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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 998 by chrisfen, Mon Jul 3 13:18:43 2006 UTC vs.
Revision 1277 by gezelter, Mon Jul 14 12:35:58 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 87 | Line 90 | namespace oopse {
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), calcBoxDipole_(false) {
93 >    nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
94 >    nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
95 >    nConstraints_(0), sman_(NULL), fortranInitialized_(false),
96 >    calcBoxDipole_(false), useAtomicVirial_(true) {
97  
98 +
99        MoleculeStamp* molStamp;
100        int nMolWithSameStamp;
101        int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
# Line 98 | Line 103 | namespace oopse {
103        CutoffGroupStamp* cgStamp;    
104        RigidBodyStamp* rbStamp;
105        int nRigidAtoms = 0;
106 +
107        std::vector<Component*> components = simParams->getComponents();
108        
109        for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
# Line 152 | Line 158 | namespace oopse {
158                                                  + nGlobalRigidBodies_;
159    
160        nGlobalMols_ = molStampIds_.size();
155 –
156 – #ifdef IS_MPI    
161        molToProcMap_.resize(nGlobalMols_);
158 – #endif
159 –
162      }
163  
164    SimInfo::~SimInfo() {
# Line 194 | Line 196 | namespace oopse {
196        nBonds_ += mol->getNBonds();
197        nBends_ += mol->getNBends();
198        nTorsions_ += mol->getNTorsions();
199 +      nInversions_ += mol->getNInversions();
200        nRigidBodies_ += mol->getNRigidBodies();
201        nIntegrableObjects_ += mol->getNIntegrableObjects();
202        nCutoffGroups_ += mol->getNCutoffGroups();
# Line 219 | Line 222 | namespace oopse {
222        nBonds_ -= mol->getNBonds();
223        nBends_ -= mol->getNBends();
224        nTorsions_ -= mol->getNTorsions();
225 +      nInversions_ -= mol->getNInversions();
226        nRigidBodies_ -= mol->getNRigidBodies();
227        nIntegrableObjects_ -= mol->getNIntegrableObjects();
228        nCutoffGroups_ -= mol->getNCutoffGroups();
# Line 354 | Line 358 | namespace oopse {
358      std::vector<Bond*>::iterator bondIter;
359      std::vector<Bend*>::iterator bendIter;
360      std::vector<Torsion*>::iterator torsionIter;
361 +    std::vector<Inversion*>::iterator inversionIter;
362      Bond* bond;
363      Bend* bend;
364      Torsion* torsion;
365 +    Inversion* inversion;
366      int a;
367      int b;
368      int c;
# Line 449 | Line 455 | namespace oopse {
455        */
456      }
457  
458 +    for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
459 +         inversion = mol->nextInversion(inversionIter)) {
460 +      a = inversion->getAtomA()->getGlobalIndex();
461 +      b = inversion->getAtomB()->getGlobalIndex();        
462 +      c = inversion->getAtomC()->getGlobalIndex();        
463 +      d = inversion->getAtomD()->getGlobalIndex();        
464 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
465 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
466 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
467 +      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
468 +
469 +      exclude_.addPairs(rigidSetA, rigidSetB);
470 +      exclude_.addPairs(rigidSetA, rigidSetC);
471 +      exclude_.addPairs(rigidSetA, rigidSetD);
472 +      exclude_.addPairs(rigidSetB, rigidSetC);
473 +      exclude_.addPairs(rigidSetB, rigidSetD);
474 +      exclude_.addPairs(rigidSetC, rigidSetD);
475 +
476 +      /*
477 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
478 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
479 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
480 +      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
481 +      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
482 +      exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
483 +        
484 +      
485 +      exclude_.addPair(a, b);
486 +      exclude_.addPair(a, c);
487 +      exclude_.addPair(a, d);
488 +      exclude_.addPair(b, c);
489 +      exclude_.addPair(b, d);
490 +      exclude_.addPair(c, d);        
491 +      */
492 +    }
493 +
494      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
495        std::vector<Atom*> atoms = rb->getAtoms();
496        for (int i = 0; i < atoms.size() -1 ; ++i) {
# Line 466 | Line 508 | namespace oopse {
508      std::vector<Bond*>::iterator bondIter;
