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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 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 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 687 | 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  
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();
699 <      boxVector[1] = globals->getBox();
700 <      boxVector[2] = globals->getBox();
701 <
702 <      info[i].setBox(boxVector);
703 <    }
704 <    else if (globals->haveDensity()){
705 <      double vol;
706 <      vol = (double) tot_nmol / globals->getDensity();
707 <      boxVector[0] = pow(vol, (1.0 / 3.0));
708 <      boxVector[1] = boxVector[0];
709 <      boxVector[2] = boxVector[0];
710 <
711 <      info[i].setBox(boxVector);
712 <    }
713 <    else{
714 <      if (!globals->haveBoxX()){
715 <        sprintf(painCave.errMsg,
716 <                "SimSetup error, no periodic BoxX size given.\n");
717 <        painCave.isFatal = 1;
718 <        simError();
719 <      }
720 <      boxVector[0] = globals->getBoxX();
721 <
722 <      if (!globals->haveBoxY()){
723 <        sprintf(painCave.errMsg,
724 <                "SimSetup error, no periodic BoxY size given.\n");
725 <        painCave.isFatal = 1;
726 <        simError();
727 <      }
728 <      boxVector[1] = globals->getBoxY();
729 <
730 <      if (!globals->haveBoxZ()){
731 <        sprintf(painCave.errMsg,
732 <                "SimSetup error, no periodic BoxZ size given.\n");
733 <        painCave.isFatal = 1;
734 <        simError();
735 <      }
736 <      boxVector[2] = globals->getBoxZ();
737 <
738 <      info[i].setBox(boxVector);
739 <    }
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 813 | 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"
818 <                "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;
822 <        smallest = info[i].boxL[0];
823 <        if (info[i].boxL[1] <= smallest)
824 <          smallest = info[i].boxL[1];
825 <        if (info[i].boxL[2] <= smallest)
826 <          smallest = info[i].boxL[2];
827 <        theEcr = 0.5 * smallest;
788 >        theEcr = 15.0;
789        }
790        else{
791          theEcr = globals->getECR();
# Line 842 | 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 857 | 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();
865 <          double smallest;
866 <          smallest = info[i].boxL[0];
867 <          if (info[i].boxL[1] <= smallest)
868 <            smallest = info[i].boxL[1];
869 <          if (info[i].boxL[2] <= smallest)
870 <            smallest = info[i].boxL[2];
871 <          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 886 | 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    }
894 –
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 914 | Line 867 | void SimSetup::initSystemCoords(void){
867      if (worldRank == 0){
868   #endif //is_mpi
869        inName = globals->getInitialConfig();
917 –      double* tempDouble = new double[1000000];
870        fileInit = new InitializeFromFile(inName);
871   #ifdef IS_MPI
872      }
# Line 926 | Line 878 | void SimSetup::initSystemCoords(void){
878      delete fileInit;
879    }
880    else{
881 < #ifdef IS_MPI
930 <
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 <
938 < #else
939 <
940 <    initFromBass();
941 <
942 <
943 < #endif
888 >    
889    }
890  
891   #ifdef IS_MPI
# Line 1158 | 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 1257 | 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 1344 | Line 1293 | void SimSetup::makeIntegrator(void){
1293    NVT<RealIntegrator>* myNVT = NULL;
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){
# Line 1447 | 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 1457 | 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 1468 | Line 1420 | void SimSetup::makeIntegrator(void){
1420          info->the_integrator = myNPTf;
1421          break;
1422  
1423 +      case NPTxyz_ENS:
1424 +        if (globals->haveZconstraints()){
1425 +          setupZConstraint(info[k]);
1426 +          myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1427 +        }
1428 +        else
1429 +          myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1430 +
1431 +        myNPTxyz->setTargetTemp(globals->getTargetTemp());
1432 +
1433 +        if (globals->haveTargetPressure())
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 +        }    
1442 +
1443 +        if (globals->haveTauThermostat())
1444 +          myNPTxyz->setTauThermostat(globals->getTauThermostat());
1445 +        else{
1446 +          sprintf(painCave.errMsg,
1447 +                  "SimSetup error: If you use an NPT\n"
1448 +                  "    ensemble, you must set tauThermostat.\n");
1449 +          painCave.isFatal = 1;
1450 +          simError();
1451 +        }
1452 +
1453 +        if (globals->haveTauBarostat())
1454 +          myNPTxyz->setTauBarostat(globals->getTauBarostat());
1455 +        else{
1456 +          sprintf(painCave.errMsg,
1457 +                  "SimSetup error: If you use an NPT\n"
1458 +                  "    ensemble, you must set tauBarostat.\n");
1459 +          painCave.isFatal = 1;
1460 +          simError();
1461 +        }
1462 +
1463 +        info->the_integrator = myNPTxyz;
1464 +        break;
1465 +
1466        default:
1467          sprintf(painCave.errMsg,
1468                  "SimSetup Error. Unrecognized ensemble in case statement.\n");

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