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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 1093 by tim, Wed Mar 17 14:22:59 2004 UTC vs.
Revision 1163 by gezelter, Wed May 12 14:30:12 2004 UTC

# Line 9 | Line 9
9   #include "parse_me.h"
10   #include "Integrator.hpp"
11   #include "simError.h"
12 + #include "RigidBody.hpp"
13   //#include "ConjugateMinimizer.hpp"
14   #include "OOPSEMinimizer.hpp"
15  
# Line 146 | Line 147 | void SimSetup::createSim(void){
147    // make the output filenames
148  
149    makeOutNames();
149 –
150 –  if (globals->haveMinimizer())
151 –    // make minimizer
152 –    makeMinimizer();
153 –  else
154 –    // make the integrator
155 –    makeIntegrator();
150    
151   #ifdef IS_MPI
152    mpiSim->mpiRefresh();
# Line 161 | Line 155 | void SimSetup::createSim(void){
155    // initialize the Fortran
156  
157    initFortran();
158 +
159 +  if (globals->haveMinimizer())
160 +    // make minimizer
161 +    makeMinimizer();
162 +  else
163 +    // make the integrator
164 +    makeIntegrator();
165 +
166   }
167  
168  
169   void SimSetup::makeMolecules(void){
170 <  int k;
171 <  int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
170 >  int i, j, k;
171 >  int exI, exJ, exK, exL, slI, slJ;
172 >  int tempI, tempJ, tempK, tempL;
173 >  int molI;
174 >  int stampID, atomOffset, rbOffset;
175    molInit molInfo;
176    DirectionalAtom* dAtom;
177 +  RigidBody* myRB;
178 +  StuntDouble* mySD;
179    LinkedAssign* extras;
180    LinkedAssign* current_extra;
181    AtomStamp* currentAtom;
182    BondStamp* currentBond;
183    BendStamp* currentBend;
184    TorsionStamp* currentTorsion;
185 <
185 >  RigidBodyStamp* currentRigidBody;
186 >  CutoffGroupStamp* currentCutoffGroup;
187 >  CutoffGroup* myCutoffGroup;
188 >  
189    bond_pair* theBonds;
190    bend_set* theBends;
191    torsion_set* theTorsions;
192  
193 +  set<int> skipList;
194 +
195 +  double phi, theta, psi;
196 +  char* molName;
197 +  char rbName[100];
198 +
199    //init the forceField paramters
200  
201    the_ff->readParams();
202  
187 –
203    // init the atoms
204  
205 <  double phi, theta, psi;
191 <  double sux, suy, suz;
192 <  double Axx, Axy, Axz, Ayx, Ayy, Ayz, Azx, Azy, Azz;
193 <  double ux, uy, uz, u, uSqr;
205 >  int nMembers, nNew, rb1, rb2;
206  
207    for (k = 0; k < nInfo; k++){
208      the_ff->setSimInfo(&(info[k]));
209  
210      atomOffset = 0;
211 <    excludeOffset = 0;
211 >
212      for (i = 0; i < info[k].n_mol; i++){
213        stampID = info[k].molecules[i].getStampID();
214 +      molName = comp_stamps[stampID]->getID();
215  
216        molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
217        molInfo.nBonds = comp_stamps[stampID]->getNBonds();
218        molInfo.nBends = comp_stamps[stampID]->getNBends();
219        molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
220 <      molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
221 <
220 >      molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
221 >      molInfo.nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
222 >      
223        molInfo.myAtoms = &(info[k].atoms[atomOffset]);
210 –      molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
211 –      molInfo.myBonds = new Bond * [molInfo.nBonds];
212 –      molInfo.myBends = new Bend * [molInfo.nBends];
213 –      molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
224  
225 +      if (molInfo.nBonds > 0)
226 +        molInfo.myBonds = new (Bond *) [molInfo.nBonds];
227 +      else
228 +        molInfo.myBonds = NULL;
229 +
230 +      if (molInfo.nBends > 0)
231 +        molInfo.myBends = new (Bend *) [molInfo.nBends];
232 +      else
233 +        molInfo.myBends = NULL;
234 +
235 +      if (molInfo.nTorsions > 0)
236 +        molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
237 +      else
238 +        molInfo.myTorsions = NULL;
239 +
240        theBonds = new bond_pair[molInfo.nBonds];
241        theBends = new bend_set[molInfo.nBends];
242        theTorsions = new torsion_set[molInfo.nTorsions];
