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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 834 by chuckv, Fri Dec 30 23:15:59 2005 UTC vs.
Revision 1089 by chrisfen, Wed Nov 1 22:22:44 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
670      useRF = 0;
671      useSF = 0;
672 +    useSP = 0;
673  
674  
675      if (simParams_->haveElectrostaticSummationMethod()) {
676        std::string myMethod = simParams_->getElectrostaticSummationMethod();
677        toUpper(myMethod);
678 <      if (myMethod == "REACTION_FIELD") {
679 <        useRF=1;
680 <      } else {
681 <        if (myMethod == "SHIFTED_FORCE") {
682 <          useSF = 1;
683 <        }
678 >      if (myMethod == "REACTION_FIELD"){
679 >        useRF = 1;
680 >      } else if (myMethod == "SHIFTED_FORCE"){
681 >        useSF = 1;
682 >      } else if (myMethod == "SHIFTED_POTENTIAL"){
683 >        useSP = 1;
684        }
685      }
686 +    
687 +    if (simParams_->haveAccumulateBoxDipole())
688 +      if (simParams_->getAccumulateBoxDipole())
689 +        useBoxDipole = 1;
690  
691      //loop over all of the atom types
692      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
# Line 740 | Line 757 | namespace oopse {
757      MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
758  
759      temp = useSF;
760 <    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
760 >    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
761  
762 +    temp = useSP;
763 +    MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
764 +
765 +    temp = useBoxDipole;
766 +    MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
767 +
768   #endif
769  
770      fInfo_.SIM_uses_PBC = usePBC;    
# Line 759 | Line 782 | namespace oopse {
782      fInfo_.SIM_uses_FLARB = useFLARB;
783      fInfo_.SIM_uses_RF = useRF;
784      fInfo_.SIM_uses_SF = useSF;
785 <
786 <    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 <
785 >    fInfo_.SIM_uses_SP = useSP;
786 >    fInfo_.SIM_uses_BoxDipole = useBoxDipole;
787    }
788  
789    void SimInfo::setupFortranSim() {
# Line 790 | Line 800 | namespace oopse {
800      }
801  
802      //calculate mass ratio of cutoff group
803 <    std::vector<double> mfact;
803 >    std::vector<RealType> mfact;
804      SimInfo::MoleculeIterator mi;
805      Molecule* mol;
806      Molecule::CutoffGroupIterator ci;
807      CutoffGroup* cg;
808      Molecule::AtomIterator ai;
809      Atom* atom;
810 <    double totalMass;
810 >    RealType totalMass;
811  
812      //to avoid memory reallocation, reserve enough space for mfact
813      mfact.reserve(getNCutoffGroups());
# Line 957 | Line 967 | namespace oopse {
967      notifyFortranCutoffPolicy(&cp);
968  
969      // Check the Skin Thickness for neighborlists
970 <    double skin;
970 >    RealType skin;
971      if (simParams_->haveSkinThickness()) {
972        skin = simParams_->getSkinThickness();
973        notifyFortranSkinThickness(&skin);
# Line 969 | Line 979 | namespace oopse {
979        if (simParams_->haveSwitchingRadius()) {
980          rsw_  = simParams_->getSwitchingRadius();
981        } else {
982 <        rsw_ = rcut_;
982 >        if (fInfo_.SIM_uses_Charges |
983 >            fInfo_.SIM_uses_Dipoles |
984 >            fInfo_.SIM_uses_RF) {
985 >          
986 >          rsw_ = 0.85 * rcut_;
987 >          sprintf(painCave.errMsg,
988 >                  "SimCreator Warning: No value was set for the switchingRadius.\n"
989 >                  "\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
990 >                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
991 >        painCave.isFatal = 0;
992 >        simError();
993 >        } else {
994 >          rsw_ = rcut_;
995 >          sprintf(painCave.errMsg,
996 >                  "SimCreator Warning: No value was set for the switchingRadius.\n"
997 >                  "\tOOPSE will use the same value as the cutoffRadius.\n"
998 >                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
999 >          painCave.isFatal = 0;
1000 >          simError();
1001 >        }
1002        }
1003 +      
1004        notifyFortranCutoffs(&rcut_, &rsw_);
1005        
1006      } else {
# Line 1027 | Line 1057 | namespace oopse {
1057      int errorOut;
1058      int esm =  NONE;
1059      int sm = UNDAMPED;
1060 <    double alphaVal;
1061 <    double dielectric;
1062 <
