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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 965 by gezelter, Mon Jan 19 21:17:39 2004 UTC vs.
Revision 1180 by chrisfen, Thu May 20 20:24:07 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 24 | Line 27
27   #define NPTxyz_ENS     4
28  
29  
30 < #define FF_DUFF 0
31 < #define FF_LJ   1
32 < #define FF_EAM  2
30 > #define FF_DUFF  0
31 > #define FF_LJ    1
32 > #define FF_EAM   2
33 > #define FF_H2O   3
34  
35   using namespace std;
36  
# Line 143 | Line 147 | void SimSetup::createSim(void){
147    // make the output filenames
148  
149    makeOutNames();
150 <
147 <  // make the integrator
148 <
149 <  makeIntegrator();
150 <
150 >  
151   #ifdef IS_MPI
152    mpiSim->mpiRefresh();
153   #endif
# Line 155 | 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 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]);
202 –      molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
203 –      molInfo.myBonds = new Bond * [molInfo.nBonds];
204 –      molInfo.myBends = new Bend * [molInfo.nBends];
205 –      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());
255            info[k].n_oriented++;
256            molInfo.myAtoms[j] = dAtom;
257  
258 <          ux = currentAtom->getOrntX();
259 <          uy = currentAtom->getOrntY();
260 <          uz = currentAtom->getOrntZ();
258 >          // Directional Atoms have standard unit vectors which are oriented
259 >          // in space using the three Euler angles.  We assume the standard
260 >          // unit vector was originally along the z axis below.
261  
262 <          uSqr = (ux * ux) + (uy * uy) + (uz * uz);
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 <          u = sqrt(uSqr);
267 <          ux = ux / u;
229 <          uy = uy / u;
230 <          uz = uz / u;
231 <
232 <          dAtom->setSUx(ux);
233 <          dAtom->setSUy(uy);
234 <          dAtom->setSUz(uz);
266 >          dAtom->setUnitFrameFromEuler(phi, theta, psi);
267 >            
268          }
269          else{
270 <          molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
271 <                                               info[k].getConfiguration());
270 >
271 >          molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
272 >
273          }
240 –        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 252 | 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  
258 –        // exclude_I must always be the smaller of the pair
259 –        if (exI > exJ){
260 –          tempEx = exI;
261 –          exI = exJ;
262 –          exJ = tempEx;
263 –        }
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);
271 < #else  // isn't MPI
272 <
273 <        info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
274 < #endif  //is_mpi
300 >        info[k].excludes->addPair(exI, exJ);
301        }
276 –      excludeOffset += molInfo.nBonds;
302  
303        //make the bends
304        for (j = 0; j < molInfo.nBends; j++){
# Line 323 | 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{
331 <          exI = theBends[j].a;
332 <          exJ = theBends[j].b;
333 <        }
334 <
335 <        // exclude_I must always be the smaller of the pair
336 <        if (exI > exJ){
337 <          tempEx = exI;
338 <          exI = exJ;
339 <          exJ = tempEx;
340 <        }
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        }
352 –      excludeOffset += molInfo.nBends;
386  
387        for (j = 0; j < molInfo.nTorsions; j++){
388          currentTorsion = comp_stamps[stampID]->getTorsion(j);
# Line 358 | 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
378 <        info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
379 < #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  
392 –
573        info[k].molecules[i].initialize(molInfo);
