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root/group/trunk/OOPSE-4/src/integrators/SMIPDForceManager.cpp
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Comparing trunk/OOPSE-4/src/integrators/SMIPDForceManager.cpp (file contents):
Revision 3469 by chuckv, Wed Oct 22 17:52:40 2008 UTC vs.
Revision 3504 by gezelter, Wed May 13 22:27:29 2009 UTC

# Line 43 | Line 43
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) {
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*/
62 <
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();
70      } else {
71        targetTemp_ = simParams->getTargetTemp();
72      }
73 <
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 <      targetPressure_ = simParams->getTargetPressure()/OOPSEConstant::pressureConvert;
81 >      // Convert pressure from atm -> amu/(fs^2*Ang)
82 >      targetPressure_ = simParams->getTargetPressure() /
83 >        OOPSEConstant::pressureConvert;
84      }
85 –
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      }
94 –
95 –
96 –
93      
94 +    if (!simParams->haveViscosity()) {
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 +    
105 +    dt_ = simParams->getDt();
106 +  
107 +    variance_ = 2.0 * OOPSEConstant::kb * targetTemp_ / dt_;
108  
109 <    //Compute initial hull
110 <    /*
101 <    surfaceMesh_->computeHull(localSites_);
102 <    Area0_ = surfaceMesh_->getArea();
103 <    int nTriangles = surfaceMesh_->getNMeshElements();
104 <    //    variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
105 <    gamma_0_ = (NumericConstant::PI * targetPressure_* targetPressure_ * Area0_ * Area0_ * simParams->getDt()) /
106 <      (4.0 * nTriangles * nTriangles* OOPSEConstant::kb*simParams->getTargetTemp());
107 <    //RealType eta0 = gamma_0/
108 <    */
109 <
110 <    // Build the hydroProp map:
111 <    std::map<std::string, HydroProp*> hydroPropMap;
112 <
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;              
115 <    bool needHydroPropFile = false;
116 <    
117 <    for (mol = info->beginMolecule(i); mol != NULL;
120 <         mol = info->nextMolecule(i)) {
114 >    Molecule::IntegrableObjectIterator  j;
115 >
116 >    for (mol = info_->beginMolecule(i); mol != NULL;
117 >         mol = info_->nextMolecule(i)) {          
118        for (integrableObject = mol->beginIntegrableObject(j);
119             integrableObject != NULL;
123 –           integrableObject = mol->nextIntegrableObject(j)) {
124 –        
125 –        if (integrableObject->isRigidBody()) {
126 –          RigidBody* rb = static_cast<RigidBody*>(integrableObject);
127 –          if (rb->getNumAtoms() > 1) needHydroPropFile = true;
128 –        }
129 –        
130 –      }
131 –    }
132 –        
133 –
134 –    if (needHydroPropFile) {              
135 –      if (simParams->haveHydroPropFile()) {
136 –        hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
137 –      } else {              
138 –        sprintf( painCave.errMsg,
139 –                 "HydroPropFile must be set to a file name if SMIPDynamics\n"
140 –                 "\tis specified for rigidBodies which contain more than one atom\n"
141 –                 "\tTo create a HydroPropFile, run the \"Hydro\" program.\n\n"
142 –                 "\tFor use with SMIPD, the default viscosity in Hydro should be\n"
143 –                 "\tset to 1.0 because the friction and random forces will be\n"
144 –                 "\tdynamically re-set assuming this is true.\n");
145 –        painCave.severity = OOPSE_ERROR;
146 –        painCave.isFatal = 1;
147 –        simError();  
148 –      }      
149 –
150 –      for (mol = info->beginMolecule(i); mol != NULL;
151 –           mol = info->nextMolecule(i)) {
152 –        for (integrableObject = mol->beginIntegrableObject(j);
153 –             integrableObject != NULL;
154 –             integrableObject = mol->nextIntegrableObject(j)) {
155 –
156 –          std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
157 –          if (iter != hydroPropMap.end()) {
158 –            hydroProps_.push_back(iter->second);
159 –          } else {
160 –            sprintf( painCave.errMsg,
161 –                     "Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
162 –            painCave.severity = OOPSE_ERROR;
163 –            painCave.isFatal = 1;
164 –            simError();  
165 –          }        
166 –        }
