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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 999 by chrisfen, Fri Jan 30 15:01:09 2004 UTC vs.
Revision 1167 by tim, Wed May 12 16:38:45 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  
16   #ifdef IS_MPI
17   #include "mpiBASS.h"
# Line 27 | Line 30
30   #define FF_DUFF  0
31   #define FF_LJ    1
32   #define FF_EAM   2
33 < #define FF_H2O 3
33 > #define FF_H2O   3
34  
35   using namespace std;
36  
# Line 144 | Line 147 | void SimSetup::createSim(void){
147    // make the output filenames
148  
149    makeOutNames();
150 <
148 <  // make the integrator
149 <
150 <  makeIntegrator();
151 <
150 >  
151   #ifdef IS_MPI
152    mpiSim->mpiRefresh();
153   #endif
# Line 156 | 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 +  RigidBodyStamp* currentRigidBody;
186 +  CutoffGroupStamp* currentCutoffGroup;
187 +  CutoffGroup* myCutoffGroup;
188 +  int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
189 +  set<int> cutoffAtomSet; //atoms belong to  cutoffgroup defined at mdl file
190  
191    bond_pair* theBonds;
192    bend_set* theBends;
193    torsion_set* theTorsions;
194  
195 +  set<int> skipList;
196 +
197 +  double phi, theta, psi;
198 +  char* molName;
199 +  char rbName[100];
200 +
201    //init the forceField paramters
202  
203    the_ff->readParams();
204  
182 –
205    // init the atoms
206  
207 <  double phi, theta, psi;
186 <  double sux, suy, suz;
187 <  double Axx, Axy, Axz, Ayx, Ayy, Ayz, Azx, Azy, Azz;
188 <  double ux, uy, uz, u, uSqr;
207 >  int nMembers, nNew, rb1, rb2;
208  
209    for (k = 0; k < nInfo; k++){
210      the_ff->setSimInfo(&(info[k]));
211  
212      atomOffset = 0;
213 <    excludeOffset = 0;
213 >
214      for (i = 0; i < info[k].n_mol; i++){
215        stampID = info[k].molecules[i].getStampID();
216 +      molName = comp_stamps[stampID]->getID();
217  
218        molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
219        molInfo.nBonds = comp_stamps[stampID]->getNBonds();
220        molInfo.nBends = comp_stamps[stampID]->getNBends();
221        molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
222 <      molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
222 >      molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
223  
224 +      nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
225 +      
226        molInfo.myAtoms = &(info[k].atoms[atomOffset]);
205 –      molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
206 –      molInfo.myBonds = new Bond * [molInfo.nBonds];
207 –      molInfo.myBends = new Bend * [molInfo.nBends];
208 –      molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
227  
228 +      if (molInfo.nBonds > 0)
229 +        molInfo.myBonds = new (Bond *) [molInfo.nBonds];
230 +      else
231 +        molInfo.myBonds = NULL;
232 +
233 +      if (molInfo.nBends > 0)
234 +        molInfo.myBends = new (Bend *) [molInfo.nBends];
235 +      else
236 +        molInfo.myBends = NULL;
237 +
238 +      if (molInfo.nTorsions > 0)
239 +        molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
240 +      else
241 +        molInfo.myTorsions = NULL;
242 +
243        theBonds = new bond_pair[molInfo.nBonds];
244        theBends = new bend_set[molInfo.nBends];
245        theTorsions = new torsion_set[molInfo.nTorsions];
246 <
246 >      
247        // make the Atoms
248  
249        for (j = 0; j < molInfo.nAtoms; j++){
250          currentAtom = comp_stamps[stampID]->getAtom(j);
251 +
252          if (currentAtom->haveOrientation()){
253            dAtom = new DirectionalAtom((j + atomOffset),
254                                        info[k].getConfiguration());
# Line 228 | Line 262 | void SimSetup::makeMolecules(void){
262            phi = currentAtom->getEulerPhi() * M_PI / 180.0;
263            theta = currentAtom->getEulerTheta() * M_PI / 180.0;
264            psi = currentAtom->getEulerPsi()* M_PI / 180.0;
265 +
266 +          dAtom->setUnitFrameFromEuler(phi, theta, psi);
267              
268 <          Axx = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
269 <          Axy = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
234 <          Axz = sin(theta) * sin(psi);
235 <          
236 <          Ayx = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
237 <          Ayy = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
238 <          Ayz = sin(theta) * cos(psi);
239 <          
240 <          Azx = sin(phi) * sin(theta);
241 <          Azy = -cos(phi) * sin(theta);
242 <          Azz = cos(theta);
268 >        }
269 >        else{
270  
271 <          sux = 0.0;
