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Comparing branches/new_design/OOPSE-2.0/src/brains/SimInfo.cpp (file contents):
Revision 1804 by tim, Tue Nov 30 19:58:25 2004 UTC vs.
Revision 1901 by tim, Tue Jan 4 22:18:36 2005 UTC

# Line 31 | Line 31
31   */
32  
33   #include <algorithm>
34 + #include <set>
35  
36   #include "brains/SimInfo.hpp"
37 + #include "math/Vector3.hpp"
38   #include "primitives/Molecule.hpp"
39 + #include "UseTheForce/doForces_interface.h"
40   #include "UseTheForce/notifyCutoffs_interface.h"
41   #include "utils/MemoryUtils.hpp"
42   #include "utils/simError.h"
43  
44 + #ifdef IS_MPI
45 + #include "UseTheForce/mpiComponentPlan.h"
46 + #include "UseTheForce/DarkSide/simParallel_interface.h"
47 + #endif
48 +
49   namespace oopse {
50  
51   SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
52 <                                ForceField* ff, Globals* globals) :
53 <                                forceField_(ff), globals_(globals), nAtoms_(0), nBonds_(0),
54 <                                nBends_(0), nTorsions_(0), nRigidBodies_(0), nIntegrableObjects_(0),
55 <                                nCutoffGroups_(0), nConstraints_(0), nZconstraint_(0), sman_(NULL),
56 <                                fortranInitialized_(false) {
52 >                                ForceField* ff, Globals* simParams) :
53 >                                forceField_(ff), simParams_(simParams),
54 >                                ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
55 >                                nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
56 >                                nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
57 >                                nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
58 >                                nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
59 >                                sman_(NULL), fortranInitialized_(false) {
60  
61 +            
62      std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
63      MoleculeStamp* molStamp;
64      int nMolWithSameStamp;
65 <    int nCutoffAtoms; // number of atoms belong to cutoff groups
66 <    int nGroups;          //total cutoff groups defined in meta-data file
67 <    CutoffGroupStamp* cgStamp;
56 <    int nAtomsInGroups;
57 <    int nCutoffGroupsInStamp;
58 <    
65 >    int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
66 >    int nGroups = 0;          //total cutoff groups defined in meta-data file
67 >    CutoffGroupStamp* cgStamp;    
68      RigidBodyStamp* rbStamp;
69 <    int nAtomsInRigidBodies;
61 <    int nRigidBodiesInStamp;
62 <    int nRigidAtoms;
63 <    int nRigidBodies;
64 <        
65 <    nGlobalAtoms_ =  0;
69 >    int nRigidAtoms = 0;
70      
67 –    nGroups = 0;
68 –    nCutoffAtoms = 0;
69 –    nRigidBodies = 0;
70 –    
71      for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
72          molStamp = i->first;
73          nMolWithSameStamp = i->second;
# Line 79 | Line 79 | SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*,
79  
80  
81          //calculate atoms in cutoff groups
82 <        nAtomsInGroups = 0;
83 <        nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
82 >        int nAtomsInGroups = 0;
83 >        int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
84          
85          for (int j=0; j < nCutoffGroupsInStamp; j++) {
86              cgStamp = molStamp->getCutoffGroup(j);
# Line 91 | Line 91 | SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*,
91          nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;            
92  
93          //calculate atoms in rigid bodies
94 <        nAtomsInRigidBodies = 0;
95 <        nRigidBodiesInStamp = molStamp->getNCutoffGroups();
94 >        int nAtomsInRigidBodies = 0;
95 >        int nRigidBodiesInStamp = molStamp->getNCutoffGroups();
96          
97          for (int j=0; j < nRigidBodiesInStamp; j++) {
98              rbStamp = molStamp->getRigidBody(j);
99 <            nRigidBodiesInStamp += rbStamp->getNMembers();
99 >            nAtomsInRigidBodies += rbStamp->getNMembers();
100          }
101  
102 <        nRigidBodies += nRigidBodiesInStamp * nMolWithSameStamp;
102 >        nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
103          nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;            
104          
105      }
# Line 110 | Line 110 | SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*,
110      //file plus the number of cutoff groups defined in meta-data file
111      nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
112  
113 <    //every free atom (atom does not belong to rigid bodies) is a rigid body
114 <    //therefore the total number of cutoff groups in the system is equal to
113 >    //every free atom (atom does not belong to rigid bodies) is an integrable object
114 >    //therefore the total number of  integrable objects in the system is equal to
115      //the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
116      //file plus the number of  rigid bodies defined in meta-data file
