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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 407 by mmeineke, Wed Mar 26 20:22:02 2003 UTC vs.
Revision 580 by gezelter, Wed Jul 9 13:56:36 2003 UTC

# Line 12 | Line 12 | SimSetup::SimSetup(){
12   #include "mpiSimulation.hpp"
13   #endif
14  
15 + // some defines for ensemble and Forcefield  cases
16 +
17 + #define NVE_ENS 0
18 + #define NVT_ENS 1
19 + #define NPTi_ENS 2
20 + #define NPTf_ENS 3
21 +
22 + #define FF_DUFF 0
23 + #define FF_LJ   1
24 +
25 +
26   SimSetup::SimSetup(){
27    stamps = new MakeStamps();
28    globals = new Globals();
# Line 66 | Line 77 | void SimSetup::createSim( void ){
77  
78    MakeStamps *the_stamps;
79    Globals* the_globals;
80 <  int i, j;
80 >  int i, j, k, globalAtomIndex;
81 >  
82 >  int ensembleCase;
83 >  int ffCase;
84 >  
85 >  ensembleCase = -1;
86 >  ffCase = -1;
87  
88    // get the stamps and globals;
89    the_stamps = stamps;
# Line 80 | Line 97 | void SimSetup::createSim( void ){
97    // get the ones we know are there, yet still may need some work.
98    n_components = the_globals->getNComponents();
99    strcpy( force_field, the_globals->getForceField() );
100 +
101 +  if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
102 +  else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
103 +  else{
104 +    sprintf( painCave.errMsg,
105 +             "SimSetup Error. Unrecognized force field -> %s\n",
106 +             force_field );
107 +    painCave.isFatal = 1;
108 +    simError();
109 +  }
110 +
111 +  // get the ensemble:
112    strcpy( ensemble, the_globals->getEnsemble() );
113 +
114 +  if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
115 +  else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
116 +  else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
117 +    ensembleCase = NPTi_ENS;
118 +  else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
119 +  else{
120 +    sprintf( painCave.errMsg,
121 +             "SimSetup Warning. Unrecognized Ensemble -> %s, "
122 +             "reverting to NVE for this simulation.\n",
123 +             ensemble );
124 +    painCave.isFatal = 0;
125 +    simError();
126 +    strcpy( ensemble, "NVE" );
127 +    ensembleCase = NVE_ENS;
128 +  }  
129    strcpy( simnfo->ensemble, ensemble );
130  
131 +
132 + //   if( !strcasecmp( ensemble, "NPT" ) ) {
133 + //     the_extendedsystem = new ExtendedSystem( simnfo );
134 + //     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
135 + //     if (the_globals->haveTargetPressure())
136 + //       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
137 + //     else {
138 + //       sprintf( painCave.errMsg,
139 + //                "SimSetup error: If you use the constant pressure\n"
140 + //                "    ensemble, you must set targetPressure.\n"
141 + //                "    This was found in the BASS file.\n");
142 + //       painCave.isFatal = 1;
143 + //       simError();
144 + //     }
145 +
146 + //     if (the_globals->haveTauThermostat())
147 + //       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
148 + //     else if (the_globals->haveQmass())
149 + //       the_extendedsystem->setQmass(the_globals->getQmass());
150 + //     else {
151 + //       sprintf( painCave.errMsg,
152 + //                "SimSetup error: If you use one of the constant temperature\n"
153 + //                "    ensembles, you must set either tauThermostat or qMass.\n"
154 + //                "    Neither of these was found in the BASS file.\n");
155 + //       painCave.isFatal = 1;
156 + //       simError();
157 + //     }
158 +
159 + //     if (the_globals->haveTauBarostat())
160 + //       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
161 + //     else {
162 + //       sprintf( painCave.errMsg,
163 + //                "SimSetup error: If you use the constant pressure\n"
164 + //                "    ensemble, you must set tauBarostat.\n"
165 + //                "    This was found in the BASS file.\n");
166 + //       painCave.isFatal = 1;
167 + //       simError();
168 + //     }
169 +
170 + //   } else if ( !strcasecmp( ensemble, "NVT") ) {
171 + //     the_extendedsystem = new ExtendedSystem( simnfo );
172 + //     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
173 +
174 + //     if (the_globals->haveTauThermostat())
175 + //       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
176 + //     else if (the_globals->haveQmass())
177 + //       the_extendedsystem->setQmass(the_globals->getQmass());
178 + //     else {
179 + //       sprintf( painCave.errMsg,
180 + //                "SimSetup error: If you use one of the constant temperature\n"
181 + //                "    ensembles, you must set either tauThermostat or qMass.\n"
182 + //                "    Neither of these was found in the BASS file.\n");
183 + //       painCave.isFatal = 1;
184 + //       simError();
185 + //     }
186 +
187    strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
188    simnfo->usePBC = the_globals->getPBC();
189            
190 +  int usesDipoles = 0;
191 +  switch( ffCase ){
192  
193 <
194 <  if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
195 <  else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
196 <  else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
197 <  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
198 <  else{
193 >  case FF_DUFF:
194 >    the_ff = new DUFF();
195 >    usesDipoles = 1;
196 >    break;
197 >
198 >  case FF_LJ:
199 >    the_ff = new LJFF();
200 >    break;
201 >
202 >  default:
203      sprintf( painCave.errMsg,
204 <             "SimSetup Error. Unrecognized force field -> %s\n",
98 <             force_field );
204 >             "SimSetup Error. Unrecognized force field in case statement.\n");
205      painCave.isFatal = 1;
206      simError();
207    }
# Line 105 | Line 211 | void SimSetup::createSim( void ){
211    MPIcheckPoint();
212   #endif // is_mpi
213  
108 –  
109 –
214    // get the components and calculate the tot_nMol and indvidual n_mol
215    the_components = the_globals->getComponents();
216    components_nmol = new int[n_components];
# Line 230 | Line 334 | void SimSetup::createSim( void ){
334    simnfo->n_torsions = tot_torsions;
335    simnfo->n_SRI = tot_SRI;
336    simnfo->n_mol = tot_nmol;
233 –
337    
338 +  simnfo->molMembershipArray = new int[tot_atoms];
339 +
340   #ifdef IS_MPI
341  
342    // divide the molecules among processors here.
