| 43 |
|
#include "integrators/SMIPDForceManager.hpp" |
| 44 |
|
#include "math/CholeskyDecomposition.hpp" |
| 45 |
|
#include "utils/OOPSEConstant.hpp" |
| 46 |
– |
#include "hydrodynamics/Sphere.hpp" |
| 47 |
– |
#include "hydrodynamics/Ellipsoid.hpp" |
| 48 |
– |
#include "utils/ElementsTable.hpp" |
| 46 |
|
#include "math/ConvexHull.hpp" |
| 47 |
|
#include "math/Triangle.hpp" |
| 48 |
|
|
| 52 |
– |
|
| 49 |
|
namespace oopse { |
| 50 |
< |
|
| 51 |
< |
SMIPDForceManager::SMIPDForceManager(SimInfo* info) : ForceManager(info), forceTolerance_(1e-6), maxIterNum_(4) { |
| 50 |
> |
|
| 51 |
> |
SMIPDForceManager::SMIPDForceManager(SimInfo* info) : ForceManager(info) { |
| 52 |
> |
|
| 53 |
|
simParams = info->getSimParams(); |
| 54 |
|
veloMunge = new Velocitizer(info); |
| 55 |
|
|
| 56 |
|
// Create Hull, Convex Hull for now, other options later. |
| 57 |
+ |
|
| 58 |
|
surfaceMesh_ = new ConvexHull(); |
| 61 |
– |
|
| 59 |
|
|
| 63 |
– |
|
| 60 |
|
/* Check that the simulation has target pressure and target |
| 61 |
< |
temperature set*/ |
| 61 |
> |
temperature set */ |
| 62 |
|
|
| 63 |
|
if (!simParams->haveTargetTemp()) { |
| 64 |
< |
sprintf(painCave.errMsg, "You can't use the SMIPDynamics integrator without a targetTemp!\n"); |
| 64 |
> |
sprintf(painCave.errMsg, |
| 65 |
> |
"SMIPDynamics error: You can't use the SMIPD integrator\n" |
| 66 |
> |
" without a targetTemp!\n"); |
| 67 |
|
painCave.isFatal = 1; |
| 68 |
|
painCave.severity = OOPSE_ERROR; |
| 69 |
|
simError(); |
| 72 |
|
} |
| 73 |
|
|
| 74 |
|
if (!simParams->haveTargetPressure()) { |
| 75 |
< |
sprintf(painCave.errMsg, "SMIPDynamics error: You can't use the SMIPD integrator\n" |
| 76 |
< |
" without a targetPressure!\n"); |
| 77 |
< |
|
| 75 |
> |
sprintf(painCave.errMsg, |
| 76 |
> |
"SMIPDynamics error: You can't use the SMIPD integrator\n" |
| 77 |
> |
" without a targetPressure!\n"); |
| 78 |
|
painCave.isFatal = 1; |
| 79 |
|
simError(); |
| 80 |
|
} else { |
| 81 |
< |
/* Convert pressure from atm -> amu/(fs^2*Ang)*/ |
| 82 |
< |
targetPressure_ = simParams->getTargetPressure()/OOPSEConstant::pressureConvert; |
| 81 |
> |
// Convert pressure from atm -> amu/(fs^2*Ang) |
| 82 |
> |
targetPressure_ = simParams->getTargetPressure() / |
| 83 |
> |
OOPSEConstant::pressureConvert; |
| 84 |
|
} |
| 86 |
– |
|
| 85 |
|
|
| 86 |
|
if (simParams->getUsePeriodicBoundaryConditions()) { |
| 87 |
< |
sprintf(painCave.errMsg, "SMIPDynamics error: You can't use the SMIPD integrator\n" |
| 88 |
< |
" with periodic boundary conditions !\n"); |
| 89 |
< |
|
| 87 |
> |
sprintf(painCave.errMsg, |
| 88 |
> |
"SMIPDynamics error: You can't use the SMIPD integrator\n" |
| 89 |
> |
" with periodic boundary conditions!\n"); |
| 90 |
|
painCave.isFatal = 1; |
| 91 |
|
simError(); |
| 92 |
|
} |
| 93 |
< |
|
| 93 |
> |
|
| 94 |
|
if (!simParams->haveViscosity()) { |
