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root/OpenMD/trunk/src/restraints/ThermoIntegrationForceManager.cpp
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Comparing trunk/src/restraints/ThermoIntegrationForceManager.cpp (file contents):
Revision 1464 by gezelter, Fri Jul 9 19:29:05 2010 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 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  
42 –
43 – #include "restraints/ThermoIntegrationForceManager.hpp"
44 –
43   #ifdef IS_MPI
44   #include <mpi.h>
45   #endif
46  
47 + #include "restraints/ThermoIntegrationForceManager.hpp"
48 +
49   namespace OpenMD {
50    
51    ThermoIntegrationForceManager::ThermoIntegrationForceManager(SimInfo* info):
# Line 95 | Line 95 | namespace OpenMD {
95      SimInfo::MoleculeIterator mi;
96      Molecule* mol;
97      Molecule::IntegrableObjectIterator ii;
98 <    StuntDouble* integrableObject;
98 >    StuntDouble* sd;
99      Vector3d frc;
100      Vector3d trq;
101      Mat3x3d tempTau;
# Line 105 | Line 105 | namespace OpenMD {
105      
106      curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
107  
108 <    // now scale forces and torques of all the integrableObjects
108 >    // now scale forces and torques of all the sds
109        
110      for (mol = info_->beginMolecule(mi); mol != NULL;
111           mol = info_->nextMolecule(mi)) {
112 <      for (integrableObject = mol->beginIntegrableObject(ii);
113 <           integrableObject != NULL;
114 <           integrableObject = mol->nextIntegrableObject(ii)) {
115 <        frc = integrableObject->getFrc();
112 >
113 >      for (sd = mol->beginIntegrableObject(ii); sd != NULL;
114 >           sd = mol->nextIntegrableObject(ii)) {
115 >
116 >        frc = sd->getFrc();
117          frc *= factor_;
118 <        integrableObject->setFrc(frc);
118 >        sd->setFrc(frc);
119          
120 <        if (integrableObject->isDirectional()){
121 <          trq = integrableObject->getTrq();
120 >        if (sd->isDirectional()){
121 >          trq = sd->getTrq();
122            trq *= factor_;
123 <          integrableObject->setTrq(trq);
123 >          sd->setTrq(trq);
124          }
125        }
126      }
127      
128 <    // set vraw to be the unmodulated potential
129 <    lrPot_ = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
130 <    curSnapshot->statData[Stats::VRAW] = lrPot_;
128 >    // set rawPotential to be the unmodulated potential
129 >    lrPot_ = curSnapshot->getLongRangePotential();
130 >    curSnapshot->setRawPotential(lrPot_);
131      
132      // modulate the potential and update the snapshot
133      lrPot_ *= factor_;
134 <    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot_;
134 >    curSnapshot->setLongRangePotential(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;
# Line 143 | Line 144 | namespace OpenMD {
144      
145      if (simParam->getUseRestraints()) {
146        // do restraints from RestraintForceManager:
146 –      //restPot_local = doRestraints(1.0 - factor_);    
147        restPot_local = doRestraints(1.0 - factor_);      
148        vHarm_local = getUnscaledPotential();
149      }
150        
151   #ifdef IS_MPI
152      RealType restPot;
153 <    MPI::COMM_WORLD.Allreduce(&restPot_local, &restPot, 1,
154 <                              MPI::REALTYPE, MPI::SUM);
155 <    MPI::COMM_WORLD.Allreduce(&vHarm_local, &vHarm_, 1,
156 <                              MPI::REALTYPE, MPI::SUM);        
153 >    MPI_Allreduce(&restPot_local, &restPot, 1,
154 >                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
155 >    MPI_Allreduce(&vHarm_local, &vHarm_, 1,
156 >                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);        
157      lrPot_ += restPot;
158   #else
159      lrPot_ += restPot_local;
# Line 161 | Line 161 | namespace OpenMD {
161   #endif
162  
163      // give the final values to stats
164 <    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot_;
165 <    curSnapshot->statData[Stats::VHARM] = vHarm_;
164 >    curSnapshot->setLongRangePotential(lrPot_);
165 >    curSnapshot->setRestraintPotential(vHarm_);
166    }  
167   }

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