1060 >    RealType alphaVal;
1061 >    RealType dielectric;
1062 >    
1063      errorOut = isError;
1034 –    alphaVal = simParams_->getDampingAlpha();
1035 –    dielectric = simParams_->getDielectric();
1064  
1065      if (simParams_->haveElectrostaticSummationMethod()) {
1066        std::string myMethod = simParams_->getElectrostaticSummationMethod();
# Line 1049 | Line 1077 | namespace oopse {
1077              if (myMethod == "SHIFTED_FORCE") {            
1078                esm = SHIFTED_FORCE;
1079              } else {
1080 <              if (myMethod == "REACTION_FIELD") {            
1080 >              if (myMethod == "REACTION_FIELD") {
1081                  esm = REACTION_FIELD;
1082 +                dielectric = simParams_->getDielectric();
1083 +                if (!simParams_->haveDielectric()) {
1084 +                  // throw warning
1085 +                  sprintf( painCave.errMsg,
1086 +                           "SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1087 +                           "\tA default value of %f will be used for the dielectric.\n", dielectric);
1088 +                  painCave.isFatal = 0;
1089 +                  simError();
1090 +                }
1091                } else {
1092                  // throw error        
1093                  sprintf( painCave.errMsg,
# Line 1077 | Line 1114 | namespace oopse {
1114          if (myScreen == "DAMPED") {
1115            sm = DAMPED;
1116            if (!simParams_->haveDampingAlpha()) {
1117 <            //throw error
1117 >            // first set a cutoff dependent alpha value
1118 >            // we assume alpha depends linearly with rcut from 0 to 20.5 ang
1119 >            alphaVal = 0.5125 - rcut_* 0.025;
1120 >            // for values rcut > 20.5, alpha is zero
1121 >            if (alphaVal < 0) alphaVal = 0;
1122 >
1123 >            // throw warning
1124              sprintf( painCave.errMsg,
1125                       "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1126 <                     "\tA default value of %f (1/ang) will be used.\n", alphaVal);
1126 >                     "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1127              painCave.isFatal = 0;
1128              simError();
1129 +          } else {
1130 +            alphaVal = simParams_->getDampingAlpha();
1131            }
1132 +          
1133          } else {
1134            // throw error        
1135            sprintf( painCave.errMsg,
# Line 1098 | Line 1144 | namespace oopse {
1144      }
1145      
1146      // let's pass some summation method variables to fortran
1147 <    setElectrostaticSumMethod( &esm );
1147 >    setElectrostaticSummationMethod( &esm );
1148      setFortranElectrostaticMethod( &esm );
1149      setScreeningMethod( &sm );
1150      setDampingAlpha( &alphaVal );
# Line 1132 | Line 1178 | namespace oopse {
1178  
1179    }
1180  
1181 +  void SimInfo::setupAccumulateBoxDipole() {    
1182 +
1183 +    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1184 +    if ( simParams_->haveAccumulateBoxDipole() )
1185 +      if ( simParams_->getAccumulateBoxDipole() ) {
1186 +        setAccumulateBoxDipole();
1187 +        calcBoxDipole_ = true;
1188 +      }
1189 +
1190 +  }
1191 +
1192    void SimInfo::addProperty(GenericData* genData) {
1193      properties_.addProperty(genData);  
1194    }
# Line 1188 | Line 1245 | namespace oopse {
1245      Molecule* mol;
1246  
1247      Vector3d comVel(0.0);
1248 <    double totalMass = 0.0;
1248 >    RealType totalMass = 0.0;
1249      
1250  
1251      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1252 <      double mass = mol->getMass();
1252 >      RealType mass = mol->getMass();
1253        totalMass += mass;
1254        comVel += mass * mol->getComVel();
1255      }  
1256  
1257   #ifdef IS_MPI
1258 <    double tmpMass = totalMass;
1258 >    RealType tmpMass = totalMass;
1259      Vector3d tmpComVel(comVel);    
1260 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1261 <    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1260 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1261 >    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1262   #endif
1263  
1264      comVel /= totalMass;
# Line 1214 | Line 1271 | namespace oopse {
1271      Molecule* mol;
1272  
1273      Vector3d com(0.0);
1274 <    double totalMass = 0.0;
