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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 962 by tim, Mon Jan 19 18:36:21 2004 UTC vs.
Revision 1139 by gezelter, Wed Apr 28 22:06:29 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  
187    bond_pair* theBonds;
188    bend_set* theBends;
189    torsion_set* theTorsions;
190  
191 +  set<int> skipList;
192  
193 +  double phi, theta, psi;
194 +  char* molName;
195 +  char rbName[100];
196 +
197    //init the forceField paramters
198  
199    the_ff->readParams();
200  
182
201    // init the atoms
202  
203 <  double ux, uy, uz, u, uSqr;
203 >  int nMembers, nNew, rb1, rb2;
204  
205    for (k = 0; k < nInfo; k++){
206      the_ff->setSimInfo(&(info[k]));
207  
208      atomOffset = 0;
209 <    excludeOffset = 0;
209 >
210      for (i = 0; i < info[k].n_mol; i++){
211        stampID = info[k].molecules[i].getStampID();
212 +      molName = comp_stamps[stampID]->getID();
213  
214        molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
215        molInfo.nBonds = comp_stamps[stampID]->getNBonds();
216        molInfo.nBends = comp_stamps[stampID]->getNBends();
217        molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
218 <      molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
219 <
218 >      molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
219 >      
220        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];
221  
222 +      if (molInfo.nBonds > 0)
223 +        molInfo.myBonds = new (Bond *) [molInfo.nBonds];
224 +      else
225 +        molInfo.myBonds = NULL;
226 +
227 +      if (molInfo.nBends > 0)
228 +        molInfo.myBends = new (Bend *) [molInfo.nBends];
229 +      else
230 +        molInfo.myBends = NULL;
231 +
232 +      if (molInfo.nTorsions > 0)
233 +        molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
234 +      else
235 +        molInfo.myTorsions = NULL;
236 +
237        theBonds = new bond_pair[molInfo.nBonds];
238        theBends = new bend_set[molInfo.nBends];
239        theTorsions = new torsion_set[molInfo.nTorsions];
240 <
240 >      
241        // make the Atoms
242  
243        for (j = 0; j < molInfo.nAtoms; j++){
244          currentAtom = comp_stamps[stampID]->getAtom(j);
245 +
246          if (currentAtom->haveOrientation()){
247            dAtom = new DirectionalAtom((j + atomOffset),
248                                        info[k].getConfiguration());
249            info[k].n_oriented++;
250            molInfo.myAtoms[j] = dAtom;
251  
252 <          ux = currentAtom->getOrntX();
253 <          uy = currentAtom->getOrntY();
254 <          uz = currentAtom->getOrntZ();
252 >          // Directional Atoms have standard unit vectors which are oriented
253 >          // in space using the three Euler angles.  We assume the standard
254 >          // unit vector was originally along the z axis below.
255  
256 <          uSqr = (ux * ux) + (uy * uy) + (uz * uz);
257 <
258 <          u = sqrt(uSqr);
259 <          ux = ux / u;
260 <          uy = uy / u;
261 <          uz = uz / u;
231 <
232 <          dAtom->setSUx(ux);
233 <          dAtom->setSUy(uy);
234 <          dAtom->setSUz(uz);
256 >          phi = currentAtom->getEulerPhi() * M_PI / 180.0;
257 >          theta = currentAtom->getEulerTheta() * M_PI / 180.0;
258 >          psi = currentAtom->getEulerPsi()* M_PI / 180.0;
259 >
260 >          dAtom->setUnitFrameFromEuler(phi, theta, psi);
261 >            
262          }
263          else{
264 <          molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
265 <                                               info[k].getConfiguration());
264 >
265 >          molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
266 >
267          }
240        molInfo.myAtoms[j]->setType(currentAtom->getType());
268  
269 +        molInfo.myAtoms[j]->setType(currentAtom->getType());
270   #ifdef IS_MPI
271  
272 <        molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
272 >        molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
273  
274   #endif // is_mpi
275        }
# Line 252 | Line 280 | void SimSetup::makeMolecules(void){
280          theBonds[j].a = currentBond->getA() + atomOffset;
281          theBonds[j].b = currentBond->getB() + atomOffset;
282  
283 <        exI = theBonds[j].a;
284 <        exJ = theBonds[j].b;
283 >        tempI = theBonds[j].a;
284 >        tempJ = theBonds[j].b;
285  
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        }
286   #ifdef IS_MPI
287 <        tempEx = exI;
288 <        exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
289 <        tempEx = exJ;
290 <        exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
287 >        exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
288 >        exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
289 > #else
290 >        exI = tempI + 1;
291 >        exJ = tempJ + 1;
292 > #endif
293  
294 <        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
294 >        info[k].excludes->addPair(exI, exJ);
295        }
276      excludeOffset += molInfo.nBonds;
296  
297        //make the bends
298        for (j = 0; j < molInfo.nBends; j++){
