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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 878 by chrisfen, Wed Feb 1 20:54:46 2006 UTC vs.
Revision 1126 by gezelter, Fri Apr 6 21:53:43 2007 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 >    useAtomicVirial_(true) {
97  
98        MoleculeStamp* molStamp;
99        int nMolWithSameStamp;
# Line 290 | Line 294 | namespace oopse {
294  
295    }
296  
297 +  int SimInfo::getFdf() {
298 + #ifdef IS_MPI
299 +    MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
300 + #else
301 +    fdf_ = fdf_local;
302 + #endif
303 +    return fdf_;
304 +  }
305 +    
306    void SimInfo::calcNdfRaw() {
307      int ndfRaw_local;
308  
# Line 590 | Line 603 | namespace oopse {
603      //setup fortran force field
604      /** @deprecate */    
605      int isError = 0;
606 +    
607 +    setupCutoff();
608      
609      setupElectrostaticSummationMethod( isError );
610      setupSwitchingFunction();
611 +    setupAccumulateBoxDipole();
612  
613      if(isError){
614        sprintf( painCave.errMsg,
# Line 600 | Line 616 | namespace oopse {
616        painCave.isFatal = 1;
617        simError();
618      }
603 –  
604 –    
605 –    setupCutoff();
619  
620      calcNdf();
621      calcNdfRaw();
# Line 652 | Line 665 | namespace oopse {
665      int usePBC = simParams_->getUsePeriodicBoundaryConditions();
666      int useRF;
667      int useSF;
668 +    int useSP;
669 +    int useBoxDipole;
670 +
671      std::string myMethod;
672  
673      // set the useRF logical
674      useRF = 0;
675      useSF = 0;
676 +    useSP = 0;
677  
678  
679      if (simParams_->haveElectrostaticSummationMethod()) {
680        std::string myMethod = simParams_->getElectrostaticSummationMethod();
681        toUpper(myMethod);
682 <      if (myMethod == "REACTION_FIELD") {
683 <        useRF=1;
684 <      } else {
685 <        if (myMethod == "SHIFTED_FORCE") {
686 <          useSF = 1;
687 <        }
682 >      if (myMethod == "REACTION_FIELD"){
683 >        useRF = 1;
684 >      } else if (myMethod == "SHIFTED_FORCE"){
685 >        useSF = 1;
686 >      } else if (myMethod == "SHIFTED_POTENTIAL"){
687 >        useSP = 1;
688        }
689      }
690 +    
691 +    if (simParams_->haveAccumulateBoxDipole())
692 +      if (simParams_->getAccumulateBoxDipole())
693 +        useBoxDipole = 1;
694  
695 +    useAtomicVirial_ = simParams_->getUseAtomicVirial();
696 +
697      //loop over all of the atom types
698      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
699        useLennardJones |= (*i)->isLennardJones();
# Line 740 | Line 763 | namespace oopse {
763      MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
764  
765      temp = useSF;
766 <    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
766 >    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
767  
768 +    temp = useSP;
769 +    MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
770 +
771 +    temp = useBoxDipole;
772 +    MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
773 +
774 +    temp = useAtomicVirial_;
775 +    MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
776 +
777   #endif
778  
779      fInfo_.SIM_uses_PBC = usePBC;    
# Line 759 | Line 791 | namespace oopse {
791      fInfo_.SIM_uses_FLARB = useFLARB;
792      fInfo_.SIM_uses_RF = useRF;
793      fInfo_.SIM_uses_SF = useSF;
794 <
795 <    if( myMethod == "REACTION_FIELD") {
796 <      
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 <
794 >    fInfo_.SIM_uses_SP = useSP;
795 >    fInfo_.SIM_uses_BoxDipole = useBoxDipole;
796 >    fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
797    }
798  
799    void SimInfo::setupFortranSim() {
# Line 790 | Line 810 | namespace oopse {
810      }
811  
812      //calculate mass ratio of cutoff group
813 <    std::vector<double> mfact;
813 >    std::vector<RealType> mfact;
814      SimInfo::MoleculeIterator mi;
815      Molecule* mol;
816      Molecule::CutoffGroupIterator ci;
817      CutoffGroup* cg;
818      Molecule::AtomIterator ai;
819      Atom* atom;
820 <    double totalMass;
820 >    RealType totalMass;
821  
822      //to avoid memory reallocation, reserve enough space for mfact
823      mfact.reserve(getNCutoffGroups());
# Line 858 | Line 878 | namespace oopse {
878               "succesfully sent the simulation information to fortran.\n");
879      MPIcheckPoint();
880   #endif // is_mpi
881 +
882 +    // Setup number of neighbors in neighbor list if present
883 +    if (simParams_->haveNeighborListNeighbors()) {
884 +      int nlistNeighbors = simParams_->getNeighborListNeighbors();
885 +      setNeighbors(&nlistNeighbors);
886 +    }
887 +  
888 +
889    }
890  
891  
# Line 957 | Line 985 | namespace oopse {
985      notifyFortranCutoffPolicy(&cp);
986  
987      // Check the Skin Thickness for neighborlists
988 <    double skin;
988 >    RealType skin;
989      if (simParams_->haveSkinThickness()) {
990        skin = simParams_->getSkinThickness();
991        notifyFortranSkinThickness(&skin);
# Line 976 | Line 1004 | namespace oopse {
1004            rsw_ = 0.85 * rcut_;
1005            sprintf(painCave.errMsg,
1006                    "SimCreator Warning: No value was set for the switchingRadius.\n"