343    
344    mpiSim = new mpiSimulation( simnfo );
345    
241 –  
242 –
346    globalIndex = mpiSim->divideLabor();
347  
245 –
246 –
348    // set up the local variables
349    
350    int localMol, allMol;
351    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
352 +
353 +  int* mol2proc = mpiSim->getMolToProcMap();
354 +  int* molCompType = mpiSim->getMolComponentType();
355    
356    allMol = 0;
357    localMol = 0;
# Line 255 | Line 359 | void SimSetup::createSim( void ){
359    local_bonds = 0;
360    local_bends = 0;
361    local_torsions = 0;
362 +  globalAtomIndex = 0;
363 +
364 +
365    for( i=0; i<n_components; i++ ){
366  
367      for( j=0; j<components_nmol[i]; j++ ){
368        
369 <      if( mpiSim->getMyMolStart() <= allMol &&
263 <          allMol <= mpiSim->getMyMolEnd() ){
369 >      if( mol2proc[allMol] == worldRank ){
370          
371          local_atoms +=    comp_stamps[i]->getNAtoms();
372          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 268 | Line 374 | void SimSetup::createSim( void ){
374          local_torsions += comp_stamps[i]->getNTorsions();
375          localMol++;
376        }      
377 <      allMol++;
377 >      for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
378 >        simnfo->molMembershipArray[globalAtomIndex] = allMol;
379 >        globalAtomIndex++;
380 >      }
381 >
382 >      allMol++;      
383      }
384    }
385    local_SRI = local_bonds + local_bends + local_torsions;
386    
276 –
387    simnfo->n_atoms = mpiSim->getMyNlocal();  
388    
389    if( local_atoms != simnfo->n_atoms ){
390      sprintf( painCave.errMsg,
391               "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
392 <             " localAtom (%d) are note equal.\n",
392 >             " localAtom (%d) are not equal.\n",
393               simnfo->n_atoms,
394               local_atoms );
395      painCave.isFatal = 1;
# Line 304 | Line 414 | void SimSetup::createSim( void ){
414    Atom::createArrays(simnfo->n_atoms);
415    the_atoms = new Atom*[simnfo->n_atoms];
416    the_molecules = new Molecule[simnfo->n_mol];
417 +  int molIndex;
418  
419 +  // initialize the molecule's stampID's
420  
421 <  if( simnfo->n_SRI ){
422 <    the_sris = new SRI*[simnfo->n_SRI];
423 <    the_excludes = new int[2 * simnfo->n_SRI];
421 > #ifdef IS_MPI
422 >  
423 >
424 >  molIndex = 0;
425 >  for(i=0; i<mpiSim->getTotNmol(); i++){
426 >    
427 >    if(mol2proc[i] == worldRank ){
428 >      the_molecules[molIndex].setStampID( molCompType[i] );
429 >      the_molecules[molIndex].setMyIndex( molIndex );
430 >      the_molecules[molIndex].setGlobalIndex( i );
431 >      molIndex++;
432 >    }
433 >  }
434 >
435 > #else // is_mpi
436 >  
437 >  molIndex = 0;
438 >  globalAtomIndex = 0;
439 >  for(i=0; i<n_components; i++){
440 >    for(j=0; j<components_nmol[i]; j++ ){
441 >      the_molecules[molIndex].setStampID( i );
442 >      the_molecules[molIndex].setMyIndex( molIndex );
443 >      the_molecules[molIndex].setGlobalIndex( molIndex );
444 >      for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
445 >        simnfo->molMembershipArray[globalAtomIndex] = molIndex;
446 >        globalAtomIndex++;
447 >      }
448 >      molIndex++;
449 >    }
450 >  }
451 >    
452 >
453 > #endif // is_mpi
454 >
455 >
456 >  if( simnfo->n_SRI ){
457 >    
458 >    Exclude::createArray(simnfo->n_SRI);
459 >    the_excludes = new Exclude*[simnfo->n_SRI];
460 >    for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
461      simnfo->globalExcludes = new int;
462 <    simnfo->n_exclude = tot_SRI;
462 >    simnfo->n_exclude = simnfo->n_SRI;
463    }
464    else{
465      
466 <    the_excludes = new int[2];
467 <    the_excludes[0] = 0;
468 <    the_excludes[1] = 0;
466 >    Exclude::createArray( 1 );
467 >    the_excludes = new Exclude*;
468 >    the_excludes[0] = new Exclude(0);
469 >    the_excludes[0]->setPair( 0,0 );
470      simnfo->globalExcludes = new int;
471      simnfo->globalExcludes[0] = 0;
472 <
323 <    simnfo->n_exclude = 1;
472 >    simnfo->n_exclude = 0;
473    }
474  
475    // set the arrays into the SimInfo object
476  
477    simnfo->atoms = the_atoms;
478 <  simnfo->sr_interactions = the_sris;
478 >  simnfo->molecules = the_molecules;
479    simnfo->nGlobalExcludes = 0;
480    simnfo->excludes = the_excludes;
481  
482  
483    // get some of the tricky things that may still be in the globals
484  
485 <  
485 >  double boxVector[3];
486    if( the_globals->haveBox() ){
487 <    simnfo->box_x = the_globals->getBox();
488 <    simnfo->box_y = the_globals->getBox();