243 <
243 >      
244        // make the Atoms
245  
246        for (j = 0; j < molInfo.nAtoms; j++){
247          currentAtom = comp_stamps[stampID]->getAtom(j);
248 +
249          if (currentAtom->haveOrientation()){
250            dAtom = new DirectionalAtom((j + atomOffset),
251                                        info[k].getConfiguration());
# Line 233 | Line 259 | void SimSetup::makeMolecules(void){
259            phi = currentAtom->getEulerPhi() * M_PI / 180.0;
260            theta = currentAtom->getEulerTheta() * M_PI / 180.0;
261            psi = currentAtom->getEulerPsi()* M_PI / 180.0;
262 +
263 +          dAtom->setUnitFrameFromEuler(phi, theta, psi);
264              
265 <          Axx = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
266 <          Axy = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
239 <          Axz = sin(theta) * sin(psi);
240 <          
241 <          Ayx = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
242 <          Ayy = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
243 <          Ayz = sin(theta) * cos(psi);
244 <          
245 <          Azx = sin(phi) * sin(theta);
246 <          Azy = -cos(phi) * sin(theta);
247 <          Azz = cos(theta);
265 >        }
266 >        else{
267  
268 <          sux = 0.0;
250 <          suy = 0.0;
251 <          suz = 1.0;
268 >          molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
269  
253 –          ux = (Axx * sux) + (Ayx * suy) + (Azx * suz);
254 –          uy = (Axy * sux) + (Ayy * suy) + (Azy * suz);
255 –          uz = (Axz * sux) + (Ayz * suy) + (Azz * suz);
256 –
257 –          uSqr = (ux * ux) + (uy * uy) + (uz * uz);
258 –
259 –          u = sqrt(uSqr);
260 –          ux = ux / u;
261 –          uy = uy / u;
262 –          uz = uz / u;
263 –
264 –          dAtom->setSUx(ux);
265 –          dAtom->setSUy(uy);
266 –          dAtom->setSUz(uz);
270          }
268 –        else{
269 –          molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
270 –                                               info[k].getConfiguration());
271 –        }
272 –        molInfo.myAtoms[j]->setType(currentAtom->getType());
271  
272 +        molInfo.myAtoms[j]->setType(currentAtom->getType());
273   #ifdef IS_MPI
274  
275 <        molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
275 >        molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
276  
277   #endif // is_mpi
278        }
# Line 284 | Line 283 | void SimSetup::makeMolecules(void){
283          theBonds[j].a = currentBond->getA() + atomOffset;
284          theBonds[j].b = currentBond->getB() + atomOffset;
285  
286 <        exI = theBonds[j].a;
287 <        exJ = theBonds[j].b;
286 >        tempI = theBonds[j].a;
287 >        tempJ = theBonds[j].b;
288  
290 –        // exclude_I must always be the smaller of the pair
291 –        if (exI > exJ){
292 –          tempEx = exI;
293 –          exI = exJ;
294 –          exJ = tempEx;
295 –        }
289   #ifdef IS_MPI
290 <        tempEx = exI;
291 <        exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
292 <        tempEx = exJ;
293 <        exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
290 >        exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
291 >        exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
292 > #else
293 >        exI = tempI + 1;
294 >        exJ = tempJ + 1;
295 > #endif
296  
297 <        info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
303 < #else  // isn't MPI
304 <
305 <        info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
306 < #endif  //is_mpi
297 >        info[k].excludes->addPair(exI, exJ);
298        }
308 –      excludeOffset += molInfo.nBonds;
299  
300        //make the bends
301        for (j = 0; j < molInfo.nBends; j++){
# Line 355 | Line 345 | void SimSetup::makeMolecules(void){
345            }
346          }
347  
348 <        if (!theBends[j].isGhost){
349 <          exI = theBends[j].a;
350 <          exJ = theBends[j].c;
351 <        }
352 <        else{