574  
575  
# Line 397 | 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
407 –
408 –  // clean up the forcefield
587  
410 –  the_ff->calcRcut();
411 –  the_ff->cleanMe();
588   }
589  
590   void SimSetup::initFromBass(void){
# Line 608 | Line 784 | void SimSetup::gatherInfo(void){
784    }
785    else if (!strcasecmp(force_field, "EAM")){
786      ffCase = FF_EAM;
787 +  }
788 +  else if (!strcasecmp(force_field, "WATER")){
789 +    ffCase = FF_H2O;
790    }
791    else{
792      sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
# Line 692 | 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 702 | 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 738 | Line 917 | void SimSetup::gatherInfo(void){
917      if (globals->haveSampleTime()){
918        info[i].sampleTime = globals->getSampleTime();
919        info[i].statusTime = info[i].sampleTime;
741 –      info[i].thermalTime = info[i].sampleTime;
920      }
921      else{
922        info[i].sampleTime = globals->getRunTime();
923        info[i].statusTime = info[i].sampleTime;
746 –      info[i].thermalTime = info[i].sampleTime;
924      }
925  
926      if (globals->haveStatusTime()){
# Line 752 | 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 769 | Line 948 | void SimSetup::gatherInfo(void){
948  
949      info[i].useInitXSstate = globals->getUseInitXSstate();
950      info[i].orthoTolerance = globals->getOrthoBoxTolerance();
951 <    
951 >
952 >    // check for thermodynamic integration
953 >    if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
954 >      info[i].thermIntLambda = globals->getThermIntLambda();
955 >      info[i].thermIntK = globals->getThermIntK();
956 >      info[i].useThermInt = 1;
957 >      
958 >      Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
959 >      info[i].restraint = myRestraint;
960 >    }
961    }
962    
963    //setup seed for random number generator
# Line 811 | Line 999 | void SimSetup::gatherInfo(void){
999    for (int i = 0; i < nInfo; i++){
1000      info[i].setSeed(seedValue);
1001    }
1002 <
1002 >  
1003   #ifdef IS_MPI
1004 <  strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
1004 >  strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1005    MPIcheckPoint();
1006   #endif // is_mpi
1007   }
# Line 822 | Line 1010 | void SimSetup::finalInfoCheck(void){
1010   void SimSetup::finalInfoCheck(void){
1011    int index;
1012    int usesDipoles;
1013 +  int usesCharges;
1014    int i;
1015  
1016    for (i = 0; i < nInfo; i++){
# Line 833 | Line 1022 | void SimSetup::finalInfoCheck(void){
1022        usesDipoles = (info[i].atoms[index])->hasDipole();
1023        index++;
1024      }
1025 <
1025 >    index = 0;
1026 >    usesCharges = 0;
1027 >    while ((index < info[i].n_atoms) && !usesCharges){
1028 >      usesCharges= (info[i].atoms[index])->hasCharge();
1029 >      index++;
1030 >    }
1031   #ifdef IS_MPI
1032      int myUse = usesDipoles;
1033      MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1034   #endif //is_mpi
1035  
1036 <    double theEcr, theEst;
1036 >    double theRcut, theRsw;
1037  
1038 +    if (globals->haveRcut()) {
1039 +      theRcut = globals->getRcut();
1040 +
1041 +      if (globals->haveRsw())
1042 +        theRsw = globals->getRsw();
1043 +      else
1044 +        theRsw = theRcut;
1045 +      
1046 +      info[i].setDefaultRcut(theRcut, theRsw);
1047 +
1048 +    } else {
1049 +      
1050 +      the_ff->calcRcut();
1051 +      theRcut = info[i].getRcut();
1052 +
1053 +      if (globals->haveRsw())
1054 +        theRsw = globals->getRsw();
1055 +      else
1056 +        theRsw = theRcut;
1057 +      
1058 +      info[i].setDefaultRcut(theRcut, theRsw);
1059 +    }
1060 +
1061      if (globals->getUseRF()){
1062        info[i].useReactionField = 1;
1063 <
1064 <      if (!globals->haveECR()){