245 <          suy = 0.0;
246 <          suz = 1.0;
271 >          molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
272  
248 –          ux = (Axx * sux) + (Ayx * suy) + (Azx * suz);
249 –          uy = (Axy * sux) + (Ayy * suy) + (Azy * suz);
250 –          uz = (Axz * sux) + (Ayz * suy) + (Azz * suz);
251 –
252 –          uSqr = (ux * ux) + (uy * uy) + (uz * uz);
253 –
254 –          u = sqrt(uSqr);
255 –          ux = ux / u;
256 –          uy = uy / u;
257 –          uz = uz / u;
258 –
259 –          dAtom->setSUx(ux);
260 –          dAtom->setSUy(uy);
261 –          dAtom->setSUz(uz);
273          }
263 –        else{
264 –          molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
265 –                                               info[k].getConfiguration());
266 –        }
267 –        molInfo.myAtoms[j]->setType(currentAtom->getType());
274  
275 +        molInfo.myAtoms[j]->setType(currentAtom->getType());
276   #ifdef IS_MPI
277  
278 <        molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
278 >        molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
279  
280   #endif // is_mpi
281        }
# Line 279 | Line 286 | void SimSetup::makeMolecules(void){
286          theBonds[j].a = currentBond->getA() + atomOffset;
287          theBonds[j].b = currentBond->getB() + atomOffset;
288  
289 <        exI = theBonds[j].a;
290 <        exJ = theBonds[j].b;
289 >        tempI = theBonds[j].a;
290 >        tempJ = theBonds[j].b;
291  
285 –        // exclude_I must always be the smaller of the pair
286 –        if (exI > exJ){
287 –          tempEx = exI;
288 –          exI = exJ;
289 –          exJ = tempEx;
290 –        }
292   #ifdef IS_MPI
293 <        tempEx = exI;
294 <        exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
295 <        tempEx = exJ;
296 <        exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
293 >        exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
294 >        exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
295 > #else
296 >        exI = tempI + 1;
297 >        exJ = tempJ + 1;
298 > #endif
299  
300 <        info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
298 < #else  // isn't MPI
299 <
300 <        info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
301 < #endif  //is_mpi
300 >        info[k].excludes->addPair(exI, exJ);
301        }
303 –      excludeOffset += molInfo.nBonds;
302  
303        //make the bends
304        for (j = 0; j < molInfo.nBends; j++){
# Line 350 | Line 348 | void SimSetup::makeMolecules(void){
348            }
349          }
350  
351 <        if (!theBends[j].isGhost){
352 <          exI = theBends[j].a;
353 <          exJ = theBends[j].c;
354 <        }
355 <        else{
358 <          exI = theBends[j].a;
359 <          exJ = theBends[j].b;
360 <        }
361 <
362 <        // exclude_I must always be the smaller of the pair
363 <        if (exI > exJ){
364 <          tempEx = exI;
365 <          exI = exJ;
366 <          exJ = tempEx;
367 <        }
351 >        if (theBends[j].isGhost) {
352 >          
353 >          tempI = theBends[j].a;
354 >          tempJ = theBends[j].b;
355 >          
356   #ifdef IS_MPI
357 <        tempEx = exI;
358 <        exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
359 <        tempEx = exJ;
360 <        exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
357 >          exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
358 >          exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
359 > #else
360 >          exI = tempI + 1;
361 >          exJ = tempJ + 1;
362 > #endif          
363 >          info[k].excludes->addPair(exI, exJ);
364  
365 <        info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
366 < #else  // isn't MPI
367 <        info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
368 < #endif  //is_mpi
365 >        } else {
366 >
367 >          tempI = theBends[j].a;
368 >          tempJ = theBends[j].b;
369 >          tempK = theBends[j].c;
370 >          
371 > #ifdef IS_MPI
372 >          exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
373 >          exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
374 >          exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
375 > #else
376 >          exI = tempI + 1;
377 >          exJ = tempJ + 1;
378 >          exK = tempK + 1;
379 > #endif
380 >          
381 >          info[k].excludes->addPair(exI, exK);
382 >          info[k].excludes->addPair(exI, exJ);
383 >          info[k].excludes->addPair(exJ, exK);
384 >        }
385        }
379 –      excludeOffset += molInfo.nBends;
