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root/OpenMD/branches/development/src/brains/SimInfo.cpp
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Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1503 by gezelter, Sat Oct 2 19:54:41 2010 UTC vs.
Revision 1532 by gezelter, Wed Dec 29 19:59:21 2010 UTC

# Line 54 | Line 54
54   #include "math/Vector3.hpp"
55   #include "primitives/Molecule.hpp"
56   #include "primitives/StuntDouble.hpp"
57 – #include "UseTheForce/fCutoffPolicy.h"
58 – #include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
57   #include "UseTheForce/doForces_interface.h"
58   #include "UseTheForce/DarkSide/neighborLists_interface.h"
61 – #include "UseTheForce/DarkSide/switcheroo_interface.h"
59   #include "utils/MemoryUtils.hpp"
60   #include "utils/simError.h"
61   #include "selection/SelectionManager.hpp"
62   #include "io/ForceFieldOptions.hpp"
63   #include "UseTheForce/ForceField.hpp"
64 + #include "nonbonded/SwitchingFunction.hpp"
65  
66  
67   #ifdef IS_MPI
# Line 71 | Line 69
69   #include "UseTheForce/DarkSide/simParallel_interface.h"
70   #endif
71  
72 + using namespace std;
73   namespace OpenMD {
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 –    return result;
83 –  }
74    
75    SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
76      forceField_(ff), simParams_(simParams),
# Line 90 | Line 80 | namespace OpenMD {
80      nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
81      nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
82      nConstraints_(0), sman_(NULL), fortranInitialized_(false),
83 <    calcBoxDipole_(false), useAtomicVirial_(true) {
84 <
85 <
86 <      MoleculeStamp* molStamp;
87 <      int nMolWithSameStamp;
88 <      int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
89 <      int nGroups = 0;      //total cutoff groups defined in meta-data file
90 <      CutoffGroupStamp* cgStamp;    
91 <      RigidBodyStamp* rbStamp;
92 <      int nRigidAtoms = 0;
93 <
94 <      std::vector<Component*> components = simParams->getComponents();
83 >    calcBoxDipole_(false), useAtomicVirial_(true) {    
84 >    
85 >    MoleculeStamp* molStamp;
86 >    int nMolWithSameStamp;
87 >    int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
88 >    int nGroups = 0;       //total cutoff groups defined in meta-data file
89 >    CutoffGroupStamp* cgStamp;    
90 >    RigidBodyStamp* rbStamp;
91 >    int nRigidAtoms = 0;
92 >    
93 >    vector<Component*> components = simParams->getComponents();
94 >    
95 >    for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
96 >      molStamp = (*i)->getMoleculeStamp();
97 >      nMolWithSameStamp = (*i)->getNMol();
98        
99 <      for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
100 <        molStamp = (*i)->getMoleculeStamp();
101 <        nMolWithSameStamp = (*i)->getNMol();
102 <        
103 <        addMoleculeStamp(molStamp, nMolWithSameStamp);
104 <
105 <        //calculate atoms in molecules
106 <        nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;  
107 <
108 <        //calculate atoms in cutoff groups
109 <        int nAtomsInGroups = 0;
110 <        int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
118 <        
119 <        for (int j=0; j < nCutoffGroupsInStamp; j++) {
120 <          cgStamp = molStamp->getCutoffGroupStamp(j);
121 <          nAtomsInGroups += cgStamp->getNMembers();
122 <        }
123 <
124 <        nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
125 <
126 <        nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;            
127 <
128 <        //calculate atoms in rigid bodies
129 <        int nAtomsInRigidBodies = 0;
130 <        int nRigidBodiesInStamp = molStamp->getNRigidBodies();
131 <        
132 <        for (int j=0; j < nRigidBodiesInStamp; j++) {
133 <          rbStamp = molStamp->getRigidBodyStamp(j);
134 <          nAtomsInRigidBodies += rbStamp->getNMembers();
135 <        }
136 <
137 <        nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
138 <        nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;            
139 <        
99 >      addMoleculeStamp(molStamp, nMolWithSameStamp);
100 >      
101 >      //calculate atoms in molecules
102 >      nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;  
103 >      
104 >      //calculate atoms in cutoff groups
105 >      int nAtomsInGroups = 0;
106 >      int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
107 >      
108 >      for (int j=0; j < nCutoffGroupsInStamp; j++) {
109 >        cgStamp = molStamp->getCutoffGroupStamp(j);
110 >        nAtomsInGroups += cgStamp->getNMembers();
111        }
112 <
113 <      //every free atom (atom does not belong to cutoff groups) is a cutoff
114 <      //group therefore the total number of cutoff groups in the system is
115 <      //equal to the total number of atoms minus number of atoms belong to
116 <      //cutoff group defined in meta-data file plus the number of cutoff
117 <      //groups defined in meta-data file
118 <      nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
119 <
120 <      //every free atom (atom does not belong to rigid bodies) is an
121 <      //integrable object therefore the total number of integrable objects
