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root/OpenMD/trunk/src/brains/SimInfo.cpp
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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 853 by chrisfen, Thu Jan 12 16:47:25 2006 UTC vs.
Revision 1103 by chuckv, Fri Dec 29 20:21:53 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"
60   #include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
61   #include "UseTheForce/doForces_interface.h"
62 + #include "UseTheForce/DarkSide/neighborLists_interface.h"
63   #include "UseTheForce/DarkSide/electrostatic_interface.h"
64   #include "UseTheForce/DarkSide/switcheroo_interface.h"
65   #include "utils/MemoryUtils.hpp"
# Line 66 | Line 68
68   #include "io/ForceFieldOptions.hpp"
69   #include "UseTheForce/ForceField.hpp"
70  
71 +
72   #ifdef IS_MPI
73   #include "UseTheForce/mpiComponentPlan.h"
74   #include "UseTheForce/DarkSide/simParallel_interface.h"
# Line 84 | Line 87 | namespace oopse {
87    
88    SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
89      forceField_(ff), simParams_(simParams),
90 <    ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
90 >    ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
91      nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
92      nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
93      nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
94      nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
95 <    sman_(NULL), fortranInitialized_(false) {
95 >    sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false) {
96  
97        MoleculeStamp* molStamp;
98        int nMolWithSameStamp;
# Line 290 | Line 293 | namespace oopse {
293  
294    }
295  
296 +  int SimInfo::getFdf() {
297 + #ifdef IS_MPI
298 +    MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
299 + #else
300 +    fdf_ = fdf_local;
301 + #endif
302 +    return fdf_;
303 +  }
304 +    
305    void SimInfo::calcNdfRaw() {
306      int ndfRaw_local;
307  
# Line 591 | Line 603 | namespace oopse {
603      /** @deprecate */    
604      int isError = 0;
605      
606 +    setupCutoff();
607 +    
608      setupElectrostaticSummationMethod( isError );
609      setupSwitchingFunction();
610 +    setupAccumulateBoxDipole();
611  
612      if(isError){
613        sprintf( painCave.errMsg,
# Line 600 | Line 615 | namespace oopse {
615        painCave.isFatal = 1;
616        simError();
617      }
603 –  
604 –    
605 –    setupCutoff();
618  
619      calcNdf();
620      calcNdfRaw();
# Line 652 | Line 664 | namespace oopse {
664      int usePBC = simParams_->getUsePeriodicBoundaryConditions();
665      int useRF;
666      int useSF;
667 +    int useSP;
668 +    int useBoxDipole;
669      std::string myMethod;
670  
671      // set the useRF logical
672      useRF = 0;
673      useSF = 0;
674 +    useSP = 0;
675  
676  
677      if (simParams_->haveElectrostaticSummationMethod()) {
678        std::string myMethod = simParams_->getElectrostaticSummationMethod();
679        toUpper(myMethod);
680 <      if (myMethod == "REACTION_FIELD") {
681 <        useRF=1;
682 <      } else {
683 <        if (myMethod == "SHIFTED_FORCE") {
684 <          useSF = 1;
685 <        }
680 >      if (myMethod == "REACTION_FIELD"){
681 >        useRF = 1;
682 >      } else if (myMethod == "SHIFTED_FORCE"){
683 >        useSF = 1;
684 >      } else if (myMethod == "SHIFTED_POTENTIAL"){
685 >        useSP = 1;
686        }
687      }
688 +    
689 +    if (simParams_->haveAccumulateBoxDipole())
690 +      if (simParams_->getAccumulateBoxDipole())
691 +        useBoxDipole = 1;
692  
693      //loop over all of the atom types
694      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
# Line 740 | Line 759 | namespace oopse {
759      MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
760  
761      temp = useSF;
762 <    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
762 >    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
763  
764 +    temp = useSP;
765 +    MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
766 +
767 +    temp = useBoxDipole;
768 +    MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
769 +
770   #endif
771  
772      fInfo_.SIM_uses_PBC = usePBC;    
