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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 3459 by chuckv, Tue Oct 7 17:12:48 2008 UTC vs.
Revision 3517 by gezelter, Thu Jul 23 18:49:45 2009 UTC

# Line 41 | Line 41
41   #include <fstream>
42   #include <iostream>
43   #include "integrators/SMIPDForceManager.hpp"
44 – #include "math/CholeskyDecomposition.hpp"
44   #include "utils/OOPSEConstant.hpp"
46 – #include "hydrodynamics/Sphere.hpp"
47 – #include "hydrodynamics/Ellipsoid.hpp"
48 – #include "utils/ElementsTable.hpp"
45   #include "math/ConvexHull.hpp"
46   #include "math/Triangle.hpp"
47  
52 –
48   namespace oopse {
49  
50 <  SMIPDForceManager::SMIPDForceManager(SimInfo* info) : ForceManager(info), forceTolerance_(1e-6), maxIterNum_(4) {
50 >  SMIPDForceManager::SMIPDForceManager(SimInfo* info) : ForceManager(info) {
51 >
52      simParams = info->getSimParams();
53      veloMunge = new Velocitizer(info);
54      
55      // Create Hull, Convex Hull for now, other options later.
56 +    
57      surfaceMesh_ = new ConvexHull();
58      
62 –    
59      /* Check that the simulation has target pressure and target
60 <       temperature set*/
61 <
60 >       temperature set */
61 >    
62      if (!simParams->haveTargetTemp()) {
63 <      sprintf(painCave.errMsg, "You can't use the SMIPDynamics integrator without a targetTemp!\n");
63 >      sprintf(painCave.errMsg,
64 >              "SMIPDynamics error: You can't use the SMIPD integrator\n"
65 >              "\twithout a targetTemp (K)!\n");      
66        painCave.isFatal = 1;
67        painCave.severity = OOPSE_ERROR;
68        simError();
69      } else {
70        targetTemp_ = simParams->getTargetTemp();
71      }
72 <
72 >    
73      if (!simParams->haveTargetPressure()) {
74 <      sprintf(painCave.errMsg, "SMIPDynamics error: You can't use the SMIPD integrator\n"
75 <              "   without a targetPressure!\n");
76 <      
74 >      sprintf(painCave.errMsg,
75 >              "SMIPDynamics error: You can't use the SMIPD integrator\n"
76 >              "\twithout a targetPressure (atm)!\n");      
77        painCave.isFatal = 1;
78        simError();
79      } else {
80 <      targetPressure_ = simParams->getTargetPressure();
80 >      // Convert pressure from atm -> amu/(fs^2*Ang)
81 >      targetPressure_ = simParams->getTargetPressure() /
82 >        OOPSEConstant::pressureConvert;
83      }
84 –
84    
85      if (simParams->getUsePeriodicBoundaryConditions()) {
86 <      sprintf(painCave.errMsg, "SMIPDynamics error: You can't use the SMIPD integrator\n"
87 <              "   with periodic boundary conditions !\n");
88 <      
86 >      sprintf(painCave.errMsg,
87 >              "SMIPDynamics error: You can't use the SMIPD integrator\n"
88 >              "\twith periodic boundary conditions!\n");    
89        painCave.isFatal = 1;
90        simError();
91      }
92 +    
93 +    if (!simParams->haveThermalConductivity()) {
94 +      sprintf(painCave.errMsg,
95 +              "SMIPDynamics error: You can't use the SMIPD integrator\n"
96 +              "\twithout a thermalConductivity (W m^-1 K^-1)!\n");
97 +      painCave.isFatal = 1;
98 +      painCave.severity = OOPSE_ERROR;
99 +      simError();
100 +    }else{
101 +      thermalConductivity_ = simParams->getThermalConductivity() *
102 +        OOPSEConstant::thermalConductivityConvert;
103 +    }
104  
105 +    if (!simParams->haveThermalLength()) {
106 +      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{
113 +      thermalLength_ = simParams->getThermalLength();
114 +    }
115 +    
116 +    dt_ = simParams->getDt();
117 +  
118 +    variance_ = 2.0 * OOPSEConstant::kb * targetTemp_ / dt_;