117 <    nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nRigidBodies;
117 >    nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
118  
119 –    //initialize globalGroupMembership_, every element of this array will be 0
120 –    globalGroupMembership_.insert(globalGroupMembership_.end(), nGlobalAtoms_, 0);
121 –
119      nGlobalMols_ = molStampIds_.size();
120  
121   #ifdef IS_MPI    
# Line 133 | Line 130 | SimInfo::~SimInfo() {
130      MemoryUtils::deleteVectorOfPointer(moleculeStamps_);
131      
132      delete sman_;
133 <    delete globals_;
133 >    delete simParams_;
134      delete forceField_;
135  
136   }
# Line 143 | Line 140 | bool SimInfo::addMolecule(Molecule* mol) {
140      MoleculeIterator i;
141  
142      i = molecules_.find(mol->getGlobalIndex());
143 <    if (i != molecules_.end() ) {
143 >    if (i == molecules_.end() ) {
144  
145 <        molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
145 >        molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
146          
147          nAtoms_ += mol->getNAtoms();
148          nBonds_ += mol->getNBonds();
# Line 154 | Line 151 | bool SimInfo::addMolecule(Molecule* mol) {
151          nRigidBodies_ += mol->getNRigidBodies();
152          nIntegrableObjects_ += mol->getNIntegrableObjects();
153          nCutoffGroups_ += mol->getNCutoffGroups();
154 <        nConstraints_ += mol->getNConstraints();
154 >        nConstraints_ += mol->getNConstraintPairs();
155  
156 +        addExcludePairs(mol);
157 +        
158          return true;
159      } else {
160          return false;
# Line 177 | Line 176 | bool SimInfo::removeMolecule(Molecule* mol) {
176          nRigidBodies_ -= mol->getNRigidBodies();
177          nIntegrableObjects_ -= mol->getNIntegrableObjects();
178          nCutoffGroups_ -= mol->getNCutoffGroups();
179 <        nConstraints_ -= mol->getNConstraints();
179 >        nConstraints_ -= mol->getNConstraintPairs();
180  
181 +        removeExcludePairs(mol);
182          molecules_.erase(mol->getGlobalIndex());
183  
184          delete mol;
# Line 389 | Line 389 | void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp
389      int curStampId;
390  
391      //index from 0
392 <    curStampId = molStampIds_.size();
392 >    curStampId = moleculeStamps_.size();
393  
394      moleculeStamps_.push_back(molStamp);
395      molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
# Line 405 | Line 405 | void SimInfo::update() {
405  
406      setupFortranSim();
407  
408 +    //setup fortran force field
409 +    /** @deprecate */    
410 +    int isError = 0;
411 +    initFortranFF( &fInfo_.SIM_uses_RF , &isError );
412 +    if(isError){
413 +        sprintf( painCave.errMsg,
414 +         "ForceField error: There was an error initializing the forceField in fortran.\n" );
415 +        painCave.isFatal = 1;
416 +        simError();
417 +    }
418 +  
419 +    
420      setupCutoff();
421  
410 –    //notify fortran whether reaction field is used or not. It is deprecated now
411 –    //int isError = 0;
412 –    //initFortranFF( &useReactionField, &isError );
413 –
414 –    //if(isError){
415 –    //    sprintf( painCave.errMsg,
416 –    //    "SimCreator::initFortran() error: There was an error initializing the forceField in fortran.\n" );
417 –    //    painCave.isFatal = 1;
418 –    //    simError();
419 –    //}
420 –    
422      calcNdf();
423      calcNdfRaw();
424      calcNdfTrans();
# Line 460 | Line 461 | void SimInfo::setupSimType() {
461      int useFLARB = 0; //it is not in AtomType yet
462      int useDirectionalAtom = 0;    
463      int useElectrostatics = 0;
464 <    //usePBC and useRF are from globals
465 <    bool usePBC = globals_->getPBC();
466 <    bool useRF = globals_->getUseRF();
464 >    //usePBC and useRF are from simParams
465 >    int usePBC = simParams_->getPBC();
466 >    int useRF = simParams_->getUseRF();
467  
468      //loop over all of the atom types
469      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
# Line 541 | Line 542 | void SimInfo::setupSimType() {
542  
543      if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
544  
545 <        if (globals_->haveDielectric()) {
546 <            fInfo_.dielect = globals_->getDielectric();
545 >        if (simParams_->haveDielectric()) {
546 >            fInfo_.dielect = simParams_->getDielectric();
547          } else {
548              sprintf(painCave.errMsg,
549                      "SimSetup Error: No Dielectric constant was set.\n"
# Line 611 | Line 612 | void SimInfo::setupFortranSim() {
612      //molMembershipArray is filled by SimCreator    
613      std::vector<int> molMembershipArray(nGlobalAtoms_);
614      for (int i = 0; i < nGlobalAtoms_; i++) {
615 <        molMembershipArray.push_back(globalMolMembership_[i] + 1);
615 >        molMembershipArray[i] = globalMolMembership_[i] + 1;
616      }
617      
618      //setup fortran simulation
# Line 679 | Line 680 | void SimInfo::setupFortranParallel() {
680      parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
681      parallelData.nGroupsLocal = getNCutoffGroups();
682      parallelData.myNode = worldRank;