363 <          exI = theBends[j].a;
364 <          exJ = theBends[j].b;
365 <        }
366 <
367 <        // exclude_I must always be the smaller of the pair
368 <        if (exI > exJ){
369 <          tempEx = exI;
370 <          exI = exJ;
371 <          exJ = tempEx;
372 <        }
348 >        if (theBends[j].isGhost) {
349 >          
350 >          tempI = theBends[j].a;
351 >          tempJ = theBends[j].b;
352 >          
353   #ifdef IS_MPI
354 <        tempEx = exI;
355 <        exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
356 <        tempEx = exJ;
357 <        exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
354 >          exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
355 >          exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
356 > #else
357 >          exI = tempI + 1;
358 >          exJ = tempJ + 1;
359 > #endif          
360 >          info[k].excludes->addPair(exI, exJ);
361  
362 <        info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
363 < #else  // isn't MPI
364 <        info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
365 < #endif  //is_mpi
362 >        } else {
363 >
364 >          tempI = theBends[j].a;
365 >          tempJ = theBends[j].b;
366 >          tempK = theBends[j].c;
367 >          
368 > #ifdef IS_MPI
369 >          exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
370 >          exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
371 >          exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
372 > #else
373 >          exI = tempI + 1;
374 >          exJ = tempJ + 1;
375 >          exK = tempK + 1;
376 > #endif
377 >          
378 >          info[k].excludes->addPair(exI, exK);
379 >          info[k].excludes->addPair(exI, exJ);
380 >          info[k].excludes->addPair(exJ, exK);
381 >        }
382        }
384 –      excludeOffset += molInfo.nBends;
383  
384        for (j = 0; j < molInfo.nTorsions; j++){
385          currentTorsion = comp_stamps[stampID]->getTorsion(j);
# Line 390 | Line 388 | void SimSetup::makeMolecules(void){
388          theTorsions[j].c = currentTorsion->getC() + atomOffset;
389          theTorsions[j].d = currentTorsion->getD() + atomOffset;
390  
391 <        exI = theTorsions[j].a;
392 <        exJ = theTorsions[j].d;
391 >        tempI = theTorsions[j].a;      
392 >        tempJ = theTorsions[j].b;
393 >        tempK = theTorsions[j].c;
394 >        tempL = theTorsions[j].d;
395  
396 –        // exclude_I must always be the smaller of the pair
397 –        if (exI > exJ){
398 –          tempEx = exI;
399 –          exI = exJ;
400 –          exJ = tempEx;
401 –        }
396   #ifdef IS_MPI
397 <        tempEx = exI;
398 <        exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
399 <        tempEx = exJ;
400 <        exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
397 >        exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
398 >        exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
399 >        exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
400 >        exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
401 > #else
402 >        exI = tempI + 1;
403 >        exJ = tempJ + 1;
404 >        exK = tempK + 1;
405 >        exL = tempL + 1;
406 > #endif
407  
408 <        info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
409 < #else  // isn't MPI
410 <        info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
411 < #endif  //is_mpi
408 >        info[k].excludes->addPair(exI, exJ);
409 >        info[k].excludes->addPair(exI, exK);
410 >        info[k].excludes->addPair(exI, exL);        
411 >        info[k].excludes->addPair(exJ, exK);
412 >        info[k].excludes->addPair(exJ, exL);
413 >        info[k].excludes->addPair(exK, exL);
414        }
413 –      excludeOffset += molInfo.nTorsions;
415  
416 +      
417 +      molInfo.myRigidBodies.clear();
418 +      
419 +      for (j = 0; j < molInfo.nRigidBodies; j++){
420  
421 <      // send the arrays off to the forceField for init.
