# | Line 1 | Line 1 | |
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1 | < | #include <iostream> |
2 | < | #include <fstream> |
3 | < | #include <cstdlib> |
4 | < | #include <cmath> |
5 | < | #include <cstring> |
6 | < | |
1 | > | /* |
2 | > | * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
3 | > | * |
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 | #ifdef IS_MPI | |
43 | #include <mpi.h> | |
44 | #endif | |
45 | ||
11 | – | #ifdef PROFILE |
12 | – | #include "profiling/mdProfile.hpp" |
13 | – | #endif // PROFILE |
14 | – | |
46 | #include "utils/simError.h" | |
47 | < | #include "brains/SimSetup.hpp" |
47 | > | #include "brains/Register.hpp" |
48 | > | #include "brains/SimCreator.hpp" |
49 | #include "brains/SimInfo.hpp" | |
50 | < | #include "primitives/Atom.hpp" |
50 | > | #include "constraints/ZconstraintForceManager.hpp" |
51 | > | #include "integrators/IntegratorFactory.hpp" |
52 | #include "integrators/Integrator.hpp" | |
53 | < | #include "brains/Thermo.hpp" |
54 | < | #include "io/ReadWrite.hpp" |
55 | < | #include "minimizers/OOPSEMinimizer.hpp" |
53 | > | #include "minimizers/MinimizerFactory.hpp" |
54 | > | #include "minimizers/Minimizer.hpp" |
55 | > | using namespace oopse; |
56 | ||
24 | – | char* program_name; |
25 | – | using namespace std; |
26 | – | |
57 | int main(int argc,char* argv[]){ | |
28 | – | |
29 | – | char* in_name; |
30 | – | SimSetup* startMe; |
31 | – | SimInfo* entry_plug; |
58 | ||
59 | // first things first, all of the initializations | |
60 | ||
# | Line 38 | Line 64 | int main(int argc,char* argv[]){ | |
64 | ||
65 | initSimError(); // the error handler | |
66 | srand48( 1337 ); // the random number generator. | |
41 | – | |
42 | – | #ifdef PROFILE |
43 | – | initProfile(); |
44 | – | #endif //profile |
67 | ||
46 | – | // check command line arguments, and set the input file |
47 | – | |
48 | – | program_name = argv[0]; // save the program name in case we need it |
49 | – | |
68 | #ifdef IS_MPI | |
69 | if( worldRank == 0 ){ | |
70 | #endif | |
# | Line 55 | Line 73 | int main(int argc,char* argv[]){ | |
73 | " | ____ ____ ____ _____ ______ The OpenSource, Object-oriented |\n" << | |
74 | " | / __ \\/ __ \\/ __ \\/ ___// ____/ Parallel Simulation Engine. |\n" << | |
75 | " | / / / / / / / /_/ /\\__ \\/ __/ |\n" << | |
76 | < | " | / /_/ / /_/ / ____/___/ / /___ Copyright 2004 by the |\n" << |
76 | > | " | / /_/ / /_/ / ____/___/ / /___ Copyright 2004-2005 by the |\n" << |
77 | " | \\____/\\____/_/ /____/_____/ University of Notre Dame. |\n" << | |
78 | " | http://www.oopse.org |\n" << | |
79 | " | |\n" << | |
# | Line 65 | Line 83 | int main(int argc,char* argv[]){ | |
83 | " | Any published work resulting from the use of this code must cite the |\n" << | |
84 | " | following paper: M. A. Meineke, C. F. Vardeman II, T. Lin, |\n" << | |
85 | " | C. J. Fennell, and J. D. Gezelter, |\n" << | |
86 | < | " | J. Comp. Chem. XX, XXXX (2004). |\n" << |
86 | > | " | J. Comput. Chem. 26, pp. 252-271 (2005). |\n" << |
87 | " +----------------------------------------------------------------------+\n" << | |
88 | "\n"; | |
89 | ||
# | Line 78 | Line 96 | int main(int argc,char* argv[]){ | |
96 | } | |
97 | #endif | |
98 | ||
81 | – | in_name = argv[1]; |
82 | – | |
99 | #ifdef IS_MPI | |
100 | strcpy( checkPointMsg, "Successful number of arguments" ); | |
101 | MPIcheckPoint(); | |
102 | #endif | |
103 | + | |
104 | + | |
105 | + | |
106 | + | //register forcefields, integrators and minimizers |
107 | + | registerAll(); |
108 | + | |
109 | + | //create simulation model |
110 | + | SimCreator creator; |
111 | + | SimInfo* info = creator.createSim(argv[1]); |
112 | + | Globals* simParams = info->getSimParams(); |
113 | + | |
114 | + | if (simParams->haveMinimizer() && simParams->haveEnsemble()) { |
115 | + | sprintf(painCave.errMsg, "Minimizer keyword and Ensemble keyword can not exist together\n"); |
116 | + | painCave.isFatal = 1; |
117 | + | simError(); |
118 | + | } |
119 | ||
120 | < | // create the simulation objects, and get the show on the road |
120 | > | if (simParams->haveMinimizer()) { |
121 | > | //create minimizer |
122 | > | Minimizer* myMinimizer = MinimizerFactory::getInstance()->createMinimizer(simParams->getMinimizer(), info); |
123 | ||
124 | < | entry_plug = new SimInfo(); |
125 | < | startMe = new SimSetup(); |
124 | > | if (myMinimizer == NULL) { |
125 | > | sprintf(painCave.errMsg, "Minimizer Factory can not create %s Minimizer\n", |
126 | > | simParams->getMinimizer()); |
127 | > | painCave.isFatal = 1; |
128 | > | simError(); |
129 | > | } |
130 | ||
131 | < | startMe->setSimInfo( entry_plug ); |
131 | > | myMinimizer->minimize(); |
132 | > | delete myMinimizer; |
133 | > | } else if (simParams->haveEnsemble()) { |
134 | > | //create Integrator |
135 | ||
136 | < | #ifdef PROFILE |
96 | < | startProfile( pro1 ); |
97 | < | #endif //profile |
136 | > | Integrator* myIntegrator = IntegratorFactory::getInstance()->createIntegrator(simParams->getEnsemble(), info); |
137 | ||
138 | < | startMe->parseFile( in_name ); |
138 | > | if (myIntegrator == NULL) { |
139 | > | sprintf(painCave.errMsg, "Integrator Factory can not create %s Integrator\n", |
140 | > | simParams->getEnsemble()); |
141 | > | painCave.isFatal = 1; |
142 | > | simError(); |
143 | > | } |
144 | > | |
145 | > | //Thermodynamic Integration Method |
146 | > | //ForceManager* fman = new ThermodynamicForceManager(info); |
147 | > | //myIntegrator->setForceManager(fman); |
148 | ||
101 | – | #ifdef PROFILE |
102 | – | endProfile( pro1 ); |
103 | – | |
104 | – | startProfile( pro2 ); |
105 | – | #endif //profile |
149 | ||
150 | < | startMe->createSim(); |
151 | < | delete startMe; |
150 | > | //Zconstraint-Method |
151 | > | if (simParams->haveZconstraints()) { |
152 | > | info->setNZconstraint(simParams->getNzConstraints()); |
153 | > | ForceManager* fman = new ZconstraintForceManager(info); |
154 | > | myIntegrator->setForceManager(fman); |
155 | > | } |
156 | > | |
157 | > | myIntegrator->integrate(); |
158 | > | delete myIntegrator; |
159 | > | }else { |
160 | > | sprintf(painCave.errMsg, "Integrator Factory can not create %s Integrator\n", |
161 | > | simParams->getEnsemble()); |
162 | > | painCave.isFatal = 1; |
163 | > | simError(); |
164 | > | } |
165 | ||
110 | – | #ifdef PROFILE |
111 | – | endProfile( pro2 ); |
112 | – | |
113 | – | startProfile( pro3 ); |
114 | – | #endif //profile |
166 | ||
167 | < | if (!entry_plug->has_minimizer) |
168 | < | entry_plug->the_integrator->integrate(); |
118 | < | else |
119 | < | entry_plug->the_minimizer->minimize(); |
120 | < | #ifdef PROFILE |
121 | < | endProfile( pro3 ); |
122 | < | |
123 | < | writeProfiles(); |
124 | < | #endif //profile |
167 | > | |
168 | > | delete info; |
169 | ||
170 | #ifdef IS_MPI | |
171 | strcpy( checkPointMsg, "Oh what a lovely Tea Party!" ); | |
172 | MPIcheckPoint(); | |
173 | ||
174 | < | MPI_Finalize(); |
174 | > | MPI_Finalize(); |
175 | #endif | |
176 | ||
177 | return 0 ; |
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