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root/OpenMD/branches/development/src/applications/hydrodynamics/Hydro.cpp

Comparing:
trunk/src/applications/hydrodynamics/Hydro.cpp (file contents), Revision 891 by tim, Wed Feb 22 20:35:16 2006 UTC vs.
branches/development/src/applications/hydrodynamics/Hydro.cpp (file contents), Revision 1725 by gezelter, Sat May 26 18:13:43 2012 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]  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>
#	Line 47 | Line 48
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	<	using namespace oopse;
64	<
65	<	/** Register different hydrodynamics models */
63	>	struct SDShape{
64	>	StuntDouble* sd;
65	>	Shape* shape;
66	>	};
67		void registerHydrodynamicsModels();
68	+	void writeHydroProps(std::ostream& os);
69
61	–	bool calcHydrodynamicsProp(const std::string& modelType, Molecule* mol, const DynamicProperty& param, const std::string& prefix,double viscosity);
62	–
70		int main(int argc, char* argv[]){
64	–	//register force fields
65	–	registerForceFields();
71		registerHydrodynamicsModels();
72
73		gengetopt_args_info args_info;
#	Line 83 | Line 88 | int main(int argc, char* argv[]){
88		exit(1);
89		}
90
86	–	mdFileName = dumpFileName;
87	–	mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
88	–
91		if (args_info.output_given){
92		prefix = args_info.output_arg;
93		} else {
94	<	prefix = "hydro";
94	>	prefix = getPrefix(dumpFileName);
95		}
96	<
97	<	DynamicProperty param;
96	<	if (args_info.sigma_given) {
97	<	param.insert(DynamicProperty::value_type("Sigma", args_info.sigma_arg));
98	<	}
99	<
100	<
96	>	std::string outputFilename = prefix + ".diff";
97	>
98		//parse md file and set up the system
99		SimCreator creator;
100	<	SimInfo* info = creator.createSim(mdFileName, true);
100	>	SimInfo* info = creator.createSim(dumpFileName, true);
101
102		SimInfo::MoleculeIterator mi;
103		Molecule* mol;
104	<	Molecule::RigidBodyIterator ri;
105	<	RigidBody* rb;
106	<	//update atoms of rigidbody
107	<	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
108	<
109	<	//change the positions of atoms which belong to the rigidbodies
110	<	for (rb = mol->beginRigidBody(ri); rb != NULL; rb = mol->nextRigidBody(ri)) {
111	<	rb->updateAtoms();
112	<	}
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	<	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
124	<	calcHydrodynamicsProp(args_info.model_arg, mol, param, prefix, args_info.viscosity_arg);
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	<	delete info;
134	<
135	<	}
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	<	void registerHydrodynamicsModels() {
139	<	HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<RoughShell>("RoughShell"));
140	<	HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<BeadModel>("BeadModel"));
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	<	}
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	<	bool calcHydrodynamicsProp(const std::string& modelType, Molecule* mol, const DynamicProperty& param, const std::string& prefix,double viscosity) {
151	<	HydrodynamicsModel* hydroModel = HydrodynamicsModelFactory::getInstance()->createHydrodynamicsModel(modelType, mol, param);
152	<	bool ret = false;
135	<	if (hydroModel == NULL) {
136	<	std::cout << "Integrator Factory can not create " << modelType <<std::endl;
137	<	}
150	>	}
151	>	}
152	>	}
153
154	<	if (hydroModel->calcHydrodyanmicsProps(viscosity)) {
155	<	ret = true;
156	<	std::stringstream outputDiffTensor;
157	<	outputDiffTensor << prefix << "_" << mol->getType() << ".diff";
158	<	std::ofstream ofs;
159	<	ofs.open(outputDiffTensor.str().c_str());
160	<	hydroModel->writeDiffCenterAndDiffTensor(ofs);
161	<	ofs.close();
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 << "_" << mol->getType() << ".xyz";
174	<	ofs.open(outputBeads.str().c_str());
175	<	hydroModel->writeBeads(ofs);
173	>	outputBeads << prefix << "_" << model->getStuntDoubleName() << ".xyz";
174	>	ofs.open(outputBeads.str().c_str());
175	>	model->writeBeads(ofs);
176		ofs.close();
153	–	}
177
178	<	delete hydroModel;
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	<	return ret;
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	+	}

Comparing:
trunk/src/applications/hydrodynamics/Hydro.cpp (property svn:keywords), Revision 891 by tim, Wed Feb 22 20:35:16 2006 UTC vs.
branches/development/src/applications/hydrodynamics/Hydro.cpp (property svn:keywords), Revision 1725 by gezelter, Sat May 26 18:13:43 2012 UTC

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