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Comparing trunk/src/applications/hydrodynamics/Hydro.cpp (file contents):
Revision 891 by tim, Wed Feb 22 20:35:16 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 47 | Line 47
47   #include "applications/hydrodynamics/HydrodynamicsModel.hpp"
48   #include "applications/hydrodynamics/HydrodynamicsModelCreator.hpp"
49   #include "applications/hydrodynamics/HydrodynamicsModelFactory.hpp"
50 + #include "applications/hydrodynamics/AnalyticalModel.hpp"
51   #include "applications/hydrodynamics/BeadModel.hpp"
52   #include "applications/hydrodynamics/RoughShell.hpp"
53 + #include "applications/hydrodynamics/ShapeBuilder.hpp"
54   #include "brains/Register.hpp"
55   #include "brains/SimCreator.hpp"
56   #include "brains/SimInfo.hpp"
57 + #include "utils/StringUtils.hpp"
58 + #include "utils/simError.h"
59 + #include "utils/MemoryUtils.hpp"
60 + using namespace OpenMD;
61  
62 < using namespace oopse;
63 <
64 < /** Register different hydrodynamics models */
62 > struct SDShape{
63 >    StuntDouble* sd;
64 >    Shape* shape;
65 > };
66   void registerHydrodynamicsModels();
67 + void writeHydroProps(std::ostream& os);
68  
61 – bool calcHydrodynamicsProp(const std::string& modelType, Molecule* mol, const DynamicProperty& param, const std::string& prefix,double viscosity);
62 –
69   int main(int argc, char* argv[]){
70    //register force fields
71    registerForceFields();    
# Line 83 | Line 89 | int main(int argc, char* argv[]){
89      exit(1);
90    }
91    
86 –  mdFileName = dumpFileName;
87 –  mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
88 –
92    if (args_info.output_given){
93      prefix = args_info.output_arg;
94    } else {
95 <    prefix = "hydro";    
95 >    prefix = getPrefix(dumpFileName);    
96    }
97 <
98 <  DynamicProperty param;
96 <  if (args_info.sigma_given) {
97 <    param.insert(DynamicProperty::value_type("Sigma", args_info.sigma_arg));
98 <  }
99 <  
100 <  
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;
105 <  Molecule::RigidBodyIterator ri;
106 <  RigidBody* rb;
107 <    //update atoms of rigidbody
108 <  for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
109 <      
110 <      //change the positions of atoms which belong to the rigidbodies
111 <      for (rb = mol->beginRigidBody(ri); rb != NULL; rb = mol->nextRigidBody(ri)) {
112 <        rb->updateAtoms();
113 <      }
105 >  Molecule::IntegrableObjectIterator  ii;
106 >  StuntDouble* integrableObject;
107 >  Mat3x3d identMat;
108 >  identMat(0,0) = 1.0;
109 >  identMat(1,1) = 1.0;
110 >  identMat(2,2) = 1.0;
111 >
112 >  Globals* simParams = info->getSimParams();
113 >  RealType temperature;
114 >  RealType viscosity;
115 >
116 >  if (simParams->haveViscosity()) {
117 >    viscosity = simParams->getViscosity();
118 >  } else {
119 >    sprintf(painCave.errMsg, "viscosity must be set\n");
120 >    painCave.isFatal = 1;
121 >    simError();  
122    }
123 <    
124 <  for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
125 <    calcHydrodynamicsProp(args_info.model_arg, mol, param, prefix, args_info.viscosity_arg);
123 >
124 >  if (simParams->haveTargetTemp()) {
125 >    temperature = simParams->getTargetTemp();
126 >  } else {
127 >    sprintf(painCave.errMsg, "target temperature must be set\n");
128 >    painCave.isFatal = 1;
129 >    simError();  
130    }
131 +
132 +  std::map<std::string, SDShape> uniqueStuntDoubles;
133    
134 <  delete info;
135 <  
136 < }
134 >  for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
135 >      for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
136 >           integrableObject = mol->nextIntegrableObject(ii)) {
137 >          if (uniqueStuntDoubles.find(integrableObject->getType()) ==  uniqueStuntDoubles.end()) {
138  
139 < void registerHydrodynamicsModels() {
140 <    HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<RoughShell>("RoughShell"));
141 <    HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<BeadModel>("BeadModel"));
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 < }
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 < bool calcHydrodynamicsProp(const std::string& modelType, Molecule* mol, const DynamicProperty& param, const std::string& prefix,double viscosity) {
152 <    HydrodynamicsModel* hydroModel = HydrodynamicsModelFactory::getInstance()->createHydrodynamicsModel(modelType, mol, param);
153 <    bool ret = false;
135 <    if (hydroModel == NULL) {
136 <        std::cout << "Integrator Factory can not create " << modelType <<std::endl;
137 <    }    
151 >          }
152 >        }
153 >  }
154  
155 <    if (hydroModel->calcHydrodyanmicsProps(viscosity)) {
156 <        ret = true;
157 <        std::stringstream outputDiffTensor;
158 <        outputDiffTensor << prefix << "_" << mol->getType() << ".diff";
159 <        std::ofstream ofs;
160 <        ofs.open(outputDiffTensor.str().c_str());
161 <        hydroModel->writeDiffCenterAndDiffTensor(ofs);
162 <        ofs.close();
155 >
156 >  
157 >  std::map<std::string, SDShape>::iterator si;
158 >  for (si = uniqueStuntDoubles.begin(); si != uniqueStuntDoubles.end(); ++si) {
159 >      HydrodynamicsModel* model;
160 >      Shape* shape = si->second.shape;
161 >      StuntDouble* sd = si->second.sd;;
162 >      if (args_info.model_given) {  
163 >        model = HydrodynamicsModelFactory::getInstance()->createHydrodynamicsModel(args_info.model_arg, sd, info);
164 >      } else if (shape->hasAnalyticalSolution()) {
165 >        model = new AnalyticalModel(sd, info);
166 >      } else {
167 >        model = new BeadModel(sd, info);
168 >      }
169 >
170 >        model->init();
171          
172 +        std::ofstream ofs;
173          std::stringstream outputBeads;
174 <        outputBeads << prefix << "_" << mol->getType() << ".xyz";
175 <        ofs.open(outputBeads.str().c_str());
176 <        hydroModel->writeBeads(ofs);
174 >        outputBeads << prefix << "_" << model->getStuntDoubleName() << ".xyz";
175 >        ofs.open(outputBeads.str().c_str());        
176 >        model->writeBeads(ofs);
177          ofs.close();
153 –    }
178  
179 <    delete hydroModel;
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  
191 <    return ret;    
191 >
192 >  //MemoryUtils::deletePointers(shapes);
193 >  delete info;
194 >  
195   }
196 +
197 + void registerHydrodynamicsModels() {
198 +    HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<RoughShell>("RoughShell"));
199 +    HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<BeadModel>("BeadModel"));
200 +    HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<AnalyticalModel>("AnalyticalModel"));
201 +
202 + }

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