| 95 |
< |
sprintf(painCave.errMsg, "You can't use SMIPDynamics without a viscosity!\n"); |
| 95 |
> |
sprintf(painCave.errMsg, |
| 96 |
> |
"SMIPDynamics error: You can't use the SMIPD integrator\n" |
| 97 |
> |
" without a viscosity!\n"); |
| 98 |
|
painCave.isFatal = 1; |
| 99 |
|
painCave.severity = OOPSE_ERROR; |
| 100 |
|
simError(); |
| 101 |
|
}else{ |
| 102 |
|
viscosity_ = simParams->getViscosity(); |
| 103 |
|
} |
| 104 |
< |
|
| 104 |
> |
|
| 105 |
|
dt_ = simParams->getDt(); |
| 106 |
+ |
|
| 107 |
+ |
variance_ = 2.0 * OOPSEConstant::kb * targetTemp_ / dt_; |
| 108 |
|
|
| 109 |
< |
|
| 110 |
< |
|
| 109 |
< |
//Compute initial hull |
| 110 |
< |
/* |
| 111 |
< |
surfaceMesh_->computeHull(localSites_); |
| 112 |
< |
Area0_ = surfaceMesh_->getArea(); |
| 113 |
< |
int nTriangles = surfaceMesh_->getNMeshElements(); |
| 114 |
< |
// variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt(); |
| 115 |
< |
gamma_0_ = (NumericConstant::PI * targetPressure_* targetPressure_ * Area0_ * Area0_ * simParams->getDt()) / |
| 116 |
< |
(4.0 * nTriangles * nTriangles* OOPSEConstant::kb*simParams->getTargetTemp()); |
| 117 |
< |
//RealType eta0 = gamma_0/ |
| 118 |
< |
*/ |
| 119 |
< |
|
| 120 |
< |
|
| 109 |
> |
// Build a vector of integrable objects to determine if the are |
| 110 |
> |
// surface atoms |
| 111 |
|
Molecule* mol; |
| 112 |
|
StuntDouble* integrableObject; |
| 113 |
|
SimInfo::MoleculeIterator i; |
| 114 |
< |
Molecule::IntegrableObjectIterator j; |
| 114 |
> |
Molecule::IntegrableObjectIterator j; |
| 115 |
|
|
| 116 |
< |
|
| 117 |
< |
|
| 118 |
< |
/* Compute hull first time through to get the area of t=0*/ |
| 119 |
< |
|
| 130 |
< |
//Build a vector of integrable objects to determine if the are surface atoms |
| 131 |
< |
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
| 132 |
< |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 116 |
> |
for (mol = info_->beginMolecule(i); mol != NULL; |
| 117 |
> |
mol = info_->nextMolecule(i)) { |
| 118 |
> |
for (integrableObject = mol->beginIntegrableObject(j); |
| 119 |
> |
integrableObject != NULL; |
| 120 |
|
integrableObject = mol->nextIntegrableObject(j)) { |
| 121 |
|
localSites_.push_back(integrableObject); |
| 122 |
|
} |
| 123 |
< |
} |
| 137 |
< |
|
| 138 |
< |
|
| 123 |
> |
} |
| 124 |
|
} |
| 140 |
– |
|
| 141 |
– |
std::map<std::string, HydroProp*> SMIPDForceManager::parseFrictionFile(const std::string& filename) { |
| 142 |
– |
std::map<std::string, HydroProp*> props; |
| 143 |
– |
std::ifstream ifs(filename.c_str()); |
| 144 |
– |
if (ifs.is_open()) { |
| 145 |
– |
|
| 146 |
– |
} |
| 147 |
– |
|
| 148 |
– |
const unsigned int BufferSize = 65535; |
| 149 |
– |
char buffer[BufferSize]; |
| 150 |
– |
while (ifs.getline(buffer, BufferSize)) { |
| 151 |
– |
HydroProp* currProp = new HydroProp(buffer); |
| 152 |
– |
