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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 1203 by gezelter, Thu May 27 18:59:17 2004 UTC

# Line 183 | Line 183 | void SimSetup::makeMolecules(void){
183    BendStamp* currentBend;
184    TorsionStamp* currentTorsion;
185    RigidBodyStamp* currentRigidBody;
186 +  CutoffGroupStamp* currentCutoffGroup;
187 +  CutoffGroup* myCutoffGroup;
188 +  int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
189 +  set<int> cutoffAtomSet; //atoms belong to  cutoffgroup defined at mdl file
190  
191    bond_pair* theBonds;
192    bend_set* theBends;
# Line 216 | Line 220 | void SimSetup::makeMolecules(void){
220        molInfo.nBends = comp_stamps[stampID]->getNBends();
221        molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
222        molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
223 +
224 +      nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
225        
226        molInfo.myAtoms = &(info[k].atoms[atomOffset]);
227  
228        if (molInfo.nBonds > 0)
229 <        molInfo.myBonds = new (Bond *) [molInfo.nBonds];
229 >        molInfo.myBonds = new Bond*[molInfo.nBonds];
230        else
231          molInfo.myBonds = NULL;
232  
233        if (molInfo.nBends > 0)
234 <        molInfo.myBends = new (Bend *) [molInfo.nBends];
234 >        molInfo.myBends = new Bend*[molInfo.nBends];
235        else
236          molInfo.myBends = NULL;
237  
238        if (molInfo.nTorsions > 0)
239 <        molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
239 >        molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
240        else
241          molInfo.myTorsions = NULL;
242  
# Line 464 | Line 470 | void SimSetup::makeMolecules(void){
470              // used for the exclude list:
471              
472   #ifdef IS_MPI
473 <            exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
474 <            exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
473 >            exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
474 >            exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
475   #else
476 <            exI = tempI + 1;
477 <            exJ = tempJ + 1;
476 >            exI = molInfo.myAtoms[tempI]->getIndex() + 1;
477 >            exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
478   #endif
479              
480              info[k].excludes->addPair(exI, exJ);
# Line 481 | Line 487 | void SimSetup::makeMolecules(void){
487        }
488        
489  
490 +      //create cutoff group for molecule
491 +
492 +      cutoffAtomSet.clear();
493 +      molInfo.myCutoffGroups.clear();
494 +      
495 +      for (j = 0; j < nCutoffGroups; j++){
496 +
497 +        currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
498 +        nMembers = currentCutoffGroup->getNMembers();
499 +
500 +        myCutoffGroup = new CutoffGroup();
501 +        
502 +        for (int cg = 0; cg < nMembers; cg++) {
503 +
504 +          // molI is atom numbering inside this molecule
505 +          molI = currentCutoffGroup->getMember(cg);    
506 +
507 +          // tempI is atom numbering on local processor
508 +          tempI = molI + atomOffset;
509 +          
510 +          myCutoffGroup->addAtom(info[k].atoms[tempI]);          
511 +
512 +          cutoffAtomSet.insert(tempI);
513 +        }
514 +
515 +        molInfo.myCutoffGroups.push_back(myCutoffGroup);
516 +      }//end for (j = 0; j < molInfo.nCutoffGroups; j++)
517 +
518 +      //creat a cutoff group for every atom  in current molecule which does not belong to cutoffgroup defined at mdl file
519 +
520 +      for(j = 0; j < molInfo.nAtoms; j++){
521 +
522 +        if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
523 +          myCutoffGroup = new CutoffGroup();
524 +          myCutoffGroup->addAtom(molInfo.myAtoms[j]);
525 +          molInfo.myCutoffGroups.push_back(myCutoffGroup);
526 +        }
527 +          
528 +      }
529 +
530 +              
531 +
532 +
533        // After this is all set up, scan through the atoms to
534        // see if they can be added to the integrableObjects:
535  
# Line 535 | Line 584 | void SimSetup::makeMolecules(void){
584    sprintf(checkPointMsg, "all molecules initialized succesfully");
585    MPIcheckPoint();
586   #endif // is_mpi
538 –
539 –  // clean up the forcefield
540 –
541 –  if (!globals->haveLJrcut()){
542 –
543 –    the_ff->calcRcut();
544 –
545 –  } else {
546 –    
547 –    the_ff->setRcut( globals->getLJrcut() );
548 –  }
587  
550 –  the_ff->cleanMe();
588   }
589  
590   void SimSetup::initFromBass(void){
# Line 834 | Line 871 | void SimSetup::gatherInfo(void){
871    }
872  
873    //check whether sample time, status time, thermal time and reset time are divisble by dt
