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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 3473 by chuckv, Fri Nov 14 15:44:34 2008 UTC vs.
Revision 3481 by gezelter, Wed Nov 26 14:26:17 2008 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) {
51  
55 –  SMIPDForceManager::SMIPDForceManager(SimInfo* info) : ForceManager(info), forceTolerance_(1e-6), maxIterNum_(4) {
52      simParams = info->getSimParams();
57 –    veloMunge = new Velocitizer(info);
53      
54      // Create Hull, Convex Hull for now, other options later.
55 +    
56      surfaceMesh_ = new ConvexHull();
61 –
57      
63 –    
58      /* Check that the simulation has target pressure and target
59         temperature set*/
60 <
60 >    
61      if (!simParams->haveTargetTemp()) {
62 <      sprintf(painCave.errMsg, "You can't use the SMIPDynamics integrator without a targetTemp!\n");
62 >      sprintf(painCave.errMsg,
63 >              "SMIPDynamics error: You can't use the SMIPD integrator\n"
64 >              "   without a targetTemp!\n");      
65        painCave.isFatal = 1;
66        painCave.severity = OOPSE_ERROR;
67        simError();
68      } else {
69        targetTemp_ = simParams->getTargetTemp();
70      }
71 <
71 >    
72      if (!simParams->haveTargetPressure()) {
73 <      sprintf(painCave.errMsg, "SMIPDynamics error: You can't use the SMIPD integrator\n"
74 <              "   without a targetPressure!\n");
75 <      
73 >      sprintf(painCave.errMsg,
74 >              "SMIPDynamics error: You can't use the SMIPD integrator\n"
75 >              "   without a targetPressure!\n");      
76        painCave.isFatal = 1;
77        simError();
78      } else {
79 <      targetPressure_ = simParams->getTargetPressure()/OOPSEConstant::pressureConvert;
79 >      // Convert pressure from atm -> amu/(fs^2*Ang)
80 >      targetPressure_ = simParams->getTargetPressure() /
81 >        OOPSEConstant::pressureConvert;
82      }
85 –
83    
84      if (simParams->getUsePeriodicBoundaryConditions()) {
85 <      sprintf(painCave.errMsg, "SMIPDynamics error: You can't use the SMIPD integrator\n"
86 <              "   with periodic boundary conditions !\n");
87 <      
85 >      sprintf(painCave.errMsg,
86 >              "SMIPDynamics error: You can't use the SMIPD integrator\n"
87 >              "   with periodic boundary conditions!\n");    
88        painCave.isFatal = 1;
89        simError();
90      }
91 <
91 >    
92      if (!simParams->haveViscosity()) {
93 <      sprintf(painCave.errMsg, "You can't use SMIPDynamics without a viscosity!\n");
93 >      sprintf(painCave.errMsg,
94 >              "SMIPDynamics error: You can't use the SMIPD integrator\n"
95 >              "   without a viscosity!\n");
96        painCave.isFatal = 1;
97        painCave.severity = OOPSE_ERROR;
98        simError();
99 +    }else{
100 +      viscosity_ = simParams->getViscosity();
101      }
101 –
102 –
102      
103 +    dt_ = simParams->getDt();
104 +  
105 +    variance_ = 2.0 * OOPSEConstant::kb * targetTemp_ / dt_;
106  
105 –    //Compute initial hull
106 –    /*
107 –    surfaceMesh_->computeHull(localSites_);
108 –    Area0_ = surfaceMesh_->getArea();
109 –    int nTriangles = surfaceMesh_->getNMeshElements();
110 –    //    variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
111 –    gamma_0_ = (NumericConstant::PI * targetPressure_* targetPressure_ * Area0_ * Area0_ * simParams->getDt()) /
112 –      (4.0 * nTriangles * nTriangles* OOPSEConstant::kb*simParams->getTargetTemp());
113 –    //RealType eta0 = gamma_0/
114 –    */
115 –
116 –    // Build the hydroProp map:
117 –    std::map<std::string, HydroProp*> hydroPropMap;
118 –
107      Molecule* mol;
108      StuntDouble* integrableObject;
109      SimInfo::MoleculeIterator i;
110 <    Molecule::IntegrableObjectIterator  j;              
123 <    bool needHydroPropFile = false;
124 <    
125 <    for (mol = info->beginMolecule(i); mol != NULL;
126 <         mol = info->nextMolecule(i)) {
127 <      for (integrableObject = mol->beginIntegrableObject(j);
128 <           integrableObject != NULL;
129 <           integrableObject = mol->nextIntegrableObject(j)) {
130 <        
131 <        if (integrableObject->isRigidBody()) {
132 <          RigidBody* rb = static_cast<RigidBody*>(integrableObject);
133 <          if (rb->getNumAtoms() > 1) needHydroPropFile = true;
134 <        }
135 <        
