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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 1108 by tim, Wed Apr 14 15:37:41 2004 UTC vs.
Revision 1330 by gezelter, Fri Jul 16 16:29:44 2004 UTC

# Line 10 | Line 10
10   #include "Integrator.hpp"
11   #include "simError.h"
12   #include "RigidBody.hpp"
13 – //#include "ConjugateMinimizer.hpp"
13   #include "OOPSEMinimizer.hpp"
14 + #include "ConstraintElement.hpp"
15 + #include "ConstraintPair.hpp"
16 + #include "ConstraintManager.hpp"
17  
18   #ifdef IS_MPI
19   #include "mpiBASS.h"
# Line 147 | Line 149 | void SimSetup::createSim(void){
149    // make the output filenames
150  
151    makeOutNames();
150 –
151 –  if (globals->haveMinimizer())
152 –    // make minimizer
153 –    makeMinimizer();
154 –  else
155 –    // make the integrator
156 –    makeIntegrator();
152    
153   #ifdef IS_MPI
154    mpiSim->mpiRefresh();
# Line 162 | Line 157 | void SimSetup::createSim(void){
157    // initialize the Fortran
158  
159    initFortran();
160 +
161 +  //creat constraint manager
162 +  for(int i = 0; i < nInfo; i++)
163 +    info[i].consMan = new ConstraintManager(&info[i]);
164 +
165 +  if (globals->haveMinimizer())
166 +    // make minimizer
167 +    makeMinimizer();
168 +  else
169 +    // make the integrator
170 +    makeIntegrator();
171 +
172   }
173  
174  
# Line 169 | Line 176 | void SimSetup::makeMolecules(void){
176    int i, j, k;
177    int exI, exJ, exK, exL, slI, slJ;
178    int tempI, tempJ, tempK, tempL;
179 <  int molI;
180 <  int stampID, atomOffset, rbOffset;
179 >  int molI, globalID;
180 >  int stampID, atomOffset, rbOffset, groupOffset;
181    molInit molInfo;
182    DirectionalAtom* dAtom;
183    RigidBody* myRB;
# Line 182 | Line 189 | void SimSetup::makeMolecules(void){
189    BendStamp* currentBend;
190    TorsionStamp* currentTorsion;
191    RigidBodyStamp* currentRigidBody;
192 +  CutoffGroupStamp* currentCutoffGroup;
193 +  CutoffGroup* myCutoffGroup;
194 +  int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
195 +  set<int> cutoffAtomSet; //atoms belong to  cutoffgroup defined at mdl file
196  
197    bond_pair* theBonds;
198    bend_set* theBends;
# Line 193 | Line 204 | void SimSetup::makeMolecules(void){
204    char* molName;
205    char rbName[100];
206  
207 +  ConstraintPair* consPair; //constraint pair
208 +  ConstraintElement* consElement1;  //first element of constraint pair
209 +  ConstraintElement* consElement2;  //second element of constraint pair
210 +  int whichRigidBody;
211 +  int consAtomIndex;  //index of constraint atom in rigid body's atom array
212 +  vector<pair<int, int> > jointAtoms;
213 +  double bondLength2;
214    //init the forceField paramters
215  
216    the_ff->readParams();
# Line 204 | Line 222 | void SimSetup::makeMolecules(void){
222    for (k = 0; k < nInfo; k++){
223      the_ff->setSimInfo(&(info[k]));
224  
225 + #ifdef IS_MPI
226 +    info[k].globalGroupMembership = new int[mpiSim->getNAtomsGlobal()];
227 +    for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
228 +      info[k].globalGroupMembership[i] = 0;
229 + #else
230 +    info[k].globalGroupMembership = new int[info[k].n_atoms];
231 +    for (i = 0; i < info[k].n_atoms; i++)
232 +      info[k].globalGroupMembership[i] = 0;
233 + #endif
234 +
235      atomOffset = 0;
236 +    groupOffset = 0;
237  
238      for (i = 0; i < info[k].n_mol; i++){
239        stampID = info[k].molecules[i].getStampID();
# Line 215 | Line 244 | void SimSetup::makeMolecules(void){
244        molInfo.nBends = comp_stamps[stampID]->getNBends();
245        molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
246        molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
247 +
248 +      nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
249        
250        molInfo.myAtoms = &(info[k].atoms[atomOffset]);
251  
252        if (molInfo.nBonds > 0)
253 <        molInfo.myBonds = new (Bond *) [molInfo.nBonds];
253 >        molInfo.myBonds = new Bond*[molInfo.nBonds];
254        else
255          molInfo.myBonds = NULL;
256  
257        if (molInfo.nBends > 0)
258 <        molInfo.myBends = new (Bend *) [molInfo.nBends];
258 >        molInfo.myBends = new Bend*[molInfo.nBends];
259        else
260          molInfo.myBends = NULL;
261  
262        if (molInfo.nTorsions > 0)
263 <        molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
263 >        molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
264        else
265          molInfo.myTorsions = NULL;
266  
# Line 262 | Line 293 | void SimSetup::makeMolecules(void){
293          else{
294  
295            molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
296 +
297          }
298  
299          molInfo.myAtoms[j]->setType(currentAtom->getType());