421 >        currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
422 >        nMembers = currentRigidBody->getNMembers();
423 >
424 >        // Create the Rigid Body:
425 >
426 >        myRB = new RigidBody();
427 >
428 >        sprintf(rbName,"%s_RB_%d", molName, j);
429 >        myRB->setType(rbName);
430 >        
431 >        for (rb1 = 0; rb1 < nMembers; rb1++) {
432 >
433 >          // molI is atom numbering inside this molecule
434 >          molI = currentRigidBody->getMember(rb1);    
435 >
436 >          // tempI is atom numbering on local processor
437 >          tempI = molI + atomOffset;
438 >
439 >          // currentAtom is the AtomStamp (which we need for
440 >          // rigid body reference positions)
441 >          currentAtom = comp_stamps[stampID]->getAtom(molI);
442 >
443 >          // When we add to the rigid body, add the atom itself and
444 >          // the stamp info:
445 >
446 >          myRB->addAtom(info[k].atoms[tempI], currentAtom);
447 >          
448 >          // Add this atom to the Skip List for the integrators
449 > #ifdef IS_MPI
450 >          slI = info[k].atoms[tempI]->getGlobalIndex();
451 > #else
452 >          slI = tempI;
453 > #endif
454 >          skipList.insert(slI);
455 >          
456 >        }
457 >        
458 >        for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
459 >          for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
460 >            
461 >            tempI = currentRigidBody->getMember(rb1);
462 >            tempJ = currentRigidBody->getMember(rb2);
463 >            
464 >            // Some explanation is required here.
465 >            // Fortran indexing starts at 1, while c indexing starts at 0
466 >            // Also, in parallel computations, the GlobalIndex is
467 >            // used for the exclude list:
468 >            
469 > #ifdef IS_MPI
470 >            exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
471 >            exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
472 > #else
473 >            exI = molInfo.myAtoms[tempI]->getIndex() + 1;
474 >            exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
475 > #endif
476 >            
477 >            info[k].excludes->addPair(exI, exJ);
478 >            
479 >          }
480 >        }
481  
482 +        molInfo.myRigidBodies.push_back(myRB);
483 +        info[k].rigidBodies.push_back(myRB);
484 +      }
485 +      
486 +
487 +      //create cutoff group for molecule
488 +      molInfo.myCutoffGroups.clear();
489 +      for (j = 0; j < molInfo.nCutoffGroups; j++){
490 +
491 +        currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
492 +        nMembers = currentCutoffGroup->getNMembers();
493 +
494 +        myCutoffGroup = new CutoffGroup();
495 +        
496 +        for (int cg = 0; cg < nMembers; cg++) {
497 +
498 +          // molI is atom numbering inside this molecule
499 +          molI = currentCutoffGroup->getMember(cg);    
500 +
501 +          // tempI is atom numbering on local processor
502 +          tempI = molI + atomOffset;
503 +
504 +          myCutoffGroup->addAtom(info[k].atoms[tempI]);          
505 +        }
506 +
507 +        molInfo.myCutoffGroups.push_back(myCutoffGroup);
508 +      }//end for (j = 0; j < molInfo.nCutoffGroups; j++)
509 +      
510 +
511 +
512 +      // After this is all set up, scan through the atoms to
513 +      // see if they can be added to the integrableObjects:
514 +
515 +      molInfo.myIntegrableObjects.clear();
516 +      
517 +
518 +      for (j = 0; j < molInfo.nAtoms; j++){
519 +
520 + #ifdef IS_MPI
521 +        slJ = molInfo.myAtoms[j]->getGlobalIndex();
522 + #else
523 +        slJ = j+atomOffset;
524 + #endif
525 +
526 +        // if they aren't on the skip list, then they can be integrated
527 +
528 +        if (skipList.find(slJ) == skipList.end()) {
529 +          mySD = (StuntDouble *) molInfo.myAtoms[j];
530 +          info[k].integrableObjects.push_back(mySD);
531 +          molInfo.myIntegrableObjects.push_back(mySD);
532 +        }
533 +      }
534 +
535 +      // all rigid bodies are integrated:
536 +
537 +      for (j = 0; j < molInfo.nRigidBodies; j++) {
538 +        mySD = (StuntDouble *) molInfo.myRigidBodies[j];
539 +        info[k].integrableObjects.push_back(mySD);      
540 +        molInfo.myIntegrableObjects.push_back(mySD);
541 +      }
542 +    
543 +      
544 +      // send the arrays off to the forceField for init.
