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Revision 1569 by gezelter, Thu May 26 13:55:04 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 58 | Line 59
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"
64 + #ifdef IS_MPI
65 + #include <mpi.h>
66 + #endif
67  
68   using namespace std;
69   namespace OpenMD {
# Line 68 | 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), topologyDone_(false),
78 >    nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false),
79      calcBoxDipole_(false), useAtomicVirial_(true) {    
80      
81      MoleculeStamp* molStamp;
# Line 125 | 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
128 –    std::cerr << "nGA = " << nGlobalAtoms_ << "\n";
129 –    std::cerr << "nCA = " << nCutoffAtoms << "\n";
130 –    std::cerr << "nG = " << nGroups << "\n";
132  
133      nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
133 –
134 –    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 226 | 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 247 | Line 250 | namespace OpenMD {
250              ndf_local += 3;
251            }
252          }
250 –            
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 287 | namespace OpenMD {
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() {
311      int ndfRaw_local;
312  
# Line 680 | 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 699 | 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
703 <    // (some will be redundant with the ones found locally):
704 <    int count;
705 <    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 745 | 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 +    
828 +    requiresPrepair_ = usesMetallicAtoms_ ? true : false;
829 +    requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
830 +    requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;    
831    }
832  
833  
# Line 824 | Line 882 | namespace OpenMD {
882      Atom* atom;
883      RealType totalMass;
884  
885 <    //to avoid memory reallocation, reserve enough space for massFactors_
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_.reserve(getNCutoffGroups());
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;
# Line 835 | Line 900 | namespace OpenMD {
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 <            massFactors_.push_back(atom->getMass()/totalMass);
903 >          if (totalMass != 0)
904 >            massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
905            else
906 <            massFactors_.push_back( 1.0 );
906 >            massFactors_[atom->getLocalIndex()] = 1.0;
907          }
908        }      
909      }
# Line 865 | Line 930 | namespace OpenMD {
930      int* oneThreeList = oneThreeInteractions_.getPairList();
931      int* oneFourList = oneFourInteractions_.getPairList();
932  
868 –    //setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray_[0],
869 –    //               &nExclude, excludeList,
870 –    //               &nOneTwo, oneTwoList,
871 –    //               &nOneThree, oneThreeList,
872 –    //               &nOneFour, oneFourList,
873 –    //               &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
874 –    //               &fortranGlobalGroupMembership[0], &isError);
875 –    
933      topologyDone_ = true;
934    }
935  
# Line 1157 | 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 1173 | 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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