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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 845 by gezelter, Thu Oct 30 18:59:20 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 102 | Line 103 | void SimSetup::createSim(void){
103  
104    sysObjectsCreation();
105  
105 –  // check on the post processing info
106 –
107 –  finalInfoCheck();
108 –
106    // initialize the system coordinates
107  
108 <  if (!isInfoArray){
108 >  if ( !initSuspend ){
109      initSystemCoords();
110 +
111 +    if( !(globals->getUseInitTime()) )
112 +      info[0].currentTime = 0.0;
113    }  
114  
115 +  // check on the post processing info
116 +
117 +  finalInfoCheck();
118 +
119    // make the output filenames
120  
121    makeOutNames();
# 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;
609 <  }
610 <  else if (!strcasecmp(ensemble, "NPTfm")){
611 <    ensembleCase = NPTfm_ENS;
611 >  else if (!strcasecmp(ensemble, "NPTxyz")){
612 >    ensembleCase = NPTxyz_ENS;
613    }
614    else{
615      sprintf(painCave.errMsg,
# Line 688 | Line 689 | void SimSetup::gatherInfo(void){
689        info[i].thermalTime = globals->getThermalTime();
690      }
691  
692 <    // check for the temperature set flag
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
699 +    
700      if (globals->haveTempSet())
701        info[i].setTemp = globals->getTempSet();
702 <
696 <    // get some of the tricky things that may still be in the globals
697 <
698 <    double boxVector[3];
699 <    if (globals->haveBox()){
700 <      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 <    }
702 >    
703    }
704 <
704 >  
705    //setup seed for random number generator
706    int seedValue;
707  
# Line 844 | Line 805 | void SimSetup::finalInfoCheck(void){
805          theEst = globals->getEST();
806        }
807  
808 <      info[i].setEcr(theEcr, theEst);
808 >      info[i].setDefaultEcr(theEcr, theEst);
809  
810        if (!globals->haveDielectric()){
811          sprintf(painCave.errMsg,
# Line 889 | Line 850 | void SimSetup::finalInfoCheck(void){
850            theEst = globals->getEST();
851          }
852  
853 <        info[i].setEcr(theEcr, theEst);
853 >        info[i].setDefaultEcr(theEcr, theEst);
854        }
855      }
856 +    info[i].checkCutOffs();
857    }
858  
859   #ifdef IS_MPI
# Line 916 | Line 878 | void SimSetup::initSystemCoords(void){
878      if (worldRank == 0){
879   #endif //is_mpi
880        inName = globals->getInitialConfig();
919 –      double* tempDouble = new double[1000000];
881        fileInit = new InitializeFromFile(inName);
882   #ifdef IS_MPI
883      }
# Line 934 | Line 895 | void SimSetup::initSystemCoords(void){
895  
896      sprintf(painCave.errMsg,
897              "Cannot intialize a parallel simulation without an initial configuration file.\n");
898 <    painCave.isFatal;
898 >    painCave.isFatal = 1;;
899      simError();
900  
901   #else
# Line 1160 | Line 1121 | void SimSetup::calcSysValues(void){
1121   }
1122  
1123   void SimSetup::calcSysValues(void){
1124 <  int i, j, k;
1124 >  int i;
1125  
1126    int* molMembershipArray;
1127  
# Line 1259 | Line 1220 | void SimSetup::makeSysArrays(void){
1220  
1221  
1222   void SimSetup::makeSysArrays(void){
1223 <  int i, j, k, l;
1223 >
1224 > #ifndef IS_MPI
1225 >  int k, j;
1226 > #endif // is_mpi
1227 >  int i, l;
1228  
1229    Atom** the_atoms;
1230    Molecule* the_molecules;
# Line 1342 | Line 1307 | void SimSetup::makeIntegrator(void){
1307   void SimSetup::makeIntegrator(void){
1308    int k;
1309  
1310 +  NVE<RealIntegrator>* myNVE = NULL;
1311    NVT<RealIntegrator>* myNVT = NULL;
1312 <  NPTi<RealIntegrator>* myNPTi = NULL;
1313 <  NPTf<RealIntegrator>* myNPTf = NULL;
1314 <  NPTim<RealIntegrator>* myNPTim = NULL;
1349 <  NPTfm<RealIntegrator>* myNPTfm = NULL;
