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/* |
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* Copyright (c) 2008 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/SMIPDForceManager.hpp" |
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#include "utils/OOPSEConstant.hpp" |
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#include "math/ConvexHull.hpp" |
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#include "math/Triangle.hpp" |
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|
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namespace oopse { |
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|
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SMIPDForceManager::SMIPDForceManager(SimInfo* info) : ForceManager(info) { |
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|
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simParams = info->getSimParams(); |
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thermo = new Thermo(info); |
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veloMunge = new Velocitizer(info); |
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|
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// Create Hull, Convex Hull for now, other options later. |
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|
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surfaceMesh_ = new ConvexHull(); |
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|
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/* Check that the simulation has target pressure and target |
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temperature set */ |
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|
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if (!simParams->haveTargetTemp()) { |
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sprintf(painCave.errMsg, |
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"SMIPDynamics error: You can't use the SMIPD integrator\n" |
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" without a targetTemp!\n"); |
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painCave.isFatal = 1; |
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painCave.severity = OOPSE_ERROR; |
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simError(); |
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} else { |
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targetTemp_ = simParams->getTargetTemp(); |
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} |
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|
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if (!simParams->haveTargetPressure()) { |
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sprintf(painCave.errMsg, |
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"SMIPDynamics error: You can't use the SMIPD integrator\n" |
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" without a targetPressure!\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} else { |
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// Convert pressure from atm -> amu/(fs^2*Ang) |
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targetPressure_ = simParams->getTargetPressure() / |
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OOPSEConstant::pressureConvert; |
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} |
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|
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if (simParams->getUsePeriodicBoundaryConditions()) { |
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sprintf(painCave.errMsg, |
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"SMIPDynamics error: You can't use the SMIPD integrator\n" |
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" with periodic boundary conditions!\n"); |
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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->haveThermalConductivity()) { |
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sprintf(painCave.errMsg, |
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"SMIPDynamics error: You can't use the SMIPD integrator\n" |
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" without a thermalConductivity!\n"); |
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painCave.isFatal = 1; |
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painCave.severity = OOPSE_ERROR; |
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simError(); |
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}else{ |
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thermalConductivity_ = simParams->getThermalConductivity(); |
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} |
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|
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if (!simParams->haveThermalLength()) { |
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sprintf(painCave.errMsg, |
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"SMIPDynamics error: You can't use the SMIPD integrator\n" |
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" without a thermalLength!\n"); |
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painCave.isFatal = 1; |
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painCave.severity = OOPSE_ERROR; |
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simError(); |
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}else{ |
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thermalLength_ = simParams->getThermalLength(); |
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} |
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|
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dt_ = simParams->getDt(); |
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|
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variance_ = 2.0 * OOPSEConstant::kb * targetTemp_ / dt_; |
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|
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// Build a vector of integrable objects to determine if the are |
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// surface atoms |
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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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|
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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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localSites_.push_back(integrableObject); |
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} |
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} |
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} |
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|
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void SMIPDForceManager::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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|
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// Compute surface Mesh |
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surfaceMesh_->computeHull(localSites_); |
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|
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// Get total area and number of surface stunt doubles |
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RealType area = surfaceMesh_->getArea(); |
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int nSurfaceSDs = surfaceMesh_->getNs(); |
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std::vector<Triangle> sMesh = surfaceMesh_->getMesh(); |
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int nTriangles = sMesh.size(); |
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|
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// Generate all of the necessary random forces |
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std::vector<RealType> randNums = genTriangleForces(nTriangles, variance_); |
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|
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RealType instaTemp = thermo->getTemperature(); |
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|
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// Loop over the mesh faces and apply external pressure to each |
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// of the faces |
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std::vector<Triangle>::iterator face; |
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std::vector<StuntDouble*>::iterator vertex; |
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int thisFacet = 0; |
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for (face = sMesh.begin(); face != sMesh.end(); ++face){ |
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|
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Triangle thisTriangle = *face; |
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std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices(); |
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RealType thisArea = thisTriangle.getArea(); |
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Vector3d unitNormal = thisTriangle.getNormal(); |
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unitNormal.normalize(); |
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Vector3d centroid = thisTriangle.getCentroid(); |
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Vector3d facetVel = thisTriangle.getFacetVelocity(); |
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RealType thisMass = thisTriangle.getFacetMass(); |
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|
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// gamma is the drag coefficient normal to the face of the triangle |
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RealType gamma = thermalConductivity_ * thisMass * thisArea |
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/ (2.0 * thermalLength_ * OOPSEConstant::kb); |
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|
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gamma *= fabs(1.0 - targetTemp_/instaTemp); |
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|
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RealType extPressure = - (targetPressure_ * thisArea) / |
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OOPSEConstant::energyConvert; |
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|
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RealType randomForce = randNums[thisFacet++] * sqrt(gamma); |
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RealType dragForce = -gamma * dot(facetVel, unitNormal); |
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|
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Vector3d langevinForce = (extPressure + randomForce + dragForce) * |
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unitNormal; |
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|
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// Apply triangle force to stuntdouble vertices |
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for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex){ |
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if ((*vertex) != NULL){ |
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Vector3d vertexForce = langevinForce / 3.0; |
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(*vertex)->addFrc(vertexForce); |
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if ((*vertex)->isDirectional()){ |
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Vector3d vertexPos = (*vertex)->getPos(); |
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Vector3d vertexCentroidVector = vertexPos - centroid; |
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(*vertex)->addTrq(cross(vertexCentroidVector,vertexForce)); |
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} |
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} |
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} |
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} |
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|
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veloMunge->removeComDrift(); |
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veloMunge->removeAngularDrift(); |
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|
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Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
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currSnapshot->setVolume(surfaceMesh_->getVolume()); |
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ForceManager::postCalculation(needStress); |
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} |
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|
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|
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std::vector<RealType> SMIPDForceManager::genTriangleForces(int nTriangles, |
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RealType variance) |
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{ |
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|
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// zero fill the random vector before starting: |
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std::vector<RealType> gaussRand; |
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gaussRand.resize(nTriangles); |
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std::fill(gaussRand.begin(), gaussRand.end(), 0.0); |
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|
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#ifdef IS_MPI |
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if (worldRank == 0) { |
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#endif |
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for (int i = 0; i < nTriangles; i++) { |
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gaussRand[i] = randNumGen_.randNorm(0.0, variance); |
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} |
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#ifdef IS_MPI |
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} |
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#endif |
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|
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// push these out to the other processors |
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|
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#ifdef IS_MPI |
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if (worldRank == 0) { |
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MPI::COMM_WORLD.Bcast(&gaussRand[0], nTriangles, MPI::REALTYPE, 0); |
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} else { |
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MPI::COMM_WORLD.Bcast(&gaussRand[0], nTriangles, MPI::REALTYPE, 0); |
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} |
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#endif |
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|
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return gaussRand; |
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} |
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} |
