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Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1489 by gezelter, Tue Aug 10 18:34:59 2010 UTC vs.
Revision 1569 by gezelter, Thu May 26 13:55:04 2011 UTC

# Line 49 | Line 49
49  
50   #include "brains/ForceManager.hpp"
51   #include "primitives/Molecule.hpp"
52 – #include "UseTheForce/doForces_interface.h"
52   #define __OPENMD_C
54 – #include "UseTheForce/DarkSide/fInteractionMap.h"
53   #include "utils/simError.h"
54   #include "primitives/Bond.hpp"
55   #include "primitives/Bend.hpp"
56   #include "primitives/Torsion.hpp"
57   #include "primitives/Inversion.hpp"
58 + #include "nonbonded/NonBondedInteraction.hpp"
59 + #include "parallel/ForceMatrixDecomposition.hpp"
60  
61 + using namespace std;
62   namespace OpenMD {
63    
64 <  ForceManager::ForceManager(SimInfo * info) : info_(info),
64 <                                               NBforcesInitialized_(false) {
65 <    lj_ = LJ::Instance();
66 <    lj_->setForceField(info_->getForceField());
64 >  ForceManager::ForceManager(SimInfo * info) : info_(info) {
65  
66 <    gb_ = GB::Instance();
67 <    gb_->setForceField(info_->getForceField());
68 <
69 <    sticky_ = Sticky::Instance();
70 <    sticky_->setForceField(info_->getForceField());
73 <
74 <    eam_ = EAM::Instance();
75 <    eam_->setForceField(info_->getForceField());
76 <
77 <    sc_ = SC::Instance();
78 <    sc_->setForceField(info_->getForceField());
66 > #ifdef IS_MPI
67 >    fDecomp_ = new ForceMatrixDecomposition(info_);
68 > #else
69 >    // fDecomp_ = new ForceSerialDecomposition(info);
70 > #endif
71    }
72 <
72 >  
73    void ForceManager::calcForces() {
74      
75 <    if (!info_->isFortranInitialized()) {
75 >    if (!info_->isTopologyDone()) {
76        info_->update();
77 +      interactionMan_->setSimInfo(info_);
78 +      interactionMan_->initialize();
79 +      swfun_ = interactionMan_->getSwitchingFunction();
80 +      fDecomp_->distributeInitialData();
81 +      info_->prepareTopology();
82      }
83      
84 <    preCalculation();
85 <    
86 <    calcShortRangeInteraction();
90 <
91 <    calcLongRangeInteraction();
92 <
84 >    preCalculation();  
85 >    shortRangeInteractions();
86 >    longRangeInteractions();
87      postCalculation();
88      
89    }
# Line 101 | Line 95 | namespace OpenMD {
95      Atom* atom;
96      Molecule::RigidBodyIterator rbIter;
97      RigidBody* rb;
98 +    Molecule::CutoffGroupIterator ci;
99 +    CutoffGroup* cg;
100      
101      // forces are zeroed here, before any are accumulated.
106 –    // NOTE: do not rezero the forces in Fortran.
102      
103      for (mol = info_->beginMolecule(mi); mol != NULL;
104           mol = info_->nextMolecule(mi)) {
# Line 116 | Line 111 | namespace OpenMD {
111             rb = mol->nextRigidBody(rbIter)) {
112          rb->zeroForcesAndTorques();
113        }        
114 <          
114 >
115 >      if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
116 >        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
117 >            cg = mol->nextCutoffGroup(ci)) {
118 >          //calculate the center of mass of cutoff group
119 >          cg->updateCOM();
120 >        }
121 >      }      
122      }
123 <    
123 >  
124      // Zero out the stress tensor
125      tau *= 0.0;
126      
127    }
128    
129 <  void ForceManager::calcShortRangeInteraction() {
129 >  void ForceManager::shortRangeInteractions() {
130      Molecule* mol;
131      RigidBody* rb;
132      Bond* bond;
# Line 166 | Line 168 | namespace OpenMD {
168          RealType currBendPot = bend->getPotential();          
169          
170          bendPotential += bend->getPotential();
171 <        std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
171 >        map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
172          if (i == bendDataSets.end()) {
173            BendDataSet dataSet;
174            dataSet.prev.angle = dataSet.curr.angle = angle;
175            dataSet.prev.potential = dataSet.curr.potential = currBendPot;
176            dataSet.deltaV = 0.0;
177 <          bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
177 >          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
178          }else {
179            i->second.prev.angle = i->second.curr.angle;
180            i->second.prev.potential = i->second.curr.potential;
# Line 189 | Line 191 | namespace OpenMD {
191          torsion->calcForce(angle);
192          RealType currTorsionPot = torsion->getPotential();
193          torsionPotential += torsion->getPotential();
194 <        std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
194 >        map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
195          if (i == torsionDataSets.end()) {
196            TorsionDataSet dataSet;
197            dataSet.prev.angle = dataSet.curr.angle = angle;
