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root/OpenMD/trunk/src/brains/ForceManager.cpp
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Comparing trunk/src/brains/ForceManager.cpp (file contents):
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC vs.
Revision 1987 by gezelter, Thu Apr 17 19:07:31 2014 UTC

# Line 99 | Line 99 | namespace OpenMD {
99     *      Use the maximum suggested value that was found.
100     *
101     * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, TAYLOR_SHIFTED,
102 <   *                        or SHIFTED_POTENTIAL)
102 >   *                        SHIFTED_POTENTIAL, or EWALD_FULL)
103     *      If cutoffMethod was explicitly set, use that choice.
104     *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
105     *
# Line 172 | Line 172 | namespace OpenMD {
172      stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
173      stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
174      stringToCutoffMethod["TAYLOR_SHIFTED"] = TAYLOR_SHIFTED;
175 +    stringToCutoffMethod["EWALD_FULL"] = EWALD_FULL;
176    
177      if (simParams_->haveCutoffMethod()) {
178        string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
# Line 182 | Line 183 | namespace OpenMD {
183                  "ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
184                  "\tShould be one of: "
185                  "HARD, SWITCHED, SHIFTED_POTENTIAL, TAYLOR_SHIFTED,\n"
186 <                "\tor SHIFTED_FORCE\n",
186 >                "\tSHIFTED_FORCE, or EWALD_FULL\n",
187                  cutMeth.c_str());
188          painCave.isFatal = 1;
189          painCave.severity = OPENMD_ERROR;
# Line 228 | Line 229 | namespace OpenMD {
229              cutoffMethod_ = SHIFTED_FORCE;
230            } else if (myMethod == "TAYLOR_SHIFTED") {
231              cutoffMethod_ = TAYLOR_SHIFTED;
232 +          } else if (myMethod == "EWALD_FULL") {
233 +            cutoffMethod_ = EWALD_FULL;
234            }
235          
236            if (simParams_->haveSwitchingRadius())
237              rSwitch_ = simParams_->getSwitchingRadius();
238  
239            if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE" ||
240 <              myMethod == "TAYLOR_SHIFTED") {
240 >              myMethod == "TAYLOR_SHIFTED" || myMethod == "EWALD_FULL") {
241              if (simParams_->haveSwitchingRadius()){
242                sprintf(painCave.errMsg,
243                        "ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
# Line 634 | Line 637 | namespace OpenMD {
637      // Collect from all nodes.  This should eventually be moved into a
638      // SystemDecomposition, but this is a better place than in
639      // Thermo to do the collection.
640 <    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
641 <                              MPI::SUM);
642 <    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
643 <                              MPI::SUM);
644 <    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
645 <                              MPI::REALTYPE, MPI::SUM);
646 <    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
647 <                              MPI::REALTYPE, MPI::SUM);
640 >
641 >    MPI_Allreduce(MPI_IN_PLACE, &bondPotential, 1, MPI_REALTYPE,
642 >                  MPI_SUM, MPI_COMM_WORLD);
643 >    MPI_Allreduce(MPI_IN_PLACE, &bendPotential, 1, MPI_REALTYPE,
644 >                  MPI_SUM, MPI_COMM_WORLD);
645 >    MPI_Allreduce(MPI_IN_PLACE, &torsionPotential, 1,
646 >                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
647 >    MPI_Allreduce(MPI_IN_PLACE, &inversionPotential, 1,
648 >                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
649   #endif
650  
651      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
# Line 663 | Line 667 | namespace OpenMD {
667      DataStorage* config = &(curSnapshot->atomData);
668      DataStorage* cgConfig = &(curSnapshot->cgData);
669  
670 +
671      //calculate the center of mass of cutoff group
672  
673      SimInfo::MoleculeIterator mi;
# Line 695 | Line 700 | namespace OpenMD {
700      RealType vij;
701      Vector3d fij, fg, f1;
702      tuple3<RealType, RealType, RealType> cuts;
703 <    RealType rCutSq;
703 >    RealType rCut, rCutSq, rListSq;
704      bool in_switching_region;
705      RealType sw, dswdr, swderiv;
706      vector<int> atomListColumn, atomListRow;
# Line 705 | Line 710 | namespace OpenMD {
710      RealType vpair;
711      RealType dVdFQ1(0.0);
712      RealType dVdFQ2(0.0);
708 –    Vector3d eField1(0.0);
709 –    Vector3d eField2(0.0);
713      potVec longRangePotential(0.0);
714 +    RealType reciprocalPotential(0.0);
715      potVec workPot(0.0);
716      potVec exPot(0.0);
717 +    Vector3d eField1(0.0);
718 +    Vector3d eField2(0.0);
719      vector<int>::iterator ia, jb;
720  
721      int loopStart, loopEnd;
722 <
722 >    
723 >    idat.rcut = &rCut;
724      idat.vdwMult = &vdwMult;
725      idat.electroMult = &electroMult;
726      idat.pot = &workPot;
# Line 746 | Line 753 | namespace OpenMD {
753          if (update_nlist) {
754            if (!usePeriodicBoundaryConditions_)
755              Mat3x3d bbox = thermo->getBoundingBox();
756 <          neighborList = fDecomp_->buildNeighborList();
756 >          fDecomp_->buildNeighborList(neighborList_);
757          }
758        }
759  
760 <      for (vector<pair<int, int> >::iterator it = neighborList.begin();
761 <             it != neighborList.end(); ++it) {
760 >      for (vector<pair<int, int> >::iterator it = neighborList_.begin();
761 >             it != neighborList_.end(); ++it) {
762                  
763          cg1 = (*it).first;
764          cg2 = (*it).second;
765          
766 <        cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
766 >        fDecomp_->getGroupCutoffs(cg1, cg2, rCut, rCutSq, rListSq);
767  
768          d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
769  
770 <        curSnapshot->wrapVector(d_grp);        
770 >        // already wrapped in the getIntergroupVector call:
771 >        // curSnapshot->wrapVector(d_grp);        
772          rgrpsq = d_grp.lengthSquare();
765 –        rCutSq = cuts.second;
773  
774          if (rgrpsq < rCutSq) {
768 –          idat.rcut = &cuts.first;
775            if (iLoop == PAIR_LOOP) {
776              vij = 0.0;
777              fij.zero();
# Line 822 | Line 828 | namespace OpenMD {
828                
829                  r = sqrt( *(idat.r2) );
830                  idat.rij = &r;
831 <              
831 >
832                  if (iLoop == PREPAIR_LOOP) {
833                    interactionMan_->doPrePair(idat);
834                  } else {
# Line 918 | Line 924 | namespace OpenMD {
924          }
925        }
926      }
927 <  
927 >    
928      // collects pairwise information
929      fDecomp_->collectData();
930 +    if (cutoffMethod_ == EWALD_FULL) {
931 +      interactionMan_->doReciprocalSpaceSum(reciprocalPotential);
932 +
933 +      curSnapshot->setReciprocalPotential(reciprocalPotential);
934 +    }
935          
936      if (info_->requiresSelfCorrection()) {
937        for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
# Line 942 | Line 953 | namespace OpenMD {
953  
954    }
955  
945 –  
956    void ForceManager::postCalculation() {
957  
958      vector<Perturbation*>::iterator pi;
# Line 968 | Line 978 | namespace OpenMD {
978      }
979      
980   #ifdef IS_MPI
981 <    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
982 <                              MPI::REALTYPE, MPI::SUM);
981 >    MPI_Allreduce(MPI_IN_PLACE, stressTensor.getArrayPointer(), 9,
982 >                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
983   #endif
984      curSnapshot->setStressTensor(stressTensor);
985      

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