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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 734 by chuckv, Tue Nov 15 16:05:38 2005 UTC vs.
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC

# Line 48 | Line 48
48  
49   #include <algorithm>
50   #include <set>
51 + #include <map>
52  
53   #include "brains/SimInfo.hpp"
54   #include "math/Vector3.hpp"
# Line 58 | Line 59
59   #include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
60   #include "UseTheForce/doForces_interface.h"
61   #include "UseTheForce/DarkSide/electrostatic_interface.h"
61 – #include "UseTheForce/notifyCutoffs_interface.h"
62   #include "UseTheForce/DarkSide/switcheroo_interface.h"
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 70 | Line 72 | namespace oopse {
72   #endif
73  
74   namespace oopse {
75 +  std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
76 +    std::map<int, std::set<int> >::iterator i = container.find(index);
77 +    std::set<int> result;
78 +    if (i != container.end()) {
79 +        result = i->second;
80 +    }
81  
82 <  SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
83 <                   ForceField* ff, Globals* simParams) :
84 <    stamps_(stamps), forceField_(ff), simParams_(simParams),
85 <    ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
82 >    return result;
83 >  }
84 >  
85 >  SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
86 >    forceField_(ff), simParams_(simParams),
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) {
93  
84 –            
85 –      std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
94        MoleculeStamp* molStamp;
95        int nMolWithSameStamp;
96        int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
# Line 90 | Line 98 | namespace oopse {
98        CutoffGroupStamp* cgStamp;    
99        RigidBodyStamp* rbStamp;
100        int nRigidAtoms = 0;
101 <    
102 <      for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
103 <        molStamp = i->first;
104 <        nMolWithSameStamp = i->second;
101 >      std::vector<Component*> components = simParams->getComponents();
102 >      
103 >      for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
104 >        molStamp = (*i)->getMoleculeStamp();
105 >        nMolWithSameStamp = (*i)->getNMol();
106          
107          addMoleculeStamp(molStamp, nMolWithSameStamp);
108  
109          //calculate atoms in molecules
110          nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;  
111  
103 –
112          //calculate atoms in cutoff groups
113          int nAtomsInGroups = 0;
114          int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
115          
116          for (int j=0; j < nCutoffGroupsInStamp; j++) {
117 <          cgStamp = molStamp->getCutoffGroup(j);
117 >          cgStamp = molStamp->getCutoffGroupStamp(j);
118            nAtomsInGroups += cgStamp->getNMembers();
119          }
120  
# Line 119 | Line 127 | namespace oopse {
127          int nRigidBodiesInStamp = molStamp->getNRigidBodies();
128          
129          for (int j=0; j < nRigidBodiesInStamp; j++) {
130 <          rbStamp = molStamp->getRigidBody(j);
130 >          rbStamp = molStamp->getRigidBodyStamp(j);
131            nAtomsInRigidBodies += rbStamp->getNMembers();
132          }
133  
# Line 158 | Line 166 | namespace oopse {
166      }
167      molecules_.clear();
168        
161 –    delete stamps_;
169      delete sman_;
170      delete simParams_;
171      delete forceField_;
# Line 265 | Line 272 | namespace oopse {
272            }
273          }
274              
275 <      }//end for (integrableObject)
276 <    }// end for (mol)
275 >      }
276 >    }
277      
278      // n_constraints is local, so subtract them on each processor
279      ndf_local -= nConstraints_;
# Line 283 | 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 345 | Line 361 | namespace oopse {
361      int b;
362      int c;
363      int d;
364 +
365 +    std::map<int, std::set<int> > atomGroups;
366 +
367 +    Molecule::RigidBodyIterator rbIter;
368 +    RigidBody* rb;
369 +    Molecule::IntegrableObjectIterator ii;
370 +    StuntDouble* integrableObject;
371      
372 +    for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
373 +           integrableObject = mol->nextIntegrableObject(ii)) {
374 +
375 +      if (integrableObject->isRigidBody()) {
376 +          rb = static_cast<RigidBody*>(integrableObject);
377 +          std::vector<Atom*> atoms = rb->getAtoms();
378 +          std::set<int> rigidAtoms;