136 <      }
137 <    }
138 <        
110 >    Molecule::IntegrableObjectIterator  j;              
111  
112 <    if (needHydroPropFile) {              
113 <      if (simParams->haveHydroPropFile()) {
142 <        hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
143 <      } else {              
144 <        sprintf( painCave.errMsg,
145 <                 "HydroPropFile must be set to a file name if SMIPDynamics\n"
146 <                 "\tis specified for rigidBodies which contain more than one atom\n"
147 <                 "\tTo create a HydroPropFile, run the \"Hydro\" program.\n\n"
148 <                 "\tFor use with SMIPD, the default viscosity in Hydro should be\n"
149 <                 "\tset to 1.0 because the friction and random forces will be\n"
150 <                 "\tdynamically re-set assuming this is true.\n");
151 <        painCave.severity = OOPSE_ERROR;
152 <        painCave.isFatal = 1;
153 <        simError();  
154 <      }      
112 >    // Build a vector of integrable objects to determine if the are
113 >    // surface atoms
114  
115 <      for (mol = info->beginMolecule(i); mol != NULL;
116 <           mol = info->nextMolecule(i)) {
117 <        for (integrableObject = mol->beginIntegrableObject(j);
118 <             integrableObject != NULL;
160 <             integrableObject = mol->nextIntegrableObject(j)) {
161 <
162 <          std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
163 <          if (iter != hydroPropMap.end()) {
164 <            hydroProps_.push_back(iter->second);
165 <          } else {
166 <            sprintf( painCave.errMsg,
167 <                     "Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
168 <            painCave.severity = OOPSE_ERROR;
169 <            painCave.isFatal = 1;
170 <            simError();  
171 <          }        
172 <        }
173 <      }
174 <    } else {
175 <      
176 <      std::map<std::string, HydroProp*> hydroPropMap;
177 <      for (mol = info->beginMolecule(i); mol != NULL;
178 <           mol = info->nextMolecule(i)) {
179 <        for (integrableObject = mol->beginIntegrableObject(j);
180 <             integrableObject != NULL;
181 <             integrableObject = mol->nextIntegrableObject(j)) {
182 <          Shape* currShape = NULL;
183 <
184 <          if (integrableObject->isAtom()){
185 <            Atom* atom = static_cast<Atom*>(integrableObject);
186 <            AtomType* atomType = atom->getAtomType();
187 <            if (atomType->isGayBerne()) {
188 <              DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);              
189 <              GenericData* data = dAtomType->getPropertyByName("GayBerne");
190 <              if (data != NULL) {
191 <                GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
192 <                
193 <                if (gayBerneData != NULL) {  
194 <                  GayBerneParam gayBerneParam = gayBerneData->getData();
195 <                  currShape = new Ellipsoid(V3Zero,
196 <                                            gayBerneParam.GB_l / 2.0,
197 <                                            gayBerneParam.GB_d / 2.0,
198 <                                            Mat3x3d::identity());
199 <                } else {
200 <                  sprintf( painCave.errMsg,
201 <                           "Can not cast GenericData to GayBerneParam\n");
202 <                  painCave.severity = OOPSE_ERROR;
203 <                  painCave.isFatal = 1;
204 <                  simError();  
205 <                }
206 <              } else {
207 <                sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n");
208 <                painCave.severity = OOPSE_ERROR;
209 <                painCave.isFatal = 1;
210 <                simError();    
211 <              }
212 <            } else {
213 <              if (atomType->isLennardJones()){
214 <                GenericData* data = atomType->getPropertyByName("LennardJones");
215 <                if (data != NULL) {
216 <                  LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
217 <                  if (ljData != NULL) {
218 <                    LJParam ljParam = ljData->getData();
219 <                    currShape = new Sphere(atom->getPos(), 2.0);
220 <                  } else {
221 <                    sprintf( painCave.errMsg,
222 <                             "Can not cast GenericData to LJParam\n");
