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trunk/src/brains/SimInfo.cpp (file contents), Revision 1103 by chuckv, Fri Dec 29 20:21:53 2006 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

# Line 6 | Line 6
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
28   * arising out of the use of or inability to use software, even if the
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31 + *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
35 + *                                                                      
36 + * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37 + * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 + * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 + * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 + * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   /**
# Line 54 | Line 55
55   #include "math/Vector3.hpp"
56   #include "primitives/Molecule.hpp"
57   #include "primitives/StuntDouble.hpp"
57 #include "UseTheForce/fCutoffPolicy.h"
58 #include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
59 #include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
60 #include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
61 #include "UseTheForce/doForces_interface.h"
62 #include "UseTheForce/DarkSide/neighborLists_interface.h"
63 #include "UseTheForce/DarkSide/electrostatic_interface.h"
64 #include "UseTheForce/DarkSide/switcheroo_interface.h"
58   #include "utils/MemoryUtils.hpp"
59   #include "utils/simError.h"
60   #include "selection/SelectionManager.hpp"
61   #include "io/ForceFieldOptions.hpp"
62   #include "UseTheForce/ForceField.hpp"
63 <
71 <
63 > #include "nonbonded/SwitchingFunction.hpp"
64   #ifdef IS_MPI
65 < #include "UseTheForce/mpiComponentPlan.h"
66 < #include "UseTheForce/DarkSide/simParallel_interface.h"
75 < #endif
65 > #include <mpi.h>
66 > #endif
67  
68 < namespace oopse {
69 <  std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
79 <    std::map<int, std::set<int> >::iterator i = container.find(index);
80 <    std::set<int> result;
81 <    if (i != container.end()) {
82 <        result = i->second;
83 <    }
84 <
85 <    return result;
86 <  }
68 > using namespace std;
69 > namespace OpenMD {
70    
71    SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
72      forceField_(ff), simParams_(simParams),
73      ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74      nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75      nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
76 <    nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
77 <    nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
78 <    sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false) {
79 <
80 <      MoleculeStamp* molStamp;
81 <      int nMolWithSameStamp;
82 <      int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
83 <      int nGroups = 0;      //total cutoff groups defined in meta-data file
84 <      CutoffGroupStamp* cgStamp;    
85 <      RigidBodyStamp* rbStamp;
86 <      int nRigidAtoms = 0;
87 <      std::vector<Component*> components = simParams->getComponents();
76 >    nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
77 >    nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
78 >    nConstraints_(0), sman_(NULL), topologyDone_(false),
79 >    calcBoxDipole_(false), useAtomicVirial_(true) {    
80 >    
81 >    MoleculeStamp* molStamp;
82 >    int nMolWithSameStamp;
83 >    int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
84 >    int nGroups = 0;       //total cutoff groups defined in meta-data file
85 >    CutoffGroupStamp* cgStamp;    
86 >    RigidBodyStamp* rbStamp;
87 >    int nRigidAtoms = 0;
88 >    
89 >    vector<Component*> components = simParams->getComponents();
90 >    
91 >    for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
92 >      molStamp = (*i)->getMoleculeStamp();
93 >      nMolWithSameStamp = (*i)->getNMol();
94        
95 <      for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
96 <        molStamp = (*i)->getMoleculeStamp();
97 <        nMolWithSameStamp = (*i)->getNMol();
98 <        
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();
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 <        
95 >      addMoleculeStamp(molStamp, nMolWithSameStamp);
96 >      
97 >      //calculate atoms in molecules
98 >      nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;  
99 >      
100 >      //calculate atoms in cutoff groups
101 >      int nAtomsInGroups = 0;
102 >      int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
103 >      
104 >      for (int j=0; j < nCutoffGroupsInStamp; j++) {
105 >        cgStamp = molStamp->getCutoffGroupStamp(j);
106 >        nAtomsInGroups += cgStamp->getNMembers();
107        }
108 <
109 <      //every free atom (atom does not belong to cutoff groups) is a cutoff
110 <      //group therefore the total number of cutoff groups in the system is
111 <      //equal to the total number of atoms minus number of atoms belong to
112 <      //cutoff group defined in meta-data file plus the number of cutoff
113 <      //groups defined in meta-data file
114 <      nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
115 <
116 <      //every free atom (atom does not belong to rigid bodies) is an
117 <      //integrable object therefore the total number of integrable objects
118 <      //in the system is equal to the total number of atoms minus number of
119 <      //atoms belong to rigid body defined in meta-data file plus the number
120 <      //of rigid bodies defined in meta-data file
121 <      nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
122 <                                                + nGlobalRigidBodies_;
123 <  
124 <      nGlobalMols_ = molStampIds_.size();
158 <
159 < #ifdef IS_MPI    
160 <      molToProcMap_.resize(nGlobalMols_);
161 < #endif
162 <
108 >      
109 >      nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
110 >      
111 >      nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;            
112 >      
113 >      //calculate atoms in rigid bodies
114 >      int nAtomsInRigidBodies = 0;
115 >      int nRigidBodiesInStamp = molStamp->getNRigidBodies();
116 >      
117 >      for (int j=0; j < nRigidBodiesInStamp; j++) {
118 >        rbStamp = molStamp->getRigidBodyStamp(j);
119 >        nAtomsInRigidBodies += rbStamp->getNMembers();
120 >      }
121 >      
122 >      nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
123 >      nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;            
124 >      
125      }
126 +    
127 +    //every free atom (atom does not belong to cutoff groups) is a cutoff
128 +    //group therefore the total number of cutoff groups in the system is
129 +    //equal to the total number of atoms minus number of atoms belong to
130 +    //cutoff group defined in meta-data file plus the number of cutoff
131 +    //groups defined in meta-data file
132  
133 +    nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
134 +    
135 +    //every free atom (atom does not belong to rigid bodies) is an
136 +    //integrable object therefore the total number of integrable objects
137 +    //in the system is equal to the total number of atoms minus number of
138 +    //atoms belong to rigid body defined in meta-data file plus the number
139 +    //of rigid bodies defined in meta-data file
140 +    nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
141 +      + nGlobalRigidBodies_;
142 +    
143 +    nGlobalMols_ = molStampIds_.size();
144 +    molToProcMap_.resize(nGlobalMols_);
145 +  }
146 +  
147    SimInfo::~SimInfo() {
148 <    std::map<int, Molecule*>::iterator i;
148 >    map<int, Molecule*>::iterator i;
149      for (i = molecules_.begin(); i != molecules_.end(); ++i) {
150        delete i->second;
151      }
# Line 174 | Line 156 | namespace oopse {
156      delete forceField_;
157    }
158  
177  int SimInfo::getNGlobalConstraints() {
178    int nGlobalConstraints;
179 #ifdef IS_MPI
