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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 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
Revision 1045 by chrisfen, Thu Sep 21 18:25:17 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 63 | Line 64
64   #include "utils/MemoryUtils.hpp"
65   #include "utils/simError.h"
66   #include "selection/SelectionManager.hpp"
67 + #include "io/ForceFieldOptions.hpp"
68 + #include "UseTheForce/ForceField.hpp"
69  
70   #ifdef IS_MPI
71   #include "UseTheForce/mpiComponentPlan.h"
# Line 82 | 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 288 | 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 589 | 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 598 | Line 613 | namespace oopse {
613        painCave.isFatal = 1;
614        simError();
615      }
601 –  
602 –    
603 –    setupCutoff();
616  
617      calcNdf();
618      calcNdfRaw();
# Line 650 | 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 660 | 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 738 | 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 757 | 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 788 | 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 920 | 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 946 | 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 958 | 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 1016 | Line 1071 | namespace oopse {
1071      int errorOut;
1072      int esm =  NONE;
1073      int sm = UNDAMPED;
1074 <    double alphaVal;
1075 <    double dielectric;
1076 <
1074 >    RealType alphaVal;
1075 >    RealType dielectric;
1076 >    
1077      errorOut = isError;
1023 –    alphaVal = simParams_->getDampingAlpha();
1078      dielectric = simParams_->getDielectric();
1079  
1080      if (simParams_->haveElectrostaticSummationMethod()) {
# Line 1066 | Line 1120 | namespace oopse {
1120          if (myScreen == "DAMPED") {
1121            sm = DAMPED;
1122            if (!simParams_->haveDampingAlpha()) {
1123 <            //throw error
1123 >            // first set a cutoff dependent alpha value
1124 >            // we assume alpha depends linearly with rcut from 0 to 20.5 ang
1125 >            alphaVal = 0.5125 - rcut_* 0.025;
1126 >            // for values rcut > 20.5, alpha is zero
1127 >            if (alphaVal < 0) alphaVal = 0;
1128 >
1129 >            // throw warning
1130              sprintf( painCave.errMsg,
1131                       "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1132 <                     "\tA default value of %f (1/ang) will be used.\n", alphaVal);
1132 >                     "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1133              painCave.isFatal = 0;
1134              simError();
1135            }
# Line 1088 | Line 1148 | namespace oopse {
1148      
1149      // let's pass some summation method variables to fortran
1150      setElectrostaticSummationMethod( &esm );
1151 <    notifyFortranElectrostaticMethod( &esm );
1151 >    setFortranElectrostaticMethod( &esm );
1152      setScreeningMethod( &sm );
1153      setDampingAlpha( &alphaVal );
1154      setReactionFieldDielectric( &dielectric );
# Line 1121 | Line 1181 | namespace oopse {
1181  
1182    }
1183  
1184 +  void SimInfo::setupAccumulateBoxDipole() {    
1185 +
1186 +    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1187 +    if ( simParams_->haveAccumulateBoxDipole() )
1188 +      if ( simParams_->getAccumulateBoxDipole() ) {
1189 +        setAccumulateBoxDipole();
1190 +        calcBoxDipole_ = true;
1191 +      }
1192 +
1193 +  }
1194 +
1195    void SimInfo::addProperty(GenericData* genData) {
1196      properties_.addProperty(genData);  
1197    }
# Line 1177 | Line 1248 | namespace oopse {
1248      Molecule* mol;
1249  
1250      Vector3d comVel(0.0);
1251 <    double totalMass = 0.0;
1251 >    RealType totalMass = 0.0;
1252      
1253  
1254      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1255 <      double mass = mol->getMass();
1255 >      RealType mass = mol->getMass();
1256        totalMass += mass;
1257        comVel += mass * mol->getComVel();
1258      }  
1259  
1260   #ifdef IS_MPI
1261 <    double tmpMass = totalMass;
1261 >    RealType tmpMass = totalMass;
1262      Vector3d tmpComVel(comVel);    
1263 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1264 <    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1263 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1264 >    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1265   #endif
