| 1 |
/* |
| 2 |
* Copyright (c) 2008 The University of Notre Dame. All Rights Reserved. |
| 3 |
* |
| 4 |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
* redistribute this software in source and binary code form, provided |
| 7 |
* that the following conditions are met: |
| 8 |
* |
| 9 |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
* publication of scientific results based in part on use of the |
| 11 |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
* the article in which the program was described (Matthew |
| 13 |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
* |
| 18 |
* 2. Redistributions of source code must retain the above copyright |
| 19 |
* notice, this list of conditions and the following disclaimer. |
| 20 |
* |
| 21 |
* 3. Redistributions in binary form must reproduce the above copyright |
| 22 |
* notice, this list of conditions and the following disclaimer in the |
| 23 |
* documentation and/or other materials provided with the |
| 24 |
* distribution. |
| 25 |
* |
| 26 |
* This software is provided "AS IS," without a warranty of any |
| 27 |
* kind. All express or implied conditions, representations and |
| 28 |
* warranties, including any implied warranty of merchantability, |
| 29 |
* fitness for a particular purpose or non-infringement, are hereby |
| 30 |
* excluded. The University of Notre Dame and its licensors shall not |
| 31 |
* be liable for any damages suffered by licensee as a result of |
| 32 |
* using, modifying or distributing the software or its |
| 33 |
* derivatives. In no event will the University of Notre Dame or its |
| 34 |
* licensors be liable for any lost revenue, profit or data, or for |
| 35 |
* direct, indirect, special, consequential, incidental or punitive |
| 36 |
* damages, however caused and regardless of the theory of liability, |
| 37 |
* arising out of the use of or inability to use software, even if the |
| 38 |
* University of Notre Dame has been advised of the possibility of |
| 39 |
* such damages. |
| 40 |
*/ |
| 41 |
#include <fstream> |
| 42 |
#include <iostream> |
| 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" |
| 49 |
#include "math/ConvexHull.hpp" |
| 50 |
#include "math/Triangle.hpp" |
| 51 |
|
| 52 |
|
| 53 |
namespace oopse { |
| 54 |
|
| 55 |
SMIPDForceManager::SMIPDForceManager(SimInfo* info) : ForceManager(info), forceTolerance_(1e-6), maxIterNum_(4) { |
| 56 |
simParams = info->getSimParams(); |
| 57 |
veloMunge = new Velocitizer(info); |
| 58 |
|
| 59 |
// Create Hull, Convex Hull for now, other options later. |
| 60 |
surfaceMesh_ = new ConvexHull(); |
| 61 |
|
| 62 |
|
| 63 |
/* Check that the simulation has target pressure and target |
| 64 |
temperature set*/ |
| 65 |
|
| 66 |
if (!simParams->haveTargetTemp()) { |
| 67 |
sprintf(painCave.errMsg, "You can't use the SMIPDynamics integrator without a targetTemp!\n"); |
| 68 |
painCave.isFatal = 1; |
| 69 |
painCave.severity = OOPSE_ERROR; |
| 70 |
simError(); |
| 71 |
} else { |
| 72 |
targetTemp_ = simParams->getTargetTemp(); |
| 73 |
} |
| 74 |
|
| 75 |
if (!simParams->haveTargetPressure()) { |
| 76 |
sprintf(painCave.errMsg, "SMIPDynamics error: You can't use the SMIPD integrator\n" |
| 77 |
" without a targetPressure!\n"); |
| 78 |
|
| 79 |
painCave.isFatal = 1; |
| 80 |
simError(); |
| 81 |
} else { |
| 82 |