379 +          for (int i = 0; i < atoms.size(); ++i) {
380 +            rigidAtoms.insert(atoms[i]->getGlobalIndex());
381 +          }
382 +          for (int i = 0; i < atoms.size(); ++i) {
383 +            atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
384 +          }      
385 +      } else {
386 +        std::set<int> oneAtomSet;
387 +        oneAtomSet.insert(integrableObject->getGlobalIndex());
388 +        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
389 +      }
390 +    }  
391 +
392 +    
393 +    
394      for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
395        a = bond->getAtomA()->getGlobalIndex();
396        b = bond->getAtomB()->getGlobalIndex();        
# Line 356 | Line 401 | namespace oopse {
401        a = bend->getAtomA()->getGlobalIndex();
402        b = bend->getAtomB()->getGlobalIndex();        
403        c = bend->getAtomC()->getGlobalIndex();
404 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
405 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
406 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
407  
408 <      exclude_.addPair(a, b);
409 <      exclude_.addPair(a, c);
410 <      exclude_.addPair(b, c);        
408 >      exclude_.addPairs(rigidSetA, rigidSetB);
409 >      exclude_.addPairs(rigidSetA, rigidSetC);
410 >      exclude_.addPairs(rigidSetB, rigidSetC);
411 >      
412 >      //exclude_.addPair(a, b);
413 >      //exclude_.addPair(a, c);
414 >      //exclude_.addPair(b, c);        
415      }
416  
417      for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
# Line 367 | Line 419 | namespace oopse {
419        b = torsion->getAtomB()->getGlobalIndex();        
420        c = torsion->getAtomC()->getGlobalIndex();        
421        d = torsion->getAtomD()->getGlobalIndex();        
422 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
423 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
424 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
425 +      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
426  
427 +      exclude_.addPairs(rigidSetA, rigidSetB);
428 +      exclude_.addPairs(rigidSetA, rigidSetC);
429 +      exclude_.addPairs(rigidSetA, rigidSetD);
430 +      exclude_.addPairs(rigidSetB, rigidSetC);
431 +      exclude_.addPairs(rigidSetB, rigidSetD);
432 +      exclude_.addPairs(rigidSetC, rigidSetD);
433 +
434 +      /*
435 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
436 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
437 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
438 +      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
439 +      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
440 +      exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
441 +        
442 +      
443        exclude_.addPair(a, b);
444        exclude_.addPair(a, c);
445        exclude_.addPair(a, d);
446        exclude_.addPair(b, c);
447        exclude_.addPair(b, d);
448        exclude_.addPair(c, d);        
449 +      */
450      }
451  
379 –    Molecule::RigidBodyIterator rbIter;
380 –    RigidBody* rb;
452      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
453        std::vector<Atom*> atoms = rb->getAtoms();
454        for (int i = 0; i < atoms.size() -1 ; ++i) {
# Line 402 | Line 473 | namespace oopse {
473      int b;
474      int c;
475      int d;
476 +
477 +    std::map<int, std::set<int> > atomGroups;
478 +
479 +    Molecule::RigidBodyIterator rbIter;
480 +    RigidBody* rb;
481 +    Molecule::IntegrableObjectIterator ii;
482 +    StuntDouble* integrableObject;
483      
484 +    for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
485 +           integrableObject = mol->nextIntegrableObject(ii)) {
486 +
487 +      if (integrableObject->isRigidBody()) {
488 +          rb = static_cast<RigidBody*>(integrableObject);
489 +          std::vector<Atom*> atoms = rb->getAtoms();
490 +          std::set<int> rigidAtoms;
491 +          for (int i = 0; i < atoms.size(); ++i) {
492 +            rigidAtoms.insert(atoms[i]->getGlobalIndex());
493 +          }
494 +          for (int i = 0; i < atoms.size(); ++i) {
495 +            atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
496 +          }      
497 +      } else {
498 +        std::set<int> oneAtomSet;
499 +        oneAtomSet.insert(integrableObject->getGlobalIndex());
500 +        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
501 +      }
502 +    }  
503 +
504 +    
505      for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
506        a = bond->getAtomA()->getGlobalIndex();