489 <    simnfo->box_z = the_globals->getBox();
487 >    boxVector[0] = the_globals->getBox();
488 >    boxVector[1] = the_globals->getBox();
489 >    boxVector[2] = the_globals->getBox();
490 >    
491 >    simnfo->setBox( boxVector );
492    }
493    else if( the_globals->haveDensity() ){
494  
495      double vol;
496      vol = (double)tot_nmol / the_globals->getDensity();
497 <    simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
498 <    simnfo->box_y = simnfo->box_x;
499 <    simnfo->box_z = simnfo->box_x;
497 >     boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
498 >     boxVector[1] = boxVector[0];
499 >     boxVector[2] = boxVector[0];
500 >
501 >    simnfo->setBox( boxVector );
502    }
503    else{
504      if( !the_globals->haveBoxX() ){
# Line 354 | Line 507 | void SimSetup::createSim( void ){
507        painCave.isFatal = 1;
508        simError();
509      }
510 <    simnfo->box_x = the_globals->getBoxX();
510 >    boxVector[0] = the_globals->getBoxX();
511  
512      if( !the_globals->haveBoxY() ){
513        sprintf( painCave.errMsg,
# Line 362 | Line 515 | void SimSetup::createSim( void ){
515        painCave.isFatal = 1;
516        simError();
517      }
518 <    simnfo->box_y = the_globals->getBoxY();
518 >    boxVector[1] = the_globals->getBoxY();
519  
520      if( !the_globals->haveBoxZ() ){
521        sprintf( painCave.errMsg,
# Line 370 | Line 523 | void SimSetup::createSim( void ){
523        painCave.isFatal = 1;
524        simError();
525      }
526 <    simnfo->box_z = the_globals->getBoxZ();
526 >    boxVector[2] = the_globals->getBoxZ();
527 >
528 >    simnfo->setBox( boxVector );
529    }
530  
531   #ifdef IS_MPI
# Line 383 | Line 538 | void SimSetup::createSim( void ){
538  
539    the_ff->setSimInfo( simnfo );
540  
541 <  makeAtoms();
541 >  makeMolecules();
542    simnfo->identArray = new int[simnfo->n_atoms];
543    for(i=0; i<simnfo->n_atoms; i++){
544      simnfo->identArray[i] = the_atoms[i]->getIdent();
545    }
546    
392 –  if( tot_bonds ){
393 –    makeBonds();
394 –  }
395 –
396 –  if( tot_bends ){
397 –    makeBends();
398 –  }
399 –
400 –  if( tot_torsions ){
401 –    makeTorsions();
402 –  }
403 –
404 –
547    if (the_globals->getUseRF() ) {
548      simnfo->useReactionField = 1;
549    
# Line 413 | Line 555 | void SimSetup::createSim( void ){
555        painCave.isFatal = 0;
556        simError();
557        double smallest;
558 <      smallest = simnfo->box_x;
559 <      if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
560 <      if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
558 >      smallest = simnfo->boxLx;
559 >      if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
560 >      if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
561        simnfo->ecr = 0.5 * smallest;
562      } else {
563        simnfo->ecr        = the_globals->getECR();
# Line 443 | Line 585 | void SimSetup::createSim( void ){
585      }
586      simnfo->dielectric = the_globals->getDielectric();  
587    } else {
588 <    if (simnfo->n_dipoles) {
588 >    if (usesDipoles) {
589        
590        if( !the_globals->haveECR() ){
591          sprintf( painCave.errMsg,
592 <                 "SimSetup Warning: using default value of 1/2 the smallest"
592 >                 "SimSetup Warning: using default value of 1/2 the smallest "
593                   "box length for the electrostaticCutoffRadius.\n"
594                   "I hope you have a very fast processor!\n");
595          painCave.isFatal = 0;
596          simError();
597          double smallest;
598 <        smallest = simnfo->box_x;
599 <        if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
600 <        if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
598 >        smallest = simnfo->boxLx;
599 >        if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
600 >        if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
601          simnfo->ecr = 0.5 * smallest;
602        } else {
603          simnfo->ecr        = the_globals->getECR();
# Line 463 | Line 605 | void SimSetup::createSim( void ){
605        
606        if( !the_globals->haveEST() ){
607          sprintf( painCave.errMsg,
608 <                 "SimSetup Warning: using default value of 5% of the"
608 >                 "SimSetup Warning: using default value of 5%% of the "
609                   "electrostaticCutoffRadius for the "
610                   "electrostaticSkinThickness\n"
611                   );
# Line 634 | Line 776 | void SimSetup::createSim( void ){
776    if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