# Line 323 | Line 342 | void SimSetup::makeMolecules(void){
342            }
343          }
344  
345 <        if (!theBends[j].isGhost){
346 <          exI = theBends[j].a;
347 <          exJ = theBends[j].c;
348 <        }
349 <        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 <        }
345 >        if (theBends[j].isGhost) {
346 >          
347 >          tempI = theBends[j].a;
348 >          tempJ = theBends[j].b;
349 >          
350   #ifdef IS_MPI
351 <        tempEx = exI;
352 <        exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
353 <        tempEx = exJ;
354 <        exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
351 >          exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
352 >          exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
353 > #else
354 >          exI = tempI + 1;
355 >          exJ = tempJ + 1;
356 > #endif          
357 >          info[k].excludes->addPair(exI, exJ);
358  
359 <        info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
360 < #else  // isn't MPI
361 <        info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
362 < #endif  //is_mpi
359 >        } else {
360 >
361 >          tempI = theBends[j].a;
362 >          tempJ = theBends[j].b;
363 >          tempK = theBends[j].c;
364 >          
365 > #ifdef IS_MPI
366 >          exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
367 >          exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
368 >          exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
369 > #else
370 >          exI = tempI + 1;
371 >          exJ = tempJ + 1;
372 >          exK = tempK + 1;
373 > #endif
374 >          
375 >          info[k].excludes->addPair(exI, exK);
376 >          info[k].excludes->addPair(exI, exJ);
377 >          info[k].excludes->addPair(exJ, exK);
378 >        }
379        }
352      excludeOffset += molInfo.nBends;
380  
381        for (j = 0; j < molInfo.nTorsions; j++){
382          currentTorsion = comp_stamps[stampID]->getTorsion(j);
# Line 358 | Line 385 | void SimSetup::makeMolecules(void){
385          theTorsions[j].c = currentTorsion->getC() + atomOffset;
386          theTorsions[j].d = currentTorsion->getD() + atomOffset;
387  
388 <        exI = theTorsions[j].a;
389 <        exJ = theTorsions[j].d;
388 >        tempI = theTorsions[j].a;      
389 >        tempJ = theTorsions[j].b;
390 >        tempK = theTorsions[j].c;
391 >        tempL = theTorsions[j].d;
392  
393 <        // exclude_I must always be the smaller of the pair
394 <        if (exI > exJ){
395 <          tempEx = exI;
396 <          exI = exJ;
397 <          exJ = tempEx;
393 > #ifdef IS_MPI
394 >        exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
395 >        exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
396 >        exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
397 >        exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
398 > #else
399 >        exI = tempI + 1;
400 >        exJ = tempJ + 1;
401 >        exK = tempK + 1;
402 >        exL = tempL + 1;
403 > #endif
404 >
405 >        info[k].excludes->addPair(exI, exJ);
406 >        info[k].excludes->addPair(exI, exK);
407 >        info[k].excludes->addPair(exI, exL);        
408 >        info[k].excludes->addPair(exJ, exK);
409 >        info[k].excludes->addPair(exJ, exL);
410 >        info[k].excludes->addPair(exK, exL);
411 >      }
412 >
413 >      
414 >      molInfo.myRigidBodies.clear();
415 >      
416 >      for (j = 0; j < molInfo.nRigidBodies; j++){
417 >
418 >        currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
419 >        nMembers = currentRigidBody->getNMembers();
420 >
421 >        // Create the Rigid Body:
422 >
423 >        myRB = new RigidBody();
424 >
425 >        sprintf(rbName,"%s_RB_%d", molName, j);
426 >        myRB->setType(rbName);
427 >        
428 >        for (rb1 = 0; rb1 < nMembers; rb1++) {
429 >
430 >          // molI is atom numbering inside this molecule
431 >          molI = currentRigidBody->getMember(rb1);    
432 >
433 >          // tempI is atom numbering on local processor
434 >          tempI = molI + atomOffset;
435 >
436 >          // currentAtom is the AtomStamp (which we need for
437 >          // rigid body reference positions)
438 >          currentAtom = comp_stamps[stampID]->getAtom(molI);
439 >
440 >          // When we add to the rigid body, add the atom itself and
441 >          // the stamp info:
442 >
443 >          myRB->addAtom(info[k].atoms[tempI], currentAtom);
444 >          
445 >          // Add this atom to the Skip List for the integrators
446 > #ifdef IS_MPI
447 >          slI = info[k].atoms[tempI]->getGlobalIndex();
448 > #else
449 >          slI = tempI;
450 > #endif
451 >          skipList.insert(slI);
452 >          
453          }
454 +        
455 +        for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
456 +          for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
457 +            
458 +            tempI = currentRigidBody->getMember(rb1);
459 +            tempJ = currentRigidBody->getMember(rb2);
460 +            
461 +            // Some explanation is required here.