507        b = bond->getAtomB()->getGlobalIndex();        
# Line 414 | Line 513 | namespace oopse {
513        b = bend->getAtomB()->getGlobalIndex();        
514        c = bend->getAtomC()->getGlobalIndex();
515  
516 <      exclude_.removePair(a, b);
517 <      exclude_.removePair(a, c);
518 <      exclude_.removePair(b, c);        
516 >      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
517 >      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
518 >      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
519 >
520 >      exclude_.removePairs(rigidSetA, rigidSetB);
521 >      exclude_.removePairs(rigidSetA, rigidSetC);
522 >      exclude_.removePairs(rigidSetB, rigidSetC);
523 >      
524 >      //exclude_.removePair(a, b);
525 >      //exclude_.removePair(a, c);
526 >      //exclude_.removePair(b, c);        
527      }
528  
529      for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
# Line 425 | Line 532 | namespace oopse {
532        c = torsion->getAtomC()->getGlobalIndex();        
533        d = torsion->getAtomD()->getGlobalIndex();        
534  
535 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
536 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
537 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
538 +      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
539 +
540 +      exclude_.removePairs(rigidSetA, rigidSetB);
541 +      exclude_.removePairs(rigidSetA, rigidSetC);
542 +      exclude_.removePairs(rigidSetA, rigidSetD);
543 +      exclude_.removePairs(rigidSetB, rigidSetC);
544 +      exclude_.removePairs(rigidSetB, rigidSetD);
545 +      exclude_.removePairs(rigidSetC, rigidSetD);
546 +
547 +      /*
548 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
549 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
550 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
551 +      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
552 +      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
553 +      exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
554 +
555 +      
556        exclude_.removePair(a, b);
557        exclude_.removePair(a, c);
558        exclude_.removePair(a, d);
559        exclude_.removePair(b, c);
560        exclude_.removePair(b, d);
561        exclude_.removePair(c, d);        
562 +      */
563      }
564  
436 –    Molecule::RigidBodyIterator rbIter;
437 –    RigidBody* rb;
565      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
566        std::vector<Atom*> atoms = rb->getAtoms();
567        for (int i = 0; i < atoms.size() -1 ; ++i) {
# Line 672 | Line 799 | namespace oopse {
799      }
800  
801      //calculate mass ratio of cutoff group
802 <    std::vector<double> mfact;
802 >    std::vector<RealType> mfact;
803      SimInfo::MoleculeIterator mi;
804      Molecule* mol;
805      Molecule::CutoffGroupIterator ci;
806      CutoffGroup* cg;
807      Molecule::AtomIterator ai;
808      Atom* atom;
809 <    double totalMass;
809 >    RealType totalMass;
810  
811      //to avoid memory reallocation, reserve enough space for mfact
812      mfact.reserve(getNCutoffGroups());
# Line 802 | Line 929 | namespace oopse {
929  
930   #endif
931  
932 <  double SimInfo::calcMaxCutoffRadius() {
932 >  void SimInfo::setupCutoff() {          
933 >    
934 >    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
935  
936 <
937 <    std::set<AtomType*> atomTypes;
809 <    std::set<AtomType*>::iterator i;
810 <    std::vector<double> cutoffRadius;
811 <
812 <    //get the unique atom types
813 <    atomTypes = getUniqueAtomTypes();
936 >    // Check the cutoff policy
937 >    int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
938  
939 <    //query the max cutoff radius among these atom types
940 <    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
941 <      cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
939 >    std::string myPolicy;
940 >    if (forceFieldOptions_.haveCutoffPolicy()){
941 >      myPolicy = forceFieldOptions_.getCutoffPolicy();
942 >    }else if (simParams_->haveCutoffPolicy()) {
943 >      myPolicy = simParams_->getCutoffPolicy();
944      }
945  
946 <    double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
821 < #ifdef IS_MPI
822 <    //pick the max cutoff radius among the processors
823 < #endif
824 <
825 <    return maxCutoffRadius;
826 <  }
827 <
828 <  void SimInfo::getCutoff(double& rcut, double& rsw) {
829 <    
830 <    if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
831 <        
832 <      if (!simParams_->haveCutoffRadius()){
