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Comparing:
trunk/src/restraints/ThermoIntegrationForceManager.cpp (file contents), Revision 1360 by cli2, Mon Sep 7 16:31:51 2009 UTC vs.
branches/development/src/restraints/ThermoIntegrationForceManager.cpp (file contents), Revision 1723 by gezelter, Thu May 24 20:59:54 2012 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 46 | Line 47
47   #include <mpi.h>
48   #endif
49  
50 < namespace oopse {
50 > namespace OpenMD {
51    
52    ThermoIntegrationForceManager::ThermoIntegrationForceManager(SimInfo* info):
53      RestraintForceManager(info){
# Line 60 | Line 61 | namespace oopse {
61        tIntLambda_ = 1.0;
62        sprintf(painCave.errMsg,
63                "ThermoIntegration error: the transformation parameter\n"
64 <              "\t(lambda) was not specified. OOPSE will use a default\n"
64 >              "\t(lambda) was not specified. OpenMD will use a default\n"
65                "\tvalue of %f. To set lambda, use the \n"
66                "\tthermodynamicIntegrationLambda variable.\n",
67                tIntLambda_);
# Line 75 | Line 76 | namespace oopse {
76        tIntK_ = 1.0;
77        sprintf(painCave.errMsg,
78                "ThermoIntegration Warning: the tranformation parameter\n"
79 <              "\texponent (k) was not specified. OOPSE will use a default\n"
79 >              "\texponent (k) was not specified. OpenMD will use a default\n"
80                "\tvalue of %f. To set k, use the thermodynamicIntegrationK\n"
81                "\tvariable.\n",
82                tIntK_);
# Line 90 | Line 91 | namespace oopse {
91    ThermoIntegrationForceManager::~ThermoIntegrationForceManager(){
92    }
93    
94 <  void ThermoIntegrationForceManager::calcForces(bool needPotential,
94 <                                                 bool needStress){
94 >  void ThermoIntegrationForceManager::calcForces(){
95      Snapshot* curSnapshot;
96      SimInfo::MoleculeIterator mi;
97      Molecule* mol;
# Line 102 | Line 102 | namespace oopse {
102      Mat3x3d tempTau;
103      
104      // perform the standard calcForces first
105 <    ForceManager::calcForces(needPotential, needStress);
105 >    ForceManager::calcForces();
106      
107      curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
108  
# Line 134 | Line 134 | namespace oopse {
134      curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot_;
135      
136      // scale the pressure tensor
137 <    tempTau = curSnapshot->statData.getTau();
137 >    tempTau = curSnapshot->getStressTensor();
138      tempTau *= factor_;
139 <    curSnapshot->statData.setTau(tempTau);
139 >    curSnapshot->setStressTensor(tempTau);
140  
141      // now, on to the applied restraining potentials (if needed):
142      RealType restPot_local = 0.0;

Comparing:
trunk/src/restraints/ThermoIntegrationForceManager.cpp (property svn:keywords), Revision 1360 by cli2, Mon Sep 7 16:31:51 2009 UTC vs.
branches/development/src/restraints/ThermoIntegrationForceManager.cpp (property svn:keywords), Revision 1723 by gezelter, Thu May 24 20:59:54 2012 UTC

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