targetPressure_ = simParams->getTargetPressure(); |
| 83 |
} |
| 84 |
|
| 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 |
|
| 90 |
painCave.isFatal = 1; |
| 91 |
simError(); |
| 92 |
} |
| 93 |
|
| 94 |
|
| 95 |
// Build the hydroProp map: |
| 96 |
std::map<std::string, HydroProp*> hydroPropMap; |
| 97 |
|
| 98 |
Molecule* mol; |
| 99 |
StuntDouble* integrableObject; |
| 100 |
SimInfo::MoleculeIterator i; |
| 101 |
Molecule::IntegrableObjectIterator j; |
| 102 |
bool needHydroPropFile = false; |
| 103 |
|
| 104 |
for (mol = info->beginMolecule(i); mol != NULL; |
| 105 |
mol = info->nextMolecule(i)) { |
| 106 |
for (integrableObject = mol->beginIntegrableObject(j); |
| 107 |
integrableObject != NULL; |
| 108 |
integrableObject = mol->nextIntegrableObject(j)) { |
| 109 |
|
| 110 |
if (integrableObject->isRigidBody()) { |
| 111 |
RigidBody* rb = static_cast<RigidBody*>(integrableObject); |
| 112 |
if (rb->getNumAtoms() > 1) needHydroPropFile = true; |
| 113 |
} |
| 114 |
|
| 115 |
} |
| 116 |
} |
| 117 |
|
| 118 |
|
| 119 |
if (needHydroPropFile) { |
| 120 |
if (simParams->haveHydroPropFile()) { |
| 121 |
hydroPropMap = parseFrictionFile(simParams->getHydroPropFile()); |
| 122 |
} else { |
| 123 |
sprintf( painCave.errMsg, |
| 124 |
"HydroPropFile must be set to a file name if SMIPDynamics\n" |
| 125 |
"\tis specified for rigidBodies which contain more than one atom\n" |
| 126 |
"\tTo create a HydroPropFile, run the \"Hydro\" program.\n\n" |
| 127 |
"\tFor use with SMIPD, the default viscosity in Hydro should be\n" |
| 128 |
"\tset to 1.0 because the friction and random forces will be\n" |
| 129 |
"\tdynamically re-set assuming this is true.\n"); |
| 130 |
painCave.severity = OOPSE_ERROR; |
| 131 |
painCave.isFatal = 1; |
| 132 |
simError(); |
| 133 |
} |
| 134 |
|
| 135 |
for (mol = info->beginMolecule(i); mol != NULL; |
| 136 |
mol = info->nextMolecule(i)) { |
| 137 |
for (integrableObject = mol->beginIntegrableObject(j); |
| 138 |
integrableObject != NULL; |
| 139 |
integrableObject = mol->nextIntegrableObject(j)) { |
| 140 |
|
| 141 |
std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType()); |
| 142 |
if (iter != hydroPropMap.end()) { |
| 143 |
hydroProps_.push_back(iter->second); |
| 144 |
} else { |
| 145 |
sprintf( painCave.errMsg, |
| 146 |
"Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str()); |
| 147 |
painCave.severity = OOPSE_ERROR; |
| 148 |
painCave.isFatal = 1; |
| 149 |
simError(); |
| 150 |
} |
| 151 |
} |
| 152 |
} |
| 153 |
} else { |
| 154 |
|
| 155 |
std::map<std::string, HydroProp*> hydroPropMap; |
| 156 |
for (mol = info->beginMolecule(i); mol != NULL; |
| 157 |
mol = info->nextMolecule(i)) { |
| 158 |
for (integrableObject = mol->beginIntegrableObject(j); |
| 159 |
integrableObject != NULL; |
| 160 |
integrableObject = mol->nextIntegrableObject(j)) { |
| 161 |
Shape* currShape = NULL; |
| 162 |
|
| 163 |
if (integrableObject->isAtom()){ |
| 164 |
Atom* atom = static_cast<Atom*>(integrableObject); |
| 165 |
AtomType* atomType = atom->getAtomType(); |
| 166 |
if (atomType->isGayBerne()) { |
| 167 |
DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType); |
| 168 |
GenericData* data = dAtomType->getPropertyByName("GayBerne"); |
| 169 |
if (data != NULL) { |
| 170 |
GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data); |
| 171 |
|
| 172 |