833 <        sprintf(painCave.errMsg,
834 <                "SimCreator Warning: No value was set for the cutoffRadius.\n"
835 <                "\tOOPSE will use a default value of 15.0 angstroms"
836 <                "\tfor the cutoffRadius.\n");
837 <        painCave.isFatal = 0;
838 <        simError();
839 <        rcut = 15.0;
840 <      } else{
841 <        rcut = simParams_->getCutoffRadius();
842 <      }
843 <
844 <      if (!simParams_->haveSwitchingRadius()){
845 <        sprintf(painCave.errMsg,
846 <                "SimCreator Warning: No value was set for switchingRadius.\n"
847 <                "\tOOPSE will use a default value of\n"
848 <                "\t0.85 * cutoffRadius for the switchingRadius\n");
849 <        painCave.isFatal = 0;
850 <        simError();
851 <        rsw = 0.85 * rcut;
852 <      } else{
853 <        rsw = simParams_->getSwitchingRadius();
854 <      }
855 <
856 <    } else {
857 <      // if charge, dipole or reaction field is not used and the cutofff radius is not specified in
858 <      //meta-data file, the maximum cutoff radius calculated from forcefiled will be used
859 <        
860 <      if (simParams_->haveCutoffRadius()) {
861 <        rcut = simParams_->getCutoffRadius();
862 <      } else {
863 <        //set cutoff radius to the maximum cutoff radius based on atom types in the whole system
864 <        rcut = calcMaxCutoffRadius();
865 <      }
866 <
867 <      if (simParams_->haveSwitchingRadius()) {
868 <        rsw  = simParams_->getSwitchingRadius();
869 <      } else {
870 <        rsw = rcut;
871 <      }
872 <    
873 <    }
874 <  }
875 <
876 <  void SimInfo::setupCutoff() {    
877 <    getCutoff(rcut_, rsw_);    
878 <    double rnblist = rcut_ + 1; // skin of neighbor list
879 <
880 <    //Pass these cutoff radius etc. to fortran. This function should be called once and only once
881 <    
882 <    int cp =  TRADITIONAL_CUTOFF_POLICY;
883 <    if (simParams_->haveCutoffPolicy()) {
884 <      std::string myPolicy = simParams_->getCutoffPolicy();
946 >    if (!myPolicy.empty()){
947        toUpper(myPolicy);
948        if (myPolicy == "MIX") {
949          cp = MIX_CUTOFF_POLICY;
# Line 900 | Line 962 | namespace oopse {
962            }    
963          }          
964        }
965 <    }
965 >    }          
966 >    notifyFortranCutoffPolicy(&cp);
967  
968 <
968 >    // Check the Skin Thickness for neighborlists
969 >    RealType skin;
970      if (simParams_->haveSkinThickness()) {
971 <      double skinThickness = simParams_->getSkinThickness();
972 <    }
971 >      skin = simParams_->getSkinThickness();
972 >      notifyFortranSkinThickness(&skin);
973 >    }            
974 >        
975 >    // Check if the cutoff was set explicitly:
976 >    if (simParams_->haveCutoffRadius()) {
977 >      rcut_ = simParams_->getCutoffRadius();
978 >      if (simParams_->haveSwitchingRadius()) {
979 >        rsw_  = simParams_->getSwitchingRadius();
980 >      } else {
981 >        if (fInfo_.SIM_uses_Charges |
982 >            fInfo_.SIM_uses_Dipoles |
983 >            fInfo_.SIM_uses_RF) {
984 >          
985 >          rsw_ = 0.85 * rcut_;
986 >          sprintf(painCave.errMsg,
987 >                  "SimCreator Warning: No value was set for the switchingRadius.\n"
988 >                  "\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
989 >                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
990 >        painCave.isFatal = 0;
991 >        simError();
992 >        } else {
993 >          rsw_ = rcut_;
994 >          sprintf(painCave.errMsg,
995 >                  "SimCreator Warning: No value was set for the switchingRadius.\n"
996 >                  "\tOOPSE will use the same value as the cutoffRadius.\n"
997 >                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
998 >          painCave.isFatal = 0;
999 >          simError();
1000 >        }
1001 >      }
1002 >      
1003 >      notifyFortranCutoffs(&rcut_, &rsw_);
1004 >      
1005 >    } else {
1006 >      
1007 >      // For electrostatic atoms, we'll assume a large safe value:
1008 >      if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1009 >        sprintf(painCave.errMsg,
1010 >                "SimCreator Warning: No value was set for the cutoffRadius.\n"
1011 >                "\tOOPSE will use a default value of 15.0 angstroms"
1012 >                "\tfor the cutoffRadius.\n");
1013 >        painCave.isFatal = 0;
1014 >        simError();
1015 >        rcut_ = 15.0;
1016 >      
