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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 616 by mmeineke, Tue Jul 15 18:52:16 2003 UTC vs.
Revision 645 by tim, Tue Jul 22 19:54:52 2003 UTC

# Line 398 | Line 398 | void SimSetup::initFromBass( void ){
398      have_extra =1;
399  
400      n_cells = (int)temp3 - 1;
401 <    cellx = info->boxLx / temp3;
402 <    celly = info->boxLy / temp3;
403 <    cellz = info->boxLz / temp3;
401 >    cellx = info->boxL[0] / temp3;
402 >    celly = info->boxL[1] / temp3;
403 >    cellz = info->boxL[2] / temp3;
404      n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
405      temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
406      n_per_extra = (int)ceil( temp1 );
# Line 415 | Line 415 | void SimSetup::initFromBass( void ){
415    }
416    else{
417      n_cells = (int)temp3;
418 <    cellx = info->boxLx / temp3;
419 <    celly = info->boxLy / temp3;
420 <    cellz = info->boxLz / temp3;
418 >    cellx = info->boxL[0] / temp3;
419 >    celly = info->boxL[1] / temp3;
420 >    cellz = info->boxL[2] / temp3;
421    }
422  
423    current_mol = 0;
# Line 762 | Line 762 | void SimSetup::finalInfoCheck( void ){
762    MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
763   #endif //is_mpi
764  
765 +  double theEcr, theEst;
766  
767    if (globals->getUseRF() ) {
768      info->useReactionField = 1;
# Line 774 | Line 775 | void SimSetup::finalInfoCheck( void ){
775        painCave.isFatal = 0;
776        simError();
777        double smallest;
778 <      smallest = info->boxLx;
779 <      if (info->boxLy <= smallest) smallest = info->boxLy;
780 <      if (info->boxLz <= smallest) smallest = info->boxLz;
781 <      info->ecr = 0.5 * smallest;
778 >      smallest = info->boxL[0];
779 >      if (info->boxL[1] <= smallest) smallest = info->boxL[1];
780 >      if (info->boxL[2] <= smallest) smallest = info->boxL[2];
781 >      theEcr = 0.5 * smallest;
782      } else {
783 <      info->ecr        = globals->getECR();
783 >      theEcr = globals->getECR();
784      }
785  
786      if( !globals->haveEST() ){
# Line 789 | Line 790 | void SimSetup::finalInfoCheck( void ){
790                 );
791        painCave.isFatal = 0;
792        simError();
793 <      info->est = 0.05 * info->ecr;
793 >      theEst = 0.05 * theEcr;
794      } else {
795 <      info->est        = globals->getEST();
795 >      theEst= globals->getEST();
796      }
797 +
798 +    info->setEcr( theEcr, theEst );
799      
800      if(!globals->haveDielectric() ){
801        sprintf( painCave.errMsg,
# Line 808 | Line 811 | void SimSetup::finalInfoCheck( void ){
811      if (usesDipoles) {
812        
813        if( !globals->haveECR() ){
814 <        sprintf( painCave.errMsg,
815 <                 "SimSetup Warning: using default value of 1/2 the smallest "
816 <                 "box length for the electrostaticCutoffRadius.\n"
817 <                 "I hope you have a very fast processor!\n");
818 <        painCave.isFatal = 0;
819 <        simError();
820 <        double smallest;
821 <        smallest = info->boxLx;
822 <        if (info->boxLy <= smallest) smallest = info->boxLy;
823 <        if (info->boxLz <= smallest) smallest = info->boxLz;
824 <        info->ecr = 0.5 * smallest;
814 >        sprintf( painCave.errMsg,
815 >                 "SimSetup Warning: using default value of 1/2 the smallest "
816 >                 "box length for the electrostaticCutoffRadius.\n"
817 >                 "I hope you have a very fast processor!\n");
818 >        painCave.isFatal = 0;
819 >        simError();
820 >        double smallest;
821 >        smallest = info->boxL[0];
822 >        if (info->boxL[1] <= smallest) smallest = info->boxL[1];
823 >        if (info->boxL[2] <= smallest) smallest = info->boxL[2];