545 +      
546        the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
547        the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
548        the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
549        the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
550                                   theTorsions);
551  
424 –
552        info[k].molecules[i].initialize(molInfo);
553  
554  
# Line 429 | Line 556 | void SimSetup::makeMolecules(void){
556        delete[] theBonds;
557        delete[] theBends;
558        delete[] theTorsions;
559 <    }
559 >    }    
560    }
561  
562   #ifdef IS_MPI
# Line 437 | Line 564 | void SimSetup::makeMolecules(void){
564    MPIcheckPoint();
565   #endif // is_mpi
566  
440 –  // clean up the forcefield
441 –
442 –  the_ff->calcRcut();
443 –  the_ff->cleanMe();
567   }
568  
569   void SimSetup::initFromBass(void){
# Line 727 | Line 850 | void SimSetup::gatherInfo(void){
850    }
851  
852    //check whether sample time, status time, thermal time and reset time are divisble by dt
853 <  if (!isDivisible(globals->getSampleTime(), globals->getDt())){
853 >  if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
854      sprintf(painCave.errMsg,
855              "Sample time is not divisible by dt.\n"
856              "\tThis will result in samples that are not uniformly\n"
# Line 737 | Line 860 | void SimSetup::gatherInfo(void){
860      simError();    
861    }
862  
863 <  if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
863 >  if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
864      sprintf(painCave.errMsg,
865              "Status time is not divisible by dt.\n"
866              "\tThis will result in status reports that are not uniformly\n"
# Line 773 | Line 896 | void SimSetup::gatherInfo(void){
896      if (globals->haveSampleTime()){
897        info[i].sampleTime = globals->getSampleTime();
898        info[i].statusTime = info[i].sampleTime;
776 –      info[i].thermalTime = info[i].sampleTime;
899      }
900      else{
901        info[i].sampleTime = globals->getRunTime();
902        info[i].statusTime = info[i].sampleTime;
781 –      info[i].thermalTime = info[i].sampleTime;
903      }
904  
905      if (globals->haveStatusTime()){
# Line 787 | Line 908 | void SimSetup::gatherInfo(void){
908  
909      if (globals->haveThermalTime()){
910        info[i].thermalTime = globals->getThermalTime();
911 +    } else {
912 +      info[i].thermalTime = globals->getRunTime();
913      }
914  
915      info[i].resetIntegrator = 0;
# Line 857 | Line 980 | void SimSetup::finalInfoCheck(void){
980   void SimSetup::finalInfoCheck(void){
981    int index;
982    int usesDipoles;
983 +  int usesCharges;
984    int i;
985  
986    for (i = 0; i < nInfo; i++){
# Line 868 | Line 992 | void SimSetup::finalInfoCheck(void){
992        usesDipoles = (info[i].atoms[index])->hasDipole();
993        index++;
994      }
995 <
995 >    index = 0;
996 >    usesCharges = 0;
997 >    while ((index < info[i].n_atoms) && !usesCharges){
998 >      usesCharges= (info[i].atoms[index])->hasCharge();
999 >      index++;
1000 >    }
1001   #ifdef IS_MPI
1002      int myUse = usesDipoles;
1003      MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1004   #endif //is_mpi
1005  
1006 <    double theEcr, theEst;
1006 >    double theRcut, theRsw;
1007  
1008 <    if (globals->getUseRF()){
1009 <      info[i].useReactionField = 1;
1008 >    if (globals->haveRcut()) {
1009 >      theRcut = globals->getRcut();