122 <      //in the system is equal to the total number of atoms minus number of
123 <      //atoms belong to rigid body defined in meta-data file plus the number
124 <      //of rigid bodies defined in meta-data file
125 <      nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
126 <                                                + nGlobalRigidBodies_;
127 <  
128 <      nGlobalMols_ = molStampIds_.size();
129 <      molToProcMap_.resize(nGlobalMols_);
130 <    }
131 <
112 >      
113 >      nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
114 >      
115 >      nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;            
116 >      
117 >      //calculate atoms in rigid bodies
118 >      int nAtomsInRigidBodies = 0;
119 >      int nRigidBodiesInStamp = molStamp->getNRigidBodies();
120 >      
121 >      for (int j=0; j < nRigidBodiesInStamp; j++) {
122 >        rbStamp = molStamp->getRigidBodyStamp(j);
123 >        nAtomsInRigidBodies += rbStamp->getNMembers();
124 >      }
125 >      
126 >      nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
127 >      nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;            
128 >      
129 >    }
130 >    
131 >    //every free atom (atom does not belong to cutoff groups) is a cutoff
132 >    //group therefore the total number of cutoff groups in the system is
133 >    //equal to the total number of atoms minus number of atoms belong to
134 >    //cutoff group defined in meta-data file plus the number of cutoff
135 >    //groups defined in meta-data file
136 >    nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
137 >    
138 >    //every free atom (atom does not belong to rigid bodies) is an
139 >    //integrable object therefore the total number of integrable objects
140 >    //in the system is equal to the total number of atoms minus number of
141 >    //atoms belong to rigid body defined in meta-data file plus the number
142 >    //of rigid bodies defined in meta-data file
143 >    nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
144 >      + nGlobalRigidBodies_;
145 >    
146 >    nGlobalMols_ = molStampIds_.size();
147 >    molToProcMap_.resize(nGlobalMols_);
148 >  }
149 >  
150    SimInfo::~SimInfo() {
151 <    std::map<int, Molecule*>::iterator i;
151 >    map<int, Molecule*>::iterator i;
152      for (i = molecules_.begin(); i != molecules_.end(); ++i) {
153        delete i->second;
154      }
# Line 170 | Line 159 | namespace OpenMD {
159      delete forceField_;
160    }
161  
173 –  int SimInfo::getNGlobalConstraints() {
174 –    int nGlobalConstraints;
175 – #ifdef IS_MPI
176 –    MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
177 –                  MPI_COMM_WORLD);    
178 – #else
179 –    nGlobalConstraints =  nConstraints_;
180 – #endif
181 –    return nGlobalConstraints;
182 –  }
162  
163    bool SimInfo::addMolecule(Molecule* mol) {
164      MoleculeIterator i;
165 <
165 >    
166      i = molecules_.find(mol->getGlobalIndex());
167      if (i == molecules_.end() ) {
168 <
169 <      molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
170 <        
168 >      
169 >      molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
170 >      
171        nAtoms_ += mol->getNAtoms();
172        nBonds_ += mol->getNBonds();
173        nBends_ += mol->getNBends();
# Line 198 | Line 177 | namespace OpenMD {
177        nIntegrableObjects_ += mol->getNIntegrableObjects();
178        nCutoffGroups_ += mol->getNCutoffGroups();
179        nConstraints_ += mol->getNConstraintPairs();
180 <
180 >      
181        addInteractionPairs(mol);
182 <  
182 >      
183        return true;
184      } else {
185        return false;
186      }
187    }
188 <
188 >  
189    bool SimInfo::removeMolecule(Molecule* mol) {
190      MoleculeIterator i;
191      i = molecules_.find(mol->getGlobalIndex());
# Line 234 | Line 213 | namespace OpenMD {
213      } else {
214        return false;
215      }
237 –
238 –
216    }    
217  
218          
# Line 253 | Line 230 | namespace OpenMD {
230    void SimInfo::calcNdf() {
231      int ndf_local;
232      MoleculeIterator i;
233 <    std::vector<StuntDouble*>::iterator j;
233 >    vector<StuntDouble*>::iterator j;
234      Molecule* mol;
235      StuntDouble* integrableObject;
236  
# Line 304 | Line 281 | namespace OpenMD {
281      int ndfRaw_local;
282  
283      MoleculeIterator i;
284 <    std::vector<StuntDouble*>::iterator j;
284 >    vector<StuntDouble*>::iterator j;
285      Molecule* mol;
286      StuntDouble* integrableObject;
287  
# Line 353 | Line 330 | namespace OpenMD {
330  
331    void SimInfo::addInteractionPairs(Molecule* mol) {
332      ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
333 <    std::vector<Bond*>::iterator bondIter;
334 <    std::vector<Bend*>::iterator bendIter;
335 <    std::vector<Torsion*>::iterator torsionIter;
336 <    std::vector<Inversion*>::iterator inversionIter;
333 >    vector<Bond*>::iterator bondIter;
334 >    vector<Bend*>::iterator bendIter;
335 >    vector<Torsion*>::iterator torsionIter;
336 >    vector<Inversion*>::iterator inversionIter;
337      Bond* bond;
338      Bend* bend;
339      Torsion* torsion;
# Line 374 | Line 351 | namespace OpenMD {
351      // always be excluded.  These are done at the bottom of this
352      // function.