if (gayBerneData != NULL) { |
| 173 |
GayBerneParam gayBerneParam = gayBerneData->getData(); |
| 174 |
currShape = new Ellipsoid(V3Zero, |
| 175 |
gayBerneParam.GB_l / 2.0, |
| 176 |
gayBerneParam.GB_d / 2.0, |
| 177 |
Mat3x3d::identity()); |
| 178 |
} else { |
| 179 |
sprintf( painCave.errMsg, |
| 180 |
"Can not cast GenericData to GayBerneParam\n"); |
| 181 |
painCave.severity = OOPSE_ERROR; |
| 182 |
painCave.isFatal = 1; |
| 183 |
simError(); |
| 184 |
} |
| 185 |
} else { |
| 186 |
sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n"); |
| 187 |
painCave.severity = OOPSE_ERROR; |
| 188 |
painCave.isFatal = 1; |
| 189 |
simError(); |
| 190 |
} |
| 191 |
} else { |
| 192 |
if (atomType->isLennardJones()){ |
| 193 |
GenericData* data = atomType->getPropertyByName("LennardJones"); |
| 194 |
if (data != NULL) { |
| 195 |
LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data); |
| 196 |
if (ljData != NULL) { |
| 197 |
LJParam ljParam = ljData->getData(); |
| 198 |
currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0); |
| 199 |
} else { |
| 200 |
sprintf( painCave.errMsg, |
| 201 |
"Can not cast GenericData to LJParam\n"); |
| 202 |
painCave.severity = OOPSE_ERROR; |
| 203 |
painCave.isFatal = 1; |
| 204 |
simError(); |
| 205 |
} |
| 206 |
} |
| 207 |
} else { |
| 208 |
int aNum = etab.GetAtomicNum((atom->getType()).c_str()); |
| 209 |
if (aNum != 0) { |
| 210 |
currShape = new Sphere(atom->getPos(), etab.GetVdwRad(aNum)); |
| 211 |
} else { |
| 212 |
sprintf( painCave.errMsg, |
| 213 |
"Could not find atom type in default element.txt\n"); |
| 214 |
painCave.severity = OOPSE_ERROR; |
| 215 |
painCave.isFatal = 1; |
| 216 |
simError(); |
| 217 |
} |
| 218 |
} |
| 219 |
} |
| 220 |
} |
| 221 |
HydroProp* currHydroProp = currShape->getHydroProp(1.0,simParams->getTargetTemp()); |
| 222 |
std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType()); |
| 223 |
if (iter != hydroPropMap.end()) |
| 224 |
hydroProps_.push_back(iter->second); |
| 225 |
else { |
| 226 |
currHydroProp->complete(); |
| 227 |
hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(integrableObject->getType(), currHydroProp)); |
| 228 |
hydroProps_.push_back(currHydroProp); |
| 229 |
} |
| 230 |
} |
| 231 |
} |
| 232 |
} |
| 233 |
|
| 234 |
/* Compute hull first time through to get the area of t=0*/ |
| 235 |
|
| 236 |
/* Build a vector of integrable objects to determine if the are surface atoms */ |
| 237 |
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
| 238 |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 239 |
integrableObject = mol->nextIntegrableObject(j)) { |
| 240 |
localSites_.push_back(integrableObject); |
| 241 |
} |
| 242 |
} |
| 243 |
|
| 244 |
surfaceMesh_->computeHull(localSites_); |
| 245 |
Area0_ = surfaceMesh_->getArea(); |
| 246 |
//variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt(); |
| 247 |
|
| 248 |
} |
| 249 |
|
| 250 |
std::map<std::string, HydroProp*> SMIPDForceManager::parseFrictionFile(const std::string& filename) { |
| 251 |
std::map<std::string, HydroProp*> props; |
| 252 |
std::ifstream ifs(filename.c_str()); |
| 253 |
if (ifs.is_open()) { |
| 254 |
|
| 255 |
} |
| 256 |
|
| 257 |
const unsigned int BufferSize = 65535; |
| 258 |
char buffer[BufferSize]; |
| 259 |
while (ifs.getline(buffer, BufferSize)) { |
| 260 |
HydroProp* currProp = new HydroProp(buffer); |
