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Revision 1536 by gezelter, Wed Jan 5 14:49:05 2011 UTC vs.
Revision 1744 by gezelter, Tue Jun 5 18:07:08 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"
62 > #include "brains/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
132 +
133      nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
134      
135      //every free atom (atom does not belong to rigid bodies) is an
# Line 227 | 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 248 | Line 250 | namespace OpenMD {
250              ndf_local += 3;
251            }
252          }
251 –            
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 +    ndfLocal_ = ndf_local;
263 +    cerr << "ndfLocal_ = " << ndfLocal_ << "\n";
264 +
265      // n_constraints is local, so subtract them on each processor
266      ndf_local -= nConstraints_;
267  
268   #ifdef IS_MPI
269      MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
270 +    MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
271   #else
272      ndf_ = ndf_local;
273 +    nGlobalFluctuatingCharges_ = nfq_local;
274   #endif
275  
276      // nZconstraints_ is global, as are the 3 COM translations for the
# Line 274 | Line 286 | namespace OpenMD {
286      fdf_ = fdf_local;
287   #endif
288      return fdf_;
289 +  }
290 +  
291 +  unsigned int SimInfo::getNLocalCutoffGroups(){
292 +    int nLocalCutoffAtoms = 0;
293 +    Molecule* mol;
294 +    MoleculeIterator mi;
295 +    CutoffGroup* cg;
296 +    Molecule::CutoffGroupIterator ci;
297 +    
298 +    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
299 +      
300 +      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
301 +           cg = mol->nextCutoffGroup(ci)) {
302 +        nLocalCutoffAtoms += cg->getNumAtom();
303 +        
304 +      }        
305 +    }
306 +    
307 +    return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
308    }
309      
310    void SimInfo::calcNdfRaw() {
# Line 681 | Line 712 | namespace OpenMD {
712      Atom* atom;
713      set<AtomType*> atomTypes;
714      
715 <    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {      
716 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
715 >    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
716 >      for(atom = mol->beginAtom(ai); atom != NULL;
717 >          atom = mol->nextAtom(ai)) {
718          atomTypes.insert(atom->getAtomType());
719        }      
720      }    
721 <
721 >    
722   #ifdef IS_MPI
723  
724      // loop over the found atom types on this processor, and add their
725      // numerical idents to a vector:
726 <
726 >    
727      vector<int> foundTypes;
728      set<AtomType*>::iterator i;
729      for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
# Line 700 | Line 732 | namespace OpenMD {
732      // count_local holds the number of found types on this processor
733      int count_local = foundTypes.size();
734  
735 <    // count holds the total number of found types on all processors
704 <    // (some will be redundant with the ones found locally):
705 <    int count;
706 <    MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
735 >    int nproc = MPI::COMM_WORLD.Get_size();
736  
737 <    // create a vector to hold the globally found types, and resize it:
738 <    vector<int> ftGlobal;
739 <    ftGlobal.resize(count);
740 <    vector<int> counts;
737 >    // we need arrays to hold the counts and displacement vectors for
738 >    // all processors
739 >    vector<int> counts(nproc, 0);
740 >    vector<int> disps(nproc, 0);
741  
742 <    int nproc = MPI::COMM_WORLD.Get_size();
743 <    counts.resize(nproc);
744 <    vector<int> disps;
745 <    disps.resize(nproc);
742 >    // fill the counts array
743 >    MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
744 >                              1, MPI::INT);
745 >  
746 >    // use the processor counts to compute the displacement array
747 >    disps[0] = 0;    
748 >    int totalCount = counts[0];
749 >    for (int iproc = 1; iproc < nproc; iproc++) {
750 >      disps[iproc] = disps[iproc-1] + counts[iproc-1];
751 >      totalCount += counts[iproc];
752 >    }
753  
754 <    // now spray out the foundTypes to all the other processors:
754 >    // we need a (possibly redundant) set of all found types:
755 >    vector<int> ftGlobal(totalCount);
756      
757 +    // now spray out the foundTypes to all the other processors:    
758      MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
759 <                               &ftGlobal[0], &counts[0], &disps[0], MPI::INT);
759 >                               &ftGlobal[0], &counts[0], &disps[0],
760 >                               MPI::INT);
761  
762 +    vector<int>::iterator j;
763 +
764      // foundIdents is a stl set, so inserting an already found ident
765      // will have no effect.
