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Revision 1544 by gezelter, Fri Mar 18 19:31:52 2011 UTC vs.
Revision 1715 by gezelter, Tue May 22 21:55:31 2012 UTC

# Line 36 | Line 36
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).                        
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 54 | Line 55
55   #include "math/Vector3.hpp"
56   #include "primitives/Molecule.hpp"
57   #include "primitives/StuntDouble.hpp"
57 – #include "UseTheForce/DarkSide/neighborLists_interface.h"
58 – #include "UseTheForce/doForces_interface.h"
58   #include "utils/MemoryUtils.hpp"
59   #include "utils/simError.h"
60   #include "selection/SelectionManager.hpp"
61   #include "io/ForceFieldOptions.hpp"
62   #include "UseTheForce/ForceField.hpp"
63   #include "nonbonded/SwitchingFunction.hpp"
65 –
64   #ifdef IS_MPI
65 < #include "UseTheForce/mpiComponentPlan.h"
66 < #include "UseTheForce/DarkSide/simParallel_interface.h"
69 < #endif
65 > #include <mpi.h>
66 > #endif
67  
68   using namespace std;
69   namespace OpenMD {
# Line 75 | Line 72 | namespace OpenMD {
72      forceField_(ff), simParams_(simParams),
73      ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74      nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75 <    nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
75 >    nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), nGlobalFluctuatingCharges_(0),
76      nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
77      nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
78 <    nConstraints_(0), sman_(NULL), fortranInitialized_(false),
78 >    nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false),
79      calcBoxDipole_(false), useAtomicVirial_(true) {    
80      
81      MoleculeStamp* molStamp;
# Line 132 | Line 129 | namespace OpenMD {
129      //equal to the total number of atoms minus number of atoms belong to
130      //cutoff group defined in meta-data file plus the number of cutoff
131      //groups defined in meta-data file
135 –    std::cerr << "nGA = " << nGlobalAtoms_ << "\n";
136 –    std::cerr << "nCA = " << nCutoffAtoms << "\n";
137 –    std::cerr << "nG = " << nGroups << "\n";
132  
133      nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
140 –
141 –    std::cerr << "nGCG = " << nGlobalCutoffGroups_ << "\n";
134      
135      //every free atom (atom does not belong to rigid bodies) is an
136      //integrable object therefore the total number of integrable objects
# Line 233 | Line 225 | namespace OpenMD {
225  
226  
227    void SimInfo::calcNdf() {
228 <    int ndf_local;
228 >    int ndf_local, nfq_local;
229      MoleculeIterator i;
230      vector<StuntDouble*>::iterator j;
231 +    vector<Atom*>::iterator k;
232 +
233      Molecule* mol;
234      StuntDouble* integrableObject;
235 +    Atom* atom;
236  
237      ndf_local = 0;
238 +    nfq_local = 0;
239      
240      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
241        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
# Line 254 | Line 250 | namespace OpenMD {
250              ndf_local += 3;
251            }
252          }
257 –            
253        }
254 +      for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
255 +           atom = mol->nextFluctuatingCharge(k)) {
256 +        if (atom->isFluctuatingCharge()) {
257 +          nfq_local++;
258 +        }
259 +      }
260      }
261      
262      // n_constraints is local, so subtract them on each processor
# Line 263 | Line 264 | namespace OpenMD {
264  
265   #ifdef IS_MPI
266      MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
267 +    MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
268   #else
269      ndf_ = ndf_local;
270 +    nGlobalFluctuatingCharges_ = nfq_local;
271   #endif
272  
273      // nZconstraints_ is global, as are the 3 COM translations for the
# Line 281 | Line 284 | namespace OpenMD {
284   #endif
285      return fdf_;
286    }
287 +  
288 +  unsigned int SimInfo::getNLocalCutoffGroups(){
289 +    int nLocalCutoffAtoms = 0;
290 +    Molecule* mol;
291 +    MoleculeIterator mi;
292 +    CutoffGroup* cg;
293 +    Molecule::CutoffGroupIterator ci;
294      
295 +    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