1010  
1011 <      if (!globals->haveECR()){
1011 >      if (globals->haveRsw())
1012 >        theRsw = globals->getRsw();
1013 >      else
1014 >        theRsw = theRcut;
1015 >      
1016 >      info[i].setDefaultRcut(theRcut, theRsw);
1017 >
1018 >    } else {
1019 >      
1020 >      the_ff->calcRcut();
1021 >      theRcut = info[i].getRcut();
1022 >
1023 >      if (globals->haveRsw())
1024 >        theRsw = globals->getRsw();
1025 >      else
1026 >        theRsw = theRcut;
1027 >      
1028 >      info[i].setDefaultRcut(theRcut, theRsw);
1029 >    }
1030 >
1031 >    if (globals->getUseRF()){
1032 >      info[i].useReactionField = 1;
1033 >      
1034 >      if (!globals->haveRcut()){
1035          sprintf(painCave.errMsg,
1036 <                "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1036 >                "SimSetup Warning: No value was set for the cutoffRadius.\n"
1037                  "\tOOPSE will use a default value of 15.0 angstroms"
1038 <                "\tfor the electrostaticCutoffRadius.\n");
1038 >                "\tfor the cutoffRadius.\n");
1039          painCave.isFatal = 0;
1040          simError();
1041 <        theEcr = 15.0;
1041 >        theRcut = 15.0;
1042        }
1043        else{
1044 <        theEcr = globals->getECR();
1044 >        theRcut = globals->getRcut();
1045        }
1046  
1047 <      if (!globals->haveEST()){
1047 >      if (!globals->haveRsw()){
1048          sprintf(painCave.errMsg,
1049 <                "SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1049 >                "SimSetup Warning: No value was set for switchingRadius.\n"
1050                  "\tOOPSE will use a default value of\n"
1051 <                "\t0.05 * electrostaticCutoffRadius\n"
900 <                "\tfor the electrostaticSkinThickness\n");
1051 >                "\t0.95 * cutoffRadius for the switchingRadius\n");
1052          painCave.isFatal = 0;
1053          simError();
1054 <        theEst = 0.05 * theEcr;
1054 >        theRsw = 0.95 * theRcut;
1055        }
1056        else{
1057 <        theEst = globals->getEST();
1057 >        theRsw = globals->getRsw();
1058        }
1059  
1060 <      info[i].setDefaultEcr(theEcr, theEst);
1060 >      info[i].setDefaultRcut(theRcut, theRsw);
1061  
1062        if (!globals->haveDielectric()){
1063          sprintf(painCave.errMsg,
# Line 919 | Line 1070 | void SimSetup::finalInfoCheck(void){
1070        info[i].dielectric = globals->getDielectric();
1071      }
1072      else{
1073 <      if (usesDipoles){
1074 <        if (!globals->haveECR()){
1073 >      if (usesDipoles || usesCharges){
1074 >
1075 >        if (!globals->haveRcut()){
1076            sprintf(painCave.errMsg,
1077 <                  "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1077 >                  "SimSetup Warning: No value was set for the cutoffRadius.\n"
1078                    "\tOOPSE will use a default value of 15.0 angstroms"
1079 <                  "\tfor the electrostaticCutoffRadius.\n");
1080 <          painCave.isFatal = 0;
1081 <          simError();
1082 <          theEcr = 15.0;
1083 <        }
1079 >                  "\tfor the cutoffRadius.\n");
1080 >          painCave.isFatal = 0;
1081 >          simError();
1082 >          theRcut = 15.0;
1083 >      }
1084          else{
1085 <          theEcr = globals->getECR();
1085 >          theRcut = globals->getRcut();
1086          }
1087 <        
1088 <        if (!globals->haveEST()){
1087 >        
1088 >        if (!globals->haveRsw()){