223 <                    painCave.severity = OOPSE_ERROR;
224 <                    painCave.isFatal = 1;
225 <                    simError();          
226 <                  }      
227 <                }
228 <              } else {
229 <                int aNum = etab.GetAtomicNum((atom->getType()).c_str());
230 <                if (aNum != 0) {
231 <                  currShape = new Sphere(atom->getPos(), 2.0);
232 <                } else {
233 <                  sprintf( painCave.errMsg,
234 <                           "Could not find atom type in default element.txt\n");
235 <                  painCave.severity = OOPSE_ERROR;
236 <                  painCave.isFatal = 1;
237 <                  simError();          
238 <                }
239 <              }
240 <            }
241 <          }
242 <          HydroProp* currHydroProp = currShape->getHydroProp(1.0,simParams->getTargetTemp());
243 <          std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
244 <          if (iter != hydroPropMap.end())
245 <            hydroProps_.push_back(iter->second);
246 <          else {
247 <            currHydroProp->complete();
248 <            hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(integrableObject->getType(), currHydroProp));
249 <            hydroProps_.push_back(currHydroProp);
250 <          }
251 <        }
252 <      }
253 <    }
254 <
255 <    /* Compute hull first time through to get the area of t=0*/
256 <
257 <    //Build a vector of integrable objects to determine if the are surface atoms
258 <    for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {          
259 <      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
115 >    for (mol = info_->beginMolecule(i); mol != NULL;
116 >         mol = info_->nextMolecule(i)) {          
117 >      for (integrableObject = mol->beginIntegrableObject(j);
118 >           integrableObject != NULL;
119             integrableObject = mol->nextIntegrableObject(j)) {  
120          localSites_.push_back(integrableObject);
121        }
122 <    }
264 <
265 <
122 >    }  
123    }  
124 <
268 <  std::map<std::string, HydroProp*> SMIPDForceManager::parseFrictionFile(const std::string& filename) {
269 <    std::map<std::string, HydroProp*> props;
270 <    std::ifstream ifs(filename.c_str());
271 <    if (ifs.is_open()) {
272 <      
273 <    }
274 <    
275 <    const unsigned int BufferSize = 65535;
276 <    char buffer[BufferSize];  
277 <    while (ifs.getline(buffer, BufferSize)) {
278 <      HydroProp* currProp = new HydroProp(buffer);
279 <      props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
280 <    }
281 <
282 <    return props;
283 <  }
284 <  
124 >  
125    void SMIPDForceManager::postCalculation(bool needStress){
126      SimInfo::MoleculeIterator i;
127      Molecule::IntegrableObjectIterator  j;
128      Molecule* mol;
129      StuntDouble* integrableObject;
290 –    RealType mass;
291 –    Vector3d pos;
292 –    Vector3d frc;
293 –    Mat3x3d A;
294 –    Mat3x3d Atrans;
295 –    Vector3d Tb;
296 –    Vector3d ji;
297 –    unsigned int index = 0;
298 –    int fdf;
130    
131 <    fdf = 0;
301 <  
302 <    /*Compute surface Mesh*/
131 >    // Compute surface Mesh
132      surfaceMesh_->computeHull(localSites_);
304 –
305 –    /* Get area and number of surface stunt doubles and compute new variance */
306 –     RealType area = surfaceMesh_->getArea();
307 –     int nSurfaceSDs = surfaceMesh_->getNs();
308 –
133      
134 +    // Get total area and number of surface stunt doubles
135 +    RealType area = surfaceMesh_->getArea();
136 +    int nSurfaceSDs = surfaceMesh_->getNs();        
137      std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
138      int nTriangles = sMesh.size();
139 <
139 >        
140 >    // Generate all of the necessary random forces
141 >    std::vector<RealType>  randNums = genTriangleForces(nTriangles, variance_);
142  
143 <
315 <     /* Compute variance for random forces */
316 <  
317 <
318 <
319 <
320 <    std::vector<RealType>  randNums = genTriangleForces(nTriangles, 1.0);
321 <
322 <    /* Loop over the mesh faces and apply random force to each of the faces*/
323 <    
324 <    
143 >    // Loop over the mesh faces and apply random force to each of the faces
144      std::vector<Triangle>::iterator face;
145      std::vector<StuntDouble*>::iterator vertex;