353  
354 <    std::map<int, std::set<int> > atomGroups;
354 >    map<int, set<int> > atomGroups;
355      Molecule::RigidBodyIterator rbIter;
356      RigidBody* rb;
357      Molecule::IntegrableObjectIterator ii;
# Line 386 | Line 363 | namespace OpenMD {
363        
364        if (integrableObject->isRigidBody()) {
365          rb = static_cast<RigidBody*>(integrableObject);
366 <        std::vector<Atom*> atoms = rb->getAtoms();
367 <        std::set<int> rigidAtoms;
366 >        vector<Atom*> atoms = rb->getAtoms();
367 >        set<int> rigidAtoms;
368          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
369            rigidAtoms.insert(atoms[i]->getGlobalIndex());
370          }
371          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
372 <          atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
372 >          atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
373          }      
374        } else {
375 <        std::set<int> oneAtomSet;
375 >        set<int> oneAtomSet;
376          oneAtomSet.insert(integrableObject->getGlobalIndex());
377 <        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
377 >        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
378        }
379      }  
380            
# Line 500 | Line 477 | namespace OpenMD {
477  
478      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
479           rb = mol->nextRigidBody(rbIter)) {
480 <      std::vector<Atom*> atoms = rb->getAtoms();
480 >      vector<Atom*> atoms = rb->getAtoms();
481        for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
482          for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
483            a = atoms[i]->getGlobalIndex();
# Line 514 | Line 491 | namespace OpenMD {
491  
492    void SimInfo::removeInteractionPairs(Molecule* mol) {
493      ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
494 <    std::vector<Bond*>::iterator bondIter;
495 <    std::vector<Bend*>::iterator bendIter;
496 <    std::vector<Torsion*>::iterator torsionIter;
497 <    std::vector<Inversion*>::iterator inversionIter;
494 >    vector<Bond*>::iterator bondIter;
495 >    vector<Bend*>::iterator bendIter;
496 >    vector<Torsion*>::iterator torsionIter;
497 >    vector<Inversion*>::iterator inversionIter;
498      Bond* bond;
499      Bend* bend;
500      Torsion* torsion;
# Line 527 | Line 504 | namespace OpenMD {
504      int c;
505      int d;
506  
507 <    std::map<int, std::set<int> > atomGroups;
507 >    map<int, set<int> > atomGroups;
508      Molecule::RigidBodyIterator rbIter;
509      RigidBody* rb;
510      Molecule::IntegrableObjectIterator ii;
# Line 539 | Line 516 | namespace OpenMD {
516        
517        if (integrableObject->isRigidBody()) {
518          rb = static_cast<RigidBody*>(integrableObject);
519 <        std::vector<Atom*> atoms = rb->getAtoms();
520 <        std::set<int> rigidAtoms;
519 >        vector<Atom*> atoms = rb->getAtoms();
520 >        set<int> rigidAtoms;
521          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
522            rigidAtoms.insert(atoms[i]->getGlobalIndex());
523          }
524          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
525 <          atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
525 >          atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
526          }      
527        } else {
528 <        std::set<int> oneAtomSet;
528 >        set<int> oneAtomSet;
529          oneAtomSet.insert(integrableObject->getGlobalIndex());
530 <        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
530 >        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
531        }
532      }  
533  
# Line 653 | Line 630 | namespace OpenMD {
630  
631      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
632           rb = mol->nextRigidBody(rbIter)) {
633 <      std::vector<Atom*> atoms = rb->getAtoms();
633 >      vector<Atom*> atoms = rb->getAtoms();
634        for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
635          for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
636            a = atoms[i]->getGlobalIndex();
# Line 676 | Line 653 | namespace OpenMD {
653      molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
654    }
655  
679 –  void SimInfo::update() {
656  
657 <    setupSimType();
657 >  /**
658 >   * update
659 >   *
660 >   *  Performs the global checks and variable settings after the objects have been
661 >   *  created.
662 >   *
663 >   */
664 >  void SimInfo::update() {
665 >    
666 >    setupSimVariables();
667 >    setupCutoffs();
668 >    setupSwitching();
669 >    setupElectrostatics();
670 >    setupNeighborlists();
671  
672   #ifdef IS_MPI
673      setupFortranParallel();
674   #endif
686 –
675      setupFortranSim();
676 +    fortranInitialized_ = true;
677  
689 –    //setup fortran force field
690 –    /** @deprecate */    
691 –    int isError = 0;
692 –    
693 –    setupCutoff();
694 –    
695 –    setupElectrostaticSummationMethod( isError );
696 –    setupSwitchingFunction();
697 –    setupAccumulateBoxDipole();
698 –
699 –    if(isError){
700 –      sprintf( painCave.errMsg,
701 –               "ForceField error: There was an error initializing the forceField in fortran.\n" );
702 –      painCave.isFatal = 1;
703 –      simError();
704 –    }
705 –
678      calcNdf();
679      calcNdfRaw();
680      calcNdfTrans();
709 –
710 –    fortranInitialized_ = true;
681    }
682 <
683 <  std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
682 >  
683 >  set<AtomType*> SimInfo::getSimulatedAtomTypes() {
684      SimInfo::MoleculeIterator mi;
685      Molecule* mol;
686      Molecule::AtomIterator ai;
687      Atom* atom;
688 <    std::set<AtomType*> atomTypes;
689 <
690 <    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
721 <
688 >    set<AtomType*> atomTypes;
689 >    
690 >    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {      
691        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
692          atomTypes.insert(atom->getAtomType());
693 <      }
694 <        
726 <    }
727 <
693 >      }      
694 >    }    
695      return atomTypes;        
696    }
697  
698 <  void SimInfo::setupSimType() {
699 <    std::set<AtomType*>::iterator i;
700 <    std::set<AtomType*> atomTypes;
701 <    atomTypes = getUniqueAtomTypes();
698 >  /**
699 >   * setupCutoffs
700 >   *
701 >   * Sets the values of cutoffRadius and cutoffMethod
702 >   *
703 >   * cutoffRadius : realType
704 >   *  If the cutoffRadius was explicitly set, use that value.
705 >   *  If the cutoffRadius was not explicitly set:
706 >   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
707 >   *      No electrostatic atoms?  Poll the atom types present in the
708 >   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
709 >   *      Use the maximum suggested value that was found.
710 >   *
711 >   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
712 >   *      If cutoffMethod was explicitly set, use that choice.
