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Comparing:
trunk/src/integrators/Integrator.hpp (file contents), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/integrators/Integrator.hpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 + * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   /**
# Line 54 | Line 55
55   #include "restraints/ThermoIntegrationForceManager.hpp"
56   #include "io/DumpWriter.hpp"
57   #include "io/StatWriter.hpp"
57 – #include "io/RestWriter.hpp"
58   #include "integrators/Velocitizer.hpp"
59 + #include "integrators/RNEMD.hpp"
60  
61 < namespace oopse {
61 > namespace OpenMD {
62  
63  
64    /**
# Line 80 | Line 81 | namespace oopse {
81      }
82  
83      void setForceManager(ForceManager* forceMan) {
84 +
85        if (forceMan_ != forceMan && forceMan_  != NULL) {
86          delete forceMan_;
87        }
# Line 87 | Line 89 | namespace oopse {
89      }
90  
91      void setVelocitizer(Velocitizer* velocitizer) {
92 <      if (velocitizer_ != velocitizer && velocitizer_  != NULL) {
92 >      if (velocitizer_ != velocitizer && velocitizer_ != NULL) {
93          delete velocitizer_;
94        }
95 <      velocitizer_  = velocitizer;
95 >      velocitizer_ = velocitizer;
96      }
97 <        
97 >
98 >    void setRNEMD(RNEMD* rnemd) {
99 >      if (rnemd_ != rnemd && rnemd_  != NULL) {
100 >        delete rnemd_;
101 >      }
102 >      rnemd_ = rnemd;
103 >    }
104 >    
105    protected:
106  
107      Integrator(SimInfo* info);
# Line 110 | Line 119 | namespace oopse {
119      ForceManager* forceMan_;
120      bool needPotential;
121      bool needStress;
122 <        
122 >    bool needReset;    
123      Velocitizer* velocitizer_;
124 +    RNEMD* rnemd_;
125      bool needVelocityScaling;
126 <    double targetScalingTemp;
126 >    RealType targetScalingTemp;
127 >
128 >    bool useRNEMD;    
129      
130      DumpWriter* dumpWriter;
131      StatWriter* statWriter;
120 –    RestWriter* restWriter;
132      Thermo thermo;
133  
134 <    double runTime;
135 <    double sampleTime;
136 <    double statusTime;
137 <    double thermalTime;
138 <    double dt;
134 >    RealType runTime;
135 >    RealType sampleTime;
136 >    RealType statusTime;
137 >    RealType thermalTime;
138 >    RealType resetTime;
139 >    RealType RNEMD_exchangeTime;
140 >    RealType dt;
141  
142      Snapshot* currentSnapshot_; //During the integration, the address of currentSnapshot Will not change
143  
144          
145    private:
146          
147 <    virtual double calcConservedQuantity() = 0;
147 >    virtual RealType calcConservedQuantity() = 0;
148          
149      virtual DumpWriter* createDumpWriter() = 0;
150  

Comparing:
trunk/src/integrators/Integrator.hpp (property svn:keywords), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/integrators/Integrator.hpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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