766      set<int> foundIdents;
767 <    vector<int>::iterator j;
767 >
768      for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
769        foundIdents.insert((*j));
770      
771      // now iterate over the foundIdents and get the actual atom types
772      // that correspond to these:
773      set<int>::iterator it;
774 <    for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
774 >    for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
775        atomTypes.insert( forceField_->getAtomType((*it)) );
776  
777   #endif
778 <    
778 >
779      return atomTypes;        
780    }
781  
# Line 746 | Line 787 | namespace OpenMD {
787        if ( simParams_->getAccumulateBoxDipole() ) {
788          calcBoxDipole_ = true;      
789        }
790 <
790 >    
791      set<AtomType*>::iterator i;
792      set<AtomType*> atomTypes;
793      atomTypes = getSimulatedAtomTypes();    
794      int usesElectrostatic = 0;
795      int usesMetallic = 0;
796      int usesDirectional = 0;
797 +    int usesFluctuatingCharges =  0;
798      //loop over all of the atom types
799      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
800        usesElectrostatic |= (*i)->isElectrostatic();
801        usesMetallic |= (*i)->isMetal();
802        usesDirectional |= (*i)->isDirectional();
803 +      usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
804      }
805 <
805 >    
806   #ifdef IS_MPI    
807      int temp;
808      temp = usesDirectional;
809      MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
810 <
810 >    
811      temp = usesMetallic;
812      MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
813 <
813 >    
814      temp = usesElectrostatic;
815      MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816 +
817 +    temp = usesFluctuatingCharges;
818 +    MPI_Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
819 + #else
820 +
821 +    usesDirectionalAtoms_ = usesDirectional;
822 +    usesMetallicAtoms_ = usesMetallic;
823 +    usesElectrostaticAtoms_ = usesElectrostatic;
824 +    usesFluctuatingCharges_ = usesFluctuatingCharges;
825 +
826   #endif
827 <    fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;    
828 <    fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
829 <    fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
830 <    fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
778 <    fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
779 <    fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
827 >    
828 >    requiresPrepair_ = usesMetallicAtoms_ ? true : false;
829 >    requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
830 >    requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;    
831    }
832  
833 <  void SimInfo::setupFortran() {
834 <    int isError;
835 <    int nExclude, nOneTwo, nOneThree, nOneFour;
836 <    vector<int> fortranGlobalGroupMembership;
833 >
834 >  vector<int> SimInfo::getGlobalAtomIndices() {
835 >    SimInfo::MoleculeIterator mi;
836 >    Molecule* mol;
837 >    Molecule::AtomIterator ai;
838 >    Atom* atom;
839 >
840 >    vector<int> GlobalAtomIndices(getNAtoms(), 0);
841      
842 <    isError = 0;
842 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
843 >      
844 >      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
845 >        GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
846 >      }
847 >    }
848 >    return GlobalAtomIndices;
849 >  }
850  
851 <    //globalGroupMembership_ is filled by SimCreator    
852 <    for (int i = 0; i < nGlobalAtoms_; i++) {
853 <      fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
851 >
852 >  vector<int> SimInfo::getGlobalGroupIndices() {
853 >    SimInfo::MoleculeIterator mi;
854 >    Molecule* mol;
855 >    Molecule::CutoffGroupIterator ci;
856 >    CutoffGroup* cg;
857 >
858 >    vector<int> GlobalGroupIndices;
859 >    
860 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
861 >      
862 >      //local index of cutoff group is trivial, it only depends on the
863 >      //order of travesing
864 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
865 >           cg = mol->nextCutoffGroup(ci)) {
866 >        GlobalGroupIndices.push_back(cg->getGlobalIndex());
867 >      }        
868      }
869 +    return GlobalGroupIndices;
870 +  }
871  
872 +
873 +  void SimInfo::prepareTopology() {
874 +    int nExclude, nOneTwo, nOneThree, nOneFour;
875 +
876      //calculate mass ratio of cutoff group
795 –    vector<RealType> mfact;
877      SimInfo::MoleculeIterator mi;
878      Molecule* mol;
879      Molecule::CutoffGroupIterator ci;
# Line 801 | Line 882 | namespace OpenMD {
882      Atom* atom;
883      RealType totalMass;
884  
885 <    //to avoid memory reallocation, reserve enough space for mfact
886 <    mfact.reserve(getNCutoffGroups());
885 >    /**
886 >     * The mass factor is the relative mass of an atom to the total
887 >     * mass of the cutoff group it belongs to.  By default, all atoms
888 >     * are their own cutoff groups, and therefore have mass factors of
889 >     * 1.  We need some special handling for massless atoms, which
890 >     * will be treated as carrying the entire mass of the cutoff
891 >     * group.
892 >     */
893 >    massFactors_.clear();
894 >    massFactors_.resize(getNAtoms(), 1.0);
895      
896      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
897 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
897 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
898 >           cg = mol->nextCutoffGroup(ci)) {
899  
900          totalMass = cg->getMass();
901          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
902            // Check for massless groups - set mfact to 1 if true
903 <          if (totalMass != 0)
904 <            mfact.push_back(atom->getMass()/totalMass);
903 >          if (totalMass != 0)
904 >            massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
905            else
906 <            mfact.push_back( 1.0 );
906 >            massFactors_[atom->getLocalIndex()] = 1.0;
907          }
908        }      
909      }
910  
911 <    //fill ident array of local atoms (it is actually ident of
822 <    //AtomType, it is so confusing !!!)