268 –
300   #ifdef IS_MPI
270 –
301          molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
272 –
302   #endif // is_mpi
303        }
304  
# Line 409 | Line 438 | void SimSetup::makeMolecules(void){
438          info[k].excludes->addPair(exK, exL);
439        }
440  
441 +      
442 +      molInfo.myRigidBodies.clear();
443 +      
444        for (j = 0; j < molInfo.nRigidBodies; j++){
445  
446          currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
# Line 418 | Line 450 | void SimSetup::makeMolecules(void){
450  
451          myRB = new RigidBody();
452  
453 <        sprintf(rbName,"%s_RB_%s", molName, j);
453 >        sprintf(rbName,"%s_RB_%d", molName, j);
454          myRB->setType(rbName);
455          
456          for (rb1 = 0; rb1 < nMembers; rb1++) {
# Line 460 | Line 492 | void SimSetup::makeMolecules(void){
492              // used for the exclude list:
493              
494   #ifdef IS_MPI
495 <            exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
496 <            exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
495 >            exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
496 >            exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
497   #else
498 <            exI = tempI + 1;
499 <            exJ = tempJ + 1;
498 >            exI = molInfo.myAtoms[tempI]->getIndex() + 1;
499 >            exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
500   #endif
501              
502              info[k].excludes->addPair(exI, exJ);
# Line 477 | Line 509 | void SimSetup::makeMolecules(void){
509        }
510        
511  
512 +      //create cutoff group for molecule
513 +
514 +      cutoffAtomSet.clear();
515 +      molInfo.myCutoffGroups.clear();
516 +      
517 +      for (j = 0; j < nCutoffGroups; j++){
518 +
519 +        currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
520 +        nMembers = currentCutoffGroup->getNMembers();
521 +
522 +        myCutoffGroup = new CutoffGroup();
523 +        
524 + #ifdef IS_MPI
525 +        myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
526 + #else
527 +        myCutoffGroup->setGlobalIndex(groupOffset);
528 + #endif
529 +        
530 +        for (int cg = 0; cg < nMembers; cg++) {
531 +
532 +          // molI is atom numbering inside this molecule
533 +          molI = currentCutoffGroup->getMember(cg);    
534 +
535 +          // tempI is atom numbering on local processor
536 +          tempI = molI + atomOffset;
537 +
538 + #ifdef IS_MPI
539 +          globalID = info[k].atoms[tempI]->getGlobalIndex();
540 +          info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
541 + #else
542 +          globalID = info[k].atoms[tempI]->getIndex();
543 +          info[k].globalGroupMembership[globalID] = groupOffset;
544 + #endif                    
545 +          myCutoffGroup->addAtom(info[k].atoms[tempI]);
546 +          cutoffAtomSet.insert(tempI);
547 +        }
548 +        
549 +        molInfo.myCutoffGroups.push_back(myCutoffGroup);
550 +        groupOffset++;
551 +
552 +      }//end for (j = 0; j < molInfo.nCutoffGroups; j++)
553 +      
554 +      
555 +      // create a cutoff group for every atom in current molecule which
556 +      // does not belong to cutoffgroup defined at mdl file
557 +      
558 +      for(j = 0; j < molInfo.nAtoms; j++){
559 +        
560 +        if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
561 +          myCutoffGroup = new CutoffGroup();
562 +          myCutoffGroup->addAtom(molInfo.myAtoms[j]);
563 +          
564 + #ifdef IS_MPI
565 +          myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
566 +          globalID = info[k].atoms[atomOffset + j]->getGlobalIndex();
567 +          info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
568 + #else
569 +          myCutoffGroup->setGlobalIndex(groupOffset);
570 +          globalID = info[k].atoms[atomOffset + j]->getIndex();
571 +          info[k].globalGroupMembership[globalID] = groupOffset;
572 + #endif
573 +          molInfo.myCutoffGroups.push_back(myCutoffGroup);
574 +          groupOffset++;
575 +        }          
576 +      }
577 +
578        // After this is all set up, scan through the atoms to
579        // see if they can be added to the integrableObjects:
580  
581 +      molInfo.myIntegrableObjects.clear();
582 +      
583 +
584        for (j = 0; j < molInfo.nAtoms; j++){
585  
586   #ifdef IS_MPI
# Line 504 | Line 605 | void SimSetup::makeMolecules(void){
605          info[k].integrableObjects.push_back(mySD);      
606          molInfo.myIntegrableObjects.push_back(mySD);
607        }
608 <    
508 <      
608 >        
609        // send the arrays off to the forceField for init.