386  
387        for (j = 0; j < molInfo.nTorsions; j++){
388          currentTorsion = comp_stamps[stampID]->getTorsion(j);
# Line 385 | Line 391 | void SimSetup::makeMolecules(void){
391          theTorsions[j].c = currentTorsion->getC() + atomOffset;
392          theTorsions[j].d = currentTorsion->getD() + atomOffset;
393  
394 <        exI = theTorsions[j].a;
395 <        exJ = theTorsions[j].d;
394 >        tempI = theTorsions[j].a;      
395 >        tempJ = theTorsions[j].b;
396 >        tempK = theTorsions[j].c;
397 >        tempL = theTorsions[j].d;
398  
399 <        // exclude_I must always be the smaller of the pair
400 <        if (exI > exJ){
401 <          tempEx = exI;
402 <          exI = exJ;
403 <          exJ = tempEx;
399 > #ifdef IS_MPI
400 >        exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
401 >        exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
402 >        exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
403 >        exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
404 > #else
405 >        exI = tempI + 1;
406 >        exJ = tempJ + 1;
407 >        exK = tempK + 1;
408 >        exL = tempL + 1;
409 > #endif
410 >
411 >        info[k].excludes->addPair(exI, exJ);
412 >        info[k].excludes->addPair(exI, exK);
413 >        info[k].excludes->addPair(exI, exL);        
414 >        info[k].excludes->addPair(exJ, exK);
415 >        info[k].excludes->addPair(exJ, exL);
416 >        info[k].excludes->addPair(exK, exL);
417 >      }
418 >
419 >      
420 >      molInfo.myRigidBodies.clear();
421 >      
422 >      for (j = 0; j < molInfo.nRigidBodies; j++){
423 >
424 >        currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
425 >        nMembers = currentRigidBody->getNMembers();
426 >
427 >        // Create the Rigid Body:
428 >
429 >        myRB = new RigidBody();
430 >
431 >        sprintf(rbName,"%s_RB_%d", molName, j);
432 >        myRB->setType(rbName);
433 >        
434 >        for (rb1 = 0; rb1 < nMembers; rb1++) {
435 >
436 >          // molI is atom numbering inside this molecule
437 >          molI = currentRigidBody->getMember(rb1);    
438 >
439 >          // tempI is atom numbering on local processor
440 >          tempI = molI + atomOffset;
441 >
442 >          // currentAtom is the AtomStamp (which we need for
443 >          // rigid body reference positions)
444 >          currentAtom = comp_stamps[stampID]->getAtom(molI);
445 >
446 >          // When we add to the rigid body, add the atom itself and
447 >          // the stamp info:
448 >
449 >          myRB->addAtom(info[k].atoms[tempI], currentAtom);
450 >          
451 >          // Add this atom to the Skip List for the integrators
452 > #ifdef IS_MPI
453 >          slI = info[k].atoms[tempI]->getGlobalIndex();
454 > #else
455 >          slI = tempI;
456 > #endif
457 >          skipList.insert(slI);
458 >          
459          }
460 +        
461 +        for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
462 +          for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
463 +            
464 +            tempI = currentRigidBody->getMember(rb1);
465 +            tempJ = currentRigidBody->getMember(rb2);
466 +            
467 +            // Some explanation is required here.
468 +            // Fortran indexing starts at 1, while c indexing starts at 0
469 +            // Also, in parallel computations, the GlobalIndex is
470 +            // used for the exclude list:
471 +            
472   #ifdef IS_MPI
473 <        tempEx = exI;
474 <        exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
475 <        tempEx = exJ;
476 <        exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
473 >            exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
474 >            exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
475 > #else
476 >            exI = molInfo.myAtoms[tempI]->getIndex() + 1;
477 >            exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
478 > #endif
479 >            
480 >            info[k].excludes->addPair(exI, exJ);
481 >            
482 >          }
483 >        }
484  
485 <        info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
486 < #else  // isn't MPI
405 <        info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
406 < #endif  //is_mpi
485 >        molInfo.myRigidBodies.push_back(myRB);
486 >        info[k].rigidBodies.push_back(myRB);
487        }
488 <      excludeOffset += molInfo.nTorsions;
488 >      
489  
490 +      //create cutoff group for molecule
491  
492 <      // send the arrays off to the forceField for init.