777  
778  
779 < //   // make the longe range forces and the integrator
780 <
781 < //   new AllLong( simnfo );
782 <
783 <  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
642 <  if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
643 <  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
644 <  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
779 >  // make the integrator
780 >  
781 >  
782 >  NVT* myNVT = NULL;
783 >  switch( ensembleCase ){
784  
785 +  case NVE_ENS:
786 +    new NVE( simnfo, the_ff );
787 +    break;
788  
789 +  case NVT_ENS:
790 +    myNVT = new NVT( simnfo, the_ff );
791 +    myNVT->setTargetTemp(the_globals->getTargetTemp());
792  
793 +    if (the_globals->haveTauThermostat())
794 +      myNVT->setTauThermostat(the_globals->getTauThermostat());
795 + //     else if (the_globals->haveQmass())
796 + //       myNVT->setQmass(the_globals->getQmass());
797 +    else {
798 +      sprintf( painCave.errMsg,
799 +               "SimSetup error: If you use the NVT\n"
800 +               "    ensemble, you must set either tauThermostat or qMass.\n"
801 +               "    Neither of these was found in the BASS file.\n");
802 +      painCave.isFatal = 1;
803 +      simError();
804 +    }
805 +    break;
806 +
807 +  default:
808 +    sprintf( painCave.errMsg,
809 +             "SimSetup Error. Unrecognized ensemble in case statement.\n");
810 +    painCave.isFatal = 1;
811 +    simError();
812 +  }
813 +
814 +
815 + #ifdef IS_MPI
816 +  mpiSim->mpiRefresh();
817 + #endif
818 +
819    // initialize the Fortran
820 <  
820 >
821 >
822    simnfo->refreshSim();
823    
824    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 674 | Line 846 | void SimSetup::makeMolecules( void ){
846  
847   void SimSetup::makeMolecules( void ){
848  
849 <  int i, j, exI, exJ, tempEx, stampID, atomOffset;
849 >  int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
850    molInit info;
851    DirectionalAtom* dAtom;
852 +  LinkedAssign* extras;
853 +  LinkedAssign* current_extra;
854    AtomStamp* currentAtom;
855    BondStamp* currentBond;
856    BendStamp* currentBend;
857    TorsionStamp* currentTorsion;
858 +
859 +  bond_pair* theBonds;
860 +  bend_set* theBends;
861 +  torsion_set* theTorsions;
862 +
863    
864    //init the forceField paramters
865  
866    the_ff->readParams();
867  
868    
869 <  // init the molecules
869 >  // init the atoms
870  
871 +  double ux, uy, uz, u, uSqr;
872 +  
873    atomOffset = 0;
874 +  excludeOffset = 0;
875    for(i=0; i<simnfo->n_mol; i++){
876      
877      stampID = the_molecules[i].getStampID();
# Line 698 | Line 880 | void SimSetup::makeMolecules( void ){
880      info.nBonds    = comp_stamps[stampID]->getNBonds();
881      info.nBends    = comp_stamps[stampID]->getNBends();
882      info.nTorsions = comp_stamps[stampID]->getNTorsions();
883 <    
883 >    info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
884 >
885      info.myAtoms = &the_atoms[atomOffset];
886 +    info.myExcludes = &the_excludes[excludeOffset];
887      info.myBonds = new Bond*[info.nBonds];
888      info.myBends = new Bend*[info.nBends];
889 <    info.myTorsions = new Torsions*[info.nTorsions];
889 >    info.myTorsions = new Torsion*[info.nTorsions];
890  
891      theBonds = new bond_pair[info.nBonds];
892      theBends = new bend_set[info.nBends];
# Line 712 | Line 896 | void SimSetup::makeMolecules( void ){
896      
897      for(j=0; j<info.nAtoms; j++){
898        
899 <      currentAtom = theComponents[stampID]->getAtom( j );
899 >      currentAtom = comp_stamps[stampID]->getAtom( j );
900        if( currentAtom->haveOrientation() ){
901          
902          dAtom = new DirectionalAtom(j + atomOffset);
# Line 747 | Line 931 | void SimSetup::makeMolecules( void ){
931      }
932      
933      // make the bonds
934 <    for(j=0; j<nBonds; j++){
934 >    for(j=0; j<info.nBonds; j++){
935        
936        currentBond = comp_stamps[stampID]->getBond( j );
937        theBonds[j].a = currentBond->getA() + atomOffset;
938        theBonds[j].b = currentBond->getB() + atomOffset;
939  
940 <      exI = theBonds[i].a;
941 <      exJ = theBonds[i].b;
940 >      exI = theBonds[j].a;
941 >      exJ = theBonds[j].b;
942  
943        // exclude_I must always be the smaller of the pair
944        if( exI > exJ ){
# Line 763 | Line 947 | void SimSetup::makeMolecules( void ){
947          exJ = tempEx;
948        }
949   #ifdef IS_MPI
950 +      tempEx = exI;
951 +      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
952 +      tempEx = exJ;