610        
611        the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
# Line 514 | Line 614 | void SimSetup::makeMolecules(void){
614        the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
615                                   theTorsions);
616  
517 –      info[k].molecules[i].initialize(molInfo);
617  
618 +      //creat ConstraintPair.
619 +      molInfo.myConstraintPairs.clear();
620 +      
621 +      for (j = 0; j < molInfo.nBonds; j++){
622  
623 +        //if bond is constrained bond, add it into constraint pair
624 +        if(molInfo.myBonds[j]->is_constrained()){
625 +
626 +          //if both atoms are in the same rigid body, just skip it
627 +          currentBond = comp_stamps[stampID]->getBond(j);
628 +          
629 +          if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){
630 +
631 +            tempI = currentBond->getA() + atomOffset;
632 +            if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex))
633 +              consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
634 +            else
635 +               consElement1 = new ConstraintAtom(info[k].atoms[tempI]);      
636 +
637 +            tempJ =  currentBond->getB() + atomOffset;
638 +            if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex))
639 +              consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
640 +            else
641 +               consElement2 = new ConstraintAtom(info[k].atoms[tempJ]);    
642 +
643 +            bondLength2 = molInfo.myBonds[j]->get_constraint()->get_dsqr();            
644 +            consPair = new DistanceConstraintPair(consElement1, consElement2, bondLength2);
645 +
646 +            molInfo.myConstraintPairs.push_back(consPair);
647 +          }
648 +        }//end if(molInfo.myBonds[j]->is_constrained())
649 +      }  
650 +      
651 +      //loop over rigid bodies, if two rigid bodies share same joint, creat a JointConstraintPair
652 +      for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){
653 +        for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){
654 +          
655 +          jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2);
656 +
657 +          for(size_t m = 0; m < jointAtoms.size(); m++){          
658 +            consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first);
659 +            consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second);
660 +
661 +            consPair = new JointConstraintPair(consElement1, consElement2);  
662 +            molInfo.myConstraintPairs.push_back(consPair);            
663 +          }
664 +
665 +        }
666 +      }
667 +      
668 +
669 +      info[k].molecules[i].initialize(molInfo);
670 +      
671 +      
672        atomOffset += molInfo.nAtoms;
673        delete[] theBonds;
674        delete[] theBends;
675        delete[] theTorsions;
676 <    }    
677 <  }
676 >    }
677 >
678 >
679 >
680 > #ifdef IS_MPI    
681 >    // Since the globalGroupMembership has been zero filled and we've only
682 >    // poked values into the atoms we know, we can do an Allreduce
683 >    // to get the full globalGroupMembership array (We think).
684 >    // This would be prettier if we could use MPI_IN_PLACE like the MPI-2
685 >    // docs said we could.