874 <  if (!isDivisible(globals->getSampleTime(), globals->getDt())){
874 >  if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
875      sprintf(painCave.errMsg,
876              "Sample time is not divisible by dt.\n"
877              "\tThis will result in samples that are not uniformly\n"
# Line 844 | Line 881 | void SimSetup::gatherInfo(void){
881      simError();    
882    }
883  
884 <  if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
884 >  if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
885      sprintf(painCave.errMsg,
886              "Status time is not divisible by dt.\n"
887              "\tThis will result in status reports that are not uniformly\n"
# Line 880 | Line 917 | void SimSetup::gatherInfo(void){
917      if (globals->haveSampleTime()){
918        info[i].sampleTime = globals->getSampleTime();
919        info[i].statusTime = info[i].sampleTime;
883 –      info[i].thermalTime = info[i].sampleTime;
920      }
921      else{
922        info[i].sampleTime = globals->getRunTime();
923        info[i].statusTime = info[i].sampleTime;
888 –      info[i].thermalTime = info[i].sampleTime;
924      }
925  
926      if (globals->haveStatusTime()){
# Line 894 | Line 929 | void SimSetup::gatherInfo(void){
929  
930      if (globals->haveThermalTime()){
931        info[i].thermalTime = globals->getThermalTime();
932 +    } else {
933 +      info[i].thermalTime = globals->getRunTime();
934      }
935  
936      info[i].resetIntegrator = 0;
# Line 911 | Line 948 | void SimSetup::gatherInfo(void){
948  
949      info[i].useInitXSstate = globals->getUseInitXSstate();
950      info[i].orthoTolerance = globals->getOrthoBoxTolerance();
951 <    
951 >
952 >    // check for thermodynamic integration
953 >    if (globals->getUseThermInt()) {
954 >      if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
955 >        info[i].useThermInt = globals->getUseThermInt();
956 >        info[i].thermIntLambda = globals->getThermIntLambda();
957 >        info[i].thermIntK = globals->getThermIntK();
958 >        
959 >        Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
960 >        info[i].restraint = myRestraint;
961 >      }
962 >      else {
963 >        sprintf(painCave.errMsg,
964 >                "SimSetup Error:\n"
965 >                "\tKeyword useThermInt was set to 'true' but\n"
966 >                "\tthermodynamicIntegrationLambda (and/or\n"
967 >                "\tthermodynamicIntegrationK) was not specified.\n"
968 >                "\tPlease provide a lambda value and k value in your .bass file.\n");
969 >        painCave.isFatal = 1;
970 >        simError();    
971 >      }
972 >    }
973 >    else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
974 >        sprintf(painCave.errMsg,
975 >                "SimSetup Warning: If you want to use Thermodynamic\n"
976 >                "\tIntegration, set useThermInt to 'true' in your .bass file.\n"
977 >                "\tThe useThermInt keyword is 'false' by default, so your\n"
978 >                "\tlambda and/or k values are being ignored.\n");
979 >        painCave.isFatal = 0;
980 >        simError();  
981 >    }
982    }
983    
984    //setup seed for random number generator
# Line 987 | Line 1054 | void SimSetup::finalInfoCheck(void){
1054      MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1055   #endif //is_mpi
1056  
1057 <    double theEcr, theEst;
1057 >    double theRcut, theRsw;
1058  
1059 +    if (globals->haveRcut()) {
1060 +      theRcut = globals->getRcut();
1061 +
1062 +      if (globals->haveRsw())
1063 +        theRsw = globals->getRsw();
1064 +      else
1065 +        theRsw = theRcut;
1066 +      
1067 +      info[i].setDefaultRcut(theRcut, theRsw);
1068 +
1069 +    } else {
1070 +      
1071 +      the_ff->calcRcut();
1072 +      theRcut = info[i].getRcut();
1073 +
1074 +      if (globals->haveRsw())
1075 +        theRsw = globals->getRsw();
1076 +      else
1077 +        theRsw = theRcut;
1078 +      
1079 +      info[i].setDefaultRcut(theRcut, theRsw);
1080 +    }
1081 +
1082      if (globals->getUseRF()){
1083        info[i].useReactionField = 1;
1084 <
1085 <      if (!globals->haveECR()){
1084 >      
1085 >      if (!globals->haveRcut()){
1086          sprintf(painCave.errMsg,
1087 <                "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1087 >                "SimSetup Warning: No value was set for the cutoffRadius.\n"
1088                  "\tOOPSE will use a default value of 15.0 angstroms"
1089 <                "\tfor the electrostaticCutoffRadius.\n");
1089 >                "\tfor the cutoffRadius.\n");
1090          painCave.isFatal = 0;
1091          simError();
1092 <        theEcr = 15.0;
1092 >        theRcut = 15.0;
1093        }
1094        else{