953 +      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
954        
955 <      the_excludes[index*2] =    
768 <        the_atoms[exI]->getGlobalIndex() + 1;
769 <      the_excludes[index*2 + 1] =
770 <        the_atoms[exJ]->getGlobalIndex() + 1;
771 <      
955 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
956   #else  // isn't MPI
773 –      
774 –      the_excludes[index*2] =     exI + 1;
775 –      the_excludes[index*2 + 1] = exJ + 1;
776 –      // fortran index from 1 (hence the +1 in the indexing)
957  
958 +      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
959   #endif  //is_mpi
960 <    
961 <  }
960 >    }
961 >    excludeOffset += info.nBonds;
962  
963 <
964 <
965 <
966 <
967 <
968 <
969 <
789 <
790 <
791 <
792 <
793 <
794 <
795 <
796 < void SimSetup::makeAtoms( void ){
797 <
798 <  int i, j, k, index;
799 <  double ux, uy, uz, uSqr, u;
800 <  AtomStamp* current_atom;
801 <
802 <  DirectionalAtom* dAtom;
803 <  int molIndex, molStart, molEnd, nMemb, lMolIndex;
804 <
805 <  lMolIndex = 0;
806 <  molIndex = 0;
807 <  index = 0;
808 <  for( i=0; i<n_components; i++ ){
809 <
810 <    for( j=0; j<components_nmol[i]; j++ ){
811 <
812 < #ifdef IS_MPI
813 <      if( mpiSim->getMyMolStart() <= molIndex &&
814 <          molIndex <= mpiSim->getMyMolEnd() ){
815 < #endif // is_mpi        
816 <
817 <        molStart = index;
818 <        nMemb = comp_stamps[i]->getNAtoms();
819 <        for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
963 >    //make the bends
964 >    for(j=0; j<info.nBends; j++){
965 >      
966 >      currentBend = comp_stamps[stampID]->getBend( j );
967 >      theBends[j].a = currentBend->getA() + atomOffset;
968 >      theBends[j].b = currentBend->getB() + atomOffset;
969 >      theBends[j].c = currentBend->getC() + atomOffset;
970            
971 <          current_atom = comp_stamps[i]->getAtom( k );
822 <          if( current_atom->haveOrientation() ){
971 >      if( currentBend->haveExtras() ){
972              
973 <            dAtom = new DirectionalAtom(index);
974 <            simnfo->n_oriented++;
826 <            the_atoms[index] = dAtom;
827 <            
828 <            ux = current_atom->getOrntX();
829 <            uy = current_atom->getOrntY();
830 <            uz = current_atom->getOrntZ();
831 <            
832 <            uSqr = (ux * ux) + (uy * uy) + (uz * uz);
833 <            
834 <            u = sqrt( uSqr );
835 <            ux = ux / u;
836 <            uy = uy / u;
837 <            uz = uz / u;
973 >        extras = currentBend->getExtras();
974 >        current_extra = extras;
975              
976 <            dAtom->setSUx( ux );
977 <            dAtom->setSUy( uy );
978 <            dAtom->setSUz( uz );
976 >        while( current_extra != NULL ){
977 >          if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
978 >                
979 >            switch( current_extra->getType() ){
980 >              
981 >            case 0:
982 >              theBends[j].ghost =
983 >                current_extra->getInt() + atomOffset;
984 >              theBends[j].isGhost = 1;
985 >              break;
986 >                  
987 >            case 1:
988 >              theBends[j].ghost =
989 >                (int)current_extra->getDouble() + atomOffset;
990 >              theBends[j].isGhost = 1;
991 >              break;
992 >              
993 >            default:
994 >              sprintf( painCave.errMsg,
995 >                       "SimSetup Error: ghostVectorSource was neither a "
996 >                       "double nor an int.\n"
997 >                       "-->Bend[%d] in %s\n",
998 >                       j, comp_stamps[stampID]->getID() );
999 >              painCave.isFatal = 1;
1000 >              simError();
1001 >            }
1002            }
1003 +          
1004            else{
1005 <            the_atoms[index] = new GeneralAtom(index);
1005 >            
1006 >            sprintf( painCave.errMsg,
1007 >                     "SimSetup Error: unhandled bend assignment:\n"
1008 >                     "    -->%s in Bend[%d] in %s\n",
1009 >                     current_extra->getlhs(),
1010 >                     j, comp_stamps[stampID]->getID() );
1011 >            painCave.isFatal = 1;
1012 >            simError();
1013            }
846 –          the_atoms[index]->setType( current_atom->getType() );
847 –          the_atoms[index]->setIndex( index );
1014            
1015 <          // increment the index and repeat;
850 <          index++;
1015 >          current_extra = current_extra->getNext();
1016          }
1017 +      }
1018 +          