462 +            // Fortran indexing starts at 1, while c indexing starts at 0
463 +            // Also, in parallel computations, the GlobalIndex is
464 +            // used for the exclude list:
465 +            
466   #ifdef IS_MPI
467 <        tempEx = exI;
468 <        exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
469 <        tempEx = exJ;
470 <        exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
467 >            exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
468 >            exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
469 > #else
470 >            exI = molInfo.myAtoms[tempI]->getIndex() + 1;
471 >            exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
472 > #endif
473 >            
474 >            info[k].excludes->addPair(exI, exJ);
475 >            
476 >          }
477 >        }
478  
479 <        info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
480 < #else  // isn't MPI
378 <        info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
379 < #endif  //is_mpi
479 >        molInfo.myRigidBodies.push_back(myRB);
480 >        info[k].rigidBodies.push_back(myRB);
481        }
482 <      excludeOffset += molInfo.nTorsions;
482 >      
483  
484 +      // After this is all set up, scan through the atoms to
485 +      // see if they can be added to the integrableObjects:
486  
487 <      // send the arrays off to the forceField for init.
487 >      molInfo.myIntegrableObjects.clear();
488 >      
489 >
490 >      for (j = 0; j < molInfo.nAtoms; j++){
491 >
492 > #ifdef IS_MPI
493 >        slJ = molInfo.myAtoms[j]->getGlobalIndex();
494 > #else
495 >        slJ = j+atomOffset;
496 > #endif
497 >
498 >        // if they aren't on the skip list, then they can be integrated
499 >
500 >        if (skipList.find(slJ) == skipList.end()) {
501 >          mySD = (StuntDouble *) molInfo.myAtoms[j];
502 >          info[k].integrableObjects.push_back(mySD);
503 >          molInfo.myIntegrableObjects.push_back(mySD);
504 >        }
505 >      }
506  
507 +      // all rigid bodies are integrated:
508 +
509 +      for (j = 0; j < molInfo.nRigidBodies; j++) {
510 +        mySD = (StuntDouble *) molInfo.myRigidBodies[j];
511 +        info[k].integrableObjects.push_back(mySD);      
512 +        molInfo.myIntegrableObjects.push_back(mySD);
513 +      }
514 +    
515 +      
516 +      // send the arrays off to the forceField for init.
517 +      
518        the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
519        the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
520        the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
521        the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
522                                   theTorsions);
523  
392
524        info[k].molecules[i].initialize(molInfo);
525  
526  
# Line 397 | Line 528 | void SimSetup::makeMolecules(void){
528        delete[] theBonds;
529        delete[] theBends;
530        delete[] theTorsions;
531 <    }
531 >    }    
532    }
533  
534   #ifdef IS_MPI
# Line 407 | Line 538 | void SimSetup::makeMolecules(void){
538  
539    // clean up the forcefield
540  
541 <  the_ff->calcRcut();
541 >  if (!globals->haveLJrcut()){
542 >
543 >    the_ff->calcRcut();
544 >
545 >  } else {
546 >    
547 >    the_ff->setRcut( globals->getLJrcut() );
548 >  }
549 >
550    the_ff->cleanMe();
551   }
552  
# Line 609 | Line 748 | void SimSetup::gatherInfo(void){
748    else if (!strcasecmp(force_field, "EAM")){
749      ffCase = FF_EAM;
750    }
751 +  else if (!strcasecmp(force_field, "WATER")){
752 +    ffCase = FF_H2O;
753 +  }
754    else{
755      sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
756              force_field);
# Line 637 | Line 779 | void SimSetup::gatherInfo(void){
779    }
780    else{
781      sprintf(painCave.errMsg,
782 <            "SimSetup Warning. Unrecognized Ensemble -> %s, "
783 <            "reverting to NVE for this simulation.\n",
782 >            "SimSetup Warning. Unrecognized Ensemble -> %s \n"
783 >            "\treverting to NVE for this simulation.\n",
784              ensemble);
785           painCave.isFatal = 0;
786           simError();
# Line 670 | Line 812 | void SimSetup::gatherInfo(void){
812        if (!the_components[i]->haveNMol()){
813          // we have a problem
814          sprintf(painCave.errMsg,
815 <                "SimSetup Error. No global NMol or component NMol"
816 <                " given. Cannot calculate the number of atoms.\n");
815 >                "SimSetup Error. No global NMol or component NMol given.\n"
816 >                "\tCannot calculate the number of atoms.\n");
817          painCave.isFatal = 1;
