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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 3463 by chuckv, Thu Oct 16 18:25:36 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();
59      
62 –    
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();
81 >      // Convert pressure from atm -> amu/(fs^2*Ang)
82 >      targetPressure_ = simParams->getTargetPressure() /
83 >        OOPSEConstant::pressureConvert;
84      }
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 <      
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 +    
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 <
110 <    // Build the hydroProp map:
96 <    std::map<std::string, HydroProp*> hydroPropMap;
97 <
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;
105 <         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;
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(simParams->getViscosity(),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;
120             integrableObject = mol->nextIntegrableObject(j)) {  
121          localSites_.push_back(integrableObject);
122        }
123 <    }
243 <
244 <    surfaceMesh_->computeHull(localSites_);
245 <    Area0_ = surfaceMesh_->getArea();
246 <    variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
247 <    
123 >    }  
124    }  
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 –  }
125    
126    void SMIPDForceManager::postCalculation(bool needStress){
127      SimInfo::MoleculeIterator i;
128      Molecule::IntegrableObjectIterator  j;
129      Molecule* mol;
130      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;
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();
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 <     /* Compute variance for random forces */
142 <    
143 <     RealType TD_variance = sqrt(2.0*NumericConstant::PI)*((targetPressure_/OOPSEConstant::pressureConvert)*area/nSurfaceSDs)
144 <       /OOPSEConstant::energyConvert;
145 <    
146 <    std::vector<Triangle*> sMesh = surfaceMesh_->getMesh();
297 <    std::vector<RealType>  randNums = genTriangleForces(sMesh.size(),TD_variance);
298 <    
299 <    /* Loop over the mesh faces and apply random force to each of the faces*/
300 <    
301 <    
302 <    std::vector<Triangle*>::iterator face;
141 >    // Generate all of the necessary random forces
142 >    std::vector<Vector3d>  randNums = genTriangleForces(nTriangles, variance_);
143 >
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 <      
154 <      /* Get Random Force */
311 <      Vector3d unitNormal = thisTriangle->getNormal();
151 >      Triangle thisTriangle = *face;
152 >      std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();
153 >      RealType thisArea = thisTriangle.getArea();
154 >      Vector3d unitNormal = thisTriangle.getNormal();
155        unitNormal.normalize();
156 <      Vector3d randomForce = -randNums[thisNumber] * unitNormal;
157 <      Vector3d centroid = thisTriangle->getCentroid();
156 >      Vector3d centroid = thisTriangle.getCentroid();
157 >      Vector3d facetVel = thisTriangle.getFacetVelocity();
158  
159 <      for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex){
159 >      Mat3x3d hydroTensor = thisTriangle.computeHydrodynamicTensor(viscosity_);
160  
161 <         // mass = integrableObject->getMass();
162 <        Vector3d vertexForce = randomForce/3.0;
163 <        (*vertex)->addFrc(vertexForce);
321 <        if (integrableObject->isDirectional()){
322 <          Vector3d vertexPos = (*vertex)->getPos();
323 <          Vector3d vertexCentroidVector = vertexPos - centroid;
324 <          (*vertex)->addTrq(cross(vertexCentroidVector,vertexForce));
325 <        }
326 <          
327 <      }
328 <    }
161 >      hydroTensor *= OOPSEConstant::viscoConvert;
162 >      Mat3x3d S;
163 >      CholeskyDecomposition(hydroTensor, S);
164  
165 <    /* Now loop over all surface particles and apply the drag*/
165 >      Vector3d extPressure = -unitNormal*(targetPressure_ * thisArea)/OOPSEConstant::energyConvert;      
166 >      Vector3d randomForce = S * randNums[thisFacet++];
167 >      Vector3d dragForce = -hydroTensor * facetVel;
168  
169 <    std::vector<StuntDouble*> surfaceSDs = surfaceMesh_->getSurfaceAtoms();
333 <    for (vertex = surfaceSDs.begin(); vertex != surfaceSDs.end(); ++vertex){
334 <      integrableObject = *vertex;
335 <      mass = integrableObject->getMass();
336 <      if (integrableObject->isDirectional()){
337 <        
338 <        // preliminaries for directional objects:
339 <        
340 <        A = integrableObject->getA();
341 <        Atrans = A.transpose();
342 <        Vector3d rcrLab = Atrans * hydroProps_[index]->getCOR();  
343 <        //apply random force and torque at center of resistance
169 >      Vector3d langevinForce = (extPressure + randomForce + dragForce);
170  
171 <        Vector3d randomForceBody;
172 <        Vector3d randomTorqueBody;
173 <        genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
174 <        Vector3d randomForceLab = Atrans * randomForceBody;
175 <        Vector3d randomTorqueLab = Atrans * randomTorqueBody;
176 <        integrableObject->addFrc(randomForceLab);            
177 <        integrableObject->addTrq(randomTorqueLab + cross(rcrLab, randomForceLab ));            
178 <        
179 <
354 <        
355 <        Mat3x3d I = integrableObject->getI();
356 <        Vector3d omegaBody;
357 <        
358 <        // What remains contains velocity explicitly, but the velocity required
359 <        // is at the full step: v(t + h), while we have initially the velocity
360 <        // at the half step: v(t + h/2).  We need to iterate to converge the
361 <        // friction force and friction torque vectors.