296 +      
297 +      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
298 +           cg = mol->nextCutoffGroup(ci)) {
299 +        nLocalCutoffAtoms += cg->getNumAtom();
300 +        
301 +      }        
302 +    }
303 +    
304 +    return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
305 +  }
306 +    
307    void SimInfo::calcNdfRaw() {
308      int ndfRaw_local;
309  
# Line 687 | Line 709 | namespace OpenMD {
709      Atom* atom;
710      set<AtomType*> atomTypes;
711      
712 <    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {      
713 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
712 >    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
713 >      for(atom = mol->beginAtom(ai); atom != NULL;
714 >          atom = mol->nextAtom(ai)) {
715          atomTypes.insert(atom->getAtomType());
716        }      
717      }    
718 <
718 >    
719   #ifdef IS_MPI
720  
721      // loop over the found atom types on this processor, and add their
722      // numerical idents to a vector:
723 <
723 >    
724      vector<int> foundTypes;
725      set<AtomType*>::iterator i;
726      for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
# Line 706 | Line 729 | namespace OpenMD {
729      // count_local holds the number of found types on this processor
730      int count_local = foundTypes.size();
731  
709 –    // count holds the total number of found types on all processors
710 –    // (some will be redundant with the ones found locally):
711 –    int count;
712 –    MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
713 –
714 –    // create a vector to hold the globally found types, and resize it:
715 –    vector<int> ftGlobal;
716 –    ftGlobal.resize(count);
717 –    vector<int> counts;
718 –
732      int nproc = MPI::COMM_WORLD.Get_size();
720 –    counts.resize(nproc);
721 –    vector<int> disps;
722 –    disps.resize(nproc);
733  
734 <    // now spray out the foundTypes to all the other processors:
734 >    // we need arrays to hold the counts and displacement vectors for
735 >    // all processors
736 >    vector<int> counts(nproc, 0);
737 >    vector<int> disps(nproc, 0);
738 >
739 >    // fill the counts array
740 >    MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
741 >                              1, MPI::INT);
742 >  
743 >    // use the processor counts to compute the displacement array
744 >    disps[0] = 0;    
745 >    int totalCount = counts[0];
746 >    for (int iproc = 1; iproc < nproc; iproc++) {
747 >      disps[iproc] = disps[iproc-1] + counts[iproc-1];
748 >      totalCount += counts[iproc];
749 >    }
750 >
751 >    // we need a (possibly redundant) set of all found types:
752 >    vector<int> ftGlobal(totalCount);
753      
754 +    // now spray out the foundTypes to all the other processors:    
755      MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
756 <                               &ftGlobal[0], &counts[0], &disps[0], MPI::INT);
756 >                               &ftGlobal[0], &counts[0], &disps[0],
757 >                               MPI::INT);
758  
759 +    vector<int>::iterator j;
760 +
761      // foundIdents is a stl set, so inserting an already found ident
762      // will have no effect.
763      set<int> foundIdents;
764 <    vector<int>::iterator j;
764 >
765      for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
766        foundIdents.insert((*j));
767      
768      // now iterate over the foundIdents and get the actual atom types
769      // that correspond to these:
770      set<int>::iterator it;
771 <    for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
771 >    for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
772        atomTypes.insert( forceField_->getAtomType((*it)) );
773  
774   #endif
775 <    
775 >
776      return atomTypes;        
777    }
778  
# Line 752 | Line 784 | namespace OpenMD {
784        if ( simParams_->getAccumulateBoxDipole() ) {
785          calcBoxDipole_ = true;      
786        }
787 <
787 >    
788      set<AtomType*>::iterator i;
789      set<AtomType*> atomTypes;
790      atomTypes = getSimulatedAtomTypes();    
791      int usesElectrostatic = 0;
792      int usesMetallic = 0;
793      int usesDirectional = 0;
