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Comparing trunk/src/applications/hydrodynamics/Hydro.cpp (file contents):
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

# Line 36 | Line 36
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   #include <iostream>
# Line 60 | Line 61 | struct SDShape{
61   using namespace OpenMD;
62  
63   struct SDShape{
64 <    StuntDouble* sd;
65 <    Shape* shape;
64 >  StuntDouble* sd;
65 >  Shape* shape;
66   };
67   void registerHydrodynamicsModels();
68   void writeHydroProps(std::ostream& os);
69  
70   int main(int argc, char* argv[]){
70 –  //register force fields
71 –  registerForceFields();    
71    registerHydrodynamicsModels();
72    
73    gengetopt_args_info args_info;
# Line 103 | Line 102 | int main(int argc, char* argv[]){
102    SimInfo::MoleculeIterator mi;
103    Molecule* mol;
104    Molecule::IntegrableObjectIterator  ii;
105 <  StuntDouble* integrableObject;
105 >  StuntDouble* sd;
106    Mat3x3d identMat;
107    identMat(0,0) = 1.0;
108    identMat(1,1) = 1.0;
# Line 131 | Line 130 | int main(int argc, char* argv[]){
130  
131    std::map<std::string, SDShape> uniqueStuntDoubles;
132    
133 <  for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
134 <      for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
135 <           integrableObject = mol->nextIntegrableObject(ii)) {
136 <          if (uniqueStuntDoubles.find(integrableObject->getType()) ==  uniqueStuntDoubles.end()) {
137 <
138 <            integrableObject->setPos(V3Zero);
139 <            integrableObject->setA(identMat);
140 <            if (integrableObject->isRigidBody()) {
141 <                RigidBody* rb = static_cast<RigidBody*>(integrableObject);
142 <                rb->updateAtoms();
143 <            }
144 <
145 <            SDShape tmp;
146 <            tmp.shape = ShapeBuilder::createShape(integrableObject);
147 <            tmp.sd = integrableObject;    
148 <            uniqueStuntDoubles.insert(std::map<std::string, SDShape>::value_type(integrableObject->getType(), tmp));
149 <
150 <          }
151 <        }
133 >  for (mol = info->beginMolecule(mi); mol != NULL;
134 >       mol = info->nextMolecule(mi)) {
135 >    
136 >    for (sd = mol->beginIntegrableObject(ii); sd != NULL;
137 >         sd = mol->nextIntegrableObject(ii)) {
138 >      
139 >      if (uniqueStuntDoubles.find(sd->getType()) ==  uniqueStuntDoubles.end()) {
140 >        
141 >        sd->setPos(V3Zero);
142 >        sd->setA(identMat);
143 >        if (sd->isRigidBody()) {
144 >          RigidBody* rb = static_cast<RigidBody*>(sd);
145 >          rb->updateAtoms();
146 >        }
147 >        
148 >        SDShape tmp;
149 >        tmp.shape = ShapeBuilder::createShape(sd);
150 >        tmp.sd = sd;    
151 >        uniqueStuntDoubles.insert(std::map<std::string, SDShape>::value_type(sd->getType(), tmp));
152 >        
153 >      }
154 >    }
155    }
154 –
155 –
156    
157 +  
158 +  
159    std::map<std::string, SDShape>::iterator si;
160    for (si = uniqueStuntDoubles.begin(); si != uniqueStuntDoubles.end(); ++si) {
161 <      HydrodynamicsModel* model;
162 <      Shape* shape = si->second.shape;
163 <      StuntDouble* sd = si->second.sd;;
164 <      if (args_info.model_given) {  
165 <        model = HydrodynamicsModelFactory::getInstance()->createHydrodynamicsModel(args_info.model_arg, sd, info);
166 <      } else if (shape->hasAnalyticalSolution()) {
167 <        model = new AnalyticalModel(sd, info);
168 <      } else {
169 <        model = new BeadModel(sd, info);
170 <      }
171 <
172 <        model->init();
161 >    HydrodynamicsModel* model;
162 >    Shape* shape = si->second.shape;
163 >    StuntDouble* sd = si->second.sd;;
164 >    if (args_info.model_given) {  
165 >      model = HydrodynamicsModelFactory::getInstance()->createHydrodynamicsModel(args_info.model_arg, sd, info);
166 >    } else if (shape->hasAnalyticalSolution()) {
167 >      model = new AnalyticalModel(sd, info);
168 >    } else {
169 >      model = new BeadModel(sd, info);
170 >    }
171 >    
172 >    model->init();
173 >    
174 >    std::ofstream ofs;
175 >    std::stringstream outputBeads;
176 >    outputBeads << prefix << "_" << model->getStuntDoubleName() << ".xyz";
177 >    ofs.open(outputBeads.str().c_str());        
178 >    model->writeBeads(ofs);
179 >    ofs.close();
180 >    
181 >    //if beads option is turned on, skip the calculation
182 >    if (!args_info.beads_flag) {
183 >      model->calcHydroProps(shape, viscosity, temperature);
184 >      std::ofstream outputDiff;
185 >      outputDiff.open(outputFilename.c_str());
186 >      model->writeHydroProps(outputDiff);
187 >      outputDiff.close();
188 >    }
189          
190 <        std::ofstream ofs;
173 <        std::stringstream outputBeads;
174 <        outputBeads << prefix << "_" << model->getStuntDoubleName() << ".xyz";
175 <        ofs.open(outputBeads.str().c_str());        
176 <        model->writeBeads(ofs);
177 <        ofs.close();
178 <
179 <        //if beads option is turned on, skip the calculation
180 <        if (!args_info.beads_flag) {
181 <          model->calcHydroProps(shape, viscosity, temperature);
182 <          std::ofstream outputDiff;
183 <          outputDiff.open(outputFilename.c_str());
184 <          model->writeHydroProps(outputDiff);
185 <          outputDiff.close();
186 <        }
187 <        
188 <        delete model;
190 >    delete model;
191    }
192  
193  
# Line 195 | Line 197 | void registerHydrodynamicsModels() {
197   }
198  
199   void registerHydrodynamicsModels() {
200 <    HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<RoughShell>("RoughShell"));
201 <    HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<BeadModel>("BeadModel"));
202 <    HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<AnalyticalModel>("AnalyticalModel"));
201 <
200 >  HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<RoughShell>("RoughShell"));
201 >  HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<BeadModel>("BeadModel"));
202 >  HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<AnalyticalModel>("AnalyticalModel"));
203   }

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