props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp)); |
| 153 |
– |
} |
| 154 |
– |
|
| 155 |
– |
return props; |
| 156 |
– |
} |
| 125 |
|
|
| 126 |
|
void SMIPDForceManager::postCalculation(bool needStress){ |
| 127 |
|
SimInfo::MoleculeIterator i; |
| 128 |
|
Molecule::IntegrableObjectIterator j; |
| 129 |
|
Molecule* mol; |
| 130 |
|
StuntDouble* integrableObject; |
| 163 |
– |
RealType mass; |
| 164 |
– |
Vector3d pos; |
| 165 |
– |
Vector3d frc; |
| 166 |
– |
Mat3x3d A; |
| 167 |
– |
Mat3x3d Atrans; |
| 168 |
– |
Vector3d Tb; |
| 169 |
– |
Vector3d ji; |
| 170 |
– |
unsigned int index = 0; |
| 171 |
– |
int fdf; |
| 172 |
– |
|
| 173 |
– |
fdf = 0; |
| 131 |
|
|
| 132 |
< |
/*Compute surface Mesh*/ |
| 132 |
> |
// Compute surface Mesh |
| 133 |
|
surfaceMesh_->computeHull(localSites_); |
| 134 |
|
|
| 135 |
< |
/* Get area and number of surface stunt doubles and compute new variance */ |
| 136 |
< |
RealType area = surfaceMesh_->getArea(); |
| 137 |
< |
int nSurfaceSDs = surfaceMesh_->getNs(); |
| 181 |
< |
|
| 182 |
< |
|
| 135 |
> |
// Get total area and number of surface stunt doubles |
| 136 |
> |
RealType area = surfaceMesh_->getArea(); |
| 137 |
> |
int nSurfaceSDs = surfaceMesh_->getNs(); |
| 138 |
|
std::vector<Triangle> sMesh = surfaceMesh_->getMesh(); |
| 139 |
|
int nTriangles = sMesh.size(); |
| 140 |
|
|
| 141 |
+ |
// Generate all of the necessary random forces |
| 142 |
+ |
std::vector<Vector3d> randNums = genTriangleForces(nTriangles, variance_); |
| 143 |
|
|
| 144 |
< |
|
| 145 |
< |
/* Compute variance for random forces */ |
| 189 |
< |
std::vector<RealType> randNums = genTriangleForces(nTriangles, 1.0); |
| 190 |
< |
|
| 191 |
< |
/* Loop over the mesh faces and apply random force to each of the faces*/ |
| 144 |
> |
// Loop over the mesh faces and apply external pressure to each |
| 145 |
> |
// of the faces |
| 146 |
|
std::vector<Triangle>::iterator face; |
| 147 |
|
std::vector<StuntDouble*>::iterator vertex; |
| 148 |
< |
int thisNumber = 0; |
| 148 |
> |
int thisFacet = 0; |
| 149 |
|
for (face = sMesh.begin(); face != sMesh.end(); ++face){ |
| 150 |
|
|
| 151 |
|
Triangle thisTriangle = *face; |
| 152 |
|
std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices(); |
| 153 |
|
RealType thisArea = thisTriangle.getArea(); |
| 200 |
– |
// RealType sigma_t = sqrt(NumericConstant::PI/2.0)*((targetPressure_)*thisArea) /OOPSEConstant::energyConvert; |
| 201 |
– |
// gamma_t_ = (NumericConstant::PI * targetPressure_* targetPressure_ * thisArea * thisArea * simParams->getDt()) /(4.0 * OOPSEConstant::kB*simParams->getTargetTemp()); |
| 202 |
– |
|
| 203 |
– |
/* Get Random Force */ |
| 154 |
|
Vector3d unitNormal = thisTriangle.getNormal(); |
| 155 |
|
unitNormal.normalize(); |
| 206 |
– |
//Vector3d randomForce = -randNums[thisNumber] * sigma_t * unitNormal; |
| 156 |
|
