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root/OpenMD/trunk/src/brains/SimInfo.cpp
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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 1908 by gezelter, Fri Jul 19 21:25:45 2013 UTC vs.
Revision 1987 by gezelter, Thu Apr 17 19:07:31 2014 UTC

# Line 47 | Line 47
47   * @version 1.0
48   */
49  
50 + #ifdef IS_MPI
51 + #include <mpi.h>
52 + #endif
53   #include <algorithm>
54   #include <set>
55   #include <map>
# Line 61 | Line 64
64   #include "io/ForceFieldOptions.hpp"
65   #include "brains/ForceField.hpp"
66   #include "nonbonded/SwitchingFunction.hpp"
64 – #ifdef IS_MPI
65 – #include <mpi.h>
66 – #endif
67  
68   using namespace std;
69   namespace OpenMD {
# Line 72 | 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), nGlobalFluctuatingCharges_(0),
76 <    nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
75 >    nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
76 >    nGlobalFluctuatingCharges_(0), nGlobalBonds_(0), nGlobalBends_(0),
77 >    nGlobalTorsions_(0), nGlobalInversions_(0), nGlobalConstraints_(0),
78 >    nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nInversions_(0),
79      nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
80 <    nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false),
81 <    calcBoxDipole_(false), useAtomicVirial_(true) {    
80 >    nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL),
81 >    topologyDone_(false), calcBoxDipole_(false), useAtomicVirial_(true),
82 >    hasNGlobalConstraints_(false) {    
83      
84      MoleculeStamp* molStamp;
85      int nMolWithSameStamp;
# Line 103 | Line 106 | namespace OpenMD {
106        addMoleculeStamp(molStamp, nMolWithSameStamp);
107        
108        //calculate atoms in molecules
109 <      nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;  
109 >      nGlobalAtoms_ += molStamp->getNAtoms() * nMolWithSameStamp;
110 >      nGlobalBonds_ += molStamp->getNBonds() * nMolWithSameStamp;
111 >      nGlobalBends_ += molStamp->getNBends() * nMolWithSameStamp;
112 >      nGlobalTorsions_ += molStamp->getNTorsions() * nMolWithSameStamp;
113 >      nGlobalInversions_ += molStamp->getNInversions() * nMolWithSameStamp;
114        
115        //calculate atoms in cutoff groups
116        int nAtomsInGroups = 0;
# Line 275 | Line 282 | namespace OpenMD {
282      ndf_local -= nConstraints_;
283  
284   #ifdef IS_MPI
285 <    MPI::COMM_WORLD.Allreduce(&ndf_local, &ndf_, 1, MPI::INT,MPI::SUM);
286 <    MPI::COMM_WORLD.Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
287 <                              MPI::INT, MPI::SUM);
285 >    MPI_Allreduce(&ndf_local, &ndf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
286 >    MPI_Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
287 >      MPI_INT, MPI_SUM, MPI_COMM_WORLD);
288   #else
289      ndf_ = ndf_local;
290      nGlobalFluctuatingCharges_ = nfq_local;
# Line 291 | Line 298 | namespace OpenMD {
298  
299    int SimInfo::getFdf() {
300   #ifdef IS_MPI
301 <    MPI::COMM_WORLD.Allreduce(&fdf_local, &fdf_, 1, MPI::INT, MPI::SUM);
301 >    MPI_Allreduce(&fdf_local, &fdf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
302   #else
303      fdf_ = fdf_local;
304   #endif
# Line 347 | Line 354 | namespace OpenMD {
354      }
355      
356   #ifdef IS_MPI
357 <    MPI::COMM_WORLD.Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI::INT, MPI::SUM);
357 >    MPI_Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
358   #else
359      ndfRaw_ = ndfRaw_local;
360   #endif
# Line 358 | Line 365 | namespace OpenMD {
365  
366      ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
367  
361 –
368   #ifdef IS_MPI
369 <    MPI::COMM_WORLD.Allreduce(&ndfTrans_local, &ndfTrans_, 1,
370 <                              MPI::INT, MPI::SUM);
369 >    MPI_Allreduce(&ndfTrans_local, &ndfTrans_, 1, MPI_INT, MPI_SUM,
370 >                  MPI_COMM_WORLD);
371   #else
372      ndfTrans_ = ndfTrans_local;
373   #endif
374  
375      ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
370 –
376    }
377  
378    void SimInfo::addInteractionPairs(Molecule* mol) {
# Line 418 | Line 423 | namespace OpenMD {
423          atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));        
424        }
425      }  
426 +
427            
428      for (bond= mol->beginBond(bondIter); bond != NULL;
429           bond = mol->nextBond(bondIter)) {
# Line 703 | Line 709 | namespace OpenMD {
709     */
710    void SimInfo::update() {  
711      setupSimVariables();
712 +    calcNConstraints();
713      calcNdf();
714      calcNdfRaw();
715      calcNdfTrans();
# Line 742 | Line 749 | namespace OpenMD {
749      // count_local holds the number of found types on this processor
750      int count_local = foundTypes.size();
751  
752 <    int nproc = MPI::COMM_WORLD.Get_size();
752 >    int nproc;
753 >    MPI_Comm_size( MPI_COMM_WORLD, &nproc);
754  
755      // we need arrays to hold the counts and displacement vectors for
756      // all processors
# Line 750 | Line 758 | namespace OpenMD {
758      vector<int> disps(nproc, 0);
759  
760      // fill the counts array
761 <    MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
762 <                              1, MPI::INT);
761 >    MPI_Allgather(&count_local, 1, MPI_INT, &counts[0],
762 >                  1, MPI_INT, MPI_COMM_WORLD);
763    
764      // use the processor counts to compute the displacement array
765      disps[0] = 0;    
# Line 765 | Line 773 | namespace OpenMD {
773      vector<int> ftGlobal(totalCount);
774      
775      // now spray out the foundTypes to all the other processors:    
