr(1,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Xirtr(1,2) = tokenizer.nextTokenAsDouble(); |
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currProp.Xirtr(2,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Xirtr(2,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Xirtr(2,2) = tokenizer.nextTokenAsDouble(); |
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|
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currProp.Xirrr(0,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Xirrr(0,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Xirrr(0,2) = tokenizer.nextTokenAsDouble(); |
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currProp.Xirrr(1,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Xirrr(1,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Xirrr(1,2) = tokenizer.nextTokenAsDouble(); |
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currProp.Xirrr(2,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Xirrr(2,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Xirrr(2,2) = tokenizer.nextTokenAsDouble(); |
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|
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SquareMatrix<RealType, 6> Xir; |
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Xir.setSubMatrix(0, 0, currProp.Xirtt); |
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Xir.setSubMatrix(0, 3, currProp.Xirrt); |
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Xir.setSubMatrix(3, 0, currProp.Xirtr); |
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Xir.setSubMatrix(3, 3, currProp.Xirrr); |
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CholeskyDecomposition(Xir, currProp.S); |
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|
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props.insert(std::map<std::string, HydroProp>::value_type(atomName, currProp)); |
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} |
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} |
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|
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return props; |
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} |
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|
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void LDForceManager::postCalculation() { |
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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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Vector3d vel; |
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Vector3d pos; |
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Vector3d frc; |
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Mat3x3d A; |
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Mat3x3d Atrans; |
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Vector3d Tb; |
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Vector3d ji; |
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RealType mass; |
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unsigned int index = 0; |
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bool doLangevinForces; |
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bool freezeMolecule; |
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int fdf; |
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|
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fdf = 0; |
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for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
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|
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if (sphericalBoundaryConditions_) { |
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|
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Vector3d molPos = mol->getCom(); |
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RealType molRad = molPos.length(); |
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|
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doLangevinForces = false; |
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freezeMolecule = false; |
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|
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if (molRad > langevinBufferRadius_) { |
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doLangevinForces = true; |
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freezeMolecule = false; |
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} |
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if (molRad > frozenBufferRadius_) { |
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doLangevinForces = false; |
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freezeMolecule = true; |
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} |
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} |
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|
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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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Mat3x3d I = integrableObject->getI(); |
| 358 |
Vector3d angMom = integrableObject->getJ(); |
| 359 |
Vector3d omega; |
| 360 |
|
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if (integrableObject->isLinear()) { |
| 362 |
int linearAxis = integrableObject->linearAxis(); |
| 363 |
int l = (linearAxis +1 )%3; |
| 364 |
int m = (linearAxis +2 )%3; |
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omega[l] = angMom[l] /I(l, l); |
| 366 |
omega[m] = angMom[m] /I(m, m); |
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|
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} else { |
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omega[0] = angMom[0] /I(0, 0); |
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omega[1] = angMom[1] /I(1, 1); |
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omega[2] = angMom[2] /I(2, 2); |
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} |
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|
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//apply friction force and torque at center of resistance |
| 375 |
A = integrableObject->getA(); |
| 376 |
Atrans = A.transpose(); |
| 377 |
Vector3d rcr = Atrans * hydroProps_[index].cor; |
| 378 |
Vector3d vcdLab = vel + cross(omega, rcr); |
| 379 |
Vector3d vcdBody = A* vcdLab; |
| 380 |
Vector3d frictionForceBody = -(hydroProps_[index].Xirtt * vcdBody + hydroProps_[index].Xirrt * omega); |
| 381 |
Vector3d frictionForceLab = Atrans*frictionForceBody; |
| 382 |
integrableObject->addFrc(frictionForceLab); |
| 383 |
Vector3d frictionTorqueBody = - (hydroProps_[index].Xirtr * vcdBody + hydroProps_[index].Xirrr * omega); |
| 384 |
Vector3d frictionTorqueLab = Atrans*frictionTorqueBody; |
| 385 |
integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab)); |
| 386 |
|
| 387 |
//apply random force and torque at center of resistance |
| 388 |
Vector3d randomForceBody; |
| 389 |
Vector3d randomTorqueBody; |
| 390 |
genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_); |
| 391 |
Vector3d randomForceLab = Atrans*randomForceBody; |
| 392 |
Vector3d randomTorqueLab = Atrans* randomTorqueBody; |
| 393 |
integrableObject->addFrc(randomForceLab); |
| 394 |
integrableObject->addTrq(randomTorqueLab + cross(rcr, randomForceLab )); |
| 395 |
|
| 396 |
} else { |
| 397 |
//spherical atom |
| 398 |
Vector3d frictionForce = -(hydroProps_[index].Xirtt *vel); |
| 399 |
Vector3d randomForce; |
| 400 |
Vector3d randomTorque; |
| 401 |
genRandomForceAndTorque(randomForce, randomTorque, index, variance_); |
| 402 |
|
| 403 |
integrableObject->addFrc(frictionForce+randomForce); |
| 404 |
} |
| 405 |
} |
| 406 |
|
| 407 |
++index; |
| 408 |
|
| 409 |
} |
| 410 |
} |
| 411 |
info_->setFdf(fdf); |
| 412 |
|
| 413 |
ForceManager::postCalculation(); |
| 414 |
} |
| 415 |
|
| 416 |
void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) { |
| 417 |
|
| 418 |
|
| 419 |
Vector<RealType, 6> Z; |
| 420 |
Vector<RealType, 6> generalForce; |
| 421 |
|
| 422 |
|
| 423 |
Z[0] = randNumGen_.randNorm(0, variance); |
| 424 |
Z[1] = randNumGen_.randNorm(0, variance); |
| 425 |
Z[2] = randNumGen_.randNorm(0, variance); |
| 426 |
Z[3] = randNumGen_.randNorm(0, variance); |
| 427 |
Z[4] = randNumGen_.randNorm(0, variance); |
| 428 |
Z[5] = randNumGen_.randNorm(0, variance); |
| 429 |
|
| 430 |
|
| 431 |
generalForce = hydroProps_[index].S*Z; |
| 432 |
|
| 433 |
force[0] = generalForce[0]; |
| 434 |
force[1] = generalForce[1]; |
| 435 |
force[2] = generalForce[2]; |
| 436 |
torque[0] = generalForce[3]; |
| 437 |
torque[1] = generalForce[4]; |
| 438 |
torque[2] = generalForce[5]; |
| 439 |
|
| 440 |
} |
| 441 |
|
| 442 |
} |