509      std::vector<Bend*>::iterator bendIter;
510      std::vector<Torsion*>::iterator torsionIter;
511 +    std::vector<Inversion*>::iterator inversionIter;
512      Bond* bond;
513      Bend* bend;
514      Torsion* torsion;
515 +    Inversion* inversion;
516      int a;
517      int b;
518      int c;
# Line 562 | Line 606 | namespace oopse {
606        */
607      }
608  
609 +    for (inversion= mol->beginInversion(inversionIter); inversion != NULL; inversion = mol->nextInversion(inversionIter)) {
610 +      a = inversion->getAtomA()->getGlobalIndex();
611 +      b = inversion->getAtomB()->getGlobalIndex();        
612 +      c = inversion->getAtomC()->getGlobalIndex();        
613 +      d = inversion->getAtomD()->getGlobalIndex();        
614 +
615 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
616 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
617 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
618 +      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
619 +
620 +      exclude_.removePairs(rigidSetA, rigidSetB);
621 +      exclude_.removePairs(rigidSetA, rigidSetC);
622 +      exclude_.removePairs(rigidSetA, rigidSetD);
623 +      exclude_.removePairs(rigidSetB, rigidSetC);
624 +      exclude_.removePairs(rigidSetB, rigidSetD);
625 +      exclude_.removePairs(rigidSetC, rigidSetD);
626 +
627 +      /*
628 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
629 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
630 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
631 +      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
632 +      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
633 +      exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
634 +
635 +      
636 +      exclude_.removePair(a, b);
637 +      exclude_.removePair(a, c);
638 +      exclude_.removePair(a, d);
639 +      exclude_.removePair(b, c);
640 +      exclude_.removePair(b, d);
641 +      exclude_.removePair(c, d);        
642 +      */
643 +    }
644 +
645      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
646        std::vector<Atom*> atoms = rb->getAtoms();
647        for (int i = 0; i < atoms.size() -1 ; ++i) {
# Line 600 | Line 680 | namespace oopse {
680      /** @deprecate */    
681      int isError = 0;
682      
683 +    setupCutoff();
684 +    
685      setupElectrostaticSummationMethod( isError );
686      setupSwitchingFunction();
687      setupAccumulateBoxDipole();
# Line 610 | Line 692 | namespace oopse {
692        painCave.isFatal = 1;
693        simError();
694      }
613 –  
614 –    
615 –    setupCutoff();
695  
696      calcNdf();
697      calcNdfRaw();
# Line 664 | Line 743 | namespace oopse {
743      int useSF;
744      int useSP;
745      int useBoxDipole;
746 +
747      std::string myMethod;
748  
749      // set the useRF logical
750      useRF = 0;
751      useSF = 0;
752 +    useSP = 0;
753  
754  
755      if (simParams_->haveElectrostaticSummationMethod()) {
756        std::string myMethod = simParams_->getElectrostaticSummationMethod();
757        toUpper(myMethod);
758        if (myMethod == "REACTION_FIELD"){
759 <        useRF=1;
759 >        useRF = 1;
760        } else if (myMethod == "SHIFTED_FORCE"){
761          useSF = 1;
762        } else if (myMethod == "SHIFTED_POTENTIAL"){
# Line 687 | Line 768 | namespace oopse {
768        if (simParams_->getAccumulateBoxDipole())
769          useBoxDipole = 1;
770  
771 +    useAtomicVirial_ = simParams_->getUseAtomicVirial();
772 +
773      //loop over all of the atom types
774      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
775        useLennardJones |= (*i)->isLennardJones();
# Line 764 | Line 847 | namespace oopse {
847      temp = useBoxDipole;
848      MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
849  
850 +    temp = useAtomicVirial_;
851 +    MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
852 +
853   #endif
854  
855      fInfo_.SIM_uses_PBC = usePBC;    
# Line 783 | Line 869 | namespace oopse {
869      fInfo_.SIM_uses_SF = useSF;
870      fInfo_.SIM_uses_SP = useSP;
871      fInfo_.SIM_uses_BoxDipole = useBoxDipole;
872 <
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 <
872 >    fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
873    }
874  
875    void SimInfo::setupFortranSim() {
# Line 864 | Line 936 | namespace oopse {
936      int nGlobalExcludes = 0;
937      int* globalExcludes = NULL;