1312 >  NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1313 >  NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1314 >  NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1315    
1316    for (k = 0; k < nInfo; k++){
1317      switch (ensembleCase){
1318        case NVE_ENS:
1319          if (globals->haveZconstraints()){
1320            setupZConstraint(info[k]);
1321 <          new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1321 >          myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1322          }
1323 <        else
1324 <          new NVE<RealIntegrator>(&(info[k]), the_ff);
1323 >        else{
1324 >          myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1325 >        }
1326 >        
1327 >        info->the_integrator = myNVE;
1328          break;
1329  
1330        case NVT_ENS:
# Line 1378 | Line 1346 | void SimSetup::makeIntegrator(void){
1346            painCave.isFatal = 1;
1347            simError();
1348          }
1349 +
1350 +        info->the_integrator = myNVT;
1351          break;
1352  
1353        case NPTi_ENS:
1354          if (globals->haveZconstraints()){
1355            setupZConstraint(info[k]);
1356 <          myNPTi = new ZConstraint<NPTi<RealIntegrator> >(&(info[k]), the_ff);
1356 >          myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1357          }
1358          else
1359 <          myNPTi = new NPTi<RealIntegrator>(&(info[k]), the_ff);
1359 >          myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1360  
1361          myNPTi->setTargetTemp(globals->getTargetTemp());
1362  
# Line 1419 | Line 1389 | void SimSetup::makeIntegrator(void){
1389            painCave.isFatal = 1;
1390            simError();
1391          }
1392 +
1393 +        info->the_integrator = myNPTi;
1394          break;
1395  
1396        case NPTf_ENS:
1397          if (globals->haveZconstraints()){
1398            setupZConstraint(info[k]);
1399 <          myNPTf = new ZConstraint<NPTf<RealIntegrator> >(&(info[k]), the_ff);
1399 >          myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1400          }
1401          else
1402 <          myNPTf = new NPTf<RealIntegrator>(&(info[k]), the_ff);
1402 >          myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1403  
1404          myNPTf->setTargetTemp(globals->getTargetTemp());
1405  
# Line 1443 | Line 1415 | void SimSetup::makeIntegrator(void){
1415  
1416          if (globals->haveTauThermostat())
1417            myNPTf->setTauThermostat(globals->getTauThermostat());
1418 +
1419          else{
1420            sprintf(painCave.errMsg,
1421                    "SimSetup error: If you use an NPT\n"
# Line 1453 | Line 1426 | void SimSetup::makeIntegrator(void){
1426  
1427          if (globals->haveTauBarostat())
1428            myNPTf->setTauBarostat(globals->getTauBarostat());
1429 +
1430          else{
1431            sprintf(painCave.errMsg,
1432                    "SimSetup error: If you use an NPT\n"
# Line 1460 | Line 1434 | void SimSetup::makeIntegrator(void){
1434            painCave.isFatal = 1;
1435            simError();
1436          }
1437 +
1438 +        info->the_integrator = myNPTf;
1439          break;
1440  
1441 <      case NPTim_ENS:
1441 >      case NPTxyz_ENS:
1442          if (globals->haveZconstraints()){
1443            setupZConstraint(info[k]);
1444 <          myNPTim = new ZConstraint<NPTim<RealIntegrator> >(&(info[k]), the_ff);
1444 >          myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1445          }
1446          else
1447 <          myNPTim = new NPTim<RealIntegrator>(&(info[k]), the_ff);
1447 >          myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1448  
1449 <        myNPTim->setTargetTemp(globals->getTargetTemp());
1449 >        myNPTxyz->setTargetTemp(globals->getTargetTemp());
1450  
1451          if (globals->haveTargetPressure())
