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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 1505 by gezelter, Sun Oct 3 22:18:59 2010 UTC vs.
Revision 1534 by gezelter, Wed Dec 29 21:53:28 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  
68 –
66   #ifdef IS_MPI
67   #include "UseTheForce/mpiComponentPlan.h"
68   #include "UseTheForce/DarkSide/simParallel_interface.h"
69   #endif
70  
71 + using namespace std;
72   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 –  }
73    
74    SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
75      forceField_(ff), simParams_(simParams),
# Line 90 | Line 79 | namespace OpenMD {
79      nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
80      nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
81      nConstraints_(0), sman_(NULL), fortranInitialized_(false),
82 <    calcBoxDipole_(false), useAtomicVirial_(true) {
83 <
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 <      std::vector<Component*> components = simParams->getComponents();
82 >    calcBoxDipole_(false), useAtomicVirial_(true) {    
83 >    
84 >    MoleculeStamp* molStamp;
85 >    int nMolWithSameStamp;
86 >    int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
87 >    int nGroups = 0;       //total cutoff groups defined in meta-data file
88 >    CutoffGroupStamp* cgStamp;    
89 >    RigidBodyStamp* rbStamp;
90 >    int nRigidAtoms = 0;
91 >    
92 >    vector<Component*> components = simParams->getComponents();
93 >    
94 >    for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
95 >      molStamp = (*i)->getMoleculeStamp();
96 >      nMolWithSameStamp = (*i)->getNMol();
97        
98 <      for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
99 <        molStamp = (*i)->getMoleculeStamp();
100 <        nMolWithSameStamp = (*i)->getNMol();
101 <        
102 <        addMoleculeStamp(molStamp, nMolWithSameStamp);
103 <
104 <        //calculate atoms in molecules
105 <        nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;  
106 <
107 <        //calculate atoms in cutoff groups
108 <        int nAtomsInGroups = 0;
109 <        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 <        
98 >      addMoleculeStamp(molStamp, nMolWithSameStamp);
99 >      
100 >      //calculate atoms in molecules
101 >      nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;  
102 >      
103 >      //calculate atoms in cutoff groups
104 >      int nAtomsInGroups = 0;
105 >      int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
106 >      
107 >      for (int j=0; j < nCutoffGroupsInStamp; j++) {
108 >        cgStamp = molStamp->getCutoffGroupStamp(j);
109 >        nAtomsInGroups += cgStamp->getNMembers();
110        }
111 <
112 <      //every free atom (atom does not belong to cutoff groups) is a cutoff
113 <      //group therefore the total number of cutoff groups in the system is
114 <      //equal to the total number of atoms minus number of atoms belong to
115 <      //cutoff group defined in meta-data file plus the number of cutoff
116 <      //groups defined in meta-data file
117 <      nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
118 <
119 <      //every free atom (atom does not belong to rigid bodies) is an
120 <      //integrable object therefore the total number of integrable objects
121 <      //in the system is equal to the total number of atoms minus number of
122 <      //atoms belong to rigid body defined in meta-data file plus the number
123 <      //of rigid bodies defined in meta-data file
124 <      nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
125 <                                                + nGlobalRigidBodies_;
126 <  
127 <      nGlobalMols_ = molStampIds_.size();
128 <      molToProcMap_.resize(nGlobalMols_);
129 <    }
130 <
111 >      
112 >      nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
113 >      
114 >      nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;            
115 >      
116 >      //calculate atoms in rigid bodies
117 >      int nAtomsInRigidBodies = 0;
118 >      int nRigidBodiesInStamp = molStamp->getNRigidBodies();
119 >      
120 >      for (int j=0; j < nRigidBodiesInStamp; j++) {
121 >        rbStamp = molStamp->getRigidBodyStamp(j);
122 >        nAtomsInRigidBodies += rbStamp->getNMembers();
123 >      }
124 >      
125 >      nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
126 >      nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;            
127 >      
128 >    }
129 >    
130 >    //every free atom (atom does not belong to cutoff groups) is a cutoff
131 >    //group therefore the total number of cutoff groups in the system is
132 >    //equal to the total number of atoms minus number of atoms belong to
133 >    //cutoff group defined in meta-data file plus the number of cutoff
134 >    //groups defined in meta-data file
135 >    nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
136 >    
137 >    //every free atom (atom does not belong to rigid bodies) is an
138 >    //integrable object therefore the total number of integrable objects
139 >    //in the system is equal to the total number of atoms minus number of
140 >    //atoms belong to rigid body defined in meta-data file plus the number
141 >    //of rigid bodies defined in meta-data file
142 >    nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
143 >      + nGlobalRigidBodies_;
144 >    
145 >    nGlobalMols_ = molStampIds_.size();
146 >    molToProcMap_.resize(nGlobalMols_);
147 >  }
148 >  
149    SimInfo::~SimInfo() {
150 <    std::map<int, Molecule*>::iterator i;
150 >    map<int, Molecule*>::iterator i;
151      for (i = molecules_.begin(); i != molecules_.end(); ++i) {
152        delete i->second;
153      }
# Line 170 | Line 158 | namespace OpenMD {
158      delete forceField_;
159    }
160  
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 –  }
161  
162    bool SimInfo::addMolecule(Molecule* mol) {
163      MoleculeIterator i;
164 <
164 >    
165      i = molecules_.find(mol->getGlobalIndex());
166      if (i == molecules_.end() ) {
167 <
168 <      molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
169 <        
167 >      
168 >      molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
169 >      
170        nAtoms_ += mol->getNAtoms();
171        nBonds_ += mol->getNBonds();
172        nBends_ += mol->getNBends();