146      int thisNumber = 0;
# Line 330 | Line 149 | namespace oopse {
149        Triangle thisTriangle = *face;
150        std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();
151        RealType thisArea = thisTriangle.getArea();
333 –      // RealType sigma_t = sqrt(NumericConstant::PI/2.0)*((targetPressure_)*thisArea) /OOPSEConstant::energyConvert;
334 –      // gamma_t_ = (NumericConstant::PI * targetPressure_* targetPressure_ * thisArea * thisArea * simParams->getDt()) /(4.0 * OOPSEConstant::kB*simParams->getTargetTemp());
335 –
336 –      /* Get Random Force */
152        Vector3d unitNormal = thisTriangle.getNormal();
153        unitNormal.normalize();
154 <      //Vector3d randomForce = -randNums[thisNumber] * sigma_t * unitNormal;
154 >
155        Vector3d centroid = thisTriangle.getCentroid();
156        Vector3d facetVel = thisTriangle.getFacetVelocity();
157 <      RealType hydroLength = thisTriangle.getIncircleRadius()*2.0/3.14;
158 <
344 <      RealType f_normal = simParams->getViscosity()*hydroLength*1.439326479e4*OOPSEConstant::energyConvert;
345 <      RealType extPressure = -(targetPressure_ * thisArea);
346 <      RealType randomForce = randNums[thisNumber] * f_normal * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
347 <      RealType dragForce = -f_normal * dot(facetVel, unitNormal);      
348 <      Vector3d langevinForce = (extPressure + randomForce + dragForce) * unitNormal;
157 >      RealType hydroLength = thisTriangle.getIncircleRadius() * 2.0 /
158 >        NumericConstant::PI;
159        
160 <      //      Vector3d dragForce = - gamma_t_ * dot(facetVel, unitNormal) * unitNormal / OOPSEConstant::energyConvert;
161 <      
162 <      //std::cout << "randomForce " << randomForce << " dragForce " << dragForce <<  " hydro  " << hydroLength << std::endl;
160 >      // gamma is the drag coefficient normal to the face of the triangle      
161 >      RealType gamma = viscosity_ * hydroLength *
162 >        OOPSEConstant::viscoConvert;
163  
164 +      RealType extPressure = - (targetPressure_ * thisArea) /
165 +        OOPSEConstant::energyConvert;
166  
167 <      for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex){
168 <        if ((*vertex) != NULL){
357 <          // mass = integrableObject->getMass();
358 <          Vector3d vertexForce = langevinForce/3.0;
359 <          (*vertex)->addFrc(vertexForce);
167 >      RealType randomForce = randNums[thisNumber++] * sqrt(gamma);
168 >      RealType dragForce = -gamma * dot(facetVel, unitNormal);
169  
170 <          if ((*vertex)->isDirectional()){
171 <
170 >      Vector3d langevinForce = (extPressure + randomForce + dragForce) * unitNormal;
171 >      
172 >      // Apply triangle force to stuntdouble vertices
173 >      for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex) {
174 >        if ((*vertex) != NULL) {
175 >          Vector3d vertexForce = langevinForce / 3.0;
176 >          (*vertex)->addFrc(vertexForce);          
177 >          if ((*vertex)->isDirectional()) {
178              Vector3d vertexPos = (*vertex)->getPos();
179              Vector3d vertexCentroidVector = vertexPos - centroid;
180              (*vertex)->addTrq(cross(vertexCentroidVector,vertexForce));
# Line 367 | Line 182 | namespace oopse {
182          }  
183        }
184      }
185 <
371 <    /* Now loop over all surface particles and apply the drag*/
372 <    /*
373 <    std::vector<StuntDouble*> surfaceSDs = surfaceMesh_->getSurfaceAtoms();
374 <    for (vertex = surfaceSDs.begin(); vertex != surfaceSDs.end(); ++vertex){
375 <      integrableObject = *vertex;
376 <      mass = integrableObject->getMass();
377 <      if (integrableObject->isDirectional()){
378 <        
379 <        // preliminaries for directional objects:
380 <        
381 <        A = integrableObject->getA();
382 <        Atrans = A.transpose();
383 <        Vector3d rcrLab = Atrans * hydroProps_[index]->getCOR();  
384 <        //apply random force and torque at center of resistance
385 <        Mat3x3d I = integrableObject->getI();
386 <        Vector3d omegaBody;
387 <        
388 <        // What remains contains velocity explicitly, but the velocity required
389 <        // is at the full step: v(t + h), while we have initially the velocity
390 <        // at the half step: v(t + h/2).  We need to iterate to converge the
391 <        // friction force and friction torque vectors.
