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

Comparing:
trunk/src/applications/hydrodynamics/Hydro.cpp (file contents), Revision 892 by tim, Thu Feb 23 23:16:43 2006 UTC vs.
branches/development/src/applications/hydrodynamics/Hydro.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 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, StuntDouble* sd, const DynamicProperty& param, std::ostream& os,  const std::string& prefix);
62	–
70		int main(int argc, char* argv[]){
71		//register force fields
72		registerForceFields();
#	Line 83 | Line 90 | int main(int argc, char* argv[]){
90		exit(1);
91		}
92
86	–	mdFileName = dumpFileName;
87	–	mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
88	–
93		if (args_info.output_given){
94		prefix = args_info.output_arg;
95		} else {
96	<	prefix = "hydro";
96	>	prefix = getPrefix(dumpFileName);
97		}
98		std::string outputFilename = prefix + ".diff";
99	<
96	<	DynamicProperty param;
97	<	param.insert(DynamicProperty::value_type("Viscosity", args_info.viscosity_arg));
98	<	param.insert(DynamicProperty::value_type("Temperature", args_info.temperature_arg));
99	<
100	<	if (args_info.sigma_given) {
101	<	param.insert(DynamicProperty::value_type("Sigma", args_info.sigma_arg));
102	<	}
103	<
104	<
99	>
100		//parse md file and set up the system
101		SimCreator creator;
102	<	SimInfo* info = creator.createSim(mdFileName, true);
102	>	SimInfo* info = creator.createSim(dumpFileName, true);
103
104		SimInfo::MoleculeIterator mi;
105		Molecule* mol;
#	Line 114 | Line 109 | int main(int argc, char* argv[]){
109		identMat(0,0) = 1.0;
110		identMat(1,1) = 1.0;
111		identMat(2,2) = 1.0;
112	<
112	>
113	>	Globals* simParams = info->getSimParams();
114	>	RealType temperature;
115	>	RealType viscosity;
116	>
117	>	if (simParams->haveViscosity()) {
118	>	viscosity = simParams->getViscosity();
119	>	} else {
120	>	sprintf(painCave.errMsg, "viscosity must be set\n");
121	>	painCave.isFatal = 1;
122	>	simError();
123	>	}
124	>
125	>	if (simParams->haveTargetTemp()) {
126	>	temperature = simParams->getTargetTemp();
127	>	} else {
128	>	sprintf(painCave.errMsg, "target temperature must be set\n");
129	>	painCave.isFatal = 1;
130	>	simError();
131	>	}
132
133	<	std::map<std::string, StuntDouble*> uniqueStuntDoubles;
133	>	std::map<std::string, SDShape> uniqueStuntDoubles;
134
135		for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
136		for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
137		integrableObject = mol->nextIntegrableObject(ii)) {
138		if (uniqueStuntDoubles.find(integrableObject->getType()) ==  uniqueStuntDoubles.end()) {
139	<	uniqueStuntDoubles.insert(std::map<std::string, StuntDouble*>::value_type(integrableObject->getType(), integrableObject));
139	>
140		integrableObject->setPos(V3Zero);
141		integrableObject->setA(identMat);
142		if (integrableObject->isRigidBody()) {
143		RigidBody* rb = static_cast<RigidBody*>(integrableObject);
144		rb->updateAtoms();
145		}
146	+
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		}
153		}
154		}
155
156	<	std::map<std::string, StuntDouble*>::iterator iter;
137	<	std::ofstream outputDiff(outputFilename.c_str());
138	<	for (iter = uniqueStuntDoubles.begin(); iter != uniqueStuntDoubles.end(); ++iter) {
139	<	calcHydrodynamicsProp(args_info.model_arg, iter->second, param, outputDiff, prefix);
140	<	}
156	>
157
158	+	std::map<std::string, SDShape>::iterator si;
159	+	for (si = uniqueStuntDoubles.begin(); si != uniqueStuntDoubles.end(); ++si) {
160	+	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	+
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	+	model->calcHydroProps(shape, viscosity, temperature);
183	+	std::ofstream outputDiff;
184	+	outputDiff.open(outputFilename.c_str());
185	+	model->writeHydroProps(outputDiff);
186	+	outputDiff.close();
187	+	}
188	+
189	+	delete model;
190	+	}
191	+
192	+
193	+	//MemoryUtils::deletePointers(shapes);
194		delete info;
195
196		}
#	Line 146 | Line 198 | void registerHydrodynamicsModels() {
198		void registerHydrodynamicsModels() {
199		HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<RoughShell>("RoughShell"));
200		HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<BeadModel>("BeadModel"));
201	+	HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<AnalyticalModel>("AnalyticalModel"));
202
203		}
151	–
152	–	bool calcHydrodynamicsProp(const std::string& modelType, StuntDouble* sd, const DynamicProperty& param, std::ostream& os, const std::string& prefix) {
153	–	HydrodynamicsModel* hydroModel = HydrodynamicsModelFactory::getInstance()->createHydrodynamicsModel(modelType, sd, param);
154	–	bool ret = false;
155	–	if (hydroModel == NULL) {
156	–	std::cout << "Integrator Factory can not create " << modelType <<std::endl;
157	–	}
158	–
159	–	if (hydroModel->calcHydrodyanmicsProps()) {
160	–	ret = true;
161	–	hydroModel->writeDiffCenterAndDiffTensor(os);
162	–
163	–	std::ofstream ofs;
164	–	std::stringstream outputBeads;
165	–	outputBeads << prefix << "_" << sd->getType() << ".xyz";
166	–	ofs.open(outputBeads.str().c_str());
167	–	hydroModel->writeBeads(ofs);
168	–	ofs.close();
169	–	}
170	–
171	–	delete hydroModel;
172	–
173	–	return ret;
174	–	}

Comparing:
trunk/src/applications/hydrodynamics/Hydro.cpp (property svn:keywords), Revision 892 by tim, Thu Feb 23 23:16:43 2006 UTC vs.
branches/development/src/applications/hydrodynamics/Hydro.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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