167 –      }
168 –    } else {
169 –      
170 –      std::map<std::string, HydroProp*> hydroPropMap;
171 –      for (mol = info->beginMolecule(i); mol != NULL;
172 –           mol = info->nextMolecule(i)) {
173 –        for (integrableObject = mol->beginIntegrableObject(j);
174 –             integrableObject != NULL;
175 –             integrableObject = mol->nextIntegrableObject(j)) {
176 –          Shape* currShape = NULL;
177 –
178 –          if (integrableObject->isAtom()){
179 –            Atom* atom = static_cast<Atom*>(integrableObject);
180 –            AtomType* atomType = atom->getAtomType();
181 –            if (atomType->isGayBerne()) {
182 –              DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);              
183 –              GenericData* data = dAtomType->getPropertyByName("GayBerne");
184 –              if (data != NULL) {
185 –                GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
186 –                
187 –                if (gayBerneData != NULL) {  
188 –                  GayBerneParam gayBerneParam = gayBerneData->getData();
189 –                  currShape = new Ellipsoid(V3Zero,
190 –                                            gayBerneParam.GB_l / 2.0,
191 –                                            gayBerneParam.GB_d / 2.0,
192 –                                            Mat3x3d::identity());
193 –                } else {
194 –                  sprintf( painCave.errMsg,
195 –                           "Can not cast GenericData to GayBerneParam\n");
196 –                  painCave.severity = OOPSE_ERROR;
197 –                  painCave.isFatal = 1;
198 –                  simError();  
199 –                }
200 –              } else {
201 –                sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n");
202 –                painCave.severity = OOPSE_ERROR;
203 –                painCave.isFatal = 1;
204 –                simError();    
205 –              }
206 –            } else {
207 –              if (atomType->isLennardJones()){
208 –                GenericData* data = atomType->getPropertyByName("LennardJones");
209 –                if (data != NULL) {
210 –                  LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
211 –                  if (ljData != NULL) {
212 –                    LJParam ljParam = ljData->getData();
213 –                    currShape = new Sphere(atom->getPos(), 2.0);
214 –                  } else {
215 –                    sprintf( painCave.errMsg,
216 –                             "Can not cast GenericData to LJParam\n");
217 –                    painCave.severity = OOPSE_ERROR;
218 –                    painCave.isFatal = 1;
219 –                    simError();          
220 –                  }      
221 –                }
222 –              } else {
223 –                int aNum = etab.GetAtomicNum((atom->getType()).c_str());
224 –                if (aNum != 0) {
225 –                  currShape = new Sphere(atom->getPos(), 2.0);
226 –                } else {
227 –                  sprintf( painCave.errMsg,
228 –                           "Could not find atom type in default element.txt\n");
229 –                  painCave.severity = OOPSE_ERROR;
230 –                  painCave.isFatal = 1;
231 –                  simError();          
232 –                }
233 –              }
234 –            }
235 –          }
236 –          HydroProp* currHydroProp = currShape->getHydroProp(1.0,simParams->getTargetTemp());
237 –          std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
238 –          if (iter != hydroPropMap.end())
239 –            hydroProps_.push_back(iter->second);
240 –          else {
241 –            currHydroProp->complete();
242 –            hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(integrableObject->getType(), currHydroProp));
243 –            hydroProps_.push_back(currHydroProp);
244 –          }
245 –        }
246 –      }
247 –    }
248 –
249 –    /* Compute hull first time through to get the area of t=0*/
250 –
251 –    //Build a vector of integrable objects to determine if the are surface atoms
252 –    for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {          
253 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
120             integrableObject = mol->nextIntegrableObject(j)) {  
121          localSites_.push_back(integrableObject);