1063 >      
1064 >      if (!globals->haveRcut()){
1065          sprintf(painCave.errMsg,
1066 <                "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1066 >                "SimSetup Warning: No value was set for the cutoffRadius.\n"
1067                  "\tOOPSE will use a default value of 15.0 angstroms"
1068 <                "\tfor the electrostaticCutoffRadius.\n");
1068 >                "\tfor the cutoffRadius.\n");
1069          painCave.isFatal = 0;
1070          simError();
1071 <        theEcr = 15.0;
1071 >        theRcut = 15.0;
1072        }
1073        else{
1074 <        theEcr = globals->getECR();
1074 >        theRcut = globals->getRcut();
1075        }
1076  
1077 <      if (!globals->haveEST()){
1077 >      if (!globals->haveRsw()){
1078          sprintf(painCave.errMsg,
1079 <                "SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1079 >                "SimSetup Warning: No value was set for switchingRadius.\n"
1080                  "\tOOPSE will use a default value of\n"
1081 <                "\t0.05 * electrostaticCutoffRadius\n"
865 <                "\tfor the electrostaticSkinThickness\n");
1081 >                "\t0.95 * cutoffRadius for the switchingRadius\n");
1082          painCave.isFatal = 0;
1083          simError();
1084 <        theEst = 0.05 * theEcr;
1084 >        theRsw = 0.95 * theRcut;
1085        }
1086        else{
1087 <        theEst = globals->getEST();
1087 >        theRsw = globals->getRsw();
1088        }
1089  
1090 <      info[i].setDefaultEcr(theEcr, theEst);
1090 >      info[i].setDefaultRcut(theRcut, theRsw);
1091  
1092        if (!globals->haveDielectric()){
1093          sprintf(painCave.errMsg,
# Line 884 | Line 1100 | void SimSetup::finalInfoCheck(void){
1100        info[i].dielectric = globals->getDielectric();
1101      }
1102      else{
1103 <      if (usesDipoles){
1104 <        if (!globals->haveECR()){
1103 >      if (usesDipoles || usesCharges){
1104 >
1105 >        if (!globals->haveRcut()){
1106            sprintf(painCave.errMsg,
1107 <                  "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1107 >                  "SimSetup Warning: No value was set for the cutoffRadius.\n"
1108                    "\tOOPSE will use a default value of 15.0 angstroms"
1109 <                  "\tfor the electrostaticCutoffRadius.\n");
1110 <          painCave.isFatal = 0;
1111 <          simError();
1112 <          theEcr = 15.0;
1113 <        }
1109 >                  "\tfor the cutoffRadius.\n");
1110 >          painCave.isFatal = 0;
1111 >          simError();
1112 >          theRcut = 15.0;
1113 >      }
1114          else{
1115 <          theEcr = globals->getECR();
1115 >          theRcut = globals->getRcut();
1116          }
1117 <        
1118 <        if (!globals->haveEST()){
1117 >        
1118 >        if (!globals->haveRsw()){
1119            sprintf(painCave.errMsg,
1120 <                  "SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1120 >                  "SimSetup Warning: No value was set for switchingRadius.\n"
1121                    "\tOOPSE will use a default value of\n"
1122 <                  "\t0.05 * electrostaticCutoffRadius\n"
906 <                  "\tfor the electrostaticSkinThickness\n");
1122 >                  "\t0.95 * cutoffRadius for the switchingRadius\n");
1123            painCave.isFatal = 0;
1124            simError();
1125 <          theEst = 0.05 * theEcr;
1125 >          theRsw = 0.95 * theRcut;
1126          }
1127          else{
1128 <          theEst = globals->getEST();
1128 >          theRsw = globals->getRsw();
1129          }
1130 +        
1131 +        info[i].setDefaultRcut(theRcut, theRsw);
1132          
915 –        info[i].setDefaultEcr(theEcr, theEst);
1133        }
1134      }
1135    }