492 >      cutoffAtomSet.clear();
493 >      molInfo.myCutoffGroups.clear();
494 >      
495 >      for (j = 0; j < nCutoffGroups; j++){
496 >
497 >        currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
498 >        nMembers = currentCutoffGroup->getNMembers();
499 >
500 >        myCutoffGroup = new CutoffGroup();
501 >        
502 >        for (int cg = 0; cg < nMembers; cg++) {
503 >
504 >          // molI is atom numbering inside this molecule
505 >          molI = currentCutoffGroup->getMember(cg);    
506 >
507 >          // tempI is atom numbering on local processor
508 >          tempI = molI + atomOffset;
509 >          
510 >          myCutoffGroup->addAtom(info[k].atoms[tempI]);          
511 >
512 >          cutoffAtomSet.insert(tempI);
513 >        }
514 >
515 >        molInfo.myCutoffGroups.push_back(myCutoffGroup);
516 >      }//end for (j = 0; j < molInfo.nCutoffGroups; j++)
517 >
518 >      //creat a cutoff group for every atom  in current molecule which does not belong to cutoffgroup defined at mdl file
519 >
520 >      for(j = 0; j < molInfo.nAtoms; j++){
521 >
522 >        if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
523 >          myCutoffGroup = new CutoffGroup();
524 >          myCutoffGroup->addAtom(molInfo.myAtoms[j]);
525 >          molInfo.myCutoffGroups.push_back(myCutoffGroup);
526 >        }
527 >          
528 >      }
529 >
530 >              
531  
532 +
533 +      // After this is all set up, scan through the atoms to
534 +      // see if they can be added to the integrableObjects:
535 +
536 +      molInfo.myIntegrableObjects.clear();
537 +      
538 +
539 +      for (j = 0; j < molInfo.nAtoms; j++){
540 +
541 + #ifdef IS_MPI
542 +        slJ = molInfo.myAtoms[j]->getGlobalIndex();
543 + #else
544 +        slJ = j+atomOffset;
545 + #endif
546 +
547 +        // if they aren't on the skip list, then they can be integrated
548 +
549 +        if (skipList.find(slJ) == skipList.end()) {
550 +          mySD = (StuntDouble *) molInfo.myAtoms[j];
551 +          info[k].integrableObjects.push_back(mySD);
552 +          molInfo.myIntegrableObjects.push_back(mySD);
553 +        }
554 +      }
555 +
556 +      // all rigid bodies are integrated:
557 +
558 +      for (j = 0; j < molInfo.nRigidBodies; j++) {
559 +        mySD = (StuntDouble *) molInfo.myRigidBodies[j];
560 +        info[k].integrableObjects.push_back(mySD);      
561 +        molInfo.myIntegrableObjects.push_back(mySD);
562 +      }
563 +    
564 +      
565 +      // send the arrays off to the forceField for init.
566 +      
567        the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
568        the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
569        the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
570        the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
571                                   theTorsions);
572  
419 –
573        info[k].molecules[i].initialize(molInfo);
574  
575  
# Line 424 | Line 577 | void SimSetup::makeMolecules(void){
577        delete[] theBonds;
578        delete[] theBends;
579        delete[] theTorsions;
580 <    }
580 >    }    
581    }
582  
583   #ifdef IS_MPI
584    sprintf(checkPointMsg, "all molecules initialized succesfully");
585    MPIcheckPoint();
586   #endif // is_mpi
434 –
435 –  // clean up the forcefield
587  
437 –  the_ff->calcRcut();
438 –  the_ff->cleanMe();
588   }
589  
590   void SimSetup::initFromBass(void){
# Line 722 | Line 871 | void SimSetup::gatherInfo(void){
871    }
872  
873    //check whether sample time, status time, thermal time and reset time are divisble by dt
874 <  if (!isDivisible(globals->getSampleTime(), globals->getDt())){
874 >  if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
875      sprintf(painCave.errMsg,
876              "Sample time is not divisible by dt.\n"
877              "\tThis will result in samples that are not uniformly\n"
# Line 732 | Line 881 | void SimSetup::gatherInfo(void){
881      simError();    
882    }
883  
884 <  if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
884 >  if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
885      sprintf(painCave.errMsg,