180    MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
181                  MPI_COMM_WORLD);    
182 #else
183    nGlobalConstraints =  nConstraints_;
184 #endif
185    return nGlobalConstraints;
186  }
159  
160    bool SimInfo::addMolecule(Molecule* mol) {
161      MoleculeIterator i;
162 <
162 >    
163      i = molecules_.find(mol->getGlobalIndex());
164      if (i == molecules_.end() ) {
165 <
166 <      molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
167 <        
165 >      
166 >      molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
167 >      
168        nAtoms_ += mol->getNAtoms();
169        nBonds_ += mol->getNBonds();
170        nBends_ += mol->getNBends();
171        nTorsions_ += mol->getNTorsions();
172 +      nInversions_ += mol->getNInversions();
173        nRigidBodies_ += mol->getNRigidBodies();
174        nIntegrableObjects_ += mol->getNIntegrableObjects();
175        nCutoffGroups_ += mol->getNCutoffGroups();
176        nConstraints_ += mol->getNConstraintPairs();
177 <
178 <      addExcludePairs(mol);
179 <        
177 >      
178 >      addInteractionPairs(mol);
179 >      
180        return true;
181      } else {
182        return false;
183      }
184    }
185 <
185 >  
186    bool SimInfo::removeMolecule(Molecule* mol) {
187      MoleculeIterator i;
188      i = molecules_.find(mol->getGlobalIndex());
# Line 222 | Line 195 | namespace oopse {
195        nBonds_ -= mol->getNBonds();
196        nBends_ -= mol->getNBends();
197        nTorsions_ -= mol->getNTorsions();
198 +      nInversions_ -= mol->getNInversions();
199        nRigidBodies_ -= mol->getNRigidBodies();
200        nIntegrableObjects_ -= mol->getNIntegrableObjects();
201        nCutoffGroups_ -= mol->getNCutoffGroups();
202        nConstraints_ -= mol->getNConstraintPairs();
203  
204 <      removeExcludePairs(mol);
204 >      removeInteractionPairs(mol);
205        molecules_.erase(mol->getGlobalIndex());
206  
207        delete mol;
# Line 236 | Line 210 | namespace oopse {
210      } else {
211        return false;
212      }
239
240
213    }    
214  
215          
# Line 255 | Line 227 | namespace oopse {
227    void SimInfo::calcNdf() {
228      int ndf_local;
229      MoleculeIterator i;
230 <    std::vector<StuntDouble*>::iterator j;
230 >    vector<StuntDouble*>::iterator j;
231      Molecule* mol;
232      StuntDouble* integrableObject;
233  
# Line 301 | Line 273 | namespace oopse {
273   #endif
274      return fdf_;
275    }
276 +  
277 +  unsigned int SimInfo::getNLocalCutoffGroups(){
278 +    int nLocalCutoffAtoms = 0;
279 +    Molecule* mol;
280 +    MoleculeIterator mi;
281 +    CutoffGroup* cg;
282 +    Molecule::CutoffGroupIterator ci;
283      
284 +    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
285 +      
286 +      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
287 +           cg = mol->nextCutoffGroup(ci)) {
288 +        nLocalCutoffAtoms += cg->getNumAtom();
289 +        
290 +      }        
291 +    }
292 +    
293 +    return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
294 +  }
295 +    
296    void SimInfo::calcNdfRaw() {
297      int ndfRaw_local;
298  
299      MoleculeIterator i;
300 <    std::vector<StuntDouble*>::iterator j;
300 >    vector<StuntDouble*>::iterator j;
301      Molecule* mol;
302      StuntDouble* integrableObject;
303  
# Line 353 | Line 344 | namespace oopse {
344  
345    }
346  
347 <  void SimInfo::addExcludePairs(Molecule* mol) {
348 <    std::vector<Bond*>::iterator bondIter;
349 <    std::vector<Bend*>::iterator bendIter;
350 <    std::vector<Torsion*>::iterator torsionIter;
347 >  void SimInfo::addInteractionPairs(Molecule* mol) {
348 >    ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
349 >    vector<Bond*>::iterator bondIter;
350 >    vector<Bend*>::iterator bendIter;
351 >    vector<Torsion*>::iterator torsionIter;
352 >    vector<Inversion*>::iterator inversionIter;
353      Bond* bond;
354      Bend* bend;
355      Torsion* torsion;
356 +    Inversion* inversion;
357      int a;
358      int b;
359      int c;
360      int d;
361  
362 <    std::map<int, std::set<int> > atomGroups;
362 >    // atomGroups can be used to add special interaction maps between
363 >    // groups of atoms that are in two separate rigid bodies.
364 >    // However, most site-site interactions between two rigid bodies
365 >    // are probably not special, just the ones between the physically
366 >    // bonded atoms.  Interactions *within* a single rigid body should
367 >    // always be excluded.  These are done at the bottom of this
368 >    // function.
369  
370 +    map<int, set<int> > atomGroups;
371      Molecule::RigidBodyIterator rbIter;
372      RigidBody* rb;
373      Molecule::IntegrableObjectIterator ii;
374      StuntDouble* integrableObject;
375      
376 <    for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
377 <           integrableObject = mol->nextIntegrableObject(ii)) {
378 <
376 >    for (integrableObject = mol->beginIntegrableObject(ii);
377 >         integrableObject != NULL;
378 >         integrableObject = mol->nextIntegrableObject(ii)) {
379 >      
380        if (integrableObject->isRigidBody()) {
381 <          rb = static_cast<RigidBody*>(integrableObject);
382 <          std::vector<Atom*> atoms = rb->getAtoms();
383 <          std::set<int> rigidAtoms;
384 <          for (int i = 0; i < atoms.size(); ++i) {
385 <            rigidAtoms.insert(atoms[i]->getGlobalIndex());
386 <          }
387 <          for (int i = 0; i < atoms.size(); ++i) {
388 <            atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
389 <          }      
390 <      } else {
391 <        std::set<int> oneAtomSet;
381 >        rb = static_cast<RigidBody*>(integrableObject);
382 >        vector<Atom*> atoms = rb->getAtoms();
383 >        set<int> rigidAtoms;
384 >        for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
385 >          rigidAtoms.insert(atoms[i]->getGlobalIndex());
386 >        }
387 >        for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
388 >          atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
389 >        }      
390 >      } else {
391 >        set<int> oneAtomSet;
392          oneAtomSet.insert(integrableObject->getGlobalIndex());
393 <        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
393 >        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
394        }
395      }  
396 +          
397 +    for (bond= mol->beginBond(bondIter); bond != NULL;
398 +         bond = mol->nextBond(bondIter)) {
399  
395    
396    
397    for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
400        a = bond->getAtomA()->getGlobalIndex();
401 <      b = bond->getAtomB()->getGlobalIndex();        
402 <      exclude_.addPair(a, b);
401 >      b = bond->getAtomB()->getGlobalIndex();  
402 >    
403 >      if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
404 >        oneTwoInteractions_.addPair(a, b);
405 >      } else {
406 >        excludedInteractions_.addPair(a, b);
407 >      }
408      }
409  
410 <    for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
410 >    for (bend= mol->beginBend(bendIter); bend != NULL;
411 >         bend = mol->nextBend(bendIter)) {
412 >
413        a = bend->getAtomA()->getGlobalIndex();
414        b = bend->getAtomB()->getGlobalIndex();        
415        c = bend->getAtomC()->getGlobalIndex();
407      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
408      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
409      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
410
411      exclude_.addPairs(rigidSetA, rigidSetB);
412      exclude_.addPairs(rigidSetA, rigidSetC);
413      exclude_.addPairs(rigidSetB, rigidSetC);
416        
417 <      //exclude_.addPair(a, b);
418 <      //exclude_.addPair(a, c);
419 <      //exclude_.addPair(b, c);        
417 >      if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
418 >        oneTwoInteractions_.addPair(a, b);      
419 >        oneTwoInteractions_.addPair(b, c);
