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root/OpenMD/branches/development/src/brains/SimInfo.cpp
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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 764 by gezelter, Mon Nov 21 22:59:21 2005 UTC vs.
Revision 998 by chrisfen, Mon Jul 3 13:18:43 2006 UTC

# Line 63 | Line 63
63   #include "utils/MemoryUtils.hpp"
64   #include "utils/simError.h"
65   #include "selection/SelectionManager.hpp"
66 + #include "io/ForceFieldOptions.hpp"
67 + #include "UseTheForce/ForceField.hpp"
68  
69   #ifdef IS_MPI
70   #include "UseTheForce/mpiComponentPlan.h"
# Line 80 | Line 82 | namespace oopse {
82      return result;
83    }
84    
85 <  SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
86 <                   ForceField* ff, Globals* simParams) :
87 <    stamps_(stamps), forceField_(ff), simParams_(simParams),
86 <    ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
85 >  SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
86 >    forceField_(ff), simParams_(simParams),
87 >    ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
88      nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
89      nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
90      nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
91      nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
92 <    sman_(NULL), fortranInitialized_(false) {
92 >    sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false) {
93  
93 –            
94 –      std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
94        MoleculeStamp* molStamp;
95        int nMolWithSameStamp;
96        int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
# Line 99 | Line 98 | namespace oopse {
98        CutoffGroupStamp* cgStamp;    
99        RigidBodyStamp* rbStamp;
100        int nRigidAtoms = 0;
101 <    
102 <      for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
103 <        molStamp = i->first;
104 <        nMolWithSameStamp = i->second;
101 >      std::vector<Component*> components = simParams->getComponents();
102 >      
103 >      for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
104 >        molStamp = (*i)->getMoleculeStamp();
105 >        nMolWithSameStamp = (*i)->getNMol();
106          
107          addMoleculeStamp(molStamp, nMolWithSameStamp);
108  
109          //calculate atoms in molecules
110          nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;  
111 –
111  
112          //calculate atoms in cutoff groups
113          int nAtomsInGroups = 0;
114          int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
115          
116          for (int j=0; j < nCutoffGroupsInStamp; j++) {
117 <          cgStamp = molStamp->getCutoffGroup(j);
117 >          cgStamp = molStamp->getCutoffGroupStamp(j);
118            nAtomsInGroups += cgStamp->getNMembers();
119          }
120  
# Line 128 | Line 127 | namespace oopse {
127          int nRigidBodiesInStamp = molStamp->getNRigidBodies();
128          
129          for (int j=0; j < nRigidBodiesInStamp; j++) {
130 <          rbStamp = molStamp->getRigidBody(j);
130 >          rbStamp = molStamp->getRigidBodyStamp(j);
131            nAtomsInRigidBodies += rbStamp->getNMembers();
132          }
133  
# Line 167 | Line 166 | namespace oopse {
166      }
167      molecules_.clear();
168        
170 –    delete stamps_;
169      delete sman_;
170      delete simParams_;
171      delete forceField_;
# Line 274 | Line 272 | namespace oopse {
272            }
273          }
274              
275 <      }//end for (integrableObject)
276 <    }// end for (mol)
275 >      }
276 >    }
277      
278      // n_constraints is local, so subtract them on each processor
279      ndf_local -= nConstraints_;
# Line 292 | Line 290 | namespace oopse {
290  
291    }
292  
293 +  int SimInfo::getFdf() {
294 + #ifdef IS_MPI
295 +    MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
296 + #else
297 +    fdf_ = fdf_local;
298 + #endif
299 +    return fdf_;
300 +  }
301 +    
302    void SimInfo::calcNdfRaw() {
303      int ndfRaw_local;
304  
# Line 595 | Line 602 | namespace oopse {
602      
603      setupElectrostaticSummationMethod( isError );
604      setupSwitchingFunction();
605 +    setupAccumulateBoxDipole();
606  
607      if(isError){
608        sprintf( painCave.errMsg,
# Line 654 | Line 662 | namespace oopse {
662      int usePBC = simParams_->getUsePeriodicBoundaryConditions();
663      int useRF;
664      int useSF;
665 +    int useSP;
666 +    int useBoxDipole;
667      std::string myMethod;
668  
669      // set the useRF logical
# Line 664 | Line 674 | namespace oopse {
674      if (simParams_->haveElectrostaticSummationMethod()) {
675        std::string myMethod = simParams_->getElectrostaticSummationMethod();
676        toUpper(myMethod);
677 <      if (myMethod == "REACTION_FIELD") {
677 >      if (myMethod == "REACTION_FIELD"){
678          useRF=1;
679 <      } else {
680 <        if (myMethod == "SHIFTED_FORCE") {
681 <          useSF = 1;
682 <        }
