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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 722 by tim, Tue Aug 26 20:02:29 2003 UTC vs.
Revision 859 by mmeineke, Mon Nov 10 21:50:36 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;
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  
703 <    // get some of the tricky things that may still be in the globals
703 >    // check for the extended State init
704  
705 <    double boxVector[3];
706 <    if (globals->haveBox()){
707 <      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 <    }
705 >    info[i].useInitXSstate = globals->getUseInitXSstate();
706 >    info[i].orthoTolerance = globals->getOrthoBoxTolerance();
707 >    
708    }
709 <
709 >  
710    //setup seed for random number generator
711    int seedValue;
712  
# Line 815 | Line 781 | void SimSetup::finalInfoCheck(void){
781  
782        if (!globals->haveECR()){
783          sprintf(painCave.errMsg,
784 <                "SimSetup Warning: using default value of 1/2 the smallest "
785 <                "box length for the electrostaticCutoffRadius.\n"
820 <                "I hope you have a very fast processor!\n");
784 >                "SimSetup Warning: using default value of 15.0 angstroms"
785 >                "box length for the electrostaticCutoffRadius.\n");
786          painCave.isFatal = 0;
787          simError();
788 <        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;
788 >        theEcr = 15.0;
789        }
790        else{
791          theEcr = globals->getECR();
# Line 844 | Line 803 | void SimSetup::finalInfoCheck(void){
803          theEst = globals->getEST();
804        }
805  
806 <      info[i].setEcr(theEcr, theEst);
806 >      info[i].setDefaultEcr(theEcr, theEst);
807  
808        if (!globals->haveDielectric()){
809          sprintf(painCave.errMsg,
# Line 859 | Line 818 | void SimSetup::finalInfoCheck(void){
818        if (usesDipoles){
819          if (!globals->haveECR()){
820            sprintf(painCave.errMsg,
821 <                  "SimSetup Warning: using default value of 1/2 the smallest "
822 <                  "box length for the electrostaticCutoffRadius.\n"
823 <                  "I hope you have a very fast processor!\n");
824 <          painCave.isFatal = 0;
825 <          simError();
867 <          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;
821 >                  "SimSetup Warning: using default value of 15.0 angstroms"
822 >                  "box length for the electrostaticCutoffRadius.\n");
823 >          painCave.isFatal = 0;
824 >          simError();
825 >          theEcr = 15.0;
826          }
827          else{
828            theEcr = globals->getECR();
829          }
830 <
830 >        
831          if (!globals->haveEST()){
832            sprintf(painCave.errMsg,
833                    "SimSetup Warning: using default value of 0.05 * the "
# Line 888 | Line 840 | void SimSetup::finalInfoCheck(void){
840          else{
841            theEst = globals->getEST();
842          }
843 <
844 <        info[i].setEcr(theEcr, theEst);
843 >        
844 >        info[i].setDefaultEcr(theEcr, theEst);
845        }
846      }
847    }
896 –
848   #ifdef IS_MPI
849    strcpy(checkPointMsg, "post processing checks out");
850    MPIcheckPoint();
851   #endif // is_mpi
852   }
853 <
853 >  
854   void SimSetup::initSystemCoords(void){
855    int i;
856  
# Line 916 | Line 867 | void SimSetup::initSystemCoords(void){
867      if (worldRank == 0){
868   #endif //is_mpi
869        inName = globals->getInitialConfig();
919 –      double* tempDouble = new double[1000000];
870        fileInit = new InitializeFromFile(inName);
871   #ifdef IS_MPI
872      }
# Line 928 | Line 878 | void SimSetup::initSystemCoords(void){
878      delete fileInit;
879    }
880    else{
881 < #ifdef IS_MPI
932 <
881 >    
882      // no init from bass
883 <
883 >    
884      sprintf(painCave.errMsg,
885 <            "Cannot intialize a parallel simulation without an initial configuration file.\n");
886 <    painCave.isFatal;
