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root/OpenMD/trunk/src/applications/oopse/oopse.cpp
Revision: 1360
Committed: Mon Sep 7 16:31:51 2009 UTC (15 years, 10 months ago) by cli2
File size: 7314 byte(s)
Log Message:
Added new restraint infrastructure
Added MolecularRestraints
Added ObjectRestraints
Added RestraintStamp
Updated thermodynamic integration to use ObjectRestraints
Added Quaternion mathematics for twist swing decompositions
Significantly updated RestWriter and RestReader to use dump-like files
Added selections for x, y, and z coordinates of atoms
Removed monolithic Restraints class
Fixed a few bugs in gradients of Euler angles in DirectionalAtom and RigidBody
Added some rotational capabilities to prinicpalAxisCalculator

File Contents

# User Rev Content
1 gezelter 507 /*
2 gezelter 861 * Copyright (c) 2006 The University of Notre Dame. All Rights Reserved.
3 gezelter 246 *
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. 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
19     * notice, this list of conditions and the following disclaimer.
20     *
21     * 3. Redistributions in binary form must reproduce the above copyright
22     * notice, this list of conditions and the following disclaimer in the
23     * documentation and/or other materials provided with the
24     * distribution.
25     *
26     * This software is provided "AS IS," without a warranty of any
27     * kind. All express or implied conditions, representations and
28     * warranties, including any implied warranty of merchantability,
29     * fitness for a particular purpose or non-infringement, are hereby
30     * excluded. The University of Notre Dame and its licensors shall not
31     * be liable for any damages suffered by licensee as a result of
32     * using, modifying or distributing the software or its
33     * derivatives. In no event will the University of Notre Dame or its
34     * licensors be liable for any lost revenue, profit or data, or for
35     * direct, indirect, special, consequential, incidental or punitive
36     * damages, however caused and regardless of the theory of liability,
37     * arising out of the use of or inability to use software, even if the
38     * University of Notre Dame has been advised of the possibility of
39     * such damages.
40     */
41    
42 tim 12 #ifdef IS_MPI
43     #include <mpi.h>
44     #endif
45    
46 cli2 1290 #include <fstream>
47 tim 12 #include "utils/simError.h"
48 chrisfen 691 #include "utils/CaseConversion.hpp"
49 gezelter 246 #include "brains/Register.hpp"
50     #include "brains/SimCreator.hpp"
51 tim 12 #include "brains/SimInfo.hpp"
52 gezelter 246 #include "constraints/ZconstraintForceManager.hpp"
53 cli2 1360 #include "restraints/RestraintForceManager.hpp"
54 gezelter 246 #include "integrators/IntegratorFactory.hpp"
55 tim 12 #include "integrators/Integrator.hpp"
56 gezelter 246 #include "minimizers/MinimizerFactory.hpp"
57     #include "minimizers/Minimizer.hpp"
58 chrisfen 993 #include "restraints/ThermoIntegrationForceManager.hpp"
59    
60 gezelter 246 using namespace oopse;
61 tim 12
62 cli2 1290
63 tim 12 int main(int argc,char* argv[]){
64 cli2 1290
65 tim 12 // first things first, all of the initializations
66    
67     #ifdef IS_MPI
68     MPI_Init( &argc, &argv ); // the MPI communicators
69     #endif
70    
71     initSimError(); // the error handler
72     srand48( 1337 ); // the random number generator.