818          simError();
819        }
# Line 692 | Line 834 | void SimSetup::gatherInfo(void){
834    }
835  
836    //check whether sample time, status time, thermal time and reset time are divisble by dt
837 <  if (!isDivisible(globals->getSampleTime(), globals->getDt())){
837 >  if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
838      sprintf(painCave.errMsg,
839 <              "Sample time is not divisible by dt \n");
839 >            "Sample time is not divisible by dt.\n"
840 >            "\tThis will result in samples that are not uniformly\n"
841 >            "\tdistributed in time.  If this is a problem, change\n"
842 >            "\tyour sampleTime variable.\n");
843      painCave.isFatal = 0;
844      simError();    
845    }
846  
847 <  if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
847 >  if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
848      sprintf(painCave.errMsg,
849 <              "Status time is not divisible by dt\n");
849 >            "Status time is not divisible by dt.\n"
850 >            "\tThis will result in status reports that are not uniformly\n"
851 >            "\tdistributed in time.  If this is a problem, change \n"
852 >            "\tyour statusTime variable.\n");
853      painCave.isFatal = 0;
854      simError();    
855    }
856  
857    if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
858      sprintf(painCave.errMsg,
859 <              "Thermal time is not divisible by dt\n");
859 >            "Thermal time is not divisible by dt.\n"
860 >            "\tThis will result in thermalizations that are not uniformly\n"
861 >            "\tdistributed in time.  If this is a problem, change \n"
862 >            "\tyour thermalTime variable.\n");
863      painCave.isFatal = 0;
864      simError();    
865    }  
866  
867    if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
868      sprintf(painCave.errMsg,
869 <              "Reset time is not divisible by dt\n");
869 >            "Reset time is not divisible by dt.\n"
870 >            "\tThis will result in integrator resets that are not uniformly\n"
871 >            "\tdistributed in time.  If this is a problem, change\n"
872 >            "\tyour resetTime variable.\n");
873      painCave.isFatal = 0;
874      simError();    
875    }
# Line 726 | Line 880 | void SimSetup::gatherInfo(void){
880      if (globals->haveSampleTime()){
881        info[i].sampleTime = globals->getSampleTime();
882        info[i].statusTime = info[i].sampleTime;
729      info[i].thermalTime = info[i].sampleTime;
883      }
884      else{
885        info[i].sampleTime = globals->getRunTime();
886        info[i].statusTime = info[i].sampleTime;
734      info[i].thermalTime = info[i].sampleTime;
887      }
888  
889      if (globals->haveStatusTime()){
# Line 740 | Line 892 | void SimSetup::gatherInfo(void){
892  
893      if (globals->haveThermalTime()){
894        info[i].thermalTime = globals->getThermalTime();
895 +    } else {
896 +      info[i].thermalTime = globals->getRunTime();
897      }
898  
899      info[i].resetIntegrator = 0;
# Line 757 | Line 911 | void SimSetup::gatherInfo(void){
911  
912      info[i].useInitXSstate = globals->getUseInitXSstate();
913      info[i].orthoTolerance = globals->getOrthoBoxTolerance();
914 +    info[i].useMolecularCutoffs = globals->getUseMolecularCutoffs();
915 +
916      
917    }
918    
# Line 799 | Line 955 | void SimSetup::gatherInfo(void){
955    for (int i = 0; i < nInfo; i++){
956      info[i].setSeed(seedValue);
957    }
958 <
958 >  
959   #ifdef IS_MPI
960 <  strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
960 >  strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
961    MPIcheckPoint();
962   #endif // is_mpi
963   }
# Line 810 | Line 966 | void SimSetup::finalInfoCheck(void){
966   void SimSetup::finalInfoCheck(void){
967    int index;
968    int usesDipoles;
969 +  int usesCharges;
970    int i;
971  
972    for (i = 0; i < nInfo; i++){
# Line 821 | Line 978 | void SimSetup::finalInfoCheck(void){
978        usesDipoles = (info[i].atoms[index])->hasDipole();
979        index++;
980      }
981 <
981 >    index = 0;
982 >    usesCharges = 0;
983 >    while ((index < info[i].n_atoms) && !usesCharges){
984 >      usesCharges= (info[i].atoms[index])->hasCharge();
985 >      index++;
986 >    }
987   #ifdef IS_MPI
988      int myUse = usesDipoles;
989      MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
# Line 834 | Line 996 | void SimSetup::finalInfoCheck(void){
996  
997        if (!globals->haveECR()){
998          sprintf(painCave.errMsg,
999 <                "SimSetup Warning: using default value of 15.0 angstroms"
1000 <                "box length for the electrostaticCutoffRadius.\n");
