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[]){
  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:	1725
Committed:	Sat May 26 18:13:43 2012 UTC (12 years, 11 months ago) by gezelter
File size:	7194 byte(s)
Log Message:	Individual ForceField classes have been removed (they were essentially all duplicates anyway). ForceField has moved to brains, and since only one force field is in play at any time, the ForceFieldFactory and Register methods have been removed.
#	Content
1	/*
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. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
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.
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	*
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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
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	#include "applications/hydrodynamics/AnalyticalModel.hpp"
52	#include "applications/hydrodynamics/BeadModel.hpp"
53	#include "applications/hydrodynamics/RoughShell.hpp"
54	#include "applications/hydrodynamics/ShapeBuilder.hpp"
55	#include "brains/Register.hpp"
56	#include "brains/SimCreator.hpp"
57	#include "brains/SimInfo.hpp"
58	#include "utils/StringUtils.hpp"
59	#include "utils/simError.h"
60	#include "utils/MemoryUtils.hpp"
61	using namespace OpenMD;
62
63	struct SDShape{
64	StuntDouble* sd;
65	Shape* shape;
66	};
67	void registerHydrodynamicsModels();
68	void writeHydroProps(std::ostream& os);
69
70	int main(int argc, char* argv[]){
71	registerHydrodynamicsModels();
72
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	prefix = getPrefix(dumpFileName);
95	}
96	std::string outputFilename = prefix + ".diff";
97
98	//parse md file and set up the system
99	SimCreator creator;
100	SimInfo* info = creator.createSim(dumpFileName, true);
101
102	SimInfo::MoleculeIterator mi;
103	Molecule* mol;
104	Molecule::IntegrableObjectIterator ii;
105	StuntDouble* integrableObject;
106	Mat3x3d identMat;
107	identMat(0,0) = 1.0;
108	identMat(1,1) = 1.0;
109	identMat(2,2) = 1.0;
110
111	Globals* simParams = info->getSimParams();
112	RealType temperature;
113	RealType viscosity;
114
115	if (simParams->haveViscosity()) {
116	viscosity = simParams->getViscosity();
117	} else {
118	sprintf(painCave.errMsg, "viscosity must be set\n");
119	painCave.isFatal = 1;
120	simError();
121	}
122
123	if (simParams->haveTargetTemp()) {
124	temperature = simParams->getTargetTemp();
125	} else {
126	sprintf(painCave.errMsg, "target temperature must be set\n");
127	painCave.isFatal = 1;
128	simError();
129	}
130
131	std::map<std::string, SDShape> uniqueStuntDoubles;
132
133	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
134	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
135	integrableObject = mol->nextIntegrableObject(ii)) {
136	if (uniqueStuntDoubles.find(integrableObject->getType()) == uniqueStuntDoubles.end()) {
137
138	integrableObject->setPos(V3Zero);
139	integrableObject->setA(identMat);
140	if (integrableObject->isRigidBody()) {
141	RigidBody* rb = static_cast<RigidBody*>(integrableObject);
142	rb->updateAtoms();
143	}
144
145	SDShape tmp;
146	tmp.shape = ShapeBuilder::createShape(integrableObject);
147	tmp.sd = integrableObject;
148	uniqueStuntDoubles.insert(std::map<std::string, SDShape>::value_type(integrableObject->getType(), tmp));
149
150	}
151	}
152	}
153
154
155
156	std::map<std::string, SDShape>::iterator si;
157	for (si = uniqueStuntDoubles.begin(); si != uniqueStuntDoubles.end(); ++si) {
158	HydrodynamicsModel* model;
159	Shape* shape = si->second.shape;
160	StuntDouble* sd = si->second.sd;;
161	if (args_info.model_given) {
162	model = HydrodynamicsModelFactory::getInstance()->createHydrodynamicsModel(args_info.model_arg, sd, info);
163	} else if (shape->hasAnalyticalSolution()) {
164	model = new AnalyticalModel(sd, info);
165	} else {
166	model = new BeadModel(sd, info);
167	}
168
169	model->init();
170
171	std::ofstream ofs;
172	std::stringstream outputBeads;
173	outputBeads << prefix << "_" << model->getStuntDoubleName() << ".xyz";
174	ofs.open(outputBeads.str().c_str());
175	model->writeBeads(ofs);
176	ofs.close();
177
178	//if beads option is turned on, skip the calculation
179	if (!args_info.beads_flag) {
180	model->calcHydroProps(shape, viscosity, temperature);
181	std::ofstream outputDiff;
182	outputDiff.open(outputFilename.c_str());
183	model->writeHydroProps(outputDiff);
184	outputDiff.close();
185	}
186
187	delete model;
188	}
189
190
191	//MemoryUtils::deletePointers(shapes);
192	delete info;
193
194	}
195
196	void registerHydrodynamicsModels() {
197	HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<RoughShell>("RoughShell"));
198	HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<BeadModel>("BeadModel"));
199	HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<AnalyticalModel>("AnalyticalModel"));
200
201	}