# Line 198 | Line 176 | namespace OpenMD {
176        nIntegrableObjects_ += mol->getNIntegrableObjects();
177        nCutoffGroups_ += mol->getNCutoffGroups();
178        nConstraints_ += mol->getNConstraintPairs();
179 <
179 >      
180        addInteractionPairs(mol);
181 <  
181 >      
182        return true;
183      } else {
184        return false;
185      }
186    }
187 <
187 >  
188    bool SimInfo::removeMolecule(Molecule* mol) {
189      MoleculeIterator i;
190      i = molecules_.find(mol->getGlobalIndex());
# Line 234 | Line 212 | namespace OpenMD {
212      } else {
213        return false;
214      }
237 –
238 –
215    }    
216  
217          
# Line 253 | Line 229 | namespace OpenMD {
229    void SimInfo::calcNdf() {
230      int ndf_local;
231      MoleculeIterator i;
232 <    std::vector<StuntDouble*>::iterator j;
232 >    vector<StuntDouble*>::iterator j;
233      Molecule* mol;
234      StuntDouble* integrableObject;
235  
# Line 304 | Line 280 | namespace OpenMD {
280      int ndfRaw_local;
281  
282      MoleculeIterator i;
283 <    std::vector<StuntDouble*>::iterator j;
283 >    vector<StuntDouble*>::iterator j;
284      Molecule* mol;
285      StuntDouble* integrableObject;
286  
# Line 353 | Line 329 | namespace OpenMD {
329  
330    void SimInfo::addInteractionPairs(Molecule* mol) {
331      ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
332 <    std::vector<Bond*>::iterator bondIter;
333 <    std::vector<Bend*>::iterator bendIter;
334 <    std::vector<Torsion*>::iterator torsionIter;
335 <    std::vector<Inversion*>::iterator inversionIter;
332 >    vector<Bond*>::iterator bondIter;
333 >    vector<Bend*>::iterator bendIter;
334 >    vector<Torsion*>::iterator torsionIter;
335 >    vector<Inversion*>::iterator inversionIter;
336      Bond* bond;
337      Bend* bend;
338      Torsion* torsion;
# Line 374 | Line 350 | namespace OpenMD {
350      // always be excluded.  These are done at the bottom of this
351      // function.
352  
353 <    std::map<int, std::set<int> > atomGroups;
353 >    map<int, set<int> > atomGroups;
354      Molecule::RigidBodyIterator rbIter;
355      RigidBody* rb;
356      Molecule::IntegrableObjectIterator ii;
# Line 386 | Line 362 | namespace OpenMD {
362        
363        if (integrableObject->isRigidBody()) {
364          rb = static_cast<RigidBody*>(integrableObject);
365 <        std::vector<Atom*> atoms = rb->getAtoms();
366 <        std::set<int> rigidAtoms;
365 >        vector<Atom*> atoms = rb->getAtoms();
366 >        set<int> rigidAtoms;
367          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
368            rigidAtoms.insert(atoms[i]->getGlobalIndex());
369          }
370          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
371 <          atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
371 >          atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
372          }      
373        } else {
374 <        std::set<int> oneAtomSet;
374 >        set<int> oneAtomSet;
375          oneAtomSet.insert(integrableObject->getGlobalIndex());
376 <        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
376 >        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
377        }
378      }  
379            
# Line 500 | Line 476 | namespace OpenMD {
476  
477      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
478           rb = mol->nextRigidBody(rbIter)) {
479 <      std::vector<Atom*> atoms = rb->getAtoms();
479 >      vector<Atom*> atoms = rb->getAtoms();
480        for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
481          for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
482            a = atoms[i]->getGlobalIndex();
# Line 514 | Line 490 | namespace OpenMD {
490  
491    void SimInfo::removeInteractionPairs(Molecule* mol) {
492      ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
493 <    std::vector<Bond*>::iterator bondIter;
494 <    std::vector<Bend*>::iterator bendIter;
495 <    std::vector<Torsion*>::iterator torsionIter;
496 <    std::vector<Inversion*>::iterator inversionIter;
493 >    vector<Bond*>::iterator bondIter;
494 >    vector<Bend*>::iterator bendIter;
495 >    vector<Torsion*>::iterator torsionIter;
496 >    vector<Inversion*>::iterator inversionIter;
497      Bond* bond;
498      Bend* bend;
499      Torsion* torsion;
# Line 527 | Line 503 | namespace OpenMD {
503      int c;
504      int d;
505  
506 <    std::map<int, std::set<int> > atomGroups;
506 >    map<int, set<int> > atomGroups;
507      Molecule::RigidBodyIterator rbIter;
508      RigidBody* rb;
509      Molecule::IntegrableObjectIterator ii;
# Line 539 | Line 515 | namespace OpenMD {
515        
516        if (integrableObject->isRigidBody()) {
517          rb = static_cast<RigidBody*>(integrableObject);
518 <        std::vector<Atom*> atoms = rb->getAtoms();
519 <        std::set<int> rigidAtoms;
518 >        vector<Atom*> atoms = rb->getAtoms();
519 >        set<int> rigidAtoms;
520          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
521            rigidAtoms.insert(atoms[i]->getGlobalIndex());
522          }
523          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
524 <          atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
524 >          atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
525          }      
526        } else {
527 <        std::set<int> oneAtomSet;
527 >        set<int> oneAtomSet;
528          oneAtomSet.insert(integrableObject->getGlobalIndex());
529 <        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
529 >        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
530        }
531      }  
532  
# Line 653 | Line 629 | namespace OpenMD {
629  
630      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
631           rb = mol->nextRigidBody(rbIter)) {
632 <      std::vector<Atom*> atoms = rb->getAtoms();
632 >      vector<Atom*> atoms = rb->getAtoms();
633        for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
634          for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
635            a = atoms[i]->getGlobalIndex();
# Line 676 | Line 652 | namespace OpenMD {
652      molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
653    }
654  
655 +
656 +  /**
657 +   * update
658 +   *
659 +   *  Performs the global checks and variable settings after the objects have been
660 +   *  created.