999 >                "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1000 >                "\tOOPSE will use a default value of 15.0 angstroms"
1001 >                "\tfor the electrostaticCutoffRadius.\n");
1002          painCave.isFatal = 0;
1003          simError();
1004          theEcr = 15.0;
# Line 846 | Line 1009 | void SimSetup::finalInfoCheck(void){
1009  
1010        if (!globals->haveEST()){
1011          sprintf(painCave.errMsg,
1012 <                "SimSetup Warning: using default value of 0.05 * the "
1013 <                "electrostaticCutoffRadius for the electrostaticSkinThickness\n");
1012 >                "SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1013 >                "\tOOPSE will use a default value of\n"
1014 >                "\t0.05 * electrostaticCutoffRadius\n"
1015 >                "\tfor the electrostaticSkinThickness\n");
1016          painCave.isFatal = 0;
1017          simError();
1018          theEst = 0.05 * theEcr;
# Line 860 | Line 1025 | void SimSetup::finalInfoCheck(void){
1025  
1026        if (!globals->haveDielectric()){
1027          sprintf(painCave.errMsg,
1028 <                "SimSetup Error: You are trying to use Reaction Field without"
1029 <                "setting a dielectric constant!\n");
1028 >                "SimSetup Error: No Dielectric constant was set.\n"
1029 >                "\tYou are trying to use Reaction Field without"
1030 >                "\tsetting a dielectric constant!\n");
1031          painCave.isFatal = 1;
1032          simError();
1033        }
1034        info[i].dielectric = globals->getDielectric();
1035      }
1036      else{
1037 <      if (usesDipoles){
1037 >      if (usesDipoles || usesCharges){
1038          if (!globals->haveECR()){
1039            sprintf(painCave.errMsg,
1040 <                  "SimSetup Warning: using default value of 15.0 angstroms"
1041 <                  "box length for the electrostaticCutoffRadius.\n");
1040 >                  "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1041 >                  "\tOOPSE will use a default value of 15.0 angstroms"
1042 >                  "\tfor the electrostaticCutoffRadius.\n");
1043            painCave.isFatal = 0;
1044            simError();
1045            theEcr = 15.0;
# Line 883 | Line 1050 | void SimSetup::finalInfoCheck(void){
1050          
1051          if (!globals->haveEST()){
1052            sprintf(painCave.errMsg,
1053 <                  "SimSetup Warning: using default value of 0.05 * the "
1054 <                  "electrostaticCutoffRadius for the "
1055 <                  "electrostaticSkinThickness\n");
1053 >                  "SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1054 >                  "\tOOPSE will use a default value of\n"
1055 >                  "\t0.05 * electrostaticCutoffRadius\n"
1056 >                  "\tfor the electrostaticSkinThickness\n");
1057            painCave.isFatal = 0;
1058            simError();
1059            theEst = 0.05 * theEcr;
# Line 1090 | Line 1258 | void SimSetup::createFF(void){
1258  
1259      case FF_EAM:
1260        the_ff = new EAM_FF();
1261 +      break;
1262 +
1263 +    case FF_H2O:
1264 +      the_ff = new WATER();
1265        break;
1266  
1267      default:
# Line 1164 | Line 1336 | void SimSetup::calcSysValues(void){
1336    tot_bonds = 0;
1337    tot_bends = 0;
1338    tot_torsions = 0;
1339 +  tot_rigid = 0;
1340    for (i = 0; i < n_components; i++){
1341      tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1342      tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1343      tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1344      tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1345 +    tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1346    }
1347 <
1347 >  
1348    tot_SRI = tot_bonds + tot_bends + tot_torsions;
1349    molMembershipArray = new int[tot_atoms];
1350  
# Line 1192 | Line 1366 | void SimSetup::mpiMolDivide(void){
1366    int i, j, k;
1367    int localMol, allMol;
1368    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1369 +  int local_rigid;
1370 +  vector<int> globalMolIndex;
1371  
1372    mpiSim = new mpiSimulation(info);
1373  
1374 <  globalIndex = mpiSim->divideLabor();
1374 >  mpiSim->divideLabor();
1375 >  globalAtomIndex = mpiSim->getGlobalAtomIndex();
1376 >  //globalMolIndex = mpiSim->getGlobalMolIndex();
1377  
1378    // set up the local variables
1379  
# Line 1208 | Line 1386 | void SimSetup::mpiMolDivide(void){
1386    local_bonds = 0;
1387    local_bends = 0;
1388    local_torsions = 0;
1389 <  globalAtomIndex = 0;
1389 >  local_rigid = 0;
1390 >  globalAtomCounter = 0;