392 <        
393 <        // this is the velocity at the half-step:
394 <        
395 <        Vector3d vel =integrableObject->getVel();
396 <        Vector3d angMom = integrableObject->getJ();
397 <        
398 <        //estimate velocity at full-step using everything but friction forces:          
399 <        
400 <        frc = integrableObject->getFrc();
401 <        Vector3d velStep = vel + (dt2_ /mass * OOPSEConstant::energyConvert) * frc;
402 <        
403 <        Tb = integrableObject->lab2Body(integrableObject->getTrq());
404 <        Vector3d angMomStep = angMom + (dt2_ * OOPSEConstant::energyConvert) * Tb;                            
405 <        
406 <        Vector3d omegaLab;
407 <        Vector3d vcdLab;
408 <        Vector3d vcdBody;
409 <        Vector3d frictionForceBody;
410 <        Vector3d frictionForceLab(0.0);
411 <        Vector3d oldFFL;  // used to test for convergence
412 <        Vector3d frictionTorqueBody(0.0);
413 <        Vector3d oldFTB;  // used to test for convergence
414 <        Vector3d frictionTorqueLab;
415 <        RealType fdot;
416 <        RealType tdot;
417 <
418 <        //iteration starts here:
419 <        
420 <        for (int k = 0; k < maxIterNum_; k++) {
421 <          
422 <          if (integrableObject->isLinear()) {
423 <            int linearAxis = integrableObject->linearAxis();
424 <            int l = (linearAxis +1 )%3;
425 <            int m = (linearAxis +2 )%3;
426 <            omegaBody[l] = angMomStep[l] /I(l, l);
427 <            omegaBody[m] = angMomStep[m] /I(m, m);
428 <            
429 <          } else {
430 <            omegaBody[0] = angMomStep[0] /I(0, 0);
431 <            omegaBody[1] = angMomStep[1] /I(1, 1);
432 <            omegaBody[2] = angMomStep[2] /I(2, 2);
433 <          }
434 <          
435 <          omegaLab = Atrans * omegaBody;
436 <          
437 <          // apply friction force and torque at center of resistance
438 <          
439 <          vcdLab = velStep + cross(omegaLab, rcrLab);      
440 <          vcdBody = A * vcdLab;
441 <          frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omegaBody);
442 <          oldFFL = frictionForceLab;
443 <          frictionForceLab = Atrans * frictionForceBody;
444 <          oldFTB = frictionTorqueBody;
445 <          frictionTorqueBody = -(hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omegaBody);
446 <          frictionTorqueLab = Atrans * frictionTorqueBody;
447 <          
448 <          // re-estimate velocities at full-step using friction forces:
449 <              
450 <          velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * (frc + frictionForceLab);
451 <          angMomStep = angMom + (dt2_ * OOPSEConstant::energyConvert) * (Tb + frictionTorqueBody);
452 <
453 <          // check for convergence (if the vectors have converged, fdot and tdot will both be 1.0):
454 <              
455 <          fdot = dot(frictionForceLab, oldFFL) / frictionForceLab.lengthSquare();
456 <          tdot = dot(frictionTorqueBody, oldFTB) / frictionTorqueBody.lengthSquare();
457 <          
458 <          if (fabs(1.0 - fdot) <= forceTolerance_ && fabs(1.0 - tdot) <= forceTolerance_)
459 <            break; // iteration ends here
460 <        }
461 <        
462 <        integrableObject->addFrc(frictionForceLab);
463 <        integrableObject->addTrq(frictionTorqueLab + cross(rcrLab, frictionForceLab));
464 <
465 <            
466 <      } else {
467 <        //spherical atom
468 <
469 <        // What remains contains velocity explicitly, but the velocity required
470 <        // is at the full step: v(t + h), while we have initially the velocity
471 <        // at the half step: v(t + h/2).  We need to iterate to converge the
472 <        // friction force vector.