1095 <        theEcr = globals->getECR();
1095 >        theRcut = globals->getRcut();
1096        }
1097  
1098 <      if (!globals->haveEST()){
1098 >      if (!globals->haveRsw()){
1099          sprintf(painCave.errMsg,
1100 <                "SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1100 >                "SimSetup Warning: No value was set for switchingRadius.\n"
1101                  "\tOOPSE will use a default value of\n"
1102 <                "\t0.05 * electrostaticCutoffRadius\n"
1013 <                "\tfor the electrostaticSkinThickness\n");
1102 >                "\t0.95 * cutoffRadius for the switchingRadius\n");
1103          painCave.isFatal = 0;
1104          simError();
1105 <        theEst = 0.05 * theEcr;
1105 >        theRsw = 0.95 * theRcut;
1106        }
1107        else{
1108 <        theEst = globals->getEST();
1108 >        theRsw = globals->getRsw();
1109        }
1110  
1111 <      info[i].setDefaultEcr(theEcr, theEst);
1111 >      info[i].setDefaultRcut(theRcut, theRsw);
1112  
1113        if (!globals->haveDielectric()){
1114          sprintf(painCave.errMsg,
# Line 1033 | Line 1122 | void SimSetup::finalInfoCheck(void){
1122      }
1123      else{
1124        if (usesDipoles || usesCharges){
1125 <        if (!globals->haveECR()){
1125 >
1126 >        if (!globals->haveRcut()){
1127            sprintf(painCave.errMsg,
1128 <                  "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1128 >                  "SimSetup Warning: No value was set for the cutoffRadius.\n"
1129                    "\tOOPSE will use a default value of 15.0 angstroms"
1130 <                  "\tfor the electrostaticCutoffRadius.\n");
1131 <          painCave.isFatal = 0;
1132 <          simError();
1133 <          theEcr = 15.0;
1134 <        }
1130 >                  "\tfor the cutoffRadius.\n");
1131 >          painCave.isFatal = 0;
1132 >          simError();
1133 >          theRcut = 15.0;
1134 >      }
1135          else{
1136 <          theEcr = globals->getECR();
1136 >          theRcut = globals->getRcut();
1137          }
1138 <        
1139 <        if (!globals->haveEST()){
1138 >        
1139 >        if (!globals->haveRsw()){
1140            sprintf(painCave.errMsg,
1141 <                  "SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1141 >                  "SimSetup Warning: No value was set for switchingRadius.\n"
1142                    "\tOOPSE will use a default value of\n"
1143 <                  "\t0.05 * electrostaticCutoffRadius\n"
1054 <                  "\tfor the electrostaticSkinThickness\n");
1143 >                  "\t0.95 * cutoffRadius for the switchingRadius\n");
1144            painCave.isFatal = 0;
1145            simError();
1146 <          theEst = 0.05 * theEcr;
1146 >          theRsw = 0.95 * theRcut;
1147          }
1148          else{
1149 <          theEst = globals->getEST();
1149 >          theRsw = globals->getRsw();
1150          }
1151 +        
1152 +        info[i].setDefaultRcut(theRcut, theRsw);
1153          
1063 –        info[i].setDefaultEcr(theEcr, theEst);
1154        }
1155      }
1156    }
# Line 1068 | Line 1158 | void SimSetup::finalInfoCheck(void){
1158    strcpy(checkPointMsg, "post processing checks out");
1159    MPIcheckPoint();
1160   #endif // is_mpi
1161 +
1162 +  // clean up the forcefield
1163 +  the_ff->cleanMe();
1164   }
1165    
1166   void SimSetup::initSystemCoords(void){
# Line 1195 | Line 1288 | void SimSetup::makeOutNames(void){
1288          }
1289          else{
1290            strcat(info[k].statusName, ".stat");
1291 +        }
1292 +      }
1293 +
1294 +      strcpy(info[k].rawPotName, inFileName);
1295 +      nameLength = strlen(info[k].rawPotName);
1296 +      endTest = &(info[k].rawPotName[nameLength - 5]);
1297 +      if (!strcmp(endTest, ".bass")){
1298 +        strcpy(endTest, ".raw");
1299 +      }
1300 +      else if (!strcmp(endTest, ".BASS")){
1301 +        strcpy(endTest, ".raw");
1302 +      }
1303 +      else{
1304 +        endTest = &(info[k].rawPotName[nameLength - 4]);
1305 +        if (!strcmp(endTest, ".bss")){
1306 +          strcpy(endTest, ".raw");
1307          }
1308 +        else if (!strcmp(endTest, ".mdl")){
1309 +          strcpy(endTest, ".raw");
1310 +        }
1311 +        else{
1312 +          strcat(info[k].rawPotName, ".raw");
1313 +        }
1314        }
1315  
1316   #ifdef IS_MPI
# Line 1282 | Line 1397 | void SimSetup::compList(void){
1397    LinkedMolStamp* headStamp = new LinkedMolStamp();
1398    LinkedMolStamp* currentStamp = NULL;
1399    comp_stamps = new MoleculeStamp * [n_components];
1400 +  bool haveCutoffGroups;
1401  
1402 +  haveCutoffGroups = false;
1403 +  
1404    // make an array of molecule stamps that match the components used.