198            dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
199            dataSet.deltaV = 0.0;
200 <          torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
200 >          torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
201          }else {
202            i->second.prev.angle = i->second.curr.angle;
203            i->second.prev.potential = i->second.curr.potential;
# Line 205 | Line 207 | namespace OpenMD {
207                                     i->second.prev.potential);
208          }      
209        }      
210 <
210 >      
211        for (inversion = mol->beginInversion(inversionIter);
212             inversion != NULL;
213             inversion = mol->nextInversion(inversionIter)) {
# Line 213 | Line 215 | namespace OpenMD {
215          inversion->calcForce(angle);
216          RealType currInversionPot = inversion->getPotential();
217          inversionPotential += inversion->getPotential();
218 <        std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
218 >        map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
219          if (i == inversionDataSets.end()) {
220            InversionDataSet dataSet;
221            dataSet.prev.angle = dataSet.curr.angle = angle;
222            dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
223            dataSet.deltaV = 0.0;
224 <          inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
224 >          inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
225          }else {
226            i->second.prev.angle = i->second.curr.angle;
227            i->second.prev.potential = i->second.curr.potential;
# Line 238 | Line 240 | namespace OpenMD {
240      curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
241      curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
242      curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
243 <    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
242 <    
243 >    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;    
244    }
245    
246 <  void ForceManager::calcLongRangeInteraction() {
246 <    Snapshot* curSnapshot;
247 <    DataStorage* config;
248 <    RealType* frc;
249 <    RealType* pos;
250 <    RealType* trq;
251 <    RealType* A;
252 <    RealType* electroFrame;
253 <    RealType* rc;
254 <    RealType* particlePot;
255 <    
256 <    //get current snapshot from SimInfo
257 <    curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
258 <    
259 <    //get array pointers
260 <    config = &(curSnapshot->atomData);
261 <    frc = config->getArrayPointer(DataStorage::dslForce);
262 <    pos = config->getArrayPointer(DataStorage::dslPosition);
263 <    trq = config->getArrayPointer(DataStorage::dslTorque);
264 <    A   = config->getArrayPointer(DataStorage::dslAmat);
265 <    electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
266 <    particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
246 >  void ForceManager::longRangeInteractions() {
247  
248 <    //calculate the center of mass of cutoff group
249 <    SimInfo::MoleculeIterator mi;
250 <    Molecule* mol;
251 <    Molecule::CutoffGroupIterator ci;
252 <    CutoffGroup* cg;
253 <    Vector3d com;
254 <    std::vector<Vector3d> rcGroup;
255 <    
256 <    if(info_->getNCutoffGroups() > 0){
257 <      
258 <      for (mol = info_->beginMolecule(mi); mol != NULL;
259 <           mol = info_->nextMolecule(mi)) {
260 <        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
261 <            cg = mol->nextCutoffGroup(ci)) {
282 <          cg->getCOM(com);
283 <          rcGroup.push_back(com);
284 <        }
285 <      }// end for (mol)
286 <      
287 <      rc = rcGroup[0].getArrayPointer();
248 >    // some of this initial stuff will go away:
249 >    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
250 >    DataStorage* config = &(curSnapshot->atomData);
251 >    DataStorage* cgConfig = &(curSnapshot->cgData);
252 >    RealType* frc = config->getArrayPointer(DataStorage::dslForce);
253 >    RealType* pos = config->getArrayPointer(DataStorage::dslPosition);
254 >    RealType* trq = config->getArrayPointer(DataStorage::dslTorque);
255 >    RealType* A = config->getArrayPointer(DataStorage::dslAmat);
256 >    RealType* electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
257 >    RealType* particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
258 >    RealType* rc;    
259 >
260 >    if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
261 >      rc = cgConfig->getArrayPointer(DataStorage::dslPosition);
262      } else {
263        // center of mass of the group is the same as position of the atom  
264        // if cutoff group does not exist
# Line 292 | Line 266 | namespace OpenMD {
266      }
267      
268      //initialize data before passing to fortran
269 <    RealType longRangePotential[LR_POT_TYPES];
