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root/OpenMD/trunk/src/brains/SimInfo.cpp
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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 834 by chuckv, Fri Dec 30 23:15:59 2005 UTC vs.
Revision 1050 by chrisfen, Fri Sep 22 22:19:59 2006 UTC

# Line 53 | Line 53
53   #include "brains/SimInfo.hpp"
54   #include "math/Vector3.hpp"
55   #include "primitives/Molecule.hpp"
56 + #include "primitives/StuntDouble.hpp"
57   #include "UseTheForce/fCutoffPolicy.h"
58   #include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
59   #include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
# Line 84 | Line 85 | namespace oopse {
85    
86    SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
87      forceField_(ff), simParams_(simParams),
88 <    ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
88 >    ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
89      nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
90      nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
91      nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
92      nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
93 <    sman_(NULL), fortranInitialized_(false) {
93 >    sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false) {
94  
95        MoleculeStamp* molStamp;
96        int nMolWithSameStamp;
# Line 290 | Line 291 | namespace oopse {
291  
292    }
293  
294 +  int SimInfo::getFdf() {
295 + #ifdef IS_MPI
296 +    MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
297 + #else
298 +    fdf_ = fdf_local;
299 + #endif
300 +    return fdf_;
301 +  }
302 +    
303    void SimInfo::calcNdfRaw() {
304      int ndfRaw_local;
305  
# Line 591 | Line 601 | namespace oopse {
601      /** @deprecate */    
602      int isError = 0;
603      
604 +    setupCutoff();
605 +    
606      setupElectrostaticSummationMethod( isError );
607      setupSwitchingFunction();
608 +    setupAccumulateBoxDipole();
609  
610      if(isError){
611        sprintf( painCave.errMsg,
# Line 600 | Line 613 | namespace oopse {
613        painCave.isFatal = 1;
614        simError();
615      }
603 –  
604 –    
605 –    setupCutoff();
616  
617      calcNdf();
618      calcNdfRaw();
# Line 652 | 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 662 | 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 740 | 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 759 | Line 781 | namespace oopse {
781      fInfo_.SIM_uses_FLARB = useFLARB;
782      fInfo_.SIM_uses_RF = useRF;
783      fInfo_.SIM_uses_SF = useSF;
784 <
785 <    if( myMethod == "REACTION_FIELD") {
764 <      
765 <      if (simParams_->haveDielectric()) {
766 <        fInfo_.dielect = simParams_->getDielectric();
767 <      } else {
768 <        sprintf(painCave.errMsg,
769 <                "SimSetup Error: No Dielectric constant was set.\n"
770 <                "\tYou are trying to use Reaction Field without"
771 <                "\tsetting a dielectric constant!\n");
772 <        painCave.isFatal = 1;
773 <        simError();
774 <      }      
775 <    }
776 <
784 >    fInfo_.SIM_uses_SP = useSP;
785 >    fInfo_.SIM_uses_BoxDipole = useBoxDipole;
786    }
787  
788    void SimInfo::setupFortranSim() {
# Line 790 | Line 799 | namespace oopse {
799      }
800  
801      //calculate mass ratio of cutoff group
802 <    std::vector<double> mfact;
802 >    std::vector<RealType> mfact;
803      SimInfo::MoleculeIterator mi;
804      Molecule* mol;
805      Molecule::CutoffGroupIterator ci;
806      CutoffGroup* cg;
807      Molecule::AtomIterator ai;
808      Atom* atom;
809 <    double totalMass;
809 >    RealType totalMass;
810  
811      //to avoid memory reallocation, reserve enough space for mfact
812      mfact.reserve(getNCutoffGroups());
# Line 957 | Line 966 | namespace oopse {
966      notifyFortranCutoffPolicy(&cp);
967  
968      // Check the Skin Thickness for neighborlists
969 <    double skin;
969 >    RealType skin;
970      if (simParams_->haveSkinThickness()) {
971        skin = simParams_->getSkinThickness();
972        notifyFortranSkinThickness(&skin);
# Line 969 | Line 978 | namespace oopse {
978        if (simParams_->haveSwitchingRadius()) {
979          rsw_  = simParams_->getSwitchingRadius();
980        } else {
981 <        rsw_ = rcut_;
981 >        if (fInfo_.SIM_uses_Charges |
982 >            fInfo_.SIM_uses_Dipoles |
983 >            fInfo_.SIM_uses_RF) {
984 >          
985 >          rsw_ = 0.85 * rcut_;
986 >          sprintf(painCave.errMsg,
987 >                  "SimCreator Warning: No value was set for the switchingRadius.\n"
988 >                  "\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
