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root/OpenMD/trunk/src/brains/SimInfo.cpp
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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 998 by chrisfen, Mon Jul 3 13:18:43 2006 UTC vs.
Revision 1241 by gezelter, Fri Apr 25 15:14:47 2008 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 89 | Line 92 | namespace oopse {
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), calcBoxDipole_(false) {
95 >    sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false),
96 >    useAtomicVirial_(true) {
97  
98        MoleculeStamp* molStamp;
99        int nMolWithSameStamp;
# Line 152 | Line 156 | namespace oopse {
156                                                  + nGlobalRigidBodies_;
157    
158        nGlobalMols_ = molStampIds_.size();
155 –
156 – #ifdef IS_MPI    
159        molToProcMap_.resize(nGlobalMols_);
158 – #endif
159 –
160      }
161  
162    SimInfo::~SimInfo() {
# Line 600 | Line 600 | namespace oopse {
600      /** @deprecate */    
601      int isError = 0;
602      
603 +    setupCutoff();
604 +    
605      setupElectrostaticSummationMethod( isError );
606      setupSwitchingFunction();
607      setupAccumulateBoxDipole();
# Line 610 | Line 612 | namespace oopse {
612        painCave.isFatal = 1;
613        simError();
614      }
613 –  
614 –    
615 –    setupCutoff();
615  
616      calcNdf();
617      calcNdfRaw();
# Line 664 | Line 663 | namespace oopse {
663      int useSF;
664      int useSP;
665      int useBoxDipole;
666 +
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;
679 >        useRF = 1;
680        } else if (myMethod == "SHIFTED_FORCE"){
681          useSF = 1;
682        } else if (myMethod == "SHIFTED_POTENTIAL"){
# Line 687 | Line 688 | namespace oopse {
688        if (simParams_->getAccumulateBoxDipole())
689          useBoxDipole = 1;
690  
691 +    useAtomicVirial_ = simParams_->getUseAtomicVirial();
692 +
693      //loop over all of the atom types
694      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
695        useLennardJones |= (*i)->isLennardJones();
# Line 764 | Line 767 | namespace oopse {
767      temp = useBoxDipole;
768      MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
769  
770 +    temp = useAtomicVirial_;
771 +    MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
772 +
773   #endif
774  
775      fInfo_.SIM_uses_PBC = usePBC;    
# Line 783 | Line 789 | namespace oopse {
789      fInfo_.SIM_uses_SF = useSF;
790      fInfo_.SIM_uses_SP = useSP;
791      fInfo_.SIM_uses_BoxDipole = useBoxDipole;
792 <
787 <    if( myMethod == "REACTION_FIELD") {
788 <      
789 <      if (simParams_->haveDielectric()) {
790 <        fInfo_.dielect = simParams_->getDielectric();
791 <      } else {
792 <        sprintf(painCave.errMsg,
793 <                "SimSetup Error: No Dielectric constant was set.\n"
794 <                "\tYou are trying to use Reaction Field without"
795 <                "\tsetting a dielectric constant!\n");
796 <        painCave.isFatal = 1;
797 <        simError();
798 <      }      
799 <    }
800 <
792 >    fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
793    }
794  
795    void SimInfo::setupFortranSim() {
# Line 864 | Line 856 | namespace oopse {
856      int nGlobalExcludes = 0;
857      int* globalExcludes = NULL;
858      int* excludeList = exclude_.getExcludeList();
859 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
860 <                   &nGlobalExcludes, globalExcludes, &molMembershipArray[0],
861 <                   &mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
862 <
859 >    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
860 >                   &nExclude, excludeList , &nGlobalExcludes, globalExcludes,
861 >                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
862 >                   &fortranGlobalGroupMembership[0], &isError);
863 >    