| 261 |
props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp)); |
| 262 |
} |
| 263 |
|
| 264 |
return props; |
| 265 |
} |
| 266 |
|
| 267 |
void SMIPDForceManager::postCalculation(bool needStress){ |
| 268 |
SimInfo::MoleculeIterator i; |
| 269 |
Molecule::IntegrableObjectIterator j; |
| 270 |
Molecule* mol; |
| 271 |
StuntDouble* integrableObject; |
| 272 |
RealType mass; |
| 273 |
Vector3d pos; |
| 274 |
Vector3d frc; |
| 275 |
Mat3x3d A; |
| 276 |
Mat3x3d Atrans; |
| 277 |
Vector3d Tb; |
| 278 |
Vector3d ji; |
| 279 |
unsigned int index = 0; |
| 280 |
int fdf; |
| 281 |
|
| 282 |
fdf = 0; |
| 283 |
|
| 284 |
/*Compute surface Mesh*/ |
| 285 |
surfaceMesh_->computeHull(localSites_); |
| 286 |
|
| 287 |
/* Get area and number of surface stunt doubles and compute new variance */ |
| 288 |
RealType area = surfaceMesh_->getArea(); |
| 289 |
int nSurfaceSDs = surfaceMesh_->getNs(); |
| 290 |
|
| 291 |
/* Compute variance for random forces */ |
| 292 |
|
| 293 |
variance_ = sqrt(2.0*NumericConstant::PI)*((targetPressure_/OOPSEConstant::pressureConvert)*area/nSurfaceSDs); |
| 294 |
|
| 295 |
std::vector<Triangle*> sMesh = surfaceMesh_->getMesh(); |
| 296 |
std::vector<RealType> randNums = genTriangleForces(sMesh.size(),variance_); |
| 297 |
|
| 298 |
/* Loop over the mesh faces and apply random force to each of the faces*/ |
| 299 |
|
| 300 |
|
| 301 |
std::vector<Triangle*>::iterator face; |
| 302 |
std::vector<StuntDouble*>::iterator vertex; |
| 303 |
int thisNumber = 0; |
| 304 |
for (face = sMesh.begin(); face != sMesh.end(); ++face){ |
| 305 |
|
| 306 |
Triangle* thisTriangle = *face; |
| 307 |
std::vector<StuntDouble*> vertexSDs = thisTriangle->getVertices(); |
| 308 |
|
| 309 |
/* Get Random Force */ |
| 310 |
Vector3d unitNormal = thisTriangle->getNormal(); |
| 311 |
unitNormal.normalize(); |
| 312 |
Vector3d randomForce = -randNums[thisNumber] * unitNormal; |
| 313 |
|
| 314 |
for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex){ |
| 315 |
|
| 316 |
// mass = integrableObject->getMass(); |
| 317 |
|
| 318 |
(*vertex)->addFrc(randomForce/3.0); |
| 319 |
} |
| 320 |
} |
| 321 |
|
| 322 |
/* Now loop over all surface particles and apply the drag*/ |
| 323 |
|
| 324 |
std::vector<StuntDouble*> surfaceSDs = surfaceMesh_->getSurfaceAtoms(); |
| 325 |
for (vertex = surfaceSDs.begin(); vertex != surfaceSDs.end(); ++vertex){ |
| 326 |
integrableObject = *vertex; |
| 327 |
mass = integrableObject->getMass(); |
| 328 |
if (integrableObject->isDirectional()){ |
| 329 |
|
| 330 |
// preliminaries for directional objects: |
| 331 |
|
| 332 |
A = integrableObject->getA(); |
| 333 |
Atrans = A.transpose(); |
| 334 |
Vector3d rcrLab = Atrans * hydroProps_[index]->getCOR(); |
| 335 |
|
| 336 |
|
| 337 |
Mat3x3d I = integrableObject->getI(); |
| 338 |
Vector3d omegaBody; |
| 339 |
|
| 340 |
// What remains contains velocity explicitly, but the velocity required |
| 341 |
// is at the full step: v(t + h), while we have initially the velocity |
| 342 |
// at the half step: v(t + h/2). We need to iterate to converge the |
| 343 |
// friction force and friction torque vectors. |
| 344 |
|
| 345 |
// this is the velocity at the half-step: |
| 346 |
|
| 347 |
Vector3d vel =integrableObject->getVel(); |
| 348 |
Vector3d angMom = integrableObject->getJ(); |
| 349 |
|
