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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 <iostream> |
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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 "utils/ElementsTable.hpp" |
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|
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namespace oopse { |
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|
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LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info), forceTolerance_(1e-6), maxIterNum_(4) { |
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simParams = info->getSimParams(); |
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veloMunge = new Velocitizer(info); |
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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 Dynamics\n" |
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"\tis specified for rigidBodies which contain more than one atom\n" |
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"\tTo create a HydroPropFile, run the \"Hydro\" program.\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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|
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if (integrableObject->isAtom()){ |
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Atom* atom = static_cast<Atom*>(integrableObject); |
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AtomType* atomType = atom->getAtomType(); |
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if (atomType->isGayBerne()) { |
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DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType); |
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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_l / 2.0, |
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gayBerneParam.GB_d / 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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} else { |
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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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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 aNum = etab.GetAtomicNum((atom->getType()).c_str()); |
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if (aNum != 0) { |
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currShape = new Sphere(atom->getPos(), etab.GetVdwRad(aNum)); |
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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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HydroProp* currHydroProp = currShape->getHydroProp(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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currHydroProp->complete(); |
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hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(integrableObject->getType(), currHydroProp)); |
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hydroProps_.push_back(currHydroProp); |
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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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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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HydroProp* currProp = new HydroProp(buffer); |
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props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp)); |
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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(bool needStress){ |
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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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RealType mass; |
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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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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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|
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for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
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|
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doLangevinForces = true; |
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freezeMolecule = false; |
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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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|
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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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mass = integrableObject->getMass(); |
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if (integrableObject->isDirectional()){ |
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|
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// preliminaries for directional objects: |
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|
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A = integrableObject->getA(); |
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Atrans = A.transpose(); |
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Vector3d rcrLab = Atrans * hydroProps_[index]->getCOR(); |
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|
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//apply random force and torque at center of resistance |
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|
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Vector3d randomForceBody; |
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Vector3d randomTorqueBody; |
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genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_); |
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Vector3d randomForceLab = Atrans * randomForceBody; |
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Vector3d randomTorqueLab = Atrans * randomTorqueBody; |
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integrableObject->addFrc(randomForceLab); |
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integrableObject->addTrq(randomTorqueLab + cross(rcrLab, randomForceLab )); |
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|
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Mat3x3d I = integrableObject->getI(); |
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Vector3d omegaBody; |
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|
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// What remains contains velocity explicitly, but the velocity required |
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// is at the full step: v(t + h), while we have initially the velocity |
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// at the half step: v(t + h/2). We need to iterate to converge the |
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// friction force and friction torque vectors. |
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|
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// this is the velocity at the half-step: |
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|
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Vector3d vel =integrableObject->getVel(); |
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Vector3d angMom = integrableObject->getJ(); |
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|
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//estimate velocity at full-step using everything but friction forces: |
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|
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frc = integrableObject->getFrc(); |
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Vector3d velStep = vel + (dt2_ /mass * OOPSEConstant::energyConvert) * frc; |
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|
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Tb = integrableObject->lab2Body(integrableObject->getTrq()); |
