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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
 
#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 oopse;

struct SDShape{
    StuntDouble* sd;
    Shape* shape;
};
void registerHydrodynamicsModels();

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);
  }
  
  mdFileName = dumpFileName;
  mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";

  if (args_info.output_given){
    prefix = args_info.output_arg;
  } else {
    prefix = getPrefix(mdFileName);    
  }
  std::string outputFilename = prefix + ".diff";
    
  //parse md file and set up the system
  SimCreator creator;
  SimInfo* info = creator.createSim(mdFileName, 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();
  double temperature;
  double 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::ofstream outputDiff(outputFilename.c_str());
  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) {
            shape->calcHydroProps(model, viscosity, temperature);
            model->writeHydroProps(outputDiff);
        }

        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:	945
Committed:	Tue Apr 25 02:09:01 2006 UTC (19 years ago) by gezelter
Original Path:	*trunk/src/applications/hydrodynamics/Hydro.cpp*
File size:	7144 byte(s)
Log Message:	Adding spherical boundary conditions to LD integrator
#	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			* 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
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			#include <iostream>
43			#include <fstream>
44			#include <string>
45
46			#include "applications/hydrodynamics/HydroCmd.h"
47			#include "applications/hydrodynamics/HydrodynamicsModel.hpp"
48			#include "applications/hydrodynamics/HydrodynamicsModelCreator.hpp"
49			#include "applications/hydrodynamics/HydrodynamicsModelFactory.hpp"
50	tim	906	#include "applications/hydrodynamics/AnalyticalModel.hpp"
51	tim	891	#include "applications/hydrodynamics/BeadModel.hpp"
52			#include "applications/hydrodynamics/RoughShell.hpp"
53	tim	906	#include "applications/hydrodynamics/ShapeBuilder.hpp"
54	tim	891	#include "brains/Register.hpp"
55			#include "brains/SimCreator.hpp"
56			#include "brains/SimInfo.hpp"
57	tim	906	#include "utils/StringUtils.hpp"
58			#include "utils/simError.h"
59			#include "utils/MemoryUtils.hpp"
60	tim	891	using namespace oopse;
61
62	tim	906	struct SDShape{
63			StuntDouble* sd;
64			Shape* shape;
65			};
66	tim	891	void registerHydrodynamicsModels();
67
68			int main(int argc, char* argv[]){
69			//register force fields
70			registerForceFields();
71	tim	907	registerHydrodynamicsModels();
72	tim	891
73			gengetopt_args_info args_info;
74			std::string dumpFileName;
75			std::string mdFileName;
76			std::string prefix;
77
78			//parse the command line option
79			if (cmdline_parser (argc, argv, &args_info) != 0) {
80			exit(1) ;
81			}
82
83			//get the dumpfile name and meta-data file name
84			if (args_info.input_given){
85			dumpFileName = args_info.input_arg;
86			} else {
87			std::cerr << "Does not have input file name" << std::endl;
88			exit(1);
89			}
90
91			mdFileName = dumpFileName;
92			mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
93
94			if (args_info.output_given){
95			prefix = args_info.output_arg;
96			} else {
97	tim	906	prefix = getPrefix(mdFileName);
98	tim	891	}
99	tim	892	std::string outputFilename = prefix + ".diff";
100	tim	906
101	tim	891	//parse md file and set up the system
102			SimCreator creator;
103			SimInfo* info = creator.createSim(mdFileName, true);
104
105			SimInfo::MoleculeIterator mi;
106			Molecule* mol;
107	tim	892	Molecule::IntegrableObjectIterator ii;
108			StuntDouble* integrableObject;
109			Mat3x3d identMat;
110			identMat(0,0) = 1.0;
111			identMat(1,1) = 1.0;
112			identMat(2,2) = 1.0;
113	tim	906
114			Globals* simParams = info->getSimParams();
115			double temperature;
116			double viscosity;
117
118			if (simParams->haveViscosity()) {
119			viscosity = simParams->getViscosity();
120			} else {
121	tim	907	sprintf(painCave.errMsg, "viscosity must be set\n");
122	tim	906	painCave.isFatal = 1;
123			simError();
124			}
125
126			if (simParams->haveTargetTemp()) {
127			temperature = simParams->getTargetTemp();
128			} else {
129	gezelter	945	sprintf(painCave.errMsg, "target temperature must be set\n");
130	tim	906	painCave.isFatal = 1;
131			simError();
132			}
133	tim	892
134	tim	906	std::map<std::string, SDShape> uniqueStuntDoubles;
135	tim	892
136	tim	891	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
137	tim	892	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
138			integrableObject = mol->nextIntegrableObject(ii)) {
139			if (uniqueStuntDoubles.find(integrableObject->getType()) == uniqueStuntDoubles.end()) {
140	tim	906
141	tim	892	integrableObject->setPos(V3Zero);
142			integrableObject->setA(identMat);
143			if (integrableObject->isRigidBody()) {
144			RigidBody* rb = static_cast<RigidBody*>(integrableObject);
145			rb->updateAtoms();
146			}
147	tim	921
148			SDShape tmp;
149			tmp.shape = ShapeBuilder::createShape(integrableObject);
150			tmp.sd = integrableObject;
151			uniqueStuntDoubles.insert(std::map<std::string, SDShape>::value_type(integrableObject->getType(), tmp));
152
153	tim	892	}
154			}
155	tim	891	}
156	tim	892
157	tim	906
158
159	tim	892	std::ofstream outputDiff(outputFilename.c_str());
160	tim	906	std::map<std::string, SDShape>::iterator si;
161	tim	907	for (si = uniqueStuntDoubles.begin(); si != uniqueStuntDoubles.end(); ++si) {
162	tim	906	HydrodynamicsModel* model;
163			Shape* shape = si->second.shape;
164			StuntDouble* sd = si->second.sd;;
165			if (args_info.model_given) {
166			model = HydrodynamicsModelFactory::getInstance()->createHydrodynamicsModel(args_info.model_arg, sd, info);
167			} else if (shape->hasAnalyticalSolution()) {
168			model = new AnalyticalModel(sd, info);
169			} else {
170			model = new BeadModel(sd, info);
171			}
172	tim	921
173			model->init();
174
175			std::ofstream ofs;
176			std::stringstream outputBeads;
177			outputBeads << prefix << "_" << model->getStuntDoubleName() << ".xyz";
178			ofs.open(outputBeads.str().c_str());
179			model->writeBeads(ofs);
180			ofs.close();
181
182			//if beads option is turned on, skip the calculation
183			if (!args_info.beads_flag) {
184			shape->calcHydroProps(model, viscosity, temperature);
185			model->writeHydroProps(outputDiff);
186			}
187
188	tim	906	delete model;
189	tim	891	}
190	tim	906
191
192			//MemoryUtils::deletePointers(shapes);
193	tim	891	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	tim	906	HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<AnalyticalModel>("AnalyticalModel"));
201	tim	891
202			}
203