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, 234107 (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[]){
  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* sd;
  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 (sd = mol->beginIntegrableObject(ii); sd != NULL;
         sd = mol->nextIntegrableObject(ii)) {
      
      if (uniqueStuntDoubles.find(sd->getType()) ==  uniqueStuntDoubles.end()) {
        
        sd->setPos(V3Zero);
        sd->setA(identMat);
        if (sd->isRigidBody()) {
          RigidBody* rb = static_cast<RigidBody*>(sd);
          rb->updateAtoms();
        }
        
        SDShape tmp;
        tmp.shape = ShapeBuilder::createShape(sd);
        tmp.sd = sd;    
        uniqueStuntDoubles.insert(std::map<std::string, SDShape>::value_type(sd->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:	1850
Committed:	Wed Feb 20 15:39:39 2013 UTC (12 years, 2 months ago) by gezelter
File size:	6959 byte(s)
Log Message:	Fixed a widespread typo in the license
#	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	gezelter	1850	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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	gezelter	1769	StuntDouble* sd;
65			Shape* shape;
66	tim	906	};
67	tim	891	void registerHydrodynamicsModels();
68	gezelter	972	void writeHydroProps(std::ostream& os);
69	tim	891
70			int main(int argc, char* argv[]){
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			if (args_info.output_given){
92			prefix = args_info.output_arg;
93			} else {
94	gezelter	1027	prefix = getPrefix(dumpFileName);
95	tim	891	}
96	tim	892	std::string outputFilename = prefix + ".diff";
97	tim	906
98	tim	891	//parse md file and set up the system
99			SimCreator creator;
100	gezelter	1027	SimInfo* info = creator.createSim(dumpFileName, true);
101	tim	891
102			SimInfo::MoleculeIterator mi;
103			Molecule* mol;
104	tim	892	Molecule::IntegrableObjectIterator ii;
105	gezelter	1769	StuntDouble* sd;
106	tim	892	Mat3x3d identMat;
107			identMat(0,0) = 1.0;
108			identMat(1,1) = 1.0;
109			identMat(2,2) = 1.0;
110	tim	906
111			Globals* simParams = info->getSimParams();
112	tim	977	RealType temperature;
113			RealType viscosity;
114	tim	906
115			if (simParams->haveViscosity()) {
116			viscosity = simParams->getViscosity();
117			} else {
118	tim	907	sprintf(painCave.errMsg, "viscosity must be set\n");
119	tim	906	painCave.isFatal = 1;
120			simError();
121			}
122
123			if (simParams->haveTargetTemp()) {
124			temperature = simParams->getTargetTemp();
125			} else {
126	gezelter	945	sprintf(painCave.errMsg, "target temperature must be set\n");
127	tim	906	painCave.isFatal = 1;
128			simError();
129			}
130	tim	892
131	tim	906	std::map<std::string, SDShape> uniqueStuntDoubles;
132	tim	892
133	gezelter	1769	for (mol = info->beginMolecule(mi); mol != NULL;
134			mol = info->nextMolecule(mi)) {
135
136			for (sd = mol->beginIntegrableObject(ii); sd != NULL;
137			sd = mol->nextIntegrableObject(ii)) {
138
139			if (uniqueStuntDoubles.find(sd->getType()) == uniqueStuntDoubles.end()) {
140
141			sd->setPos(V3Zero);
142			sd->setA(identMat);
143			if (sd->isRigidBody()) {
144			RigidBody* rb = static_cast<RigidBody*>(sd);
145			rb->updateAtoms();
146			}
147
148			SDShape tmp;
149			tmp.shape = ShapeBuilder::createShape(sd);
150			tmp.sd = sd;
151			uniqueStuntDoubles.insert(std::map<std::string, SDShape>::value_type(sd->getType(), tmp));
152
153			}
154			}
155	tim	891	}
156	tim	906
157	gezelter	1769
158
159	tim	906	std::map<std::string, SDShape>::iterator si;
160	tim	907	for (si = uniqueStuntDoubles.begin(); si != uniqueStuntDoubles.end(); ++si) {
161	gezelter	1769	HydrodynamicsModel* model;
162			Shape* shape = si->second.shape;
163			StuntDouble* sd = si->second.sd;;
164			if (args_info.model_given) {
165			model = HydrodynamicsModelFactory::getInstance()->createHydrodynamicsModel(args_info.model_arg, sd, info);
166			} else if (shape->hasAnalyticalSolution()) {
167			model = new AnalyticalModel(sd, info);
168			} else {
169			model = new BeadModel(sd, info);
170			}
171
172			model->init();
173
174			std::ofstream ofs;
175			std::stringstream outputBeads;
176			outputBeads << prefix << "_" << model->getStuntDoubleName() << ".xyz";
177			ofs.open(outputBeads.str().c_str());
178			model->writeBeads(ofs);
179			ofs.close();
180
181			//if beads option is turned on, skip the calculation
182			if (!args_info.beads_flag) {
183			model->calcHydroProps(shape, viscosity, temperature);
184			std::ofstream outputDiff;
185			outputDiff.open(outputFilename.c_str());
186			model->writeHydroProps(outputDiff);
187			outputDiff.close();
188			}
189	tim	921
190	gezelter	1769	delete model;
191	tim	891	}
192	tim	906
193
194			//MemoryUtils::deletePointers(shapes);
195	tim	891	delete info;
196
197			}
198
199			void registerHydrodynamicsModels() {
200	gezelter	1769	HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<RoughShell>("RoughShell"));
201			HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<BeadModel>("BeadModel"));
202			HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<AnalyticalModel>("AnalyticalModel"));
203	tim	891	}