420 >      } else {
421 >        excludedInteractions_.addPair(a, b);
422 >        excludedInteractions_.addPair(b, c);
423 >      }
424 >
425 >      if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
426 >        oneThreeInteractions_.addPair(a, c);      
427 >      } else {
428 >        excludedInteractions_.addPair(a, c);
429 >      }
430      }
431  
432 <    for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
432 >    for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
433 >         torsion = mol->nextTorsion(torsionIter)) {
434 >
435        a = torsion->getAtomA()->getGlobalIndex();
436        b = torsion->getAtomB()->getGlobalIndex();        
437        c = torsion->getAtomC()->getGlobalIndex();        
438 <      d = torsion->getAtomD()->getGlobalIndex();        
425 <      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
426 <      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
427 <      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
428 <      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
438 >      d = torsion->getAtomD()->getGlobalIndex();      
439  
440 <      exclude_.addPairs(rigidSetA, rigidSetB);
441 <      exclude_.addPairs(rigidSetA, rigidSetC);
442 <      exclude_.addPairs(rigidSetA, rigidSetD);
443 <      exclude_.addPairs(rigidSetB, rigidSetC);
444 <      exclude_.addPairs(rigidSetB, rigidSetD);
445 <      exclude_.addPairs(rigidSetC, rigidSetD);
440 >      if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
441 >        oneTwoInteractions_.addPair(a, b);      
442 >        oneTwoInteractions_.addPair(b, c);
443 >        oneTwoInteractions_.addPair(c, d);
444 >      } else {
445 >        excludedInteractions_.addPair(a, b);
446 >        excludedInteractions_.addPair(b, c);
447 >        excludedInteractions_.addPair(c, d);
448 >      }
449  
450 <      /*
451 <      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
452 <      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
453 <      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
454 <      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
455 <      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
456 <      exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
457 <        
458 <      
459 <      exclude_.addPair(a, b);
460 <      exclude_.addPair(a, c);
461 <      exclude_.addPair(a, d);
462 <      exclude_.addPair(b, c);
450 <      exclude_.addPair(b, d);
451 <      exclude_.addPair(c, d);        
452 <      */
450 >      if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
451 >        oneThreeInteractions_.addPair(a, c);      
452 >        oneThreeInteractions_.addPair(b, d);      
453 >      } else {
454 >        excludedInteractions_.addPair(a, c);
455 >        excludedInteractions_.addPair(b, d);
456 >      }
457 >
458 >      if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
459 >        oneFourInteractions_.addPair(a, d);      
460 >      } else {
461 >        excludedInteractions_.addPair(a, d);
462 >      }
463      }
464  
465 <    for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
466 <      std::vector<Atom*> atoms = rb->getAtoms();
467 <      for (int i = 0; i < atoms.size() -1 ; ++i) {
468 <        for (int j = i + 1; j < atoms.size(); ++j) {
465 >    for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
466 >         inversion = mol->nextInversion(inversionIter)) {
467 >
468 >      a = inversion->getAtomA()->getGlobalIndex();
469 >      b = inversion->getAtomB()->getGlobalIndex();        
470 >      c = inversion->getAtomC()->getGlobalIndex();        
471 >      d = inversion->getAtomD()->getGlobalIndex();        
472 >
473 >      if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
474 >        oneTwoInteractions_.addPair(a, b);      
475 >        oneTwoInteractions_.addPair(a, c);
476 >        oneTwoInteractions_.addPair(a, d);
477 >      } else {
478 >        excludedInteractions_.addPair(a, b);
479 >        excludedInteractions_.addPair(a, c);
480 >        excludedInteractions_.addPair(a, d);
481 >      }
482 >
483 >      if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
484 >        oneThreeInteractions_.addPair(b, c);    
485 >        oneThreeInteractions_.addPair(b, d);    
486 >        oneThreeInteractions_.addPair(c, d);      
487 >      } else {
488 >        excludedInteractions_.addPair(b, c);
489 >        excludedInteractions_.addPair(b, d);
490 >        excludedInteractions_.addPair(c, d);
491 >      }
492 >    }
493 >
494 >    for (rb = mol->beginRigidBody(rbIter); rb != NULL;
495 >         rb = mol->nextRigidBody(rbIter)) {
496 >      vector<Atom*> atoms = rb->getAtoms();
497 >      for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
498 >        for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
499            a = atoms[i]->getGlobalIndex();
500            b = atoms[j]->getGlobalIndex();
501 <          exclude_.addPair(a, b);
501 >          excludedInteractions_.addPair(a, b);
502          }
503        }
504      }        
505  
506    }
507  
508 <  void SimInfo::removeExcludePairs(Molecule* mol) {
509 <    std::vector<Bond*>::iterator bondIter;
510 <    std::vector<Bend*>::iterator bendIter;
511 <    std::vector<Torsion*>::iterator torsionIter;
508 >  void SimInfo::removeInteractionPairs(Molecule* mol) {
509 >    ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
510 >    vector<Bond*>::iterator bondIter;
511 >    vector<Bend*>::iterator bendIter;
512 >    vector<Torsion*>::iterator torsionIter;
513 >    vector<Inversion*>::iterator inversionIter;
514      Bond* bond;
515      Bend* bend;
516      Torsion* torsion;
517 +    Inversion* inversion;
518      int a;
519      int b;
520      int c;
521      int d;
522  
523 <    std::map<int, std::set<int> > atomGroups;
481 <
523 >    map<int, set<int> > atomGroups;
524      Molecule::RigidBodyIterator rbIter;
525      RigidBody* rb;
526      Molecule::IntegrableObjectIterator ii;
527      StuntDouble* integrableObject;
528      
529 <    for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
530 <           integrableObject = mol->nextIntegrableObject(ii)) {
531 <
529 >    for (integrableObject = mol->beginIntegrableObject(ii);
530 >         integrableObject != NULL;
531 >         integrableObject = mol->nextIntegrableObject(ii)) {
532 >      
533        if (integrableObject->isRigidBody()) {
534 <          rb = static_cast<RigidBody*>(integrableObject);
535 <          std::vector<Atom*> atoms = rb->getAtoms();
536 <          std::set<int> rigidAtoms;
537 <          for (int i = 0; i < atoms.size(); ++i) {
538 <            rigidAtoms.insert(atoms[i]->getGlobalIndex());
539 <          }
540 <          for (int i = 0; i < atoms.size(); ++i) {
541 <            atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
542 <          }      
534 >        rb = static_cast<RigidBody*>(integrableObject);
535 >        vector<Atom*> atoms = rb->getAtoms();
536 >        set<int> rigidAtoms;
537 >        for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
538 >          rigidAtoms.insert(atoms[i]->getGlobalIndex());
539 >        }
540 >        for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
541 >          atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
542 >        }      
543        } else {
544 <        std::set<int> oneAtomSet;
544 >        set<int> oneAtomSet;
545          oneAtomSet.insert(integrableObject->getGlobalIndex());
546 <        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
546 >        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
547        }
548      }  
549  
550 <    
551 <    for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
550 >    for (bond= mol->beginBond(bondIter); bond != NULL;
551 >         bond = mol->nextBond(bondIter)) {
552 >      
553        a = bond->getAtomA()->getGlobalIndex();
554 <      b = bond->getAtomB()->getGlobalIndex();        
555 <      exclude_.removePair(a, b);
554 >      b = bond->getAtomB()->getGlobalIndex();  
555 >    