# Line 920 | Line 1137 | void SimSetup::finalInfoCheck(void){
1137    strcpy(checkPointMsg, "post processing checks out");
1138    MPIcheckPoint();
1139   #endif // is_mpi
1140 +
1141 +  // clean up the forcefield
1142 +  the_ff->cleanMe();
1143   }
1144    
1145   void SimSetup::initSystemCoords(void){
# Line 1050 | Line 1270 | void SimSetup::makeOutNames(void){
1270          }
1271        }
1272  
1273 +      strcpy(info[k].rawPotName, inFileName);
1274 +      nameLength = strlen(info[k].rawPotName);
1275 +      endTest = &(info[k].rawPotName[nameLength - 5]);
1276 +      if (!strcmp(endTest, ".bass")){
1277 +        strcpy(endTest, ".raw");
1278 +      }
1279 +      else if (!strcmp(endTest, ".BASS")){
1280 +        strcpy(endTest, ".raw");
1281 +      }
1282 +      else{
1283 +        endTest = &(info[k].rawPotName[nameLength - 4]);
1284 +        if (!strcmp(endTest, ".bss")){
1285 +          strcpy(endTest, ".raw");
1286 +        }
1287 +        else if (!strcmp(endTest, ".mdl")){
1288 +          strcpy(endTest, ".raw");
1289 +        }
1290 +        else{
1291 +          strcat(info[k].rawPotName, ".raw");
1292 +        }
1293 +      }
1294 +
1295   #ifdef IS_MPI
1296  
1297      }
# Line 1110 | Line 1352 | void SimSetup::createFF(void){
1352        the_ff = new EAM_FF();
1353        break;
1354  
1355 +    case FF_H2O:
1356 +      the_ff = new WATER();
1357 +      break;
1358 +
1359      default:
1360        sprintf(painCave.errMsg,
1361                "SimSetup Error. Unrecognized force field in case statement.\n");
# Line 1130 | Line 1376 | void SimSetup::compList(void){
1376    LinkedMolStamp* headStamp = new LinkedMolStamp();
1377    LinkedMolStamp* currentStamp = NULL;
1378    comp_stamps = new MoleculeStamp * [n_components];
1379 +  bool haveCutoffGroups;
1380  
1381 +  haveCutoffGroups = false;
1382 +  
1383    // make an array of molecule stamps that match the components used.
1384    // also extract the used stamps out into a separate linked list
1385  
# Line 1165 | Line 1414 | void SimSetup::compList(void){
1414        headStamp->add(currentStamp);
1415        comp_stamps[i] = headStamp->match(id);
1416      }
1417 +
1418 +    if(comp_stamps[i]->getNCutoffGroups() > 0)
1419 +      haveCutoffGroups = true;    
1420    }
1421 +    
1422 +  for (i = 0; i < nInfo; i++)
1423 +    info[i].haveCutoffGroups = haveCutoffGroups;
1424  
1425   #ifdef IS_MPI
1426    strcpy(checkPointMsg, "Component stamps successfully extracted\n");
# Line 1182 | Line 1437 | void SimSetup::calcSysValues(void){
1437    tot_bonds = 0;
1438    tot_bends = 0;
1439    tot_torsions = 0;
1440 +  tot_rigid = 0;
1441    for (i = 0; i < n_components; i++){
1442      tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1443      tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1444      tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1445      tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1446 +    tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1447    }
1448 <
1448 >  
1449    tot_SRI = tot_bonds + tot_bends + tot_torsions;
1450    molMembershipArray = new int[tot_atoms];
1451  
# Line 1210 | Line 1467 | void SimSetup::mpiMolDivide(void){
1467    int i, j, k;
1468    int localMol, allMol;
1469    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1470 +  int local_rigid;
1471 +  vector<int> globalMolIndex;
1472  
1473    mpiSim = new mpiSimulation(info);
1474  
1475 <  globalIndex = mpiSim->divideLabor();
1475 >  mpiSim->divideLabor();
1476 >  globalAtomIndex = mpiSim->getGlobalAtomIndex();
1477 >  //globalMolIndex = mpiSim->getGlobalMolIndex();
1478  
1479    // set up the local variables
1480  
# Line 1226 | Line 1487 | void SimSetup::mpiMolDivide(void){
1487    local_bonds = 0;
1488    local_bends = 0;
1489    local_torsions = 0;
1490 <  globalAtomIndex = 0;
