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/* |
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* Copyright (c) 2008, 2009, 2010 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. 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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* 2. 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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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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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/PhysicalConstants.hpp" |
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#include "math/ConvexHull.hpp" |
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#include "math/AlphaHull.hpp" |
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#include "math/Triangle.hpp" |
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#include "math/CholeskyDecomposition.hpp" |
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#ifdef IS_MPI |
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#include <mpi.h> |
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#endif |
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|
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namespace OpenMD { |
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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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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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stringToEnumMap_["Convex"] = hullConvex; |
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stringToEnumMap_["AlphaShape"] = hullAlphaShape; |
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stringToEnumMap_["Unknown"] = hullUnknown; |
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|
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const std::string ht = simParams->getHULL_Method(); |
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|
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|
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|
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std::map<std::string, HullTypeEnum>::iterator iter; |
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iter = stringToEnumMap_.find(ht); |
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hullType_ = (iter == stringToEnumMap_.end()) ? SMIPDForceManager::hullUnknown : iter->second; |
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if (hullType_ == hullUnknown) { |
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std::cerr << "WARNING! Hull Type Unknown!\n"; |
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} |
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|
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switch(hullType_) { |
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case hullConvex : |
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surfaceMesh_ = new ConvexHull(); |
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break; |
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case hullAlphaShape : |
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surfaceMesh_ = new AlphaHull(simParams->getAlpha()); |
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break; |
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case hullUnknown : |
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default : |
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break; |
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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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"\twithout a targetTemp (K)!\n"); |
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painCave.isFatal = 1; |
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painCave.severity = OPENMD_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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"\twithout a targetPressure (atm)!\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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PhysicalConstants::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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"\twith 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->haveViscosity()) { |
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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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"\twithout a viscosity!\n"); |
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painCave.isFatal = 1; |
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painCave.severity = OPENMD_ERROR; |
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simError(); |
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}else{ |
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viscosity_ = simParams->getViscosity(); |
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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 * PhysicalConstants::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(){ |
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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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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<Vector3d> randNums = genTriangleForces(nTriangles, variance_); |
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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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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.getUnitNormal(); |
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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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Mat3x3d hydroTensor = thisTriangle.computeHydrodynamicTensor(viscosity_); |
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|
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hydroTensor *= PhysicalConstants::viscoConvert; |
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Mat3x3d S; |
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CholeskyDecomposition(hydroTensor, S); |
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|
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Vector3d extPressure = -unitNormal * (targetPressure_ * thisArea) / |
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PhysicalConstants::energyConvert; |
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|
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Vector3d randomForce = S * randNums[thisFacet++]; |
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Vector3d dragForce = -hydroTensor * facetVel; |
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|
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Vector3d langevinForce = (extPressure + randomForce + dragForce); |
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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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} |
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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(); |
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} |
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|
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|
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std::vector<Vector3d> 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<Vector3d> gaussRand; |
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gaussRand.resize(nTriangles); |
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std::fill(gaussRand.begin(), gaussRand.end(), V3Zero); |
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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][0] = randNumGen_.randNorm(0.0, variance); |
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gaussRand[i][1] = randNumGen_.randNorm(0.0, variance); |
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gaussRand[i][2] = 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*3, MPI::REALTYPE, 0); |
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} else { |
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MPI::COMM_WORLD.Bcast(&gaussRand[0], nTriangles*3, 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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} |