989 >                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
990 >        painCave.isFatal = 0;
991 >        simError();
992 >        } else {
993 >          rsw_ = rcut_;
994 >          sprintf(painCave.errMsg,
995 >                  "SimCreator Warning: No value was set for the switchingRadius.\n"
996 >                  "\tOOPSE will use the same value as the cutoffRadius.\n"
997 >                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
998 >          painCave.isFatal = 0;
999 >          simError();
1000 >        }
1001        }
1002 +      
1003        notifyFortranCutoffs(&rcut_, &rsw_);
1004        
1005      } else {
# Line 1027 | Line 1056 | namespace oopse {
1056      int errorOut;
1057      int esm =  NONE;
1058      int sm = UNDAMPED;
1059 <    double alphaVal;
1060 <    double dielectric;
1061 <
1059 >    RealType alphaVal;
1060 >    RealType dielectric;
1061 >    
1062      errorOut = isError;
1034 –    alphaVal = simParams_->getDampingAlpha();
1035 –    dielectric = simParams_->getDielectric();
1063  
1064      if (simParams_->haveElectrostaticSummationMethod()) {
1065        std::string myMethod = simParams_->getElectrostaticSummationMethod();
# Line 1049 | Line 1076 | namespace oopse {
1076              if (myMethod == "SHIFTED_FORCE") {            
1077                esm = SHIFTED_FORCE;
1078              } else {
1079 <              if (myMethod == "REACTION_FIELD") {            
1079 >              if (myMethod == "REACTION_FIELD") {
1080                  esm = REACTION_FIELD;
1081 +                dielectric = simParams_->getDielectric();
1082 +                if (!simParams_->haveDielectric()) {
1083 +                  // throw warning
1084 +                  sprintf( painCave.errMsg,
1085 +                           "SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1086 +                           "\tA default value of %f will be used for the dielectric.\n", dielectric);
1087 +                  painCave.isFatal = 0;
1088 +                  simError();
1089 +                }
1090                } else {
1091                  // throw error        
1092                  sprintf( painCave.errMsg,
# Line 1077 | Line 1113 | namespace oopse {
1113          if (myScreen == "DAMPED") {
1114            sm = DAMPED;
1115            if (!simParams_->haveDampingAlpha()) {
1116 <            //throw error
1116 >            // first set a cutoff dependent alpha value
1117 >            // we assume alpha depends linearly with rcut from 0 to 20.5 ang
1118 >            alphaVal = 0.5125 - rcut_* 0.025;
1119 >            // for values rcut > 20.5, alpha is zero
1120 >            if (alphaVal < 0) alphaVal = 0;
1121 >
1122 >            // throw warning
1123              sprintf( painCave.errMsg,
1124                       "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1125 <                     "\tA default value of %f (1/ang) will be used.\n", alphaVal);
1125 >                     "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1126              painCave.isFatal = 0;
1127              simError();
1128            }
# Line 1098 | Line 1140 | namespace oopse {
1140      }
1141      
1142      // let's pass some summation method variables to fortran
1143 <    setElectrostaticSumMethod( &esm );
1143 >    setElectrostaticSummationMethod( &esm );
1144      setFortranElectrostaticMethod( &esm );
1145      setScreeningMethod( &sm );
1146      setDampingAlpha( &alphaVal );
# Line 1132 | Line 1174 | namespace oopse {
1174  
1175    }
1176  
1177 +  void SimInfo::setupAccumulateBoxDipole() {    
1178 +
1179 +    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1180 +    if ( simParams_->haveAccumulateBoxDipole() )
1181 +      if ( simParams_->getAccumulateBoxDipole() ) {
1182 +        setAccumulateBoxDipole();
1183 +        calcBoxDipole_ = true;
1184 +      }
1185 +
1186 +  }
1187 +
1188    void SimInfo::addProperty(GenericData* genData) {
1189      properties_.addProperty(genData);  
1190    }
# Line 1188 | Line 1241 | namespace oopse {
1241      Molecule* mol;
1242  
1243      Vector3d comVel(0.0);
1244 <    double totalMass = 0.0;
1244 >    RealType totalMass = 0.0;
1245      
1246  
1247      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1248 <      double mass = mol->getMass();
1248 >      RealType mass = mol->getMass();
1249        totalMass += mass;
1250        comVel += mass * mol->getComVel();
1251      }  
1252  
1253   #ifdef IS_MPI
1254 <    double tmpMass = totalMass;
1254 >    RealType tmpMass = totalMass;
1255      Vector3d tmpComVel(comVel);    
