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Comparing:
trunk/src/minimizers/Minimizer.cpp (file contents), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/minimizers/Minimizer.cpp (file contents), Revision 1627 by gezelter, Tue Sep 13 22:05:04 2011 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, 24107 (2008).          
39 + * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41  
42   #include <cmath>
# Line 45 | Line 45
45   #include "io/StatWriter.hpp"
46   #include "minimizers/Minimizer.hpp"
47   #include "primitives/Molecule.hpp"
48 < namespace oopse {
48 > #ifdef IS_MPI
49 > #include <mpi.h>
50 > #endif
51 > namespace OpenMD {
52    RealType dotProduct(const std::vector<RealType>& v1, const std::vector<RealType>& v2) {
53      if (v1.size() != v2.size()) {
54  
# Line 64 | Line 67 | namespace oopse {
67      info(rhs), usingShake(false) {
68  
69        forceMan = new ForceManager(info);
70 <      paramSet= new MinimizerParameterSet(info),
68 <        calcDim();
70 >      paramSet= new MinimizerParameterSet(info), calcDim();
71        curX = getCoor();
72        curG.resize(ndim);
73  
# Line 830 | Line 832 | namespace oopse {
832      int convgStatus;
833      int stepStatus;
834      int maxIter;
835 <    int writeFrq;
835 >    int writeFreq;
836      int nextWriteIter;
837      Snapshot* curSnapshot =info->getSnapshotManager()->getCurrentSnapshot();
838      DumpWriter dumpWriter(info);    
# Line 841 | Line 843 | namespace oopse {
843  
844      init();
845  
846 <    writeFrq = paramSet->getWriteFrq();
846 >    writeFreq = paramSet->getWriteFreq();
847  
848 <    nextWriteIter = writeFrq;
848 >    nextWriteIter = writeFreq;
849  
850      maxIter = paramSet->getMaxIteration();
851  
# Line 871 | Line 873 | namespace oopse {
873        curSnapshot->increaseTime(1);    
874          
875        if (curIter == nextWriteIter) {
876 <        nextWriteIter += writeFrq;
876 >        nextWriteIter += writeFreq;
877          calcF();
878 <        dumpWriter.writeDump();
878 >        dumpWriter.writeDumpAndEor();
879          statWriter.writeStat(curSnapshot->statData);
880        }
881  
# Line 903 | Line 905 | namespace oopse {
905  
906  
907    RealType Minimizer::calcPotential() {
908 <    forceMan->calcForces(true, false);
908 >    forceMan->calcForces();
909  
910      Snapshot* curSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
911      RealType potential_local = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] +

Comparing:
trunk/src/minimizers/Minimizer.cpp (property svn:keywords), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/minimizers/Minimizer.cpp (property svn:keywords), Revision 1627 by gezelter, Tue Sep 13 22:05:04 2011 UTC

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

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