applications/hydrodynamics/Hydro.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#include <iostream>
#include <fstream>
#include <string>

#include "applications/hydrodynamics/HydroCmd.h"
#include "applications/hydrodynamics/HydrodynamicsModel.hpp"
#include "applications/hydrodynamics/HydrodynamicsModelCreator.hpp"
#include "applications/hydrodynamics/HydrodynamicsModelFactory.hpp"
#include "applications/hydrodynamics/AnalyticalModel.hpp"
#include "applications/hydrodynamics/BeadModel.hpp"
#include "applications/hydrodynamics/RoughShell.hpp"
#include "applications/hydrodynamics/ShapeBuilder.hpp"
#include "brains/Register.hpp"
#include "brains/SimCreator.hpp"
#include "brains/SimInfo.hpp"
#include "utils/StringUtils.hpp"
#include "utils/simError.h"
#include "utils/MemoryUtils.hpp"
using namespace OpenMD;

struct SDShape{
    StuntDouble* sd;
    Shape* shape;
};
void registerHydrodynamicsModels();
void writeHydroProps(std::ostream& os);

int main(int argc, char* argv[]){
  //register force fields
  registerForceFields();    
  registerHydrodynamicsModels();
  
  gengetopt_args_info args_info;
  std::string dumpFileName;
  std::string mdFileName;
  std::string prefix;
  
  //parse the command line option
  if (cmdline_parser (argc, argv, &args_info) != 0) {
    exit(1) ;
  }
  
  //get the dumpfile name and meta-data file name
  if (args_info.input_given){
    dumpFileName = args_info.input_arg;
  } else {
    std::cerr << "Does not have input file name" << std::endl;
    exit(1);
  }
  
  if (args_info.output_given){
    prefix = args_info.output_arg;
  } else {
    prefix = getPrefix(dumpFileName);    
  }
  std::string outputFilename = prefix + ".diff";
    
  //parse md file and set up the system
  SimCreator creator;
  SimInfo* info = creator.createSim(dumpFileName, true);
    
  SimInfo::MoleculeIterator mi;
  Molecule* mol;
  Molecule::IntegrableObjectIterator  ii;
  StuntDouble* integrableObject;
  Mat3x3d identMat;
  identMat(0,0) = 1.0;
  identMat(1,1) = 1.0;
  identMat(2,2) = 1.0;

  Globals* simParams = info->getSimParams();
  RealType temperature;
  RealType viscosity;

  if (simParams->haveViscosity()) {
    viscosity = simParams->getViscosity();
  } else {
    sprintf(painCave.errMsg, "viscosity must be set\n");
    painCave.isFatal = 1;
    simError();  
  }

  if (simParams->haveTargetTemp()) {
    temperature = simParams->getTargetTemp();
  } else {
    sprintf(painCave.errMsg, "target temperature must be set\n");
    painCave.isFatal = 1;
    simError();  
  }
 
  std::map<std::string, SDShape> uniqueStuntDoubles;
  
  for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
      for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
           integrableObject = mol->nextIntegrableObject(ii)) {
          if (uniqueStuntDoubles.find(integrableObject->getType()) ==  uniqueStuntDoubles.end()) {

            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));

          }
        }
  }


  std::map<std::string, SDShape>::iterator si;
  for (si = uniqueStuntDoubles.begin(); si != uniqueStuntDoubles.end(); ++si) {
      HydrodynamicsModel* model;
      Shape* shape = si->second.shape;
      StuntDouble* sd = si->second.sd;;
      if (args_info.model_given) {  
        model = HydrodynamicsModelFactory::getInstance()->createHydrodynamicsModel(args_info.model_arg, sd, info);
      } else if (shape->hasAnalyticalSolution()) {
        model = new AnalyticalModel(sd, info);
      } else {
        model = new BeadModel(sd, info);
      }

        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);
          std::ofstream outputDiff;
          outputDiff.open(outputFilename.c_str());
          model->writeHydroProps(outputDiff);
          outputDiff.close();
        }
        
        delete model;
  }


  //MemoryUtils::deletePointers(shapes);
  delete info;
   
}

void registerHydrodynamicsModels() {
    HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<RoughShell>("RoughShell"));
    HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<BeadModel>("BeadModel"));
    HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<AnalyticalModel>("AnalyticalModel"));