1391  
1213
1392    for (i = 0; i < n_components; i++){
1393      for (j = 0; j < components_nmol[i]; j++){
1394        if (mol2proc[allMol] == worldRank){
# Line 1218 | Line 1396 | void SimSetup::mpiMolDivide(void){
1396          local_bonds += comp_stamps[i]->getNBonds();
1397          local_bends += comp_stamps[i]->getNBends();
1398          local_torsions += comp_stamps[i]->getNTorsions();
1399 +        local_rigid += comp_stamps[i]->getNRigidBodies();
1400          localMol++;
1401        }      
1402        for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1403 <        info[0].molMembershipArray[globalAtomIndex] = allMol;
1404 <        globalAtomIndex++;
1403 >        info[0].molMembershipArray[globalAtomCounter] = allMol;
1404 >        globalAtomCounter++;
1405        }
1406  
1407        allMol++;
# Line 1231 | Line 1410 | void SimSetup::mpiMolDivide(void){
1410    local_SRI = local_bonds + local_bends + local_torsions;
1411  
1412    info[0].n_atoms = mpiSim->getMyNlocal();  
1413 +  
1414  
1415    if (local_atoms != info[0].n_atoms){
1416      sprintf(painCave.errMsg,
1417 <            "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1418 <            " localAtom (%d) are not equal.\n",
1417 >            "SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1418 >            "\tlocalAtom (%d) are not equal.\n",
1419              info[0].n_atoms, local_atoms);
1420      painCave.isFatal = 1;
1421      simError();
# Line 1263 | Line 1443 | void SimSetup::makeSysArrays(void){
1443  
1444    Atom** the_atoms;
1445    Molecule* the_molecules;
1266  Exclude** the_excludes;
1446  
1268
1447    for (l = 0; l < nInfo; l++){
1448      // create the atom and short range interaction arrays
1449  
# Line 1291 | Line 1469 | void SimSetup::makeSysArrays(void){
1469   #else // is_mpi
1470  
1471      molIndex = 0;
1472 <    globalAtomIndex = 0;
1472 >    globalAtomCounter = 0;
1473      for (i = 0; i < n_components; i++){
1474        for (j = 0; j < components_nmol[i]; j++){
1475          the_molecules[molIndex].setStampID(i);
1476          the_molecules[molIndex].setMyIndex(molIndex);
1477          the_molecules[molIndex].setGlobalIndex(molIndex);
1478          for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1479 <          info[l].molMembershipArray[globalAtomIndex] = molIndex;
1480 <          globalAtomIndex++;
1479 >          info[l].molMembershipArray[globalAtomCounter] = molIndex;
1480 >          globalAtomCounter++;
1481          }
1482          molIndex++;
1483        }
# Line 1308 | Line 1486 | void SimSetup::makeSysArrays(void){
1486  
1487   #endif // is_mpi
1488  
1489 <
1490 <    if (info[l].n_SRI){
1491 <      Exclude::createArray(info[l].n_SRI);
1314 <      the_excludes = new Exclude * [info[l].n_SRI];
1315 <      for (int ex = 0; ex < info[l].n_SRI; ex++){
1316 <        the_excludes[ex] = new Exclude(ex);
1317 <      }
1318 <      info[l].globalExcludes = new int;
1319 <      info[l].n_exclude = info[l].n_SRI;
1320 <    }
1321 <    else{
1322 <      Exclude::createArray(1);
1323 <      the_excludes = new Exclude * ;
1324 <      the_excludes[0] = new Exclude(0);
1325 <      the_excludes[0]->setPair(0, 0);
1326 <      info[l].globalExcludes = new int;
1327 <      info[l].globalExcludes[0] = 0;
1328 <      info[l].n_exclude = 0;
1329 <    }
1330 <
1489 >    info[l].globalExcludes = new int;
1490 >    info[l].globalExcludes[0] = 0;
1491 >    
1492      // set the arrays into the SimInfo object
1493  
1494      info[l].atoms = the_atoms;
1495      info[l].molecules = the_molecules;
1496      info[l].nGlobalExcludes = 0;
1336    info[l].excludes = the_excludes;
1497  
1498      the_ff->setSimInfo(info);
1499    }
# Line 1377 | Line 1537 | void SimSetup::makeIntegrator(void){
1537          else{
1538            sprintf(painCave.errMsg,
1539                    "SimSetup error: If you use the NVT\n"
1540 <                  "    ensemble, you must set tauThermostat.\n");
1540 >                  "\tensemble, you must set tauThermostat.\n");
1541            painCave.isFatal = 1;
1542            simError();
1543          }
# Line 1400 | Line 1560 | void SimSetup::makeIntegrator(void){
1560          else{
1561            sprintf(painCave.errMsg,
1562                    "SimSetup error: If you use a constant pressure\n"
1563 <                  "    ensemble, you must set targetPressure in the BASS file.\n");
1563 >                  "\tensemble, you must set targetPressure in the BASS file.\n");
1564            painCave.isFatal = 1;
1565            simError();
1566          }
# Line 1410 | Line 1570 | void SimSetup::makeIntegrator(void){
1570          else{
1571            sprintf(painCave.errMsg,