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Vector3d angMomStep = angMom + (dt2_ * OOPSEConstant::energyConvert) * Tb; |
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|
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Vector3d omegaLab; |
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Vector3d vcdLab; |
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Vector3d vcdBody; |
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Vector3d frictionForceBody; |
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Vector3d frictionForceLab(0.0); |
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Vector3d oldFFL; // used to test for convergence |
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Vector3d frictionTorqueBody(0.0); |
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Vector3d oldFTB; // used to test for convergence |
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Vector3d frictionTorqueLab; |
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RealType fdot; |
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RealType tdot; |
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|
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//iteration starts here: |
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|
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for (int k = 0; k < maxIterNum_; k++) { |
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|
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if (integrableObject->isLinear()) { |
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int linearAxis = integrableObject->linearAxis(); |
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int l = (linearAxis +1 )%3; |
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int m = (linearAxis +2 )%3; |
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omegaBody[l] = angMomStep[l] /I(l, l); |
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omegaBody[m] = angMomStep[m] /I(m, m); |
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|
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} else { |
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omegaBody[0] = angMomStep[0] /I(0, 0); |
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omegaBody[1] = angMomStep[1] /I(1, 1); |
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omegaBody[2] = angMomStep[2] /I(2, 2); |
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} |
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|
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omegaLab = Atrans * omegaBody; |
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|
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// apply friction force and torque at center of resistance |
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|
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vcdLab = velStep + cross(omegaLab, rcrLab); |
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vcdBody = A * vcdLab; |
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frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omegaBody); |
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oldFFL = frictionForceLab; |
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frictionForceLab = Atrans * frictionForceBody; |
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oldFTB = frictionTorqueBody; |
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frictionTorqueBody = -(hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omegaBody); |
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frictionTorqueLab = Atrans * frictionTorqueBody; |
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|
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// re-estimate velocities at full-step using friction forces: |
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|
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velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * (frc + frictionForceLab); |
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angMomStep = angMom + (dt2_ * OOPSEConstant::energyConvert) * (Tb + frictionTorqueBody); |
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|
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// check for convergence (if the vectors have converged, fdot and tdot will both be 1.0): |
| 382 |
|
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fdot = dot(frictionForceLab, oldFFL) / frictionForceLab.lengthSquare(); |
| 384 |
tdot = dot(frictionTorqueBody, oldFTB) / frictionTorqueBody.lengthSquare(); |
| 385 |
|
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if (fabs(1.0 - fdot) <= forceTolerance_ && fabs(1.0 - tdot) <= forceTolerance_) |
| 387 |
break; // iteration ends here |
| 388 |
} |
| 389 |
|
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integrableObject->addFrc(frictionForceLab); |
| 391 |
integrableObject->addTrq(frictionTorqueLab + cross(rcrLab, frictionForceLab)); |
| 392 |
|
| 393 |
|
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} else { |
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//spherical atom |
| 396 |
|
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Vector3d randomForce; |
| 398 |
Vector3d randomTorque; |
| 399 |
genRandomForceAndTorque(randomForce, randomTorque, index, variance_); |
| 400 |
integrableObject->addFrc(randomForce); |
| 401 |
|
| 402 |
// What remains contains velocity explicitly, but the velocity required |
| 403 |
// is at the full step: v(t + h), while we have initially the velocity |
| 404 |
// at the half step: v(t + h/2). We need to iterate to converge the |
| 405 |
// friction force vector. |
| 406 |
|
| 407 |
// this is the velocity at the half-step: |
| 408 |
|
| 409 |
Vector3d vel =integrableObject->getVel(); |
| 410 |
|
| 411 |
//estimate velocity at full-step using everything but friction forces: |
| 412 |
|
| 413 |
frc = integrableObject->getFrc(); |
| 414 |
Vector3d velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * frc; |
| 415 |
|
| 416 |
Vector3d frictionForce(0.0); |
| 417 |
Vector3d oldFF; // used to test for convergence |
| 418 |
RealType fdot; |
| 419 |
|
| 420 |
//iteration starts here: |
| 421 |
|
| 422 |
for (int k = 0; k < maxIterNum_; k++) { |
| 423 |
|
| 424 |
oldFF = frictionForce; |
| 425 |
frictionForce = -hydroProps_[index]->getXitt() * velStep; |
| 426 |
|
| 427 |
// re-estimate velocities at full-step using friction forces: |
| 428 |
|
| 429 |
velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * (frc + frictionForce); |
| 430 |
|
| 431 |
// check for convergence (if the vector has converged, fdot will be 1.0): |
| 432 |
|
| 433 |
fdot = dot(frictionForce, oldFF) / frictionForce.lengthSquare(); |
| 434 |
|
| 435 |
if (fabs(1.0 - fdot) <= forceTolerance_) |
| 436 |
break; // iteration ends here |
| 437 |
} |
| 438 |
|
| 439 |
integrableObject->addFrc(frictionForce); |
| 440 |
|
| 441 |
} |
| 442 |
} |
| 443 |
|
| 444 |
++index; |
| 445 |
|
| 446 |
} |
| 447 |
} |
| 448 |
|
| 449 |
info_->setFdf(fdf); |
| 450 |
veloMunge->removeComDrift(); |
| 451 |
// Remove angular drift if we are not using periodic boundary conditions. |
| 452 |
if(!simParams->getUsePeriodicBoundaryConditions()) |
| 453 |
veloMunge->removeAngularDrift(); |
| 454 |
|
| 455 |
ForceManager::postCalculation(needStress); |
| 456 |
} |
| 457 |
|
| 458 |
void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) { |
| 459 |
|
| 460 |
|
| 461 |
Vector<RealType, 6> Z; |
| 462 |
Vector<RealType, 6> generalForce; |
| 463 |
|
| 464 |
Z[0] = randNumGen_.randNorm(0, variance); |
| 465 |
Z[1] = randNumGen_.randNorm(0, variance); |
| 466 |
Z[2] = randNumGen_.randNorm(0, variance); |
| 467 |
Z[3] = randNumGen_.randNorm(0, variance); |
| 468 |
Z[4] = randNumGen_.randNorm(0, variance); |
| 469 |
Z[5] = randNumGen_.randNorm(0, variance); |
| 470 |
|
| 471 |
generalForce = hydroProps_[index]->getS()*Z; |
| 472 |
|
| 473 |
force[0] = generalForce[0]; |
| 474 |
force[1] = generalForce[1]; |
| 475 |
force[2] = generalForce[2]; |
| 476 |
torque[0] = generalForce[3]; |
| 477 |
torque[1] = generalForce[4]; |
| 478 |
torque[2] = generalForce[5]; |
| 479 |
|
| 480 |
} |
| 481 |
|
| 482 |
} |