| 350 |
//estimate velocity at full-step using everything but friction forces: |
| 351 |
|
| 352 |
frc = integrableObject->getFrc(); |
| 353 |
Vector3d velStep = vel + (dt2_ /mass * OOPSEConstant::energyConvert) * frc; |
| 354 |
|
| 355 |
Tb = integrableObject->lab2Body(integrableObject->getTrq()); |
| 356 |
Vector3d angMomStep = angMom + (dt2_ * OOPSEConstant::energyConvert) * Tb; |
| 357 |
|
| 358 |
Vector3d omegaLab; |
| 359 |
Vector3d vcdLab; |
| 360 |
Vector3d vcdBody; |
| 361 |
Vector3d frictionForceBody; |
| 362 |
Vector3d frictionForceLab(0.0); |
| 363 |
Vector3d oldFFL; // used to test for convergence |
| 364 |
Vector3d frictionTorqueBody(0.0); |
| 365 |
Vector3d oldFTB; // used to test for convergence |
| 366 |
Vector3d frictionTorqueLab; |
| 367 |
RealType fdot; |
| 368 |
RealType tdot; |
| 369 |
|
| 370 |
//iteration starts here: |
| 371 |
|
| 372 |
for (int k = 0; k < maxIterNum_; k++) { |
| 373 |
|
| 374 |
if (integrableObject->isLinear()) { |
| 375 |
int linearAxis = integrableObject->linearAxis(); |
| 376 |
int l = (linearAxis +1 )%3; |
| 377 |
int m = (linearAxis +2 )%3; |
| 378 |
omegaBody[l] = angMomStep[l] /I(l, l); |
| 379 |
omegaBody[m] = angMomStep[m] /I(m, m); |
| 380 |
|
| 381 |
} else { |
| 382 |
omegaBody[0] = angMomStep[0] /I(0, 0); |
| 383 |
omegaBody[1] = angMomStep[1] /I(1, 1); |
| 384 |
omegaBody[2] = angMomStep[2] /I(2, 2); |
| 385 |
} |
| 386 |
|
| 387 |
omegaLab = Atrans * omegaBody; |
| 388 |
|
| 389 |
// apply friction force and torque at center of resistance |
| 390 |
|
| 391 |
vcdLab = velStep + cross(omegaLab, rcrLab); |
| 392 |
vcdBody = A * vcdLab; |
| 393 |
frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omegaBody); |
| 394 |
oldFFL = frictionForceLab; |
| 395 |
frictionForceLab = Atrans * frictionForceBody; |
| 396 |
oldFTB = frictionTorqueBody; |
| 397 |
frictionTorqueBody = -(hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omegaBody); |
| 398 |
frictionTorqueLab = Atrans * frictionTorqueBody; |
| 399 |
|
| 400 |
// re-estimate velocities at full-step using friction forces: |
| 401 |
|
| 402 |
velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * (frc + frictionForceLab); |
| 403 |
angMomStep = angMom + (dt2_ * OOPSEConstant::energyConvert) * (Tb + frictionTorqueBody); |
| 404 |
|
| 405 |
// check for convergence (if the vectors have converged, fdot and tdot will both be 1.0): |
| 406 |
|
| 407 |
fdot = dot(frictionForceLab, oldFFL) / frictionForceLab.lengthSquare(); |
| 408 |
tdot = dot(frictionTorqueBody, oldFTB) / frictionTorqueBody.lengthSquare(); |
| 409 |
|
| 410 |
if (fabs(1.0 - fdot) <= forceTolerance_ && fabs(1.0 - tdot) <= forceTolerance_) |
| 411 |
break; // iteration ends here |
| 412 |
} |
| 413 |
|
| 414 |
integrableObject->addFrc(frictionForceLab); |
| 415 |
integrableObject->addTrq(frictionTorqueLab + cross(rcrLab, frictionForceLab)); |
| 416 |
|
| 417 |
|
| 418 |
} else { |
| 419 |
//spherical atom |
| 420 |
|
| 421 |
|
| 422 |
// What remains contains velocity explicitly, but the velocity required |
| 423 |
// is at the full step: v(t + h), while we have initially the velocity |
| 424 |
// at the half step: v(t + h/2). We need to iterate to converge the |
| 425 |
// friction force vector. |
| 426 |
|
| 427 |
// this is the velocity at the half-step: |
| 428 |
|
| 429 |
Vector3d vel =integrableObject->getVel(); |
