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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 736 by tim, Thu Aug 28 21:09:47 2003 UTC vs.
Revision 965 by gezelter, Mon Jan 19 21:17:39 2004 UTC

# Line 1 | Line 1
1   #include <algorithm>
2 < #include <cstdlib>
2 > #include <stdlib.h>
3   #include <iostream>
4 < #include <cmath>
4 > #include <math.h>
5   #include <string>
6   #include <sprng.h>
7 –
7   #include "SimSetup.hpp"
8   #include "ReadWrite.hpp"
9   #include "parse_me.h"
# Line 22 | Line 21
21   #define NVT_ENS        1
22   #define NPTi_ENS       2
23   #define NPTf_ENS       3
24 < #define NPTim_ENS      4
26 < #define NPTfm_ENS      5
24 > #define NPTxyz_ENS     4
25  
26 +
27   #define FF_DUFF 0
28   #define FF_LJ   1
29   #define FF_EAM  2
30  
31   using namespace std;
32  
33 + /**
34 + * Check whether dividend is divisble by divisor or not
35 + */
36 + bool isDivisible(double dividend, double divisor){
37 +  double tolerance = 0.000001;
38 +  double quotient;
39 +  double diff;
40 +  int intQuotient;
41 +  
42 +  quotient = dividend / divisor;
43 +
44 +  if (quotient < 0)
45 +    quotient = -quotient;
46 +
47 +  intQuotient = int (quotient + tolerance);
48 +
49 +  diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
50 +
51 +  if (diff <= tolerance)
52 +    return true;
53 +  else
54 +    return false;  
55 + }
56 +
57   SimSetup::SimSetup(){
58 +  
59 +  initSuspend = false;
60    isInfoArray = 0;
61    nInfo = 1;
62  
# Line 54 | Line 79 | void SimSetup::setSimInfo(SimInfo* the_info, int theNi
79    info = the_info;
80    nInfo = theNinfo;
81    isInfoArray = 1;
82 +  initSuspend = true;
83   }
84  
85  
# Line 92 | Line 118 | void SimSetup::createSim(void){
118   #endif // is_mpi
119  
120   void SimSetup::createSim(void){
95 –  int i, j, k, globalAtomIndex;
121  
122    // gather all of the information from the Bass file
123  
# Line 108 | Line 133 | void SimSetup::createSim(void){
133  
134    // initialize the system coordinates
135  
136 <  if (!isInfoArray){
136 >  if ( !initSuspend ){
137      initSystemCoords();
138 +
139 +    if( !(globals->getUseInitTime()) )
140 +      info[0].currentTime = 0.0;
141    }  
142  
143    // make the output filenames
# Line 131 | Line 159 | void SimSetup::makeMolecules(void){
159  
160  
161   void SimSetup::makeMolecules(void){
162 <  int k, l;
162 >  int k;
163    int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
164    molInit molInfo;
165    DirectionalAtom* dAtom;
# Line 553 | Line 581 | void SimSetup::gatherInfo(void){
581  
582  
583   void SimSetup::gatherInfo(void){
584 <  int i, j, k;
584 >  int i;
585  
586    ensembleCase = -1;
587    ffCase = -1;
# Line 604 | Line 632 | void SimSetup::gatherInfo(void){
632    else if (!strcasecmp(ensemble, "NPTf")){
633      ensembleCase = NPTf_ENS;
634    }
635 <  else if (!strcasecmp(ensemble, "NPTim")){
636 <    ensembleCase = NPTim_ENS;
609 <  }
610 <  else if (!strcasecmp(ensemble, "NPTfm")){
611 <    ensembleCase = NPTfm_ENS;
635 >  else if (!strcasecmp(ensemble, "NPTxyz")){
636 >    ensembleCase = NPTxyz_ENS;
637    }
638    else{
639      sprintf(painCave.errMsg,
640 <            "SimSetup Warning. Unrecognized Ensemble -> %s, "
641 <            "reverting to NVE for this simulation.\n",
640 >            "SimSetup Warning. Unrecognized Ensemble -> %s \n"
641 >            "\treverting to NVE for this simulation.\n",
642              ensemble);
643           painCave.isFatal = 0;
644           simError();
# Line 645 | Line 670 | void SimSetup::gatherInfo(void){
670        if (!the_components[i]->haveNMol()){
671          // we have a problem
672          sprintf(painCave.errMsg,
673 <                "SimSetup Error. No global NMol or component NMol"
674 <                " given. Cannot calculate the number of atoms.\n");
673 >                "SimSetup Error. No global NMol or component NMol given.\n"
