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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 814 by mmeineke, Thu Oct 23 19:57:25 2003 UTC

# Line 4 | Line 4
4   #include <cmath>
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
# Line 92 | Line 91 | void SimSetup::createSim(void){
91   #endif // is_mpi
92  
93   void SimSetup::createSim(void){
95 –  int i, j, k, globalAtomIndex;
94  
95    // gather all of the information from the Bass file
96  
# Line 110 | Line 108 | void SimSetup::createSim(void){
108  
109    if (!isInfoArray){
110      initSystemCoords();
111 +
112 +    if( !(globals->getUseInitTime()) )
113 +      info[0].currentTime = 0.0;
114    }  
115  
116    // make the output filenames
# Line 131 | Line 132 | void SimSetup::makeMolecules(void){
132  
133  
134   void SimSetup::makeMolecules(void){
135 <  int k, l;
135 >  int k;
136    int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
137    molInit molInfo;
138    DirectionalAtom* dAtom;
# Line 553 | Line 554 | void SimSetup::gatherInfo(void){
554  
555  
556   void SimSetup::gatherInfo(void){
557 <  int i, j, k;
557 >  int i;
558  
559    ensembleCase = -1;
560    ffCase = -1;
# Line 604 | Line 605 | void SimSetup::gatherInfo(void){
605    else if (!strcasecmp(ensemble, "NPTf")){
606      ensembleCase = NPTf_ENS;
607    }
608 <  else if (!strcasecmp(ensemble, "NPTim")){
609 <    ensembleCase = NPTim_ENS;
609 <  }
610 <  else if (!strcasecmp(ensemble, "NPTfm")){
611 <    ensembleCase = NPTfm_ENS;
608 >  else if (!strcasecmp(ensemble, "NPTxyz")){
609 >    ensembleCase = NPTxyz_ENS;
610    }
611    else{
612      sprintf(painCave.errMsg,
# Line 686 | Line 684 | void SimSetup::gatherInfo(void){
684  
685      if (globals->haveThermalTime()){
686        info[i].thermalTime = globals->getThermalTime();
687 +    }
688 +
689 +    info[i].resetIntegrator = 0;
690 +    if( globals->haveResetTime() ){
691 +      info[i].resetTime = globals->getResetTime();
692 +      info[i].resetIntegrator = 1;
693      }
694  
695      // check for the temperature set flag
# Line 916 | Line 920 | void SimSetup::initSystemCoords(void){
920      if (worldRank == 0){
921   #endif //is_mpi
922        inName = globals->getInitialConfig();
919 –      double* tempDouble = new double[1000000];
923        fileInit = new InitializeFromFile(inName);
924   #ifdef IS_MPI
925      }
# Line 934 | Line 937 | void SimSetup::initSystemCoords(void){
937  
938      sprintf(painCave.errMsg,
939              "Cannot intialize a parallel simulation without an initial configuration file.\n");
940 <    painCave.isFatal;
940 >    painCave.isFatal = 1;;
941      simError();
942  
943   #else
# Line 1160 | Line 1163 | void SimSetup::calcSysValues(void){
1163   }
1164  
1165   void SimSetup::calcSysValues(void){
1166 <  int i, j, k;
1166 >  int i;
1167  
1168    int* molMembershipArray;
1169  
# Line 1259 | Line 1262 | void SimSetup::makeSysArrays(void){
1262  
1263  
1264   void SimSetup::makeSysArrays(void){
1265 <  int i, j, k, l;
1265 >
1266 > #ifndef IS_MPI
1267 >  int k, j;
1268 > #endif // is_mpi
1269 >  int i, l;
1270  
1271    Atom** the_atoms;
1272    Molecule* the_molecules;
# Line 1342 | Line 1349 | void SimSetup::makeIntegrator(void){
1349   void SimSetup::makeIntegrator(void){
1350    int k;
1351  
1352 +  NVE<RealIntegrator>* myNVE = NULL;
1353    NVT<RealIntegrator>* myNVT = NULL;
1354 <  NPTi<RealIntegrator>* myNPTi = NULL;
1355 <  NPTf<RealIntegrator>* myNPTf = NULL;
1356 <  NPTim<RealIntegrator>* myNPTim = NULL;
1349 <  NPTfm<RealIntegrator>* myNPTfm = NULL;
1354 >  NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1355 >  NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1356 >  NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1357    
1358    for (k = 0; k < nInfo; k++){
1359      switch (ensembleCase){
1360        case NVE_ENS:
1361          if (globals->haveZconstraints()){
1362            setupZConstraint(info[k]);
1363 <          new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1363 >          myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1364          }
1365 <        else
1366 <          new NVE<RealIntegrator>(&(info[k]), the_ff);
1365 >        else{
1366 >          myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1367 >        }
1368 >        
1369 >        info->the_integrator = myNVE;
1370          break;
1371  
1372        case NVT_ENS:
# Line 1378 | Line 1388 | void SimSetup::makeIntegrator(void){
1388            painCave.isFatal = 1;
1389            simError();
1390          }
1391 +
1392 +        info->the_integrator = myNVT;
1393          break;
1394  
1395        case NPTi_ENS:
1396          if (globals->haveZconstraints()){
1397            setupZConstraint(info[k]);