73    
74     #ifdef IS_MPI
75     if( worldRank == 0 ){
76     #endif
77     std::cerr <<
78     " +----------------------------------------------------------------------+\n" <<
79     " | ____ ____ ____ _____ ______ The OpenSource, Object-oriented |\n" <<
80     " | / __ \\/ __ \\/ __ \\/ ___// ____/ Parallel Simulation Engine. |\n" <<
81     " | / / / / / / / /_/ /\\__ \\/ __/ |\n" <<
82 gezelter 1249 " | / /_/ / /_/ / ____/___/ / /___ Copyright 2004-2008 by the |\n" <<
83 tim 12 " | \\____/\\____/_/ /____/_____/ University of Notre Dame. |\n" <<
84 gezelter 510 " | |\n" <<
85 gezelter 509 " | version " <<
86     OOPSE_VERSION_MAJOR << "." << OOPSE_VERSION_MINOR << "." << OOPSE_VERSION_TINY <<
87     " http://www.oopse.org |\n" <<
88 tim 12 " | |\n" <<
89     " | OOPSE is an OpenScience project. All source code is available for |\n" <<
90     " | any use subject to only one condition: |\n" <<
91     " | |\n" <<
92     " | Any published work resulting from the use of this code must cite the |\n" <<
93     " | following paper: M. A. Meineke, C. F. Vardeman II, T. Lin, |\n" <<
94     " | C. J. Fennell, and J. D. Gezelter, |\n" <<
95 gezelter 266 " | J. Comput. Chem. 26, pp. 252-271 (2005). |\n" <<
96 tim 12 " +----------------------------------------------------------------------+\n" <<
97     "\n";
98    
99     if( argc < 2 ){
100     strcpy( painCave.errMsg, "Error, a meta-data file is needed to run.\n" );
101     painCave.isFatal = 1;
102     simError();
103     }
104     #ifdef IS_MPI
105     }
106     #endif
107    
108     strcpy( checkPointMsg, "Successful number of arguments" );
109 gezelter 1241 errorCheckPoint();
110 gezelter 246
111 gezelter 507 //register forcefields, integrators and minimizers
112     registerAll();
113 gezelter 246
114 gezelter 507 //create simulation model
115     SimCreator creator;
116     SimInfo* info = creator.createSim(argv[1]);
117     Globals* simParams = info->getSimParams();
118 gezelter 246
119 gezelter 507 if (simParams->haveMinimizer() && simParams->haveEnsemble()) {
120     sprintf(painCave.errMsg, "Minimizer keyword and Ensemble keyword can not exist together\n");
121     painCave.isFatal = 1;
122     simError();
123     }
124 tim 12
125 gezelter 507 if (simParams->haveMinimizer()) {
126     //create minimizer
127 chrisfen 691 Minimizer* myMinimizer = MinimizerFactory::getInstance()->createMinimizer(toUpperCopy(simParams->getMinimizer()), info);
128 tim 12
129 gezelter 507 if (myMinimizer == NULL) {
130     sprintf(painCave.errMsg, "Minimizer Factory can not create %s Minimizer\n",
131 tim 665 simParams->getMinimizer().c_str());
132 gezelter 507 painCave.isFatal = 1;
133     simError();
134     }
135 tim 12
136 gezelter 507 myMinimizer->minimize();
137     delete myMinimizer;
138     } else if (simParams->haveEnsemble()) {
139     //create Integrator
140 tim 12
141 chrisfen 691 Integrator* myIntegrator = IntegratorFactory::getInstance()->createIntegrator(toUpperCopy(simParams->getEnsemble()), info);
142 chrisfen 704
143 gezelter 507 if (myIntegrator == NULL) {
144     sprintf(painCave.errMsg, "Integrator Factory can not create %s Integrator\n",
145 tim 665 simParams->getEnsemble().c_str());
146 gezelter 507 painCave.isFatal = 1;
147     simError();
148     }
149 gezelter 246
150 gezelter 507 //Thermodynamic Integration Method
151 chrisfen 993 //set the force manager for thermodynamic integration if specified
152 cli2 1360 if (simParams->getUseThermodynamicIntegration()){
153 chrisfen 993 ForceManager* fman = new ThermoIntegrationForceManager(info);
154     myIntegrator->setForceManager(fman);
155     }
156 tim 12
157 cli2 1360 // Restraints
158     if (simParams->getUseRestraints() && !simParams->getUseThermodynamicIntegration()) {
159     ForceManager* fman = new RestraintForceManager(info);
160     myIntegrator->setForceManager(fman);
161     }
162    
163 gezelter 507 //Zconstraint-Method
164 tim 770 if (simParams->getNZconsStamps() > 0) {
165     info->setNZconstraint(simParams->getNZconsStamps());
166 gezelter 507 ForceManager* fman = new ZconstraintForceManager(info);
167     myIntegrator->setForceManager(fman);
168     }
169 gezelter 246
170 gezelter 507 myIntegrator->integrate();
171     delete myIntegrator;
172     }else {
173     sprintf(painCave.errMsg, "Integrator Factory can not create %s Integrator\n",
174 tim 665 simParams->getEnsemble().c_str());
175 gezelter 507 painCave.isFatal = 1;
176     simError();
177     }
178 gezelter 246
179 gezelter 507 delete info;
180 tim 12
181 gezelter 1241
182     strcpy( checkPointMsg, "Great googly moogly! It worked!" );
183     errorCheckPoint();
184    
185     #ifdef IS_MPI
186 gezelter 246 MPI_Finalize();
187 tim 12 #endif
188    
189     return 0 ;
190     }