713 >   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
714 >   */
715 >  void SimInfo::setupCutoffs() {
716      
717 <    int useLennardJones = 0;
718 <    int useElectrostatic = 0;
719 <    int useEAM = 0;
720 <    int useSC = 0;
721 <    int useCharge = 0;
722 <    int useDirectional = 0;
723 <    int useDipole = 0;
724 <    int useGayBerne = 0;
725 <    int useSticky = 0;
726 <    int useStickyPower = 0;
727 <    int useShape = 0;
728 <    int useFLARB = 0; //it is not in AtomType yet
729 <    int useDirectionalAtom = 0;    
730 <    int useElectrostatics = 0;
731 <    //usePBC and useRF are from simParams
732 <    int usePBC = simParams_->getUsePeriodicBoundaryConditions();
733 <    int useRF;
734 <    int useSF;
735 <    int useSP;
736 <    int useBoxDipole;
717 >    if (simParams_->haveCutoffRadius()) {
718 >      cutoffRadius_ = simParams_->getCutoffRadius();
719 >    } else {      
720 >      if (usesElectrostaticAtoms_) {
721 >        sprintf(painCave.errMsg,
722 >                "SimInfo: No value was set for the cutoffRadius.\n"
723 >                "\tOpenMD will use a default value of 12.0 angstroms"
724 >                "\tfor the cutoffRadius.\n");
725 >        painCave.isFatal = 0;
726 >        painCave.severity = OPENMD_INFO;
727 >        simError();
728 >        cutoffRadius_ = 12.0;
729 >      } else {
730 >        RealType thisCut;
731 >        set<AtomType*>::iterator i;
732 >        set<AtomType*> atomTypes;
733 >        atomTypes = getSimulatedAtomTypes();        
734 >        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
735 >          thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
736 >          cutoffRadius_ = max(thisCut, cutoffRadius_);
737 >        }
738 >        sprintf(painCave.errMsg,
739 >                "SimInfo: No value was set for the cutoffRadius.\n"
740 >                "\tOpenMD will use %lf angstroms.\n",
741 >                cutoffRadius_);
742 >        painCave.isFatal = 0;
743 >        painCave.severity = OPENMD_INFO;
744 >        simError();
745 >      }            
746 >    }
747  
748 <    std::string myMethod;
748 >    InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
749  
750 <    // set the useRF logical
751 <    useRF = 0;
752 <    useSF = 0;
753 <    useSP = 0;
754 <    useBoxDipole = 0;
750 >    map<string, CutoffMethod> stringToCutoffMethod;
751 >    stringToCutoffMethod["HARD"] = HARD;
752 >    stringToCutoffMethod["SWITCHING_FUNCTION"] = SWITCHING_FUNCTION;
753 >    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
754 >    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
755 >  
756 >    if (simParams_->haveCutoffMethod()) {
757 >      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
758 >      map<string, CutoffMethod>::iterator i;
759 >      i = stringToCutoffMethod.find(cutMeth);
760 >      if (i == stringToCutoffMethod.end()) {
761 >        sprintf(painCave.errMsg,
762 >                "SimInfo: Could not find chosen cutoffMethod %s\n"
763 >                "\tShould be one of: "
764 >                "HARD, SWITCHING_FUNCTION, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
765 >                cutMeth.c_str());
766 >        painCave.isFatal = 1;
767 >        painCave.severity = OPENMD_ERROR;
768 >        simError();
769 >      } else {
770 >        cutoffMethod_ = i->second;
771 >      }
772 >    } else {
773 >      sprintf(painCave.errMsg,
774 >              "SimInfo: No value was set for the cutoffMethod.\n"
775 >              "\tOpenMD will use SHIFTED_FORCE.\n");
776 >        painCave.isFatal = 0;
777 >        painCave.severity = OPENMD_INFO;
778 >        simError();
779 >        cutoffMethod_ = SHIFTED_FORCE;        
780 >    }
781  
782 +    InteractionManager::Instance()->setCutoffMethod(cutoffMethod_);
783 +  }
784 +  
785 +  /**
786 +   * setupSwitching
787 +   *
788 +   * Sets the values of switchingRadius and
789 +   *  If the switchingRadius was explicitly set, use that value (but check it)
790 +   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
791 +   */
792 +  void SimInfo::setupSwitching() {
793 +    
794 +    if (simParams_->haveSwitchingRadius()) {
795 +      switchingRadius_ = simParams_->getSwitchingRadius();
796 +      if (switchingRadius_ > cutoffRadius_) {        
797 +        sprintf(painCave.errMsg,
798 +                "SimInfo: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
799 +                switchingRadius_, cutoffRadius_);
800 +        painCave.isFatal = 1;
801 +        painCave.severity = OPENMD_ERROR;
802 +        simError();
803 +      }
804 +    } else {      
805 +      switchingRadius_ = 0.85 * cutoffRadius_;
806 +      sprintf(painCave.errMsg,
807 +              "SimInfo: No value was set for the switchingRadius.\n"
808 +              "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
809 +              "\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
810 +      painCave.isFatal = 0;
811 +      painCave.severity = OPENMD_WARNING;
812 +      simError();
813 +    }          
814 +  
815 +    InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
816  
817 <    if (simParams_->haveElectrostaticSummationMethod()) {
818 <      std::string myMethod = simParams_->getElectrostaticSummationMethod();
819 <      toUpper(myMethod);
820 <      if (myMethod == "REACTION_FIELD"){
821 <        useRF = 1;
822 <      } else if (myMethod == "SHIFTED_FORCE"){
823 <        useSF = 1;
824 <      } else if (myMethod == "SHIFTED_POTENTIAL"){
825 <        useSP = 1;
817 >    SwitchingFunctionType ft;
818 >    
819 >    if (simParams_->haveSwitchingFunctionType()) {
820 >      string funcType = simParams_->getSwitchingFunctionType();