1398 <          myNPTi = new ZConstraint<NPTi<RealIntegrator> >(&(info[k]), the_ff);
1398 >          myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1399          }
1400          else
1401 <          myNPTi = new NPTi<RealIntegrator>(&(info[k]), the_ff);
1401 >          myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1402  
1403          myNPTi->setTargetTemp(globals->getTargetTemp());
1404  
# Line 1419 | Line 1431 | void SimSetup::makeIntegrator(void){
1431            painCave.isFatal = 1;
1432            simError();
1433          }
1434 +
1435 +        info->the_integrator = myNPTi;
1436          break;
1437  
1438        case NPTf_ENS:
1439          if (globals->haveZconstraints()){
1440            setupZConstraint(info[k]);
1441 <          myNPTf = new ZConstraint<NPTf<RealIntegrator> >(&(info[k]), the_ff);
1441 >          myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1442          }
1443          else
1444 <          myNPTf = new NPTf<RealIntegrator>(&(info[k]), the_ff);
1444 >          myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1445  
1446          myNPTf->setTargetTemp(globals->getTargetTemp());
1447  
# Line 1460 | Line 1474 | void SimSetup::makeIntegrator(void){
1474            painCave.isFatal = 1;
1475            simError();
1476          }
1463 –        break;
1477  
1478 <      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());
1477 <        else{
1478 <          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,
1489 <                  "SimSetup error: If you use an NPT\n"
1490 <                  "    ensemble, you must set tauThermostat.\n");
1491 <          painCave.isFatal = 1;
1492 <          simError();
1493 <        }
1494 <
1495 <        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 <        }
1478 >        info->the_integrator = myNPTf;
1479          break;
1480  
1481 <      case NPTfm_ENS:
1481 >      case NPTxyz_ENS:
1482          if (globals->haveZconstraints()){
1483            setupZConstraint(info[k]);
1484 <          myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >(&(info[k]), the_ff);
1484 >          myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1485          }
1486          else
1487 <          myNPTfm = new NPTfm<RealIntegrator>(&(info[k]), the_ff);
1487 >          myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1488  
1489 <        myNPTfm->setTargetTemp(globals->getTargetTemp());
1489 >        myNPTxyz->setTargetTemp(globals->getTargetTemp());
1490  
1491          if (globals->haveTargetPressure())
1492 <          myNPTfm->setTargetPressure(globals->getTargetPressure());
1492 >          myNPTxyz->setTargetPressure(globals->getTargetPressure());
1493          else{
1494            sprintf(painCave.errMsg,
1495                    "SimSetup error: If you use a constant pressure\n"
1496                    "    ensemble, you must set targetPressure in the BASS file.\n");
1497            painCave.isFatal = 1;
1498            simError();
1499 <        }
1499 >        }    
1500  
1501          if (globals->haveTauThermostat())
1502 <          myNPTfm->setTauThermostat(globals->getTauThermostat());
1502 >          myNPTxyz->setTauThermostat(globals->getTauThermostat());
1503          else{
1504            sprintf(painCave.errMsg,
1505                    "SimSetup error: If you use an NPT\n"
# Line 1534 | Line 1509 | void SimSetup::makeIntegrator(void){
1509          }
1510  
1511          if (globals->haveTauBarostat())
1512 <          myNPTfm->setTauBarostat(globals->getTauBarostat());
1512 >          myNPTxyz->setTauBarostat(globals->getTauBarostat());
1513          else{
1514            sprintf(painCave.errMsg,
1515                    "SimSetup error: If you use an NPT\n"
# Line 1542 | Line 1517 | void SimSetup::makeIntegrator(void){
1517            painCave.isFatal = 1;
1518            simError();
1519          }
1520 +
1521 +        info->the_integrator = myNPTxyz;
1522          break;
1523  
1524        default:
# Line 1615 | Line 1592 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1592    }
1593    theInfo.addProperty(zconsTol);
1594  
1595 <  //set Force Substraction Policy
1595 >  //set Force Subtraction Policy
1596    StringData* zconsForcePolicy = new StringData();
1597    zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1598  
# Line 1624 | Line 1601 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1601    }
1602    else{
1603      sprintf(painCave.errMsg,
1604 <            "ZConstraint Warning: User does not set force substraction policy, "
1604 >            "ZConstraint Warning: User does not set force Subtraction policy, "
1605              "PolicyByMass is used\n");
1606      painCave.isFatal = 0;
1607      simError();

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