686  
687 < #ifdef IS_MPI
528 <  sprintf(checkPointMsg, "all molecules initialized succesfully");
529 <  MPIcheckPoint();
530 < #endif // is_mpi
687 >    int* ggMjunk = new int[mpiSim->getNAtomsGlobal()];    
688  
689 <  // clean up the forcefield
689 >    MPI_Allreduce(info[k].globalGroupMembership,
690 >                  ggMjunk,
691 >                  mpiSim->getNAtomsGlobal(),
692 >                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
693  
694 <  if (!globals->haveLJrcut()){
694 >    for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
695 >      info[k].globalGroupMembership[i] = ggMjunk[i];
696  
697 <    the_ff->calcRcut();
537 <
538 <  } else {
697 >    delete[] ggMjunk;
698      
699 <    the_ff->setRcut( globals->getLJrcut() );
699 > #endif
700 >
701 >
702 >
703    }
704  
705 <  the_ff->cleanMe();
705 > #ifdef IS_MPI
706 >  sprintf(checkPointMsg, "all molecules initialized succesfully");
707 >  MPIcheckPoint();
708 > #endif // is_mpi
709 >
710   }
711  
712   void SimSetup::initFromBass(void){
# Line 750 | Line 916 | void SimSetup::gatherInfo(void){
916           painCave.isFatal = 1;
917           simError();
918    }
919 <
920 <    // get the ensemble
919 >  if (globals->haveForceFieldVariant()) {
920 >    strcpy(forcefield_variant, globals->getForceFieldVariant());
921 >    has_forcefield_variant = 1;
922 >  }
923 >  
924 >  // get the ensemble
925  
926    strcpy(ensemble, globals->getEnsemble());
927  
# Line 827 | Line 997 | void SimSetup::gatherInfo(void){
997    }
998  
999    //check whether sample time, status time, thermal time and reset time are divisble by dt
1000 <  if (!isDivisible(globals->getSampleTime(), globals->getDt())){
1000 >  if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
1001      sprintf(painCave.errMsg,
1002              "Sample time is not divisible by dt.\n"
1003              "\tThis will result in samples that are not uniformly\n"
# Line 837 | Line 1007 | void SimSetup::gatherInfo(void){
1007      simError();    
1008    }
1009  
1010 <  if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
1010 >  if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
1011      sprintf(painCave.errMsg,
1012              "Status time is not divisible by dt.\n"
1013              "\tThis will result in status reports that are not uniformly\n"
# Line 873 | Line 1043 | void SimSetup::gatherInfo(void){
1043      if (globals->haveSampleTime()){
1044        info[i].sampleTime = globals->getSampleTime();
1045        info[i].statusTime = info[i].sampleTime;
876 –      info[i].thermalTime = info[i].sampleTime;
1046      }
1047      else{
1048        info[i].sampleTime = globals->getRunTime();
1049        info[i].statusTime = info[i].sampleTime;
881 –      info[i].thermalTime = info[i].sampleTime;
1050      }
1051  
1052      if (globals->haveStatusTime()){
# Line 887 | Line 1055 | void SimSetup::gatherInfo(void){
1055  
1056      if (globals->haveThermalTime()){
1057        info[i].thermalTime = globals->getThermalTime();
1058 +    } else {
1059 +      info[i].thermalTime = globals->getRunTime();
1060      }
1061  
1062      info[i].resetIntegrator = 0;
# Line 904 | Line 1074 | void SimSetup::gatherInfo(void){
1074  
1075      info[i].useInitXSstate = globals->getUseInitXSstate();
1076      info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1077 <    
1077 >
1078 >    // check for thermodynamic integration
1079 >    if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
1080 >      if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1081 >        info[i].useSolidThermInt = globals->getUseSolidThermInt();
1082 >        info[i].thermIntLambda = globals->getThermIntLambda();
1083 >        info[i].thermIntK = globals->getThermIntK();
1084 >        
1085 >        Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
1086 >        info[i].restraint = myRestraint;
1087 >      }
1088 >      else {
1089 >        sprintf(painCave.errMsg,
1090 >                "SimSetup Error:\n"
1091 >                "\tKeyword useSolidThermInt was set to 'true' but\n"
1092 >                "\tthermodynamicIntegrationLambda (and/or\n"