}
Revision:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	7249 byte(s)
Log Message:	updated copyright notices
#	User	Rev	Content
1	tim	891	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	tim	891	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	891	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
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	gezelter	1390	*
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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	891	*/
42
43			#include <iostream>
44			#include <fstream>
45			#include <string>
46
47			#include "applications/hydrodynamics/HydroCmd.h"
48			#include "applications/hydrodynamics/HydrodynamicsModel.hpp"
49			#include "applications/hydrodynamics/HydrodynamicsModelCreator.hpp"
50			#include "applications/hydrodynamics/HydrodynamicsModelFactory.hpp"
51	tim	906	#include "applications/hydrodynamics/AnalyticalModel.hpp"
52	tim	891	#include "applications/hydrodynamics/BeadModel.hpp"
53			#include "applications/hydrodynamics/RoughShell.hpp"
54	tim	906	#include "applications/hydrodynamics/ShapeBuilder.hpp"
55	tim	891	#include "brains/Register.hpp"
56			#include "brains/SimCreator.hpp"
57			#include "brains/SimInfo.hpp"
58	tim	906	#include "utils/StringUtils.hpp"
59			#include "utils/simError.h"
60			#include "utils/MemoryUtils.hpp"
61	gezelter	1390	using namespace OpenMD;
62	tim	891
63	tim	906	struct SDShape{
64			StuntDouble* sd;
65			Shape* shape;
66			};
67	tim	891	void registerHydrodynamicsModels();
68	gezelter	972	void writeHydroProps(std::ostream& os);
69	tim	891
70			int main(int argc, char* argv[]){
71			//register force fields
72			registerForceFields();
73	tim	907	registerHydrodynamicsModels();
74	tim	891
75			gengetopt_args_info args_info;
76			std::string dumpFileName;
77			std::string mdFileName;
78			std::string prefix;
79
80			//parse the command line option
81			if (cmdline_parser (argc, argv, &args_info) != 0) {
82			exit(1) ;
83			}
84
85			//get the dumpfile name and meta-data file name
86			if (args_info.input_given){
87			dumpFileName = args_info.input_arg;
88			} else {
89			std::cerr << "Does not have input file name" << std::endl;
90			exit(1);
91			}
92
93			if (args_info.output_given){
94			prefix = args_info.output_arg;
95			} else {
96	gezelter	1027	prefix = getPrefix(dumpFileName);
97	tim	891	}
98	tim	892	std::string outputFilename = prefix + ".diff";
99	tim	906
100	tim	891	//parse md file and set up the system
101			SimCreator creator;
102	gezelter	1027	SimInfo* info = creator.createSim(dumpFileName, true);
103	tim	891
104			SimInfo::MoleculeIterator mi;
105			Molecule* mol;
106	tim	892	Molecule::IntegrableObjectIterator ii;
107			StuntDouble* integrableObject;
108			Mat3x3d identMat;
109			identMat(0,0) = 1.0;
110			identMat(1,1) = 1.0;
111			identMat(2,2) = 1.0;
112	tim	906
113			Globals* simParams = info->getSimParams();
114	tim	977	RealType temperature;
115			RealType viscosity;
116	tim	906
117			if (simParams->haveViscosity()) {
118			viscosity = simParams->getViscosity();
119			} else {
120	tim	907	sprintf(painCave.errMsg, "viscosity must be set\n");
121	tim	906	painCave.isFatal = 1;
122			simError();
123			}
124
125			if (simParams->haveTargetTemp()) {
126			temperature = simParams->getTargetTemp();
127			} else {
128	gezelter	945	sprintf(painCave.errMsg, "target temperature must be set\n");
129	tim	906	painCave.isFatal = 1;
130			simError();
131			}
132	tim	892
133	tim	906	std::map<std::string, SDShape> uniqueStuntDoubles;
134	tim	892
135	tim	891	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
136	tim	892	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
137			integrableObject = mol->nextIntegrableObject(ii)) {
138			if (uniqueStuntDoubles.find(integrableObject->getType()) == uniqueStuntDoubles.end()) {
139	tim	906
140	tim	892	integrableObject->setPos(V3Zero);
141			integrableObject->setA(identMat);
142			if (integrableObject->isRigidBody()) {
143			RigidBody* rb = static_cast<RigidBody*>(integrableObject);
144			rb->updateAtoms();
145			}
146	tim	921
147			SDShape tmp;
148			tmp.shape = ShapeBuilder::createShape(integrableObject);
149			tmp.sd = integrableObject;
150			uniqueStuntDoubles.insert(std::map<std::string, SDShape>::value_type(integrableObject->getType(), tmp));
151
152	tim	892	}
153			}
154	tim	891	}
155	tim	892
156	tim	906
157
158			std::map<std::string, SDShape>::iterator si;
159	tim	907	for (si = uniqueStuntDoubles.begin(); si != uniqueStuntDoubles.end(); ++si) {
160	tim	906	HydrodynamicsModel* model;
161			Shape* shape = si->second.shape;
162			StuntDouble* sd = si->second.sd;;
163			if (args_info.model_given) {
164			model = HydrodynamicsModelFactory::getInstance()->createHydrodynamicsModel(args_info.model_arg, sd, info);
165			} else if (shape->hasAnalyticalSolution()) {
166			model = new AnalyticalModel(sd, info);
167			} else {
168			model = new BeadModel(sd, info);
169			}
170	tim	921
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	gezelter	972	model->calcHydroProps(shape, viscosity, temperature);
183	xsun	1177	std::ofstream outputDiff;
184			outputDiff.open(outputFilename.c_str());
185	gezelter	972	model->writeHydroProps(outputDiff);
186	xsun	1177	outputDiff.close();
187	tim	921	}
188	gezelter	972
189	tim	906	delete model;
190	tim	891	}
191	tim	906
192
193			//MemoryUtils::deletePointers(shapes);
194	tim	891	delete info;
195
196			}
197
198			void registerHydrodynamicsModels() {
199			HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<RoughShell>("RoughShell"));
200			HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<BeadModel>("BeadModel"));
201	tim	906	HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<AnalyticalModel>("AnalyticalModel"));
202	tim	891
203			}