473 <        
474 <        // this is the velocity at the half-step:
475 <        
476 <        Vector3d vel =integrableObject->getVel();
477 <        
478 <        //estimate velocity at full-step using everything but friction forces:          
479 <        
480 <        frc = integrableObject->getFrc();
481 <        Vector3d velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * frc;
482 <        
483 <        Vector3d frictionForce(0.0);
484 <        Vector3d oldFF;  // used to test for convergence
485 <        RealType fdot;
486 <        
487 <        //iteration starts here:
488 <        
489 <        for (int k = 0; k < maxIterNum_; k++) {
490 <          
491 <          oldFF = frictionForce;                            
492 <          frictionForce = -hydroProps_[index]->getXitt() * velStep;
493 <          //frictionForce = -gamma_t*velStep;
494 <          // re-estimate velocities at full-step using friction forces:
495 <          
496 <          velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * (frc + frictionForce);
497 <          
498 <          // check for convergence (if the vector has converged, fdot will be 1.0):
499 <          
500 <          fdot = dot(frictionForce, oldFF) / frictionForce.lengthSquare();
501 <          
502 <          if (fabs(1.0 - fdot) <= forceTolerance_)
503 <            break; // iteration ends here
504 <        }
505 <        
506 <        integrableObject->addFrc(frictionForce);
507 <        
508 <        
509 <      }
510 <  
511 <      
512 <  }
513 <    */
185 >    
186      Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
187      currSnapshot->setVolume(surfaceMesh_->getVolume());    
188      ForceManager::postCalculation(needStress);  
189    }
190  
191 <  void SMIPDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
191 >  std::vector<RealType> SMIPDForceManager::genTriangleForces(int nTriangles,
192 >                                                             RealType variance) {
193  
521 –    
522 –    Vector<RealType, 6> Z;
523 –    Vector<RealType, 6> generalForce;
524 –    
525 –
526 –    Z[0] = randNumGen_.randNorm(0, variance);
527 –    Z[1] = randNumGen_.randNorm(0, variance);
528 –    Z[2] = randNumGen_.randNorm(0, variance);
529 –    Z[3] = randNumGen_.randNorm(0, variance);
530 –    Z[4] = randNumGen_.randNorm(0, variance);
531 –    Z[5] = randNumGen_.randNorm(0, variance);
532 –    
533 –    generalForce = hydroProps_[index]->getS()*Z;
534 –    
535 –    force[0] = generalForce[0];
536 –    force[1] = generalForce[1];
537 –    force[2] = generalForce[2];
538 –    torque[0] = generalForce[3];
539 –    torque[1] = generalForce[4];
540 –    torque[2] = generalForce[5];
541 –    
542 – }
543 –  std::vector<RealType> SMIPDForceManager::genTriangleForces(int nTriangles, RealType variance) {
544 –
194      // zero fill the random vector before starting:
195      std::vector<RealType> gaussRand;
196      gaussRand.resize(nTriangles);
197      std::fill(gaussRand.begin(), gaussRand.end(), 0.0);
198 <
550 <
198 >  
199   #ifdef IS_MPI
200      if (worldRank == 0) {
201   #endif
202        for (int i = 0; i < nTriangles; i++) {
203 <        //gaussRand[i] = fabs(randNumGen_.randNorm(0.0, 1.0));    
556 <        gaussRand[i] = randNumGen_.randNorm(0.0, 1.0);    
203 >        gaussRand[i] = randNumGen_.randNorm(0.0, variance);
204        }
205   #ifdef IS_MPI
206      }
# Line 563 | Line 210 | namespace oopse {
210  
211   #ifdef IS_MPI
212      if (worldRank == 0) {
213 <      MPI_Bcast(&gaussRand[0], nTriangles, MPI_REAL, 0, MPI_COMM_WORLD);
213 >      MPI_Bcast(&gaussRand[0], nTriangles, MPI_REALTYPE, 0, MPI_COMM_WORLD);
214      } else {
215 <      MPI_Bcast(&gaussRand[0], nTriangles, MPI_REAL, 0, MPI_COMM_WORLD);
215 >      MPI_Bcast(&gaussRand[0], nTriangles, MPI_REALTYPE, 0, MPI_COMM_WORLD);
216      }
217   #endif
218    
572 –    for (int i = 0; i < nTriangles; i++) {
573 –      gaussRand[i] = gaussRand[i] * variance;
574 –    }
575 –  
219      return gaussRand;
220    }
578 –
579 –
580 –
581 –
582 –
221   }

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