661 +   *
662 +   */
663    void SimInfo::update() {
664 +    
665 +    setupSimVariables();
666 +    setupCutoffs();
667 +    setupSwitching();
668 +    setupElectrostatics();
669 +    setupNeighborlists();
670  
681 –    setupSimType();
682 –
671   #ifdef IS_MPI
672      setupFortranParallel();
673   #endif
686 –
674      setupFortranSim();
675 +    fortranInitialized_ = true;
676  
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 –
677      calcNdf();
678      calcNdfRaw();
679      calcNdfTrans();
709 –
710 –    fortranInitialized_ = true;
680    }
681 <
682 <  std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
681 >  
682 >  set<AtomType*> SimInfo::getSimulatedAtomTypes() {
683      SimInfo::MoleculeIterator mi;
684      Molecule* mol;
685      Molecule::AtomIterator ai;
686      Atom* atom;
687 <    std::set<AtomType*> atomTypes;
688 <
689 <    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
721 <
687 >    set<AtomType*> atomTypes;
688 >    
689 >    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {      
690        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
691          atomTypes.insert(atom->getAtomType());
692 <      }
693 <        
726 <    }
727 <
692 >      }      
693 >    }    
694      return atomTypes;        
695    }
696  
697 <  void SimInfo::setupSimType() {
698 <    std::set<AtomType*>::iterator i;
699 <    std::set<AtomType*> atomTypes;
700 <    atomTypes = getUniqueAtomTypes();
697 >  /**
698 >   * setupCutoffs
699 >   *
700 >   * Sets the values of cutoffRadius and cutoffMethod
701 >   *
702 >   * cutoffRadius : realType
703 >   *  If the cutoffRadius was explicitly set, use that value.
704 >   *  If the cutoffRadius was not explicitly set:
705 >   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
706 >   *      No electrostatic atoms?  Poll the atom types present in the
707 >   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
708 >   *      Use the maximum suggested value that was found.
709 >   *
710 >   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
711 >   *      If cutoffMethod was explicitly set, use that choice.
712 >   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
713 >   */
714 >  void SimInfo::setupCutoffs() {
715      
716 <    int useLennardJones = 0;
717 <    int useElectrostatic = 0;
718 <    int useEAM = 0;
719 <    int useSC = 0;
720 <    int useCharge = 0;
721 <    int useDirectional = 0;
722 <    int useDipole = 0;
723 <    int useGayBerne = 0;
724 <    int useSticky = 0;
725 <    int useStickyPower = 0;
726 <    int useShape = 0;
727 <    int useFLARB = 0; //it is not in AtomType yet
728 <    int useDirectionalAtom = 0;    
729 <    int useElectrostatics = 0;
730 <    //usePBC and useRF are from simParams
731 <    int usePBC = simParams_->getUsePeriodicBoundaryConditions();
732 <    int useRF;
733 <    int useSF;
734 <    int useSP;
735 <    int useBoxDipole;
716 >    if (simParams_->haveCutoffRadius()) {
717 >      cutoffRadius_ = simParams_->getCutoffRadius();
718 >    } else {      
719 >      if (usesElectrostaticAtoms_) {
720 >        sprintf(painCave.errMsg,
721 >                "SimInfo: No value was set for the cutoffRadius.\n"
722 >                "\tOpenMD will use a default value of 12.0 angstroms"
723 >                "\tfor the cutoffRadius.\n");
724 >        painCave.isFatal = 0;
725 >        painCave.severity = OPENMD_INFO;
726 >        simError();
727 >        cutoffRadius_ = 12.0;
728 >      } else {
729 >        RealType thisCut;
730 >        set<AtomType*>::iterator i;
731 >        set<AtomType*> atomTypes;
732 >        atomTypes = getSimulatedAtomTypes();        
733 >        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
734 >          thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
735 >          cutoffRadius_ = max(thisCut, cutoffRadius_);
736 >        }
737 >        sprintf(painCave.errMsg,
738 >                "SimInfo: No value was set for the cutoffRadius.\n"
739 >                "\tOpenMD will use %lf angstroms.\n",
740 >                cutoffRadius_);
741 >        painCave.isFatal = 0;
742 >        painCave.severity = OPENMD_INFO;
743 >        simError();
744 >      }            
745 >    }
746  
747 <    std::string myMethod;
748 <
749 <    // set the useRF logical
750 <    useRF = 0;
751 <    useSF = 0;
752 <    useSP = 0;
753 <    useBoxDipole = 0;
754 <
755 <    if (simParams_->haveElectrostaticSummationMethod()) {
756 <      std::string myMethod = simParams_->getElectrostaticSummationMethod();
757 <      toUpper(myMethod);
758 <      if (myMethod == "REACTION_FIELD"){
759 <        useRF = 1;
760 <      } else if (myMethod == "SHIFTED_FORCE"){
761 <        useSF = 1;
762 <      } else if (myMethod == "SHIFTED_POTENTIAL"){
763 <        useSP = 1;
747 >    map<string, CutoffMethod> stringToCutoffMethod;
748 >    stringToCutoffMethod["HARD"] = HARD;
749 >    stringToCutoffMethod["SWITCHING_FUNCTION"] = SWITCHING_FUNCTION;
750 >    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