362 <        
363 <        // this is the velocity at the half-step:
364 <        
365 <        Vector3d vel =integrableObject->getVel();
366 <        Vector3d angMom = integrableObject->getJ();
367 <        
368 <        //estimate velocity at full-step using everything but friction forces:          
369 <        
370 <        frc = integrableObject->getFrc();
371 <        Vector3d velStep = vel + (dt2_ /mass * OOPSEConstant::energyConvert) * frc;
372 <        
373 <        Tb = integrableObject->lab2Body(integrableObject->getTrq());
374 <        Vector3d angMomStep = angMom + (dt2_ * OOPSEConstant::energyConvert) * Tb;                            
375 <        
376 <        Vector3d omegaLab;
377 <        Vector3d vcdLab;
378 <        Vector3d vcdBody;
379 <        Vector3d frictionForceBody;
380 <        Vector3d frictionForceLab(0.0);
381 <        Vector3d oldFFL;  // used to test for convergence
382 <        Vector3d frictionTorqueBody(0.0);
383 <        Vector3d oldFTB;  // used to test for convergence
384 <        Vector3d frictionTorqueLab;
385 <        RealType fdot;
386 <        RealType tdot;
387 <
388 <        //iteration starts here:
389 <        
390 <        for (int k = 0; k < maxIterNum_; k++) {
391 <          
392 <          if (integrableObject->isLinear()) {
393 <            int linearAxis = integrableObject->linearAxis();
394 <            int l = (linearAxis +1 )%3;
395 <            int m = (linearAxis +2 )%3;
396 <            omegaBody[l] = angMomStep[l] /I(l, l);
397 <            omegaBody[m] = angMomStep[m] /I(m, m);
398 <            
399 <          } else {
400 <            omegaBody[0] = angMomStep[0] /I(0, 0);
401 <            omegaBody[1] = angMomStep[1] /I(1, 1);
402 <            omegaBody[2] = angMomStep[2] /I(2, 2);
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));
180            }
181 <          
405 <          omegaLab = Atrans * omegaBody;
406 <          
407 <          // apply friction force and torque at center of resistance
408 <          
409 <          vcdLab = velStep + cross(omegaLab, rcrLab);      
410 <          vcdBody = A * vcdLab;
411 <          frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omegaBody);
412 <          oldFFL = frictionForceLab;
413 <          frictionForceLab = Atrans * frictionForceBody;
414 <          oldFTB = frictionTorqueBody;
415 <          frictionTorqueBody = -(hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omegaBody);
416 <          frictionTorqueLab = Atrans * frictionTorqueBody;
417 <          
418 <          // re-estimate velocities at full-step using friction forces:
419 <              
420 <          velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * (frc + frictionForceLab);
421 <          angMomStep = angMom + (dt2_ * OOPSEConstant::energyConvert) * (Tb + frictionTorqueBody);
422 <
423 <          // check for convergence (if the vectors have converged, fdot and tdot will both be 1.0):
424 <              
425 <          fdot = dot(frictionForceLab, oldFFL) / frictionForceLab.lengthSquare();
426 <          tdot = dot(frictionTorqueBody, oldFTB) / frictionTorqueBody.lengthSquare();
427 <          
428 <          if (fabs(1.0 - fdot) <= forceTolerance_ && fabs(1.0 - tdot) <= forceTolerance_)
429 <            break; // iteration ends here
430 <        }
431 <        
432 <        integrableObject->addFrc(frictionForceLab);
433 <        integrableObject->addTrq(frictionTorqueLab + cross(rcrLab, frictionForceLab));
434 <
435 <            
436 <      } else {
437 <        //spherical atom
438 <
439 <        Vector3d randomForce;
440 <        Vector3d randomTorque;
441 <        genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
442 <        integrableObject->addFrc(randomForce);  
443 <        
444 <        // What remains contains velocity explicitly, but the velocity required
445 <        // is at the full step: v(t + h), while we have initially the velocity
446 <        // at the half step: v(t + h/2).  We need to iterate to converge the
447 <        // friction force vector.