556 >      if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
557 >        oneTwoInteractions_.removePair(a, b);
558 >      } else {
559 >        excludedInteractions_.removePair(a, b);
560 >      }
561      }
562  
563 <    for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
563 >    for (bend= mol->beginBend(bendIter); bend != NULL;
564 >         bend = mol->nextBend(bendIter)) {
565 >
566        a = bend->getAtomA()->getGlobalIndex();
567        b = bend->getAtomB()->getGlobalIndex();        
568        c = bend->getAtomC()->getGlobalIndex();
518
519      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
520      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
521      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
522
523      exclude_.removePairs(rigidSetA, rigidSetB);
524      exclude_.removePairs(rigidSetA, rigidSetC);
525      exclude_.removePairs(rigidSetB, rigidSetC);
569        
570 <      //exclude_.removePair(a, b);
571 <      //exclude_.removePair(a, c);
572 <      //exclude_.removePair(b, c);        
570 >      if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
571 >        oneTwoInteractions_.removePair(a, b);      
572 >        oneTwoInteractions_.removePair(b, c);
573 >      } else {
574 >        excludedInteractions_.removePair(a, b);
575 >        excludedInteractions_.removePair(b, c);
576 >      }
577 >
578 >      if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
579 >        oneThreeInteractions_.removePair(a, c);      
580 >      } else {
581 >        excludedInteractions_.removePair(a, c);
582 >      }
583      }
584  
585 <    for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
585 >    for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
586 >         torsion = mol->nextTorsion(torsionIter)) {
587 >
588        a = torsion->getAtomA()->getGlobalIndex();
589        b = torsion->getAtomB()->getGlobalIndex();        
590        c = torsion->getAtomC()->getGlobalIndex();        
591 <      d = torsion->getAtomD()->getGlobalIndex();        
591 >      d = torsion->getAtomD()->getGlobalIndex();      
592 >  
593 >      if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
594 >        oneTwoInteractions_.removePair(a, b);      
595 >        oneTwoInteractions_.removePair(b, c);
596 >        oneTwoInteractions_.removePair(c, d);
597 >      } else {
598 >        excludedInteractions_.removePair(a, b);
599 >        excludedInteractions_.removePair(b, c);
600 >        excludedInteractions_.removePair(c, d);
601 >      }
602  
603 <      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
604 <      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
605 <      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
606 <      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
603 >      if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
604 >        oneThreeInteractions_.removePair(a, c);      
605 >        oneThreeInteractions_.removePair(b, d);      
606 >      } else {
607 >        excludedInteractions_.removePair(a, c);
608 >        excludedInteractions_.removePair(b, d);
609 >      }
610  
611 <      exclude_.removePairs(rigidSetA, rigidSetB);
612 <      exclude_.removePairs(rigidSetA, rigidSetC);
613 <      exclude_.removePairs(rigidSetA, rigidSetD);
614 <      exclude_.removePairs(rigidSetB, rigidSetC);
615 <      exclude_.removePairs(rigidSetB, rigidSetD);
616 <      exclude_.removePairs(rigidSetC, rigidSetD);
611 >      if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
612 >        oneFourInteractions_.removePair(a, d);      
613 >      } else {
614 >        excludedInteractions_.removePair(a, d);
615 >      }
616 >    }
617  
618 <      /*
619 <      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
552 <      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
553 <      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
554 <      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
555 <      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
556 <      exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
618 >    for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
619 >         inversion = mol->nextInversion(inversionIter)) {
620  
621 <      
622 <      exclude_.removePair(a, b);
623 <      exclude_.removePair(a, c);
624 <      exclude_.removePair(a, d);
625 <      exclude_.removePair(b, c);
626 <      exclude_.removePair(b, d);
627 <      exclude_.removePair(c, d);        
628 <      */
621 >      a = inversion->getAtomA()->getGlobalIndex();
622 >      b = inversion->getAtomB()->getGlobalIndex();        
623 >      c = inversion->getAtomC()->getGlobalIndex();        
624 >      d = inversion->getAtomD()->getGlobalIndex();        
625 >
626 >      if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
627 >        oneTwoInteractions_.removePair(a, b);      
628 >        oneTwoInteractions_.removePair(a, c);
629 >        oneTwoInteractions_.removePair(a, d);
630 >      } else {
631 >        excludedInteractions_.removePair(a, b);
632 >        excludedInteractions_.removePair(a, c);
633 >        excludedInteractions_.removePair(a, d);
634 >      }
635 >
636 >      if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
637 >        oneThreeInteractions_.removePair(b, c);    
638 >        oneThreeInteractions_.removePair(b, d);    
639 >        oneThreeInteractions_.removePair(c, d);      
640 >      } else {
641 >        excludedInteractions_.removePair(b, c);
642 >        excludedInteractions_.removePair(b, d);
643 >        excludedInteractions_.removePair(c, d);
644 >      }
645      }
646  
647 <    for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
648 <      std::vector<Atom*> atoms = rb->getAtoms();
649 <      for (int i = 0; i < atoms.size() -1 ; ++i) {
650 <        for (int j = i + 1; j < atoms.size(); ++j) {
647 >    for (rb = mol->beginRigidBody(rbIter); rb != NULL;
648 >         rb = mol->nextRigidBody(rbIter)) {
649 >      vector<Atom*> atoms = rb->getAtoms();
650 >      for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
651 >        for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
652            a = atoms[i]->getGlobalIndex();
653            b = atoms[j]->getGlobalIndex();
654 <          exclude_.removePair(a, b);
654 >          excludedInteractions_.removePair(a, b);
655          }
656        }
657      }        
658 <
658 >    
659    }
660 <
661 <
660 >  
661 >  
662    void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
663      int curStampId;
664 <
664 >    
665      //index from 0
666      curStampId = moleculeStamps_.size();
667  
# Line 589 | Line 669 | namespace oopse {
669      molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
670    }
671  
592  void SimInfo::update() {
672  
673 <    setupSimType();
674 <
675 < #ifdef IS_MPI
676 <    setupFortranParallel();
677 < #endif
678 <
679 <    setupFortranSim();
680 <
681 <    //setup fortran force field
603 <    /** @deprecate */    
604 <    int isError = 0;
605 <    
606 <    setupCutoff();
607 <    
608 <    setupElectrostaticSummationMethod( isError );
609 <    setupSwitchingFunction();
610 <    setupAccumulateBoxDipole();
611 <
612 <    if(isError){
613 <      sprintf( painCave.errMsg,
614 <               "ForceField error: There was an error initializing the forceField in fortran.\n" );
615 <      painCave.isFatal = 1;
616 <      simError();
617 <    }
618 <
673 >  /**
674 >   * update
675 >   *
676 >   *  Performs the global checks and variable settings after the
677 >   *  objects have been created.
678 >   *
679 >   */
680 >  void SimInfo::update() {  
681 >    setupSimVariables();
682      calcNdf();
683      calcNdfRaw();
684      calcNdfTrans();
622
623    fortranInitialized_ = true;
685    }
686 <
687 <  std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
686 >  
687 >  /**
688 >   * getSimulatedAtomTypes
689 >   *
690 >   * Returns an STL set of AtomType* that are actually present in this
691 >   * simulation.  Must query all processors to assemble this information.