269 >    RealType longRangePotential[N_INTERACTION_FAMILIES];
270      RealType lrPot = 0.0;
297 –    Vector3d totalDipole;
271      int isError = 0;
272  
273 <    for (int i=0; i<LR_POT_TYPES;i++){
273 >    // dangerous to iterate over enums, but we'll live on the edge:
274 >    for (int i = NO_FAMILY; i != N_INTERACTION_FAMILIES; ++i){
275        longRangePotential[i]=0.0; //Initialize array
276      }
277 <    
278 <    doForceLoop(pos,
279 <                rc,
280 <                A,
281 <                electroFrame,
282 <                frc,
283 <                trq,
284 <                tau.getArrayPointer(),
285 <                longRangePotential,
286 <                particlePot,
287 <                &isError );
288 <    
289 <    if( isError ){
290 <      sprintf( painCave.errMsg,
291 <               "Error returned from the fortran force calculation.\n" );
292 <      painCave.isFatal = 1;
293 <      simError();
277 >
278 >    // new stuff starts here:
279 >
280 >    fDecomp_->distributeData();
281 >
282 >    int cg1, cg2, atom1, atom2;
283 >    Vector3d d_grp, dag;
284 >    RealType rgrpsq, rgrp;
285 >    RealType vij;
286 >    Vector3d fij, fg;
287 >    pair<int, int> gtypes;
288 >    RealType rCutSq;
289 >    bool in_switching_region;
290 >    RealType sw, dswdr, swderiv;
291 >    vector<int> atomListColumn, atomListRow, atomListLocal;
292 >    InteractionData idat;
293 >    SelfData sdat;
294 >    RealType mf;
295 >
296 >    int loopStart, loopEnd;
297 >
298 >    loopEnd = PAIR_LOOP;
299 >    if (info_->requiresPrepair() ) {
300 >      loopStart = PREPAIR_LOOP;
301 >    } else {
302 >      loopStart = PAIR_LOOP;
303      }
304 <    for (int i=0; i<LR_POT_TYPES;i++){
305 <      lrPot += longRangePotential[i]; //Quick hack
323 <    }
324 <    
325 <    // grab the simulation box dipole moment if specified
326 <    if (info_->getCalcBoxDipole()){
327 <      getAccumulatedBoxDipole(totalDipole.getArrayPointer());
304 >
305 >    for (int iLoop = loopStart; iLoop < loopEnd; iLoop++) {
306        
307 <      curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
308 <      curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
309 <      curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
307 >      if (iLoop == loopStart) {
308 >        bool update_nlist = fDecomp_->checkNeighborList();
309 >        if (update_nlist)
310 >          neighborList = fDecomp_->buildNeighborList();
311 >      }
312 >
313 >      for (vector<pair<int, int> >::iterator it = neighborList.begin();
314 >             it != neighborList.end(); ++it) {
315 >        
316 >        cg1 = (*it).first;
317 >        cg2 = (*it).second;
318 >
319 >        gtypes = fDecomp_->getGroupTypes(cg1, cg2);
320 >        d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
321 >        curSnapshot->wrapVector(d_grp);        
322 >        rgrpsq = d_grp.lengthSquare();
323 >        rCutSq = groupCutoffMap[gtypes].first;
324 >
325 >        if (rgrpsq < rCutSq) {
326 >          *(idat.rcut) = groupCutoffMap[gtypes].second;
327 >          if (iLoop == PAIR_LOOP) {
328 >            vij *= 0.0;
329 >            fij = V3Zero;
330 >          }
331 >          
332 >          in_switching_region = swfun_->getSwitch(rgrpsq, *(idat.sw), dswdr,
333 >                                                  rgrp);              
334 >          atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
335 >          atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
336 >
337 >          for (vector<int>::iterator ia = atomListRow.begin();
338 >               ia != atomListRow.end(); ++ia) {            
339 >            atom1 = (*ia);
340 >            
341 >            for (vector<int>::iterator jb = atomListColumn.begin();
342 >                 jb != atomListColumn.end(); ++jb) {              
343 >              atom2 = (*jb);
344 >              
345 >              if (!fDecomp_->skipAtomPair(atom1, atom2)) {
346 >                
347 >                idat = fDecomp_->fillInteractionData(atom1, atom2);
348 >
349 >                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
350 >                  *(idat.d) = d_grp;
351 >                  *(idat.r2) = rgrpsq;
352 >                } else {
353 >                  *(idat.d) = fDecomp_->getInteratomicVector(atom1, atom2);
354 >                  curSnapshot->wrapVector( *(idat.d) );
355 >                  *(idat.r2) = idat.d->lengthSquare();
356 >                }
357 >                
358 >                *(idat.rij) = sqrt( *(idat.r2) );
359 >              
360 >                if (iLoop == PREPAIR_LOOP) {
361 >                  interactionMan_->doPrePair(idat);
362 >                } else {
363 >                  interactionMan_->doPair(idat);
364 >                  vij += *(idat.vpair);
365 >                  fij += *(idat.f1);
