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root/group/branches/no-template-branch/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 733 by tim, Wed Aug 27 19:23:29 2003 UTC vs.
Revision 829 by gezelter, Tue Oct 28 16:03:37 2003 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
# Line 32 | Line 31 | SimSetup::SimSetup(){
31   using namespace std;
32  
33   SimSetup::SimSetup(){
34 +  
35 +  initSuspend = false;
36    isInfoArray = 0;
37    nInfo = 1;
38  
# Line 54 | Line 55 | void SimSetup::setSimInfo(SimInfo* the_info, int theNi
55    info = the_info;
56    nInfo = theNinfo;
57    isInfoArray = 1;
58 +  initSuspend = true;
59   }
60  
61  
# Line 92 | Line 94 | void SimSetup::createSim(void){
94   #endif // is_mpi
95  
96   void SimSetup::createSim(void){
95 –  int i, j, k, globalAtomIndex;
97  
98    // gather all of the information from the Bass file
99  
# Line 108 | Line 109 | void SimSetup::createSim(void){
109  
110    // initialize the system coordinates
111  
112 <  if (!isInfoArray){
112 >  if ( !initSuspend ){
113      initSystemCoords();
114 +
115 +    if( !(globals->getUseInitTime()) )
116 +      info[0].currentTime = 0.0;
117    }  
118  
119    // make the output filenames
# Line 131 | Line 135 | void SimSetup::makeMolecules(void){
135  
136  
137   void SimSetup::makeMolecules(void){
138 <  int k, l;
138 >  int k;
139    int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
140    molInit molInfo;
141    DirectionalAtom* dAtom;
# Line 553 | Line 557 | void SimSetup::gatherInfo(void){
557  
558  
559   void SimSetup::gatherInfo(void){
560 <  int i, j, k;
560 >  int i;
561  
562    ensembleCase = -1;
563    ffCase = -1;
# Line 604 | Line 608 | void SimSetup::gatherInfo(void){
608    else if (!strcasecmp(ensemble, "NPTf")){
609      ensembleCase = NPTf_ENS;
610    }
611 <  else if (!strcasecmp(ensemble, "NPTim")){
612 <    ensembleCase = NPTim_ENS;
611 >  else if (!strcasecmp(ensemble, "NPTxyz")){
612 >    ensembleCase = NPTxyz_ENS;
613    }
610 –  else if (!strcasecmp(ensemble, "NPTfm")){
611 –    ensembleCase = NPTfm_ENS;
612 –  }
614    else{
615      sprintf(painCave.errMsg,
616              "SimSetup Warning. Unrecognized Ensemble -> %s, "
# Line 686 | Line 687 | void SimSetup::gatherInfo(void){
687  
688      if (globals->haveThermalTime()){
689        info[i].thermalTime = globals->getThermalTime();
690 +    }
691 +
692 +    info[i].resetIntegrator = 0;
693 +    if( globals->haveResetTime() ){
694 +      info[i].resetTime = globals->getResetTime();
695 +      info[i].resetIntegrator = 1;
696      }
697  
698      // check for the temperature set flag
# Line 916 | Line 923 | void SimSetup::initSystemCoords(void){
923      if (worldRank == 0){
924   #endif //is_mpi
925        inName = globals->getInitialConfig();
919 –      double* tempDouble = new double[1000000];
926        fileInit = new InitializeFromFile(inName);
927   #ifdef IS_MPI
928      }
# Line 934 | Line 940 | void SimSetup::initSystemCoords(void){
940  
941      sprintf(painCave.errMsg,
942              "Cannot intialize a parallel simulation without an initial configuration file.\n");
943 <    painCave.isFatal;
943 >    painCave.isFatal = 1;;
944      simError();
945  
946   #else
# Line 1160 | Line 1166 | void SimSetup::calcSysValues(void){
1166   }
1167  
1168   void SimSetup::calcSysValues(void){
1169 <  int i, j, k;
1169 >  int i;
1170  
1171    int* molMembershipArray;
1172  
# Line 1259 | Line 1265 | void SimSetup::makeSysArrays(void){
1265  
1266  
1267   void SimSetup::makeSysArrays(void){
1268 <  int i, j, k, l;
1268 >
1269 > #ifndef IS_MPI
1270 >  int k, j;
1271 > #endif // is_mpi
1272 >  int i, l;
1273  
1274    Atom** the_atoms;
1275    Molecule* the_molecules;
# Line 1342 | Line 1352 | void SimSetup::makeIntegrator(void){
1352   void SimSetup::makeIntegrator(void){
1353    int k;
1354  
1355 +  NVE<RealIntegrator>* myNVE = NULL;
1356    NVT<RealIntegrator>* myNVT = NULL;
1357 <  NPTi<RealIntegrator>* myNPTi = NULL;
1358 <  NPTf<RealIntegrator>* myNPTf = NULL;
1359 <  NPTim<RealIntegrator>* myNPTim = NULL;
1349 <  NPTfm<RealIntegrator>* myNPTfm = NULL;
1357 >  NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1358 >  NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1359 >  NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1360    
1361    for (k = 0; k < nInfo; k++){
1362      switch (ensembleCase){
1363        case NVE_ENS:
1364          if (globals->haveZconstraints()){
1365            setupZConstraint(info[k]);
1366 <          new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1366 >          myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1367          }
1368 <        else
1369 <          new NVE<RealIntegrator>(&(info[k]), the_ff);
1368 >        else{
1369 >          myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1370 >        }
1371 >        
1372 >        info->the_integrator = myNVE;
1373          break;
1374  
1375        case NVT_ENS:
# Line 1378 | Line 1391 | void SimSetup::makeIntegrator(void){
1391            painCave.isFatal = 1;
1392            simError();
1393          }
1394 +
1395 +        info->the_integrator = myNVT;
1396          break;
1397  
1398        case NPTi_ENS:
1399          if (globals->haveZconstraints()){
1400            setupZConstraint(info[k]);
1401 <          myNPTi = new ZConstraint<NPTi<RealIntegrator> >(&(info[k]), the_ff);
1401 >          myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1402          }