692 >   *
693 >   */
694 >  set<AtomType*> SimInfo::getSimulatedAtomTypes() {
695      SimInfo::MoleculeIterator mi;
696      Molecule* mol;
697      Molecule::AtomIterator ai;
698      Atom* atom;
699 <    std::set<AtomType*> atomTypes;
700 <
699 >    set<AtomType*> atomTypes;
700 >    
701      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
702 <
703 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
702 >      for(atom = mol->beginAtom(ai); atom != NULL;
703 >          atom = mol->nextAtom(ai)) {
704          atomTypes.insert(atom->getAtomType());
705 <      }
706 <        
705 >      }      
706 >    }    
707 >    
708 > #ifdef IS_MPI
709 >
710 >    // loop over the found atom types on this processor, and add their
711 >    // numerical idents to a vector:
712 >    
713 >    vector<int> foundTypes;
714 >    set<AtomType*>::iterator i;
715 >    for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
716 >      foundTypes.push_back( (*i)->getIdent() );
717 >
718 >    // count_local holds the number of found types on this processor
719 >    int count_local = foundTypes.size();
720 >
721 >    int nproc = MPI::COMM_WORLD.Get_size();
722 >
723 >    // we need arrays to hold the counts and displacement vectors for
724 >    // all processors
725 >    vector<int> counts(nproc, 0);
726 >    vector<int> disps(nproc, 0);
727 >
728 >    // fill the counts array
729 >    MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
730 >                              1, MPI::INT);
731 >  
732 >    // use the processor counts to compute the displacement array
733 >    disps[0] = 0;    
734 >    int totalCount = counts[0];
735 >    for (int iproc = 1; iproc < nproc; iproc++) {
736 >      disps[iproc] = disps[iproc-1] + counts[iproc-1];
737 >      totalCount += counts[iproc];
738      }
739  
740 <    return atomTypes;        
741 <  }
643 <
644 <  void SimInfo::setupSimType() {
645 <    std::set<AtomType*>::iterator i;
646 <    std::set<AtomType*> atomTypes;
647 <    atomTypes = getUniqueAtomTypes();
740 >    // we need a (possibly redundant) set of all found types:
741 >    vector<int> ftGlobal(totalCount);
742      
743 <    int useLennardJones = 0;
744 <    int useElectrostatic = 0;
745 <    int useEAM = 0;
746 <    int useSC = 0;
653 <    int useCharge = 0;
654 <    int useDirectional = 0;
655 <    int useDipole = 0;
656 <    int useGayBerne = 0;
657 <    int useSticky = 0;
658 <    int useStickyPower = 0;
659 <    int useShape = 0;
660 <    int useFLARB = 0; //it is not in AtomType yet
661 <    int useDirectionalAtom = 0;    
662 <    int useElectrostatics = 0;
663 <    //usePBC and useRF are from simParams
664 <    int usePBC = simParams_->getUsePeriodicBoundaryConditions();
665 <    int useRF;
666 <    int useSF;
667 <    int useSP;
668 <    int useBoxDipole;
669 <    std::string myMethod;
743 >    // now spray out the foundTypes to all the other processors:    
744 >    MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
745 >                               &ftGlobal[0], &counts[0], &disps[0],
746 >                               MPI::INT);
747  
748 <    // set the useRF logical
672 <    useRF = 0;
673 <    useSF = 0;
674 <    useSP = 0;
748 >    vector<int>::iterator j;
749  
750 +    // foundIdents is a stl set, so inserting an already found ident
751 +    // will have no effect.
752 +    set<int> foundIdents;
753  
754 <    if (simParams_->haveElectrostaticSummationMethod()) {
755 <      std::string myMethod = simParams_->getElectrostaticSummationMethod();
679 <      toUpper(myMethod);
680 <      if (myMethod == "REACTION_FIELD"){
681 <        useRF = 1;
682 <      } else if (myMethod == "SHIFTED_FORCE"){
683 <        useSF = 1;
684 <      } else if (myMethod == "SHIFTED_POTENTIAL"){
685 <        useSP = 1;
686 <      }
687 <    }
754 >    for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
755 >      foundIdents.insert((*j));
756      
757 <    if (simParams_->haveAccumulateBoxDipole())
758 <      if (simParams_->getAccumulateBoxDipole())
759 <        useBoxDipole = 1;
757 >    // now iterate over the foundIdents and get the actual atom types
758 >    // that correspond to these:
759 >    set<int>::iterator it;
760 >    for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
761 >      atomTypes.insert( forceField_->getAtomType((*it)) );
762 >
763 > #endif
764  
765 +    return atomTypes;        
766 +  }
767 +
768 +  void SimInfo::setupSimVariables() {
769 +    useAtomicVirial_ = simParams_->getUseAtomicVirial();
770 +    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
771 +    calcBoxDipole_ = false;
772 +    if ( simParams_->haveAccumulateBoxDipole() )
773 +      if ( simParams_->getAccumulateBoxDipole() ) {
774 +        calcBoxDipole_ = true;      
775 +      }
776 +    
777 +    set<AtomType*>::iterator i;
778 +    set<AtomType*> atomTypes;
779 +    atomTypes = getSimulatedAtomTypes();    
780 +    int usesElectrostatic = 0;
781 +    int usesMetallic = 0;
782 +    int usesDirectional = 0;
783      //loop over all of the atom types
784      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
785 <      useLennardJones |= (*i)->isLennardJones();
786 <      useElectrostatic |= (*i)->isElectrostatic();
787 <      useEAM |= (*i)->isEAM();
698 <      useSC |= (*i)->isSC();
699 <      useCharge |= (*i)->isCharge();
700 <      useDirectional |= (*i)->isDirectional();
701 <      useDipole |= (*i)->isDipole();
702 <      useGayBerne |= (*i)->isGayBerne();
703 <      useSticky |= (*i)->isSticky();
704 <      useStickyPower |= (*i)->isStickyPower();
705 <      useShape |= (*i)->isShape();
785 >      usesElectrostatic |= (*i)->isElectrostatic();
786 >      usesMetallic |= (*i)->isMetal();
787 >      usesDirectional |= (*i)->isDirectional();
788      }
789 <
708 <    if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
709 <      useDirectionalAtom = 1;
710 <    }
711 <
712 <    if (useCharge || useDipole) {
713 <      useElectrostatics = 1;
714 <    }
715 <
789 >    
790   #ifdef IS_MPI    
791      int temp;
792 <
793 <    temp = usePBC;
720 <    MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
721 <
722 <    temp = useDirectionalAtom;
723 <    MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
724 <
725 <    temp = useLennardJones;
726 <    MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
727 <
728 <    temp = useElectrostatics;
729 <    MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
730 <
731 <    temp = useCharge;
732 <    MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
733 <
734 <    temp = useDipole;
735 <    MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
736 <
737 <    temp = useSticky;
738 <    MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
739 <
740 <    temp = useStickyPower;
741 <    MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
792 >    temp = usesDirectional;
793 >    MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
794      
795 <    temp = useGayBerne;
796 <    MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
795 >    temp = usesMetallic;
796 >    MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
797 >    
798 >    temp = usesElectrostatic;
799 >    MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
800 > #else
801  
802 <    temp = useEAM;
803 <    MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