1490 >  local_rigid = 0;
1491 >  globalAtomCounter = 0;
1492  
1231 –
1493    for (i = 0; i < n_components; i++){
1494      for (j = 0; j < components_nmol[i]; j++){
1495        if (mol2proc[allMol] == worldRank){
# Line 1236 | Line 1497 | void SimSetup::mpiMolDivide(void){
1497          local_bonds += comp_stamps[i]->getNBonds();
1498          local_bends += comp_stamps[i]->getNBends();
1499          local_torsions += comp_stamps[i]->getNTorsions();
1500 +        local_rigid += comp_stamps[i]->getNRigidBodies();
1501          localMol++;
1502        }      
1503        for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1504 <        info[0].molMembershipArray[globalAtomIndex] = allMol;
1505 <        globalAtomIndex++;
1504 >        info[0].molMembershipArray[globalAtomCounter] = allMol;
1505 >        globalAtomCounter++;
1506        }
1507  
1508        allMol++;
# Line 1249 | Line 1511 | void SimSetup::mpiMolDivide(void){
1511    local_SRI = local_bonds + local_bends + local_torsions;
1512  
1513    info[0].n_atoms = mpiSim->getMyNlocal();  
1514 +  
1515  
1516    if (local_atoms != info[0].n_atoms){
1517      sprintf(painCave.errMsg,
# Line 1281 | Line 1544 | void SimSetup::makeSysArrays(void){
1544  
1545    Atom** the_atoms;
1546    Molecule* the_molecules;
1284 –  Exclude** the_excludes;
1547  
1286 –
1548    for (l = 0; l < nInfo; l++){
1549      // create the atom and short range interaction arrays
1550  
# Line 1309 | Line 1570 | void SimSetup::makeSysArrays(void){
1570   #else // is_mpi
1571  
1572      molIndex = 0;
1573 <    globalAtomIndex = 0;
1573 >    globalAtomCounter = 0;
1574      for (i = 0; i < n_components; i++){
1575        for (j = 0; j < components_nmol[i]; j++){
1576          the_molecules[molIndex].setStampID(i);
1577          the_molecules[molIndex].setMyIndex(molIndex);
1578          the_molecules[molIndex].setGlobalIndex(molIndex);
1579          for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1580 <          info[l].molMembershipArray[globalAtomIndex] = molIndex;
1581 <          globalAtomIndex++;
1580 >          info[l].molMembershipArray[globalAtomCounter] = molIndex;
1581 >          globalAtomCounter++;
1582          }
1583          molIndex++;
1584        }
# Line 1326 | Line 1587 | void SimSetup::makeSysArrays(void){
1587  
1588   #endif // is_mpi
1589  
1590 <
1591 <    if (info[l].n_SRI){
1592 <      Exclude::createArray(info[l].n_SRI);
1332 <      the_excludes = new Exclude * [info[l].n_SRI];
1333 <      for (int ex = 0; ex < info[l].n_SRI; ex++){
1334 <        the_excludes[ex] = new Exclude(ex);
1335 <      }
1336 <      info[l].globalExcludes = new int;
1337 <      info[l].n_exclude = info[l].n_SRI;
1338 <    }
1339 <    else{
1340 <      Exclude::createArray(1);
1341 <      the_excludes = new Exclude * ;
1342 <      the_excludes[0] = new Exclude(0);
1343 <      the_excludes[0]->setPair(0, 0);
1344 <      info[l].globalExcludes = new int;
1345 <      info[l].globalExcludes[0] = 0;
1346 <      info[l].n_exclude = 0;
1347 <    }
1348 <
1590 >    info[l].globalExcludes = new int;
1591 >    info[l].globalExcludes[0] = 0;
1592 >    
1593      // set the arrays into the SimInfo object
1594  
1595      info[l].atoms = the_atoms;
1596      info[l].molecules = the_molecules;
1597      info[l].nGlobalExcludes = 0;
1598 <    info[l].excludes = the_excludes;
1355 <
1598 >    
1599      the_ff->setSimInfo(info);
1600    }
1601   }
# Line 1625 | Line 1868 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1868  
1869    theInfo.addProperty(zconsForcePolicy);
1870  
1871 +  //set zcons gap
1872 +  DoubleData* zconsGap = new DoubleData();
1873 +  zconsGap->setID(ZCONSGAP_ID);
1874 +
1875 +  if (globals->haveZConsGap()){
1876 +    zconsGap->setData(globals->getZconsGap());
1877 +    theInfo.addProperty(zconsGap);  
1878 +  }
