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Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1849 by gezelter, Wed Feb 20 13:52:51 2013 UTC vs.
Revision 1877 by gezelter, Thu Jun 6 15:43:35 2013 UTC

# Line 35 | Line 35
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).          
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39   * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40   * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
# Line 67 | Line 67 | namespace OpenMD {
67   using namespace std;
68   namespace OpenMD {
69    
70 <  ForceManager::ForceManager(SimInfo * info) : info_(info) {
70 >  ForceManager::ForceManager(SimInfo * info) : info_(info), switcher_(NULL),
71 >                                               initialized_(false) {
72      forceField_ = info_->getForceField();
73      interactionMan_ = new InteractionManager();
74      fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
75 +    thermo = new Thermo(info_);
76    }
77  
78 +  ForceManager::~ForceManager() {
79 +    perturbations_.clear();
80 +    
81 +    delete switcher_;
82 +    delete interactionMan_;
83 +    delete fDecomp_;
84 +    delete thermo;
85 +  }
86 +  
87    /**
88     * setupCutoffs
89     *
# Line 87 | Line 98 | namespace OpenMD {
98     *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
99     *      Use the maximum suggested value that was found.
100     *
101 <   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
101 >   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, TAYLOR_SHIFTED,
102     *                        or SHIFTED_POTENTIAL)
103     *      If cutoffMethod was explicitly set, use that choice.
104     *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
# Line 160 | Line 171 | namespace OpenMD {
171      stringToCutoffMethod["SWITCHED"] = SWITCHED;
172      stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
173      stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
174 +    stringToCutoffMethod["TAYLOR_SHIFTED"] = TAYLOR_SHIFTED;
175    
176      if (simParams_->haveCutoffMethod()) {
177        string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
# Line 169 | Line 181 | namespace OpenMD {
181          sprintf(painCave.errMsg,
182                  "ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
183                  "\tShould be one of: "
184 <                "HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
184 >                "HARD, SWITCHED, SHIFTED_POTENTIAL, TAYLOR_SHIFTED,\n"
185 >                "\tor SHIFTED_FORCE\n",
186                  cutMeth.c_str());
187          painCave.isFatal = 1;
188          painCave.severity = OPENMD_ERROR;
# Line 213 | Line 226 | namespace OpenMD {
226              cutoffMethod_ = SHIFTED_POTENTIAL;
227            } else if (myMethod == "SHIFTED_FORCE") {
228              cutoffMethod_ = SHIFTED_FORCE;
229 +          } else if (myMethod == "TAYLOR_SHIFTED") {
230 +            cutoffMethod_ = TAYLOR_SHIFTED;
231            }
232          
233            if (simParams_->haveSwitchingRadius())
234              rSwitch_ = simParams_->getSwitchingRadius();
235  
236 <          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
236 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE" ||
237 >              myMethod == "TAYLOR_SHIFTED") {
238              if (simParams_->haveSwitchingRadius()){
239                sprintf(painCave.errMsg,
240                        "ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
# Line 433 | Line 449 | namespace OpenMD {
449        perturbations_.push_back(eField);
450      }
451  
452 +    usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
453 +    
454      fDecomp_->distributeInitialData();
455 <
455 >    
456      initialized_ = true;
457 <
457 >    
458    }
459 <
459 >  
460    void ForceManager::calcForces() {
461      
462      if (!initialized_) initialize();
463 <
463 >    
464      preCalculation();  
465      shortRangeInteractions();
466      longRangeInteractions();
# Line 641 | Line 659 | namespace OpenMD {
659    
660    void ForceManager::longRangeInteractions() {
661  
644 –
662      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
663      DataStorage* config = &(curSnapshot->atomData);
664      DataStorage* cgConfig = &(curSnapshot->cgData);
# Line 681 | Line 698 | namespace OpenMD {
698      RealType rCutSq;
699      bool in_switching_region;
700      RealType sw, dswdr, swderiv;
701 <    vector<int> atomListColumn, atomListRow, atomListLocal;
701 >    vector<int> atomListColumn, atomListRow;
702      InteractionData idat;
703      SelfData sdat;
704      RealType mf;
# Line 711 | Line 728 | namespace OpenMD {
728      idat.f1 = &f1;
729      idat.sw = &sw;
730      idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
731 <    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
731 >    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE || cutoffMethod_ == TAYLOR_SHIFTED) ? true : false;
732      idat.doParticlePot = doParticlePot_;
733      idat.doElectricField = doElectricField_;
734      sdat.doParticlePot = doParticlePot_;
# Line 726 | Line 743 | namespace OpenMD {
743      
744        if (iLoop == loopStart) {
745          bool update_nlist = fDecomp_->checkNeighborList();
746 <        if (update_nlist)
746 >        if (update_nlist) {
747 >          if (!usePeriodicBoundaryConditions_)
748 >            Mat3x3d bbox = thermo->getBoundingBox();
749            neighborList = fDecomp_->buildNeighborList();
750 <      }            
750 >        }
751 >      }
752  
753        for (vector<pair<int, int> >::iterator it = neighborList.begin();
754               it != neighborList.end(); ++it) {
# Line 748 | Line 768 | namespace OpenMD {
768            idat.rcut = &cuts.first;
769            if (iLoop == PAIR_LOOP) {
770              vij = 0.0;
771 <            fij = V3Zero;
772 <            eField1 = V3Zero;
773 <            eField2 = V3Zero;
771 >            fij.zero();
772 >            eField1.zero();
773 >            eField2.zero();
774            }
775            
776            in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
# Line 775 | Line 795 | namespace OpenMD {
795                  vpair = 0.0;
796                  workPot = 0.0;
797                  exPot = 0.0;
798 <                f1 = V3Zero;
798 >                f1.zero();
799                  dVdFQ1 = 0.0;
800                  dVdFQ2 = 0.0;
801  

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