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Comparing trunk/src/integrators/Integrator.cpp (file contents):
Revision 1330 by skuang, Thu Mar 19 21:03:36 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 "brains/Snapshot.hpp"
43   #include "integrators/Integrator.hpp"
44   #include "utils/simError.h"
45 < namespace oopse {
45 > namespace OpenMD {
46    Integrator::Integrator(SimInfo* info)
47      : info_(info), forceMan_(NULL) , needPotential(false), needStress(false),
48        needReset(false), velocitizer_(NULL), needVelocityScaling(false),
# Line 96 | Line 96 | namespace oopse {
96          needReset = true;
97          resetTime = simParams->getResetTime();
98        }
99 –
100 –
101 –     if (simParams->haveUseRNEMD()) {
102 –        if (simParams->getUseRNEMD()) {
103 –           useRNEMD = simParams->getUseRNEMD();
104 –           if (simParams->haveRNEMD_swapTime()) {
105 –              RNEMD_swapTime = simParams->getRNEMD_swapTime();
106 –           }
107 –         }
108 –      }
99        
100        // Create a default ForceManager: If the subclass wants to use
101        // a different ForceManager, use setForceManager
# Line 126 | Line 116 | namespace oopse {
116  
117          }
118        }
119 <    
119 >      
120        // Create a default a velocitizer: If the subclass wants to use
121        // a different velocitizer, use setVelocitizer
122        velocitizer_ = new Velocitizer(info);
133 –      // Create a default a RNEMD.
134 –      rnemd_ = new RNEMD(info);
135 –    
136 –    }
123  
124 +      if (simParams->haveUseRNEMD()) {
125 +        if (simParams->getUseRNEMD()) {
126 +          // Create a default a RNEMD.
127 +          rnemd_ = new RNEMD(info);
128 +          useRNEMD = simParams->getUseRNEMD();
129 +          if (simParams->haveRNEMD_exchangeTime()) {
130 +            RNEMD_exchangeTime = simParams->getRNEMD_exchangeTime();
131 +          }
132 +        }
133 +      }
134 +  }
135 +  
136    Integrator::~Integrator(){
137      delete forceMan_;
138      delete velocitizer_;

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