802 >    usesDirectionalAtoms_ = usesDirectional;
803 >    usesMetallicAtoms_ = usesMetallic;
804 >    usesElectrostaticAtoms_ = usesElectrostatic;
805  
806 <    temp = useSC;
750 <    MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
806 > #endif
807      
808 <    temp = useShape;
809 <    MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
808 >    requiresPrepair_ = usesMetallicAtoms_ ? true : false;
809 >    requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
810 >    requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;    
811 >  }
812  
755    temp = useFLARB;
756    MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
813  
814 <    temp = useRF;
815 <    MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
814 >  vector<int> SimInfo::getGlobalAtomIndices() {
815 >    SimInfo::MoleculeIterator mi;
816 >    Molecule* mol;
817 >    Molecule::AtomIterator ai;
818 >    Atom* atom;
819  
820 <    temp = useSF;
821 <    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
820 >    vector<int> GlobalAtomIndices(getNAtoms(), 0);
821 >    
822 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
823 >      
824 >      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
825 >        GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
826 >      }
827 >    }
828 >    return GlobalAtomIndices;
829 >  }
830  
764    temp = useSP;
765    MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
831  
832 <    temp = useBoxDipole;
833 <    MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
832 >  vector<int> SimInfo::getGlobalGroupIndices() {
833 >    SimInfo::MoleculeIterator mi;
834 >    Molecule* mol;
835 >    Molecule::CutoffGroupIterator ci;
836 >    CutoffGroup* cg;
837  
838 < #endif
839 <
840 <    fInfo_.SIM_uses_PBC = usePBC;    
841 <    fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
842 <    fInfo_.SIM_uses_LennardJones = useLennardJones;
843 <    fInfo_.SIM_uses_Electrostatics = useElectrostatics;    
844 <    fInfo_.SIM_uses_Charges = useCharge;
845 <    fInfo_.SIM_uses_Dipoles = useDipole;
846 <    fInfo_.SIM_uses_Sticky = useSticky;
847 <    fInfo_.SIM_uses_StickyPower = useStickyPower;
848 <    fInfo_.SIM_uses_GayBerne = useGayBerne;
849 <    fInfo_.SIM_uses_EAM = useEAM;
782 <    fInfo_.SIM_uses_SC = useSC;
783 <    fInfo_.SIM_uses_Shapes = useShape;
784 <    fInfo_.SIM_uses_FLARB = useFLARB;
785 <    fInfo_.SIM_uses_RF = useRF;
786 <    fInfo_.SIM_uses_SF = useSF;
787 <    fInfo_.SIM_uses_SP = useSP;
788 <    fInfo_.SIM_uses_BoxDipole = useBoxDipole;
838 >    vector<int> GlobalGroupIndices;
839 >    
840 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
841 >      
842 >      //local index of cutoff group is trivial, it only depends on the
843 >      //order of travesing
844 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
845 >           cg = mol->nextCutoffGroup(ci)) {
846 >        GlobalGroupIndices.push_back(cg->getGlobalIndex());
847 >      }        
848 >    }
849 >    return GlobalGroupIndices;
850    }
851  
791  void SimInfo::setupFortranSim() {
792    int isError;
793    int nExclude;
794    std::vector<int> fortranGlobalGroupMembership;
795    
796    nExclude = exclude_.getSize();
797    isError = 0;
852  
853 <    //globalGroupMembership_ is filled by SimCreator    
854 <    for (int i = 0; i < nGlobalAtoms_; i++) {
801 <      fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
802 <    }
853 >  void SimInfo::prepareTopology() {
854 >    int nExclude, nOneTwo, nOneThree, nOneFour;
855  
856      //calculate mass ratio of cutoff group
805    std::vector<RealType> mfact;
857      SimInfo::MoleculeIterator mi;
858      Molecule* mol;
859      Molecule::CutoffGroupIterator ci;
# Line 811 | Line 862 | namespace oopse {
862      Atom* atom;
863      RealType totalMass;
864  
865 <    //to avoid memory reallocation, reserve enough space for mfact
866 <    mfact.reserve(getNCutoffGroups());
865 >    /**
866 >     * The mass factor is the relative mass of an atom to the total
867 >     * mass of the cutoff group it belongs to.  By default, all atoms
868 >     * are their own cutoff groups, and therefore have mass factors of
869 >     * 1.  We need some special handling for massless atoms, which
870 >     * will be treated as carrying the entire mass of the cutoff
871 >     * group.
872 >     */
873 >    massFactors_.clear();
874 >    massFactors_.resize(getNAtoms(), 1.0);
875      
876      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
877 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
877 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
878 >           cg = mol->nextCutoffGroup(ci)) {
879  
880          totalMass = cg->getMass();
881          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
882            // Check for massless groups - set mfact to 1 if true
883 <          if (totalMass != 0)
884 <            mfact.push_back(atom->getMass()/totalMass);
883 >          if (totalMass != 0)
884 >            massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
885            else
886 <            mfact.push_back( 1.0 );
886 >            massFactors_[atom->getLocalIndex()] = 1.0;
887          }
828
888        }      
889      }
890  
891 <    //fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
833 <    std::vector<int> identArray;
891 >    // Build the identArray_
892  
893 <    //to avoid memory reallocation, reserve enough space identArray
894 <    identArray.reserve(getNAtoms());
837 <    
893 >    identArray_.clear();
894 >    identArray_.reserve(getNAtoms());    
895      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
896        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
897 <        identArray.push_back(atom->getIdent());
897 >        identArray_.push_back(atom->getIdent());
898        }
899      }    
843
844    //fill molMembershipArray
845    //molMembershipArray is filled by SimCreator    
846    std::vector<int> molMembershipArray(nGlobalAtoms_);
847    for (int i = 0; i < nGlobalAtoms_; i++) {
848      molMembershipArray[i] = globalMolMembership_[i] + 1;
849    }
900      
901 <    //setup fortran simulation
852 <    int nGlobalExcludes = 0;
853 <    int* globalExcludes = NULL;
854 <    int* excludeList = exclude_.getExcludeList();
855 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
856 <                   &nGlobalExcludes, globalExcludes, &molMembershipArray[0],
857 <                   &mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
901 >    //scan topology
902  
903 <    if( isError ){
903 >    nExclude = excludedInteractions_.getSize();
904 >    nOneTwo = oneTwoInteractions_.getSize();
905 >    nOneThree = oneThreeInteractions_.getSize();
906 >    nOneFour = oneFourInteractions_.getSize();
907  
908 <      sprintf( painCave.errMsg,
909 <               "There was an error setting the simulation information in fortran.\n" );
910 <      painCave.isFatal = 1;
911 <      painCave.severity = OOPSE_ERROR;
865 <      simError();
866 <    }
908 >    int* excludeList = excludedInteractions_.getPairList();
909 >    int* oneTwoList = oneTwoInteractions_.getPairList();
910 >    int* oneThreeList = oneThreeInteractions_.getPairList();
911 >    int* oneFourList = oneFourInteractions_.getPairList();
912  
913 < #ifdef IS_MPI
869 <    sprintf( checkPointMsg,
870 <             "succesfully sent the simulation information to fortran.\n");