751 >    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
752 >  
753 >    if (simParams_->haveCutoffMethod()) {
754 >      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
755 >      map<string, CutoffMethod>::iterator i;
756 >      i = stringToCutoffMethod.find(cutMeth);
757 >      if (i == stringToCutoffMethod.end()) {
758 >        sprintf(painCave.errMsg,
759 >                "SimInfo: Could not find chosen cutoffMethod %s\n"
760 >                "\tShould be one of: "
761 >                "HARD, SWITCHING_FUNCTION, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
762 >                cutMeth.c_str());
763 >        painCave.isFatal = 1;
764 >        painCave.severity = OPENMD_ERROR;
765 >        simError();
766 >      } else {
767 >        cutoffMethod_ = i->second;
768        }
769 +    } else {
770 +      sprintf(painCave.errMsg,
771 +              "SimInfo: No value was set for the cutoffMethod.\n"
772 +              "\tOpenMD will use SHIFTED_FORCE.\n");
773 +        painCave.isFatal = 0;
774 +        painCave.severity = OPENMD_INFO;
775 +        simError();
776 +        cutoffMethod_ = SHIFTED_FORCE;        
777      }
778 +  }
779 +  
780 +  /**
781 +   * setupSwitching
782 +   *
783 +   * Sets the values of switchingRadius and
784 +   *  If the switchingRadius was explicitly set, use that value (but check it)
785 +   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
786 +   */
787 +  void SimInfo::setupSwitching() {
788      
789 <    if (simParams_->haveAccumulateBoxDipole())
790 <      if (simParams_->getAccumulateBoxDipole())
791 <        useBoxDipole = 1;
789 >    if (simParams_->haveSwitchingRadius()) {
790 >      switchingRadius_ = simParams_->getSwitchingRadius();
791 >      if (switchingRadius_ > cutoffRadius_) {        
792 >        sprintf(painCave.errMsg,
793 >                "SimInfo: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
794 >                switchingRadius_, cutoffRadius_);
795 >        painCave.isFatal = 1;
796 >        painCave.severity = OPENMD_ERROR;
797 >        simError();
798 >      }
799 >    } else {      
800 >      switchingRadius_ = 0.85 * cutoffRadius_;
801 >      sprintf(painCave.errMsg,
802 >              "SimInfo: No value was set for the switchingRadius.\n"
803 >              "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
804 >              "\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
805 >      painCave.isFatal = 0;
806 >      painCave.severity = OPENMD_WARNING;
807 >      simError();
808 >    }          
809 >    
810 >    if (simParams_->haveSwitchingFunctionType()) {
811 >      string funcType = simParams_->getSwitchingFunctionType();
812 >      toUpper(funcType);
813 >      if (funcType == "CUBIC") {
814 >        sft_ = cubic;
815 >      } else {
816 >        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
817 >          sft_ = fifth_order_poly;
818 >        } else {
819 >          // throw error        
820 >          sprintf( painCave.errMsg,
821 >                   "SimInfo : Unknown switchingFunctionType. (Input file specified %s .)\n"
822 >                   "\tswitchingFunctionType must be one of: "
823 >                   "\"cubic\" or \"fifth_order_polynomial\".",
824 >                   funcType.c_str() );
825 >          painCave.isFatal = 1;
826 >          painCave.severity = OPENMD_ERROR;
827 >          simError();
828 >        }          
829 >      }
830 >    }
831 >  }
832 >
833 >  /**
834 >   * setupNeighborlists
835 >   *
836 >   *  If the skinThickness was explicitly set, use that value (but check it)
837 >   *  If the skinThickness was not explicitly set: use 1.0 angstroms
838 >   */
839 >  void SimInfo::setupNeighborlists() {    
840 >    if (simParams_->haveSkinThickness()) {
841 >      skinThickness_ = simParams_->getSkinThickness();
842 >    } else {      
843 >      skinThickness_ = 1.0;
844 >      sprintf(painCave.errMsg,
845 >              "SimInfo: No value was set for the skinThickness.\n"
846 >              "\tOpenMD will use a default value of %f Angstroms\n"
847 >              "\tfor this simulation\n", skinThickness_);
848 >      painCave.severity = OPENMD_INFO;
849 >      painCave.isFatal = 0;
850 >      simError();
851 >    }            
852 >  }
853  
854 +  void SimInfo::setupSimVariables() {
855      useAtomicVirial_ = simParams_->getUseAtomicVirial();
856 +    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
857 +    calcBoxDipole_ = false;
858 +    if ( simParams_->haveAccumulateBoxDipole() )
859 +      if ( simParams_->getAccumulateBoxDipole() ) {
860 +        calcBoxDipole_ = true;      
861 +      }
862  
863 +    set<AtomType*>::iterator i;
864 +    set<AtomType*> atomTypes;
865 +    atomTypes = getSimulatedAtomTypes();    
866 +    int usesElectrostatic = 0;
867 +    int usesMetallic = 0;
868 +    int usesDirectional = 0;
869      //loop over all of the atom types
870      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
871 <      useLennardJones |= (*i)->isLennardJones();
872 <      useElectrostatic |= (*i)->isElectrostatic();