885 >            "Cannot intialize a simulation without an initial configuration file.\n");
886 >    painCave.isFatal = 1;;
887      simError();
888 <
940 < #else
941 <
942 <    initFromBass();
943 <
944 <
945 < #endif
888 >    
889    }
890  
891   #ifdef IS_MPI
# Line 1160 | Line 1103 | void SimSetup::calcSysValues(void){
1103   }
1104  
1105   void SimSetup::calcSysValues(void){
1106 <  int i, j, k;
1106 >  int i;
1107  
1108    int* molMembershipArray;
1109  
# Line 1259 | Line 1202 | void SimSetup::makeSysArrays(void){
1202  
1203  
1204   void SimSetup::makeSysArrays(void){
1205 <  int i, j, k, l;
1205 >
1206 > #ifndef IS_MPI
1207 >  int k, j;
1208 > #endif // is_mpi
1209 >  int i, l;
1210  
1211    Atom** the_atoms;
1212    Molecule* the_molecules;
# Line 1342 | Line 1289 | void SimSetup::makeIntegrator(void){
1289   void SimSetup::makeIntegrator(void){
1290    int k;
1291  
1292 +  NVE<RealIntegrator>* myNVE = NULL;
1293    NVT<RealIntegrator>* myNVT = NULL;
1294 <  NPTi<RealIntegrator>* myNPTi = NULL;
1295 <  NPTf<RealIntegrator>* myNPTf = NULL;
1296 <  NPTim<RealIntegrator>* myNPTim = NULL;
1297 <  NPTfm<RealIntegrator>* myNPTfm = NULL;
1350 <
1294 >  NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1295 >  NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1296 >  NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1297 >  
1298    for (k = 0; k < nInfo; k++){
1299      switch (ensembleCase){
1300        case NVE_ENS:
1301          if (globals->haveZconstraints()){
1302            setupZConstraint(info[k]);
1303 <          new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1303 >          myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1304          }
1305 <        else
1306 <          new NVE<RealIntegrator>(&(info[k]), the_ff);
1305 >        else{
1306 >          myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1307 >        }
1308 >        
1309 >        info->the_integrator = myNVE;
1310          break;
1311  
1312        case NVT_ENS:
# Line 1378 | Line 1328 | void SimSetup::makeIntegrator(void){
1328            painCave.isFatal = 1;
1329            simError();
1330          }
1331 +
1332 +        info->the_integrator = myNVT;
1333          break;
1334  
1335        case NPTi_ENS:
1336          if (globals->haveZconstraints()){
1337            setupZConstraint(info[k]);
1338 <          myNPTi = new ZConstraint<NPTi<RealIntegrator> >(&(info[k]), the_ff);
1338 >          myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1339          }
1340          else
1341 <          myNPTi = new NPTi<RealIntegrator>(&(info[k]), the_ff);
1341 >          myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1342  
1343          myNPTi->setTargetTemp(globals->getTargetTemp());
1344  
# Line 1419 | Line 1371 | void SimSetup::makeIntegrator(void){
1371            painCave.isFatal = 1;
1372            simError();
1373          }
1374 +
1375 +        info->the_integrator = myNPTi;
1376          break;
1377  
1378        case NPTf_ENS:
1379          if (globals->haveZconstraints()){
1380            setupZConstraint(info[k]);
1381 <          myNPTf = new ZConstraint<NPTf<RealIntegrator> >(&(info[k]), the_ff);
1381 >          myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1382          }
1383          else
1384 <          myNPTf = new NPTf<RealIntegrator>(&(info[k]), the_ff);
1384 >          myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1385  
1386          myNPTf->setTargetTemp(globals->getTargetTemp());
1387  
# Line 1443 | Line 1397 | void SimSetup::makeIntegrator(void){
1397  
1398          if (globals->haveTauThermostat())
1399            myNPTf->setTauThermostat(globals->getTauThermostat());
1400 +
1401          else{
1402            sprintf(painCave.errMsg,
1403                    "SimSetup error: If you use an NPT\n"
# Line 1453 | Line 1408 | void SimSetup::makeIntegrator(void){
1408  
1409          if (globals->haveTauBarostat())
1410            myNPTf->setTauBarostat(globals->getTauBarostat());
1411 +
1412          else{
1413            sprintf(painCave.errMsg,
1414                    "SimSetup error: If you use an NPT\n"
