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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 1113 by tim, Thu Apr 15 16:18:26 2004 UTC vs.
Revision 1157 by tim, Tue May 11 20:33:41 2004 UTC

# Line 183 | Line 183 | void SimSetup::makeMolecules(void){
183    BendStamp* currentBend;
184    TorsionStamp* currentTorsion;
185    RigidBodyStamp* currentRigidBody;
186 <
186 >  CutoffGroupStamp* currentCutoffGroup;
187 >  CutoffGroup* myCutoffGroup;
188 >  
189    bond_pair* theBonds;
190    bend_set* theBends;
191    torsion_set* theTorsions;
# Line 216 | Line 218 | void SimSetup::makeMolecules(void){
218        molInfo.nBends = comp_stamps[stampID]->getNBends();
219        molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
220        molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
221 +      molInfo.nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
222        
223        molInfo.myAtoms = &(info[k].atoms[atomOffset]);
224  
# Line 464 | Line 467 | void SimSetup::makeMolecules(void){
467              // used for the exclude list:
468              
469   #ifdef IS_MPI
470 <            exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
471 <            exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
470 >            exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
471 >            exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
472   #else
473 <            exI = tempI + 1;
474 <            exJ = tempJ + 1;
473 >            exI = molInfo.myAtoms[tempI]->getIndex() + 1;
474 >            exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
475   #endif
476              
477              info[k].excludes->addPair(exI, exJ);
# Line 479 | Line 482 | void SimSetup::makeMolecules(void){
482          molInfo.myRigidBodies.push_back(myRB);
483          info[k].rigidBodies.push_back(myRB);
484        }
485 +      
486 +
487 +      //creat cutoff group for molecule
488 +      molInfo.myCutoffGroups.clear();
489 +      for (j = 0; j < molInfo.nCutoffGroups; j++){
490 +
491 +        currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
492 +        nMembers = currentCutoffGroup->getNMembers();
493 +
494 +        myCutoffGroup = new CutoffGroup();
495 +        
496 +        for (int cg = 0; cg < nMembers; cg++) {
497 +
498 +          // molI is atom numbering inside this molecule
499 +          molI = currentCutoffGroup->getMember(cg);    
500 +
501 +          // tempI is atom numbering on local processor
502 +          tempI = molI + atomOffset;
503 +
504 +          myCutoffGroup->addAtom(info[k].atoms[tempI]);          
505 +        }
506 +
507 +        molInfo.myCutoffGroups.push_back(myCutoffGroup);
508 +      }//end for (j = 0; j < molInfo.nCutoffGroups; j++)
509        
510  
511 +
512        // After this is all set up, scan through the atoms to
513        // see if they can be added to the integrableObjects:
514  
# Line 538 | Line 566 | void SimSetup::makeMolecules(void){
566  
567    // clean up the forcefield
568  
569 <  if (!globals->haveLJrcut()){
569 >  if (!globals->haveRcut()){
570  
571      the_ff->calcRcut();
572  
573    } else {
574      
575 <    the_ff->setRcut( globals->getLJrcut() );
575 >    the_ff->setRcut( globals->getRcut() );
576    }
577  
578    the_ff->cleanMe();
# Line 834 | Line 862 | void SimSetup::gatherInfo(void){
862    }
863  
864    //check whether sample time, status time, thermal time and reset time are divisble by dt
865 <  if (!isDivisible(globals->getSampleTime(), globals->getDt())){
865 >  if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
866      sprintf(painCave.errMsg,
867              "Sample time is not divisible by dt.\n"
868              "\tThis will result in samples that are not uniformly\n"
# Line 844 | Line 872 | void SimSetup::gatherInfo(void){
872      simError();    
873    }
874  
875 <  if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
875 >  if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
876      sprintf(painCave.errMsg,
877              "Status time is not divisible by dt.\n"
878              "\tThis will result in status reports that are not uniformly\n"
# Line 880 | Line 908 | void SimSetup::gatherInfo(void){
908      if (globals->haveSampleTime()){
909        info[i].sampleTime = globals->getSampleTime();
910        info[i].statusTime = info[i].sampleTime;
883 –      info[i].thermalTime = info[i].sampleTime;
911      }
912      else{
913        info[i].sampleTime = globals->getRunTime();
914        info[i].statusTime = info[i].sampleTime;
888 –      info[i].thermalTime = info[i].sampleTime;
915      }
916  
917      if (globals->haveStatusTime()){
# Line 894 | Line 920 | void SimSetup::gatherInfo(void){
920  
921      if (globals->haveThermalTime()){
922        info[i].thermalTime = globals->getThermalTime();
923 +    } else {
924 +      info[i].thermalTime = globals->getRunTime();
925      }
926  
927      info[i].resetIntegrator = 0;
# Line 987 | Line 1015 | void SimSetup::finalInfoCheck(void){
1015      MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1016   #endif //is_mpi
1017  
1018 <    double theEcr, theEst;
1018 >    double theRcut, theRsw;
1019  
1020      if (globals->getUseRF()){
1021        info[i].useReactionField = 1;
1022  
1023 <      if (!globals->haveECR()){
1023 >      if (!globals->haveRcut()){
1024          sprintf(painCave.errMsg,