873 <      useEAM |= (*i)->isEAM();
788 <      useSC |= (*i)->isSC();
789 <      useCharge |= (*i)->isCharge();
790 <      useDirectional |= (*i)->isDirectional();
791 <      useDipole |= (*i)->isDipole();
792 <      useGayBerne |= (*i)->isGayBerne();
793 <      useSticky |= (*i)->isSticky();
794 <      useStickyPower |= (*i)->isStickyPower();
795 <      useShape |= (*i)->isShape();
871 >      usesElectrostatic |= (*i)->isElectrostatic();
872 >      usesMetallic |= (*i)->isMetal();
873 >      usesDirectional |= (*i)->isDirectional();
874      }
875  
798 –    if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
799 –      useDirectionalAtom = 1;
800 –    }
801 –
802 –    if (useCharge || useDipole) {
803 –      useElectrostatics = 1;
804 –    }
805 –
876   #ifdef IS_MPI    
877      int temp;
878 +    temp = usesDirectional;
879 +    MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
880  
881 <    temp = usePBC;
882 <    MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
881 >    temp = usesMetallic;
882 >    MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
883  
884 <    temp = useDirectionalAtom;
885 <    MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
814 <
815 <    temp = useLennardJones;
816 <    MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
817 <
818 <    temp = useElectrostatics;
819 <    MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
820 <
821 <    temp = useCharge;
822 <    MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
823 <
824 <    temp = useDipole;
825 <    MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
826 <
827 <    temp = useSticky;
828 <    MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
829 <
830 <    temp = useStickyPower;
831 <    MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
832 <    
833 <    temp = useGayBerne;
834 <    MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
835 <
836 <    temp = useEAM;
837 <    MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
838 <
839 <    temp = useSC;
840 <    MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
841 <    
842 <    temp = useShape;
843 <    MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
844 <
845 <    temp = useFLARB;
846 <    MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
847 <
848 <    temp = useRF;
849 <    MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
850 <
851 <    temp = useSF;
852 <    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
853 <
854 <    temp = useSP;
855 <    MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
856 <
857 <    temp = useBoxDipole;
858 <    MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
859 <
860 <    temp = useAtomicVirial_;
861 <    MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
862 <
884 >    temp = usesElectrostatic;
885 >    MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
886   #endif
887 <    fInfo_.SIM_uses_PBC = usePBC;    
888 <    fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
889 <    fInfo_.SIM_uses_LennardJones = useLennardJones;
890 <    fInfo_.SIM_uses_Electrostatics = useElectrostatics;    
891 <    fInfo_.SIM_uses_Charges = useCharge;
892 <    fInfo_.SIM_uses_Dipoles = useDipole;
870 <    fInfo_.SIM_uses_Sticky = useSticky;
871 <    fInfo_.SIM_uses_StickyPower = useStickyPower;
872 <    fInfo_.SIM_uses_GayBerne = useGayBerne;
873 <    fInfo_.SIM_uses_EAM = useEAM;
874 <    fInfo_.SIM_uses_SC = useSC;
875 <    fInfo_.SIM_uses_Shapes = useShape;
876 <    fInfo_.SIM_uses_FLARB = useFLARB;
877 <    fInfo_.SIM_uses_RF = useRF;
878 <    fInfo_.SIM_uses_SF = useSF;
879 <    fInfo_.SIM_uses_SP = useSP;
880 <    fInfo_.SIM_uses_BoxDipole = useBoxDipole;
881 <    fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
887 >    fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;    
888 >    fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
889 >    fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
890 >    fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
891 >    fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
892 >    fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
893    }
894  
895    void SimInfo::setupFortranSim() {
896      int isError;
897      int nExclude, nOneTwo, nOneThree, nOneFour;
898 <    std::vector<int> fortranGlobalGroupMembership;
898 >    vector<int> fortranGlobalGroupMembership;
899      
900 +    notifyFortranSkinThickness(&skinThickness_);
901 +
902 +    int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
903 +    int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
904 +    notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
905 +
906      isError = 0;
907  
908      //globalGroupMembership_ is filled by SimCreator    
# Line 894 | Line 911 | namespace OpenMD {
911      }
912  
913      //calculate mass ratio of cutoff group
914 <    std::vector<RealType> mfact;
914 >    vector<RealType> mfact;
915      SimInfo::MoleculeIterator mi;
916      Molecule* mol;
917      Molecule::CutoffGroupIterator ci;
# Line 921 | Line 938 | namespace OpenMD {
938      }