1019 +      if( !theBends[j].isGhost ){
1020 +            
1021 +        exI = theBends[j].a;
1022 +        exJ = theBends[j].c;
1023 +      }
1024 +      else{
1025          
1026 <        molEnd = index -1;
1027 <        the_molecules[lMolIndex].setNMembers( nMemb );
855 <        the_molecules[lMolIndex].setStartAtom( molStart );
856 <        the_molecules[lMolIndex].setEndAtom( molEnd );
857 <        the_molecules[lMolIndex].setStampID( i );
858 <        lMolIndex++;
859 <
860 < #ifdef IS_MPI
1026 >        exI = theBends[j].a;
1027 >        exJ = theBends[j].b;
1028        }
862 – #endif //is_mpi
1029        
1030 <      molIndex++;
1030 >      // exclude_I must always be the smaller of the pair
1031 >      if( exI > exJ ){
1032 >        tempEx = exI;
1033 >        exI = exJ;
1034 >        exJ = tempEx;
1035 >      }
1036 > #ifdef IS_MPI
1037 >      tempEx = exI;
1038 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1039 >      tempEx = exJ;
1040 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1041 >      
1042 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
1043 > #else  // isn't MPI
1044 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1045 > #endif  //is_mpi
1046      }
1047 <  }
1047 >    excludeOffset += info.nBends;
1048  
1049 < #ifdef IS_MPI
1050 <    for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
1051 <    
1052 <    delete[] globalIndex;
1049 >    for(j=0; j<info.nTorsions; j++){
1050 >      
1051 >      currentTorsion = comp_stamps[stampID]->getTorsion( j );
1052 >      theTorsions[j].a = currentTorsion->getA() + atomOffset;
1053 >      theTorsions[j].b = currentTorsion->getB() + atomOffset;
1054 >      theTorsions[j].c = currentTorsion->getC() + atomOffset;
1055 >      theTorsions[j].d = currentTorsion->getD() + atomOffset;
1056 >      
1057 >      exI = theTorsions[j].a;
1058 >      exJ = theTorsions[j].d;
1059  
1060 <    mpiSim->mpiRefresh();
1061 < #endif //IS_MPI
1062 <          
1063 <  the_ff->initializeAtoms();
1064 < }
1065 <
879 < void SimSetup::makeBonds( void ){
880 <
881 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
882 <  bond_pair* the_bonds;
883 <  BondStamp* current_bond;
884 <
885 <  the_bonds = new bond_pair[tot_bonds];
886 <  index = 0;
887 <  offset = 0;
888 <  molIndex = 0;
889 <
890 <  for( i=0; i<n_components; i++ ){
891 <
892 <    for( j=0; j<components_nmol[i]; j++ ){
893 <
1060 >      // exclude_I must always be the smaller of the pair
1061 >      if( exI > exJ ){
1062 >        tempEx = exI;
1063 >        exI = exJ;
1064 >        exJ = tempEx;
1065 >      }
1066   #ifdef IS_MPI
1067 <      if( mpiSim->getMyMolStart() <= molIndex &&
1068 <          molIndex <= mpiSim->getMyMolEnd() ){
1069 < #endif // is_mpi        
1070 <        
1071 <        for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
1072 <          
901 <          current_bond = comp_stamps[i]->getBond( k );
902 <          the_bonds[index].a = current_bond->getA() + offset;
903 <          the_bonds[index].b = current_bond->getB() + offset;
904 <
905 <          exI = the_bonds[index].a;
906 <          exJ = the_bonds[index].b;
907 <
908 <          // exclude_I must always be the smaller of the pair
909 <          if( exI > exJ ){
910 <            tempEx = exI;
911 <            exI = exJ;
912 <            exJ = tempEx;
913 <          }
914 <
915 <          
916 < #ifdef IS_MPI
917 <
918 <          the_excludes[index*2] =    
919 <            the_atoms[exI]->getGlobalIndex() + 1;
920 <          the_excludes[index*2 + 1] =
921 <            the_atoms[exJ]->getGlobalIndex() + 1;
922 <
1067 >      tempEx = exI;
1068 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1069 >      tempEx = exJ;
1070 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1071 >      
1072 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
1073   #else  // isn't MPI
1074 <          
925 <          the_excludes[index*2] =     exI + 1;
926 <          the_excludes[index*2 + 1] = exJ + 1;
927 <          // fortran index from 1 (hence the +1 in the indexing)
1074 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1075   #endif  //is_mpi
1076 <          
1077 <          // increment the index and repeat;
931 <          index++;
932 <        }
933 <        offset += comp_stamps[i]->getNAtoms();
934 <        
935 < #ifdef IS_MPI
936 <      }
937 < #endif //is_mpi
938 <      
939 <      molIndex++;
940 <    }      
941 <  }
1076 >    }
1077 >    excludeOffset += info.nTorsions;
1078  
1079 <  the_ff->initializeBonds( the_bonds );
1080 < }
1079 >    
1080 >    // send the arrays off to the forceField for init.