Vector3d centroid = thisTriangle.getCentroid(); |
| 157 |
|
Vector3d facetVel = thisTriangle.getFacetVelocity(); |
| 209 |
– |
RealType hydroLength = thisTriangle.getIncircleRadius()*2.0/NumericConstant::PI; |
| 158 |
|
|
| 159 |
< |
RealType f_normal = viscosity_*hydroLength*OOPSEConstant::viscoConvert; |
| 212 |
< |
RealType extPressure = -(targetPressure_ * thisArea)/OOPSEConstant::energyConvert; |
| 213 |
< |
RealType randomForce = randNums[thisNumber++] * sqrt(2.0 * f_normal * OOPSEConstant::kb*targetTemp_/dt_); |
| 159 |
> |
Mat3x3d hydroTensor = thisTriangle.computeHydrodynamicTensor(viscosity_); |
| 160 |
|
|
| 161 |
< |
RealType dragForce = -f_normal * dot(facetVel, unitNormal); |
| 161 |
> |
hydroTensor *= OOPSEConstant::viscoConvert; |
| 162 |
> |
Mat3x3d S; |
| 163 |
> |
CholeskyDecomposition(hydroTensor, S); |
| 164 |
|
|
| 165 |
+ |
Vector3d extPressure = -unitNormal*(targetPressure_ * thisArea)/OOPSEConstant::energyConvert; |
| 166 |
+ |
Vector3d randomForce = S * randNums[thisFacet++]; |
| 167 |
+ |
Vector3d dragForce = -hydroTensor * facetVel; |
| 168 |
|
|
| 169 |
< |
Vector3d langevinForce = (extPressure + randomForce + dragForce) * unitNormal; |
| 219 |
< |
|
| 220 |
< |
// Vector3d dragForce = - gamma_t_ * dot(facetVel, unitNormal) * unitNormal / OOPSEConstant::energyConvert; |
| 221 |
< |
|
| 222 |
< |
// std::cout << " " << randomForce << " " << f_normal << std::endl; |
| 169 |
> |
Vector3d langevinForce = (extPressure + randomForce + dragForce); |
| 170 |
|
|
| 171 |
< |
/* Apply triangle force to stuntdouble vertices */ |
| 171 |
> |
// Apply triangle force to stuntdouble vertices |
| 172 |
|
for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex){ |
| 173 |
< |
if ((*vertex) != NULL){ |
| 174 |
< |
// mass = integrableObject->getMass(); |
| 175 |
< |
Vector3d vertexForce = langevinForce/3.0; |
| 176 |
< |
(*vertex)->addFrc(vertexForce); |
| 230 |
< |
|
| 231 |
< |
if ((*vertex)->isDirectional()){ |
| 232 |
< |
|
| 173 |
> |
if ((*vertex) != NULL){ |
| 174 |
> |
Vector3d vertexForce = langevinForce / 3.0; |
| 175 |
> |
(*vertex)->addFrc(vertexForce); |
| 176 |
> |
if ((*vertex)->isDirectional()){ |
| 177 |
|
Vector3d vertexPos = (*vertex)->getPos(); |
| 178 |
|
Vector3d vertexCentroidVector = vertexPos - centroid; |
| 179 |
|
(*vertex)->addTrq(cross(vertexCentroidVector,vertexForce)); |
| 181 |
|
} |
| 182 |
|
} |
| 183 |
|
} |
| 184 |
+ |
|
| 185 |
+ |
veloMunge->removeComDrift(); |
| 186 |
+ |
veloMunge->removeAngularDrift(); |
| 187 |
|
|
| 188 |
|
Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 189 |
|
currSnapshot->setVolume(surfaceMesh_->getVolume()); |
| 190 |
|
ForceManager::postCalculation(needStress); |
| 191 |
|
} |
| 192 |
|
|
| 193 |
< |
void SMIPDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) { |
| 194 |
< |
|
| 193 |
> |
|
| 194 |
> |
std::vector<Vector3d> SMIPDForceManager::genTriangleForces(int nTriangles, |