939  
940      //fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
941 <    std::vector<int> identArray;
941 >    vector<int> identArray;
942  
943      //to avoid memory reallocation, reserve enough space identArray
944      identArray.reserve(getNAtoms());
# Line 934 | Line 951 | namespace OpenMD {
951  
952      //fill molMembershipArray
953      //molMembershipArray is filled by SimCreator    
954 <    std::vector<int> molMembershipArray(nGlobalAtoms_);
954 >    vector<int> molMembershipArray(nGlobalAtoms_);
955      for (int i = 0; i < nGlobalAtoms_; i++) {
956        molMembershipArray[i] = globalMolMembership_[i] + 1;
957      }
# Line 987 | Line 1004 | namespace OpenMD {
1004    void SimInfo::setupFortranParallel() {
1005   #ifdef IS_MPI    
1006      //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
1007 <    std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1008 <    std::vector<int> localToGlobalCutoffGroupIndex;
1007 >    vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1008 >    vector<int> localToGlobalCutoffGroupIndex;
1009      SimInfo::MoleculeIterator mi;
1010      Molecule::AtomIterator ai;
1011      Molecule::CutoffGroupIterator ci;
# Line 1038 | Line 1055 | namespace OpenMD {
1055      errorCheckPoint();
1056  
1057   #endif
1041 –  }
1042 –
1043 –  void SimInfo::setupCutoff() {          
1044 –    
1045 –    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1046 –
1047 –    // Check the cutoff policy
1048 –    int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1049 –
1050 –    // Set LJ shifting bools to false
1051 –    ljsp_ = 0;
1052 –    ljsf_ = 0;
1053 –
1054 –    std::string myPolicy;
1055 –    if (forceFieldOptions_.haveCutoffPolicy()){
1056 –      myPolicy = forceFieldOptions_.getCutoffPolicy();
1057 –    }else if (simParams_->haveCutoffPolicy()) {
1058 –      myPolicy = simParams_->getCutoffPolicy();
1059 –    }
1060 –
1061 –    if (!myPolicy.empty()){
1062 –      toUpper(myPolicy);
1063 –      if (myPolicy == "MIX") {
1064 –        cp = MIX_CUTOFF_POLICY;
1065 –      } else {
1066 –        if (myPolicy == "MAX") {
1067 –          cp = MAX_CUTOFF_POLICY;
1068 –        } else {
1069 –          if (myPolicy == "TRADITIONAL") {            
1070 –            cp = TRADITIONAL_CUTOFF_POLICY;
1071 –          } else {
1072 –            // throw error        
1073 –            sprintf( painCave.errMsg,
1074 –                     "SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1075 –            painCave.isFatal = 1;
1076 –            simError();
1077 –          }    
1078 –        }          
1079 –      }
1080 –    }          
1081 –    notifyFortranCutoffPolicy(&cp);
1082 –
1083 –    // Check the Skin Thickness for neighborlists
1084 –    RealType skin;
1085 –    if (simParams_->haveSkinThickness()) {
1086 –      skin = simParams_->getSkinThickness();
1087 –      notifyFortranSkinThickness(&skin);
1088 –    }            
1089 –        
1090 –    // Check if the cutoff was set explicitly:
1091 –    if (simParams_->haveCutoffRadius()) {
1092 –      rcut_ = simParams_->getCutoffRadius();
1093 –      if (simParams_->haveSwitchingRadius()) {
1094 –        rsw_  = simParams_->getSwitchingRadius();
1095 –      } else {
1096 –        if (fInfo_.SIM_uses_Charges |
1097 –            fInfo_.SIM_uses_Dipoles |
1098 –            fInfo_.SIM_uses_RF) {
1099 –          
1100 –          rsw_ = 0.85 * rcut_;
1101 –          sprintf(painCave.errMsg,
1102 –                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1103 –                  "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
1104 –                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1105 –        painCave.isFatal = 0;
1106 –        simError();
1107 –        } else {
1108 –          rsw_ = rcut_;
1109 –          sprintf(painCave.errMsg,
1110 –                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1111 –                  "\tOpenMD will use the same value as the cutoffRadius.\n"
1112 –                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1113 –          painCave.isFatal = 0;
1114 –          simError();
1115 –        }
1116 –      }
1117 –
1118 –      if (simParams_->haveElectrostaticSummationMethod()) {
1119 –        std::string myMethod = simParams_->getElectrostaticSummationMethod();
1120 –        toUpper(myMethod);
1121 –        
1122 –        if (myMethod == "SHIFTED_POTENTIAL") {
1123 –          ljsp_ = 1;
1124 –        } else if (myMethod == "SHIFTED_FORCE") {
1125 –          ljsf_ = 1;
1126 –        }
1127 –      }
1128 –
1129 –      notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1130 –      
1131 –    } else {
1132 –      
1133 –      // For electrostatic atoms, we'll assume a large safe value:
1134 –      if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1135 –        sprintf(painCave.errMsg,
1136 –                "SimCreator Warning: No value was set for the cutoffRadius.\n"
1137 –                "\tOpenMD will use a default value of 15.0 angstroms"
