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/* |
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* Copyright (c) 2008 The University of Notre Dame. All Rights Reserved. |
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* Copyright (c) 2008, 2009 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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#include "math/Triangle.hpp" |
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namespace oopse { |
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SMIPDForceManager::SMIPDForceManager(SimInfo* info) : ForceManager(info) { |
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simParams = info->getSimParams(); |
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veloMunge = new Velocitizer(info); |
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// Create Hull, Convex Hull for now, other options later. |
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surfaceMesh_ = new ConvexHull(); |
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/* Check that the simulation has target pressure and target |
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temperature set*/ |
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temperature set */ |
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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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"\twithout a targetTemp (K)!\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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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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"\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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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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"\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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if (!simParams->haveViscosity()) { |
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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 viscosity!\n"); |
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"\twithout a thermalConductivity (W m^-1 K^-1)!\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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viscosity_ = simParams->getViscosity(); |
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thermalConductivity_ = simParams->getThermalConductivity() * |
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OOPSEConstant::thermalConductivityConvert; |
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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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"\twithout a thermalLength (Angstroms)!\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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dt_ = simParams->getDt(); |
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variance_ = 2.0 * OOPSEConstant::kb * targetTemp_ / dt_; |
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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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Molecule::IntegrableObjectIterator j; |
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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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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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} |
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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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// Compute surface Mesh |
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surfaceMesh_->computeHull(localSites_); |
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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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// Generate all of the necessary random forces |
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std::vector<RealType> randNums = genTriangleForces(nTriangles, variance_); |
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// Loop over the mesh faces and apply random force to each of the faces |
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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 thisNumber = 0; |
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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.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 hydroLength = thisTriangle.getIncircleRadius() * 2.0 / |
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NumericConstant::PI; |
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RealType thisMass = thisTriangle.getFacetMass(); |
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// gamma is the drag coefficient normal to the face of the triangle |
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RealType gamma = viscosity_ * hydroLength * |
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OOPSEConstant::viscoConvert; |
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RealType gamma = thermalConductivity_ * thisMass * thisArea |
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/ (2.0 * thermalLength_ * OOPSEConstant::kB); |
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RealType extPressure = - (targetPressure_ * thisArea) / |
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OOPSEConstant::energyConvert; |
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RealType randomForce = randNums[thisNumber++] * sqrt(gamma); |
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RealType randomForce = randNums[thisFacet++] * sqrt(gamma); |
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RealType dragForce = -gamma * dot(facetVel, unitNormal); |
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Vector3d langevinForce = (extPressure + randomForce + dragForce) * unitNormal; |
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Vector3d langevinForce = (extPressure + randomForce + dragForce) * |
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unitNormal; |
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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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// 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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(*vertex)->addFrc(vertexForce); |
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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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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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std::vector<RealType> SMIPDForceManager::genTriangleForces(int nTriangles, |
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RealType variance) { |
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RealType variance) |
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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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#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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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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// push these out to the other processors |
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#ifdef IS_MPI |
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if (worldRank == 0) { |
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MPI_Bcast(&gaussRand[0], nTriangles, MPI_REALTYPE, 0, MPI_COMM_WORLD); |
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MPI::COMM_WORLD.Bcast(&gaussRand[0], nTriangles, MPI::REALTYPE, 0); |
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} else { |
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MPI_Bcast(&gaussRand[0], nTriangles, MPI_REALTYPE, 0, MPI_COMM_WORLD); |
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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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return gaussRand; |
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} |
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} |