1017 >        if (simParams_->haveElectrostaticSummationMethod()) {
1018 >          std::string myMethod = simParams_->getElectrostaticSummationMethod();
1019 >          toUpper(myMethod);
1020 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1021 >            if (simParams_->haveSwitchingRadius()){
1022 >              sprintf(painCave.errMsg,
1023 >                      "SimInfo Warning: A value was set for the switchingRadius\n"
1024 >                      "\teven though the electrostaticSummationMethod was\n"
1025 >                      "\tset to %s\n", myMethod.c_str());
1026 >              painCave.isFatal = 1;
1027 >              simError();            
1028 >            }
1029 >          }
1030 >        }
1031 >      
1032 >        if (simParams_->haveSwitchingRadius()){
1033 >          rsw_ = simParams_->getSwitchingRadius();
1034 >        } else {        
1035 >          sprintf(painCave.errMsg,
1036 >                  "SimCreator Warning: No value was set for switchingRadius.\n"
1037 >                  "\tOOPSE will use a default value of\n"
1038 >                  "\t0.85 * cutoffRadius for the switchingRadius\n");
1039 >          painCave.isFatal = 0;
1040 >          simError();
1041 >          rsw_ = 0.85 * rcut_;
1042 >        }
1043 >        notifyFortranCutoffs(&rcut_, &rsw_);
1044 >      } else {
1045 >        // We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1046 >        // We'll punt and let fortran figure out the cutoffs later.
1047 >        
1048 >        notifyFortranYouAreOnYourOwn();
1049  
1050 <    notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1051 <    // also send cutoff notification to electrostatics
912 <    setElectrostaticCutoffRadius(&rcut_, &rsw_);
1050 >      }
1051 >    }
1052    }
1053  
1054    void SimInfo::setupElectrostaticSummationMethod( int isError ) {    
# Line 917 | Line 1056 | namespace oopse {
1056      int errorOut;
1057      int esm =  NONE;
1058      int sm = UNDAMPED;
1059 <    double alphaVal;
1060 <    double dielectric;
1059 >    RealType alphaVal;
1060 >    RealType dielectric;
1061  
1062      errorOut = isError;
1063      alphaVal = simParams_->getDampingAlpha();
# Line 944 | Line 1083 | namespace oopse {
1083                } else {
1084                  // throw error        
1085                  sprintf( painCave.errMsg,
1086 <                         "SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"shifted_potential\", \"shifted_force\", or \"reaction_field\".", myMethod.c_str() );
1086 >                         "SimInfo error: Unknown electrostaticSummationMethod.\n"
1087 >                         "\t(Input file specified %s .)\n"
1088 >                         "\telectrostaticSummationMethod must be one of: \"none\",\n"
1089 >                         "\t\"shifted_potential\", \"shifted_force\", or \n"
1090 >                         "\t\"reaction_field\".\n", myMethod.c_str() );
1091                  painCave.isFatal = 1;
1092                  simError();
1093                }    
# Line 965 | Line 1108 | namespace oopse {
1108            if (!simParams_->haveDampingAlpha()) {
1109              //throw error
1110              sprintf( painCave.errMsg,
1111 <                     "SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal);
1111 >                     "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1112 >                     "\tA default value of %f (1/ang) will be used.\n", alphaVal);
1113              painCave.isFatal = 0;
1114              simError();
1115            }
1116          } else {
1117            // throw error        
1118            sprintf( painCave.errMsg,
1119 <                   "SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() );
1119 >                   "SimInfo error: Unknown electrostaticScreeningMethod.\n"
1120 >                   "\t(Input file specified %s .)\n"
1121 >                   "\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1122 >                   "or \"damped\".\n", myScreen.c_str() );
1123            painCave.isFatal = 1;
1124            simError();
1125          }
# Line 981 | Line 1128 | namespace oopse {
1128      
1129      // let's pass some summation method variables to fortran
1130      setElectrostaticSummationMethod( &esm );
1131 +    setFortranElectrostaticMethod( &esm );
1132      setScreeningMethod( &sm );
1133      setDampingAlpha( &alphaVal );
1134      setReactionFieldDielectric( &dielectric );
1135 <    initFortranFF( &esm, &errorOut );
1135 >    initFortranFF( &errorOut );
1136    }
1137  