1138 –                "\tfor the cutoffRadius.\n");
1139 –        painCave.isFatal = 0;
1140 –        simError();
1141 –        rcut_ = 15.0;
1142 –      
1143 –        if (simParams_->haveElectrostaticSummationMethod()) {
1144 –          std::string myMethod = simParams_->getElectrostaticSummationMethod();
1145 –          toUpper(myMethod);
1146 –          
1147 –          // For the time being, we're tethering the LJ shifted behavior to the
1148 –          // electrostaticSummationMethod keyword options
1149 –          if (myMethod == "SHIFTED_POTENTIAL") {
1150 –            ljsp_ = 1;
1151 –          } else if (myMethod == "SHIFTED_FORCE") {
1152 –            ljsf_ = 1;
1153 –          }
1154 –          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1155 –            if (simParams_->haveSwitchingRadius()){
1156 –              sprintf(painCave.errMsg,
1157 –                      "SimInfo Warning: A value was set for the switchingRadius\n"
1158 –                      "\teven though the electrostaticSummationMethod was\n"
1159 –                      "\tset to %s\n", myMethod.c_str());
1160 –              painCave.isFatal = 1;
1161 –              simError();            
1162 –            }
1163 –          }
1164 –        }
1165 –      
1166 –        if (simParams_->haveSwitchingRadius()){
1167 –          rsw_ = simParams_->getSwitchingRadius();
1168 –        } else {        
1169 –          sprintf(painCave.errMsg,
1170 –                  "SimCreator Warning: No value was set for switchingRadius.\n"
1171 –                  "\tOpenMD will use a default value of\n"
1172 –                  "\t0.85 * cutoffRadius for the switchingRadius\n");
1173 –          painCave.isFatal = 0;
1174 –          simError();
1175 –          rsw_ = 0.85 * rcut_;
1176 –        }
1177 –
1178 –        Electrostatic::setElectrostaticCutoffRadius(rcut_, rsw_);
1179 –        notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1180 –
1181 –      } else {
1182 –        // We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1183 –        // We'll punt and let fortran figure out the cutoffs later.
1184 –        
1185 –        notifyFortranYouAreOnYourOwn();
1186 –
1187 –      }
1188 –    }
1058    }
1059  
1191 –  void SimInfo::setupElectrostaticSummationMethod( int isError ) {    
1192 –    
1193 –    int errorOut;
1194 –    ElectrostaticSummationMethod esm = NONE;
1195 –    ElectrostaticScreeningMethod sm = UNDAMPED;
1196 –    RealType alphaVal;
1197 –    RealType dielectric;
1198 –    
1199 –    errorOut = isError;
1060  
1201 –    if (simParams_->haveElectrostaticSummationMethod()) {
1202 –      std::string myMethod = simParams_->getElectrostaticSummationMethod();
1203 –      toUpper(myMethod);
1204 –      if (myMethod == "NONE") {
1205 –        esm = NONE;
1206 –      } else {
1207 –        if (myMethod == "SWITCHING_FUNCTION") {
1208 –          esm = SWITCHING_FUNCTION;
1209 –        } else {
1210 –          if (myMethod == "SHIFTED_POTENTIAL") {
1211 –            esm = SHIFTED_POTENTIAL;
1212 –          } else {
1213 –            if (myMethod == "SHIFTED_FORCE") {            
1214 –              esm = SHIFTED_FORCE;
1215 –            } else {
1216 –              if (myMethod == "REACTION_FIELD") {
1217 –                esm = REACTION_FIELD;
1218 –                dielectric = simParams_->getDielectric();
1219 –                if (!simParams_->haveDielectric()) {
1220 –                  // throw warning
1221 –                  sprintf( painCave.errMsg,
1222 –                           "SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1223 –                           "\tA default value of %f will be used for the dielectric.\n", dielectric);
1224 –                  painCave.isFatal = 0;
1225 –                  simError();
1226 –                }
1227 –              } else {
1228 –                // throw error        
1229 –                sprintf( painCave.errMsg,
1230 –                         "SimInfo error: Unknown electrostaticSummationMethod.\n"
1231 –                         "\t(Input file specified %s .)\n"
1232 –                         "\telectrostaticSummationMethod must be one of: \"none\",\n"
1233 –                         "\t\"shifted_potential\", \"shifted_force\", or \n"
1234 –                         "\t\"reaction_field\".\n", myMethod.c_str() );
1235 –                painCave.isFatal = 1;
1236 –                simError();
1237 –              }    
1238 –            }          
1239 –          }
1240 –        }
1241 –      }
1242 –    }
1243 –    
1244 –    if (simParams_->haveElectrostaticScreeningMethod()) {
1245 –      std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1246 –      toUpper(myScreen);
1247 –      if (myScreen == "UNDAMPED") {
1248 –        sm = UNDAMPED;
1249 –      } else {
1250 –        if (myScreen == "DAMPED") {
1251 –          sm = DAMPED;
1252 –          if (!simParams_->haveDampingAlpha()) {
1253 –            // first set a cutoff dependent alpha value
1254 –            // we assume alpha depends linearly with rcut from 0 to 20.5 ang