886              "Status time is not divisible by dt.\n"
887              "\tThis will result in status reports that are not uniformly\n"
# Line 768 | Line 917 | void SimSetup::gatherInfo(void){
917      if (globals->haveSampleTime()){
918        info[i].sampleTime = globals->getSampleTime();
919        info[i].statusTime = info[i].sampleTime;
771 –      info[i].thermalTime = info[i].sampleTime;
920      }
921      else{
922        info[i].sampleTime = globals->getRunTime();
923        info[i].statusTime = info[i].sampleTime;
776 –      info[i].thermalTime = info[i].sampleTime;
924      }
925  
926      if (globals->haveStatusTime()){
# Line 782 | Line 929 | void SimSetup::gatherInfo(void){
929  
930      if (globals->haveThermalTime()){
931        info[i].thermalTime = globals->getThermalTime();
932 +    } else {
933 +      info[i].thermalTime = globals->getRunTime();
934      }
935  
936      info[i].resetIntegrator = 0;
# Line 841 | Line 990 | void SimSetup::gatherInfo(void){
990    for (int i = 0; i < nInfo; i++){
991      info[i].setSeed(seedValue);
992    }
993 <
993 >  
994   #ifdef IS_MPI
995    strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
996    MPIcheckPoint();
# Line 852 | Line 1001 | void SimSetup::finalInfoCheck(void){
1001   void SimSetup::finalInfoCheck(void){
1002    int index;
1003    int usesDipoles;
1004 +  int usesCharges;
1005    int i;
1006  
1007    for (i = 0; i < nInfo; i++){
# Line 863 | Line 1013 | void SimSetup::finalInfoCheck(void){
1013        usesDipoles = (info[i].atoms[index])->hasDipole();
1014        index++;
1015      }
1016 <
1016 >    index = 0;
1017 >    usesCharges = 0;
1018 >    while ((index < info[i].n_atoms) && !usesCharges){
1019 >      usesCharges= (info[i].atoms[index])->hasCharge();
1020 >      index++;
1021 >    }
1022   #ifdef IS_MPI
1023      int myUse = usesDipoles;
1024      MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1025   #endif //is_mpi
1026  
1027 <    double theEcr, theEst;
1027 >    double theRcut, theRsw;
1028  
1029 +    if (globals->haveRcut()) {
1030 +      theRcut = globals->getRcut();
1031 +
1032 +      if (globals->haveRsw())
1033 +        theRsw = globals->getRsw();
1034 +      else
1035 +        theRsw = theRcut;
1036 +      
1037 +      info[i].setDefaultRcut(theRcut, theRsw);
1038 +
1039 +    } else {
1040 +      
1041 +      the_ff->calcRcut();
1042 +      theRcut = info[i].getRcut();
1043 +
1044 +      if (globals->haveRsw())
1045 +        theRsw = globals->getRsw();
1046 +      else
1047 +        theRsw = theRcut;
1048 +      
1049 +      info[i].setDefaultRcut(theRcut, theRsw);
1050 +    }
1051 +
1052      if (globals->getUseRF()){
1053        info[i].useReactionField = 1;
1054 <
1055 <      if (!globals->haveECR()){
1054 >      
1055 >      if (!globals->haveRcut()){
1056          sprintf(painCave.errMsg,
1057 <                "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1057 >                "SimSetup Warning: No value was set for the cutoffRadius.\n"
1058                  "\tOOPSE will use a default value of 15.0 angstroms"
1059 <                "\tfor the electrostaticCutoffRadius.\n");
1059 >                "\tfor the cutoffRadius.\n");
1060          painCave.isFatal = 0;
1061          simError();
1062 <        theEcr = 15.0;
1062 >        theRcut = 15.0;
1063        }
1064        else{
1065 <        theEcr = globals->getECR();
1065 >        theRcut = globals->getRcut();
1066        }
1067  
1068 <      if (!globals->haveEST()){
1068 >      if (!globals->haveRsw()){
1069          sprintf(painCave.errMsg,
1070 <                "SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1070 >                "SimSetup Warning: No value was set for switchingRadius.\n"
1071                  "\tOOPSE will use a default value of\n"
1072 <                "\t0.05 * electrostaticCutoffRadius\n"
895 <                "\tfor the electrostaticSkinThickness\n");
1072 >                "\t0.95 * cutoffRadius for the switchingRadius\n");
1073          painCave.isFatal = 0;
1074          simError();
1075 <        theEst = 0.05 * theEcr;
1075 >        theRsw = 0.95 * theRcut;
1076        }
1077        else{
1078 <        theEst = globals->getEST();