1138    void SimInfo::setupSwitchingFunction() {    
# Line 1069 | Line 1217 | namespace oopse {
1217      Molecule* mol;
1218  
1219      Vector3d comVel(0.0);
1220 <    double totalMass = 0.0;
1220 >    RealType totalMass = 0.0;
1221      
1222  
1223      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1224 <      double mass = mol->getMass();
1224 >      RealType mass = mol->getMass();
1225        totalMass += mass;
1226        comVel += mass * mol->getComVel();
1227      }  
1228  
1229   #ifdef IS_MPI
1230 <    double tmpMass = totalMass;
1230 >    RealType tmpMass = totalMass;
1231      Vector3d tmpComVel(comVel);    
1232 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1233 <    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1232 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1233 >    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1234   #endif
1235  
1236      comVel /= totalMass;
# Line 1095 | Line 1243 | namespace oopse {
1243      Molecule* mol;
1244  
1245      Vector3d com(0.0);
1246 <    double totalMass = 0.0;
1246 >    RealType totalMass = 0.0;
1247      
1248      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1249 <      double mass = mol->getMass();
1249 >      RealType mass = mol->getMass();
1250        totalMass += mass;
1251        com += mass * mol->getCom();
1252      }  
1253  
1254   #ifdef IS_MPI
1255 <    double tmpMass = totalMass;
1255 >    RealType tmpMass = totalMass;
1256      Vector3d tmpCom(com);    
1257 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1258 <    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1257 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1258 >    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1259   #endif
1260  
1261      com /= totalMass;
# Line 1131 | Line 1279 | namespace oopse {
1279        Molecule* mol;
1280        
1281      
1282 <      double totalMass = 0.0;
1282 >      RealType totalMass = 0.0;
1283      
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           comVel += mass * mol->getComVel();          
1290        }  
1291        
1292   #ifdef IS_MPI
1293 <      double tmpMass = totalMass;
1293 >      RealType tmpMass = totalMass;
1294        Vector3d tmpCom(com);  
1295        Vector3d tmpComVel(comVel);
1296 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1297 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1298 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1296 >      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1297 >      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1298 >      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1299   #endif
1300        
1301        com /= totalMass;
# Line 1166 | Line 1314 | namespace oopse {
1314     void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1315        
1316  
1317 <      double xx = 0.0;
1318 <      double yy = 0.0;
1319 <      double zz = 0.0;
1320 <      double xy = 0.0;
1321 <      double xz = 0.0;
1322 <      double yz = 0.0;
1317 >      RealType xx = 0.0;
1318 >      RealType yy = 0.0;
1319 >      RealType zz = 0.0;
1320 >      RealType xy = 0.0;
1321 >      RealType xz = 0.0;
1322 >      RealType yz = 0.0;
1323        Vector3d com(0.0);
1324        Vector3d comVel(0.0);
1325        
# Line 1183 | Line 1331 | namespace oopse {
1331        Vector3d thisq(0.0);
1332        Vector3d thisv(0.0);
1333  
1334 <      double thisMass = 0.0;
1334 >      RealType thisMass = 0.0;
1335      
1336        
1337        
# Line 1221 | Line 1369 | namespace oopse {
1369   #ifdef IS_MPI
1370        Mat3x3d tmpI(inertiaTensor);
1371        Vector3d tmpAngMom;
1372 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1373 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1372 >      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1373 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1374   #endif
1375                
1376        return;
# Line 1243 | Line 1391 | namespace oopse {
1391        Vector3d thisr(0.0);
1392        Vector3d thisp(0.0);
1393        
1394 <      double thisMass;
1394 >      RealType thisMass;
1395        
1396        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1397          thisMass = mol->getMass();
# Line 1256 | Line 1404 | namespace oopse {
1404        
1405   #ifdef IS_MPI
1406        Vector3d tmpAngMom;
1407 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1407 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1408   #endif
1409        
1410        return angularMomentum;

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