674 >                "\tCannot calculate the number of atoms.\n");
675          painCave.isFatal = 1;
676          simError();
677        }
# Line 665 | Line 690 | void SimSetup::gatherInfo(void){
690      painCave.isFatal = 1;
691      simError();
692    }
693 +
694 +  //check whether sample time, status time, thermal time and reset time are divisble by dt
695 +  if (!isDivisible(globals->getSampleTime(), globals->getDt())){
696 +    sprintf(painCave.errMsg,
697 +            "Sample time is not divisible by dt.\n"
698 +            "\tThis will result in samples that are not uniformly\n"
699 +            "\tdistributed in time.  If this is a problem, change\n"
700 +            "\tyour sampleTime variable.\n");
701 +    painCave.isFatal = 0;
702 +    simError();    
703 +  }
704 +
705 +  if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
706 +    sprintf(painCave.errMsg,
707 +            "Status time is not divisible by dt.\n"
708 +            "\tThis will result in status reports that are not uniformly\n"
709 +            "\tdistributed in time.  If this is a problem, change \n"
710 +            "\tyour statusTime variable.\n");
711 +    painCave.isFatal = 0;
712 +    simError();    
713 +  }
714 +
715 +  if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
716 +    sprintf(painCave.errMsg,
717 +            "Thermal time is not divisible by dt.\n"
718 +            "\tThis will result in thermalizations that are not uniformly\n"
719 +            "\tdistributed in time.  If this is a problem, change \n"
720 +            "\tyour thermalTime variable.\n");
721 +    painCave.isFatal = 0;
722 +    simError();    
723 +  }  
724 +
725 +  if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
726 +    sprintf(painCave.errMsg,
727 +            "Reset time is not divisible by dt.\n"
728 +            "\tThis will result in integrator resets that are not uniformly\n"
729 +            "\tdistributed in time.  If this is a problem, change\n"
730 +            "\tyour resetTime variable.\n");
731 +    painCave.isFatal = 0;
732 +    simError();    
733 +  }
734  
735    // set the status, sample, and thermal kick times
736  
# Line 688 | Line 754 | void SimSetup::gatherInfo(void){
754        info[i].thermalTime = globals->getThermalTime();
755      }
756  
757 <    // check for the temperature set flag
757 >    info[i].resetIntegrator = 0;
758 >    if( globals->haveResetTime() ){
759 >      info[i].resetTime = globals->getResetTime();
760 >      info[i].resetIntegrator = 1;
761 >    }
762  
763 +    // check for the temperature set flag
764 +    
765      if (globals->haveTempSet())
766        info[i].setTemp = globals->getTempSet();
767  
768 <    // get some of the tricky things that may still be in the globals
768 >    // check for the extended State init
769  
770 <    double boxVector[3];
771 <    if (globals->haveBox()){
772 <      boxVector[0] = globals->getBox();
701 <      boxVector[1] = globals->getBox();
702 <      boxVector[2] = globals->getBox();
703 <
704 <      info[i].setBox(boxVector);
705 <    }
706 <    else if (globals->haveDensity()){
707 <      double vol;
708 <      vol = (double) tot_nmol / globals->getDensity();
709 <      boxVector[0] = pow(vol, (1.0 / 3.0));
710 <      boxVector[1] = boxVector[0];
711 <      boxVector[2] = boxVector[0];
712 <
713 <      info[i].setBox(boxVector);
714 <    }
715 <    else{
716 <      if (!globals->haveBoxX()){
717 <        sprintf(painCave.errMsg,
718 <                "SimSetup error, no periodic BoxX size given.\n");
719 <        painCave.isFatal = 1;
720 <        simError();
721 <      }
722 <      boxVector[0] = globals->getBoxX();
723 <
724 <      if (!globals->haveBoxY()){
725 <        sprintf(painCave.errMsg,
726 <                "SimSetup error, no periodic BoxY size given.\n");
727 <        painCave.isFatal = 1;
728 <        simError();