1078 >        theRsw = globals->getRsw();
1079        }
1080  
1081 <      info[i].setDefaultEcr(theEcr, theEst);
1081 >      info[i].setDefaultRcut(theRcut, theRsw);
1082  
1083        if (!globals->haveDielectric()){
1084          sprintf(painCave.errMsg,
# Line 914 | Line 1091 | void SimSetup::finalInfoCheck(void){
1091        info[i].dielectric = globals->getDielectric();
1092      }
1093      else{
1094 <      if (usesDipoles){
1095 <        if (!globals->haveECR()){
1094 >      if (usesDipoles || usesCharges){
1095 >
1096 >        if (!globals->haveRcut()){
1097            sprintf(painCave.errMsg,
1098 <                  "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1098 >                  "SimSetup Warning: No value was set for the cutoffRadius.\n"
1099                    "\tOOPSE will use a default value of 15.0 angstroms"
1100 <                  "\tfor the electrostaticCutoffRadius.\n");
1101 <          painCave.isFatal = 0;
1102 <          simError();
1103 <          theEcr = 15.0;
1104 <        }
1100 >                  "\tfor the cutoffRadius.\n");
1101 >          painCave.isFatal = 0;
1102 >          simError();
1103 >          theRcut = 15.0;
1104 >      }
1105          else{
1106 <          theEcr = globals->getECR();
1106 >          theRcut = globals->getRcut();
1107          }
1108 <        
1109 <        if (!globals->haveEST()){
1108 >        
1109 >        if (!globals->haveRsw()){
1110            sprintf(painCave.errMsg,
1111 <                  "SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1111 >                  "SimSetup Warning: No value was set for switchingRadius.\n"
1112                    "\tOOPSE will use a default value of\n"
1113 <                  "\t0.05 * electrostaticCutoffRadius\n"
936 <                  "\tfor the electrostaticSkinThickness\n");
1113 >                  "\t0.95 * cutoffRadius for the switchingRadius\n");
1114            painCave.isFatal = 0;
1115            simError();
1116 <          theEst = 0.05 * theEcr;
1116 >          theRsw = 0.95 * theRcut;
1117          }
1118          else{
1119 <          theEst = globals->getEST();
1119 >          theRsw = globals->getRsw();
1120          }
1121 +        
1122 +        info[i].setDefaultRcut(theRcut, theRsw);
1123          
945 –        info[i].setDefaultEcr(theEcr, theEst);
1124        }
1125      }
1126    }
# Line 950 | Line 1128 | void SimSetup::finalInfoCheck(void){
1128    strcpy(checkPointMsg, "post processing checks out");
1129    MPIcheckPoint();
1130   #endif // is_mpi
1131 +
1132 +  // clean up the forcefield
1133 +  the_ff->cleanMe();
1134   }
1135    
1136   void SimSetup::initSystemCoords(void){
# Line 1164 | Line 1345 | void SimSetup::compList(void){
1345    LinkedMolStamp* headStamp = new LinkedMolStamp();
1346    LinkedMolStamp* currentStamp = NULL;
1347    comp_stamps = new MoleculeStamp * [n_components];
1348 +  bool haveCutoffGroups;
1349  
1350 +  haveCutoffGroups = false;
1351 +  
1352    // make an array of molecule stamps that match the components used.
1353    // also extract the used stamps out into a separate linked list
1354  
# Line 1199 | Line 1383 | void SimSetup::compList(void){
1383        headStamp->add(currentStamp);
1384        comp_stamps[i] = headStamp->match(id);
1385      }
1386 +
1387 +    if(comp_stamps[i]->getNCutoffGroups() > 0)
1388 +      haveCutoffGroups = true;    
1389    }
1390 +    
1391 +  for (i = 0; i < nInfo; i++)
1392 +    info[i].haveCutoffGroups = haveCutoffGroups;
1393  
1394   #ifdef IS_MPI
1395    strcpy(checkPointMsg, "Component stamps successfully extracted\n");
# Line 1216 | Line 1406 | void SimSetup::calcSysValues(void){
1406    tot_bonds = 0;
1407    tot_bends = 0;
1408    tot_torsions = 0;
1409 +  tot_rigid = 0;
1410    for (i = 0; i < n_components; i++){
1411      tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1412      tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1413      tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1414      tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1415 +    tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1416    }
1417 <
1417 >  
1418    tot_SRI = tot_bonds + tot_bends + tot_torsions;