679 >      } else if (myMethod == "SHIFTED_FORCE"){
680 >        useSF = 1;
681 >      } else if (myMethod == "SHIFTED_POTENTIAL"){
682 >        useSP = 1;
683        }
684      }
685 +    
686 +    if (simParams_->haveAccumulateBoxDipole())
687 +      if (simParams_->getAccumulateBoxDipole())
688 +        useBoxDipole = 1;
689  
690      //loop over all of the atom types
691      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
# Line 742 | Line 756 | namespace oopse {
756      MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
757  
758      temp = useSF;
759 <    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
759 >    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
760  
761 +    temp = useSP;
762 +    MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
763 +
764 +    temp = useBoxDipole;
765 +    MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
766 +
767   #endif
768  
769      fInfo_.SIM_uses_PBC = usePBC;    
# Line 761 | Line 781 | namespace oopse {
781      fInfo_.SIM_uses_FLARB = useFLARB;
782      fInfo_.SIM_uses_RF = useRF;
783      fInfo_.SIM_uses_SF = useSF;
784 +    fInfo_.SIM_uses_SP = useSP;
785 +    fInfo_.SIM_uses_BoxDipole = useBoxDipole;
786  
787      if( myMethod == "REACTION_FIELD") {
788        
# Line 792 | Line 814 | namespace oopse {
814      }
815  
816      //calculate mass ratio of cutoff group
817 <    std::vector<double> mfact;
817 >    std::vector<RealType> mfact;
818      SimInfo::MoleculeIterator mi;
819      Molecule* mol;
820      Molecule::CutoffGroupIterator ci;
821      CutoffGroup* cg;
822      Molecule::AtomIterator ai;
823      Atom* atom;
824 <    double totalMass;
824 >    RealType totalMass;
825  
826      //to avoid memory reallocation, reserve enough space for mfact
827      mfact.reserve(getNCutoffGroups());
# Line 924 | Line 946 | namespace oopse {
946  
947    void SimInfo::setupCutoff() {          
948      
949 +    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
950 +
951      // Check the cutoff policy
952 <    int cp =  TRADITIONAL_CUTOFF_POLICY;
953 <    if (simParams_->haveCutoffPolicy()) {
954 <      std::string myPolicy = simParams_->getCutoffPolicy();
952 >    int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
953 >
954 >    std::string myPolicy;
955 >    if (forceFieldOptions_.haveCutoffPolicy()){
956 >      myPolicy = forceFieldOptions_.getCutoffPolicy();
957 >    }else if (simParams_->haveCutoffPolicy()) {
958 >      myPolicy = simParams_->getCutoffPolicy();
959 >    }
960 >
961 >    if (!myPolicy.empty()){
962        toUpper(myPolicy);
963        if (myPolicy == "MIX") {
964          cp = MIX_CUTOFF_POLICY;
# Line 950 | Line 981 | namespace oopse {
981      notifyFortranCutoffPolicy(&cp);
982  
983      // Check the Skin Thickness for neighborlists
984 <    double skin;
984 >    RealType skin;
985      if (simParams_->haveSkinThickness()) {
986        skin = simParams_->getSkinThickness();
987        notifyFortranSkinThickness(&skin);
# Line 962 | Line 993 | namespace oopse {
993        if (simParams_->haveSwitchingRadius()) {
994          rsw_  = simParams_->getSwitchingRadius();
995        } else {
996 <        rsw_ = rcut_;
996 >        if (fInfo_.SIM_uses_Charges |
997 >            fInfo_.SIM_uses_Dipoles |
998 >            fInfo_.SIM_uses_RF) {
999 >          
1000 >          rsw_ = 0.85 * rcut_;
1001 >          sprintf(painCave.errMsg,
1002 >                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1003 >                  "\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1004 >                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1005 >        painCave.isFatal = 0;
1006 >        simError();
1007 >        } else {
1008 >          rsw_ = rcut_;
1009 >          sprintf(painCave.errMsg,
1010 >                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1011 >                  "\tOOPSE will use the same value as the cutoffRadius.\n"
1012 >                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1013 >          painCave.isFatal = 0;
1014 >          simError();
1015 >        }
1016        }
1017 +      
1018        notifyFortranCutoffs(&rcut_, &rsw_);
1019        
1020      } else {
# Line 1020 | Line 1071 | namespace oopse {
1071      int errorOut;
1072      int esm =  NONE;
1073      int sm = UNDAMPED;
1074 <    double alphaVal;
1075 <    double dielectric;
1074 >    RealType alphaVal;
1075 >    RealType dielectric;
1076  
1077      errorOut = isError;
1078      alphaVal = simParams_->getDampingAlpha();
# Line 1092 | Line 1143 | namespace oopse {
1143      
1144      // let's pass some summation method variables to fortran
1145      setElectrostaticSummationMethod( &esm );
1146 <    notifyFortranElectrostaticMethod( &esm );
1146 >    setFortranElectrostaticMethod( &esm );
1147      setScreeningMethod( &sm );
1148      setDampingAlpha( &alphaVal );
1149      setReactionFieldDielectric( &dielectric );
# Line 1125 | Line 1176 | namespace oopse {
1176  
1177    }
1178  
1179 +  void SimInfo::setupAccumulateBoxDipole() {    
1180 +