1266  
1267      comVel /= totalMass;
# Line 1203 | Line 1274 | namespace oopse {
1274      Molecule* mol;
1275  
1276      Vector3d com(0.0);
1277 <    double totalMass = 0.0;
1277 >    RealType totalMass = 0.0;
1278      
1279      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1280 <      double mass = mol->getMass();
1280 >      RealType mass = mol->getMass();
1281        totalMass += mass;
1282        com += mass * mol->getCom();
1283      }  
1284  
1285   #ifdef IS_MPI
1286 <    double tmpMass = totalMass;
1286 >    RealType tmpMass = totalMass;
1287      Vector3d tmpCom(com);    
1288 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1289 <    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1288 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1289 >    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1290   #endif
1291  
1292      com /= totalMass;
# Line 1239 | Line 1310 | namespace oopse {
1310        Molecule* mol;
1311        
1312      
1313 <      double totalMass = 0.0;
1313 >      RealType totalMass = 0.0;
1314      
1315  
1316        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1317 <         double mass = mol->getMass();
1317 >         RealType mass = mol->getMass();
1318           totalMass += mass;
1319           com += mass * mol->getCom();
1320           comVel += mass * mol->getComVel();          
1321        }  
1322        
1323   #ifdef IS_MPI
1324 <      double tmpMass = totalMass;
1324 >      RealType tmpMass = totalMass;
1325        Vector3d tmpCom(com);  
1326        Vector3d tmpComVel(comVel);
1327 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1328 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1329 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1327 >      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1328 >      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1329 >      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1330   #endif
1331        
1332        com /= totalMass;
# Line 1274 | Line 1345 | namespace oopse {
1345     void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1346        
1347  
1348 <      double xx = 0.0;
1349 <      double yy = 0.0;
1350 <      double zz = 0.0;
1351 <      double xy = 0.0;
1352 <      double xz = 0.0;
1353 <      double yz = 0.0;
1348 >      RealType xx = 0.0;
1349 >      RealType yy = 0.0;
1350 >      RealType zz = 0.0;
1351 >      RealType xy = 0.0;
1352 >      RealType xz = 0.0;
1353 >      RealType yz = 0.0;
1354        Vector3d com(0.0);
1355        Vector3d comVel(0.0);
1356        
# Line 1291 | Line 1362 | namespace oopse {
1362        Vector3d thisq(0.0);
1363        Vector3d thisv(0.0);
1364  
1365 <      double thisMass = 0.0;
1365 >      RealType thisMass = 0.0;
1366      
1367        
1368        
# Line 1329 | Line 1400 | namespace oopse {
1400   #ifdef IS_MPI
1401        Mat3x3d tmpI(inertiaTensor);
1402        Vector3d tmpAngMom;
1403 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1404 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1403 >      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1404 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1405   #endif
1406                
1407        return;
# Line 1351 | Line 1422 | namespace oopse {
1422        Vector3d thisr(0.0);
1423        Vector3d thisp(0.0);
1424        
1425 <      double thisMass;
1425 >      RealType thisMass;
1426        
1427        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1428          thisMass = mol->getMass();
# Line 1364 | Line 1435 | namespace oopse {
1435        
1436   #ifdef IS_MPI
1437        Vector3d tmpAngMom;
1438 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1438 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1439   #endif
1440        
1441        return angularMomentum;
1442     }
1443    
1444 <  
1444 >  StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1445 >    return IOIndexToIntegrableObject.at(index);
1446 >  }
1447 >  
1448 >  void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1449 >    IOIndexToIntegrableObject= v;
1450 >  }
1451 >
1452 > /*
1453 >   void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1454 >      assert( v.size() == nAtoms_ + nRigidBodies_);
1455 >      sdByGlobalIndex_ = v;
1456 >    }
1457 >
1458 >    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1459 >      //assert(index < nAtoms_ + nRigidBodies_);
1460 >      return sdByGlobalIndex_.at(index);
1461 >    }  
1462 > */  
1463   }//end namespace oopse
1464  

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