1419    molMembershipArray = new int[tot_atoms];
1420  
# Line 1244 | Line 1436 | void SimSetup::mpiMolDivide(void){
1436    int i, j, k;
1437    int localMol, allMol;
1438    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1439 +  int local_rigid;
1440 +  vector<int> globalMolIndex;
1441  
1442    mpiSim = new mpiSimulation(info);
1443  
1444 <  globalIndex = mpiSim->divideLabor();
1444 >  mpiSim->divideLabor();
1445 >  globalAtomIndex = mpiSim->getGlobalAtomIndex();
1446 >  //globalMolIndex = mpiSim->getGlobalMolIndex();
1447  
1448    // set up the local variables
1449  
# Line 1260 | Line 1456 | void SimSetup::mpiMolDivide(void){
1456    local_bonds = 0;
1457    local_bends = 0;
1458    local_torsions = 0;
1459 <  globalAtomIndex = 0;
1459 >  local_rigid = 0;
1460 >  globalAtomCounter = 0;
1461  
1265 –
1462    for (i = 0; i < n_components; i++){
1463      for (j = 0; j < components_nmol[i]; j++){
1464        if (mol2proc[allMol] == worldRank){
# Line 1270 | Line 1466 | void SimSetup::mpiMolDivide(void){
1466          local_bonds += comp_stamps[i]->getNBonds();
1467          local_bends += comp_stamps[i]->getNBends();
1468          local_torsions += comp_stamps[i]->getNTorsions();
1469 +        local_rigid += comp_stamps[i]->getNRigidBodies();
1470          localMol++;
1471        }      
1472        for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1473 <        info[0].molMembershipArray[globalAtomIndex] = allMol;
1474 <        globalAtomIndex++;
1473 >        info[0].molMembershipArray[globalAtomCounter] = allMol;
1474 >        globalAtomCounter++;
1475        }
1476  
1477        allMol++;
# Line 1283 | Line 1480 | void SimSetup::mpiMolDivide(void){
1480    local_SRI = local_bonds + local_bends + local_torsions;
1481  
1482    info[0].n_atoms = mpiSim->getMyNlocal();  
1483 +  
1484  
1485    if (local_atoms != info[0].n_atoms){
1486      sprintf(painCave.errMsg,
# Line 1315 | Line 1513 | void SimSetup::makeSysArrays(void){
1513  
1514    Atom** the_atoms;
1515    Molecule* the_molecules;
1318 –  Exclude** the_excludes;
1516  
1320 –
1517    for (l = 0; l < nInfo; l++){
1518      // create the atom and short range interaction arrays
1519  
# Line 1343 | Line 1539 | void SimSetup::makeSysArrays(void){
1539   #else // is_mpi
1540  
1541      molIndex = 0;
1542 <    globalAtomIndex = 0;
1542 >    globalAtomCounter = 0;
1543      for (i = 0; i < n_components; i++){
1544        for (j = 0; j < components_nmol[i]; j++){
1545          the_molecules[molIndex].setStampID(i);
1546          the_molecules[molIndex].setMyIndex(molIndex);
1547          the_molecules[molIndex].setGlobalIndex(molIndex);
1548          for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1549 <          info[l].molMembershipArray[globalAtomIndex] = molIndex;
1550 <          globalAtomIndex++;
1549 >          info[l].molMembershipArray[globalAtomCounter] = molIndex;
1550 >          globalAtomCounter++;
1551          }
1552          molIndex++;
1553        }
# Line 1360 | Line 1556 | void SimSetup::makeSysArrays(void){
1556  
1557   #endif // is_mpi
1558  
1559 <
1560 <    if (info[l].n_SRI){
1561 <      Exclude::createArray(info[l].n_SRI);
1366 <      the_excludes = new Exclude * [info[l].n_SRI];
1367 <      for (int ex = 0; ex < info[l].n_SRI; ex++){
1368 <        the_excludes[ex] = new Exclude(ex);
1369 <      }
1370 <      info[l].globalExcludes = new int;
1371 <      info[l].n_exclude = info[l].n_SRI;
1372 <    }
1373 <    else{
1374 <      Exclude::createArray(1);
1375 <      the_excludes = new Exclude * ;
1376 <      the_excludes[0] = new Exclude(0);
1377 <      the_excludes[0]->setPair(0, 0);
1378 <      info[l].globalExcludes = new int;
1379 <      info[l].globalExcludes[0] = 0;
1380 <      info[l].n_exclude = 0;
1381 <    }
1382 <
1559 >    info[l].globalExcludes = new int;
1560 >    info[l].globalExcludes[0] = 0;
1561 >    
1562      // set the arrays into the SimInfo object
1563  
1564      info[l].atoms = the_atoms;
1565      info[l].molecules = the_molecules;
1566      info[l].nGlobalExcludes = 0;
1567 <    info[l].excludes = the_excludes;
1389 <
1567 >    
1568      the_ff->setSimInfo(info);
1569    }
1570   }