1089            sprintf(painCave.errMsg,
1090 <                  "SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1090 >                  "SimSetup Warning: No value was set for switchingRadius.\n"
1091                    "\tOOPSE will use a default value of\n"
1092 <                  "\t0.05 * electrostaticCutoffRadius\n"
941 <                  "\tfor the electrostaticSkinThickness\n");
1092 >                  "\t0.95 * cutoffRadius for the switchingRadius\n");
1093            painCave.isFatal = 0;
1094            simError();
1095 <          theEst = 0.05 * theEcr;
1095 >          theRsw = 0.95 * theRcut;
1096          }
1097          else{
1098 <          theEst = globals->getEST();
1098 >          theRsw = globals->getRsw();
1099          }
1100 +        
1101 +        info[i].setDefaultRcut(theRcut, theRsw);
1102          
950 –        info[i].setDefaultEcr(theEcr, theEst);
1103        }
1104      }
1105    }
# Line 955 | Line 1107 | void SimSetup::finalInfoCheck(void){
1107    strcpy(checkPointMsg, "post processing checks out");
1108    MPIcheckPoint();
1109   #endif // is_mpi
1110 +
1111 +  // clean up the forcefield
1112 +  the_ff->cleanMe();
1113   }
1114    
1115   void SimSetup::initSystemCoords(void){
# Line 1169 | Line 1324 | void SimSetup::compList(void){
1324    LinkedMolStamp* headStamp = new LinkedMolStamp();
1325    LinkedMolStamp* currentStamp = NULL;
1326    comp_stamps = new MoleculeStamp * [n_components];
1327 +  bool haveCutoffGroups;
1328  
1329 +  haveCutoffGroups = false;
1330 +  
1331    // make an array of molecule stamps that match the components used.
1332    // also extract the used stamps out into a separate linked list
1333  
# Line 1204 | Line 1362 | void SimSetup::compList(void){
1362        headStamp->add(currentStamp);
1363        comp_stamps[i] = headStamp->match(id);
1364      }
1365 +
1366 +    if(comp_stamps[i]->getNCutoffGroups() > 0)
1367 +      haveCutoffGroups = true;    
1368    }
1369 +    
1370 +  for (i = 0; i < nInfo; i++)
1371 +    info[i].haveCutoffGroups = haveCutoffGroups;
1372  
1373   #ifdef IS_MPI
1374    strcpy(checkPointMsg, "Component stamps successfully extracted\n");
# Line 1221 | Line 1385 | void SimSetup::calcSysValues(void){
1385    tot_bonds = 0;
1386    tot_bends = 0;
1387    tot_torsions = 0;
1388 +  tot_rigid = 0;
1389    for (i = 0; i < n_components; i++){
1390      tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1391      tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1392      tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1393      tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1394 +    tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1395    }
1396 <
1396 >  
1397    tot_SRI = tot_bonds + tot_bends + tot_torsions;
1398    molMembershipArray = new int[tot_atoms];
1399  
# Line 1249 | Line 1415 | void SimSetup::mpiMolDivide(void){
1415    int i, j, k;
1416    int localMol, allMol;
1417    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1418 +  int local_rigid;
1419 +  vector<int> globalMolIndex;
1420  
1421    mpiSim = new mpiSimulation(info);
1422  
1423 <  globalIndex = mpiSim->divideLabor();
1423 >  mpiSim->divideLabor();
1424 >  globalAtomIndex = mpiSim->getGlobalAtomIndex();
1425 >  //globalMolIndex = mpiSim->getGlobalMolIndex();
1426  
1427    // set up the local variables
1428  
# Line 1265 | Line 1435 | void SimSetup::mpiMolDivide(void){
1435    local_bonds = 0;
1436    local_bends = 0;
1437    local_torsions = 0;