| 430 |
|
| 431 |
//estimate velocity at full-step using everything but friction forces: |
| 432 |
|
| 433 |
frc = integrableObject->getFrc(); |
| 434 |
Vector3d velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * frc; |
| 435 |
|
| 436 |
Vector3d frictionForce(0.0); |
| 437 |
Vector3d oldFF; // used to test for convergence |
| 438 |
RealType fdot; |
| 439 |
|
| 440 |
//iteration starts here: |
| 441 |
|
| 442 |
for (int k = 0; k < maxIterNum_; k++) { |
| 443 |
|
| 444 |
oldFF = frictionForce; |
| 445 |
frictionForce = -hydroProps_[index]->getXitt() * velStep; |
| 446 |
|
| 447 |
// re-estimate velocities at full-step using friction forces: |
| 448 |
|
| 449 |
velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * (frc + frictionForce); |
| 450 |
|
| 451 |
// check for convergence (if the vector has converged, fdot will be 1.0): |
| 452 |
|
| 453 |
fdot = dot(frictionForce, oldFF) / frictionForce.lengthSquare(); |
| 454 |
|
| 455 |
if (fabs(1.0 - fdot) <= forceTolerance_) |
| 456 |
break; // iteration ends here |
| 457 |
} |
| 458 |
|
| 459 |
integrableObject->addFrc(frictionForce); |
| 460 |
|
| 461 |
|
| 462 |
} |
| 463 |
|
| 464 |
|
| 465 |
} |
| 466 |
Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 467 |
currSnapshot->setVolume(surfaceMesh_->getVolume()); |
| 468 |
|
| 469 |
ForceManager::postCalculation(needStress); |
| 470 |
} |
| 471 |
|
| 472 |
void SMIPDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) { |
| 473 |
|
| 474 |
|
| 475 |
Vector<RealType, 6> Z; |
| 476 |
Vector<RealType, 6> generalForce; |
| 477 |
|
| 478 |
|
| 479 |
Z[0] = randNumGen_.randNorm(0, variance); |
| 480 |
Z[1] = randNumGen_.randNorm(0, variance); |
| 481 |
Z[2] = randNumGen_.randNorm(0, variance); |
| 482 |
Z[3] = randNumGen_.randNorm(0, variance); |
| 483 |
Z[4] = randNumGen_.randNorm(0, variance); |
| 484 |
Z[5] = randNumGen_.randNorm(0, variance); |
| 485 |
|
| 486 |
generalForce = hydroProps_[index]->getS()*Z; |
| 487 |
|
| 488 |
force[0] = generalForce[0]; |
| 489 |
force[1] = generalForce[1]; |
| 490 |
force[2] = generalForce[2]; |
| 491 |
torque[0] = generalForce[3]; |
| 492 |
torque[1] = generalForce[4]; |
| 493 |
torque[2] = generalForce[5]; |
| 494 |
|
| 495 |
} |
| 496 |
std::vector<RealType> SMIPDForceManager::genTriangleForces(int nTriangles, RealType variance) { |
| 497 |
|
| 498 |
// zero fill the random vector before starting: |
| 499 |
std::vector<RealType> gaussRand; |
| 500 |
gaussRand.resize(nTriangles); |
| 501 |
std::fill(gaussRand.begin(), gaussRand.end(), 0.0); |
| 502 |
|
| 503 |
|
| 504 |
#ifdef IS_MPI |
| 505 |
if (worldRank == 0) { |
| 506 |
#endif |
| 507 |
for (int i = 0; i < nTriangles; i++) { |
| 508 |
gaussRand[i] = fabs(randNumGen_.randNorm(0.0, 1.0)); |
| 509 |
} |
| 510 |
#ifdef IS_MPI |
| 511 |
} |
| 512 |
#endif |
| 513 |
|
| 514 |
// push these out to the other processors |
| 515 |
|
| 516 |
#ifdef IS_MPI |
| 517 |
if (worldRank == 0) { |
| 518 |
MPI_Bcast(&gaussRand[0], nTriangles, MPI_REAL, 0, MPI_COMM_WORLD); |
| 519 |
} else { |
| 520 |
MPI_Bcast(&gaussRand[0], nTriangles, MPI_REAL, 0, MPI_COMM_WORLD); |
| 521 |
} |
| 522 |
#endif |
| 523 |
|
| 524 |
for (int i = 0; i < nTriangles; i++) { |
| 525 |
gaussRand[i] = gaussRand[i] * variance; |
| 526 |
} |
| 527 |
|
| 528 |
return gaussRand; |
| 529 |
} |
| 530 |
|
| 531 |
} |
