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root/group/branches/new-templateless/OOPSE/libmdtools/SimSetup.cpp
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Comparing:
trunk/OOPSE/libmdtools/SimSetup.cpp (file contents), Revision 812 by mmeineke, Wed Oct 22 21:17:32 2003 UTC vs.
branches/new-templateless/OOPSE/libmdtools/SimSetup.cpp (file contents), Revision 849 by mmeineke, Fri Oct 31 21:06:47 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 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 101 | Line 103 | void SimSetup::createSim(void){
103  
104    sysObjectsCreation();
105  
104 –  // check on the post processing info
105 –
106 –  finalInfoCheck();
107 –
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  
# Line 694 | Line 696 | void SimSetup::gatherInfo(void){
696      }
697  
698      // check for the temperature set flag
699 <
699 >    
700      if (globals->haveTempSet())
701        info[i].setTemp = globals->getTempSet();
702 <
701 <    // get some of the tricky things that may still be in the globals
702 <
703 <    double boxVector[3];
704 <    if (globals->haveBox()){
705 <      boxVector[0] = globals->getBox();
706 <      boxVector[1] = globals->getBox();
707 <      boxVector[2] = globals->getBox();
708 <
709 <      info[i].setBox(boxVector);
710 <    }
711 <    else if (globals->haveDensity()){
712 <      double vol;
713 <      vol = (double) tot_nmol / globals->getDensity();
714 <      boxVector[0] = pow(vol, (1.0 / 3.0));
715 <      boxVector[1] = boxVector[0];
716 <      boxVector[2] = boxVector[0];
717 <
718 <      info[i].setBox(boxVector);
719 <    }
720 <    else{
721 <      if (!globals->haveBoxX()){
722 <        sprintf(painCave.errMsg,
723 <                "SimSetup error, no periodic BoxX size given.\n");
724 <        painCave.isFatal = 1;
725 <        simError();
726 <      }
727 <      boxVector[0] = globals->getBoxX();
728 <
729 <      if (!globals->haveBoxY()){
730 <        sprintf(painCave.errMsg,
731 <                "SimSetup error, no periodic BoxY size given.\n");
732 <        painCave.isFatal = 1;
733 <        simError();
734 <      }
735 <      boxVector[1] = globals->getBoxY();
736 <
737 <      if (!globals->haveBoxZ()){
738 <        sprintf(painCave.errMsg,
739 <                "SimSetup error, no periodic BoxZ size given.\n");
740 <        painCave.isFatal = 1;
741 <        simError();
742 <      }
743 <      boxVector[2] = globals->getBoxZ();
744 <
745 <      info[i].setBox(boxVector);
746 <    }
702 >    
703    }
704 <
704 >  
705    //setup seed for random number generator
706    int seedValue;
707  
# Line 849 | 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 894 | 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 1350 | 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<NPT<RealIntegrator> >* myNPTi = NULL;
1313 <  NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1314 <  NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1310 >  NVE* myNVE = NULL;
1311 >  NVT* myNVT = NULL;
1312 >  NPTi* myNPTi = NULL;
1313 >  NPTf* myNPTf = NULL;
1314 >  NPTxyz* myNPTxyz = NULL;
1315    
1316    for (k = 0; k < nInfo; k++){
1317      switch (ensembleCase){
1318 <      case NVE_ENS:
1319 <        if (globals->haveZconstraints()){
1363 <          setupZConstraint(info[k]);
1364 <          myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1365 <        }
1366 <        else{
1367 <          myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1368 <        }
1318 >    case NVE_ENS:
1319 >      if (globals->haveZconstraints()){
1320          
1321 +        std::cerr << "ZConstraint is temporarily disabled\n";
1322 +        
1323 +        //      setupZConstraint(info[k]);
1324 +        //      myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1325 +      }
1326 +      
1327 + //       else{
1328 +        myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1329 + //       }
1330 +        
1331          info->the_integrator = myNVE;
1332          break;
1333 +        
1334 +    case NVT_ENS:
1335 +      if (globals->haveZconstraints()){
1336  
1337 <      case NVT_ENS:
1338 <        if (globals->haveZconstraints()){
1339 <          setupZConstraint(info[k]);
1340 <          myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1341 <        }
1337 >        std::cerr << "ZConstraint is temporarily disabled\n";
1338 >
1339 > //      setupZConstraint(info[k]);
1340 > //      myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1341 >      }
1342          else
1343            myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1344  
# Line 1458 | Line 1422 | void SimSetup::makeIntegrator(void){
1422  
1423          if (globals->haveTauThermostat())
1424            myNPTf->setTauThermostat(globals->getTauThermostat());
1425 +
1426          else{
1427            sprintf(painCave.errMsg,
1428                    "SimSetup error: If you use an NPT\n"
# Line 1468 | Line 1433 | void SimSetup::makeIntegrator(void){
1433  
1434          if (globals->haveTauBarostat())
1435            myNPTf->setTauBarostat(globals->getTauBarostat());
1436 +
1437          else{
1438            sprintf(painCave.errMsg,
1439                    "SimSetup error: If you use an NPT\n"

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