1438 <  globalAtomIndex = 0;
1438 >  local_rigid = 0;
1439 >  globalAtomCounter = 0;
1440  
1270 –
1441    for (i = 0; i < n_components; i++){
1442      for (j = 0; j < components_nmol[i]; j++){
1443        if (mol2proc[allMol] == worldRank){
# Line 1275 | Line 1445 | void SimSetup::mpiMolDivide(void){
1445          local_bonds += comp_stamps[i]->getNBonds();
1446          local_bends += comp_stamps[i]->getNBends();
1447          local_torsions += comp_stamps[i]->getNTorsions();
1448 +        local_rigid += comp_stamps[i]->getNRigidBodies();
1449          localMol++;
1450        }      
1451        for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1452 <        info[0].molMembershipArray[globalAtomIndex] = allMol;
1453 <        globalAtomIndex++;
1452 >        info[0].molMembershipArray[globalAtomCounter] = allMol;
1453 >        globalAtomCounter++;
1454        }
1455  
1456        allMol++;
# Line 1288 | Line 1459 | void SimSetup::mpiMolDivide(void){
1459    local_SRI = local_bonds + local_bends + local_torsions;
1460  
1461    info[0].n_atoms = mpiSim->getMyNlocal();  
1462 +  
1463  
1464    if (local_atoms != info[0].n_atoms){
1465      sprintf(painCave.errMsg,
# Line 1320 | Line 1492 | void SimSetup::makeSysArrays(void){
1492  
1493    Atom** the_atoms;
1494    Molecule* the_molecules;
1323 –  Exclude** the_excludes;
1495  
1325 –
1496    for (l = 0; l < nInfo; l++){
1497      // create the atom and short range interaction arrays
1498  
# Line 1348 | Line 1518 | void SimSetup::makeSysArrays(void){
1518   #else // is_mpi
1519  
1520      molIndex = 0;
1521 <    globalAtomIndex = 0;
1521 >    globalAtomCounter = 0;
1522      for (i = 0; i < n_components; i++){
1523        for (j = 0; j < components_nmol[i]; j++){
1524          the_molecules[molIndex].setStampID(i);
1525          the_molecules[molIndex].setMyIndex(molIndex);
1526          the_molecules[molIndex].setGlobalIndex(molIndex);
1527          for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1528 <          info[l].molMembershipArray[globalAtomIndex] = molIndex;
1529 <          globalAtomIndex++;
1528 >          info[l].molMembershipArray[globalAtomCounter] = molIndex;
1529 >          globalAtomCounter++;
1530          }
1531          molIndex++;
1532        }
# Line 1365 | Line 1535 | void SimSetup::makeSysArrays(void){
1535  
1536   #endif // is_mpi
1537  
1538 <
1539 <    if (info[l].n_SRI){
1540 <      Exclude::createArray(info[l].n_SRI);
1371 <      the_excludes = new Exclude * [info[l].n_SRI];
1372 <      for (int ex = 0; ex < info[l].n_SRI; ex++){
1373 <        the_excludes[ex] = new Exclude(ex);
1374 <      }
1375 <      info[l].globalExcludes = new int;
1376 <      info[l].n_exclude = info[l].n_SRI;
1377 <    }
1378 <    else{
1379 <      Exclude::createArray(1);
1380 <      the_excludes = new Exclude * ;
1381 <      the_excludes[0] = new Exclude(0);
1382 <      the_excludes[0]->setPair(0, 0);
1383 <      info[l].globalExcludes = new int;
1384 <      info[l].globalExcludes[0] = 0;
1385 <      info[l].n_exclude = 0;
1386 <    }
1387 <
1538 >    info[l].globalExcludes = new int;
1539 >    info[l].globalExcludes[0] = 0;
1540 >    
1541      // set the arrays into the SimInfo object
1542  
1543      info[l].atoms = the_atoms;
1544      info[l].molecules = the_molecules;
1545      info[l].nGlobalExcludes = 0;
1546 <    info[l].excludes = the_excludes;
1394 <
1546 >    
1547      the_ff->setSimInfo(info);
1548    }
1549   }

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