729 <      }
730 <      boxVector[1] = globals->getBoxY();
731 <
732 <      if (!globals->haveBoxZ()){
733 <        sprintf(painCave.errMsg,
734 <                "SimSetup error, no periodic BoxZ size given.\n");
735 <        painCave.isFatal = 1;
736 <        simError();
737 <      }
738 <      boxVector[2] = globals->getBoxZ();
739 <
740 <      info[i].setBox(boxVector);
741 <    }
770 >    info[i].useInitXSstate = globals->getUseInitXSstate();
771 >    info[i].orthoTolerance = globals->getOrthoBoxTolerance();
772 >    
773    }
774 <
774 >  
775    //setup seed for random number generator
776    int seedValue;
777  
# Line 815 | Line 846 | void SimSetup::finalInfoCheck(void){
846  
847        if (!globals->haveECR()){
848          sprintf(painCave.errMsg,
849 <                "SimSetup Warning: using default value of 1/2 the smallest "
850 <                "box length for the electrostaticCutoffRadius.\n"
851 <                "I hope you have a very fast processor!\n");
849 >                "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
850 >                "\tOOPSE will use a default value of 15.0 angstroms"
851 >                "\tfor the electrostaticCutoffRadius.\n");
852          painCave.isFatal = 0;
853          simError();
854 <        double smallest;
824 <        smallest = info[i].boxL[0];
825 <        if (info[i].boxL[1] <= smallest)
826 <          smallest = info[i].boxL[1];
827 <        if (info[i].boxL[2] <= smallest)
828 <          smallest = info[i].boxL[2];
829 <        theEcr = 0.5 * smallest;
854 >        theEcr = 15.0;
855        }
856        else{
857          theEcr = globals->getECR();
# Line 834 | Line 859 | void SimSetup::finalInfoCheck(void){
859  
860        if (!globals->haveEST()){
861          sprintf(painCave.errMsg,
862 <                "SimSetup Warning: using default value of 0.05 * the "
863 <                "electrostaticCutoffRadius for the electrostaticSkinThickness\n");
862 >                "SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
863 >                "\tOOPSE will use a default value of\n"
864 >                "\t0.05 * electrostaticCutoffRadius\n"
865 >                "\tfor the electrostaticSkinThickness\n");
866          painCave.isFatal = 0;
867          simError();
868          theEst = 0.05 * theEcr;
# Line 844 | Line 871 | void SimSetup::finalInfoCheck(void){
871          theEst = globals->getEST();
872        }
873  
874 <      info[i].setEcr(theEcr, theEst);
874 >      info[i].setDefaultEcr(theEcr, theEst);
875  
876        if (!globals->haveDielectric()){
877          sprintf(painCave.errMsg,
878 <                "SimSetup Error: You are trying to use Reaction Field without"
879 <                "setting a dielectric constant!\n");
878 >                "SimSetup Error: No Dielectric constant was set.\n"
879 >                "\tYou are trying to use Reaction Field without"
880 >                "\tsetting a dielectric constant!\n");
881          painCave.isFatal = 1;
882          simError();
883        }
# Line 859 | Line 887 | void SimSetup::finalInfoCheck(void){
887        if (usesDipoles){
888          if (!globals->haveECR()){
889            sprintf(painCave.errMsg,
890 <                  "SimSetup Warning: using default value of 1/2 the smallest "
891 <                  "box length for the electrostaticCutoffRadius.\n"
892 <                  "I hope you have a very fast processor!\n");
893 <          painCave.isFatal = 0;
894 <          simError();
895 <          double smallest;
868 <          smallest = info[i].boxL[0];
869 <          if (info[i].boxL[1] <= smallest)
870 <            smallest = info[i].boxL[1];
871 <          if (info[i].boxL[2] <= smallest)
872 <            smallest = info[i].boxL[2];
873 <          theEcr = 0.5 * smallest;
890 >                  "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
