ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 780 by mmeineke, Mon Sep 22 21:23:25 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 NPTxyz_ENS     4
25  
26 +
27   #define FF_DUFF 0
28   #define FF_LJ   1
29   #define FF_EAM  2
# Line 90 | Line 91 | void SimSetup::createSim(void){
91   #endif // is_mpi
92  
93   void SimSetup::createSim(void){
93 –  int i, j, k, globalAtomIndex;
94  
95    // gather all of the information from the Bass file
96  
# Line 108 | 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 129 | 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 551 | 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 601 | Line 604 | void SimSetup::gatherInfo(void){
604    }
605    else if (!strcasecmp(ensemble, "NPTf")){
606      ensembleCase = NPTf_ENS;
607 +  }
608 +  else if (!strcasecmp(ensemble, "NPTxyz")){
609 +    ensembleCase = NPTxyz_ENS;
610    }
611    else{
612      sprintf(painCave.errMsg,
# Line 914 | Line 920 | void SimSetup::initSystemCoords(void){
920      if (worldRank == 0){
921   #endif //is_mpi
922        inName = globals->getInitialConfig();
917 –      double* tempDouble = new double[1000000];
923        fileInit = new InitializeFromFile(inName);
924   #ifdef IS_MPI
925      }
# Line 932 | 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 1158 | 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 1257 | 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 1340 | 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<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 1374 | 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:
# Line 1415 | 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:
# Line 1456 | Line 1474 | void SimSetup::makeIntegrator(void){
1474            painCave.isFatal = 1;
1475            simError();
1476          }
1477 +
1478 +        info->the_integrator = myNPTf;
1479          break;
1480  
1481 +      case NPTxyz_ENS:
1482 +        if (globals->haveZconstraints()){
1483 +          setupZConstraint(info[k]);
1484 +          myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1485 +        }
1486 +        else
1487 +          myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1488 +
1489 +        myNPTxyz->setTargetTemp(globals->getTargetTemp());
1490 +
1491 +        if (globals->haveTargetPressure())
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 +        }    
1500 +
1501 +        if (globals->haveTauThermostat())
1502 +          myNPTxyz->setTauThermostat(globals->getTauThermostat());
1503 +        else{
1504 +          sprintf(painCave.errMsg,
1505 +                  "SimSetup error: If you use an NPT\n"
1506 +                  "    ensemble, you must set tauThermostat.\n");
1507 +          painCave.isFatal = 1;
1508 +          simError();
1509 +        }
1510 +
1511 +        if (globals->haveTauBarostat())
1512 +          myNPTxyz->setTauBarostat(globals->getTauBarostat());
1513 +        else{
1514 +          sprintf(painCave.errMsg,
1515 +                  "SimSetup error: If you use an NPT\n"
1516 +                  "    ensemble, you must set tauBarostat.\n");
1517 +          painCave.isFatal = 1;
1518 +          simError();
1519 +        }
1520 +
1521 +        info->the_integrator = myNPTxyz;
1522 +        break;
1523 +
1524        default:
1525          sprintf(painCave.errMsg,
1526                  "SimSetup Error. Unrecognized ensemble in case statement.\n");

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines