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root/OpenMD/trunk/src/math/ParallelRandNumGen.cpp
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Comparing trunk/src/math/ParallelRandNumGen.cpp (file contents):
Revision 392 by tim, Wed Mar 2 15:36:14 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 1 | Line 1
1 < /*
1 > /*
2   * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
4   * The University of Notre Dame grants you ("Licensee") a
# 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]  Vardeman & Gezelter, in progress (2009).                        
40   */
41  
42   #include "math/ParallelRandNumGen.hpp"
43   #ifdef IS_MPI
44   #include <mpi.h>
45 + #endif
46  
47 < namespace oopse {
47 > namespace OpenMD {
48  
49 +  int ParallelRandNumGen::nCreatedRNG_ = 0;
50  
51 +  ParallelRandNumGen::ParallelRandNumGen(const uint32& oneSeed) {
52  
50 – int ParallelRandNumGen::nCreatedRNG_ = 0;
51 –
52 – ParallelRandNumGen::ParallelRandNumGen( const uint32& oneSeed) {
53 –
53      const int masterNode = 0;
54 <    int seed = oneSeed;
54 >    unsigned long seed = oneSeed;
55 >
56 > #ifdef IS_MPI
57      MPI_Bcast(&seed, 1, MPI_UNSIGNED_LONG, masterNode, MPI_COMM_WORLD);
58 + #endif
59  
60      if (seed != oneSeed) {
61 <        sprintf(painCave.errMsg,
62 <                "Using different seed to initialize ParallelRandNumGen.\n");
63 <        painCave.isFatal = 1;;
64 <        simError();
61 >      sprintf(painCave.errMsg,
62 >              "Using different seed to initialize ParallelRandNumGen.\n");
63 >      painCave.isFatal = 1;;
64 >      simError();
65      }
66  
67      int nProcessors;
68 <    MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
69 <
70 <    //In order to generate independent random number stream, the actual seed used by random
71 <    //number generator is the seed passed to the constructor plus the number of random number
72 <    //generators which are already created.    
73 <    int newSeed = oneSeed + nCreatedRNG_;
74 <    mtRand_ = new MTRand(newSeed, nProcessors, worldRank);
75 <
68 > #ifdef IS_MPI
69 >    MPI_Comm_size( MPI_COMM_WORLD, &nProcessors);
70 >    MPI_Comm_rank( MPI_COMM_WORLD, &myRank_);
71 > #else
72 >    nProcessors = 1;
73 >    myRank_ = 0;
74 > #endif
75 >    //In order to generate independent random number stream, the
76 >    //actual seed used by random number generator is the seed passed
77 >    //to the constructor plus the number of random number generators
78 >    //which are already created.
79 >    unsigned long newSeed = oneSeed + nCreatedRNG_;
80 >    mtRand_ = new MTRand(newSeed, nProcessors, myRank_);
81 >    
82      ++nCreatedRNG_;
83 < }
83 >  }
84  
85 < ParallelRandNumGen::ParallelRandNumGen() {
85 >  ParallelRandNumGen::ParallelRandNumGen() {
86  
87      std::vector<uint32> bigSeed;
88      const int masterNode = 0;
89      int nProcessors;
90 <    MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
91 <    mtRand_ = new MTRand(nProcessors, worldRank);
90 > #ifdef IS_MPI
91 >    MPI_Comm_size( MPI_COMM_WORLD, &nProcessors);
92 >    MPI_Comm_rank( MPI_COMM_WORLD, &myRank_);
93 > #else
94 >    nProcessors = 1;
95 >    myRank_ = 0;
96 > #endif
97 >    mtRand_ = new MTRand(nProcessors, myRank_);
98  
99 <    seed();       /** @todo calling virtual function in constructor is not a good design */
100 < }
99 >    seed();       /** @todo calling virtual function in constructor is
100 >                      not a good design */
101 >  }
102  
103  
104 < void ParallelRandNumGen::seed( const uint32 oneSeed ) {
104 >  void ParallelRandNumGen::seed( const uint32 oneSeed ) {
105  
106      const int masterNode = 0;
107 <    int seed = oneSeed;
107 >    unsigned long seed = oneSeed;
108 > #ifdef IS_MPI
109      MPI_Bcast(&seed, 1, MPI_UNSIGNED_LONG, masterNode, MPI_COMM_WORLD);
110 <
110 > #endif
111      if (seed != oneSeed) {
112 <        sprintf(painCave.errMsg,
113 <                "Using different seed to initialize ParallelRandNumGen.\n");
114 <        painCave.isFatal = 1;;
115 <        simError();
112 >      sprintf(painCave.errMsg,
113 >              "Using different seed to initialize ParallelRandNumGen.\n");
114 >      painCave.isFatal = 1;;
115 >      simError();
116      }
117 <
118 <    int newSeed = oneSeed +nCreatedRNG_;
117 >    
118 >    unsigned long newSeed = oneSeed +nCreatedRNG_;
119      mtRand_->seed(newSeed);
120 <
120 >    
121      ++nCreatedRNG_;
122 < }
122 >  }
123          
124 < void ParallelRandNumGen::seed() {
124 >  void ParallelRandNumGen::seed() {
125  
126      std::vector<uint32> bigSeed;
127      int size;
128      const int masterNode = 0;
129 + #ifdef IS_MPI
130      if (worldRank == masterNode) {
131 <        bigSeed = mtRand_->generateSeeds();
115 <        size = bigSeed.size();
116 <        MPI_Bcast(&size, 1, MPI_INT, masterNode, MPI_COMM_WORLD);        
117 <        MPI_Bcast(&bigSeed[0], size, MPI_UNSIGNED_LONG, masterNode, MPI_COMM_WORLD);
131 > #endif
132  
133 +      bigSeed = mtRand_->generateSeeds();
134 +      size = bigSeed.size();
135 +
136 + #ifdef IS_MPI
137 +      MPI_Bcast(&size, 1, MPI_INT, masterNode, MPI_COMM_WORLD);        
138 +      MPI_Bcast(&bigSeed[0], size, MPI_UNSIGNED_LONG, masterNode, MPI_COMM_WORLD);
139      }else {
140 <        MPI_Bcast(&size, 1, MPI_INT, masterNode, MPI_COMM_WORLD);        
141 <        bigSeed.resize(size);
142 <        MPI_Bcast(&bigSeed[0], size, MPI_UNSIGNED_LONG, masterNode, MPI_COMM_WORLD);
140 >      MPI_Bcast(&size, 1, MPI_INT, masterNode, MPI_COMM_WORLD);        
141 >      bigSeed.resize(size);
142 >      MPI_Bcast(&bigSeed[0], size, MPI_UNSIGNED_LONG, masterNode, MPI_COMM_WORLD);
143      }
144 + #endif
145      
146      if (bigSeed.size() == 1) {
147 <        mtRand_->seed(bigSeed[0]);
147 >      mtRand_->seed(bigSeed[0]);
148      } else {
149 <        mtRand_->seed(&bigSeed[0], bigSeed.size());
149 >      mtRand_->seed(&bigSeed[0], bigSeed.size());
150      }
151  
152      ++nCreatedRNG_;
153 < }    
133 <
134 <
153 >  }        
154   }
136 –
137 – #endif

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