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root/OpenMD/trunk/src/applications/hydrodynamics/Hydro.cpp

Comparing trunk/src/applications/hydrodynamics/Hydro.cpp (file contents):
Revision 977 by tim, Thu May 25 16:27:27 2006 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 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, 234107 (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 57 | Line 58
58		#include "utils/StringUtils.hpp"
59		#include "utils/simError.h"
60		#include "utils/MemoryUtils.hpp"
61	<	using namespace oopse;
61	>	using namespace OpenMD;
62
63		struct SDShape{
64	<	StuntDouble* sd;
65	<	Shape* shape;
64	>	StuntDouble* sd;
65	>	Shape* shape;
66		};
67		void registerHydrodynamicsModels();
68		void writeHydroProps(std::ostream& os);
69
70		int main(int argc, char* argv[]){
70	–	//register force fields
71	–	registerForceFields();
71		registerHydrodynamicsModels();
72
73		gengetopt_args_info args_info;
#	Line 89 | Line 88 | int main(int argc, char* argv[]){
88		exit(1);
89		}
90
92	–	mdFileName = dumpFileName;
93	–	mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
94	–
91		if (args_info.output_given){
92		prefix = args_info.output_arg;
93		} else {
94	<	prefix = getPrefix(mdFileName);
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(mdFileName, true);
100	>	SimInfo* info = creator.createSim(dumpFileName, true);
101
102		SimInfo::MoleculeIterator mi;
103		Molecule* mol;
104		Molecule::IntegrableObjectIterator  ii;
105	<	StuntDouble* integrableObject;
105	>	StuntDouble* sd;
106		Mat3x3d identMat;
107		identMat(0,0) = 1.0;
108		identMat(1,1) = 1.0;
#	Line 134 | Line 130 | int main(int argc, char* argv[]){
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	<	}
133	>	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		}
157	–
158	–
156
157	<	std::ofstream outputDiff(outputFilename.c_str());
157	>
158	>
159		std::map<std::string, SDShape>::iterator si;
160		for (si = uniqueStuntDoubles.begin(); si != uniqueStuntDoubles.end(); ++si) {
161	<	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();
161	>	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
190	<	std::ofstream ofs;
177	<	std::stringstream outputBeads;
178	<	outputBeads << prefix << "_" << model->getStuntDoubleName() << ".xyz";
179	<	ofs.open(outputBeads.str().c_str());
180	<	model->writeBeads(ofs);
181	<	ofs.close();
182	<
183	<	//if beads option is turned on, skip the calculation
184	<	if (!args_info.beads_flag) {
185	<	model->calcHydroProps(shape, viscosity, temperature);
186	<	model->writeHydroProps(outputDiff);
187	<	}
188	<
189	<	delete model;
190	>	delete model;
191		}
192
193
#	Line 196 | Line 197 | void registerHydrodynamicsModels() {
197		}
198
199		void registerHydrodynamicsModels() {
200	<	HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<RoughShell>("RoughShell"));
201	<	HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<BeadModel>("BeadModel"));
202	<	HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<AnalyticalModel>("AnalyticalModel"));
202	<
200	>	HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<RoughShell>("RoughShell"));
201	>	HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<BeadModel>("BeadModel"));
202	>	HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<AnalyticalModel>("AnalyticalModel"));
203		}

Comparing trunk/src/applications/hydrodynamics/Hydro.cpp (property svn:keywords):
Revision 977 by tim, Thu May 25 16:27:27 2006 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 0 | Line 1
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