871 <    MPIcheckPoint();
872 < #endif // is_mpi
873 <
874 <    // Setup number of neighbors in neighbor list if present
875 <    if (simParams_->haveNeighborListNeighbors()) {
876 <      setNeighbors(simParams_->getNeighborListNeighbors());
877 <    }
878 <  
879 <
880 <  }
881 <
882 <
883 < #ifdef IS_MPI
884 <  void SimInfo::setupFortranParallel() {
885 <    
886 <    //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
887 <    std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
888 <    std::vector<int> localToGlobalCutoffGroupIndex;
889 <    SimInfo::MoleculeIterator mi;
890 <    Molecule::AtomIterator ai;
891 <    Molecule::CutoffGroupIterator ci;
892 <    Molecule* mol;
893 <    Atom* atom;
894 <    CutoffGroup* cg;
895 <    mpiSimData parallelData;
896 <    int isError;
897 <
898 <    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
899 <
900 <      //local index(index in DataStorge) of atom is important
901 <      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
902 <        localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
903 <      }
904 <
905 <      //local index of cutoff group is trivial, it only depends on the order of travesing
906 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
907 <        localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
908 <      }        
909 <        
910 <    }
911 <
912 <    //fill up mpiSimData struct
913 <    parallelData.nMolGlobal = getNGlobalMolecules();
914 <    parallelData.nMolLocal = getNMolecules();
915 <    parallelData.nAtomsGlobal = getNGlobalAtoms();
916 <    parallelData.nAtomsLocal = getNAtoms();
917 <    parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
918 <    parallelData.nGroupsLocal = getNCutoffGroups();
919 <    parallelData.myNode = worldRank;
920 <    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
921 <
922 <    //pass mpiSimData struct and index arrays to fortran
923 <    setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
924 <                    &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
925 <                    &localToGlobalCutoffGroupIndex[0], &isError);
926 <
927 <    if (isError) {
928 <      sprintf(painCave.errMsg,
929 <              "mpiRefresh errror: fortran didn't like something we gave it.\n");
930 <      painCave.isFatal = 1;
931 <      simError();
932 <    }
933 <
934 <    sprintf(checkPointMsg, " mpiRefresh successful.\n");
935 <    MPIcheckPoint();
936 <
937 <
938 <  }
939 <
940 < #endif
941 <
942 <  void SimInfo::setupCutoff() {          
943 <    
944 <    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
945 <
946 <    // Check the cutoff policy
947 <    int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
948 <
949 <    std::string myPolicy;
950 <    if (forceFieldOptions_.haveCutoffPolicy()){
951 <      myPolicy = forceFieldOptions_.getCutoffPolicy();
952 <    }else if (simParams_->haveCutoffPolicy()) {
953 <      myPolicy = simParams_->getCutoffPolicy();
954 <    }
955 <
956 <    if (!myPolicy.empty()){
957 <      toUpper(myPolicy);
958 <      if (myPolicy == "MIX") {
959 <        cp = MIX_CUTOFF_POLICY;
960 <      } else {
961 <        if (myPolicy == "MAX") {
962 <          cp = MAX_CUTOFF_POLICY;
963 <        } else {
964 <          if (myPolicy == "TRADITIONAL") {            
965 <            cp = TRADITIONAL_CUTOFF_POLICY;
966 <          } else {
967 <            // throw error        
968 <            sprintf( painCave.errMsg,
969 <                     "SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
970 <            painCave.isFatal = 1;
971 <            simError();
972 <          }    
973 <        }          
974 <      }
975 <    }          
976 <    notifyFortranCutoffPolicy(&cp);
977 <
978 <    // Check the Skin Thickness for neighborlists
979 <    RealType skin;
980 <    if (simParams_->haveSkinThickness()) {
981 <      skin = simParams_->getSkinThickness();
982 <      notifyFortranSkinThickness(&skin);
983 <    }            
984 <        
985 <    // Check if the cutoff was set explicitly:
986 <    if (simParams_->haveCutoffRadius()) {
987 <      rcut_ = simParams_->getCutoffRadius();
988 <      if (simParams_->haveSwitchingRadius()) {
989 <        rsw_  = simParams_->getSwitchingRadius();
990 <      } else {
991 <        if (fInfo_.SIM_uses_Charges |
992 <            fInfo_.SIM_uses_Dipoles |
993 <            fInfo_.SIM_uses_RF) {
994 <          
995 <          rsw_ = 0.85 * rcut_;
996 <          sprintf(painCave.errMsg,
997 <                  "SimCreator Warning: No value was set for the switchingRadius.\n"
998 <                  "\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
999 <                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1000 <        painCave.isFatal = 0;
1001 <        simError();
1002 <        } else {
1003 <          rsw_ = rcut_;
1004 <          sprintf(painCave.errMsg,
1005 <                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1006 <                  "\tOOPSE will use the same value as the cutoffRadius.\n"
1007 <                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1008 <          painCave.isFatal = 0;
1009 <          simError();
1010 <        }
1011 <      }
1012 <      
1013 <      notifyFortranCutoffs(&rcut_, &rsw_);
1014 <      
1015 <    } else {
1016 <      
1017 <      // For electrostatic atoms, we'll assume a large safe value:
1018 <      if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1019 <        sprintf(painCave.errMsg,
1020 <                "SimCreator Warning: No value was set for the cutoffRadius.\n"
1021 <                "\tOOPSE will use a default value of 15.0 angstroms"
1022 <                "\tfor the cutoffRadius.\n");
1023 <        painCave.isFatal = 0;
1024 <        simError();
1025 <        rcut_ = 15.0;
1026 <      
1027 <        if (simParams_->haveElectrostaticSummationMethod()) {
1028 <          std::string myMethod = simParams_->getElectrostaticSummationMethod();
1029 <          toUpper(myMethod);
1030 <          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1031 <            if (simParams_->haveSwitchingRadius()){
1032 <              sprintf(painCave.errMsg,
1033 <                      "SimInfo Warning: A value was set for the switchingRadius\n"
1034 <                      "\teven though the electrostaticSummationMethod was\n"
1035 <                      "\tset to %s\n", myMethod.c_str());
1036 <              painCave.isFatal = 1;
1037 <              simError();            
1038 <            }
1039 <          }
1040 <        }
1041 <      
1042 <        if (simParams_->haveSwitchingRadius()){
1043 <          rsw_ = simParams_->getSwitchingRadius();
1044 <        } else {        
1045 <          sprintf(painCave.errMsg,
1046 <                  "SimCreator Warning: No value was set for switchingRadius.\n"
1047 <                  "\tOOPSE will use a default value of\n"
1048 <                  "\t0.85 * cutoffRadius for the switchingRadius\n");
1049 <          painCave.isFatal = 0;
1050 <          simError();
1051 <          rsw_ = 0.85 * rcut_;
1052 <        }
1053 <        notifyFortranCutoffs(&rcut_, &rsw_);
1054 <      } else {
1055 <        // We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1056 <        // We'll punt and let fortran figure out the cutoffs later.