1093 >                "\tthermodynamicIntegrationK) was not specified.\n"
1094 >                "\tPlease provide a lambda value and k value in your .bass file.\n");
1095 >        painCave.isFatal = 1;
1096 >        simError();    
1097 >      }
1098 >    }
1099 >    else if(globals->getUseLiquidThermInt()) {
1100 >      if (globals->getUseSolidThermInt()) {
1101 >        sprintf( painCave.errMsg,
1102 >                 "SimSetup Warning: It appears that you have both solid and\n"
1103 >                 "\tliquid thermodynamic integration activated in your .bass\n"
1104 >                 "\tfile. To avoid confusion, specify only one technique in\n"
1105 >                 "\tyour .bass file. Liquid-state thermodynamic integration\n"
1106 >                 "\twill be assumed for the current simulation. If this is not\n"
1107 >                 "\twhat you desire, set useSolidThermInt to 'true' and\n"
1108 >                 "\tuseLiquidThermInt to 'false' in your .bass file.\n");
1109 >        painCave.isFatal = 0;
1110 >        simError();
1111 >      }
1112 >      if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1113 >        info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1114 >        info[i].thermIntLambda = globals->getThermIntLambda();
1115 >        info[i].thermIntK = globals->getThermIntK();
1116 >      }
1117 >      else {
1118 >        sprintf(painCave.errMsg,
1119 >                "SimSetup Error:\n"
1120 >                "\tKeyword useLiquidThermInt was set to 'true' but\n"
1121 >                "\tthermodynamicIntegrationLambda (and/or\n"
1122 >                "\tthermodynamicIntegrationK) was not specified.\n"
1123 >                "\tPlease provide a lambda value and k value in your .bass file.\n");
1124 >        painCave.isFatal = 1;
1125 >        simError();    
1126 >      }
1127 >    }
1128 >    else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
1129 >        sprintf(painCave.errMsg,
1130 >                "SimSetup Warning: If you want to use Thermodynamic\n"
1131 >                "\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1132 >                "\t'true' in your .bass file.  These keywords are set to\n"
1133 >                "\t'false' by default, so your lambda and/or k values are\n"
1134 >                "\tbeing ignored.\n");
1135 >        painCave.isFatal = 0;
1136 >        simError();  
1137 >    }
1138    }
1139    
1140    //setup seed for random number generator
# Line 957 | Line 1187 | void SimSetup::finalInfoCheck(void){
1187   void SimSetup::finalInfoCheck(void){
1188    int index;
1189    int usesDipoles;
1190 +  int usesCharges;
1191    int i;
1192  
1193    for (i = 0; i < nInfo; i++){
# Line 968 | Line 1199 | void SimSetup::finalInfoCheck(void){
1199        usesDipoles = (info[i].atoms[index])->hasDipole();
1200        index++;
1201      }
1202 <
1202 >    index = 0;
1203 >    usesCharges = 0;
1204 >    while ((index < info[i].n_atoms) && !usesCharges){
1205 >      usesCharges= (info[i].atoms[index])->hasCharge();
1206 >      index++;
1207 >    }
1208   #ifdef IS_MPI
1209      int myUse = usesDipoles;
1210      MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1211   #endif //is_mpi
1212  
1213 <    double theEcr, theEst;
1213 >    double theRcut, theRsw;
1214  
1215 +    if (globals->haveRcut()) {
1216 +      theRcut = globals->getRcut();
1217 +
1218 +      if (globals->haveRsw())
1219 +        theRsw = globals->getRsw();
1220 +      else
1221 +        theRsw = theRcut;
1222 +      
1223 +      info[i].setDefaultRcut(theRcut, theRsw);
1224 +
1225 +    } else {
1226 +      
1227 +      the_ff->calcRcut();
1228 +      theRcut = info[i].getRcut();
1229 +
1230 +      if (globals->haveRsw())
1231 +        theRsw = globals->getRsw();
1232 +      else
1233 +        theRsw = theRcut;
1234 +      
1235 +      info[i].setDefaultRcut(theRcut, theRsw);
1236 +    }
1237 +
1238      if (globals->getUseRF()){
1239        info[i].useReactionField = 1;
1240 <
1241 <      if (!globals->haveECR()){
1240 >      
1241 >      if (!globals->haveRcut()){
1242          sprintf(painCave.errMsg,
1243 <                "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1243 >                "SimSetup Warning: No value was set for the cutoffRadius.\n"