122        }
123 <    }
258 <
259 <
123 >    }  
124    }  
261 –
262 –  std::map<std::string, HydroProp*> SMIPDForceManager::parseFrictionFile(const std::string& filename) {
263 –    std::map<std::string, HydroProp*> props;
264 –    std::ifstream ifs(filename.c_str());
265 –    if (ifs.is_open()) {
266 –      
267 –    }
268 –    
269 –    const unsigned int BufferSize = 65535;
270 –    char buffer[BufferSize];  
271 –    while (ifs.getline(buffer, BufferSize)) {
272 –      HydroProp* currProp = new HydroProp(buffer);
273 –      props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
274 –    }
275 –
276 –    return props;
277 –  }
125    
126    void SMIPDForceManager::postCalculation(bool needStress){
127      SimInfo::MoleculeIterator i;
128      Molecule::IntegrableObjectIterator  j;
129      Molecule* mol;
130      StuntDouble* integrableObject;
284 –    RealType mass;
285 –    Vector3d pos;
286 –    Vector3d frc;
287 –    Mat3x3d A;
288 –    Mat3x3d Atrans;
289 –    Vector3d Tb;
290 –    Vector3d ji;
291 –    unsigned int index = 0;
292 –    int fdf;
293 –  
294 –    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();
302 <
303 <    
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 <
142 <
309 <     /* Compute variance for random forces */
310 <  
311 <    RealType sigma_t = sqrt(NumericConstant::PI/2.0)*((targetPressure_)*area/nTriangles)
312 <       /OOPSEConstant::energyConvert;
313 <
314 <    gamma_t_ = (NumericConstant::PI * targetPressure_* targetPressure_ * area * area * simParams->getDt()) /
315 <      (4.0 * nTriangles * nTriangles* OOPSEConstant::kB*simParams->getTargetTemp()) /OOPSEConstant::energyConvert;
141 >    // Generate all of the necessary random forces
142 >    std::vector<Vector3d>  randNums = genTriangleForces(nTriangles, variance_);
143  
144 <    std::vector<RealType>  randNums = genTriangleForces(nTriangles, sigma_t);
145 <
319 <    /* Loop over the mesh faces and apply random force to each of the faces*/
320 <    
321 <    
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 <      
330 <      /* Get Random Force */
153 >      RealType thisArea = thisTriangle.getArea();
154        Vector3d unitNormal = thisTriangle.getNormal();
155        unitNormal.normalize();
333 –      Vector3d randomForce = -randNums[thisNumber] * unitNormal;
156        Vector3d centroid = thisTriangle.getCentroid();
157 +      Vector3d facetVel = thisTriangle.getFacetVelocity();
158  
159 <      Vector3d langevinForce = randomForce - gamma_t_*thisTriangle.getFacetVelocity();
337 <      
338 <      for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex){
339 <        if ((*vertex) != NULL){
340 <          // mass = integrableObject->getMass();
341 <          Vector3d vertexForce = langevinForce/3.0;
342 <          (*vertex)->addFrc(vertexForce);
159 >      Mat3x3d hydroTensor = thisTriangle.computeHydrodynamicTensor(viscosity_);
160  
161 <          if ((*vertex)->isDirectional()){
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);
170 >
171 >      // Apply triangle force to stuntdouble vertices
172 >      for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex){
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));
# Line 349 | Line 181 | namespace oopse {
181          }  
182        }
183      }
352 –
353 –    /* Now loop over all surface particles and apply the drag*/
354 –    /*
355 –    std::vector<StuntDouble*> surfaceSDs = surfaceMesh_->getSurfaceAtoms();
356 –    for (vertex = surfaceSDs.begin(); vertex != surfaceSDs.end(); ++vertex){
357 –      integrableObject = *vertex;
358 –      mass = integrableObject->getMass();
359 –      if (integrableObject->isDirectional()){
360 –        
361 –        // preliminaries for directional objects:
362 –        
363 –        A = integrableObject->getA();
364 –        Atrans = A.transpose();
365 –        Vector3d rcrLab = Atrans * hydroProps_[index]->getCOR();  
366 –        //apply random force and torque at center of resistance
367 –        Mat3x3d I = integrableObject->getI();
368 –        Vector3d omegaBody;
369 –        
370 –        // What remains contains velocity explicitly, but the velocity required
371 –        // is at the full step: v(t + h), while we have initially the velocity
372 –        // at the half step: v(t + h/2).  We need to iterate to converge the
373 –        // friction force and friction torque vectors.