938      int* excludeList = exclude_.getExcludeList();
939 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
940 <                   &nGlobalExcludes, globalExcludes, &molMembershipArray[0],
941 <                   &mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
942 <
939 >    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
940 >                   &nExclude, excludeList , &nGlobalExcludes, globalExcludes,
941 >                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
942 >                   &fortranGlobalGroupMembership[0], &isError);
943 >    
944      if( isError ){
945 <
945 >      
946        sprintf( painCave.errMsg,
947                 "There was an error setting the simulation information in fortran.\n" );
948        painCave.isFatal = 1;
949        painCave.severity = OOPSE_ERROR;
950        simError();
951      }
952 <
953 < #ifdef IS_MPI
952 >    
953 >    
954      sprintf( checkPointMsg,
955               "succesfully sent the simulation information to fortran.\n");
956 <    MPIcheckPoint();
957 < #endif // is_mpi
956 >    
957 >    errorCheckPoint();
958 >    
959 >    // Setup number of neighbors in neighbor list if present
960 >    if (simParams_->haveNeighborListNeighbors()) {
961 >      int nlistNeighbors = simParams_->getNeighborListNeighbors();
962 >      setNeighbors(&nlistNeighbors);
963 >    }
964 >  
965 >
966    }
967  
968  
888 – #ifdef IS_MPI
969    void SimInfo::setupFortranParallel() {
970 <    
970 > #ifdef IS_MPI    
971      //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
972      std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
973      std::vector<int> localToGlobalCutoffGroupIndex;
# Line 937 | Line 1017 | namespace oopse {
1017      }
1018  
1019      sprintf(checkPointMsg, " mpiRefresh successful.\n");
1020 <    MPIcheckPoint();
1020 >    errorCheckPoint();
1021  
1022 <
1022 > #endif
1023    }
1024  
945 – #endif
946 –
1025    void SimInfo::setupCutoff() {          
1026      
1027      ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
# Line 951 | Line 1029 | namespace oopse {
1029      // Check the cutoff policy
1030      int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1031  
1032 +    // Set LJ shifting bools to false
1033 +    ljsp_ = false;
1034 +    ljsf_ = false;
1035 +
1036      std::string myPolicy;
1037      if (forceFieldOptions_.haveCutoffPolicy()){
1038        myPolicy = forceFieldOptions_.getCutoffPolicy();
# Line 1014 | Line 1096 | namespace oopse {
1096            simError();
1097          }
1098        }
1099 <      
1100 <      notifyFortranCutoffs(&rcut_, &rsw_);
1099 >
1100 >      if (simParams_->haveElectrostaticSummationMethod()) {
1101 >        std::string myMethod = simParams_->getElectrostaticSummationMethod();
1102 >        toUpper(myMethod);
1103 >        
1104 >        if (myMethod == "SHIFTED_POTENTIAL") {
1105 >          ljsp_ = true;
1106 >        } else if (myMethod == "SHIFTED_FORCE") {
1107 >          ljsf_ = true;
1108 >        }
1109 >      }
1110 >      notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1111        
1112      } else {
1113        
# Line 1032 | Line 1124 | namespace oopse {
1124          if (simParams_->haveElectrostaticSummationMethod()) {
1125            std::string myMethod = simParams_->getElectrostaticSummationMethod();
1126            toUpper(myMethod);
1127 <          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1127 >      
1128 >      // For the time being, we're tethering the LJ shifted behavior to the
1129 >      // electrostaticSummationMethod keyword options
1130 >          if (myMethod == "SHIFTED_POTENTIAL") {
1131 >            ljsp_ = true;
1132 >          } else if (myMethod == "SHIFTED_FORCE") {
1133 >            ljsf_ = true;
1134 >          }
1135 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1136              if (simParams_->haveSwitchingRadius()){
1137                sprintf(painCave.errMsg,
1138                        "SimInfo Warning: A value was set for the switchingRadius\n"
# Line 1055 | Line 1155 | namespace oopse {
1155            simError();
1156            rsw_ = 0.85 * rcut_;
1157          }
1158 <        notifyFortranCutoffs(&rcut_, &rsw_);
1158 >
1159 >        notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1160 >
1161        } else {
1162          // We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1163          // We'll punt and let fortran figure out the cutoffs later.