1081  
1082 < void SimSetup::makeBends( void ){
1082 >    the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1083 >    the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1084 >    the_ff->initializeBends( info.nBends, info.myBends, theBends );
1085 >    the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1086  
948 –  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
949 –  bend_set* the_bends;
950 –  BendStamp* current_bend;
951 –  LinkedAssign* extras;
952 –  LinkedAssign* current_extra;
953 –  
1087  
1088 <  the_bends = new bend_set[tot_bends];
956 <  index = 0;
957 <  offset = 0;
958 <  molIndex = 0;
959 <  for( i=0; i<n_components; i++ ){
960 <
961 <    for( j=0; j<components_nmol[i]; j++ ){
962 <
963 < #ifdef IS_MPI
964 <      if( mpiSim->getMyMolStart() <= molIndex &&
965 <          molIndex <= mpiSim->getMyMolEnd() ){
966 < #endif // is_mpi        
1088 >    the_molecules[i].initialize( info );
1089  
968 –        for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
969 –          
970 –          current_bend = comp_stamps[i]->getBend( k );
971 –          the_bends[index].a = current_bend->getA() + offset;
972 –          the_bends[index].b = current_bend->getB() + offset;
973 –          the_bends[index].c = current_bend->getC() + offset;
974 –          
975 –          if( current_bend->haveExtras() ){
976 –            
977 –            extras = current_bend->getExtras();
978 –            current_extra = extras;
979 –            
980 –            while( current_extra != NULL ){
981 –              if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
982 –                
983 –                switch( current_extra->getType() ){
984 –                  
985 –                case 0:
986 –                  the_bends[index].ghost =
987 –                    current_extra->getInt() + offset;
988 –                  the_bends[index].isGhost = 1;
989 –                  break;
990 –                  
991 –                case 1:
992 –                  the_bends[index].ghost =
993 –                    (int)current_extra->getDouble() + offset;
994 –                  the_bends[index].isGhost = 1;
995 –                  break;
996 –                  
997 –                default:
998 –                  sprintf( painCave.errMsg,
999 –                           "SimSetup Error: ghostVectorSource was neiter a "
1000 –                           "double nor an int.\n"
1001 –                           "-->Bend[%d] in %s\n",
1002 –                           k, comp_stamps[i]->getID() );
1003 –                  painCave.isFatal = 1;
1004 –                  simError();
1005 –                }
1006 –              }
1007 –              
1008 –              else{
1009 –                
1010 –                sprintf( painCave.errMsg,
1011 –                         "SimSetup Error: unhandled bend assignment:\n"
1012 –                         "    -->%s in Bend[%d] in %s\n",
1013 –                         current_extra->getlhs(),
1014 –                         k, comp_stamps[i]->getID() );
1015 –                painCave.isFatal = 1;
1016 –                simError();
1017 –              }
1018 –              
1019 –              current_extra = current_extra->getNext();
1020 –            }
1021 –          }
1022 –          
1023 –          if( !the_bends[index].isGhost ){
1024 –            
1025 –            exI = the_bends[index].a;
1026 –            exJ = the_bends[index].c;
1027 –          }
1028 –          else{
1029 –            
1030 –            exI = the_bends[index].a;
1031 –            exJ = the_bends[index].b;
1032 –          }
1033 –          
1034 –          // exclude_I must always be the smaller of the pair
1035 –          if( exI > exJ ){
1036 –            tempEx = exI;
1037 –            exI = exJ;
1038 –            exJ = tempEx;
1039 –          }
1090  
1091 <
1092 < #ifdef IS_MPI
1093 <
1094 <          the_excludes[(index + tot_bonds)*2] =    
1045 <            the_atoms[exI]->getGlobalIndex() + 1;
1046 <          the_excludes[(index + tot_bonds)*2 + 1] =
1047 <            the_atoms[exJ]->getGlobalIndex() + 1;
1048 <          
1049 < #else  // isn't MPI
1050 <          
1051 <          the_excludes[(index + tot_bonds)*2] =     exI + 1;
1052 <          the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