821 >      toUpper(funcType);
822 >      if (funcType == "CUBIC") {
823 >        ft = cubic;
824 >      } else {
825 >        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
826 >          ft = fifth_order_poly;
827 >        } else {
828 >          // throw error        
829 >          sprintf( painCave.errMsg,
830 >                   "SimInfo : Unknown switchingFunctionType. (Input file specified %s .)\n"
831 >                   "\tswitchingFunctionType must be one of: "
832 >                   "\"cubic\" or \"fifth_order_polynomial\".",
833 >                   funcType.c_str() );
834 >          painCave.isFatal = 1;
835 >          painCave.severity = OPENMD_ERROR;
836 >          simError();
837 >        }          
838        }
839      }
840 <    
841 <    if (simParams_->haveAccumulateBoxDipole())
842 <      if (simParams_->getAccumulateBoxDipole())
780 <        useBoxDipole = 1;
840 >
841 >    InteractionManager::Instance()->setSwitchingFunctionType(ft);
842 >  }
843  
844 +  /**
845 +   * setupSkinThickness
846 +   *
847 +   *  If the skinThickness was explicitly set, use that value (but check it)
848 +   *  If the skinThickness was not explicitly set: use 1.0 angstroms
849 +   */
850 +  void SimInfo::setupSkinThickness() {    
851 +    if (simParams_->haveSkinThickness()) {
852 +      skinThickness_ = simParams_->getSkinThickness();
853 +    } else {      
854 +      skinThickness_ = 1.0;
855 +      sprintf(painCave.errMsg,
856 +              "SimInfo Warning: No value was set for the skinThickness.\n"
857 +              "\tOpenMD will use a default value of %f Angstroms\n"
858 +              "\tfor this simulation\n", skinThickness_);
859 +      painCave.isFatal = 0;
860 +      simError();
861 +    }            
862 +  }
863 +
864 +  void SimInfo::setupSimType() {
865 +    set<AtomType*>::iterator i;
866 +    set<AtomType*> atomTypes;
867 +    atomTypes = getSimulatedAtomTypes();
868 +
869      useAtomicVirial_ = simParams_->getUseAtomicVirial();
870  
871 +    int usesElectrostatic = 0;
872 +    int usesMetallic = 0;
873 +    int usesDirectional = 0;
874      //loop over all of the atom types
875      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
876 <      useLennardJones |= (*i)->isLennardJones();
877 <      useElectrostatic |= (*i)->isElectrostatic();
878 <      useEAM |= (*i)->isEAM();
789 <      useSC |= (*i)->isSC();
790 <      useCharge |= (*i)->isCharge();
791 <      useDirectional |= (*i)->isDirectional();
792 <      useDipole |= (*i)->isDipole();
793 <      useGayBerne |= (*i)->isGayBerne();
794 <      useSticky |= (*i)->isSticky();
795 <      useStickyPower |= (*i)->isStickyPower();
796 <      useShape |= (*i)->isShape();
876 >      usesElectrostatic |= (*i)->isElectrostatic();
877 >      usesMetallic |= (*i)->isMetal();
878 >      usesDirectional |= (*i)->isDirectional();
879      }
880  
799 –    if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
800 –      useDirectionalAtom = 1;
801 –    }
802 –
803 –    if (useCharge || useDipole) {
804 –      useElectrostatics = 1;
805 –    }
806 –
881   #ifdef IS_MPI    
882      int temp;
883 +    temp = usesDirectional;
884 +    MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
885  
886 <    temp = usePBC;
887 <    MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
886 >    temp = usesMetallic;
887 >    MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
888  
889 <    temp = useDirectionalAtom;
890 <    MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
815 <
816 <    temp = useLennardJones;
817 <    MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
818 <
819 <    temp = useElectrostatics;
820 <    MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
821 <
822 <    temp = useCharge;
823 <    MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
824 <
825 <    temp = useDipole;
826 <    MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
827 <
828 <    temp = useSticky;
829 <    MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
830 <
831 <    temp = useStickyPower;
832 <    MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
833 <    
834 <    temp = useGayBerne;
835 <    MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
836 <
837 <    temp = useEAM;
838 <    MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
839 <
840 <    temp = useSC;
841 <    MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
842 <    
843 <    temp = useShape;
844 <    MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
845 <
846 <    temp = useFLARB;
847 <    MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
848 <
849 <    temp = useRF;
850 <    MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
851 <
852 <    temp = useSF;
853 <    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
854 <
855 <    temp = useSP;
856 <    MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
857 <
858 <    temp = useBoxDipole;
859 <    MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
860 <
861 <    temp = useAtomicVirial_;
862 <    MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
863 <
889 >    temp = usesElectrostatic;
890 >    MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
891   #endif
892 <
893 <    fInfo_.SIM_uses_PBC = usePBC;    
894 <    fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
895 <    fInfo_.SIM_uses_LennardJones = useLennardJones;
896 <    fInfo_.SIM_uses_Electrostatics = useElectrostatics;    
897 <    fInfo_.SIM_uses_Charges = useCharge;
871 <    fInfo_.SIM_uses_Dipoles = useDipole;
872 <    fInfo_.SIM_uses_Sticky = useSticky;
873 <    fInfo_.SIM_uses_StickyPower = useStickyPower;
874 <    fInfo_.SIM_uses_GayBerne = useGayBerne;