# Line 1658 | Line 1836 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1836    }
1837  
1838    theInfo.addProperty(zconsForcePolicy);
1839 +
1840 +  //set zcons gap
1841 +  DoubleData* zconsGap = new DoubleData();
1842 +  zconsGap->setID(ZCONSGAP_ID);
1843  
1844 +  if (globals->haveZConsGap()){
1845 +    zconsGap->setData(globals->getZconsGap());
1846 +    theInfo.addProperty(zconsGap);  
1847 +  }
1848 +
1849 +  //set zcons fixtime
1850 +  DoubleData* zconsFixtime = new DoubleData();
1851 +  zconsFixtime->setID(ZCONSFIXTIME_ID);
1852 +
1853 +  if (globals->haveZConsFixTime()){
1854 +    zconsFixtime->setData(globals->getZconsFixtime());
1855 +    theInfo.addProperty(zconsFixtime);  
1856 +  }
1857 +
1858 +  //set zconsUsingSMD
1859 +  IntData* zconsUsingSMD = new IntData();
1860 +  zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1861 +
1862 +  if (globals->haveZConsUsingSMD()){
1863 +    zconsUsingSMD->setData(globals->getZconsUsingSMD());
1864 +    theInfo.addProperty(zconsUsingSMD);  
1865 +  }
1866 +
1867    //Determine the name of ouput file and add it into SimInfo's property list
1868    //Be careful, do not use inFileName, since it is a pointer which
1869    //point to a string at master node, and slave nodes do not contain that string
# Line 1688 | Line 1893 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1893      tempParaItem.zPos = zconStamp[i]->getZpos();
1894      tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1895      tempParaItem.kRatio = zconStamp[i]->getKratio();
1896 <
1896 >    tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1897 >    tempParaItem.cantVel = zconStamp[i]->getCantVel();    
1898      zconsParaData->addItem(tempParaItem);
1899    }
1900  
# Line 1706 | Line 1912 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1912    //push data into siminfo, therefore, we can retrieve later
1913    theInfo.addProperty(zconsParaData);
1914   }
1915 +
1916 + void SimSetup::makeMinimizer(){
1917 +
1918 +  OOPSEMinimizer* myOOPSEMinimizer;
1919 +  MinimizerParameterSet* param;
1920 +  char minimizerName[100];
1921 +  
1922 +  for (int i = 0; i < nInfo; i++){
1923 +    
1924 +    //prepare parameter set for minimizer
1925 +    param = new MinimizerParameterSet();
1926 +    param->setDefaultParameter();
1927 +
1928 +    if (globals->haveMinimizer()){
1929 +      param->setFTol(globals->getMinFTol());
1930 +    }
1931 +
1932 +    if (globals->haveMinGTol()){
1933 +      param->setGTol(globals->getMinGTol());
1934 +    }
1935 +
1936 +    if (globals->haveMinMaxIter()){
1937 +      param->setMaxIteration(globals->getMinMaxIter());
1938 +    }
1939 +
1940 +    if (globals->haveMinWriteFrq()){
1941 +      param->setMaxIteration(globals->getMinMaxIter());
1942 +    }
1943 +
1944 +    if (globals->haveMinWriteFrq()){
1945 +      param->setWriteFrq(globals->getMinWriteFrq());
1946 +    }
1947 +    
1948 +    if (globals->haveMinStepSize()){
1949 +      param->setStepSize(globals->getMinStepSize());
1950 +    }
1951 +
1952 +    if (globals->haveMinLSMaxIter()){
1953 +      param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1954 +    }    
1955 +
1956 +    if (globals->haveMinLSTol()){
1957 +      param->setLineSearchTol(globals->getMinLSTol());
1958 +    }    
1959 +
1960 +    strcpy(minimizerName, globals->getMinimizer());
1961 +
1962 +    if (!strcasecmp(minimizerName, "CG")){
1963 +      myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1964 +    }
1965 +    else if (!strcasecmp(minimizerName, "SD")){
1966 +    //myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1967 +      myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1968 +    }
1969 +    else{
1970 +          sprintf(painCave.errMsg,
1971 +                  "SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1972 +          painCave.isFatal = 0;
1973 +          simError();
1974 +
1975 +      myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);          
1976 +    }
1977 +     info[i].the_integrator = myOOPSEMinimizer;
1978 +
1979 +     //store the minimizer into simInfo
1980 +     info[i].the_minimizer = myOOPSEMinimizer;
1981 +     info[i].has_minimizer = true;
1982 +  }
1983 +
1984 + }

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