# Line 1460 | Line 1416 | void SimSetup::makeIntegrator(void){
1416            painCave.isFatal = 1;
1417            simError();
1418          }
1419 +
1420 +        info->the_integrator = myNPTf;
1421          break;
1422  
1423 <      case NPTim_ENS:
1423 >      case NPTxyz_ENS:
1424          if (globals->haveZconstraints()){
1425            setupZConstraint(info[k]);
1426 <          myNPTim = new ZConstraint<NPTim<RealIntegrator> >(&(info[k]), the_ff);
1426 >          myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1427          }
1428          else
1429 <          myNPTim = new NPTim<RealIntegrator>(&(info[k]), the_ff);
1429 >          myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1430  
1431 <        myNPTim->setTargetTemp(globals->getTargetTemp());
1431 >        myNPTxyz->setTargetTemp(globals->getTargetTemp());
1432  
1433          if (globals->haveTargetPressure())
1434 <          myNPTim->setTargetPressure(globals->getTargetPressure());
1434 >          myNPTxyz->setTargetPressure(globals->getTargetPressure());
1435          else{
1436            sprintf(painCave.errMsg,
1437                    "SimSetup error: If you use a constant pressure\n"
1438                    "    ensemble, you must set targetPressure in the BASS file.\n");
1439            painCave.isFatal = 1;
1440            simError();
1441 <        }
1441 >        }    
1442  
1443          if (globals->haveTauThermostat())
1444 <          myNPTim->setTauThermostat(globals->getTauThermostat());
1444 >          myNPTxyz->setTauThermostat(globals->getTauThermostat());
1445          else{
1446            sprintf(painCave.errMsg,
1447                    "SimSetup error: If you use an NPT\n"
# Line 1493 | Line 1451 | void SimSetup::makeIntegrator(void){
1451          }
1452  
1453          if (globals->haveTauBarostat())
1454 <          myNPTim->setTauBarostat(globals->getTauBarostat());
1454 >          myNPTxyz->setTauBarostat(globals->getTauBarostat());
1455          else{
1456            sprintf(painCave.errMsg,
1457                    "SimSetup error: If you use an NPT\n"
# Line 1501 | Line 1459 | void SimSetup::makeIntegrator(void){
1459            painCave.isFatal = 1;
1460            simError();
1461          }
1504 –        break;
1462  
1463 <      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 <        }
1463 >        info->the_integrator = myNPTxyz;
1464          break;
1465  
1466        default:
# Line 1615 | Line 1534 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1534    }
1535    theInfo.addProperty(zconsTol);
1536  
1537 <  //set Force Substraction Policy
1537 >  //set Force Subtraction Policy
1538    StringData* zconsForcePolicy = new StringData();
1539    zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1540  
# Line 1624 | Line 1543 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1543    }
1544    else{
1545      sprintf(painCave.errMsg,
1546 <            "ZConstraint Warning: User does not set force substraction policy, "
1547 <            "average force substraction policy is used\n");
1546 >            "ZConstraint Warning: User does not set force Subtraction policy, "
1547 >            "PolicyByMass is used\n");
1548      painCave.isFatal = 0;
1549      simError();
1550 <    zconsForcePolicy->setData("BYNUMBER");
1550 >    zconsForcePolicy->setData("BYMASS");
1551    }
1552  
1553    theInfo.addProperty(zconsForcePolicy);
# Line 1666 | Line 1585 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1585      zconsParaData->addItem(tempParaItem);
1586    }
1587  
1588 +  //check the uniqueness of index  
1589 +  if(!zconsParaData->isIndexUnique()){
1590 +    sprintf(painCave.errMsg,
1591 +            "ZConstraint Error: molIndex is not unique\n");
1592 +    painCave.isFatal = 1;
1593 +    simError();
1594 +  }
1595 +
1596    //sort the parameters by index of molecules
1597    zconsParaData->sortByIndex();
1598 <
1598 >  
1599    //push data into siminfo, therefore, we can retrieve later
1600    theInfo.addProperty(zconsParaData);
1601   }

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