891 >                  "\tOOPSE will use a default value of 15.0 angstroms"
892 >                  "\tfor the electrostaticCutoffRadius.\n");
893 >          painCave.isFatal = 0;
894 >          simError();
895 >          theEcr = 15.0;
896          }
897          else{
898            theEcr = globals->getECR();
899          }
900 <
900 >        
901          if (!globals->haveEST()){
902            sprintf(painCave.errMsg,
903 <                  "SimSetup Warning: using default value of 0.05 * the "
904 <                  "electrostaticCutoffRadius for the "
905 <                  "electrostaticSkinThickness\n");
903 >                  "SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
904 >                  "\tOOPSE will use a default value of\n"
905 >                  "\t0.05 * electrostaticCutoffRadius\n"
906 >                  "\tfor the electrostaticSkinThickness\n");
907            painCave.isFatal = 0;
908            simError();
909            theEst = 0.05 * theEcr;
# Line 888 | Line 911 | void SimSetup::finalInfoCheck(void){
911          else{
912            theEst = globals->getEST();
913          }
914 <
915 <        info[i].setEcr(theEcr, theEst);
914 >        
915 >        info[i].setDefaultEcr(theEcr, theEst);
916        }
917      }
918    }
896 –
919   #ifdef IS_MPI
920    strcpy(checkPointMsg, "post processing checks out");
921    MPIcheckPoint();
922   #endif // is_mpi
923   }
924 <
924 >  
925   void SimSetup::initSystemCoords(void){
926    int i;
927  
# Line 916 | Line 938 | void SimSetup::initSystemCoords(void){
938      if (worldRank == 0){
939   #endif //is_mpi
940        inName = globals->getInitialConfig();
919 –      double* tempDouble = new double[1000000];
941        fileInit = new InitializeFromFile(inName);
942   #ifdef IS_MPI
943      }
# Line 928 | Line 949 | void SimSetup::initSystemCoords(void){
949      delete fileInit;
950    }
951    else{
952 < #ifdef IS_MPI
932 <
952 >    
953      // no init from bass
954 <
954 >    
955      sprintf(painCave.errMsg,
956 <            "Cannot intialize a parallel simulation without an initial configuration file.\n");
957 <    painCave.isFatal;
956 >            "Cannot intialize a simulation without an initial configuration file.\n");
957 >    painCave.isFatal = 1;;
958      simError();
959 <
940 < #else
941 <
942 <    initFromBass();
943 <
944 <
945 < #endif
959 >    
960    }
961  
962   #ifdef IS_MPI
# Line 1160 | Line 1174 | void SimSetup::calcSysValues(void){
1174   }
1175  
1176   void SimSetup::calcSysValues(void){
1177 <  int i, j, k;
1177 >  int i;
1178  
1179    int* molMembershipArray;
1180  
# Line 1238 | Line 1252 | void SimSetup::mpiMolDivide(void){
1252  
1253    if (local_atoms != info[0].n_atoms){
1254      sprintf(painCave.errMsg,
1255 <            "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1256 <            " localAtom (%d) are not equal.\n",
1255 >            "SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1256 >            "\tlocalAtom (%d) are not equal.\n",
1257              info[0].n_atoms, local_atoms);
1258      painCave.isFatal = 1;
1259      simError();
# Line 1259 | Line 1273 | void SimSetup::makeSysArrays(void){
1273  
1274  
1275   void SimSetup::makeSysArrays(void){
1276 <  int i, j, k, l;
1276 >
1277 > #ifndef IS_MPI
1278 >  int k, j;
1279 > #endif // is_mpi
1280 >  int i, l;
1281  
1282    Atom** the_atoms;
1283    Molecule* the_molecules;
# Line 1342 | Line 1360 | void SimSetup::makeIntegrator(void){
1360   void SimSetup::makeIntegrator(void){
1361    int k;
1362  
1363 +  NVE<RealIntegrator>* myNVE = NULL;
1364    NVT<RealIntegrator>* myNVT = NULL;
1365 <  NPTi<RealIntegrator>* myNPTi = NULL;
1366 <  NPTf<RealIntegrator>* myNPTf = NULL;
1367 <  NPTim<RealIntegrator>* myNPTim = NULL;
1349 <  NPTfm<RealIntegrator>* myNPTfm = NULL;