119  
120 <    // Build the hydroProp map:
121 <    std::map<std::string, HydroProp*> hydroPropMap;
97 <
120 >    // Build a vector of integrable objects to determine if the are
121 >    // surface atoms
122      Molecule* mol;
123      StuntDouble* integrableObject;
124      SimInfo::MoleculeIterator i;
125 <    Molecule::IntegrableObjectIterator  j;              
126 <    bool needHydroPropFile = false;
127 <    
128 <    for (mol = info->beginMolecule(i); mol != NULL;
105 <         mol = info->nextMolecule(i)) {
125 >    Molecule::IntegrableObjectIterator  j;
126 >
127 >    for (mol = info_->beginMolecule(i); mol != NULL;
128 >         mol = info_->nextMolecule(i)) {          
129        for (integrableObject = mol->beginIntegrableObject(j);
130             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;
131             integrableObject = mol->nextIntegrableObject(j)) {  
132          localSites_.push_back(integrableObject);
133        }
134 <    }
243 <
244 <    surfaceMesh_->computeHull(localSites_);
245 <    Area0_ = surfaceMesh_->getArea();
246 <    //variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
247 <    
134 >    }  
135    }  
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 –  }
136    
137    void SMIPDForceManager::postCalculation(bool needStress){
138      SimInfo::MoleculeIterator i;
139      Molecule::IntegrableObjectIterator  j;
140      Molecule* mol;
141      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;
142    
143 <    /*Compute surface Mesh*/
143 >    // Compute surface Mesh
144 >
145      surfaceMesh_->computeHull(localSites_);
146  
147 <    /* Get area and number of surface stunt doubles and compute new variance */
148 <     RealType area = surfaceMesh_->getArea();
149 <     int nSurfaceSDs = surfaceMesh_->getNs();
150 <
151 <     /* Compute variance for random forces */
152 <    
153 <     variance_ = sqrt(2.0*NumericConstant::PI)*((targetPressure_/OOPSEConstant::pressureConvert)*area/nSurfaceSDs);
154 <    
155 <    std::vector<Triangle*> sMesh = surfaceMesh_->getMesh();
156 <    std::vector<RealType>  randNums = genTriangleForces(sMesh.size(),variance_);
157 <    
158 <    /* Loop over the mesh faces and apply random force to each of the faces*/
299 <    
300 <    
301 <    std::vector<Triangle*>::iterator face;
147 >    // Get total area and number of surface stunt doubles
148 >    RealType area = surfaceMesh_->getArea();
149 >    int nSurfaceSDs = surfaceMesh_->getNs();
150 >    std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
151 >    int nTriangles = sMesh.size();
152 >
153 >    // Generate all of the necessary random forces
154 >    std::vector<RealType>  randNums = genTriangleForces(nTriangles, variance_);
155 >
156 >    // Loop over the mesh faces and apply external pressure to each
157 >    // of the faces
158 >    std::vector<Triangle>::iterator face;
159      std::vector<StuntDouble*>::iterator vertex;
160 <    int thisNumber = 0;
160 >    int thisFacet = 0;
161      for (face = sMesh.begin(); face != sMesh.end(); ++face){
162      
163 <      Triangle* thisTriangle = *face;
164 <      std::vector<StuntDouble*> vertexSDs = thisTriangle->getVertices();
165 <      
166 <      /* Get Random Force */
310 <      Vector3d unitNormal = thisTriangle->getNormal();
163 >      Triangle thisTriangle = *face;
164 >      std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();
165 >      RealType thisArea = thisTriangle.getArea();
166 >      Vector3d unitNormal = thisTriangle.getNormal();
167        unitNormal.normalize();
168 <      Vector3d randomForce = -randNums[thisNumber] * unitNormal;
168 >      Vector3d centroid = thisTriangle.getCentroid();