864      if( isError ){
865 <
865 >      
866        sprintf( painCave.errMsg,
867                 "There was an error setting the simulation information in fortran.\n" );
868        painCave.isFatal = 1;
869        painCave.severity = OOPSE_ERROR;
870        simError();
871      }
872 <
873 < #ifdef IS_MPI
872 >    
873 >    
874      sprintf( checkPointMsg,
875               "succesfully sent the simulation information to fortran.\n");
876 <    MPIcheckPoint();
877 < #endif // is_mpi
876 >    
877 >    errorCheckPoint();
878 >    
879 >    // Setup number of neighbors in neighbor list if present
880 >    if (simParams_->haveNeighborListNeighbors()) {
881 >      int nlistNeighbors = simParams_->getNeighborListNeighbors();
882 >      setNeighbors(&nlistNeighbors);
883 >    }
884 >  
885 >
886    }
887  
888  
888 – #ifdef IS_MPI
889    void SimInfo::setupFortranParallel() {
890 <    
890 > #ifdef IS_MPI    
891      //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
892      std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
893      std::vector<int> localToGlobalCutoffGroupIndex;
# Line 937 | Line 937 | namespace oopse {
937      }
938  
939      sprintf(checkPointMsg, " mpiRefresh successful.\n");
940 <    MPIcheckPoint();
940 >    errorCheckPoint();
941  
942 <
942 > #endif
943    }
944  
945 – #endif
946 –
945    void SimInfo::setupCutoff() {          
946      
947      ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
# Line 951 | Line 949 | namespace oopse {
949      // Check the cutoff policy
950      int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
951  
952 +    // Set LJ shifting bools to false
953 +    ljsp_ = false;
954 +    ljsf_ = false;
955 +
956      std::string myPolicy;
957      if (forceFieldOptions_.haveCutoffPolicy()){
958        myPolicy = forceFieldOptions_.getCutoffPolicy();
# Line 1014 | Line 1016 | namespace oopse {
1016            simError();
1017          }
1018        }
1019 +
1020 +      if (simParams_->haveElectrostaticSummationMethod()) {
1021 +        std::string myMethod = simParams_->getElectrostaticSummationMethod();
1022 +        toUpper(myMethod);
1023 +        
1024 +        if (myMethod == "SHIFTED_POTENTIAL") {
1025 +          ljsp_ = true;
1026 +        } else if (myMethod == "SHIFTED_FORCE") {
1027 +          ljsf_ = true;
1028 +        }
1029 +      }
1030 +      notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1031        
1018 –      notifyFortranCutoffs(&rcut_, &rsw_);
1019 –      
1032      } else {
1033        
1034        // For electrostatic atoms, we'll assume a large safe value:
# Line 1032 | Line 1044 | namespace oopse {
1044          if (simParams_->haveElectrostaticSummationMethod()) {
1045            std::string myMethod = simParams_->getElectrostaticSummationMethod();
1046            toUpper(myMethod);
1047 <          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1047 >      
1048 >      // For the time being, we're tethering the LJ shifted behavior to the
1049 >      // electrostaticSummationMethod keyword options
1050 >          if (myMethod == "SHIFTED_POTENTIAL") {
1051 >            ljsp_ = true;
1052 >          } else if (myMethod == "SHIFTED_FORCE") {
1053 >            ljsf_ = true;
1054 >          }
1055 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1056              if (simParams_->haveSwitchingRadius()){
1057                sprintf(painCave.errMsg,
1058                        "SimInfo Warning: A value was set for the switchingRadius\n"
# Line 1055 | Line 1075 | namespace oopse {
1075            simError();
1076            rsw_ = 0.85 * rcut_;
1077          }
1078 <        notifyFortranCutoffs(&rcut_, &rsw_);
1078 >
1079 >        notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1080 >
1081        } else {
1082          // We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1083          // We'll punt and let fortran figure out the cutoffs later.