824 >        theEcr = 0.5 * smallest;
825        } else {
826 <        info->ecr        = globals->getECR();
826 >        theEcr = globals->getECR();
827        }
828        
829        if( !globals->haveEST() ){
830 <        sprintf( painCave.errMsg,
831 <                 "SimSetup Warning: using default value of 5%% of the "
832 <                 "electrostaticCutoffRadius for the "
833 <                 "electrostaticSkinThickness\n"
834 <                 );
835 <        painCave.isFatal = 0;
836 <        simError();
837 <        info->est = 0.05 * info->ecr;
830 >        sprintf( painCave.errMsg,
831 >                 "SimSetup Warning: using default value of 0.05 * the "
832 >                 "electrostaticCutoffRadius for the "
833 >                 "electrostaticSkinThickness\n"
834 >                 );
835 >        painCave.isFatal = 0;
836 >        simError();
837 >        theEst = 0.05 * theEcr;
838        } else {
839 <        info->est        = globals->getEST();
839 >        theEst= globals->getEST();
840        }
841 +
842 +      info->setEcr( theEcr, theEst );
843      }
844    }  
845  
# Line 857 | Line 862 | void SimSetup::initSystemCoords( void ){
862   #ifdef IS_MPI
863       }else fileInit = new InitializeFromFile( NULL );
864   #endif
865 <   fileInit->read_xyz( info ); // default velocities on
865 >   fileInit->readInit( info ); // default velocities on
866  
867     delete fileInit;
868   }
# Line 1276 | Line 1281 | void SimSetup::makeIntegrator( void ){
1281  
1282   void SimSetup::makeIntegrator( void ){
1283  
1284 <  NVT*  myNVT = NULL;
1285 <  NPTi* myNPTi = NULL;
1286 <  NPTf* myNPTf = NULL;
1287 <  NPTim* myNPTim = NULL;
1288 <  NPTfm* myNPTfm = NULL;
1284 >  NVT<RealIntegrator>*  myNVT = NULL;
1285 >  NPTi<RealIntegrator>* myNPTi = NULL;
1286 >  NPTf<RealIntegrator>* myNPTf = NULL;
1287 >  NPTim<RealIntegrator>* myNPTim = NULL;
1288 >  NPTfm<RealIntegrator>* myNPTfm = NULL;
1289  
1290    switch( ensembleCase ){
1291  
1292    case NVE_ENS:
1293 <    new NVE( info, the_ff );
1293 >    new NVE<RealIntegrator>( info, the_ff );
1294      break;
1295  
1296    case NVT_ENS:
1297 <    myNVT = new NVT( info, the_ff );
1297 >    myNVT = new NVT<RealIntegrator>( info, the_ff );
1298      myNVT->setTargetTemp(globals->getTargetTemp());
1299  
1300      if (globals->haveTauThermostat())
# Line 1305 | Line 1310 | void SimSetup::makeIntegrator( void ){
1310      break;
1311  
1312    case NPTi_ENS:
1313 <    myNPTi = new NPTi( info, the_ff );
1313 >    myNPTi = new NPTi<RealIntegrator>( info, the_ff );
1314      myNPTi->setTargetTemp( globals->getTargetTemp() );
1315  
1316      if (globals->haveTargetPressure())
# Line 1340 | Line 1345 | void SimSetup::makeIntegrator( void ){
1345      break;
1346  
1347    case NPTf_ENS:
1348 <    myNPTf = new NPTf( info, the_ff );
1348 >    myNPTf = new NPTf<RealIntegrator>( info, the_ff );
1349      myNPTf->setTargetTemp( globals->getTargetTemp());
1350  
1351      if (globals->haveTargetPressure())
# Line 1375 | Line 1380 | void SimSetup::makeIntegrator( void ){
1380      break;
1381      
1382    case NPTim_ENS:
1383 <    myNPTim = new NPTim( info, the_ff );
1383 >    myNPTim = new NPTim<RealIntegrator>( info, the_ff );
1384      myNPTim->setTargetTemp( globals->getTargetTemp());
1385  
1386      if (globals->haveTargetPressure())
# Line 1410 | Line 1415 | void SimSetup::makeIntegrator( void ){
1415      break;
1416  
1417    case NPTfm_ENS:
1418 <    myNPTfm = new NPTfm( info, the_ff );
1418 >    myNPTfm = new NPTfm<RealIntegrator>( info, the_ff );
1419      myNPTfm->setTargetTemp( globals->getTargetTemp());
1420  
1421      if (globals->haveTargetPressure())

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