1879 +
1880 +  //set zcons fixtime
1881 +  DoubleData* zconsFixtime = new DoubleData();
1882 +  zconsFixtime->setID(ZCONSFIXTIME_ID);
1883 +
1884 +  if (globals->haveZConsFixTime()){
1885 +    zconsFixtime->setData(globals->getZconsFixtime());
1886 +    theInfo.addProperty(zconsFixtime);  
1887 +  }
1888 +
1889 +  //set zconsUsingSMD
1890 +  IntData* zconsUsingSMD = new IntData();
1891 +  zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1892 +
1893 +  if (globals->haveZConsUsingSMD()){
1894 +    zconsUsingSMD->setData(globals->getZconsUsingSMD());
1895 +    theInfo.addProperty(zconsUsingSMD);  
1896 +  }
1897 +
1898    //Determine the name of ouput file and add it into SimInfo's property list
1899    //Be careful, do not use inFileName, since it is a pointer which
1900    //point to a string at master node, and slave nodes do not contain that string
# Line 1654 | Line 1924 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1924      tempParaItem.zPos = zconStamp[i]->getZpos();
1925      tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1926      tempParaItem.kRatio = zconStamp[i]->getKratio();
1927 <
1927 >    tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1928 >    tempParaItem.cantVel = zconStamp[i]->getCantVel();    
1929      zconsParaData->addItem(tempParaItem);
1930    }
1931  
# Line 1672 | Line 1943 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1943    //push data into siminfo, therefore, we can retrieve later
1944    theInfo.addProperty(zconsParaData);
1945   }
1946 +
1947 + void SimSetup::makeMinimizer(){
1948 +
1949 +  OOPSEMinimizer* myOOPSEMinimizer;
1950 +  MinimizerParameterSet* param;
1951 +  char minimizerName[100];
1952 +  
1953 +  for (int i = 0; i < nInfo; i++){
1954 +    
1955 +    //prepare parameter set for minimizer
1956 +    param = new MinimizerParameterSet();
1957 +    param->setDefaultParameter();
1958 +
1959 +    if (globals->haveMinimizer()){
1960 +      param->setFTol(globals->getMinFTol());
1961 +    }
1962 +
1963 +    if (globals->haveMinGTol()){
1964 +      param->setGTol(globals->getMinGTol());
1965 +    }
1966 +
1967 +    if (globals->haveMinMaxIter()){
1968 +      param->setMaxIteration(globals->getMinMaxIter());
1969 +    }
1970 +
1971 +    if (globals->haveMinWriteFrq()){
1972 +      param->setMaxIteration(globals->getMinMaxIter());
1973 +    }
1974 +
1975 +    if (globals->haveMinWriteFrq()){
1976 +      param->setWriteFrq(globals->getMinWriteFrq());
1977 +    }
1978 +    
1979 +    if (globals->haveMinStepSize()){
1980 +      param->setStepSize(globals->getMinStepSize());
1981 +    }
1982 +
1983 +    if (globals->haveMinLSMaxIter()){
1984 +      param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1985 +    }    
1986 +
1987 +    if (globals->haveMinLSTol()){
1988 +      param->setLineSearchTol(globals->getMinLSTol());
1989 +    }    
1990 +
1991 +    strcpy(minimizerName, globals->getMinimizer());
1992 +
1993 +    if (!strcasecmp(minimizerName, "CG")){
1994 +      myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1995 +    }
1996 +    else if (!strcasecmp(minimizerName, "SD")){
1997 +    //myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1998 +      myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1999 +    }
2000 +    else{
2001 +          sprintf(painCave.errMsg,
2002 +                  "SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2003 +          painCave.isFatal = 0;
2004 +          simError();
2005 +
2006 +      myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);          
2007 +    }
2008 +     info[i].the_integrator = myOOPSEMinimizer;
2009 +
2010 +     //store the minimizer into simInfo
2011 +     info[i].the_minimizer = myOOPSEMinimizer;
2012 +     info[i].has_minimizer = true;
2013 +  }
2014 +
2015 + }

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