1244                  "\tOOPSE will use a default value of 15.0 angstroms"
1245 <                "\tfor the electrostaticCutoffRadius.\n");
1245 >                "\tfor the cutoffRadius.\n");
1246          painCave.isFatal = 0;
1247          simError();
1248 <        theEcr = 15.0;
1248 >        theRcut = 15.0;
1249        }
1250        else{
1251 <        theEcr = globals->getECR();
1251 >        theRcut = globals->getRcut();
1252        }
1253  
1254 <      if (!globals->haveEST()){
1254 >      if (!globals->haveRsw()){
1255          sprintf(painCave.errMsg,
1256 <                "SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1256 >                "SimSetup Warning: No value was set for switchingRadius.\n"
1257                  "\tOOPSE will use a default value of\n"
1258 <                "\t0.05 * electrostaticCutoffRadius\n"
1000 <                "\tfor the electrostaticSkinThickness\n");
1258 >                "\t0.95 * cutoffRadius for the switchingRadius\n");
1259          painCave.isFatal = 0;
1260          simError();
1261 <        theEst = 0.05 * theEcr;
1261 >        theRsw = 0.95 * theRcut;
1262        }
1263        else{
1264 <        theEst = globals->getEST();
1264 >        theRsw = globals->getRsw();
1265        }
1266  
1267 <      info[i].setDefaultEcr(theEcr, theEst);
1267 >      info[i].setDefaultRcut(theRcut, theRsw);
1268  
1269        if (!globals->haveDielectric()){
1270          sprintf(painCave.errMsg,
# Line 1019 | Line 1277 | void SimSetup::finalInfoCheck(void){
1277        info[i].dielectric = globals->getDielectric();
1278      }
1279      else{
1280 <      if (usesDipoles){
1281 <        if (!globals->haveECR()){
1280 >      if (usesDipoles || usesCharges){
1281 >
1282 >        if (!globals->haveRcut()){
1283            sprintf(painCave.errMsg,
1284 <                  "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1284 >                  "SimSetup Warning: No value was set for the cutoffRadius.\n"
1285                    "\tOOPSE will use a default value of 15.0 angstroms"
1286 <                  "\tfor the electrostaticCutoffRadius.\n");
1287 <          painCave.isFatal = 0;
1288 <          simError();
1289 <          theEcr = 15.0;
1290 <        }
1286 >                  "\tfor the cutoffRadius.\n");
1287 >          painCave.isFatal = 0;
1288 >          simError();
1289 >          theRcut = 15.0;
1290 >      }
1291          else{
1292 <          theEcr = globals->getECR();
1292 >          theRcut = globals->getRcut();
1293          }
1294 <        
1295 <        if (!globals->haveEST()){
1294 >        
1295 >        if (!globals->haveRsw()){
1296            sprintf(painCave.errMsg,
1297 <                  "SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1297 >                  "SimSetup Warning: No value was set for switchingRadius.\n"
1298                    "\tOOPSE will use a default value of\n"
1299 <                  "\t0.05 * electrostaticCutoffRadius\n"
1041 <                  "\tfor the electrostaticSkinThickness\n");
1299 >                  "\t0.95 * cutoffRadius for the switchingRadius\n");
1300            painCave.isFatal = 0;
1301            simError();
1302 <          theEst = 0.05 * theEcr;
1302 >          theRsw = 0.95 * theRcut;
1303          }
1304          else{
1305 <          theEst = globals->getEST();
1305 >          theRsw = globals->getRsw();
1306          }
1307 +        
1308 +        info[i].setDefaultRcut(theRcut, theRsw);
1309          
1050 –        info[i].setDefaultEcr(theEcr, theEst);
1310        }
1311      }
1312    }
# Line 1055 | Line 1314 | void SimSetup::finalInfoCheck(void){
1314    strcpy(checkPointMsg, "post processing checks out");
1315    MPIcheckPoint();
1316   #endif // is_mpi
1317 +
1318 +  // clean up the forcefield
1319 +  the_ff->cleanMe();
1320   }
1321    
1322   void SimSetup::initSystemCoords(void){
# Line 1182 | Line 1444 | void SimSetup::makeOutNames(void){
1444          }
1445          else{
1446            strcat(info[k].statusName, ".stat");
1447 +        }
1448 +      }
1449 +
1450 +      strcpy(info[k].rawPotName, inFileName);
