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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 809 by gezelter, Mon Dec 12 19:32:50 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 82 | Line 84 | namespace oopse {
84    
85    SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
86      forceField_(ff), simParams_(simParams),
87 <    ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
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  
94        MoleculeStamp* molStamp;
95        int nMolWithSameStamp;
# Line 288 | 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 591 | Line 602 | namespace oopse {
602      
603      setupElectrostaticSummationMethod( isError );
604      setupSwitchingFunction();
605 +    setupAccumulateBoxDipole();
606  
607      if(isError){
608        sprintf( painCave.errMsg,
# 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  
# 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;
1074 >    RealType alphaVal;
1075 >    RealType dielectric;
1076  
1077      errorOut = isError;
1078      alphaVal = simParams_->getDampingAlpha();
# Line 1087 | Line 1142 | namespace oopse {
1142      }
1143      
1144      // let's pass some summation method variables to fortran
1145 <    setElectrostaticSumMethod( &esm );
1145 >    setElectrostaticSummationMethod( &esm );
1146      setFortranElectrostaticMethod( &esm );
1147      setScreeningMethod( &sm );
1148      setDampingAlpha( &alphaVal );
# Line 1121 | 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 1177 | 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 1203 | 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 1239 | 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 1274 | 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 1291 | 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 1329 | 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 1351 | 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 1364 | 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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