1405    // also extract the used stamps out into a separate linked list
1406  
# Line 1317 | Line 1435 | void SimSetup::compList(void){
1435        headStamp->add(currentStamp);
1436        comp_stamps[i] = headStamp->match(id);
1437      }
1438 +
1439 +    if(comp_stamps[i]->getNCutoffGroups() > 0)
1440 +      haveCutoffGroups = true;    
1441    }
1442 +    
1443 +  for (i = 0; i < nInfo; i++)
1444 +    info[i].haveCutoffGroups = haveCutoffGroups;
1445  
1446   #ifdef IS_MPI
1447    strcpy(checkPointMsg, "Component stamps successfully extracted\n");
# Line 1326 | Line 1450 | void SimSetup::calcSysValues(void){
1450   }
1451  
1452   void SimSetup::calcSysValues(void){
1453 <  int i;
1453 >  int i, j;
1454 >  int ncutgroups, atomsingroups, ngroupsinstamp;
1455  
1456    int* molMembershipArray;
1457 +  CutoffGroupStamp* cg;
1458  
1459    tot_atoms = 0;
1460    tot_bonds = 0;
1461    tot_bends = 0;
1462    tot_torsions = 0;
1463    tot_rigid = 0;
1464 +  tot_groups = 0;
1465    for (i = 0; i < n_components; i++){
1466      tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1467      tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1468      tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1469      tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1470      tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1471 +
1472 +    ncutgroups = comp_stamps[i]->getNCutoffGroups();
1473 +    atomsingroups = 0;
1474 +    for (j=0; j < ncutgroups; j++) {
1475 +      cg = comp_stamps[i]->getCutoffGroup(j);
1476 +      atomsingroups += cg->getNMembers();
1477 +    }
1478 +    ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1479 +    tot_groups += components_nmol[i] * ngroupsinstamp;    
1480    }
1481    
1482    tot_SRI = tot_bonds + tot_bends + tot_torsions;
# Line 1353 | Line 1489 | void SimSetup::calcSysValues(void){
1489      info[i].n_torsions = tot_torsions;
1490      info[i].n_SRI = tot_SRI;
1491      info[i].n_mol = tot_nmol;
1492 <
1492 >    info[i].ngroup = tot_groups;
1493      info[i].molMembershipArray = molMembershipArray;
1494    }
1495   }
# Line 1365 | Line 1501 | void SimSetup::mpiMolDivide(void){
1501    int localMol, allMol;
1502    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1503    int local_rigid;
1368 –  vector<int> globalAtomIndex;
1504    vector<int> globalMolIndex;
1505  
1506    mpiSim = new mpiSimulation(info);
1507  
1508    mpiSim->divideLabor();
1509    globalAtomIndex = mpiSim->getGlobalAtomIndex();
1510 <  globalMolIndex = mpiSim->getGlobalMolIndex();
1510 >  //globalMolIndex = mpiSim->getGlobalMolIndex();
1511  
1512    // set up the local variables
1513  
# Line 1408 | Line 1543 | void SimSetup::mpiMolDivide(void){
1543    }
1544    local_SRI = local_bonds + local_bends + local_torsions;
1545  
1546 <  info[0].n_atoms = mpiSim->getMyNlocal();  
1546 >  info[0].n_atoms = mpiSim->getNAtomsLocal();  
1547    
1548  
1549    if (local_atoms != info[0].n_atoms){
# Line 1456 | Line 1591 | void SimSetup::makeSysArrays(void){
1591  
1592  
1593      molIndex = 0;
1594 <    for (i = 0; i < mpiSim->getTotNmol(); i++){
1594 >    for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1595        if (mol2proc[i] == worldRank){
1596          the_molecules[molIndex].setStampID(molCompType[i]);
1597          the_molecules[molIndex].setMyIndex(molIndex);
# Line 1493 | Line 1628 | void SimSetup::makeSysArrays(void){
1628      info[l].atoms = the_atoms;
1629      info[l].molecules = the_molecules;
1630      info[l].nGlobalExcludes = 0;
1631 <
1631 >    
1632      the_ff->setSimInfo(info);
1633    }
1634   }

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