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root/OpenMD/trunk/src/integrators/RNEMD.cpp
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Comparing trunk/src/integrators/RNEMD.cpp (file contents):
Revision 1368 by skuang, Mon Oct 19 13:39:04 2009 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 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 46 | Line 46
46   #include "math/Polynomial.hpp"
47   #include "primitives/Molecule.hpp"
48   #include "primitives/StuntDouble.hpp"
49 < #include "utils/OOPSEConstant.hpp"
49 > #include "utils/PhysicalConstants.hpp"
50   #include "utils/Tuple.hpp"
51  
52   #ifndef IS_MPI
# Line 57 | Line 57
57  
58   #define HONKING_LARGE_VALUE 1.0e10
59  
60 < namespace oopse {
60 > namespace OpenMD {
61    
62    RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
63  
# Line 279 | Line 279 | namespace oopse {
279            }
280            //make exchangeSum_ comparable between swap & scale
281            //temporarily without using energyConvert
282 <          //value = value * 0.5 / OOPSEConstant::energyConvert;
282 >          //value = value * 0.5 / PhysicalConstants::energyConvert;
283            value *= 0.5;
284            break;
285          case rnemdPx :
# Line 915 | Line 915 | namespace oopse {
915              valueCount_[binNo] +=3;
916            }
917          }
918 <        value = value / OOPSEConstant::energyConvert / OOPSEConstant::kb;
918 >        value = value / PhysicalConstants::energyConvert / PhysicalConstants::kb;
919  
920          break;
921        case rnemdPx :
922        case rnemdPxScale :
923          value = mass * vel[0];
924          valueCount_[binNo]++;
925 <        xVal = mass * vel.x() * vel.x() / OOPSEConstant::energyConvert
926 <          / OOPSEConstant::kb;
927 <        yVal = mass * vel.y() * vel.y() / OOPSEConstant::energyConvert
928 <          / OOPSEConstant::kb;
929 <        zVal = mass * vel.z() * vel.z() / OOPSEConstant::energyConvert
930 <          / OOPSEConstant::kb;
925 >        xVal = mass * vel.x() * vel.x() / PhysicalConstants::energyConvert
926 >          / PhysicalConstants::kb;
927 >        yVal = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
928 >          / PhysicalConstants::kb;
929 >        zVal = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
930 >          / PhysicalConstants::kb;
931          xTempHist_[binNo] += xVal;
932          yTempHist_[binNo] += yVal;
933          zTempHist_[binNo] += zVal;
# Line 1010 | Line 1010 | namespace oopse {
1010        }
1011        for (j = 0; j < rnemdLogWidth_; j++) valueCount_[j] = 0;
1012   #ifdef IS_MPI
1013 <    }
1013 >    }    
1014   #endif
1015 +
1016 +      
1017    }
1018  
1019   }

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