1572                    "SimSetup error: If you use an NPT\n"
1573 <                  "    ensemble, you must set tauThermostat.\n");
1573 >                  "\tensemble, you must set tauThermostat.\n");
1574            painCave.isFatal = 1;
1575            simError();
1576          }
# Line 1420 | Line 1580 | void SimSetup::makeIntegrator(void){
1580          else{
1581            sprintf(painCave.errMsg,
1582                    "SimSetup error: If you use an NPT\n"
1583 <                  "    ensemble, you must set tauBarostat.\n");
1583 >                  "\tensemble, you must set tauBarostat.\n");
1584            painCave.isFatal = 1;
1585            simError();
1586          }
# Line 1443 | Line 1603 | void SimSetup::makeIntegrator(void){
1603          else{
1604            sprintf(painCave.errMsg,
1605                    "SimSetup error: If you use a constant pressure\n"
1606 <                  "    ensemble, you must set targetPressure in the BASS file.\n");
1606 >                  "\tensemble, you must set targetPressure in the BASS file.\n");
1607            painCave.isFatal = 1;
1608            simError();
1609          }    
# Line 1454 | Line 1614 | void SimSetup::makeIntegrator(void){
1614          else{
1615            sprintf(painCave.errMsg,
1616                    "SimSetup error: If you use an NPT\n"
1617 <                  "    ensemble, you must set tauThermostat.\n");
1617 >                  "\tensemble, you must set tauThermostat.\n");
1618            painCave.isFatal = 1;
1619            simError();
1620          }
# Line 1465 | Line 1625 | void SimSetup::makeIntegrator(void){
1625          else{
1626            sprintf(painCave.errMsg,
1627                    "SimSetup error: If you use an NPT\n"
1628 <                  "    ensemble, you must set tauBarostat.\n");
1628 >                  "\tensemble, you must set tauBarostat.\n");
1629            painCave.isFatal = 1;
1630            simError();
1631          }
# Line 1488 | Line 1648 | void SimSetup::makeIntegrator(void){
1648          else{
1649            sprintf(painCave.errMsg,
1650                    "SimSetup error: If you use a constant pressure\n"
1651 <                  "    ensemble, you must set targetPressure in the BASS file.\n");
1651 >                  "\tensemble, you must set targetPressure in the BASS file.\n");
1652            painCave.isFatal = 1;
1653            simError();
1654          }    
# Line 1498 | Line 1658 | void SimSetup::makeIntegrator(void){
1658          else{
1659            sprintf(painCave.errMsg,
1660                    "SimSetup error: If you use an NPT\n"
1661 <                  "    ensemble, you must set tauThermostat.\n");
1661 >                  "\tensemble, you must set tauThermostat.\n");
1662            painCave.isFatal = 1;
1663            simError();
1664          }
# Line 1508 | Line 1668 | void SimSetup::makeIntegrator(void){
1668          else{
1669            sprintf(painCave.errMsg,
1670                    "SimSetup error: If you use an NPT\n"
1671 <                  "    ensemble, you must set tauBarostat.\n");
1671 >                  "\tensemble, you must set tauBarostat.\n");
1672            painCave.isFatal = 1;
1673            simError();
1674          }
# Line 1561 | Line 1721 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1721    }
1722    else{
1723      sprintf(painCave.errMsg,
1724 <            "ZConstraint error: If you use an ZConstraint\n"
1725 <            " , you must set sample time.\n");
1724 >            "ZConstraint error: If you use a ZConstraint,\n"
1725 >            "\tyou must set zconsTime.\n");
1726      painCave.isFatal = 1;
1727      simError();
1728    }
# Line 1577 | Line 1737 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1737    else{
1738      double defaultZConsTol = 0.01;
1739      sprintf(painCave.errMsg,
1740 <            "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1741 <            " , default value %f is used.\n",
1740 >            "ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1741 >            "\tOOPSE will use a default value of %f.\n"
1742 >            "\tTo set the tolerance, use the zconsTol variable.\n",
1743              defaultZConsTol);
1744      painCave.isFatal = 0;
1745      simError();      
# Line 1596 | Line 1757 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1757    }
1758    else{
1759      sprintf(painCave.errMsg,
1760 <            "ZConstraint Warning: User does not set force Subtraction policy, "
1761 <            "PolicyByMass is used\n");
1760 >            "ZConstraint Warning: No force subtraction policy was set.\n"
1761 >            "\tOOPSE will use PolicyByMass.\n"