1007 <                  "\tOOPSE will use a default value of 85\% of the cutoffRadius"
1007 >                  "\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1008                    "\tswitchingRadius = %f. for this simulation\n", rsw_);
1009          painCave.isFatal = 0;
1010          simError();
# Line 989 | Line 1017 | namespace oopse {
1017            painCave.isFatal = 0;
1018            simError();
1019          }
1020 <          
1020 >      }
1021 >      
1022        notifyFortranCutoffs(&rcut_, &rsw_);
1023        
1024      } else {
# Line 1046 | Line 1075 | namespace oopse {
1075      int errorOut;
1076      int esm =  NONE;
1077      int sm = UNDAMPED;
1078 <    double alphaVal;
1079 <    double dielectric;
1080 <
1078 >    RealType alphaVal;
1079 >    RealType dielectric;
1080 >    
1081      errorOut = isError;
1053 –    alphaVal = simParams_->getDampingAlpha();
1054 –    dielectric = simParams_->getDielectric();
1082  
1083      if (simParams_->haveElectrostaticSummationMethod()) {
1084        std::string myMethod = simParams_->getElectrostaticSummationMethod();
# Line 1068 | Line 1095 | namespace oopse {
1095              if (myMethod == "SHIFTED_FORCE") {            
1096                esm = SHIFTED_FORCE;
1097              } else {
1098 <              if (myMethod == "REACTION_FIELD") {            
1098 >              if (myMethod == "REACTION_FIELD") {
1099                  esm = REACTION_FIELD;
1100 +                dielectric = simParams_->getDielectric();
1101 +                if (!simParams_->haveDielectric()) {
1102 +                  // throw warning
1103 +                  sprintf( painCave.errMsg,
1104 +                           "SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1105 +                           "\tA default value of %f will be used for the dielectric.\n", dielectric);
1106 +                  painCave.isFatal = 0;
1107 +                  simError();
1108 +                }
1109                } else {
1110                  // throw error        
1111                  sprintf( painCave.errMsg,
# Line 1096 | Line 1132 | namespace oopse {
1132          if (myScreen == "DAMPED") {
1133            sm = DAMPED;
1134            if (!simParams_->haveDampingAlpha()) {
1135 <            //throw error
1135 >            // first set a cutoff dependent alpha value
1136 >            // we assume alpha depends linearly with rcut from 0 to 20.5 ang
1137 >            alphaVal = 0.5125 - rcut_* 0.025;
1138 >            // for values rcut > 20.5, alpha is zero
1139 >            if (alphaVal < 0) alphaVal = 0;
1140 >
1141 >            // throw warning
1142              sprintf( painCave.errMsg,
1143                       "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1144 <                     "\tA default value of %f (1/ang) will be used.\n", alphaVal);
1144 >                     "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1145              painCave.isFatal = 0;
1146              simError();
1147 +          } else {
1148 +            alphaVal = simParams_->getDampingAlpha();
1149            }
1150 +          
1151          } else {
1152            // throw error        
1153            sprintf( painCave.errMsg,
# Line 1151 | Line 1196 | namespace oopse {
1196  
1197    }
1198  
1199 +  void SimInfo::setupAccumulateBoxDipole() {    
1200 +
1201 +    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1202 +    if ( simParams_->haveAccumulateBoxDipole() )
1203 +      if ( simParams_->getAccumulateBoxDipole() ) {
1204 +        setAccumulateBoxDipole();
1205 +        calcBoxDipole_ = true;
1206 +      }
1207 +
1208 +  }
1209 +
1210    void SimInfo::addProperty(GenericData* genData) {
1211      properties_.addProperty(genData);  
1212    }
# Line 1207 | Line 1263 | namespace oopse {
1263      Molecule* mol;
1264  
1265      Vector3d comVel(0.0);
1266 <    double totalMass = 0.0;
1266 >    RealType totalMass = 0.0;
1267      
1268  
1269      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1270 <      double mass = mol->getMass();
1270 >      RealType mass = mol->getMass();
1271        totalMass += mass;
1272        comVel += mass * mol->getComVel();
1273      }  
1274  
1275   #ifdef IS_MPI
1276 <    double tmpMass = totalMass;
1276 >    RealType tmpMass = totalMass;
1277      Vector3d tmpComVel(comVel);    
1278 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1279 <    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1278 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1279 >    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1280   #endif
1281  
1282      comVel /= totalMass;
# Line 1233 | Line 1289 | namespace oopse {
1289      Molecule* mol;
1290  
1291      Vector3d com(0.0);
1292 <    double totalMass = 0.0;
1292 >    RealType totalMass = 0.0;
1293      
1294      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1295 <      double mass = mol->getMass();
1295 >      RealType mass = mol->getMass();
1296        totalMass += mass;
1297        com += mass * mol->getCom();
1298      }  
1299  
1300   #ifdef IS_MPI
1301 <    double tmpMass = totalMass;
1301 >    RealType tmpMass = totalMass;
1302      Vector3d tmpCom(com);    