1365 >  NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1366 >  NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1367 >  NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1368    
1369    for (k = 0; k < nInfo; k++){
1370      switch (ensembleCase){
1371        case NVE_ENS:
1372          if (globals->haveZconstraints()){
1373            setupZConstraint(info[k]);
1374 <          new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1374 >          myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1375          }
1376 <        else
1377 <          new NVE<RealIntegrator>(&(info[k]), the_ff);
1376 >        else{
1377 >          myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1378 >        }
1379 >        
1380 >        info->the_integrator = myNVE;
1381          break;
1382  
1383        case NVT_ENS:
# Line 1374 | Line 1395 | void SimSetup::makeIntegrator(void){
1395          else{
1396            sprintf(painCave.errMsg,
1397                    "SimSetup error: If you use the NVT\n"
1398 <                  "    ensemble, you must set tauThermostat.\n");
1398 >                  "\tensemble, you must set tauThermostat.\n");
1399            painCave.isFatal = 1;
1400            simError();
1401          }
1402 +
1403 +        info->the_integrator = myNVT;
1404          break;
1405  
1406        case NPTi_ENS:
1407          if (globals->haveZconstraints()){
1408            setupZConstraint(info[k]);
1409 <          myNPTi = new ZConstraint<NPTi<RealIntegrator> >(&(info[k]), the_ff);
1409 >          myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1410          }
1411          else
1412 <          myNPTi = new NPTi<RealIntegrator>(&(info[k]), the_ff);
1412 >          myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1413  
1414          myNPTi->setTargetTemp(globals->getTargetTemp());
1415  
# Line 1395 | Line 1418 | void SimSetup::makeIntegrator(void){
1418          else{
1419            sprintf(painCave.errMsg,
1420                    "SimSetup error: If you use a constant pressure\n"
1421 <                  "    ensemble, you must set targetPressure in the BASS file.\n");
1421 >                  "\tensemble, you must set targetPressure in the BASS file.\n");
1422            painCave.isFatal = 1;
1423            simError();
1424          }
# Line 1405 | Line 1428 | void SimSetup::makeIntegrator(void){
1428          else{
1429            sprintf(painCave.errMsg,
1430                    "SimSetup error: If you use an NPT\n"
1431 <                  "    ensemble, you must set tauThermostat.\n");
1431 >                  "\tensemble, you must set tauThermostat.\n");
1432            painCave.isFatal = 1;
1433            simError();
1434          }
# Line 1415 | Line 1438 | void SimSetup::makeIntegrator(void){
1438          else{
1439            sprintf(painCave.errMsg,
1440                    "SimSetup error: If you use an NPT\n"
1441 <                  "    ensemble, you must set tauBarostat.\n");
1441 >                  "\tensemble, you must set tauBarostat.\n");
1442            painCave.isFatal = 1;
1443            simError();
1444          }
1445 +
1446 +        info->the_integrator = myNPTi;
1447          break;
1448  
1449        case NPTf_ENS:
1450          if (globals->haveZconstraints()){
1451            setupZConstraint(info[k]);
1452 <          myNPTf = new ZConstraint<NPTf<RealIntegrator> >(&(info[k]), the_ff);
1452 >          myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1453          }
1454          else
1455 <          myNPTf = new NPTf<RealIntegrator>(&(info[k]), the_ff);
1455 >          myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1456  
1457          myNPTf->setTargetTemp(globals->getTargetTemp());
1458  
# Line 1436 | Line 1461 | void SimSetup::makeIntegrator(void){
1461          else{
1462            sprintf(painCave.errMsg,
1463                    "SimSetup error: If you use a constant pressure\n"