794 +    int usesFluctuatingCharges =  0;
795      //loop over all of the atom types
796      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
797        usesElectrostatic |= (*i)->isElectrostatic();
798        usesMetallic |= (*i)->isMetal();
799        usesDirectional |= (*i)->isDirectional();
800 +      usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
801      }
802 <
802 >    
803   #ifdef IS_MPI    
804      int temp;
805      temp = usesDirectional;
806      MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
807 <
807 >    
808      temp = usesMetallic;
809      MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
810 <
810 >    
811      temp = usesElectrostatic;
812      MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813 +
814 +    temp = usesFluctuatingCharges;
815 +    MPI_Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816 + #else
817 +
818 +    usesDirectionalAtoms_ = usesDirectional;
819 +    usesMetallicAtoms_ = usesMetallic;
820 +    usesElectrostaticAtoms_ = usesElectrostatic;
821 +    usesFluctuatingCharges_ = usesFluctuatingCharges;
822 +
823   #endif
824 <    fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;    
825 <    fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
826 <    fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
827 <    fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
784 <    fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
785 <    fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
824 >    
825 >    requiresPrepair_ = usesMetallicAtoms_ ? true : false;
826 >    requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
827 >    requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;    
828    }
829  
788 –  void SimInfo::setupFortran() {
789 –    int isError;
790 –    int nExclude, nOneTwo, nOneThree, nOneFour;
791 –    vector<int> fortranGlobalGroupMembership;
792 –    
793 –    isError = 0;
830  
831 <    //globalGroupMembership_ is filled by SimCreator    
832 <    for (int i = 0; i < nGlobalAtoms_; i++) {
833 <      fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
831 >  vector<int> SimInfo::getGlobalAtomIndices() {
832 >    SimInfo::MoleculeIterator mi;
833 >    Molecule* mol;
834 >    Molecule::AtomIterator ai;
835 >    Atom* atom;
836 >
837 >    vector<int> GlobalAtomIndices(getNAtoms(), 0);
838 >    
839 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
840 >      
841 >      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
842 >        GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
843 >      }
844      }
845 +    return GlobalAtomIndices;
846 +  }
847  
848 +
849 +  vector<int> SimInfo::getGlobalGroupIndices() {
850 +    SimInfo::MoleculeIterator mi;
851 +    Molecule* mol;
852 +    Molecule::CutoffGroupIterator ci;
853 +    CutoffGroup* cg;
854 +
855 +    vector<int> GlobalGroupIndices;
856 +    
857 +    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
858 +      
859 +      //local index of cutoff group is trivial, it only depends on the
860 +      //order of travesing
861 +      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
862 +           cg = mol->nextCutoffGroup(ci)) {
863 +        GlobalGroupIndices.push_back(cg->getGlobalIndex());
864 +      }        
865 +    }
866 +    return GlobalGroupIndices;
867 +  }
868 +
869 +
870 +  void SimInfo::prepareTopology() {
871 +    int nExclude, nOneTwo, nOneThree, nOneFour;
872 +
873      //calculate mass ratio of cutoff group
801 –    vector<RealType> mfact;
874      SimInfo::MoleculeIterator mi;
875      Molecule* mol;
876      Molecule::CutoffGroupIterator ci;
# Line 807 | Line 879 | namespace OpenMD {
879      Atom* atom;
880      RealType totalMass;
881  
882 <    //to avoid memory reallocation, reserve enough space for mfact
883 <    mfact.reserve(getNCutoffGroups());
882 >    /**
883 >     * The mass factor is the relative mass of an atom to the total
884 >     * mass of the cutoff group it belongs to.  By default, all atoms
885 >     * are their own cutoff groups, and therefore have mass factors of
886 >     * 1.  We need some special handling for massless atoms, which
887 >     * will be treated as carrying the entire mass of the cutoff
888 >     * group.