374 –        
375 –        // this is the velocity at the half-step:
184          
185 <        Vector3d vel =integrableObject->getVel();
186 <        Vector3d angMom = integrableObject->getJ();
379 <        
380 <        //estimate velocity at full-step using everything but friction forces:          
381 <        
382 <        frc = integrableObject->getFrc();
383 <        Vector3d velStep = vel + (dt2_ /mass * OOPSEConstant::energyConvert) * frc;
384 <        
385 <        Tb = integrableObject->lab2Body(integrableObject->getTrq());
386 <        Vector3d angMomStep = angMom + (dt2_ * OOPSEConstant::energyConvert) * Tb;                            
387 <        
388 <        Vector3d omegaLab;
389 <        Vector3d vcdLab;
390 <        Vector3d vcdBody;
391 <        Vector3d frictionForceBody;
392 <        Vector3d frictionForceLab(0.0);
393 <        Vector3d oldFFL;  // used to test for convergence
394 <        Vector3d frictionTorqueBody(0.0);
395 <        Vector3d oldFTB;  // used to test for convergence
396 <        Vector3d frictionTorqueLab;
397 <        RealType fdot;
398 <        RealType tdot;
185 >    veloMunge->removeComDrift();
186 >    veloMunge->removeAngularDrift();
187  
400 –        //iteration starts here:
401 –        
402 –        for (int k = 0; k < maxIterNum_; k++) {
403 –          
404 –          if (integrableObject->isLinear()) {
405 –            int linearAxis = integrableObject->linearAxis();
406 –            int l = (linearAxis +1 )%3;
407 –            int m = (linearAxis +2 )%3;
408 –            omegaBody[l] = angMomStep[l] /I(l, l);
409 –            omegaBody[m] = angMomStep[m] /I(m, m);
410 –            
411 –          } else {
412 –            omegaBody[0] = angMomStep[0] /I(0, 0);
413 –            omegaBody[1] = angMomStep[1] /I(1, 1);
414 –            omegaBody[2] = angMomStep[2] /I(2, 2);
415 –          }
416 –          
417 –          omegaLab = Atrans * omegaBody;
418 –          
419 –          // apply friction force and torque at center of resistance
420 –          
421 –          vcdLab = velStep + cross(omegaLab, rcrLab);      
422 –          vcdBody = A * vcdLab;
423 –          frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omegaBody);
424 –          oldFFL = frictionForceLab;
425 –          frictionForceLab = Atrans * frictionForceBody;
426 –          oldFTB = frictionTorqueBody;
427 –          frictionTorqueBody = -(hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omegaBody);
428 –          frictionTorqueLab = Atrans * frictionTorqueBody;
429 –          
430 –          // re-estimate velocities at full-step using friction forces:
431 –              
432 –          velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * (frc + frictionForceLab);
433 –          angMomStep = angMom + (dt2_ * OOPSEConstant::energyConvert) * (Tb + frictionTorqueBody);
434 –
435 –          // check for convergence (if the vectors have converged, fdot and tdot will both be 1.0):
436 –              
437 –          fdot = dot(frictionForceLab, oldFFL) / frictionForceLab.lengthSquare();
438 –          tdot = dot(frictionTorqueBody, oldFTB) / frictionTorqueBody.lengthSquare();
439 –          
440 –          if (fabs(1.0 - fdot) <= forceTolerance_ && fabs(1.0 - tdot) <= forceTolerance_)
441 –            break; // iteration ends here
442 –        }
443 –        
444 –        integrableObject->addFrc(frictionForceLab);
445 –        integrableObject->addTrq(frictionTorqueLab + cross(rcrLab, frictionForceLab));
446 –
447 –            
448 –      } else {
449 –        //spherical atom
450 –
451 –        // What remains contains velocity explicitly, but the velocity required
452 –        // is at the full step: v(t + h), while we have initially the velocity
453 –        // at the half step: v(t + h/2).  We need to iterate to converge the
454 –        // friction force vector.