1255 –            alphaVal = 0.5125 - rcut_* 0.025;
1256 –            // for values rcut > 20.5, alpha is zero
1257 –            if (alphaVal < 0) alphaVal = 0;
1258 –
1259 –            // throw warning
1260 –            sprintf( painCave.errMsg,
1261 –                     "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1262 –                     "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1263 –            painCave.isFatal = 0;
1264 –            simError();
1265 –          } else {
1266 –            alphaVal = simParams_->getDampingAlpha();
1267 –          }
1268 –          
1269 –        } else {
1270 –          // throw error        
1271 –          sprintf( painCave.errMsg,
1272 –                   "SimInfo error: Unknown electrostaticScreeningMethod.\n"
1273 –                   "\t(Input file specified %s .)\n"
1274 –                   "\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1275 –                   "or \"damped\".\n", myScreen.c_str() );
1276 –          painCave.isFatal = 1;
1277 –          simError();
1278 –        }
1279 –      }
1280 –    }
1281 –    
1282 –
1283 –    Electrostatic::setElectrostaticSummationMethod( esm );
1284 –    Electrostatic::setElectrostaticScreeningMethod( sm );
1285 –    Electrostatic::setDampingAlpha( alphaVal );
1286 –    Electrostatic::setReactionFieldDielectric( dielectric );
1287 –    initFortranFF( &errorOut );
1288 –  }
1289 –
1290 –  void SimInfo::setupSwitchingFunction() {    
1291 –    int ft = CUBIC;
1292 –
1293 –    if (simParams_->haveSwitchingFunctionType()) {
1294 –      std::string funcType = simParams_->getSwitchingFunctionType();
1295 –      toUpper(funcType);
1296 –      if (funcType == "CUBIC") {
1297 –        ft = CUBIC;
1298 –      } else {
1299 –        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1300 –          ft = FIFTH_ORDER_POLY;
1301 –        } else {
1302 –          // throw error        
1303 –          sprintf( painCave.errMsg,
1304 –                   "SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1305 –          painCave.isFatal = 1;
1306 –          simError();
1307 –        }          
1308 –      }
1309 –    }
1310 –
1311 –    // send switching function notification to switcheroo
1312 –    setFunctionType(&ft);
1313 –
1314 –  }
1315 –
1061    void SimInfo::setupAccumulateBoxDipole() {    
1062  
1318 –    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1319 –    if ( simParams_->haveAccumulateBoxDipole() )
1320 –      if ( simParams_->getAccumulateBoxDipole() ) {
1321 –        setAccumulateBoxDipole();
1322 –        calcBoxDipole_ = true;
1323 –      }
1063  
1064    }
1065  
# Line 1328 | Line 1067 | namespace OpenMD {
1067      properties_.addProperty(genData);  
1068    }
1069  
1070 <  void SimInfo::removeProperty(const std::string& propName) {
1070 >  void SimInfo::removeProperty(const string& propName) {
1071      properties_.removeProperty(propName);  
1072    }
1073  
# Line 1336 | Line 1075 | namespace OpenMD {
1075      properties_.clearProperties();
1076    }
1077  
1078 <  std::vector<std::string> SimInfo::getPropertyNames() {
1078 >  vector<string> SimInfo::getPropertyNames() {
1079      return properties_.getPropertyNames();  
1080    }
1081        
1082 <  std::vector<GenericData*> SimInfo::getProperties() {
1082 >  vector<GenericData*> SimInfo::getProperties() {
1083      return properties_.getProperties();
1084    }
1085  
1086 <  GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1086 >  GenericData* SimInfo::getPropertyByName(const string& propName) {
1087      return properties_.getPropertyByName(propName);
1088    }
1089  
# Line 1427 | Line 1166 | namespace OpenMD {
1166  
1167    }        
1168  
1169 <  std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1169 >  ostream& operator <<(ostream& o, SimInfo& info) {
1170  
1171      return o;
1172    }
# Line 1577 | Line 1316 | namespace OpenMD {
1316      return IOIndexToIntegrableObject.at(index);
1317    }
1318    
1319 <  void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1319 >  void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1320      IOIndexToIntegrableObject= v;
1321    }
1322  
# Line 1619 | Line 1358 | namespace OpenMD {
1358      return;
1359    }
1360   /*
1361 <   void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1361 >   void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1362        assert( v.size() == nAtoms_ + nRigidBodies_);
1363        sdByGlobalIndex_ = v;
1364      }
# Line 1629 | Line 1368 | namespace OpenMD {
1368        return sdByGlobalIndex_.at(index);
1369      }  
1370   */  
1371 +  int SimInfo::getNGlobalConstraints() {
1372 +    int nGlobalConstraints;
1373 + #ifdef IS_MPI
1374 +    MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1375 +                  MPI_COMM_WORLD);    
1376 + #else
1377 +    nGlobalConstraints =  nConstraints_;
1378 + #endif
1379 +    return nGlobalConstraints;
1380 +  }
1381 +
1382   }//end namespace OpenMD
1383  

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