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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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|
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/* |
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Provides the force manager for Isothermal-Isobaric Langevin Dynamics where the stochastic force |
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is applied to the surface atoms anisotropically so as to provide a constant pressure. The |
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surface atoms are determined by computing the convex hull and then triangulating that hull. The force |
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applied to the facets of the triangulation and mapped back onto the surface atoms. |
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See: Kohanoff et.al. CHEMPHYSCHEM,2005,6,1848-1852. |
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*/ |
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|
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#include <fstream> |
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#include <iostream> |
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#include "integrators/SMLDForceManager.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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#if defined(HAVE_QHULL) || defined(HAVE_CGAL) |
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#ifdef HAVE_QHULL |
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#include "math/ConvexHull.hpp" |
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#endif |
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|
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#ifdef HAVE_CGAL |
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#include "math/AlphaShape.hpp" |
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#endif |
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#endif |
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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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SMLDForceManager::SMLDForceManager(SimInfo* info) : ForceManager(info){ |
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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\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_d / 2.0, |
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gayBerneParam.GB_l / 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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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*> SMLDForceManager::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 SMLDForceManager::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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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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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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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(); |
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Vector3d angMom = integrableObject->getJ(); |
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Vector3d omega; |
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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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omega[l] = angMom[l] /I(l, l); |
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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 |
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A = integrableObject->getA(); |
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Atrans = A.transpose(); |
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Vector3d rcr = Atrans * hydroProps_[index]->getCOR(); |
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Vector3d vcdLab = vel + cross(omega, rcr); |
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Vector3d vcdBody = A* vcdLab; |
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Vector3d frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omega); |
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Vector3d frictionForceLab = Atrans*frictionForceBody; |
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integrableObject->addFrc(frictionForceLab); |
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Vector3d frictionTorqueBody = - (hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omega); |
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Vector3d frictionTorqueLab = Atrans*frictionTorqueBody; |
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integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab)); |
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|
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//apply random force and torque at center of resistance |
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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(rcr, randomForceLab )); |
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|
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} else { |
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//spherical atom |
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Vector3d frictionForce = -(hydroProps_[index]->getXitt() * vel); |
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Vector3d randomForce; |
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Vector3d randomTorque; |
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genRandomForceAndTorque(randomForce, randomTorque, index, variance_); |
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|
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integrableObject->addFrc(frictionForce+randomForce); |
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} |
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} |
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|
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++index; |
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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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// commented out for testing one particle |
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// veloMunge->removeComDrift(); |
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// Remove angular drift if we are not using periodic boundary conditions. |
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if(!simParams->getUsePeriodicBoundaryConditions()) |
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veloMunge->removeAngularDrift(); |
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|
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ForceManager::postCalculation(needStress); |
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} |
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|
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void SMLDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) { |
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|
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|
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Vector<RealType, 6> Z; |
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Vector<RealType, 6> generalForce; |
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|
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Z[0] = randNumGen_.randNorm(0, variance); |
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Z[1] = randNumGen_.randNorm(0, variance); |
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Z[2] = randNumGen_.randNorm(0, variance); |
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Z[3] = randNumGen_.randNorm(0, variance); |
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Z[4] = randNumGen_.randNorm(0, variance); |
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Z[5] = randNumGen_.randNorm(0, variance); |
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|
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|
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generalForce = hydroProps_[index]->getS()*Z; |
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|
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force[0] = generalForce[0]; |
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force[1] = generalForce[1]; |
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force[2] = generalForce[2]; |
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torque[0] = generalForce[3]; |
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torque[1] = generalForce[4]; |
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torque[2] = generalForce[5]; |
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|
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} |
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|
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} |