# Line 759 | Line 784 | namespace oopse {
784      fInfo_.SIM_uses_FLARB = useFLARB;
785      fInfo_.SIM_uses_RF = useRF;
786      fInfo_.SIM_uses_SF = useSF;
787 <
788 <    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 <
787 >    fInfo_.SIM_uses_SP = useSP;
788 >    fInfo_.SIM_uses_BoxDipole = useBoxDipole;
789    }
790  
791    void SimInfo::setupFortranSim() {
# Line 790 | Line 802 | namespace oopse {
802      }
803  
804      //calculate mass ratio of cutoff group
805 <    std::vector<double> mfact;
805 >    std::vector<RealType> mfact;
806      SimInfo::MoleculeIterator mi;
807      Molecule* mol;
808      Molecule::CutoffGroupIterator ci;
809      CutoffGroup* cg;
810      Molecule::AtomIterator ai;
811      Atom* atom;
812 <    double totalMass;
812 >    RealType totalMass;
813  
814      //to avoid memory reallocation, reserve enough space for mfact
815      mfact.reserve(getNCutoffGroups());
# Line 858 | Line 870 | namespace oopse {
870               "succesfully sent the simulation information to fortran.\n");
871      MPIcheckPoint();
872   #endif // is_mpi
873 +
874 +    // Setup number of neighbors in neighbor list if present
875 +    if (simParams_->haveNeighborListNeighbors()) {
876 +      setNeighbors(simParams_->getNeighborListNeighbors());
877 +    }
878 +  
879 +
880    }
881  
882  
# Line 957 | Line 976 | namespace oopse {
976      notifyFortranCutoffPolicy(&cp);
977  
978      // Check the Skin Thickness for neighborlists
979 <    double skin;
979 >    RealType skin;
980      if (simParams_->haveSkinThickness()) {
981        skin = simParams_->getSkinThickness();
982        notifyFortranSkinThickness(&skin);
# Line 969 | Line 988 | namespace oopse {
988        if (simParams_->haveSwitchingRadius()) {
989          rsw_  = simParams_->getSwitchingRadius();
990        } else {
991 <        rsw_ = rcut_;
991 >        if (fInfo_.SIM_uses_Charges |
992 >            fInfo_.SIM_uses_Dipoles |
993 >            fInfo_.SIM_uses_RF) {
994 >          
995 >          rsw_ = 0.85 * rcut_;
996 >          sprintf(painCave.errMsg,
997 >                  "SimCreator Warning: No value was set for the switchingRadius.\n"
998 >                  "\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
999 >                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1000 >        painCave.isFatal = 0;
1001 >        simError();
1002 >        } else {
1003 >          rsw_ = rcut_;
1004 >          sprintf(painCave.errMsg,
1005 >                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1006 >                  "\tOOPSE will use the same value as the cutoffRadius.\n"
1007 >                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1008 >          painCave.isFatal = 0;
1009 >          simError();
1010 >        }
1011        }
1012 +      
1013        notifyFortranCutoffs(&rcut_, &rsw_);
1014        
1015      } else {
# Line 1027 | Line 1066 | namespace oopse {
1066      int errorOut;
1067      int esm =  NONE;
1068      int sm = UNDAMPED;
1069 <    double alphaVal;
1070 <    double dielectric;
1071 <
1069 >    RealType alphaVal;
1070 >    RealType dielectric;
1071 >    
1072      errorOut = isError;
1034 –    alphaVal = simParams_->getDampingAlpha();
1035 –    dielectric = simParams_->getDielectric();
1073  
1074      if (simParams_->haveElectrostaticSummationMethod()) {
1075        std::string myMethod = simParams_->getElectrostaticSummationMethod();
# Line 1049 | Line 1086 | namespace oopse {
1086              if (myMethod == "SHIFTED_FORCE") {            
1087                esm = SHIFTED_FORCE;
1088              } else {
1089 <              if (myMethod == "REACTION_FIELD") {            
1089 >              if (myMethod == "REACTION_FIELD") {
1090                  esm = REACTION_FIELD;
1091 +                dielectric = simParams_->getDielectric();
1092 +                if (!simParams_->haveDielectric()) {
1093 +                  // throw warning
1094 +                  sprintf( painCave.errMsg,
1095 +                           "SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1096 +                           "\tA default value of %f will be used for the dielectric.\n", dielectric);
1097 +                  painCave.isFatal = 0;
1098 +                  simError();
1099 +                }
1100                } else {