# Line 1073 | Line 1175 | namespace oopse {
1175      int sm = UNDAMPED;
1176      RealType alphaVal;
1177      RealType dielectric;
1178 <
1178 >    
1179      errorOut = isError;
1078 –    alphaVal = simParams_->getDampingAlpha();
1079 –    dielectric = simParams_->getDielectric();
1180  
1181      if (simParams_->haveElectrostaticSummationMethod()) {
1182        std::string myMethod = simParams_->getElectrostaticSummationMethod();
# Line 1093 | Line 1193 | namespace oopse {
1193              if (myMethod == "SHIFTED_FORCE") {            
1194                esm = SHIFTED_FORCE;
1195              } else {
1196 <              if (myMethod == "REACTION_FIELD") {            
1196 >              if (myMethod == "REACTION_FIELD") {
1197                  esm = REACTION_FIELD;
1198 +                dielectric = simParams_->getDielectric();
1199 +                if (!simParams_->haveDielectric()) {
1200 +                  // throw warning
1201 +                  sprintf( painCave.errMsg,
1202 +                           "SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1203 +                           "\tA default value of %f will be used for the dielectric.\n", dielectric);
1204 +                  painCave.isFatal = 0;
1205 +                  simError();
1206 +                }
1207                } else {
1208                  // throw error        
1209                  sprintf( painCave.errMsg,
# Line 1121 | Line 1230 | namespace oopse {
1230          if (myScreen == "DAMPED") {
1231            sm = DAMPED;
1232            if (!simParams_->haveDampingAlpha()) {
1233 <            //throw error
1233 >            // first set a cutoff dependent alpha value
1234 >            // we assume alpha depends linearly with rcut from 0 to 20.5 ang
1235 >            alphaVal = 0.5125 - rcut_* 0.025;
1236 >            // for values rcut > 20.5, alpha is zero
1237 >            if (alphaVal < 0) alphaVal = 0;
1238 >
1239 >            // throw warning
1240              sprintf( painCave.errMsg,
1241                       "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1242 <                     "\tA default value of %f (1/ang) will be used.\n", alphaVal);
1242 >                     "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1243              painCave.isFatal = 0;
1244              simError();
1245 +          } else {
1246 +            alphaVal = simParams_->getDampingAlpha();
1247            }
1248 +          
1249          } else {
1250            // throw error        
1251            sprintf( painCave.errMsg,
# Line 1436 | Line 1554 | namespace oopse {
1554        return angularMomentum;
1555     }
1556    
1557 <  
1557 >  StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1558 >    return IOIndexToIntegrableObject.at(index);
1559 >  }
1560 >  
1561 >  void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1562 >    IOIndexToIntegrableObject= v;
1563 >  }
1564 >
1565 >  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1566 >     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1567 >     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1568 >     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1569 >  */
1570 >  void SimInfo::getGyrationalVolume(RealType &volume){
1571 >    Mat3x3d intTensor;
1572 >    RealType det;
1573 >    Vector3d dummyAngMom;
1574 >    RealType sysconstants;
1575 >    RealType geomCnst;
1576 >
1577 >    geomCnst = 3.0/2.0;
1578 >    /* Get the inertial tensor and angular momentum for free*/
1579 >    getInertiaTensor(intTensor,dummyAngMom);
1580 >    
1581 >    det = intTensor.determinant();
1582 >    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1583 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1584 >    return;
1585 >  }
1586 >
1587 >  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1588 >    Mat3x3d intTensor;
1589 >    Vector3d dummyAngMom;
1590 >    RealType sysconstants;
1591 >    RealType geomCnst;
1592 >
1593 >    geomCnst = 3.0/2.0;
1594 >    /* Get the inertial tensor and angular momentum for free*/
1595 >    getInertiaTensor(intTensor,dummyAngMom);
1596 >    
1597 >    detI = intTensor.determinant();
1598 >    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1599 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1600 >    return;
1601 >  }
1602 > /*
1603 >   void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1604 >      assert( v.size() == nAtoms_ + nRigidBodies_);
1605 >      sdByGlobalIndex_ = v;
1606 >    }
1607 >
1608 >    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1609 >      //assert(index < nAtoms_ + nRigidBodies_);
1610 >      return sdByGlobalIndex_.at(index);
1611 >    }  
1612 > */  
1613   }//end namespace oopse
1614  

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