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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 "math/CholeskyDecomposition.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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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" |
| 76 |
< |
" 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" |
| 88 |
< |
" 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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|
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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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} |
| 104 |
+ |
|
| 105 |
+ |
if (!simParams->haveThermalLength()) { |
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+ |
sprintf(painCave.errMsg, |
| 107 |
+ |
"SMIPDynamics error: You can't use the SMIPD integrator\n" |
| 108 |
+ |
"\twithout a thermalLength (Angstroms)!\n"); |
| 109 |
+ |
painCave.isFatal = 1; |
| 110 |
+ |
painCave.severity = OOPSE_ERROR; |
| 111 |
+ |
simError(); |
| 112 |
+ |
}else{ |
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+ |
thermalLength_ = simParams->getThermalLength(); |
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+ |
} |
| 115 |
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|
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dt_ = simParams->getDt(); |
| 117 |
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|
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StuntDouble* integrableObject; |
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|
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// Compute surface Mesh |
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|
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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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int nTriangles = sMesh.size(); |
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|
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// Generate all of the necessary random forces |
| 154 |
< |
std::vector<Vector3d> randNums = genTriangleForces(nTriangles, variance_); |
| 154 |
> |
std::vector<RealType> 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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unitNormal.normalize(); |
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Vector3d centroid = thisTriangle.getCentroid(); |
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|
Vector3d facetVel = thisTriangle.getFacetVelocity(); |
| 170 |
+ |
RealType thisMass = thisTriangle.getFacetMass(); |
| 171 |
|
|
| 172 |
< |
Mat3x3d hydroTensor = thisTriangle.computeHydrodynamicTensor(viscosity_); |
| 172 |
> |
// gamma is the drag coefficient normal to the face of the triangle |
| 173 |
> |
RealType gamma = thermalConductivity_ * thisMass * thisArea |
| 174 |
> |
/ (2.0 * thermalLength_ * OOPSEConstant::kB); |
| 175 |
> |
|
| 176 |
> |
RealType extPressure = - (targetPressure_ * thisArea) / |
| 177 |
> |
OOPSEConstant::energyConvert; |
| 178 |
|
|
| 179 |
< |
hydroTensor *= OOPSEConstant::viscoConvert; |
| 180 |
< |
Mat3x3d S; |
| 163 |
< |
CholeskyDecomposition(hydroTensor, S); |
| 179 |
> |
RealType randomForce = randNums[thisFacet++] * sqrt(gamma); |
| 180 |
> |
RealType dragForce = -gamma * dot(facetVel, unitNormal); |
| 181 |
|
|
| 182 |
< |
Vector3d extPressure = -unitNormal*(targetPressure_ * thisArea)/OOPSEConstant::energyConvert; |
| 183 |
< |
Vector3d randomForce = S * randNums[thisFacet++]; |
| 184 |
< |
Vector3d dragForce = -hydroTensor * facetVel; |
| 168 |
< |
|
| 169 |
< |
Vector3d langevinForce = (extPressure + randomForce + dragForce); |
| 170 |
< |
|
| 182 |
> |
Vector3d langevinForce = (extPressure + randomForce + dragForce) * |
| 183 |
> |
unitNormal; |
| 184 |
> |
|
| 185 |
|
// Apply triangle force to stuntdouble vertices |
| 186 |
|
for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex){ |
| 187 |
|
if ((*vertex) != NULL){ |
| 195 |
|
} |
| 196 |
|
} |
| 197 |
|
} |
| 198 |
< |
|
| 198 |
> |
|
| 199 |
|
veloMunge->removeComDrift(); |
| 200 |
|
veloMunge->removeAngularDrift(); |
| 201 |
< |
|
| 201 |
> |
|
| 202 |
|
Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 203 |
|
currSnapshot->setVolume(surfaceMesh_->getVolume()); |
| 204 |
|
ForceManager::postCalculation(needStress); |
| 205 |
|
} |
| 192 |
– |
|
| 206 |
|
|
| 207 |
< |
std::vector<Vector3d> SMIPDForceManager::genTriangleForces(int nTriangles, |
| 207 |
> |
|
| 208 |
> |
std::vector<RealType> SMIPDForceManager::genTriangleForces(int nTriangles, |
| 209 |
|
RealType variance) |
| 210 |
|
{ |
| 211 |
|
|
| 212 |
|
// zero fill the random vector before starting: |
| 213 |
< |
std::vector<Vector3d> gaussRand; |
| 213 |
> |
std::vector<RealType> gaussRand; |
| 214 |
|
gaussRand.resize(nTriangles); |
| 215 |
< |
std::fill(gaussRand.begin(), gaussRand.end(), V3Zero); |
| 215 |
> |
std::fill(gaussRand.begin(), gaussRand.end(), 0.0); |
| 216 |
|
|
| 217 |
|
#ifdef IS_MPI |
| 218 |
|
if (worldRank == 0) { |
| 219 |
|
#endif |
| 206 |
– |
RealType rx, ry, rz; |
| 220 |
|
for (int i = 0; i < nTriangles; i++) { |
| 221 |
< |
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; |
| 221 |
> |
gaussRand[i] = randNumGen_.randNorm(0.0, variance); |
| 222 |
|
} |
| 223 |
|
#ifdef IS_MPI |
| 224 |
|
} |
| 228 |
|
|
| 229 |
|
#ifdef IS_MPI |
| 230 |
|
if (worldRank == 0) { |
| 231 |
< |
MPI_Bcast(&gaussRand[0], nTriangles*3 , MPI_REALTYPE, 0, MPI_COMM_WORLD); |
| 231 |
> |
MPI::COMM_WORLD.Bcast(&gaussRand[0], nTriangles, MPI::REALTYPE, 0); |
| 232 |
|
} else { |
| 233 |
< |
MPI_Bcast(&gaussRand[0], nTriangles*3, MPI_REALTYPE, 0, MPI_COMM_WORLD); |
| 233 |
> |
MPI::COMM_WORLD.Bcast(&gaussRand[0], nTriangles, MPI::REALTYPE, 0); |
| 234 |
|
} |
| 235 |
|
#endif |
| 236 |
|
|