823 <    vector<int> identArray;
911 >    // Build the identArray_
912  
913 <    //to avoid memory reallocation, reserve enough space identArray
914 <    identArray.reserve(getNAtoms());
827 <    
913 >    identArray_.clear();
914 >    identArray_.reserve(getNAtoms());    
915      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
916        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
917 <        identArray.push_back(atom->getIdent());
917 >        identArray_.push_back(atom->getIdent());
918        }
919      }    
833 –
834 –    //fill molMembershipArray
835 –    //molMembershipArray is filled by SimCreator    
836 –    vector<int> molMembershipArray(nGlobalAtoms_);
837 –    for (int i = 0; i < nGlobalAtoms_; i++) {
838 –      molMembershipArray[i] = globalMolMembership_[i] + 1;
839 –    }
920      
921 <    //setup fortran simulation
921 >    //scan topology
922  
923      nExclude = excludedInteractions_.getSize();
924      nOneTwo = oneTwoInteractions_.getSize();
# Line 850 | Line 930 | namespace OpenMD {
930      int* oneThreeList = oneThreeInteractions_.getPairList();
931      int* oneFourList = oneFourInteractions_.getPairList();
932  
933 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
854 <                   &nExclude, excludeList,
855 <                   &nOneTwo, oneTwoList,
856 <                   &nOneThree, oneThreeList,
857 <                   &nOneFour, oneFourList,
858 <                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
859 <                   &fortranGlobalGroupMembership[0], &isError);
860 <    
861 <    if( isError ){
862 <      
863 <      sprintf( painCave.errMsg,
864 <               "There was an error setting the simulation information in fortran.\n" );
865 <      painCave.isFatal = 1;
866 <      painCave.severity = OPENMD_ERROR;
867 <      simError();
868 <    }
869 <    
870 <    
871 <    sprintf( checkPointMsg,
872 <             "succesfully sent the simulation information to fortran.\n");
873 <    
874 <    errorCheckPoint();
875 <    
876 <    // Setup number of neighbors in neighbor list if present
877 <    if (simParams_->haveNeighborListNeighbors()) {
878 <      int nlistNeighbors = simParams_->getNeighborListNeighbors();
879 <      setNeighbors(&nlistNeighbors);
880 <    }
881 <  
882 < #ifdef IS_MPI    
883 <    //SimInfo is responsible for creating localToGlobalAtomIndex and
884 <    //localToGlobalGroupIndex
885 <    vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
886 <    vector<int> localToGlobalCutoffGroupIndex;
887 <    mpiSimData parallelData;
888 <
889 <    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
890 <
891 <      //local index(index in DataStorge) of atom is important
892 <      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
893 <        localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
894 <      }
895 <
896 <      //local index of cutoff group is trivial, it only depends on the order of travesing
897 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
898 <        localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
899 <      }        
900 <        
901 <    }
902 <
903 <    //fill up mpiSimData struct
904 <    parallelData.nMolGlobal = getNGlobalMolecules();
905 <    parallelData.nMolLocal = getNMolecules();
906 <    parallelData.nAtomsGlobal = getNGlobalAtoms();
907 <    parallelData.nAtomsLocal = getNAtoms();
908 <    parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
909 <    parallelData.nGroupsLocal = getNCutoffGroups();
910 <    parallelData.myNode = worldRank;
911 <    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
912 <
913 <    //pass mpiSimData struct and index arrays to fortran
914 <    setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
915 <                    &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
916 <                    &localToGlobalCutoffGroupIndex[0], &isError);
917 <
918 <    if (isError) {
919 <      sprintf(painCave.errMsg,
920 <              "mpiRefresh errror: fortran didn't like something we gave it.\n");
921 <      painCave.isFatal = 1;
922 <      simError();
923 <    }
924 <
925 <    sprintf(checkPointMsg, " mpiRefresh successful.\n");
926 <    errorCheckPoint();
927 < #endif
928 <
929 <    initFortranFF(&isError);
930 <    if (isError) {
931 <      sprintf(painCave.errMsg,
932 <              "initFortranFF errror: fortran didn't like something we gave it.\n");
933 <      painCave.isFatal = 1;
934 <      simError();
935 <    }
936 <    fortranInitialized_ = true;
933 >    topologyDone_ = true;
934    }
935  
936    void SimInfo::addProperty(GenericData* genData) {
# Line 970 | Line 967 | namespace OpenMD {
967      Molecule* mol;
968      RigidBody* rb;
969      Atom* atom;
970 +    CutoffGroup* cg;
971      SimInfo::MoleculeIterator mi;
972      Molecule::RigidBodyIterator rbIter;
973 <    Molecule::AtomIterator atomIter;;
973 >    Molecule::AtomIterator atomIter;
974 >    Molecule::CutoffGroupIterator cgIter;
975  
976      for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
977          
# Line 982 | Line 981 | namespace OpenMD {
981          
982        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
983          rb->setSnapshotManager(sman_);
984 +      }
985 +
986 +      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
987 +        cg->setSnapshotManager(sman_);
988        }
989      }    
990      
# Line 1211 | Line 1214 | namespace OpenMD {
1214      
1215      det = intTensor.determinant();
1216      sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1217 <    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1217 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
1218      return;
1219    }
1220  
# Line 1227 | Line 1230 | namespace OpenMD {
1230      
1231      detI = intTensor.determinant();
1232      sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1233 <    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1233 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
1234      return;
1235    }
1236   /*

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