169 >      Vector3d facetVel = thisTriangle.getFacetVelocity();
170 >      RealType thisMass = thisTriangle.getFacetMass();
171 >
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 <      for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex){
176 >      RealType extPressure = - (targetPressure_ * thisArea) /
177 >        OOPSEConstant::energyConvert;
178  
179 <         // mass = integrableObject->getMass();
179 >      RealType randomForce = randNums[thisFacet++] * sqrt(gamma);
180 >      RealType dragForce = -gamma * dot(facetVel, unitNormal);
181  
182 <                    (*vertex)->addFrc(randomForce/3.0);          
183 <      }
184 <    }
185 <
186 <    /* Now loop over all surface particles and apply the drag*/
187 <
188 <    std::vector<StuntDouble*> surfaceSDs = surfaceMesh_->getSurfaceAtoms();
189 <    for (vertex = surfaceSDs.begin(); vertex != surfaceSDs.end(); ++vertex){
190 <      integrableObject = *vertex;
191 <      mass = integrableObject->getMass();
192 <      if (integrableObject->isDirectional()){
193 <        
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);
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){
188 >          Vector3d vertexForce = langevinForce / 3.0;
189 >          (*vertex)->addFrc(vertexForce);          
190 >          if ((*vertex)->isDirectional()){          
191 >            Vector3d vertexPos = (*vertex)->getPos();
192 >            Vector3d vertexCentroidVector = vertexPos - centroid;
193 >            (*vertex)->addTrq(cross(vertexCentroidVector,vertexForce));
194            }
195 <          
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 <        
195 >        }  
196        }
197 <      
464 <      
465 <    }
466 <    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
467 <    currSnapshot->setVolume(surfaceMesh_->getVolume());
197 >    }
198      
199 +    veloMunge->removeComDrift();
200 +    veloMunge->removeAngularDrift();
201 +    
202 +    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
203 +    currSnapshot->setVolume(surfaceMesh_->getVolume());    
204      ForceManager::postCalculation(needStress);  
205    }
206 <
207 <  void SMIPDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
208 <
206 >  
207 >  
208 >  std::vector<RealType> SMIPDForceManager::genTriangleForces(int nTriangles,
209 >                                                             RealType variance)
210 >  {
211      
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 –
212      // zero fill the random vector before starting:
213      std::vector<RealType> gaussRand;
214      gaussRand.resize(nTriangles);
215      std::fill(gaussRand.begin(), gaussRand.end(), 0.0);
216 <
503 <
216 >    
217   #ifdef IS_MPI
218      if (worldRank == 0) {
219   #endif
220        for (int i = 0; i < nTriangles; i++) {
221 <        gaussRand[i] = fabs(randNumGen_.randNorm(0.0, 1.0));    
221 >        gaussRand[i] = randNumGen_.randNorm(0.0, variance);
222        }
223   #ifdef IS_MPI
224      }
225   #endif
226 <
226 >    
227      // push these out to the other processors
228 <
228 >    
229   #ifdef IS_MPI
230      if (worldRank == 0) {
231 <      MPI_Bcast(&gaussRand[0], nTriangles, MPI_REAL, 0, MPI_COMM_WORLD);
231 >      MPI::COMM_WORLD.Bcast(&gaussRand[0], nTriangles, MPI::REALTYPE, 0);
232      } else {
233 <      MPI_Bcast(&gaussRand[0], nTriangles, MPI_REAL, 0, MPI_COMM_WORLD);
233 >      MPI::COMM_WORLD.Bcast(&gaussRand[0], nTriangles, MPI::REALTYPE, 0);
234      }
235   #endif
236 <
524 <    for (int i = 0; i < nTriangles; i++) {
525 <      gaussRand[i] = gaussRand[i] * variance;
526 <    }
527 <
236 >    
237      return gaussRand;
238    }
530 –
239   }

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