875 <    fInfo_.SIM_uses_EAM = useEAM;
876 <    fInfo_.SIM_uses_SC = useSC;
877 <    fInfo_.SIM_uses_Shapes = useShape;
878 <    fInfo_.SIM_uses_FLARB = useFLARB;
879 <    fInfo_.SIM_uses_RF = useRF;
880 <    fInfo_.SIM_uses_SF = useSF;
881 <    fInfo_.SIM_uses_SP = useSP;
882 <    fInfo_.SIM_uses_BoxDipole = useBoxDipole;
883 <    fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
892 >    fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;    
893 >    fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
894 >    fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
895 >    fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
896 >    fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
897 >    fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
898    }
899  
900    void SimInfo::setupFortranSim() {
901      int isError;
902      int nExclude, nOneTwo, nOneThree, nOneFour;
903 <    std::vector<int> fortranGlobalGroupMembership;
903 >    vector<int> fortranGlobalGroupMembership;
904      
905 +    notifyFortranSkinThickness(&skinThickness_);
906 +
907 +    int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
908 +    int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
909 +    notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
910 +
911      isError = 0;
912  
913      //globalGroupMembership_ is filled by SimCreator    
# Line 896 | Line 916 | namespace OpenMD {
916      }
917  
918      //calculate mass ratio of cutoff group
919 <    std::vector<RealType> mfact;
919 >    vector<RealType> mfact;
920      SimInfo::MoleculeIterator mi;
921      Molecule* mol;
922      Molecule::CutoffGroupIterator ci;
# Line 923 | Line 943 | namespace OpenMD {
943      }
944  
945      //fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
946 <    std::vector<int> identArray;
946 >    vector<int> identArray;
947  
948      //to avoid memory reallocation, reserve enough space identArray
949      identArray.reserve(getNAtoms());
# Line 936 | Line 956 | namespace OpenMD {
956  
957      //fill molMembershipArray
958      //molMembershipArray is filled by SimCreator    
959 <    std::vector<int> molMembershipArray(nGlobalAtoms_);
959 >    vector<int> molMembershipArray(nGlobalAtoms_);
960      for (int i = 0; i < nGlobalAtoms_; i++) {
961        molMembershipArray[i] = globalMolMembership_[i] + 1;
962      }
# Line 989 | Line 1009 | namespace OpenMD {
1009    void SimInfo::setupFortranParallel() {
1010   #ifdef IS_MPI    
1011      //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
1012 <    std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1013 <    std::vector<int> localToGlobalCutoffGroupIndex;
1012 >    vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1013 >    vector<int> localToGlobalCutoffGroupIndex;
1014      SimInfo::MoleculeIterator mi;
1015      Molecule::AtomIterator ai;
1016      Molecule::CutoffGroupIterator ci;
# Line 1042 | Line 1062 | namespace OpenMD {
1062   #endif
1063    }
1064  
1045 –  void SimInfo::setupCutoff() {          
1046 –    
1047 –    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1065  
1049 –    // Check the cutoff policy
1050 –    int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1051 –
1052 –    // Set LJ shifting bools to false
1053 –    ljsp_ = 0;
1054 –    ljsf_ = 0;
1055 –
1056 –    std::string myPolicy;
1057 –    if (forceFieldOptions_.haveCutoffPolicy()){
1058 –      myPolicy = forceFieldOptions_.getCutoffPolicy();
1059 –    }else if (simParams_->haveCutoffPolicy()) {
1060 –      myPolicy = simParams_->getCutoffPolicy();
1061 –    }
1062 –
1063 –    if (!myPolicy.empty()){
1064 –      toUpper(myPolicy);
1065 –      if (myPolicy == "MIX") {
1066 –        cp = MIX_CUTOFF_POLICY;
1067 –      } else {
1068 –        if (myPolicy == "MAX") {
1069 –          cp = MAX_CUTOFF_POLICY;
1070 –        } else {
1071 –          if (myPolicy == "TRADITIONAL") {            
1072 –            cp = TRADITIONAL_CUTOFF_POLICY;
1073 –          } else {
1074 –            // throw error        
1075 –            sprintf( painCave.errMsg,
1076 –                     "SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1077 –            painCave.isFatal = 1;
1078 –            simError();
1079 –          }    
1080 –        }          
1081 –      }
1082 –    }          
1083 –    notifyFortranCutoffPolicy(&cp);
1084 –
1085 –    // Check the Skin Thickness for neighborlists
1086 –    RealType skin;
1087 –    if (simParams_->haveSkinThickness()) {
1088 –      skin = simParams_->getSkinThickness();
1089 –      notifyFortranSkinThickness(&skin);
1090 –    }            
1091 –        
1092 –    // Check if the cutoff was set explicitly:
1093 –    if (simParams_->haveCutoffRadius()) {
1094 –      rcut_ = simParams_->getCutoffRadius();
1095 –      if (simParams_->haveSwitchingRadius()) {
1096 –        rsw_  = simParams_->getSwitchingRadius();
1097 –      } else {
1098 –        if (fInfo_.SIM_uses_Charges |
1099 –            fInfo_.SIM_uses_Dipoles |
1100 –            fInfo_.SIM_uses_RF) {
1101 –          
1102 –          rsw_ = 0.85 * rcut_;
1103 –          sprintf(painCave.errMsg,
1104 –                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1105 –                  "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
1106 –                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1107 –        painCave.isFatal = 0;
1108 –        simError();
1109 –        } else {
1110 –          rsw_ = rcut_;
1111 –          sprintf(painCave.errMsg,
1112 –                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1113 –                  "\tOpenMD will use the same value as the cutoffRadius.\n"