1053 <          // fortran index from 1 (hence the +1 in the indexing)
1054 < #endif  //is_mpi
1055 <          
1056 <          
1057 <          // increment the index and repeat;
1058 <          index++;
1059 <        }
1060 <        offset += comp_stamps[i]->getNAtoms();
1061 <        
1062 < #ifdef IS_MPI
1063 <      }
1064 < #endif //is_mpi
1065 <
1066 <      molIndex++;
1067 <    }
1091 >    atomOffset += info.nAtoms;
1092 >    delete[] theBonds;
1093 >    delete[] theBends;
1094 >    delete[] theTorsions;
1095    }
1096  
1097   #ifdef IS_MPI
1098 <  sprintf( checkPointMsg,
1072 <           "Successfully created the bends list.\n" );
1098 >  sprintf( checkPointMsg, "all molecules initialized succesfully" );
1099    MPIcheckPoint();
1100   #endif // is_mpi
1075 –  
1101  
1102 <  the_ff->initializeBends( the_bends );
1103 < }
1102 >  // clean up the forcefield
1103 >  the_ff->calcRcut();
1104 >  the_ff->cleanMe();
1105  
1080 – void SimSetup::makeTorsions( void ){
1081 –
1082 –  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1083 –  torsion_set* the_torsions;
1084 –  TorsionStamp* current_torsion;
1085 –
1086 –  the_torsions = new torsion_set[tot_torsions];
1087 –  index = 0;
1088 –  offset = 0;
1089 –  molIndex = 0;
1090 –  for( i=0; i<n_components; i++ ){
1091 –
1092 –    for( j=0; j<components_nmol[i]; j++ ){
1093 –
1094 – #ifdef IS_MPI
1095 –      if( mpiSim->getMyMolStart() <= molIndex &&
1096 –          molIndex <= mpiSim->getMyMolEnd() ){
1097 – #endif // is_mpi        
1098 –
1099 –      for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1100 –
1101 –        current_torsion = comp_stamps[i]->getTorsion( k );
1102 –        the_torsions[index].a = current_torsion->getA() + offset;
1103 –        the_torsions[index].b = current_torsion->getB() + offset;
1104 –        the_torsions[index].c = current_torsion->getC() + offset;
1105 –        the_torsions[index].d = current_torsion->getD() + offset;
1106 –
1107 –        exI = the_torsions[index].a;
1108 –        exJ = the_torsions[index].d;
1109 –
1110 –        
1111 –        // exclude_I must always be the smaller of the pair
1112 –        if( exI > exJ ){
1113 –          tempEx = exI;
1114 –          exI = exJ;
1115 –          exJ = tempEx;
1116 –        }
1117 –
1118 –
1119 – #ifdef IS_MPI
1120 –        
1121 –        the_excludes[(index + tot_bonds + tot_bends)*2] =    
1122 –          the_atoms[exI]->getGlobalIndex() + 1;
1123 –        the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1124 –          the_atoms[exJ]->getGlobalIndex() + 1;
1125 –        
1126 – #else  // isn't MPI
1127 –        
1128 –        the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1129 –        the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1130 –        // fortran indexes from 1 (hence the +1 in the indexing)
1131 – #endif  //is_mpi
1132 –        
1133 –
1134 –        // increment the index and repeat;
1135 –        index++;
1136 –      }
1137 –      offset += comp_stamps[i]->getNAtoms();
1138 –
1139 – #ifdef IS_MPI
1140 –      }
1141 – #endif //is_mpi      
1142 –
1143 –      molIndex++;
1144 –    }
1145 –  }
1146 –
1147 –  the_ff->initializeTorsions( the_torsions );
1106   }
1107  
1108   void SimSetup::initFromBass( void ){
# Line 1166 | Line 1124 | void SimSetup::initFromBass( void ){
1124      have_extra =1;
1125  
1126      n_cells = (int)temp3 - 1;
1127 <    cellx = simnfo->box_x / temp3;
1128 <    celly = simnfo->box_y / temp3;
1129 <    cellz = simnfo->box_z / temp3;
1127 >    cellx = simnfo->boxLx / temp3;
1128 >    celly = simnfo->boxLy / temp3;
1129 >    cellz = simnfo->boxLz / temp3;
1130      n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1131      temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1132      n_per_extra = (int)ceil( temp1 );
# Line 1183 | Line 1141 | void SimSetup::initFromBass( void ){
1141    }
1142    else{
1143      n_cells = (int)temp3;
1144 <    cellx = simnfo->box_x / temp3;
1145 <    celly = simnfo->box_y / temp3;
1146 <    cellz = simnfo->box_z / temp3;
1144 >    cellx = simnfo->boxLx / temp3;
1145 >    celly = simnfo->boxLy / temp3;
1146 >    cellz = simnfo->boxLz / temp3;
1147    }
1148  
1149    current_mol = 0;

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