1274 >    RealType totalMass = 0.0;
1275      
1276      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1277 <      double mass = mol->getMass();
1277 >      RealType mass = mol->getMass();
1278        totalMass += mass;
1279        com += mass * mol->getCom();
1280      }  
1281  
1282   #ifdef IS_MPI
1283 <    double tmpMass = totalMass;
1283 >    RealType tmpMass = totalMass;
1284      Vector3d tmpCom(com);    
1285 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1286 <    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1285 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1286 >    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1287   #endif
1288  
1289      com /= totalMass;
# Line 1250 | Line 1307 | namespace oopse {
1307        Molecule* mol;
1308        
1309      
1310 <      double totalMass = 0.0;
1310 >      RealType totalMass = 0.0;
1311      
1312  
1313        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1314 <         double mass = mol->getMass();
1314 >         RealType mass = mol->getMass();
1315           totalMass += mass;
1316           com += mass * mol->getCom();
1317           comVel += mass * mol->getComVel();          
1318        }  
1319        
1320   #ifdef IS_MPI
1321 <      double tmpMass = totalMass;
1321 >      RealType tmpMass = totalMass;
1322        Vector3d tmpCom(com);  
1323        Vector3d tmpComVel(comVel);
1324 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1325 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1326 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1324 >      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1325 >      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1326 >      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1327   #endif
1328        
1329        com /= totalMass;
# Line 1285 | Line 1342 | namespace oopse {
1342     void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1343        
1344  
1345 <      double xx = 0.0;
1346 <      double yy = 0.0;
1347 <      double zz = 0.0;
1348 <      double xy = 0.0;
1349 <      double xz = 0.0;
1350 <      double yz = 0.0;
1345 >      RealType xx = 0.0;
1346 >      RealType yy = 0.0;
1347 >      RealType zz = 0.0;
1348 >      RealType xy = 0.0;
1349 >      RealType xz = 0.0;
1350 >      RealType yz = 0.0;
1351        Vector3d com(0.0);
1352        Vector3d comVel(0.0);
1353        
# Line 1302 | Line 1359 | namespace oopse {
1359        Vector3d thisq(0.0);
1360        Vector3d thisv(0.0);
1361  
1362 <      double thisMass = 0.0;
1362 >      RealType thisMass = 0.0;
1363      
1364        
1365        
# Line 1340 | Line 1397 | namespace oopse {
1397   #ifdef IS_MPI
1398        Mat3x3d tmpI(inertiaTensor);
1399        Vector3d tmpAngMom;
1400 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1401 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1400 >      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1401 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1402   #endif
1403                
1404        return;
# Line 1362 | Line 1419 | namespace oopse {
1419        Vector3d thisr(0.0);
1420        Vector3d thisp(0.0);
1421        
1422 <      double thisMass;
1422 >      RealType thisMass;
1423        
1424        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1425          thisMass = mol->getMass();
# Line 1375 | Line 1432 | namespace oopse {
1432        
1433   #ifdef IS_MPI
1434        Vector3d tmpAngMom;
1435 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1435 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1436   #endif
1437        
1438        return angularMomentum;
1439     }
1440    
1441 <  
1441 >  StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1442 >    return IOIndexToIntegrableObject.at(index);
1443 >  }
1444 >  
1445 >  void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1446 >    IOIndexToIntegrableObject= v;
1447 >  }
1448 >
1449 > /*
1450 >   void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1451 >      assert( v.size() == nAtoms_ + nRigidBodies_);
1452 >      sdByGlobalIndex_ = v;
1453 >    }
1454 >
1455 >    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1456 >      //assert(index < nAtoms_ + nRigidBodies_);
1457 >      return sdByGlobalIndex_.at(index);
1458 >    }  
1459 > */  
1460   }//end namespace oopse
1461  

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