| 195 |
> |
RealType variance) |
| 196 |
> |
{ |
| 197 |
|
|
| 249 |
– |
Vector<RealType, 6> Z; |
| 250 |
– |
Vector<RealType, 6> generalForce; |
| 251 |
– |
|
| 252 |
– |
|
| 253 |
– |
Z[0] = randNumGen_.randNorm(0, variance); |
| 254 |
– |
Z[1] = randNumGen_.randNorm(0, variance); |
| 255 |
– |
Z[2] = randNumGen_.randNorm(0, variance); |
| 256 |
– |
Z[3] = randNumGen_.randNorm(0, variance); |
| 257 |
– |
Z[4] = randNumGen_.randNorm(0, variance); |
| 258 |
– |
Z[5] = randNumGen_.randNorm(0, variance); |
| 259 |
– |
|
| 260 |
– |
generalForce = hydroProps_[index]->getS()*Z; |
| 261 |
– |
|
| 262 |
– |
force[0] = generalForce[0]; |
| 263 |
– |
force[1] = generalForce[1]; |
| 264 |
– |
force[2] = generalForce[2]; |
| 265 |
– |
torque[0] = generalForce[3]; |
| 266 |
– |
torque[1] = generalForce[4]; |
| 267 |
– |
torque[2] = generalForce[5]; |
| 268 |
– |
|
| 269 |
– |
} |
| 270 |
– |
std::vector<RealType> SMIPDForceManager::genTriangleForces(int nTriangles, RealType variance) { |
| 271 |
– |
|
| 198 |
|
// zero fill the random vector before starting: |
| 199 |
< |
std::vector<RealType> gaussRand; |
| 199 |
> |
std::vector<Vector3d> gaussRand; |
| 200 |
|
gaussRand.resize(nTriangles); |
| 201 |
< |
std::fill(gaussRand.begin(), gaussRand.end(), 0.0); |
| 276 |
< |
|
| 201 |
> |
std::fill(gaussRand.begin(), gaussRand.end(), V3Zero); |
| 202 |
|
|
| 278 |
– |
|
| 203 |
|
#ifdef IS_MPI |
| 204 |
|
if (worldRank == 0) { |
| 205 |
|
#endif |
| 206 |
+ |
RealType rx, ry, rz; |
| 207 |
|
for (int i = 0; i < nTriangles; i++) { |
| 208 |
< |
//gaussRand[i] = fabs(randNumGen_.randNorm(0.0, 1.0)); |
| 209 |
< |
gaussRand[i] = randNumGen_.randNorm(0.0, 1.0); |
| 208 |
> |
rx = randNumGen_.randNorm(0.0, variance); |
| 209 |
> |
ry = randNumGen_.randNorm(0.0, variance); |
| 210 |
> |
rz = randNumGen_.randNorm(0.0, variance); |
| 211 |
> |
gaussRand[i][0] = rx; |
| 212 |
> |
gaussRand[i][1] = ry; |
| 213 |
> |
gaussRand[i][2] = rz; |
| 214 |
|
} |
| 215 |
|
#ifdef IS_MPI |
| 216 |
|
} |
| 217 |
|
#endif |
| 218 |
< |
|
| 218 |
> |
|
| 219 |
|
// push these out to the other processors |
| 220 |
< |
|
| 220 |
> |
|
| 221 |
|
#ifdef IS_MPI |
| 222 |
|
if (worldRank == 0) { |
| 223 |
< |
MPI_Bcast(&gaussRand[0], nTriangles, MPI_REAL, 0, MPI_COMM_WORLD); |
| 223 |
> |
MPI_Bcast(&gaussRand[0], nTriangles*3 , MPI_REALTYPE, 0, MPI_COMM_WORLD); |
| 224 |
|
} else { |
| 225 |
< |
MPI_Bcast(&gaussRand[0], nTriangles, MPI_REAL, 0, MPI_COMM_WORLD); |
| 225 |
> |
MPI_Bcast(&gaussRand[0], nTriangles*3, MPI_REALTYPE, 0, MPI_COMM_WORLD); |
| 226 |
|
} |
| 227 |
|
#endif |
| 228 |
< |
|
| 300 |
< |
for (int i = 0; i < nTriangles; i++) { |
| 301 |
< |
gaussRand[i] = gaussRand[i] * variance; |
| 302 |
< |
} |
| 303 |
< |
|
| 228 |
> |
|
| 229 |
|
return gaussRand; |
| 230 |
|
} |
| 306 |
– |
|
| 307 |
– |
|
| 231 |
|
} |