889 >     */
890 >    massFactors_.clear();
891 >    massFactors_.resize(getNAtoms(), 1.0);
892      
893      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
894 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
894 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
895 >           cg = mol->nextCutoffGroup(ci)) {
896  
897          totalMass = cg->getMass();
898          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
899            // Check for massless groups - set mfact to 1 if true
900 <          if (totalMass != 0)
901 <            mfact.push_back(atom->getMass()/totalMass);
900 >          if (totalMass != 0)
901 >            massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
902            else
903 <            mfact.push_back( 1.0 );
903 >            massFactors_[atom->getLocalIndex()] = 1.0;
904          }
905        }      
906      }
# Line 833 | Line 914 | namespace OpenMD {
914          identArray_.push_back(atom->getIdent());
915        }
916      }    
836 –
837 –    //fill molMembershipArray
838 –    //molMembershipArray is filled by SimCreator    
839 –    vector<int> molMembershipArray(nGlobalAtoms_);
840 –    for (int i = 0; i < nGlobalAtoms_; i++) {
841 –      molMembershipArray[i] = globalMolMembership_[i] + 1;
842 –    }
917      
918 <    //setup fortran simulation
918 >    //scan topology
919  
920      nExclude = excludedInteractions_.getSize();
921      nOneTwo = oneTwoInteractions_.getSize();
# Line 853 | Line 927 | namespace OpenMD {
927      int* oneThreeList = oneThreeInteractions_.getPairList();
928      int* oneFourList = oneFourInteractions_.getPairList();
929  
930 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
857 <                   &nExclude, excludeList,
858 <                   &nOneTwo, oneTwoList,
859 <                   &nOneThree, oneThreeList,
860 <                   &nOneFour, oneFourList,
861 <                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
862 <                   &fortranGlobalGroupMembership[0], &isError);
863 <    
864 <    if( isError ){
865 <      
866 <      sprintf( painCave.errMsg,
867 <               "There was an error setting the simulation information in fortran.\n" );
868 <      painCave.isFatal = 1;
869 <      painCave.severity = OPENMD_ERROR;
870 <      simError();
871 <    }
872 <    
873 <    
874 <    sprintf( checkPointMsg,
875 <             "succesfully sent the simulation information to fortran.\n");
876 <    
877 <    errorCheckPoint();
878 <    
879 <    // Setup number of neighbors in neighbor list if present
880 <    if (simParams_->haveNeighborListNeighbors()) {
881 <      int nlistNeighbors = simParams_->getNeighborListNeighbors();
882 <      setNeighbors(&nlistNeighbors);
883 <    }
884 <  
885 < #ifdef IS_MPI    
886 <    //SimInfo is responsible for creating localToGlobalAtomIndex and
887 <    //localToGlobalGroupIndex
888 <    vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
889 <    vector<int> localToGlobalCutoffGroupIndex;
890 <    mpiSimData parallelData;
891 <
892 <    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
893 <
894 <      //local index(index in DataStorge) of atom is important
895 <      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
896 <        localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
897 <      }
898 <
899 <      //local index of cutoff group is trivial, it only depends on the order of travesing
900 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
901 <        localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
902 <      }        
903 <        
904 <    }
905 <
906 <    //fill up mpiSimData struct
907 <    parallelData.nMolGlobal = getNGlobalMolecules();
908 <    parallelData.nMolLocal = getNMolecules();
909 <    parallelData.nAtomsGlobal = getNGlobalAtoms();
910 <    parallelData.nAtomsLocal = getNAtoms();
911 <    parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
912 <    parallelData.nGroupsLocal = getNCutoffGroups();
913 <    parallelData.myNode = worldRank;
914 <    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
915 <
916 <    //pass mpiSimData struct and index arrays to fortran
917 <    setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
918 <                    &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
919 <                    &localToGlobalCutoffGroupIndex[0], &isError);
920 <
921 <    if (isError) {
922 <      sprintf(painCave.errMsg,
923 <              "mpiRefresh errror: fortran didn't like something we gave it.\n");
924 <      painCave.isFatal = 1;
925 <      simError();
926 <    }
927 <
928 <    sprintf(checkPointMsg, " mpiRefresh successful.\n");
929 <    errorCheckPoint();
930 < #endif
931 <
932 <    initFortranFF(&isError);
933 <    if (isError) {
934 <      sprintf(painCave.errMsg,
935 <              "initFortranFF errror: fortran didn't like something we gave it.\n");
936 <      painCave.isFatal = 1;
937 <      simError();
938 <    }
939 <    fortranInitialized_ = true;
930 >    topologyDone_ = true;
931    }
932  
933    void SimInfo::addProperty(GenericData* genData) {
# Line 1220 | Line 1211 | namespace OpenMD {
1211      
1212      det = intTensor.determinant();
1213      sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1214 <    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1214 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
1215      return;
1216    }
1217  
# Line 1236 | Line 1227 | namespace OpenMD {
1227      
1228      detI = intTensor.determinant();
1229      sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1230 <    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1230 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
1231      return;
1232    }
1233   /*

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