1451 +      nameLength = strlen(info[k].rawPotName);
1452 +      endTest = &(info[k].rawPotName[nameLength - 5]);
1453 +      if (!strcmp(endTest, ".bass")){
1454 +        strcpy(endTest, ".raw");
1455 +      }
1456 +      else if (!strcmp(endTest, ".BASS")){
1457 +        strcpy(endTest, ".raw");
1458 +      }
1459 +      else{
1460 +        endTest = &(info[k].rawPotName[nameLength - 4]);
1461 +        if (!strcmp(endTest, ".bss")){
1462 +          strcpy(endTest, ".raw");
1463 +        }
1464 +        else if (!strcmp(endTest, ".mdl")){
1465 +          strcpy(endTest, ".raw");
1466          }
1467 +        else{
1468 +          strcat(info[k].rawPotName, ".raw");
1469 +        }
1470        }
1471  
1472   #ifdef IS_MPI
# Line 1234 | Line 1518 | void SimSetup::createFF(void){
1518   void SimSetup::createFF(void){
1519    switch (ffCase){
1520      case FF_DUFF:
1521 <      the_ff = new DUFF();
1521 >        the_ff = new DUFF();
1522        break;
1523  
1524      case FF_LJ:
# Line 1242 | Line 1526 | void SimSetup::createFF(void){
1526        break;
1527  
1528      case FF_EAM:
1529 <      the_ff = new EAM_FF();
1529 >      if (has_forcefield_variant)
1530 >        the_ff = new EAM_FF(forcefield_variant);
1531 >      else
1532 >        the_ff = new EAM_FF();
1533        break;
1534  
1535      case FF_H2O:
# Line 1256 | Line 1543 | void SimSetup::createFF(void){
1543        simError();
1544    }
1545  
1546 +
1547   #ifdef IS_MPI
1548    strcpy(checkPointMsg, "ForceField creation successful");
1549    MPIcheckPoint();
# Line 1269 | Line 1557 | void SimSetup::compList(void){
1557    LinkedMolStamp* headStamp = new LinkedMolStamp();
1558    LinkedMolStamp* currentStamp = NULL;
1559    comp_stamps = new MoleculeStamp * [n_components];
1560 +  bool haveCutoffGroups;
1561  
1562 +  haveCutoffGroups = false;
1563 +  
1564    // make an array of molecule stamps that match the components used.
1565    // also extract the used stamps out into a separate linked list
1566  
# Line 1304 | Line 1595 | void SimSetup::compList(void){
1595        headStamp->add(currentStamp);
1596        comp_stamps[i] = headStamp->match(id);
1597      }
1598 +
1599 +    if(comp_stamps[i]->getNCutoffGroups() > 0)
1600 +      haveCutoffGroups = true;    
1601    }
1602 +    
1603 +  for (i = 0; i < nInfo; i++)
1604 +    info[i].haveCutoffGroups = haveCutoffGroups;
1605  
1606   #ifdef IS_MPI
1607    strcpy(checkPointMsg, "Component stamps successfully extracted\n");
# Line 1313 | Line 1610 | void SimSetup::calcSysValues(void){
1610   }
1611  
1612   void SimSetup::calcSysValues(void){
1613 <  int i;
1613 >  int i, j;
1614 >  int ncutgroups, atomsingroups, ngroupsinstamp;
1615  
1616    int* molMembershipArray;
1617 +  CutoffGroupStamp* cg;
1618  
1619    tot_atoms = 0;
1620    tot_bonds = 0;
1621    tot_bends = 0;
1622    tot_torsions = 0;
1623    tot_rigid = 0;
1624 +  tot_groups = 0;
1625    for (i = 0; i < n_components; i++){
1626      tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1627      tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1628      tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1629      tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1630      tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1631 +
1632 +    ncutgroups = comp_stamps[i]->getNCutoffGroups();
1633 +    atomsingroups = 0;
1634 +    for (j=0; j < ncutgroups; j++) {
1635 +      cg = comp_stamps[i]->getCutoffGroup(j);
1636 +      atomsingroups += cg->getNMembers();
1637 +    }
1638 +    ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1639 +    tot_groups += components_nmol[i] * ngroupsinstamp;    
1640    }
1641    
1642    tot_SRI = tot_bonds + tot_bends + tot_torsions;
# Line 1340 | Line 1649 | void SimSetup::calcSysValues(void){
1649      info[i].n_torsions = tot_torsions;
1650      info[i].n_SRI = tot_SRI;
1651      info[i].n_mol = tot_nmol;
1652 <
1652 >    info[i].ngroup = tot_groups;
1653      info[i].molMembershipArray = molMembershipArray;
1654    }
1655   }
# Line 1351 | Line 1660 | void SimSetup::mpiMolDivide(void){
1660    int i, j, k;
1661    int localMol, allMol;