1025 <                "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1025 >                "SimSetup Warning: No value was set for the cutoffRadius.\n"
1026                  "\tOOPSE will use a default value of 15.0 angstroms"
1027 <                "\tfor the electrostaticCutoffRadius.\n");
1027 >                "\tfor the cutoffRadius.\n");
1028          painCave.isFatal = 0;
1029          simError();
1030 <        theEcr = 15.0;
1030 >        theRcut = 15.0;
1031        }
1032        else{
1033 <        theEcr = globals->getECR();
1033 >        theRcut = globals->getRcut();
1034        }
1035  
1036 <      if (!globals->haveEST()){
1036 >      if (!globals->haveRsw()){
1037          sprintf(painCave.errMsg,
1038 <                "SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1038 >                "SimSetup Warning: No value was set for switchingRadius.\n"
1039                  "\tOOPSE will use a default value of\n"
1040 <                "\t0.05 * electrostaticCutoffRadius\n"
1013 <                "\tfor the electrostaticSkinThickness\n");
1040 >                "\t0.95 * cutoffRadius for the switchingRadius\n");
1041          painCave.isFatal = 0;
1042          simError();
1043 <        theEst = 0.05 * theEcr;
1043 >        theRsw = 0.95 * theRcut;
1044        }
1045        else{
1046 <        theEst = globals->getEST();
1046 >        theRsw = globals->getRsw();
1047        }
1048  
1049 <      info[i].setDefaultEcr(theEcr, theEst);
1049 >      info[i].setDefaultRcut(theRcut, theRsw);
1050  
1051        if (!globals->haveDielectric()){
1052          sprintf(painCave.errMsg,
# Line 1033 | Line 1060 | void SimSetup::finalInfoCheck(void){
1060      }
1061      else{
1062        if (usesDipoles || usesCharges){
1063 <        if (!globals->haveECR()){
1063 >
1064 >        if (!globals->haveRcut()){
1065            sprintf(painCave.errMsg,
1066 <                  "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1066 >                  "SimSetup Warning: No value was set for the cutoffRadius.\n"
1067                    "\tOOPSE will use a default value of 15.0 angstroms"
1068 <                  "\tfor the electrostaticCutoffRadius.\n");
1069 <          painCave.isFatal = 0;
1070 <          simError();
1071 <          theEcr = 15.0;
1072 <        }
1068 >                  "\tfor the cutoffRadius.\n");
1069 >          painCave.isFatal = 0;
1070 >          simError();
1071 >          theRcut = 15.0;
1072 >      }
1073          else{
1074 <          theEcr = globals->getECR();
1074 >          theRcut = globals->getRcut();
1075          }
1076 <        
1077 <        if (!globals->haveEST()){
1076 >        
1077 >        if (!globals->haveRsw()){
1078            sprintf(painCave.errMsg,
1079 <                  "SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1079 >                  "SimSetup Warning: No value was set for switchingRadius.\n"
1080                    "\tOOPSE will use a default value of\n"
1081 <                  "\t0.05 * electrostaticCutoffRadius\n"
1054 <                  "\tfor the electrostaticSkinThickness\n");
1081 >                  "\t0.95 * cutoffRadius for the switchingRadius\n");
1082            painCave.isFatal = 0;
1083            simError();
1084 <          theEst = 0.05 * theEcr;
1084 >          theRsw = 0.95 * theRcut;
1085          }
1086          else{
1087 <          theEst = globals->getEST();
1087 >          theRsw = globals->getRsw();
1088          }
1089 +        
1090 +        info[i].setDefaultRcut(theRcut, theRsw);
1091          
1063 –        info[i].setDefaultEcr(theEcr, theEst);
1092        }
1093      }
1094    }
# Line 1282 | Line 1310 | void SimSetup::compList(void){
1310    LinkedMolStamp* headStamp = new LinkedMolStamp();
1311    LinkedMolStamp* currentStamp = NULL;
1312    comp_stamps = new MoleculeStamp * [n_components];
1313 +  bool haveCutoffGroups;
1314  
1315 +  haveCutoffGroups = false;
1316 +  
1317    // make an array of molecule stamps that match the components used.
1318    // also extract the used stamps out into a separate linked list
1319  
# Line 1317 | Line 1348 | void SimSetup::compList(void){
1348        headStamp->add(currentStamp);
1349        comp_stamps[i] = headStamp->match(id);
1350      }
1351 +
1352 +    if(comp_stamps[i]->getNCutoffGroups() > 0)
1353 +      haveCutoffGroups = true;    
1354    }
1355 +    
1356 +  for (i = 0; i < nInfo; i++)
1357 +    info[i].haveCutoffGroups = haveCutoffGroups;
1358  
1359   #ifdef IS_MPI
1360    strcpy(checkPointMsg, "Component stamps successfully extracted\n");
# Line 1365 | Line 1402 | void SimSetup::mpiMolDivide(void){
1402    int localMol, allMol;
1403    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1404    int local_rigid;
1368 –  vector<int> globalAtomIndex;
1405    vector<int> globalMolIndex;
1406  
1407    mpiSim = new mpiSimulation(info);
1408  
1409    mpiSim->divideLabor();
1410    globalAtomIndex = mpiSim->getGlobalAtomIndex();
1411 <  globalMolIndex = mpiSim->getGlobalMolIndex();
1411 >  //globalMolIndex = mpiSim->getGlobalMolIndex();
1412  
1413    // set up the local variables
1414  
# Line 1493 | Line 1529 | void SimSetup::makeSysArrays(void){
1529      info[l].atoms = the_atoms;
1530      info[l].molecules = the_molecules;
1531      info[l].nGlobalExcludes = 0;
1532 <
1532 >    
1533      the_ff->setSimInfo(info);
1534    }
1535   }

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