1403          else
1404 <          myNPTi = new NPTi<RealIntegrator>(&(info[k]), the_ff);
1404 >          myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1405  
1406          myNPTi->setTargetTemp(globals->getTargetTemp());
1407  
# Line 1419 | Line 1434 | void SimSetup::makeIntegrator(void){
1434            painCave.isFatal = 1;
1435            simError();
1436          }
1437 +
1438 +        info->the_integrator = myNPTi;
1439          break;
1440  
1441        case NPTf_ENS:
1442          if (globals->haveZconstraints()){
1443            setupZConstraint(info[k]);
1444 <          myNPTf = new ZConstraint<NPTf<RealIntegrator> >(&(info[k]), the_ff);
1444 >          myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1445          }
1446          else
1447 <          myNPTf = new NPTf<RealIntegrator>(&(info[k]), the_ff);
1447 >          myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1448  
1449          myNPTf->setTargetTemp(globals->getTargetTemp());
1450  
# Line 1457 | Line 1474 | void SimSetup::makeIntegrator(void){
1474            sprintf(painCave.errMsg,
1475                    "SimSetup error: If you use an NPT\n"
1476                    "    ensemble, you must set tauBarostat.\n");
1460 –          painCave.isFatal = 1;
1461 –          simError();
1462 –        }
1463 –        break;
1464 –
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());
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");
1477            painCave.isFatal = 1;
1478            simError();
1479          }
1480  
1481 <        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 <        }
1481 >        info->the_integrator = myNPTf;
1482          break;
1483  
1484 <      case NPTfm_ENS:
1484 >      case NPTxyz_ENS:
1485          if (globals->haveZconstraints()){
1486            setupZConstraint(info[k]);
1487 <          myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >(&(info[k]), the_ff);
1487 >          myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1488          }
1489          else
1490 <          myNPTfm = new NPTfm<RealIntegrator>(&(info[k]), the_ff);
1490 >          myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1491  
1492 <        myNPTfm->setTargetTemp(globals->getTargetTemp());
1492 >        myNPTxyz->setTargetTemp(globals->getTargetTemp());
1493  
1494          if (globals->haveTargetPressure())
1495 <          myNPTfm->setTargetPressure(globals->getTargetPressure());
1495 >          myNPTxyz->setTargetPressure(globals->getTargetPressure());
1496          else{
1497            sprintf(painCave.errMsg,
1498                    "SimSetup error: If you use a constant pressure\n"
1499                    "    ensemble, you must set targetPressure in the BASS file.\n");
1500            painCave.isFatal = 1;
1501            simError();
1502 <        }
1502 >        }    
1503  
1504          if (globals->haveTauThermostat())
1505 <          myNPTfm->setTauThermostat(globals->getTauThermostat());
1505 >          myNPTxyz->setTauThermostat(globals->getTauThermostat());
1506          else{
1507            sprintf(painCave.errMsg,
1508                    "SimSetup error: If you use an NPT\n"
# Line 1534 | Line 1512 | void SimSetup::makeIntegrator(void){
1512          }
1513  
1514          if (globals->haveTauBarostat())
1515 <          myNPTfm->setTauBarostat(globals->getTauBarostat());
1515 >          myNPTxyz->setTauBarostat(globals->getTauBarostat());
1516          else{
1517            sprintf(painCave.errMsg,
1518                    "SimSetup error: If you use an NPT\n"
# Line 1542 | Line 1520 | void SimSetup::makeIntegrator(void){
1520            painCave.isFatal = 1;
1521            simError();
1522          }
1523 +
1524 +        info->the_integrator = myNPTxyz;
1525          break;
1526  
1527        default:
# Line 1615 | Line 1595 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1595    }
1596    theInfo.addProperty(zconsTol);
1597  
1598 <  //set Force Substraction Policy
1598 >  //set Force Subtraction Policy
1599    StringData* zconsForcePolicy = new StringData();
1600    zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1601  
# Line 1624 | Line 1604 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1604    }
1605    else{
1606      sprintf(painCave.errMsg,
1607 <            "ZConstraint Warning: User does not set force substraction policy, "
1608 <            "average force substraction policy is used\n");
1607 >            "ZConstraint Warning: User does not set force Subtraction policy, "
1608 >            "PolicyByMass is used\n");
1609      painCave.isFatal = 0;
1610      simError();
1611 <    zconsForcePolicy->setData("BYNUMBER");
1611 >    zconsForcePolicy->setData("BYMASS");
1612    }
1613  
1614    theInfo.addProperty(zconsForcePolicy);
# Line 1666 | Line 1646 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1646      zconsParaData->addItem(tempParaItem);
1647    }
1648  
1649 +  //check the uniqueness of index  
1650 +  if(!zconsParaData->isIndexUnique()){
1651 +    sprintf(painCave.errMsg,
1652 +            "ZConstraint Error: molIndex is not unique\n");
1653 +    painCave.isFatal = 1;
1654 +    simError();
1655 +  }
1656 +
1657    //sort the parameters by index of molecules
1658    zconsParaData->sortByIndex();
1659 <
1659 >  
1660    //push data into siminfo, therefore, we can retrieve later
1661    theInfo.addProperty(zconsParaData);
1662   }

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