1464 <                  "    ensemble, you must set targetPressure in the BASS file.\n");
1464 >                  "\tensemble, you must set targetPressure in the BASS file.\n");
1465            painCave.isFatal = 1;
1466            simError();
1467          }    
1468  
1469          if (globals->haveTauThermostat())
1470            myNPTf->setTauThermostat(globals->getTauThermostat());
1471 +
1472          else{
1473            sprintf(painCave.errMsg,
1474                    "SimSetup error: If you use an NPT\n"
1475 <                  "    ensemble, you must set tauThermostat.\n");
1475 >                  "\tensemble, you must set tauThermostat.\n");
1476            painCave.isFatal = 1;
1477            simError();
1478          }
1479  
1480          if (globals->haveTauBarostat())
1481            myNPTf->setTauBarostat(globals->getTauBarostat());
1456 –        else{
1457 –          sprintf(painCave.errMsg,
1458 –                  "SimSetup error: If you use an NPT\n"
1459 –                  "    ensemble, you must set tauBarostat.\n");
1460 –          painCave.isFatal = 1;
1461 –          simError();
1462 –        }
1463 –        break;
1482  
1465 –      case NPTim_ENS:
1466 –        if (globals->haveZconstraints()){
1467 –          setupZConstraint(info[k]);
1468 –          myNPTim = new ZConstraint<NPTim<RealIntegrator> >(&(info[k]), the_ff);
1469 –        }
1470 –        else
1471 –          myNPTim = new NPTim<RealIntegrator>(&(info[k]), the_ff);
1472 –
1473 –        myNPTim->setTargetTemp(globals->getTargetTemp());
1474 –
1475 –        if (globals->haveTargetPressure())
1476 –          myNPTim->setTargetPressure(globals->getTargetPressure());
1483          else{
1484            sprintf(painCave.errMsg,
1479 –                  "SimSetup error: If you use a constant pressure\n"
1480 –                  "    ensemble, you must set targetPressure in the BASS file.\n");
1481 –          painCave.isFatal = 1;
1482 –          simError();
1483 –        }
1484 –
1485 –        if (globals->haveTauThermostat())
1486 –          myNPTim->setTauThermostat(globals->getTauThermostat());
1487 –        else{
1488 –          sprintf(painCave.errMsg,
1485                    "SimSetup error: If you use an NPT\n"
1486 <                  "    ensemble, you must set tauThermostat.\n");
1486 >                  "\tensemble, you must set tauBarostat.\n");
1487            painCave.isFatal = 1;
1488            simError();
1489          }
1490  
1491 <        if (globals->haveTauBarostat())
1496 <          myNPTim->setTauBarostat(globals->getTauBarostat());
1497 <        else{
1498 <          sprintf(painCave.errMsg,
1499 <                  "SimSetup error: If you use an NPT\n"
1500 <                  "    ensemble, you must set tauBarostat.\n");
1501 <          painCave.isFatal = 1;
1502 <          simError();
1503 <        }
1491 >        info->the_integrator = myNPTf;
1492          break;
1493  
1494 <      case NPTfm_ENS:
1494 >      case NPTxyz_ENS:
1495          if (globals->haveZconstraints()){
1496            setupZConstraint(info[k]);
1497 <          myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >(&(info[k]), the_ff);
1497 >          myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1498          }
1499          else
1500 <          myNPTfm = new NPTfm<RealIntegrator>(&(info[k]), the_ff);
1500 >          myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1501  
1502 <        myNPTfm->setTargetTemp(globals->getTargetTemp());
1502 >        myNPTxyz->setTargetTemp(globals->getTargetTemp());
1503  
1504          if (globals->haveTargetPressure())
1505 <          myNPTfm->setTargetPressure(globals->getTargetPressure());
1505 >          myNPTxyz->setTargetPressure(globals->getTargetPressure());
1506          else{
1507            sprintf(painCave.errMsg,
1508                    "SimSetup error: If you use a constant pressure\n"