455 –        
456 –        // this is the velocity at the half-step:
457 –        
458 –        Vector3d vel =integrableObject->getVel();
459 –        
460 –        //estimate velocity at full-step using everything but friction forces:          
461 –        
462 –        frc = integrableObject->getFrc();
463 –        Vector3d velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * frc;
464 –        
465 –        Vector3d frictionForce(0.0);
466 –        Vector3d oldFF;  // used to test for convergence
467 –        RealType fdot;
468 –        
469 –        //iteration starts here:
470 –        
471 –        for (int k = 0; k < maxIterNum_; k++) {
472 –          
473 –          oldFF = frictionForce;                            
474 –          frictionForce = -hydroProps_[index]->getXitt() * velStep;
475 –          //frictionForce = -gamma_t*velStep;
476 –          // re-estimate velocities at full-step using friction forces:
477 –          
478 –          velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * (frc + frictionForce);
479 –          
480 –          // check for convergence (if the vector has converged, fdot will be 1.0):
481 –          
482 –          fdot = dot(frictionForce, oldFF) / frictionForce.lengthSquare();
483 –          
484 –          if (fabs(1.0 - fdot) <= forceTolerance_)
485 –            break; // iteration ends here
486 –        }
487 –        
488 –        integrableObject->addFrc(frictionForce);
489 –        
490 –        
491 –      }
492 –  
493 –      
494 –  }
495 –    */
188      Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
189 <    currSnapshot->setVolume(surfaceMesh_->getVolume());
498 <    
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      
505 –    Vector<RealType, 6> Z;
506 –    Vector<RealType, 6> generalForce;
507 –    
508 –
509 –    Z[0] = randNumGen_.randNorm(0, variance);
510 –    Z[1] = randNumGen_.randNorm(0, variance);
511 –    Z[2] = randNumGen_.randNorm(0, variance);
512 –    Z[3] = randNumGen_.randNorm(0, variance);
513 –    Z[4] = randNumGen_.randNorm(0, variance);
514 –    Z[5] = randNumGen_.randNorm(0, variance);
515 –    
516 –    generalForce = hydroProps_[index]->getS()*Z;
517 –    
518 –    force[0] = generalForce[0];
519 –    force[1] = generalForce[1];
520 –    force[2] = generalForce[2];
521 –    torque[0] = generalForce[3];
522 –    torque[1] = generalForce[4];
523 –    torque[2] = generalForce[5];
524 –    
525 – }
526 –  std::vector<RealType> SMIPDForceManager::genTriangleForces(int nTriangles, RealType variance) {
527 –
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);
202 <
533 <
201 >    std::fill(gaussRand.begin(), gaussRand.end(), V3Zero);
202 >    
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));    
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 <
554 <    for (int i = 0; i < nTriangles; i++) {
555 <      gaussRand[i] = gaussRand[i] * variance;
556 <    }
557 <
228 >    
229      return gaussRand;
230    }
560 –
561 –
562 –
563 –
564 –
231   }

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