# Line 1073 | Line 1095 | namespace oopse {
1095      int sm = UNDAMPED;
1096      RealType alphaVal;
1097      RealType dielectric;
1098 <
1098 >    
1099      errorOut = isError;
1078 –    alphaVal = simParams_->getDampingAlpha();
1079 –    dielectric = simParams_->getDielectric();
1100  
1101      if (simParams_->haveElectrostaticSummationMethod()) {
1102        std::string myMethod = simParams_->getElectrostaticSummationMethod();
# Line 1093 | Line 1113 | namespace oopse {
1113              if (myMethod == "SHIFTED_FORCE") {            
1114                esm = SHIFTED_FORCE;
1115              } else {
1116 <              if (myMethod == "REACTION_FIELD") {            
1116 >              if (myMethod == "REACTION_FIELD") {
1117                  esm = REACTION_FIELD;
1118 +                dielectric = simParams_->getDielectric();
1119 +                if (!simParams_->haveDielectric()) {
1120 +                  // throw warning
1121 +                  sprintf( painCave.errMsg,
1122 +                           "SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1123 +                           "\tA default value of %f will be used for the dielectric.\n", dielectric);
1124 +                  painCave.isFatal = 0;
1125 +                  simError();
1126 +                }
1127                } else {
1128                  // throw error        
1129                  sprintf( painCave.errMsg,
# Line 1121 | Line 1150 | namespace oopse {
1150          if (myScreen == "DAMPED") {
1151            sm = DAMPED;
1152            if (!simParams_->haveDampingAlpha()) {
1153 <            //throw error
1153 >            // first set a cutoff dependent alpha value
1154 >            // we assume alpha depends linearly with rcut from 0 to 20.5 ang
1155 >            alphaVal = 0.5125 - rcut_* 0.025;
1156 >            // for values rcut > 20.5, alpha is zero
1157 >            if (alphaVal < 0) alphaVal = 0;
1158 >
1159 >            // throw warning
1160              sprintf( painCave.errMsg,
1161                       "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1162 <                     "\tA default value of %f (1/ang) will be used.\n", alphaVal);
1162 >                     "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1163              painCave.isFatal = 0;
1164              simError();
1165 +          } else {
1166 +            alphaVal = simParams_->getDampingAlpha();
1167            }
1168 +          
1169          } else {
1170            // throw error        
1171            sprintf( painCave.errMsg,
# Line 1436 | Line 1474 | namespace oopse {
1474        return angularMomentum;
1475     }
1476    
1477 <  
1477 >  StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1478 >    return IOIndexToIntegrableObject.at(index);
1479 >  }
1480 >  
1481 >  void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1482 >    IOIndexToIntegrableObject= v;
1483 >  }
1484 >
1485 >  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1486 >     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1487 >     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1488 >     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1489 >  */
1490 >  void SimInfo::getGyrationalVolume(RealType &volume){
1491 >    Mat3x3d intTensor;
1492 >    RealType det;
1493 >    Vector3d dummyAngMom;
1494 >    RealType sysconstants;
1495 >    RealType geomCnst;
1496 >
1497 >    geomCnst = 3.0/2.0;
1498 >    /* Get the inertial tensor and angular momentum for free*/
1499 >    getInertiaTensor(intTensor,dummyAngMom);
1500 >    
1501 >    det = intTensor.determinant();
1502 >    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1503 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1504 >    return;
1505 >  }
1506 >
1507 >  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1508 >    Mat3x3d intTensor;
1509 >    Vector3d dummyAngMom;
1510 >    RealType sysconstants;
1511 >    RealType geomCnst;
1512 >
1513 >    geomCnst = 3.0/2.0;
1514 >    /* Get the inertial tensor and angular momentum for free*/
1515 >    getInertiaTensor(intTensor,dummyAngMom);
1516 >    
1517 >    detI = intTensor.determinant();
1518 >    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1519 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1520 >    return;
1521 >  }
1522 > /*
1523 >   void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1524 >      assert( v.size() == nAtoms_ + nRigidBodies_);
1525 >      sdByGlobalIndex_ = v;
1526 >    }
1527 >
1528 >    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1529 >      //assert(index < nAtoms_ + nRigidBodies_);
1530 >      return sdByGlobalIndex_.at(index);
1531 >    }  
1532 > */  
1533   }//end namespace oopse
1534  

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