1114 –                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1115 –          painCave.isFatal = 0;
1116 –          simError();
1117 –        }
1118 –      }
1119 –
1120 –      if (simParams_->haveElectrostaticSummationMethod()) {
1121 –        std::string myMethod = simParams_->getElectrostaticSummationMethod();
1122 –        toUpper(myMethod);
1123 –        
1124 –        if (myMethod == "SHIFTED_POTENTIAL") {
1125 –          ljsp_ = 1;
1126 –        } else if (myMethod == "SHIFTED_FORCE") {
1127 –          ljsf_ = 1;
1128 –        }
1129 –      }
1130 –
1131 –      notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1132 –      
1133 –    } else {
1134 –      
1135 –      // For electrostatic atoms, we'll assume a large safe value:
1136 –      if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1137 –        sprintf(painCave.errMsg,
1138 –                "SimCreator Warning: No value was set for the cutoffRadius.\n"
1139 –                "\tOpenMD will use a default value of 15.0 angstroms"
1140 –                "\tfor the cutoffRadius.\n");
1141 –        painCave.isFatal = 0;
1142 –        simError();
1143 –        rcut_ = 15.0;
1144 –      
1145 –        if (simParams_->haveElectrostaticSummationMethod()) {
1146 –          std::string myMethod = simParams_->getElectrostaticSummationMethod();
1147 –          toUpper(myMethod);
1148 –          
1149 –          // For the time being, we're tethering the LJ shifted behavior to the
1150 –          // electrostaticSummationMethod keyword options
1151 –          if (myMethod == "SHIFTED_POTENTIAL") {
1152 –            ljsp_ = 1;
1153 –          } else if (myMethod == "SHIFTED_FORCE") {
1154 –            ljsf_ = 1;
1155 –          }
1156 –          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1157 –            if (simParams_->haveSwitchingRadius()){
1158 –              sprintf(painCave.errMsg,
1159 –                      "SimInfo Warning: A value was set for the switchingRadius\n"
1160 –                      "\teven though the electrostaticSummationMethod was\n"
1161 –                      "\tset to %s\n", myMethod.c_str());
1162 –              painCave.isFatal = 1;
1163 –              simError();            
1164 –            }
1165 –          }
1166 –        }
1167 –      
1168 –        if (simParams_->haveSwitchingRadius()){
1169 –          rsw_ = simParams_->getSwitchingRadius();
1170 –        } else {        
1171 –          sprintf(painCave.errMsg,
1172 –                  "SimCreator Warning: No value was set for switchingRadius.\n"
1173 –                  "\tOpenMD will use a default value of\n"
1174 –                  "\t0.85 * cutoffRadius for the switchingRadius\n");
1175 –          painCave.isFatal = 0;
1176 –          simError();
1177 –          rsw_ = 0.85 * rcut_;
1178 –        }
1179 –
1180 –        Electrostatic::setElectrostaticCutoffRadius(rcut_, rsw_);
1181 –        notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1182 –
1183 –      } else {
1184 –        // We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1185 –        // We'll punt and let fortran figure out the cutoffs later.
1186 –        
1187 –        notifyFortranYouAreOnYourOwn();
1188 –
1189 –      }
1190 –    }
1191 –  }
1192 –
1193 –  void SimInfo::setupElectrostaticSummationMethod( int isError ) {    
1194 –    
1195 –    int errorOut;
1196 –    ElectrostaticSummationMethod esm = NONE;
1197 –    ElectrostaticScreeningMethod sm = UNDAMPED;
1198 –    RealType alphaVal;
1199 –    RealType dielectric;
1200 –    
1201 –    errorOut = isError;
1202 –
1203 –    if (simParams_->haveElectrostaticSummationMethod()) {
1204 –      std::string myMethod = simParams_->getElectrostaticSummationMethod();
1205 –      toUpper(myMethod);
1206 –      if (myMethod == "NONE") {
1207 –        esm = NONE;
1208 –      } else {
1209 –        if (myMethod == "SWITCHING_FUNCTION") {
1210 –          esm = SWITCHING_FUNCTION;
1211 –        } else {
1212 –          if (myMethod == "SHIFTED_POTENTIAL") {
1213 –            esm = SHIFTED_POTENTIAL;
1214 –          } else {
1215 –            if (myMethod == "SHIFTED_FORCE") {            
1216 –              esm = SHIFTED_FORCE;
1217 –            } else {
1218 –              if (myMethod == "REACTION_FIELD") {
1219 –                esm = REACTION_FIELD;
1220 –                dielectric = simParams_->getDielectric();
1221 –                if (!simParams_->haveDielectric()) {
1222 –                  // throw warning
1223 –                  sprintf( painCave.errMsg,
1224 –                           "SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1225 –                           "\tA default value of %f will be used for the dielectric.\n", dielectric);
1226 –                  painCave.isFatal = 0;
1227 –                  simError();
1228 –                }
1229 –              } else {
1230 –                // throw error        
1231 –                sprintf( painCave.errMsg,
1232 –                         "SimInfo error: Unknown electrostaticSummationMethod.\n"
1233 –                         "\t(Input file specified %s .)\n"
1234 –                         "\telectrostaticSummationMethod must be one of: \"none\",\n"
1235 –                         "\t\"shifted_potential\", \"shifted_force\", or \n"
1236 –                         "\t\"reaction_field\".\n", myMethod.c_str() );
1237 –                painCave.isFatal = 1;
1238 –                simError();
1239 –              }    
1240 –            }          
1241 –          }
1242 –        }
1243 –      }
1244 –    }
1245 –    
1246 –    if (simParams_->haveElectrostaticScreeningMethod()) {
1247 –      std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1248 –      toUpper(myScreen);
