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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 782 by mmeineke, Tue Sep 23 20:34:31 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 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 52 | 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 90 | Line 118 | void SimSetup::createSim(void){
118   #endif // is_mpi
119  
120   void SimSetup::createSim(void){
93 –  int i, j, k, globalAtomIndex;
121  
122    // gather all of the information from the Bass file
123  
# Line 106 | 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 129 | 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 551 | 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 602 | Line 632 | void SimSetup::gatherInfo(void){
632    else if (!strcasecmp(ensemble, "NPTf")){
633      ensembleCase = NPTf_ENS;
634    }
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 637 | 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 657 | 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  
737    for (i = 0; i < nInfo; i++){
# Line 687 | Line 761 | void SimSetup::gatherInfo(void){
761      }
762  
763      // check for the temperature set flag
764 <
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();
699 <      boxVector[1] = globals->getBox();
700 <      boxVector[2] = globals->getBox();
701 <
702 <      info[i].setBox(boxVector);
703 <    }
704 <    else if (globals->haveDensity()){
705 <      double vol;
706 <      vol = (double) tot_nmol / globals->getDensity();
707 <      boxVector[0] = pow(vol, (1.0 / 3.0));
708 <      boxVector[1] = boxVector[0];
709 <      boxVector[2] = boxVector[0];
710 <
711 <      info[i].setBox(boxVector);
712 <    }
713 <    else{
714 <      if (!globals->haveBoxX()){
715 <        sprintf(painCave.errMsg,
716 <                "SimSetup error, no periodic BoxX size given.\n");
717 <        painCave.isFatal = 1;
718 <        simError();
719 <      }
720 <      boxVector[0] = globals->getBoxX();
721 <
722 <      if (!globals->haveBoxY()){
723 <        sprintf(painCave.errMsg,
724 <                "SimSetup error, no periodic BoxY size given.\n");
725 <        painCave.isFatal = 1;
726 <        simError();
727 <      }
728 <      boxVector[1] = globals->getBoxY();
729 <
730 <      if (!globals->haveBoxZ()){
731 <        sprintf(painCave.errMsg,
732 <                "SimSetup error, no periodic BoxZ size given.\n");
733 <        painCave.isFatal = 1;
734 <        simError();
735 <      }
736 <      boxVector[2] = globals->getBoxZ();
737 <
738 <      info[i].setBox(boxVector);
739 <    }
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 813 | 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;
822 <        smallest = info[i].boxL[0];
823 <        if (info[i].boxL[1] <= smallest)
824 <          smallest = info[i].boxL[1];
825 <        if (info[i].boxL[2] <= smallest)
826 <          smallest = info[i].boxL[2];
827 <        theEcr = 0.5 * smallest;
854 >        theEcr = 15.0;
855        }
856        else{
857          theEcr = globals->getECR();
# Line 832 | 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 842 | 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 857 | 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;
866 <          smallest = info[i].boxL[0];
867 <          if (info[i].boxL[1] <= smallest)
868 <            smallest = info[i].boxL[1];
869 <          if (info[i].boxL[2] <= smallest)
870 <            smallest = info[i].boxL[2];
871 <          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 886 | 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    }
894 –
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 914 | Line 938 | void SimSetup::initSystemCoords(void){
938      if (worldRank == 0){
939   #endif //is_mpi
940        inName = globals->getInitialConfig();
917 –      double* tempDouble = new double[1000000];
941        fileInit = new InitializeFromFile(inName);
942   #ifdef IS_MPI
943      }
# Line 926 | Line 949 | void SimSetup::initSystemCoords(void){
949      delete fileInit;
950    }
951    else{
952 < #ifdef IS_MPI
930 <
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 <
938 < #else
939 <
940 <    initFromBass();
941 <
942 <
943 < #endif
959 >    
960    }
961  
962   #ifdef IS_MPI
# Line 1158 | 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 1236 | 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 1257 | 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 1344 | Line 1364 | void SimSetup::makeIntegrator(void){
1364    NVT<RealIntegrator>* myNVT = 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){
# 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          }
# Line 1397 | 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 1407 | 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 1417 | 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          }
# Line 1440 | 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());
1482 +
1483          else{
1484            sprintf(painCave.errMsg,
1485                    "SimSetup error: If you use an NPT\n"
1486 <                  "    ensemble, you must set tauBarostat.\n");
1486 >                  "\tensemble, you must set tauBarostat.\n");
1487            painCave.isFatal = 1;
1488            simError();
1489          }
# Line 1468 | Line 1491 | void SimSetup::makeIntegrator(void){
1491          info->the_integrator = myNPTf;
1492          break;
1493  
1494 +      case NPTxyz_ENS:
1495 +        if (globals->haveZconstraints()){
1496 +          setupZConstraint(info[k]);
1497 +          myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1498 +        }
1499 +        else
1500 +          myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1501 +
1502 +        myNPTxyz->setTargetTemp(globals->getTargetTemp());
1503 +
1504 +        if (globals->haveTargetPressure())
1505 +          myNPTxyz->setTargetPressure(globals->getTargetPressure());
1506 +        else{
1507 +          sprintf(painCave.errMsg,
1508 +                  "SimSetup error: If you use a constant pressure\n"
1509 +                  "\tensemble, you must set targetPressure in the BASS file.\n");
1510 +          painCave.isFatal = 1;
1511 +          simError();
1512 +        }    
1513 +
1514 +        if (globals->haveTauThermostat())
1515 +          myNPTxyz->setTauThermostat(globals->getTauThermostat());
1516 +        else{
1517 +          sprintf(painCave.errMsg,
1518 +                  "SimSetup error: If you use an NPT\n"
1519 +                  "\tensemble, you must set tauThermostat.\n");
1520 +          painCave.isFatal = 1;
1521 +          simError();
1522 +        }
1523 +
1524 +        if (globals->haveTauBarostat())
1525 +          myNPTxyz->setTauBarostat(globals->getTauBarostat());
1526 +        else{
1527 +          sprintf(painCave.errMsg,
1528 +                  "SimSetup error: If you use an NPT\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:
1538          sprintf(painCave.errMsg,
1539                  "SimSetup Error. Unrecognized ensemble in case statement.\n");
# Line 1513 | 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 1529 | 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 1548 | Line 1615 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1615    }
1616    else{
1617      sprintf(painCave.errMsg,
1618 <            "ZConstraint Warning: User does not set force Subtraction 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 1593 | 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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