1303 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1304 <    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1303 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1304 >    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1305   #endif
1306  
1307      com /= totalMass;
# Line 1269 | Line 1325 | namespace oopse {
1325        Molecule* mol;
1326        
1327      
1328 <      double totalMass = 0.0;
1328 >      RealType totalMass = 0.0;
1329      
1330  
1331        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1332 <         double mass = mol->getMass();
1332 >         RealType mass = mol->getMass();
1333           totalMass += mass;
1334           com += mass * mol->getCom();
1335           comVel += mass * mol->getComVel();          
1336        }  
1337        
1338   #ifdef IS_MPI
1339 <      double tmpMass = totalMass;
1339 >      RealType tmpMass = totalMass;
1340        Vector3d tmpCom(com);  
1341        Vector3d tmpComVel(comVel);
1342 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1343 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1344 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1342 >      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1343 >      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1344 >      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1345   #endif
1346        
1347        com /= totalMass;
# Line 1304 | Line 1360 | namespace oopse {
1360     void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1361        
1362  
1363 <      double xx = 0.0;
1364 <      double yy = 0.0;
1365 <      double zz = 0.0;
1366 <      double xy = 0.0;
1367 <      double xz = 0.0;
1368 <      double yz = 0.0;
1363 >      RealType xx = 0.0;
1364 >      RealType yy = 0.0;
1365 >      RealType zz = 0.0;
1366 >      RealType xy = 0.0;
1367 >      RealType xz = 0.0;
1368 >      RealType yz = 0.0;
1369        Vector3d com(0.0);
1370        Vector3d comVel(0.0);
1371        
# Line 1321 | Line 1377 | namespace oopse {
1377        Vector3d thisq(0.0);
1378        Vector3d thisv(0.0);
1379  
1380 <      double thisMass = 0.0;
1380 >      RealType thisMass = 0.0;
1381      
1382        
1383        
# Line 1359 | Line 1415 | namespace oopse {
1415   #ifdef IS_MPI
1416        Mat3x3d tmpI(inertiaTensor);
1417        Vector3d tmpAngMom;
1418 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1419 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1418 >      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1419 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1420   #endif
1421                
1422        return;
# Line 1381 | Line 1437 | namespace oopse {
1437        Vector3d thisr(0.0);
1438        Vector3d thisp(0.0);
1439        
1440 <      double thisMass;
1440 >      RealType thisMass;
1441        
1442        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1443          thisMass = mol->getMass();
# Line 1394 | Line 1450 | namespace oopse {
1450        
1451   #ifdef IS_MPI
1452        Vector3d tmpAngMom;
1453 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1453 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1454   #endif
1455        
1456        return angularMomentum;
1457     }
1458    
1459 <  
1459 >  StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1460 >    return IOIndexToIntegrableObject.at(index);
1461 >  }
1462 >  
1463 >  void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1464 >    IOIndexToIntegrableObject= v;
1465 >  }
1466 >
1467 >  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1468 >     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1469 >     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1470 >     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1471 >  */
1472 >  void SimInfo::getGyrationalVolume(RealType &volume){
1473 >    Mat3x3d intTensor;
1474 >    RealType det;
1475 >    Vector3d dummyAngMom;
1476 >    RealType sysconstants;
1477 >    RealType geomCnst;
1478 >
1479 >    geomCnst = 3.0/2.0;
1480 >    /* Get the inertial tensor and angular momentum for free*/
1481 >    getInertiaTensor(intTensor,dummyAngMom);
1482 >    
1483 >    det = intTensor.determinant();
1484 >    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1485 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1486 >    return;
1487 >  }
1488 >
1489 >  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1490 >    Mat3x3d intTensor;
1491 >    Vector3d dummyAngMom;
1492 >    RealType sysconstants;
1493 >    RealType geomCnst;
1494 >
1495 >    geomCnst = 3.0/2.0;
1496 >    /* Get the inertial tensor and angular momentum for free*/
1497 >    getInertiaTensor(intTensor,dummyAngMom);
1498 >    
1499 >    detI = intTensor.determinant();
1500 >    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1501 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1502 >    return;
1503 >  }
1504 > /*
1505 >   void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1506 >      assert( v.size() == nAtoms_ + nRigidBodies_);
1507 >      sdByGlobalIndex_ = v;
1508 >    }
1509 >
1510 >    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1511 >      //assert(index < nAtoms_ + nRigidBodies_);
1512 >      return sdByGlobalIndex_.at(index);
1513 >    }  
1514 > */  
1515   }//end namespace oopse
1516  

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