366 >                  tau -= outProduct( *(idat.d), *(idat.f1));
367 >                }
368 >              }
369 >            }
370 >          }
371 >
372 >          if (iLoop == PAIR_LOOP) {
373 >            if (in_switching_region) {
374 >              swderiv = vij * dswdr / rgrp;
375 >              fg = swderiv * d_grp;
376 >
377 >              fij += fg;
378 >
379 >              if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
380 >                tau -= outProduct( *(idat.d), fg);
381 >              }
382 >          
383 >              for (vector<int>::iterator ia = atomListRow.begin();
384 >                   ia != atomListRow.end(); ++ia) {            
385 >                atom1 = (*ia);                
386 >                mf = fDecomp_->getMassFactorRow(atom1);
387 >                // fg is the force on atom ia due to cutoff group's
388 >                // presence in switching region
389 >                fg = swderiv * d_grp * mf;
390 >                fDecomp_->addForceToAtomRow(atom1, fg);
391 >
392 >                if (atomListRow.size() > 1) {
393 >                  if (info_->usesAtomicVirial()) {
394 >                    // find the distance between the atom
395 >                    // and the center of the cutoff group:
396 >                    dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
397 >                    tau -= outProduct(dag, fg);
398 >                  }
399 >                }
400 >              }
401 >              for (vector<int>::iterator jb = atomListColumn.begin();
402 >                   jb != atomListColumn.end(); ++jb) {              
403 >                atom2 = (*jb);
404 >                mf = fDecomp_->getMassFactorColumn(atom2);
405 >                // fg is the force on atom jb due to cutoff group's
406 >                // presence in switching region
407 >                fg = -swderiv * d_grp * mf;
408 >                fDecomp_->addForceToAtomColumn(atom2, fg);
409 >
410 >                if (atomListColumn.size() > 1) {
411 >                  if (info_->usesAtomicVirial()) {
412 >                    // find the distance between the atom
413 >                    // and the center of the cutoff group:
414 >                    dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
415 >                    tau -= outProduct(dag, fg);
416 >                  }
417 >                }
418 >              }
419 >            }
420 >            //if (!SIM_uses_AtomicVirial) {
421 >            //  tau -= outProduct(d_grp, fij);
422 >            //}
423 >          }
424 >        }
425 >      }
426 >
427 >      if (iLoop == PREPAIR_LOOP) {
428 >        if (info_->requiresPrepair()) {            
429 >          fDecomp_->collectIntermediateData();
430 >          atomListLocal = fDecomp_->getAtomList();
431 >          for (vector<int>::iterator ia = atomListLocal.begin();
432 >               ia != atomListLocal.end(); ++ia) {              
433 >            atom1 = (*ia);            
434 >            sdat = fDecomp_->fillSelfData(atom1);
435 >            interactionMan_->doPreForce(sdat);
436 >          }
437 >          fDecomp_->distributeIntermediateData();        
438 >        }
439 >      }
440 >
441      }
442      
443 +    fDecomp_->collectData();
444 +    
445 +    if (info_->requiresSkipCorrection() || info_->requiresSelfCorrection()) {
446 +      atomListLocal = fDecomp_->getAtomList();
447 +      for (vector<int>::iterator ia = atomListLocal.begin();
448 +           ia != atomListLocal.end(); ++ia) {              
449 +        atom1 = (*ia);    
450 +
451 +        if (info_->requiresSkipCorrection()) {
452 +          vector<int> skipList = fDecomp_->getSkipsForAtom(atom1);
453 +          for (vector<int>::iterator jb = skipList.begin();
454 +               jb != skipList.end(); ++jb) {              
455 +            atom2 = (*jb);
456 +            idat = fDecomp_->fillSkipData(atom1, atom2);
457 +            interactionMan_->doSkipCorrection(idat);
458 +          }
459 +        }
460 +          
461 +        if (info_->requiresSelfCorrection()) {
462 +          sdat = fDecomp_->fillSelfData(atom1);
463 +          interactionMan_->doSelfCorrection(sdat);
464 +        }
465 +      }
466 +    }
467 +
468 +    // dangerous to iterate over enums, but we'll live on the edge:
469 +    for (int i = NO_FAMILY; i != N_INTERACTION_FAMILIES; ++i){
470 +      lrPot += longRangePotential[i]; //Quick hack
471 +    }
472 +        
473      //store the tau and long range potential    
474      curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
475 <    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
476 <    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
475 >    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
476 >    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
477    }
478  
479    

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