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root/OpenMD/trunk/src/applications/hydrodynamics/Hydro.cpp
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Comparing trunk/src/applications/hydrodynamics/Hydro.cpp (file contents):
Revision 906 by tim, Fri Mar 17 23:20:35 2006 UTC vs.
Revision 1027 by gezelter, Wed Aug 30 21:13:57 2006 UTC

# Line 64 | Line 64 | void registerHydrodynamicsModels();
64      Shape* shape;
65   };
66   void registerHydrodynamicsModels();
67 < void calcHydrodynamicsProp(HydrodynamicsModel* model, Shape* shape,double viscosity,  double temperature, std::ostream& os, const std::string& prefix);
67 > void writeHydroProps(std::ostream& os);
68  
69   int main(int argc, char* argv[]){
70    //register force fields
71    registerForceFields();    
72 <
72 >  registerHydrodynamicsModels();
73    
74    gengetopt_args_info args_info;
75    std::string dumpFileName;
# Line 89 | Line 89 | int main(int argc, char* argv[]){
89      exit(1);
90    }
91    
92 –  mdFileName = dumpFileName;
93 –  mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
94 –
92    if (args_info.output_given){
93      prefix = args_info.output_arg;
94    } else {
95 <    prefix = getPrefix(mdFileName);    
95 >    prefix = getPrefix(dumpFileName);    
96    }
97    std::string outputFilename = prefix + ".diff";
98      
99    //parse md file and set up the system
100    SimCreator creator;
101 <  SimInfo* info = creator.createSim(mdFileName, true);
101 >  SimInfo* info = creator.createSim(dumpFileName, true);
102      
103    SimInfo::MoleculeIterator mi;
104    Molecule* mol;
# Line 113 | Line 110 | int main(int argc, char* argv[]){
110    identMat(2,2) = 1.0;
111  
112    Globals* simParams = info->getSimParams();
113 <  double temperature;
114 <  double viscosity;
113 >  RealType temperature;
114 >  RealType viscosity;
115  
116    if (simParams->haveViscosity()) {
117      viscosity = simParams->getViscosity();
118    } else {
119 <    sprintf(painCave.errMsg, "target temperature must be set\n");
119 >    sprintf(painCave.errMsg, "viscosity must be set\n");
120      painCave.isFatal = 1;
121      simError();  
122    }
# Line 127 | Line 124 | int main(int argc, char* argv[]){
124    if (simParams->haveTargetTemp()) {
125      temperature = simParams->getTargetTemp();
126    } else {
127 <    sprintf(painCave.errMsg, "viscosity must be set\n");
127 >    sprintf(painCave.errMsg, "target temperature must be set\n");
128      painCave.isFatal = 1;
129      simError();  
130    }
# Line 139 | Line 136 | int main(int argc, char* argv[]){
136             integrableObject = mol->nextIntegrableObject(ii)) {
137            if (uniqueStuntDoubles.find(integrableObject->getType()) ==  uniqueStuntDoubles.end()) {
138  
142 –            SDShape tmp;
143 –            tmp.shape = ShapeBuilder::createShape(integrableObject);
144 –            tmp.sd = integrableObject;    
145 –            uniqueStuntDoubles.insert(std::map<std::string, SDShape>::value_type(integrableObject->getType(), tmp));
139              integrableObject->setPos(V3Zero);
140              integrableObject->setA(identMat);
141              if (integrableObject->isRigidBody()) {
142                  RigidBody* rb = static_cast<RigidBody*>(integrableObject);
143                  rb->updateAtoms();
144              }
145 +
146 +            SDShape tmp;
147 +            tmp.shape = ShapeBuilder::createShape(integrableObject);
148 +            tmp.sd = integrableObject;    
149 +            uniqueStuntDoubles.insert(std::map<std::string, SDShape>::value_type(integrableObject->getType(), tmp));
150 +
151            }
152          }
153    }
# Line 157 | Line 156 | int main(int argc, char* argv[]){
156    
157    std::ofstream outputDiff(outputFilename.c_str());
158    std::map<std::string, SDShape>::iterator si;
159 <  for (si != uniqueStuntDoubles.begin(); si != uniqueStuntDoubles.end(); ++si) {
159 >  for (si = uniqueStuntDoubles.begin(); si != uniqueStuntDoubles.end(); ++si) {
160        HydrodynamicsModel* model;
161        Shape* shape = si->second.shape;
162        StuntDouble* sd = si->second.sd;;
# Line 168 | Line 167 | int main(int argc, char* argv[]){
167        } else {
168          model = new BeadModel(sd, info);
169        }
170 <        calcHydrodynamicsProp(model, shape, viscosity, temperature, outputDiff, prefix);          
170 >
171 >        model->init();
172 >        
173 >        std::ofstream ofs;
174 >        std::stringstream outputBeads;
175 >        outputBeads << prefix << "_" << model->getStuntDoubleName() << ".xyz";
176 >        ofs.open(outputBeads.str().c_str());        
177 >        model->writeBeads(ofs);
178 >        ofs.close();
179 >
180 >        //if beads option is turned on, skip the calculation
181 >        if (!args_info.beads_flag) {
182 >          model->calcHydroProps(shape, viscosity, temperature);
183 >          model->writeHydroProps(outputDiff);
184 >        }
185 >        
186          delete model;
187    }
188  
# Line 184 | Line 198 | void registerHydrodynamicsModels() {
198      HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<AnalyticalModel>("AnalyticalModel"));
199  
200   }
187 – void calcHydrodynamicsProp(HydrodynamicsModel* model, Shape* shape,double viscosity,  double temperature, std::ostream& os, const std::string& prefix) {
188 –
189 –       shape->calcHydroProps(model, viscosity, temperature);
190 –        model->writeHydroProps(os);
191 –        std::ofstream ofs;
192 –        std::stringstream outputBeads;
193 –        outputBeads << prefix << "_" << model->getStuntDoubleName() << ".xyz";
194 –        ofs.open(outputBeads.str().c_str());        
195 –        model->writeBeads(ofs);
196 –        ofs.close();
197 – }

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