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Comparing trunk/src/applications/hydrodynamics/Hydro.cpp (file contents):
Revision 891 by tim, Wed Feb 22 20:35:16 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 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)) {
104	>	Molecule::IntegrableObjectIterator  ii;
105	>	StuntDouble* sd;
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;
134	>	mol = info->nextMolecule(mi)) {
135	>
136	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
137	>	sd = mol->nextIntegrableObject(ii)) {
138
139	<	//change the positions of atoms which belong to the rigidbodies
140	<	for (rb = mol->beginRigidBody(ri); rb != NULL; rb = mol->nextRigidBody(ri)) {
141	<	rb->updateAtoms();
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		}
156	+
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	<	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
173	<	calcHydrodynamicsProp(args_info.model_arg, mol, param, prefix, args_info.viscosity_arg);
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	>	delete model;
191		}
192	<
192	>
193	>
194	>	//MemoryUtils::deletePointers(shapes);
195		delete info;
196
197		}
198
199		void registerHydrodynamicsModels() {
200	<	HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<RoughShell>("RoughShell"));
201	<	HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<BeadModel>("BeadModel"));
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		}
131	–
132	–	bool calcHydrodynamicsProp(const std::string& modelType, Molecule* mol, const DynamicProperty& param, const std::string& prefix,double viscosity) {
133	–	HydrodynamicsModel* hydroModel = HydrodynamicsModelFactory::getInstance()->createHydrodynamicsModel(modelType, mol, param);
134	–	bool ret = false;
135	–	if (hydroModel == NULL) {
136	–	std::cout << "Integrator Factory can not create " << modelType <<std::endl;
137	–	}
138	–
139	–	if (hydroModel->calcHydrodyanmicsProps(viscosity)) {
140	–	ret = true;
141	–	std::stringstream outputDiffTensor;
142	–	outputDiffTensor << prefix << "_" << mol->getType() << ".diff";
143	–	std::ofstream ofs;
144	–	ofs.open(outputDiffTensor.str().c_str());
145	–	hydroModel->writeDiffCenterAndDiffTensor(ofs);
146	–	ofs.close();
147	–
148	–	std::stringstream outputBeads;
149	–	outputBeads << prefix << "_" << mol->getType() << ".xyz";
150	–	ofs.open(outputBeads.str().c_str());
151	–	hydroModel->writeBeads(ofs);
152	–	ofs.close();
153	–	}
154	–
155	–	delete hydroModel;
156	–
157	–	return ret;
158	–	}

Comparing trunk/src/applications/hydrodynamics/Hydro.cpp (property svn:keywords):
Revision 891 by tim, Wed Feb 22 20:35:16 2006 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

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