--- trunk/src/applications/hydrodynamics/Hydro.cpp	2006/03/17 23:20:35	906
+++ trunk/src/applications/hydrodynamics/Hydro.cpp	2006/08/30 21:13:57	1027
@@ -64,12 +64,12 @@ void registerHydrodynamicsModels();
     Shape* shape;
 };
 void registerHydrodynamicsModels();
-void calcHydrodynamicsProp(HydrodynamicsModel* model, Shape* shape,double viscosity,  double temperature, std::ostream& os, const std::string& prefix);
+void writeHydroProps(std::ostream& os);
 
 int main(int argc, char* argv[]){
   //register force fields
   registerForceFields();    
-
+  registerHydrodynamicsModels();
   
   gengetopt_args_info args_info;
   std::string dumpFileName;
@@ -89,19 +89,16 @@ int main(int argc, char* argv[]){
     exit(1);
   }
   
-  mdFileName = dumpFileName;
-  mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
-
   if (args_info.output_given){
     prefix = args_info.output_arg;
   } else {
-    prefix = getPrefix(mdFileName);    
+    prefix = getPrefix(dumpFileName);    
   }
   std::string outputFilename = prefix + ".diff";
     
   //parse md file and set up the system
   SimCreator creator;
-  SimInfo* info = creator.createSim(mdFileName, true);
+  SimInfo* info = creator.createSim(dumpFileName, true);
     
   SimInfo::MoleculeIterator mi;
   Molecule* mol;
@@ -113,13 +110,13 @@ int main(int argc, char* argv[]){
   identMat(2,2) = 1.0;
 
   Globals* simParams = info->getSimParams();
-  double temperature;
-  double viscosity;
+  RealType temperature;
+  RealType viscosity;
 
   if (simParams->haveViscosity()) {
     viscosity = simParams->getViscosity();
   } else {
-    sprintf(painCave.errMsg, "target temperature must be set\n");
+    sprintf(painCave.errMsg, "viscosity must be set\n");
     painCave.isFatal = 1;
     simError();  
   }
@@ -127,7 +124,7 @@ int main(int argc, char* argv[]){
   if (simParams->haveTargetTemp()) {
     temperature = simParams->getTargetTemp();
   } else {
-    sprintf(painCave.errMsg, "viscosity must be set\n");
+    sprintf(painCave.errMsg, "target temperature must be set\n");
     painCave.isFatal = 1;
     simError();  
   }
@@ -139,16 +136,18 @@ int main(int argc, char* argv[]){
 	   integrableObject = mol->nextIntegrableObject(ii)) {
           if (uniqueStuntDoubles.find(integrableObject->getType()) ==  uniqueStuntDoubles.end()) {
 
-            SDShape tmp;
-            tmp.shape = ShapeBuilder::createShape(integrableObject);
-            tmp.sd = integrableObject;    
-            uniqueStuntDoubles.insert(std::map<std::string, SDShape>::value_type(integrableObject->getType(), tmp));
             integrableObject->setPos(V3Zero);
             integrableObject->setA(identMat);
             if (integrableObject->isRigidBody()) {
                 RigidBody* rb = static_cast<RigidBody*>(integrableObject);
                 rb->updateAtoms();
             }
+
+            SDShape tmp;
+            tmp.shape = ShapeBuilder::createShape(integrableObject);
+            tmp.sd = integrableObject;    
+            uniqueStuntDoubles.insert(std::map<std::string, SDShape>::value_type(integrableObject->getType(), tmp));
+
           }
 	}
   }
@@ -157,7 +156,7 @@ int main(int argc, char* argv[]){
   
   std::ofstream outputDiff(outputFilename.c_str());
   std::map<std::string, SDShape>::iterator si;
-  for (si != uniqueStuntDoubles.begin(); si != uniqueStuntDoubles.end(); ++si) {
+  for (si = uniqueStuntDoubles.begin(); si != uniqueStuntDoubles.end(); ++si) {
       HydrodynamicsModel* model;
       Shape* shape = si->second.shape;
       StuntDouble* sd = si->second.sd;;
@@ -168,7 +167,22 @@ int main(int argc, char* argv[]){
       } else {
         model = new BeadModel(sd, info);
       }
-        calcHydrodynamicsProp(model, shape, viscosity, temperature, outputDiff, prefix);          
+
+        model->init();
+        
+        std::ofstream ofs;
+        std::stringstream outputBeads;
+        outputBeads << prefix << "_" << model->getStuntDoubleName() << ".xyz";
+        ofs.open(outputBeads.str().c_str());        
+        model->writeBeads(ofs);
+        ofs.close();
+
+        //if beads option is turned on, skip the calculation
+        if (!args_info.beads_flag) {
+          model->calcHydroProps(shape, viscosity, temperature);
+          model->writeHydroProps(outputDiff);
+        }
+        
         delete model;
   }
 
@@ -184,14 +198,3 @@ void registerHydrodynamicsModels() {
     HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<AnalyticalModel>("AnalyticalModel"));
 
 }
-void calcHydrodynamicsProp(HydrodynamicsModel* model, Shape* shape,double viscosity,  double temperature, std::ostream& os, const std::string& prefix) {
-
-       shape->calcHydroProps(model, viscosity, temperature);
-        model->writeHydroProps(os);
-        std::ofstream ofs;
-        std::stringstream outputBeads;
-        outputBeads << prefix << "_" << model->getStuntDoubleName() << ".xyz";
-        ofs.open(outputBeads.str().c_str());        
-        model->writeBeads(ofs);
-        ofs.close();
-}