1662    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1663 <  int local_rigid;
1355 <  vector<int> globalAtomIndex;
1663 >  int local_rigid, local_groups;
1664    vector<int> globalMolIndex;
1665 +  int ncutgroups, atomsingroups, ngroupsinstamp;
1666 +  CutoffGroupStamp* cg;
1667  
1668    mpiSim = new mpiSimulation(info);
1669  
1670    mpiSim->divideLabor();
1671    globalAtomIndex = mpiSim->getGlobalAtomIndex();
1672 <  globalMolIndex = mpiSim->getGlobalMolIndex();
1672 >  globalGroupIndex = mpiSim->getGlobalGroupIndex();
1673 >  //globalMolIndex = mpiSim->getGlobalMolIndex();
1674  
1675    // set up the local variables
1676  
# Line 1373 | Line 1684 | void SimSetup::mpiMolDivide(void){
1684    local_bends = 0;
1685    local_torsions = 0;
1686    local_rigid = 0;
1687 +  local_groups = 0;
1688    globalAtomCounter = 0;
1689  
1690    for (i = 0; i < n_components; i++){
# Line 1383 | Line 1695 | void SimSetup::mpiMolDivide(void){
1695          local_bends += comp_stamps[i]->getNBends();
1696          local_torsions += comp_stamps[i]->getNTorsions();
1697          local_rigid += comp_stamps[i]->getNRigidBodies();
1698 +
1699 +        ncutgroups = comp_stamps[i]->getNCutoffGroups();
1700 +        atomsingroups = 0;
1701 +        for (k=0; k < ncutgroups; k++) {
1702 +          cg = comp_stamps[i]->getCutoffGroup(k);
1703 +          atomsingroups += cg->getNMembers();
1704 +        }
1705 +        ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups +
1706 +          ncutgroups;
1707 +        local_groups += ngroupsinstamp;    
1708 +
1709          localMol++;
1710        }      
1711        for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
# Line 1395 | Line 1718 | void SimSetup::mpiMolDivide(void){
1718    }
1719    local_SRI = local_bonds + local_bends + local_torsions;
1720  
1721 <  info[0].n_atoms = mpiSim->getMyNlocal();  
1721 >  info[0].n_atoms = mpiSim->getNAtomsLocal();  
1722    
1400 –
1723    if (local_atoms != info[0].n_atoms){
1724      sprintf(painCave.errMsg,
1725              "SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
# Line 1407 | Line 1729 | void SimSetup::mpiMolDivide(void){
1729      simError();
1730    }
1731  
1732 +  info[0].ngroup = mpiSim->getNGroupsLocal();  
1733 +  if (local_groups != info[0].ngroup){
1734 +    sprintf(painCave.errMsg,
1735 +            "SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n"
1736 +            "\tlocalGroups (%d) are not equal.\n",
1737 +            info[0].ngroup, local_groups);
1738 +    painCave.isFatal = 1;
1739 +    simError();
1740 +  }
1741 +  
1742    info[0].n_bonds = local_bonds;
1743    info[0].n_bends = local_bends;
1744    info[0].n_torsions = local_torsions;
# Line 1443 | Line 1775 | void SimSetup::makeSysArrays(void){
1775  
1776  
1777      molIndex = 0;
1778 <    for (i = 0; i < mpiSim->getTotNmol(); i++){
1778 >    for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1779        if (mol2proc[i] == worldRank){
1780          the_molecules[molIndex].setStampID(molCompType[i]);
1781          the_molecules[molIndex].setMyIndex(molIndex);
# Line 1480 | Line 1812 | void SimSetup::makeSysArrays(void){
1812      info[l].atoms = the_atoms;
1813      info[l].molecules = the_molecules;
1814      info[l].nGlobalExcludes = 0;
1815 <
1815 >    
1816      the_ff->setSimInfo(info);
1817    }
1818   }
# Line 1488 | Line 1820 | void SimSetup::makeIntegrator(void){
1820   void SimSetup::makeIntegrator(void){
1821    int k;
1822  
1823 <  NVE<RealIntegrator>* myNVE = NULL;
1824 <  NVT<RealIntegrator>* myNVT = NULL;
1825 <  NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1826 <  NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1827 <  NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1823 >  NVE<Integrator<BaseIntegrator> >* myNVE = NULL;
1824 >  NVT<Integrator<BaseIntegrator> >* myNVT = NULL;
1825 >  NPTi<NPT<Integrator<BaseIntegrator> > >* myNPTi = NULL;
1826 >  NPTf<NPT<Integrator<BaseIntegrator> > >* myNPTf = NULL;
1827 >  NPTxyz<NPT<Integrator<BaseIntegrator> > >* myNPTxyz = NULL;
1828    
1829    for (k = 0; k < nInfo; k++){
1830      switch (ensembleCase){

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