1181 +    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1182 +    if ( simParams_->haveAccumulateBoxDipole() )
1183 +      if ( simParams_->getAccumulateBoxDipole() ) {
1184 +        setAccumulateBoxDipole();
1185 +        calcBoxDipole_ = true;
1186 +      }
1187 +
1188 +  }
1189 +
1190    void SimInfo::addProperty(GenericData* genData) {
1191      properties_.addProperty(genData);  
1192    }
# Line 1181 | Line 1243 | namespace oopse {
1243      Molecule* mol;
1244  
1245      Vector3d comVel(0.0);
1246 <    double totalMass = 0.0;
1246 >    RealType totalMass = 0.0;
1247      
1248  
1249      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1250 <      double mass = mol->getMass();
1250 >      RealType mass = mol->getMass();
1251        totalMass += mass;
1252        comVel += mass * mol->getComVel();
1253      }  
1254  
1255   #ifdef IS_MPI
1256 <    double tmpMass = totalMass;
1256 >    RealType tmpMass = totalMass;
1257      Vector3d tmpComVel(comVel);    
1258 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1259 <    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1258 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1259 >    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1260   #endif
1261  
1262      comVel /= totalMass;
# Line 1207 | Line 1269 | namespace oopse {
1269      Molecule* mol;
1270  
1271      Vector3d com(0.0);
1272 <    double totalMass = 0.0;
1272 >    RealType totalMass = 0.0;
1273      
1274      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1275 <      double mass = mol->getMass();
1275 >      RealType mass = mol->getMass();
1276        totalMass += mass;
1277        com += mass * mol->getCom();
1278      }  
1279  
1280   #ifdef IS_MPI
1281 <    double tmpMass = totalMass;
1281 >    RealType tmpMass = totalMass;
1282      Vector3d tmpCom(com);    
1283 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1284 <    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1283 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1284 >    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1285   #endif
1286  
1287      com /= totalMass;
# Line 1243 | Line 1305 | namespace oopse {
1305        Molecule* mol;
1306        
1307      
1308 <      double totalMass = 0.0;
1308 >      RealType totalMass = 0.0;
1309      
1310  
1311        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1312 <         double mass = mol->getMass();
1312 >         RealType mass = mol->getMass();
1313           totalMass += mass;
1314           com += mass * mol->getCom();
1315           comVel += mass * mol->getComVel();          
1316        }  
1317        
1318   #ifdef IS_MPI
1319 <      double tmpMass = totalMass;
1319 >      RealType tmpMass = totalMass;
1320        Vector3d tmpCom(com);  
1321        Vector3d tmpComVel(comVel);
1322 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1323 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1324 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1322 >      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1323 >      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1324 >      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1325   #endif
1326        
1327        com /= totalMass;
# Line 1278 | Line 1340 | namespace oopse {
1340     void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1341        
1342  
1343 <      double xx = 0.0;
1344 <      double yy = 0.0;
1345 <      double zz = 0.0;
1346 <      double xy = 0.0;
1347 <      double xz = 0.0;
1348 <      double yz = 0.0;
1343 >      RealType xx = 0.0;
1344 >      RealType yy = 0.0;
1345 >      RealType zz = 0.0;
1346 >      RealType xy = 0.0;
1347 >      RealType xz = 0.0;
1348 >      RealType yz = 0.0;
1349        Vector3d com(0.0);
1350        Vector3d comVel(0.0);
1351        
# Line 1295 | Line 1357 | namespace oopse {
1357        Vector3d thisq(0.0);
1358        Vector3d thisv(0.0);
1359  
1360 <      double thisMass = 0.0;
1360 >      RealType thisMass = 0.0;
1361      
1362        
1363        
# Line 1333 | Line 1395 | namespace oopse {
1395   #ifdef IS_MPI
1396        Mat3x3d tmpI(inertiaTensor);
1397        Vector3d tmpAngMom;
1398 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1399 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1398 >      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1399 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1400   #endif
1401                
1402        return;
# Line 1355 | Line 1417 | namespace oopse {
1417        Vector3d thisr(0.0);
1418        Vector3d thisp(0.0);
1419        
1420 <      double thisMass;
1420 >      RealType thisMass;
1421        
1422        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1423          thisMass = mol->getMass();
# Line 1368 | Line 1430 | namespace oopse {
1430        
1431   #ifdef IS_MPI
1432        Vector3d tmpAngMom;
1433 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1433 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1434   #endif
1435        
1436        return angularMomentum;

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