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Comparing trunk/src/minimizers/Minimizer.cpp (file contents):
Revision 1231 by chuckv, Tue Mar 11 21:06:55 2008 UTC vs.
Revision 1422 by gezelter, Tue Mar 30 15:04:45 2010 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 > namespace OpenMD {
49    RealType dotProduct(const std::vector<RealType>& v1, const std::vector<RealType>& v2) {
50      if (v1.size() != v2.size()) {
51  
# Line 64 | Line 64 | namespace oopse {
64      info(rhs), usingShake(false) {
65  
66        forceMan = new ForceManager(info);
67 <      paramSet= new MinimizerParameterSet(info),
68 <        calcDim();
67 >      paramSet= new MinimizerParameterSet(info), calcDim();
68        curX = getCoor();
69        curG.resize(ndim);
70  
# Line 830 | Line 829 | namespace oopse {
829      int convgStatus;
830      int stepStatus;
831      int maxIter;
832 <    int writeFrq;
832 >    int writeFreq;
833      int nextWriteIter;
834      Snapshot* curSnapshot =info->getSnapshotManager()->getCurrentSnapshot();
835      DumpWriter dumpWriter(info);    
# Line 841 | Line 840 | namespace oopse {
840  
841      init();
842  
843 <    writeFrq = paramSet->getWriteFrq();
843 >    writeFreq = paramSet->getWriteFreq();
844  
845 <    nextWriteIter = writeFrq;
845 >    nextWriteIter = writeFreq;
846  
847      maxIter = paramSet->getMaxIteration();
848  
# Line 871 | Line 870 | namespace oopse {
870        curSnapshot->increaseTime(1);    
871          
872        if (curIter == nextWriteIter) {
873 <        nextWriteIter += writeFrq;
873 >        nextWriteIter += writeFreq;
874          calcF();
875          dumpWriter.writeDumpAndEor();
876          statWriter.writeStat(curSnapshot->statData);

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