1762 >            "\tTo set the policy, use the zconsForcePolicy variable.\n");
1763      painCave.isFatal = 0;
1764      simError();
1765      zconsForcePolicy->setData("BYMASS");
# Line 1605 | Line 1767 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1767  
1768    theInfo.addProperty(zconsForcePolicy);
1769  
1770 +  //set zcons gap
1771 +  DoubleData* zconsGap = new DoubleData();
1772 +  zconsGap->setID(ZCONSGAP_ID);
1773 +
1774 +  if (globals->haveZConsGap()){
1775 +    zconsGap->setData(globals->getZconsGap());
1776 +    theInfo.addProperty(zconsGap);  
1777 +  }
1778 +
1779 +  //set zcons fixtime
1780 +  DoubleData* zconsFixtime = new DoubleData();
1781 +  zconsFixtime->setID(ZCONSFIXTIME_ID);
1782 +
1783 +  if (globals->haveZConsFixTime()){
1784 +    zconsFixtime->setData(globals->getZconsFixtime());
1785 +    theInfo.addProperty(zconsFixtime);  
1786 +  }
1787 +
1788 +  //set zconsUsingSMD
1789 +  IntData* zconsUsingSMD = new IntData();
1790 +  zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1791 +
1792 +  if (globals->haveZConsUsingSMD()){
1793 +    zconsUsingSMD->setData(globals->getZconsUsingSMD());
1794 +    theInfo.addProperty(zconsUsingSMD);  
1795 +  }
1796 +
1797    //Determine the name of ouput file and add it into SimInfo's property list
1798    //Be careful, do not use inFileName, since it is a pointer which
1799    //point to a string at master node, and slave nodes do not contain that string
# Line 1634 | Line 1823 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1823      tempParaItem.zPos = zconStamp[i]->getZpos();
1824      tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1825      tempParaItem.kRatio = zconStamp[i]->getKratio();
1826 <
1826 >    tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1827 >    tempParaItem.cantVel = zconStamp[i]->getCantVel();    
1828      zconsParaData->addItem(tempParaItem);
1829    }
1830  
1831    //check the uniqueness of index  
1832    if(!zconsParaData->isIndexUnique()){
1833      sprintf(painCave.errMsg,
1834 <            "ZConstraint Error: molIndex is not unique\n");
1834 >            "ZConstraint Error: molIndex is not unique!\n");
1835      painCave.isFatal = 1;
1836      simError();
1837    }
# Line 1652 | Line 1842 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1842    //push data into siminfo, therefore, we can retrieve later
1843    theInfo.addProperty(zconsParaData);
1844   }
1845 +
1846 + void SimSetup::makeMinimizer(){
1847 +
1848 +  OOPSEMinimizer* myOOPSEMinimizer;
1849 +  MinimizerParameterSet* param;
1850 +  char minimizerName[100];
1851 +  
1852 +  for (int i = 0; i < nInfo; i++){
1853 +    
1854 +    //prepare parameter set for minimizer
1855 +    param = new MinimizerParameterSet();
1856 +    param->setDefaultParameter();
1857 +
1858 +    if (globals->haveMinimizer()){
1859 +      param->setFTol(globals->getMinFTol());
1860 +    }
1861 +
1862 +    if (globals->haveMinGTol()){
1863 +      param->setGTol(globals->getMinGTol());
1864 +    }
1865 +
1866 +    if (globals->haveMinMaxIter()){
1867 +      param->setMaxIteration(globals->getMinMaxIter());
1868 +    }
1869 +
1870 +    if (globals->haveMinWriteFrq()){
1871 +      param->setMaxIteration(globals->getMinMaxIter());
1872 +    }
1873 +
1874 +    if (globals->haveMinWriteFrq()){
1875 +      param->setWriteFrq(globals->getMinWriteFrq());
1876 +    }
1877 +    
1878 +    if (globals->haveMinStepSize()){
1879 +      param->setStepSize(globals->getMinStepSize());
1880 +    }
1881 +
1882 +    if (globals->haveMinLSMaxIter()){
1883 +      param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1884 +    }    
1885 +
1886 +    if (globals->haveMinLSTol()){
1887 +      param->setLineSearchTol(globals->getMinLSTol());
1888 +    }    
1889 +
1890 +    strcpy(minimizerName, globals->getMinimizer());
1891 +
1892 +    if (!strcasecmp(minimizerName, "CG")){
1893 +      myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1894 +    }
1895 +    else if (!strcasecmp(minimizerName, "SD")){
1896 +    //myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1897 +      myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1898 +    }
1899 +    else{
1900 +          sprintf(painCave.errMsg,
1901 +                  "SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1902 +          painCave.isFatal = 0;
1903 +          simError();
1904 +
1905 +      myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);          
1906 +    }
1907 +     info[i].the_integrator = myOOPSEMinimizer;
1908 +
1909 +     //store the minimizer into simInfo
1910 +     info[i].the_minimizer = myOOPSEMinimizer;
1911 +     info[i].has_minimizer = true;
1912 +  }
1913 +
1914 + }

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