1509 <                  "    ensemble, you must set targetPressure in the BASS file.\n");
1509 >                  "\tensemble, you must set targetPressure in the BASS file.\n");
1510            painCave.isFatal = 1;
1511            simError();
1512 <        }
1512 >        }    
1513  
1514          if (globals->haveTauThermostat())
1515 <          myNPTfm->setTauThermostat(globals->getTauThermostat());
1515 >          myNPTxyz->setTauThermostat(globals->getTauThermostat());
1516          else{
1517            sprintf(painCave.errMsg,
1518                    "SimSetup error: If you use an NPT\n"
1519 <                  "    ensemble, you must set tauThermostat.\n");
1519 >                  "\tensemble, you must set tauThermostat.\n");
1520            painCave.isFatal = 1;
1521            simError();
1522          }
1523  
1524          if (globals->haveTauBarostat())
1525 <          myNPTfm->setTauBarostat(globals->getTauBarostat());
1525 >          myNPTxyz->setTauBarostat(globals->getTauBarostat());
1526          else{
1527            sprintf(painCave.errMsg,
1528                    "SimSetup error: If you use an NPT\n"
1529 <                  "    ensemble, you must set tauBarostat.\n");
1529 >                  "\tensemble, you must set tauBarostat.\n");
1530            painCave.isFatal = 1;
1531            simError();
1532          }
1533 +
1534 +        info->the_integrator = myNPTxyz;
1535          break;
1536  
1537        default:
# Line 1589 | Line 1579 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1579    }
1580    else{
1581      sprintf(painCave.errMsg,
1582 <            "ZConstraint error: If you use an ZConstraint\n"
1583 <            " , you must set sample time.\n");
1582 >            "ZConstraint error: If you use a ZConstraint,\n"
1583 >            "\tyou must set zconsTime.\n");
1584      painCave.isFatal = 1;
1585      simError();
1586    }
# Line 1605 | Line 1595 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1595    else{
1596      double defaultZConsTol = 0.01;
1597      sprintf(painCave.errMsg,
1598 <            "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1599 <            " , default value %f is used.\n",
1598 >            "ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1599 >            "\tOOPSE will use a default value of %f.\n"
1600 >            "\tTo set the tolerance, use the zconsTol variable.\n",
1601              defaultZConsTol);
1602      painCave.isFatal = 0;
1603      simError();      
# Line 1615 | Line 1606 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1606    }
1607    theInfo.addProperty(zconsTol);
1608  
1609 <  //set Force Substraction Policy
1609 >  //set Force Subtraction Policy
1610    StringData* zconsForcePolicy = new StringData();
1611    zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1612  
# Line 1624 | Line 1615 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1615    }
1616    else{
1617      sprintf(painCave.errMsg,
1618 <            "ZConstraint Warning: User does not set force substraction policy, "
1619 <            "PolicyByMass is used\n");
1618 >            "ZConstraint Warning: No force subtraction policy was set.\n"
1619 >            "\tOOPSE will use PolicyByMass.\n"
1620 >            "\tTo set the policy, use the zconsForcePolicy variable.\n");
1621      painCave.isFatal = 0;
1622      simError();
1623      zconsForcePolicy->setData("BYMASS");
# Line 1669 | Line 1661 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1661    //check the uniqueness of index  
1662    if(!zconsParaData->isIndexUnique()){
1663      sprintf(painCave.errMsg,
1664 <            "ZConstraint Error: molIndex is not unique\n");
1664 >            "ZConstraint Error: molIndex is not unique!\n");
1665      painCave.isFatal = 1;
1666      simError();
1667    }

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