1452 <          myNPTim->setTargetPressure(globals->getTargetPressure());
1452 >          myNPTxyz->setTargetPressure(globals->getTargetPressure());
1453          else{
1454            sprintf(painCave.errMsg,
1455                    "SimSetup error: If you use a constant pressure\n"
1456                    "    ensemble, you must set targetPressure in the BASS file.\n");
1457            painCave.isFatal = 1;
1458            simError();
1459 <        }
1459 >        }    
1460  
1461          if (globals->haveTauThermostat())
1462 <          myNPTim->setTauThermostat(globals->getTauThermostat());
1462 >          myNPTxyz->setTauThermostat(globals->getTauThermostat());
1463          else{
1464            sprintf(painCave.errMsg,
1465                    "SimSetup error: If you use an NPT\n"
# Line 1493 | Line 1469 | void SimSetup::makeIntegrator(void){
1469          }
1470  
1471          if (globals->haveTauBarostat())
1472 <          myNPTim->setTauBarostat(globals->getTauBarostat());
1472 >          myNPTxyz->setTauBarostat(globals->getTauBarostat());
1473          else{
1474            sprintf(painCave.errMsg,
1475                    "SimSetup error: If you use an NPT\n"
# Line 1501 | Line 1477 | void SimSetup::makeIntegrator(void){
1477            painCave.isFatal = 1;
1478            simError();
1479          }
1504 –        break;
1480  
1481 <      case NPTfm_ENS:
1507 <        if (globals->haveZconstraints()){
1508 <          setupZConstraint(info[k]);
1509 <          myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >(&(info[k]), the_ff);
1510 <        }
1511 <        else
1512 <          myNPTfm = new NPTfm<RealIntegrator>(&(info[k]), the_ff);
1513 <
1514 <        myNPTfm->setTargetTemp(globals->getTargetTemp());
1515 <
1516 <        if (globals->haveTargetPressure())
1517 <          myNPTfm->setTargetPressure(globals->getTargetPressure());
1518 <        else{
1519 <          sprintf(painCave.errMsg,
1520 <                  "SimSetup error: If you use a constant pressure\n"
1521 <                  "    ensemble, you must set targetPressure in the BASS file.\n");
1522 <          painCave.isFatal = 1;
1523 <          simError();
1524 <        }
1525 <
1526 <        if (globals->haveTauThermostat())
1527 <          myNPTfm->setTauThermostat(globals->getTauThermostat());
1528 <        else{
1529 <          sprintf(painCave.errMsg,
1530 <                  "SimSetup error: If you use an NPT\n"
1531 <                  "    ensemble, you must set tauThermostat.\n");
1532 <          painCave.isFatal = 1;
1533 <          simError();
1534 <        }
1535 <
1536 <        if (globals->haveTauBarostat())
1537 <          myNPTfm->setTauBarostat(globals->getTauBarostat());
1538 <        else{
1539 <          sprintf(painCave.errMsg,
1540 <                  "SimSetup error: If you use an NPT\n"
1541 <                  "    ensemble, you must set tauBarostat.\n");
1542 <          painCave.isFatal = 1;
1543 <          simError();
1544 <        }
1481 >        info->the_integrator = myNPTxyz;
1482          break;
1483  
1484        default:
# Line 1615 | Line 1552 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1552    }
1553    theInfo.addProperty(zconsTol);
1554  
1555 <  //set Force Substraction Policy
1555 >  //set Force Subtraction Policy
1556    StringData* zconsForcePolicy = new StringData();
1557    zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1558  
# Line 1624 | Line 1561 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1561    }
1562    else{
1563      sprintf(painCave.errMsg,
1564 <            "ZConstraint Warning: User does not set force substraction policy, "
1564 >            "ZConstraint Warning: User does not set force Subtraction policy, "
1565              "PolicyByMass is used\n");
1566      painCave.isFatal = 0;
1567      simError();

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