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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 782 by mmeineke, Tue Sep 23 20:34:31 2003 UTC vs.
Revision 823 by mmeineke, Mon Oct 27 22:07:48 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 30 | Line 31 | SimSetup::SimSetup(){
31   using namespace std;
32  
33   SimSetup::SimSetup(){
34 +  
35 +  initSuspend = false;
36    isInfoArray = 0;
37    nInfo = 1;
38  
# Line 52 | 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 90 | Line 94 | void SimSetup::createSim(void){
94   #endif // is_mpi
95  
96   void SimSetup::createSim(void){
93 –  int i, j, k, globalAtomIndex;
97  
98    // gather all of the information from the Bass file
99  
# Line 106 | 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 129 | 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 551 | 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 602 | Line 608 | void SimSetup::gatherInfo(void){
608    else if (!strcasecmp(ensemble, "NPTf")){
609      ensembleCase = NPTf_ENS;
610    }
611 +  else if (!strcasecmp(ensemble, "NPTxyz")){
612 +    ensembleCase = NPTxyz_ENS;
613 +  }
614    else{
615      sprintf(painCave.errMsg,
616              "SimSetup Warning. Unrecognized Ensemble -> %s, "
# Line 914 | Line 923 | void SimSetup::initSystemCoords(void){
923      if (worldRank == 0){
924   #endif //is_mpi
925        inName = globals->getInitialConfig();
917 –      double* tempDouble = new double[1000000];
926        fileInit = new InitializeFromFile(inName);
927   #ifdef IS_MPI
928      }
# Line 932 | 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 1158 | 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 1257 | 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 1344 | Line 1356 | void SimSetup::makeIntegrator(void){
1356    NVT<RealIntegrator>* myNVT = 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){
# Line 1466 | Line 1479 | void SimSetup::makeIntegrator(void){
1479          }
1480  
1481          info->the_integrator = myNPTf;
1482 +        break;
1483 +
1484 +      case NPTxyz_ENS:
1485 +        if (globals->haveZconstraints()){
1486 +          setupZConstraint(info[k]);
1487 +          myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1488 +        }
1489 +        else
1490 +          myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1491 +
1492 +        myNPTxyz->setTargetTemp(globals->getTargetTemp());
1493 +
1494 +        if (globals->haveTargetPressure())
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 +        }    
1503 +
1504 +        if (globals->haveTauThermostat())
1505 +          myNPTxyz->setTauThermostat(globals->getTauThermostat());
1506 +        else{
1507 +          sprintf(painCave.errMsg,
1508 +                  "SimSetup error: If you use an NPT\n"
1509 +                  "    ensemble, you must set tauThermostat.\n");
1510 +          painCave.isFatal = 1;
1511 +          simError();
1512 +        }
1513 +
1514 +        if (globals->haveTauBarostat())
1515 +          myNPTxyz->setTauBarostat(globals->getTauBarostat());
1516 +        else{
1517 +          sprintf(painCave.errMsg,
1518 +                  "SimSetup error: If you use an NPT\n"
1519 +                  "    ensemble, you must set tauBarostat.\n");
1520 +          painCave.isFatal = 1;
1521 +          simError();
1522 +        }
1523 +
1524 +        info->the_integrator = myNPTxyz;
1525          break;
1526  
1527        default:

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