683 <    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData->nProcessors));
683 >    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
684  
685      //pass mpiSimData struct and index arrays to fortran
686 <    setFsimParallel(parallelData, &(parallelData->nAtomsLocal),
687 <                    &localToGlobalAtomIndex[0],  &(parallelData->nGroupsLocal),
686 >    setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
687 >                    &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
688                      &localToGlobalCutoffGroupIndex[0], &isError);
689  
690      if (isError) {
# Line 730 | Line 731 | void SimInfo::setupCutoff() {
731      
732      if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
733          
734 <        if (!globals_->haveRcut()){
734 >        if (!simParams_->haveRcut()){
735              sprintf(painCave.errMsg,
736                  "SimCreator Warning: No value was set for the cutoffRadius.\n"
737                  "\tOOPSE will use a default value of 15.0 angstroms"
# Line 739 | Line 740 | void SimInfo::setupCutoff() {
740              simError();
741              rcut_ = 15.0;
742          } else{
743 <            rcut_ = globals_->getRcut();
743 >            rcut_ = simParams_->getRcut();
744          }
745  
746 <        if (!globals_->haveRsw()){
746 >        if (!simParams_->haveRsw()){
747              sprintf(painCave.errMsg,
748                  "SimCreator Warning: No value was set for switchingRadius.\n"
749                  "\tOOPSE will use a default value of\n"
# Line 751 | Line 752 | void SimInfo::setupCutoff() {
752              simError();
753              rsw_ = 0.95 * rcut_;
754          } else{
755 <            rsw_ = globals_->getRsw();
755 >            rsw_ = simParams_->getRsw();
756          }
757  
758      } else {
759          // if charge, dipole or reaction field is not used and the cutofff radius is not specified in
760          //meta-data file, the maximum cutoff radius calculated from forcefiled will be used
761          
762 <        if (globals_->haveRcut()) {
763 <            rcut_ = globals_->getRcut();
762 >        if (simParams_->haveRcut()) {
763 >            rcut_ = simParams_->getRcut();
764          } else {
765              //set cutoff radius to the maximum cutoff radius based on atom types in the whole system
766              rcut_ = calcMaxCutoffRadius();
767          }
768  
769 <        if (globals_->haveRsw()) {
770 <            rsw_  = globals_->getRsw();
769 >        if (simParams_->haveRsw()) {
770 >            rsw_  = simParams_->getRsw();
771          } else {
772              rsw_ = rcut_;
773          }
# Line 803 | Line 804 | GenericData* SimInfo::getPropertyByName(const std::str
804      return properties_.getPropertyByName(propName);
805   }
806  
807 + void SimInfo::setSnapshotManager(SnapshotManager* sman) {
808 +    sman_ = sman;
809  
810 < std::ostream& operator <<(ostream& o, SimInfo& info) {
810 >    Molecule* mol;
811 >    RigidBody* rb;
812 >    Atom* atom;
813 >    SimInfo::MoleculeIterator mi;
814 >    Molecule::RigidBodyIterator rbIter;
815 >    Molecule::AtomIterator atomIter;;
816 >
817 >    for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
818 >        
819 >        for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
820 >            atom->setSnapshotManager(sman_);
821 >        }
822 >        
823 >        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
824 >            rb->setSnapshotManager(sman_);
825 >        }
826 >    }    
827 >    
828 > }
829  
830 + Vector3d SimInfo::getComVel(){
831 +    SimInfo::MoleculeIterator i;
832 +    Molecule* mol;
833 +
834 +    Vector3d comVel(0.0);
835 +    double totalMass = 0.0;
836 +    
837 +
838 +    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
839 +        double mass = mol->getMass();
840 +        totalMass += mass;
841 +        comVel += mass * mol->getComVel();
842 +    }  
843 +
844 + #ifdef IS_MPI
845 +    double tmpMass = totalMass;
846 +    Vector3d tmpComVel(comVel);    
847 +    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
848 +    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
849 + #endif
850 +
851 +    comVel /= totalMass;
852 +
853 +    return comVel;
854 + }
855 +
856 + Vector3d SimInfo::getCom(){
857 +    SimInfo::MoleculeIterator i;
858 +    Molecule* mol;
859 +
860 +    Vector3d com(0.0);
861 +    double totalMass = 0.0;
862 +    
863 +    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
864 +        double mass = mol->getMass();
865 +        totalMass += mass;
866 +        com += mass * mol->getCom();
867 +    }  
868 +
869 + #ifdef IS_MPI
870 +    double tmpMass = totalMass;
871 +    Vector3d tmpCom(com);    
872 +    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
873 +    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
874 + #endif
875 +
876 +    com /= totalMass;
877 +
878 +    return com;
879 +
880 + }        
881 +
882 + std::ostream& operator <<(std::ostream& o, SimInfo& info) {
883 +
884      return o;
885   }
886  
887   }//end namespace oopse
888 +

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