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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.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 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 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;
98      Molecule::IntegrableObjectIterator ii;
99 <    StuntDouble* integrableObject;
99 >    StuntDouble* sd;
100      Vector3d frc;
101      Vector3d trq;
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  
109 <    // now scale forces and torques of all the integrableObjects
109 >    // now scale forces and torques of all the sds
110        
111      for (mol = info_->beginMolecule(mi); mol != NULL;
112           mol = info_->nextMolecule(mi)) {
113 <      for (integrableObject = mol->beginIntegrableObject(ii);
114 <           integrableObject != NULL;
115 <           integrableObject = mol->nextIntegrableObject(ii)) {
116 <        frc = integrableObject->getFrc();
113 >
114 >      for (sd = mol->beginIntegrableObject(ii); sd != NULL;
115 >           sd = mol->nextIntegrableObject(ii)) {
116 >
117 >        frc = sd->getFrc();
118          frc *= factor_;
119 <        integrableObject->setFrc(frc);
119 >        sd->setFrc(frc);
120          
121 <        if (integrableObject->isDirectional()){
122 <          trq = integrableObject->getTrq();
121 >        if (sd->isDirectional()){
122 >          trq = sd->getTrq();
123            trq *= factor_;
124 <          integrableObject->setTrq(trq);
124 >          sd->setTrq(trq);
125          }
126        }
127      }
128      
129 <    // set vraw to be the unmodulated potential
130 <    lrPot_ = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
131 <    curSnapshot->statData[Stats::VRAW] = lrPot_;
129 >    // set rawPotential to be the unmodulated potential
130 >    lrPot_ = curSnapshot->getLongRangePotential();
131 >    curSnapshot->setRawPotential(lrPot_);
132      
133      // modulate the potential and update the snapshot
134      lrPot_ *= factor_;
135 <    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot_;
135 >    curSnapshot->setLongRangePotential(lrPot_);
136      
137      // scale the pressure tensor
138 <    tempTau = curSnapshot->statData.getTau();
138 >    tempTau = curSnapshot->getStressTensor();
139      tempTau *= factor_;
140 <    curSnapshot->statData.setTau(tempTau);
140 >    curSnapshot->setStressTensor(tempTau);
141  
142      // now, on to the applied restraining potentials (if needed):
143      RealType restPot_local = 0.0;
# Line 144 | Line 145 | namespace oopse {
145      
146      if (simParam->getUseRestraints()) {
147        // do restraints from RestraintForceManager:
147 –      //restPot_local = doRestraints(1.0 - factor_);    
148        restPot_local = doRestraints(1.0 - factor_);      
149        vHarm_local = getUnscaledPotential();
150      }
# Line 162 | Line 162 | namespace oopse {
162   #endif
163  
164      // give the final values to stats
165 <    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot_;
166 <    curSnapshot->statData[Stats::VHARM] = vHarm_;
165 >    curSnapshot->setLongRangePotential(lrPot_);
166 >    curSnapshot->setRestraintPotential(vHarm_);
167    }  
168   }

Comparing trunk/src/restraints/ThermoIntegrationForceManager.cpp (property svn:keywords):
Revision 1360 by cli2, Mon Sep 7 16:31:51 2009 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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