448 <        
449 <        // this is the velocity at the half-step:
450 <        
451 <        Vector3d vel =integrableObject->getVel();
452 <        
453 <        //estimate velocity at full-step using everything but friction forces:          
454 <        
455 <        frc = integrableObject->getFrc();
456 <        Vector3d velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * frc;
457 <        
458 <        Vector3d frictionForce(0.0);
459 <        Vector3d oldFF;  // used to test for convergence
460 <        RealType fdot;
461 <        
462 <        //iteration starts here:
463 <        
464 <        for (int k = 0; k < maxIterNum_; k++) {
465 <          
466 <          oldFF = frictionForce;                            
467 <          frictionForce = -hydroProps_[index]->getXitt() * velStep;
468 <          
469 <          // re-estimate velocities at full-step using friction forces:
470 <          
471 <          velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * (frc + frictionForce);
472 <          
473 <          // check for convergence (if the vector has converged, fdot will be 1.0):
474 <          
475 <          fdot = dot(frictionForce, oldFF) / frictionForce.lengthSquare();
476 <          
477 <          if (fabs(1.0 - fdot) <= forceTolerance_)
478 <            break; // iteration ends here
479 <        }
480 <        
481 <        integrableObject->addFrc(frictionForce);
482 <        
483 <        
181 >        }  
182        }
183 <      
184 <      
185 <    }
183 >    }
184 >        
185 >    veloMunge->removeComDrift();
186 >    veloMunge->removeAngularDrift();
187 >
188      Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
189 <    currSnapshot->setVolume(surfaceMesh_->getVolume());
490 <    
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      
497 –    Vector<RealType, 6> Z;
498 –    Vector<RealType, 6> generalForce;
499 –    
500 –
501 –    Z[0] = randNumGen_.randNorm(0, variance);
502 –    Z[1] = randNumGen_.randNorm(0, variance);
503 –    Z[2] = randNumGen_.randNorm(0, variance);
504 –    Z[3] = randNumGen_.randNorm(0, variance);
505 –    Z[4] = randNumGen_.randNorm(0, variance);
506 –    Z[5] = randNumGen_.randNorm(0, variance);
507 –    
508 –    generalForce = hydroProps_[index]->getS()*Z;
509 –    
510 –    force[0] = generalForce[0];
511 –    force[1] = generalForce[1];
512 –    force[2] = generalForce[2];
513 –    torque[0] = generalForce[3];
514 –    torque[1] = generalForce[4];
515 –    torque[2] = generalForce[5];
516 –    
517 – }
518 –  std::vector<RealType> SMIPDForceManager::genTriangleForces(int nTriangles, RealType variance) {
519 –
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 <
525 <
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 <
546 <    for (int i = 0; i < nTriangles; i++) {
547 <      gaussRand[i] = gaussRand[i] * variance;
548 <    }
549 <
228 >    
229      return gaussRand;
230    }
552 –
553 –
554 –
555 –
556 –
231   }

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