1101                  // throw error        
1102                  sprintf( painCave.errMsg,
# Line 1077 | Line 1123 | namespace oopse {
1123          if (myScreen == "DAMPED") {
1124            sm = DAMPED;
1125            if (!simParams_->haveDampingAlpha()) {
1126 <            //throw error
1126 >            // first set a cutoff dependent alpha value
1127 >            // we assume alpha depends linearly with rcut from 0 to 20.5 ang
1128 >            alphaVal = 0.5125 - rcut_* 0.025;
1129 >            // for values rcut > 20.5, alpha is zero
1130 >            if (alphaVal < 0) alphaVal = 0;
1131 >
1132 >            // throw warning
1133              sprintf( painCave.errMsg,
1134                       "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1135 <                     "\tA default value of %f (1/ang) will be used.\n", alphaVal);
1135 >                     "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1136              painCave.isFatal = 0;
1137              simError();
1138 +          } else {
1139 +            alphaVal = simParams_->getDampingAlpha();
1140            }
1141 +          
1142          } else {
1143            // throw error        
1144            sprintf( painCave.errMsg,
# Line 1132 | Line 1187 | namespace oopse {
1187  
1188    }
1189  
1190 +  void SimInfo::setupAccumulateBoxDipole() {    
1191 +
1192 +    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1193 +    if ( simParams_->haveAccumulateBoxDipole() )
1194 +      if ( simParams_->getAccumulateBoxDipole() ) {
1195 +        setAccumulateBoxDipole();
1196 +        calcBoxDipole_ = true;
1197 +      }
1198 +
1199 +  }
1200 +
1201    void SimInfo::addProperty(GenericData* genData) {
1202      properties_.addProperty(genData);  
1203    }
# Line 1188 | Line 1254 | namespace oopse {
1254      Molecule* mol;
1255  
1256      Vector3d comVel(0.0);
1257 <    double totalMass = 0.0;
1257 >    RealType totalMass = 0.0;
1258      
1259  
1260      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1261 <      double mass = mol->getMass();
1261 >      RealType mass = mol->getMass();
1262        totalMass += mass;
1263        comVel += mass * mol->getComVel();
1264      }  
1265  
1266   #ifdef IS_MPI
1267 <    double tmpMass = totalMass;
1267 >    RealType tmpMass = totalMass;
1268      Vector3d tmpComVel(comVel);    
1269 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1270 <    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1269 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1270 >    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1271   #endif
1272  
1273      comVel /= totalMass;
# Line 1214 | Line 1280 | namespace oopse {
1280      Molecule* mol;
1281  
1282      Vector3d com(0.0);
1283 <    double totalMass = 0.0;
1283 >    RealType totalMass = 0.0;
1284      
1285      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1286 <      double mass = mol->getMass();
1286 >      RealType mass = mol->getMass();
1287        totalMass += mass;
1288        com += mass * mol->getCom();
1289      }  
1290  
1291   #ifdef IS_MPI
1292 <    double tmpMass = totalMass;
1292 >    RealType tmpMass = totalMass;
1293      Vector3d tmpCom(com);    
1294 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1295 <    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1294 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1295 >    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1296   #endif
1297  
1298      com /= totalMass;
# Line 1250 | Line 1316 | namespace oopse {
1316        Molecule* mol;
1317        
1318      
1319 <      double totalMass = 0.0;
1319 >      RealType totalMass = 0.0;
1320      
1321  
1322        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1323 <         double mass = mol->getMass();
1323 >         RealType mass = mol->getMass();
1324           totalMass += mass;
1325           com += mass * mol->getCom();
1326           comVel += mass * mol->getComVel();          
1327        }  
1328        
1329   #ifdef IS_MPI
1330 <      double tmpMass = totalMass;
1330 >      RealType tmpMass = totalMass;
1331        Vector3d tmpCom(com);  
1332        Vector3d tmpComVel(comVel);