776 <    MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
777 <                               &ftGlobal[0], &counts[0], &disps[0],
778 <                               MPI::INT);
776 >    MPI_Allgatherv(&foundTypes[0], count_local, MPI_INT,
777 >                   &ftGlobal[0], &counts[0], &disps[0],
778 >                   MPI_INT, MPI_COMM_WORLD);
779  
780      vector<int>::iterator j;
781  
# Line 831 | Line 839 | namespace OpenMD {
839      }
840  
841   #ifdef IS_MPI
842 <    bool temp;
842 >    int temp;
843 >
844      temp = usesDirectional;
845 <    MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
846 <                              MPI::LOR);
838 <        
839 <    temp = usesMetallic;
840 <    MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
841 <                              MPI::LOR);
845 >    MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
846 >    usesDirectionalAtoms_ = (temp == 0) ? false : true;
847      
848 +    temp = usesMetallic;
849 +    MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
850 +    usesMetallicAtoms_ = (temp == 0) ? false : true;
851 +
852      temp = usesElectrostatic;
853 <    MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
854 <                              MPI::LOR);
853 >    MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
854 >    usesElectrostaticAtoms_ = (temp == 0) ? false : true;
855  
856      temp = usesFluctuatingCharges;
857 <    MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
858 <                              MPI::LOR);
857 >    MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
858 >    usesFluctuatingCharges_ = (temp == 0) ? false : true;
859   #else
860  
861      usesDirectionalAtoms_ = usesDirectional;
# Line 938 | Line 947 | namespace OpenMD {
947        }      
948      }
949  
950 <    // Build the identArray_
950 >    // Build the identArray_ and regions_
951  
952      identArray_.clear();
953 <    identArray_.reserve(getNAtoms());    
954 <    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
953 >    identArray_.reserve(getNAtoms());  
954 >    regions_.clear();
955 >    regions_.reserve(getNAtoms());
956 >
957 >    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {      
958 >      int reg = mol->getRegion();      
959        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
960          identArray_.push_back(atom->getIdent());
961 +        regions_.push_back(reg);
962        }
963      }    
964 <    
964 >      
965      topologyDone_ = true;
966    }
967  
# Line 982 | Line 996 | namespace OpenMD {
996      delete sman_;
997      sman_ = sman;
998  
985 –    Molecule* mol;
986 –    RigidBody* rb;
987 –    Atom* atom;
988 –    CutoffGroup* cg;
999      SimInfo::MoleculeIterator mi;
1000 +    Molecule::AtomIterator ai;
1001      Molecule::RigidBodyIterator rbIter;
991 –    Molecule::AtomIterator atomIter;
1002      Molecule::CutoffGroupIterator cgIter;
1003 +    Molecule::BondIterator bondIter;
1004 +    Molecule::BendIterator bendIter;
1005 +    Molecule::TorsionIterator torsionIter;
1006 +    Molecule::InversionIterator inversionIter;
1007  
1008 +    Molecule* mol;
1009 +    Atom* atom;
1010 +    RigidBody* rb;
1011 +    CutoffGroup* cg;
1012 +    Bond* bond;
1013 +    Bend* bend;
1014 +    Torsion* torsion;
1015 +    Inversion* inversion;    
1016 +
1017      for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1018          
1019 <      for (atom = mol->beginAtom(atomIter); atom != NULL;
1020 <           atom = mol->nextAtom(atomIter)) {
1019 >      for (atom = mol->beginAtom(ai); atom != NULL;
1020 >           atom = mol->nextAtom(ai)) {
1021          atom->setSnapshotManager(sman_);
1022 <      }
1000 <        
1022 >      }        
1023        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1024             rb = mol->nextRigidBody(rbIter)) {
1025          rb->setSnapshotManager(sman_);
1026        }
1005 –
1027        for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1028             cg = mol->nextCutoffGroup(cgIter)) {
1029          cg->setSnapshotManager(sman_);
1030        }
1031 <    }    
1032 <    
1031 >      for (bond = mol->beginBond(bondIter); bond != NULL;
1032 >           bond = mol->nextBond(bondIter)) {
1033 >        bond->setSnapshotManager(sman_);
1034 >      }
1035 >      for (bend = mol->beginBend(bendIter); bend != NULL;
1036 >           bend = mol->nextBend(bendIter)) {
1037 >        bend->setSnapshotManager(sman_);
1038 >      }
1039 >      for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
1040 >           torsion = mol->nextTorsion(torsionIter)) {
1041 >        torsion->setSnapshotManager(sman_);
1042 >      }
1043 >      for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
1044 >           inversion = mol->nextInversion(inversionIter)) {
1045 >        inversion->setSnapshotManager(sman_);
1046 >      }
1047 >    }
1048    }
1049  
1050  
# Line 1034 | Line 1070 | namespace OpenMD {
1070      IOIndexToIntegrableObject= v;
1071    }
1072  
1073 <  int SimInfo::getNGlobalConstraints() {
1038 <    int nGlobalConstraints;
1073 >  void SimInfo::calcNConstraints() {
1074   #ifdef IS_MPI
1075 <    MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1076 <                              MPI::INT, MPI::SUM);
1075 >    MPI_Allreduce(&nConstraints_, &nGlobalConstraints_, 1,  
1076 >                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1077   #else
1078 <    nGlobalConstraints =  nConstraints_;
1078 >    nGlobalConstraints_ =  nConstraints_;
1079   #endif
1045 –    return nGlobalConstraints;
1080    }
1081  
1082   }//end namespace OpenMD

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