1057 <        
1058 <        notifyFortranYouAreOnYourOwn();
1059 <
1060 <      }
1061 <    }
1062 <  }
1063 <
1064 <  void SimInfo::setupElectrostaticSummationMethod( int isError ) {    
1065 <    
1066 <    int errorOut;
1067 <    int esm =  NONE;
1068 <    int sm = UNDAMPED;
1069 <    RealType alphaVal;
1070 <    RealType dielectric;
1071 <    
1072 <    errorOut = isError;
1073 <
1074 <    if (simParams_->haveElectrostaticSummationMethod()) {
1075 <      std::string myMethod = simParams_->getElectrostaticSummationMethod();
1076 <      toUpper(myMethod);
1077 <      if (myMethod == "NONE") {
1078 <        esm = NONE;
1079 <      } else {
1080 <        if (myMethod == "SWITCHING_FUNCTION") {
1081 <          esm = SWITCHING_FUNCTION;
1082 <        } else {
1083 <          if (myMethod == "SHIFTED_POTENTIAL") {
1084 <            esm = SHIFTED_POTENTIAL;
1085 <          } else {
1086 <            if (myMethod == "SHIFTED_FORCE") {            
1087 <              esm = SHIFTED_FORCE;
1088 <            } else {
1089 <              if (myMethod == "REACTION_FIELD") {
1090 <                esm = REACTION_FIELD;
1091 <                dielectric = simParams_->getDielectric();
1092 <                if (!simParams_->haveDielectric()) {
1093 <                  // throw warning
1094 <                  sprintf( painCave.errMsg,
1095 <                           "SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1096 <                           "\tA default value of %f will be used for the dielectric.\n", dielectric);
1097 <                  painCave.isFatal = 0;
1098 <                  simError();
1099 <                }
1100 <              } else {
1101 <                // throw error        
1102 <                sprintf( painCave.errMsg,
1103 <                         "SimInfo error: Unknown electrostaticSummationMethod.\n"
1104 <                         "\t(Input file specified %s .)\n"
1105 <                         "\telectrostaticSummationMethod must be one of: \"none\",\n"
1106 <                         "\t\"shifted_potential\", \"shifted_force\", or \n"
1107 <                         "\t\"reaction_field\".\n", myMethod.c_str() );
1108 <                painCave.isFatal = 1;
1109 <                simError();
1110 <              }    
1111 <            }          
1112 <          }
1113 <        }
1114 <      }
1115 <    }
1116 <    
1117 <    if (simParams_->haveElectrostaticScreeningMethod()) {
1118 <      std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1119 <      toUpper(myScreen);
1120 <      if (myScreen == "UNDAMPED") {
1121 <        sm = UNDAMPED;
1122 <      } else {
1123 <        if (myScreen == "DAMPED") {
1124 <          sm = DAMPED;
1125 <          if (!simParams_->haveDampingAlpha()) {
1126 <            // first set a cutoff dependent alpha value
1127 <            // we assume alpha depends linearly with rcut from 0 to 20.5 ang
1128 <            alphaVal = 0.5125 - rcut_* 0.025;
1129 <            // for values rcut > 20.5, alpha is zero
1130 <            if (alphaVal < 0) alphaVal = 0;
1131 <
1132 <            // throw warning
1133 <            sprintf( painCave.errMsg,
1134 <                     "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1135 <                     "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1136 <            painCave.isFatal = 0;
1137 <            simError();
1138 <          } else {
1139 <            alphaVal = simParams_->getDampingAlpha();
1140 <          }
1141 <          
1142 <        } else {
1143 <          // throw error        
1144 <          sprintf( painCave.errMsg,
1145 <                   "SimInfo error: Unknown electrostaticScreeningMethod.\n"
1146 <                   "\t(Input file specified %s .)\n"
1147 <                   "\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1148 <                   "or \"damped\".\n", myScreen.c_str() );
1149 <          painCave.isFatal = 1;
1150 <          simError();
1151 <        }
1152 <      }
1153 <    }
1154 <    
1155 <    // let's pass some summation method variables to fortran
1156 <    setElectrostaticSummationMethod( &esm );
1157 <    setFortranElectrostaticMethod( &esm );
1158 <    setScreeningMethod( &sm );
1159 <    setDampingAlpha( &alphaVal );
1160 <    setReactionFieldDielectric( &dielectric );
1161 <    initFortranFF( &errorOut );
1162 <  }
1163 <
1164 <  void SimInfo::setupSwitchingFunction() {    
1165 <    int ft = CUBIC;
1166 <
1167 <    if (simParams_->haveSwitchingFunctionType()) {
1168 <      std::string funcType = simParams_->getSwitchingFunctionType();
1169 <      toUpper(funcType);
1170 <      if (funcType == "CUBIC") {
1171 <        ft = CUBIC;
1172 <      } else {
1173 <        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1174 <          ft = FIFTH_ORDER_POLY;
1175 <        } else {
1176 <          // throw error        
1177 <          sprintf( painCave.errMsg,
1178 <                   "SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1179 <          painCave.isFatal = 1;
1180 <          simError();
1181 <        }          
1182 <      }
1183 <    }
1184 <
1185 <    // send switching function notification to switcheroo
1186 <    setFunctionType(&ft);
1187 <
1188 <  }
1189 <
1190 <  void SimInfo::setupAccumulateBoxDipole() {    
1191 <
1192 <    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1193 <    if ( simParams_->haveAccumulateBoxDipole() )
1194 <      if ( simParams_->getAccumulateBoxDipole() ) {
1195 <        setAccumulateBoxDipole();
1196 <        calcBoxDipole_ = true;
1197 <      }
1198 <
913 >    topologyDone_ = true;
914    }
915  
916    void SimInfo::addProperty(GenericData* genData) {
917      properties_.addProperty(genData);  
918    }
919  
920 <  void SimInfo::removeProperty(const std::string& propName) {
920 >  void SimInfo::removeProperty(const string& propName) {
921      properties_.removeProperty(propName);  
922    }
923  
# Line 1210 | Line 925 | namespace oopse {
925      properties_.clearProperties();
926    }
927  
928 <  std::vector<std::string> SimInfo::getPropertyNames() {
928 >  vector<string> SimInfo::getPropertyNames() {
929      return properties_.getPropertyNames();  
930    }
931        
932 <  std::vector<GenericData*> SimInfo::getProperties() {
932 >  vector<GenericData*> SimInfo::getProperties() {
933      return properties_.getProperties();
934    }
935  
936 <  GenericData* SimInfo::getPropertyByName(const std::string& propName) {
936 >  GenericData* SimInfo::getPropertyByName(const string& propName) {
937      return properties_.getPropertyByName(propName);
938    }
939  
# Line 1232 | Line 947 | namespace oopse {
947      Molecule* mol;
948      RigidBody* rb;
949      Atom* atom;
950 +    CutoffGroup* cg;
951      SimInfo::MoleculeIterator mi;
952      Molecule::RigidBodyIterator rbIter;
953 <    Molecule::AtomIterator atomIter;;
953 >    Molecule::AtomIterator atomIter;
954 >    Molecule::CutoffGroupIterator cgIter;
955  
956      for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
957          
# Line 1245 | Line 962 | namespace oopse {
962        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
963          rb->setSnapshotManager(sman_);
964        }
965 +
966 +      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
967 +        cg->setSnapshotManager(sman_);
968 +      }
969      }    
970      
971    }
# Line 1301 | Line 1022 | namespace oopse {
1022  
1023    }        
1024  
1025 <  std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1025 >  ostream& operator <<(ostream& o, SimInfo& info) {
1026  
1027      return o;
1028    }
# Line 1344 | Line 1065 | namespace oopse {
1065  
1066  
1067         [  Ixx -Ixy  -Ixz ]
1068 <  J =| -Iyx  Iyy  -Iyz |
1068 >    J =| -Iyx  Iyy  -Iyz |
1069         [ -Izx -Iyz   Izz ]
1070      */
1071  
# Line 1451 | Line 1172 | namespace oopse {
1172      return IOIndexToIntegrableObject.at(index);
1173    }
1174    
1175 <  void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1175 >  void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1176      IOIndexToIntegrableObject= v;
1177    }
1178  
# Line 1493 | Line 1214 | namespace oopse {
1214      return;
1215    }
1216   /*
1217 <   void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1217 >   void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1218        assert( v.size() == nAtoms_ + nRigidBodies_);
1219        sdByGlobalIndex_ = v;
1220      }
# Line 1503 | Line 1224 | namespace oopse {
1224        return sdByGlobalIndex_.at(index);
1225      }  
1226   */  
1227 < }//end namespace oopse
1227 >  int SimInfo::getNGlobalConstraints() {
1228 >    int nGlobalConstraints;
1229 > #ifdef IS_MPI
1230 >    MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1231 >                  MPI_COMM_WORLD);    
1232 > #else
1233 >    nGlobalConstraints =  nConstraints_;
1234 > #endif
1235 >    return nGlobalConstraints;
1236 >  }
1237  
1238 + }//end namespace OpenMD
1239 +

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 1103 by chuckv, Fri Dec 29 20:21:53 2006 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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