1256 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1257 <    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1256 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1257 >    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1258   #endif
1259  
1260      comVel /= totalMass;
# Line 1214 | Line 1267 | namespace oopse {
1267      Molecule* mol;
1268  
1269      Vector3d com(0.0);
1270 <    double totalMass = 0.0;
1270 >    RealType totalMass = 0.0;
1271      
1272      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1273 <      double mass = mol->getMass();
1273 >      RealType mass = mol->getMass();
1274        totalMass += mass;
1275        com += mass * mol->getCom();
1276      }  
1277  
1278   #ifdef IS_MPI
1279 <    double tmpMass = totalMass;
1279 >    RealType tmpMass = totalMass;
1280      Vector3d tmpCom(com);    
1281 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1282 <    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1281 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1282 >    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1283   #endif
1284  
1285      com /= totalMass;
# Line 1250 | Line 1303 | namespace oopse {
1303        Molecule* mol;
1304        
1305      
1306 <      double totalMass = 0.0;
1306 >      RealType totalMass = 0.0;
1307      
1308  
1309        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1310 <         double mass = mol->getMass();
1310 >         RealType mass = mol->getMass();
1311           totalMass += mass;
1312           com += mass * mol->getCom();
1313           comVel += mass * mol->getComVel();          
1314        }  
1315        
1316   #ifdef IS_MPI
1317 <      double tmpMass = totalMass;
1317 >      RealType tmpMass = totalMass;
1318        Vector3d tmpCom(com);  
1319        Vector3d tmpComVel(comVel);
1320 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1321 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1322 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1320 >      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1321 >      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1322 >      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1323   #endif
1324        
1325        com /= totalMass;
# Line 1285 | Line 1338 | namespace oopse {
1338     void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1339        
1340  
1341 <      double xx = 0.0;
1342 <      double yy = 0.0;
1343 <      double zz = 0.0;
1344 <      double xy = 0.0;
1345 <      double xz = 0.0;
1346 <      double yz = 0.0;
1341 >      RealType xx = 0.0;
1342 >      RealType yy = 0.0;
1343 >      RealType zz = 0.0;
1344 >      RealType xy = 0.0;
1345 >      RealType xz = 0.0;
1346 >      RealType yz = 0.0;
1347        Vector3d com(0.0);
1348        Vector3d comVel(0.0);
1349        
# Line 1302 | Line 1355 | namespace oopse {
1355        Vector3d thisq(0.0);
1356        Vector3d thisv(0.0);
1357  
1358 <      double thisMass = 0.0;
1358 >      RealType thisMass = 0.0;
1359      
1360        
1361        
# Line 1340 | Line 1393 | namespace oopse {
1393   #ifdef IS_MPI
1394        Mat3x3d tmpI(inertiaTensor);
1395        Vector3d tmpAngMom;
1396 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1397 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1396 >      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1397 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1398   #endif
1399                
1400        return;
# Line 1362 | Line 1415 | namespace oopse {
1415        Vector3d thisr(0.0);
1416        Vector3d thisp(0.0);
1417        
1418 <      double thisMass;
1418 >      RealType thisMass;
1419        
1420        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1421          thisMass = mol->getMass();
# Line 1375 | Line 1428 | namespace oopse {
1428        
1429   #ifdef IS_MPI
1430        Vector3d tmpAngMom;
1431 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1431 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1432   #endif
1433        
1434        return angularMomentum;
1435     }
1436    
1437 <  
1437 >  StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1438 >    return IOIndexToIntegrableObject.at(index);
1439 >  }
1440 >  
1441 >  void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1442 >    IOIndexToIntegrableObject= v;
1443 >  }
1444 >
1445 > /*
1446 >   void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1447 >      assert( v.size() == nAtoms_ + nRigidBodies_);
1448 >      sdByGlobalIndex_ = v;
1449 >    }
1450 >
1451 >    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1452 >      //assert(index < nAtoms_ + nRigidBodies_);
1453 >      return sdByGlobalIndex_.at(index);
1454 >    }  
1455 > */  
1456   }//end namespace oopse
1457  

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