1333 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1334 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1335 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1333 >      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1334 >      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1335 >      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1336   #endif
1337        
1338        com /= totalMass;
# Line 1285 | Line 1351 | namespace oopse {
1351     void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1352        
1353  
1354 <      double xx = 0.0;
1355 <      double yy = 0.0;
1356 <      double zz = 0.0;
1357 <      double xy = 0.0;
1358 <      double xz = 0.0;
1359 <      double yz = 0.0;
1354 >      RealType xx = 0.0;
1355 >      RealType yy = 0.0;
1356 >      RealType zz = 0.0;
1357 >      RealType xy = 0.0;
1358 >      RealType xz = 0.0;
1359 >      RealType yz = 0.0;
1360        Vector3d com(0.0);
1361        Vector3d comVel(0.0);
1362        
# Line 1302 | Line 1368 | namespace oopse {
1368        Vector3d thisq(0.0);
1369        Vector3d thisv(0.0);
1370  
1371 <      double thisMass = 0.0;
1371 >      RealType thisMass = 0.0;
1372      
1373        
1374        
# Line 1340 | Line 1406 | namespace oopse {
1406   #ifdef IS_MPI
1407        Mat3x3d tmpI(inertiaTensor);
1408        Vector3d tmpAngMom;
1409 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1410 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1409 >      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1410 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1411   #endif
1412                
1413        return;
# Line 1362 | Line 1428 | namespace oopse {
1428        Vector3d thisr(0.0);
1429        Vector3d thisp(0.0);
1430        
1431 <      double thisMass;
1431 >      RealType thisMass;
1432        
1433        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1434          thisMass = mol->getMass();
# Line 1375 | Line 1441 | namespace oopse {
1441        
1442   #ifdef IS_MPI
1443        Vector3d tmpAngMom;
1444 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1444 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1445   #endif
1446        
1447        return angularMomentum;
1448     }
1449    
1450 <  
1450 >  StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1451 >    return IOIndexToIntegrableObject.at(index);
1452 >  }
1453 >  
1454 >  void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1455 >    IOIndexToIntegrableObject= v;
1456 >  }
1457 >
1458 >  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1459 >     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1460 >     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1461 >     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1462 >  */
1463 >  void SimInfo::getGyrationalVolume(RealType &volume){
1464 >    Mat3x3d intTensor;
1465 >    RealType det;
1466 >    Vector3d dummyAngMom;
1467 >    RealType sysconstants;
1468 >    RealType geomCnst;
1469 >
1470 >    geomCnst = 3.0/2.0;
1471 >    /* Get the inertial tensor and angular momentum for free*/
1472 >    getInertiaTensor(intTensor,dummyAngMom);
1473 >    
1474 >    det = intTensor.determinant();
1475 >    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1476 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1477 >    return;
1478 >  }
1479 >
1480 >  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1481 >    Mat3x3d intTensor;
1482 >    Vector3d dummyAngMom;
1483 >    RealType sysconstants;
1484 >    RealType geomCnst;
1485 >
1486 >    geomCnst = 3.0/2.0;
1487 >    /* Get the inertial tensor and angular momentum for free*/
1488 >    getInertiaTensor(intTensor,dummyAngMom);
1489 >    
1490 >    detI = intTensor.determinant();
1491 >    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1492 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1493 >    return;
1494 >  }
1495 > /*
1496 >   void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1497 >      assert( v.size() == nAtoms_ + nRigidBodies_);
1498 >      sdByGlobalIndex_ = v;
1499 >    }
1500 >
1501 >    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1502 >      //assert(index < nAtoms_ + nRigidBodies_);
1503 >      return sdByGlobalIndex_.at(index);
1504 >    }  
1505 > */  
1506   }//end namespace oopse
1507  

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