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Comparing trunk/src/restraints/Restraint.hpp (file contents):
Revision 1364 by cli2, Wed Oct 7 20:49:50 2009 UTC vs.
Revision 2020 by gezelter, Mon Sep 22 19:18:35 2014 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, 234107 (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 "math/Vector3.hpp"
56   #include <map>
57  
58 < namespace oopse {
58 > namespace OpenMD {
59    
60    class Restraint {
61    public:
# Line 68 | Line 69 | namespace oopse {
69  
70      typedef std::pair<RealType, RealType> RealPair;
71  
72 <    Restraint() : twist0_(0.0), swingX0_(0.0), swingY0_(0.0), restType_(0) {
72 >    Restraint() : twist0_(0.0), swingX0_(0.0), swingY0_(0.0), restType_(0),
73 >                  printRest_(false) {
74      }
75      
76      virtual ~Restraint() {}
# Line 94 | Line 96 | namespace oopse {
96      void setDisplacementForceConstant(RealType kDisp) {
97        kDisp_ = kDisp;
98        restType_ |= rtDisplacement;
99 <      restInfo_[rtDisplacement] = std::make_pair(0.0, 0.0);
99 >      if (printRest_) restInfo_[rtDisplacement] = std::make_pair(0.0, 0.0);
100      }
101      
102      void setTwistForceConstant(RealType kTwist) {
103        kTwist_ = kTwist/4;
104        restType_ |= rtTwist;
105 <      restInfo_[rtTwist] = std::make_pair(0.0, 0.0);
105 >      if (printRest_) restInfo_[rtTwist] = std::make_pair(0.0, 0.0);
106      }
107      
108      void setSwingXForceConstant(RealType kSwingX) {
109        kSwingX_ = kSwingX;
110        restType_ |= rtSwingX;
111 <      restInfo_[rtSwingX] = std::make_pair(0.0, 0.0);
111 >      if (printRest_) restInfo_[rtSwingX] = std::make_pair(0.0, 0.0);
112      }
113  
114      void setSwingYForceConstant(RealType kSwingY) {
115        kSwingY_ = kSwingY;
116        restType_ |= rtSwingY;
117 <      restInfo_[rtSwingY] = std::make_pair(0.0, 0.0);
117 >      if (printRest_) restInfo_[rtSwingY] = std::make_pair(0.0, 0.0);
118      }
119      
120      /* restraint angles are measured relative to the ideal structure,
# Line 122 | Line 124 | namespace oopse {
124      void setRestrainedTwistAngle(RealType twist0) {
125        twist0_ = twist0;
126        restType_ |= rtTwist;
127 <      restInfo_[rtTwist] = std::make_pair(0.0, 0.0);
127 >      if (printRest_) restInfo_[rtTwist] = std::make_pair(0.0, 0.0);
128      }
129      
130      void setRestrainedSwingXAngle(RealType swingX0) {
131        swingX0_ = swingX0;
132        restType_ |= rtSwingX;
133 <      restInfo_[rtSwingX] = std::make_pair(0.0, 0.0);
133 >      if (printRest_) restInfo_[rtSwingX] = std::make_pair(0.0, 0.0);
134      }
135  
136      void setRestrainedSwingYAngle(RealType swingY0) {
137        swingY0_ = swingY0;
138        restType_ |= rtSwingY;
139 <      restInfo_[rtSwingY] = std::make_pair(0.0, 0.0);
139 >      if (printRest_) restInfo_[rtSwingY] = std::make_pair(0.0, 0.0);
140      }
141      
142      void setPrintRestraint(bool printRest) {

Comparing trunk/src/restraints/Restraint.hpp (property svn:keywords):
Revision 1364 by cli2, Wed Oct 7 20:49:50 2009 UTC vs.
Revision 2020 by gezelter, Mon Sep 22 19:18:35 2014 UTC

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