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root/OpenMD/trunk/src/restraints/ThermoIntegrationForceManager.cpp
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Comparing trunk/src/restraints/ThermoIntegrationForceManager.cpp (file contents):
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

# Line 35 | Line 35
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).                        
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 90 | Line 91 | namespace OpenMD {
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 OpenMD {
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 OpenMD {
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   }

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