1249 –      if (myScreen == "UNDAMPED") {
1250 –        sm = UNDAMPED;
1251 –      } else {
1252 –        if (myScreen == "DAMPED") {
1253 –          sm = DAMPED;
1254 –          if (!simParams_->haveDampingAlpha()) {
1255 –            // first set a cutoff dependent alpha value
1256 –            // we assume alpha depends linearly with rcut from 0 to 20.5 ang
1257 –            alphaVal = 0.5125 - rcut_* 0.025;
1258 –            // for values rcut > 20.5, alpha is zero
1259 –            if (alphaVal < 0) alphaVal = 0;
1260 –
1261 –            // throw warning
1262 –            sprintf( painCave.errMsg,
1263 –                     "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1264 –                     "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1265 –            painCave.isFatal = 0;
1266 –            simError();
1267 –          } else {
1268 –            alphaVal = simParams_->getDampingAlpha();
1269 –          }
1270 –          
1271 –        } else {
1272 –          // throw error        
1273 –          sprintf( painCave.errMsg,
1274 –                   "SimInfo error: Unknown electrostaticScreeningMethod.\n"
1275 –                   "\t(Input file specified %s .)\n"
1276 –                   "\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1277 –                   "or \"damped\".\n", myScreen.c_str() );
1278 –          painCave.isFatal = 1;
1279 –          simError();
1280 –        }
1281 –      }
1282 –    }
1283 –    
1284 –
1285 –    Electrostatic::setElectrostaticSummationMethod( esm );
1286 –    Electrostatic::setElectrostaticScreeningMethod( sm );
1287 –    Electrostatic::setDampingAlpha( alphaVal );
1288 –    Electrostatic::setReactionFieldDielectric( dielectric );
1289 –    initFortranFF( &errorOut );
1290 –  }
1291 –
1066    void SimInfo::setupSwitchingFunction() {    
1293 –    int ft = CUBIC;
1067  
1295 –    if (simParams_->haveSwitchingFunctionType()) {
1296 –      std::string funcType = simParams_->getSwitchingFunctionType();
1297 –      toUpper(funcType);
1298 –      if (funcType == "CUBIC") {
1299 –        ft = CUBIC;
1300 –      } else {
1301 –        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1302 –          ft = FIFTH_ORDER_POLY;
1303 –        } else {
1304 –          // throw error        
1305 –          sprintf( painCave.errMsg,
1306 –                   "SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1307 –          painCave.isFatal = 1;
1308 –          simError();
1309 –        }          
1310 –      }
1311 –    }
1312 –
1313 –    // send switching function notification to switcheroo
1314 –    setFunctionType(&ft);
1315 –
1068    }
1069  
1070    void SimInfo::setupAccumulateBoxDipole() {    
# Line 1320 | Line 1072 | namespace OpenMD {
1072      // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1073      if ( simParams_->haveAccumulateBoxDipole() )
1074        if ( simParams_->getAccumulateBoxDipole() ) {
1323 –        setAccumulateBoxDipole();
1075          calcBoxDipole_ = true;
1076        }
1077  
# Line 1330 | Line 1081 | namespace OpenMD {
1081      properties_.addProperty(genData);  
1082    }
1083  
1084 <  void SimInfo::removeProperty(const std::string& propName) {
1084 >  void SimInfo::removeProperty(const string& propName) {
1085      properties_.removeProperty(propName);  
1086    }
1087  
# Line 1338 | Line 1089 | namespace OpenMD {
1089      properties_.clearProperties();
1090    }
1091  
1092 <  std::vector<std::string> SimInfo::getPropertyNames() {
1092 >  vector<string> SimInfo::getPropertyNames() {
1093      return properties_.getPropertyNames();  
1094    }
1095        
1096 <  std::vector<GenericData*> SimInfo::getProperties() {
1096 >  vector<GenericData*> SimInfo::getProperties() {
1097      return properties_.getProperties();
1098    }
1099  
1100 <  GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1100 >  GenericData* SimInfo::getPropertyByName(const string& propName) {
1101      return properties_.getPropertyByName(propName);
1102    }
1103  
# Line 1429 | Line 1180 | namespace OpenMD {
1180  
1181    }        
1182  
1183 <  std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1183 >  ostream& operator <<(ostream& o, SimInfo& info) {
1184  
1185      return o;
1186    }
# Line 1472 | Line 1223 | namespace OpenMD {
1223  
1224  
1225         [  Ixx -Ixy  -Ixz ]
1226 <  J =| -Iyx  Iyy  -Iyz |
1226 >    J =| -Iyx  Iyy  -Iyz |
1227         [ -Izx -Iyz   Izz ]
1228      */
1229  
# Line 1579 | Line 1330 | namespace OpenMD {
1330      return IOIndexToIntegrableObject.at(index);
1331    }
1332    
1333 <  void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1333 >  void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1334      IOIndexToIntegrableObject= v;
1335    }
1336  
# Line 1621 | Line 1372 | namespace OpenMD {
1372      return;
1373    }
1374   /*
1375 <   void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1375 >   void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1376        assert( v.size() == nAtoms_ + nRigidBodies_);
1377        sdByGlobalIndex_ = v;
1378      }
# Line 1631 | Line 1382 | namespace OpenMD {
1382        return sdByGlobalIndex_.at(index);
1383      }  
1384   */  
1385 +  int SimInfo::getNGlobalConstraints() {
1386 +    int nGlobalConstraints;
1387 + #ifdef IS_MPI
1388 +    MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1389 +                  MPI_COMM_WORLD);    
1390 + #else
1391 +    nGlobalConstraints =  nConstraints_;
1392 + #endif
1393 +    return nGlobalConstraints;
1394 +  }
1395 +
1396   }//end namespace OpenMD
1397  

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