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Comparing trunk/src/applications/hydrodynamics/Hydro.cpp (file contents):
Revision 907 by tim, Fri Mar 17 23:51:54 2006 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 6 | Line 6
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
28   * arising out of the use of or inability to use software, even if the
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31 + *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
35 + *                                                                      
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).                        
40   */
41  
42   #include <iostream>
# Line 57 | Line 57
57   #include "utils/StringUtils.hpp"
58   #include "utils/simError.h"
59   #include "utils/MemoryUtils.hpp"
60 < using namespace oopse;
60 > using namespace OpenMD;
61  
62   struct SDShape{
63      StuntDouble* sd;
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
# 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();
# Line 127 | Line 124 | int main(int argc, char* argv[]){
124    if (simParams->haveTargetTemp()) {
125      temperature = simParams->getTargetTemp();
126    } else {
127 <    sprintf(painCave.errMsg, "target temperaturemust 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    }
154  
155  
156    
158 –  std::ofstream outputDiff(outputFilename.c_str());
157    std::map<std::string, SDShape>::iterator si;
158    for (si = uniqueStuntDoubles.begin(); si != uniqueStuntDoubles.end(); ++si) {
159        HydrodynamicsModel* model;
# Line 168 | Line 166 | int main(int argc, char* argv[]){
166        } else {
167          model = new BeadModel(sd, info);
168        }
169 <        calcHydrodynamicsProp(model, shape, viscosity, temperature, outputDiff, prefix);          
169 >
170 >        model->init();
171 >        
172 >        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;
189    }
190  
# Line 184 | Line 200 | void registerHydrodynamicsModels() {
200      HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<AnalyticalModel>("AnalyticalModel"));
201  
202   }
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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