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root/group/trunk/OOPSE-1.0/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE-1.0/libmdtools/SimSetup.cpp (file contents):
Revision 1334 by gezelter, Fri Jul 16 18:58:03 2004 UTC vs.
Revision 1419 by gezelter, Tue Jul 27 18:14:16 2004 UTC

# Line 57 | Line 57 | bool isDivisible(double dividend, double divisor){
57      return false;  
58   }
59  
60 + string getPrefix(const string& str ){
61 +  string prefix;
62 +  string suffix;
63 +  int pos;
64 +
65 +  pos = str.rfind(".");
66 +
67 +  if (pos >= 0) {
68 +     prefix = str.substr(0, pos);
69 +     suffix = str.substr(pos, str.size());
70 +
71 +     // leave .bass there in case we've reverted to old habits
72 +     if (LowerCase(suffix) == ".md" || LowerCase(suffix) == ".bass")
73 +       return prefix;
74 +     else
75 +       return str;
76 +    
77 +  } else
78 +    return str;
79 + };
80 +
81 +
82   SimSetup::SimSetup(){
83    
84    initSuspend = false;
# Line 122 | Line 144 | void SimSetup::createSim(void){
144  
145   void SimSetup::createSim(void){
146  
147 <  // gather all of the information from the Bass file
147 >  // gather all of the information from the meta-data file
148  
149    gatherInfo();
150  
# Line 645 | Line 667 | void SimSetup::makeMolecules(void){
667   #endif // is_mpi
668  
669   }
648 –
649 – void SimSetup::initFromBass(void){
650 –  int i, j, k;
651 –  int n_cells;
652 –  double cellx, celly, cellz;
653 –  double temp1, temp2, temp3;
654 –  int n_per_extra;
655 –  int n_extra;
656 –  int have_extra, done;
657 –
658 –  double vel[3];
659 –  vel[0] = 0.0;
660 –  vel[1] = 0.0;
661 –  vel[2] = 0.0;
670  
663 –  temp1 = (double) tot_nmol / 4.0;
664 –  temp2 = pow(temp1, (1.0 / 3.0));
665 –  temp3 = ceil(temp2);
666 –
667 –  have_extra = 0;
668 –  if (temp2 < temp3){
669 –    // we have a non-complete lattice
670 –    have_extra = 1;
671 –
672 –    n_cells = (int) temp3 - 1;
673 –    cellx = info[0].boxL[0] / temp3;
674 –    celly = info[0].boxL[1] / temp3;
675 –    cellz = info[0].boxL[2] / temp3;
676 –    n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
677 –    temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
678 –    n_per_extra = (int) ceil(temp1);
679 –
680 –    if (n_per_extra > 4){
681 –      sprintf(painCave.errMsg,
682 –              "SimSetup error. There has been an error in constructing"
683 –              " the non-complete lattice.\n");
684 –      painCave.isFatal = 1;
685 –      simError();
686 –    }
687 –  }
688 –  else{
689 –    n_cells = (int) temp3;
690 –    cellx = info[0].boxL[0] / temp3;
691 –    celly = info[0].boxL[1] / temp3;
692 –    cellz = info[0].boxL[2] / temp3;
693 –  }
694 –
695 –  current_mol = 0;
696 –  current_comp_mol = 0;
697 –  current_comp = 0;
698 –  current_atom_ndx = 0;
699 –
700 –  for (i = 0; i < n_cells ; i++){
701 –    for (j = 0; j < n_cells; j++){
702 –      for (k = 0; k < n_cells; k++){
703 –        makeElement(i * cellx, j * celly, k * cellz);
704 –
705 –        makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
706 –
707 –        makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
708 –
709 –        makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
710 –      }
711 –    }
712 –  }
713 –
714 –  if (have_extra){
715 –    done = 0;
716 –
717 –    int start_ndx;
718 –    for (i = 0; i < (n_cells + 1) && !done; i++){
719 –      for (j = 0; j < (n_cells + 1) && !done; j++){
720 –        if (i < n_cells){
721 –          if (j < n_cells){
722 –            start_ndx = n_cells;
723 –          }
724 –          else
725 –            start_ndx = 0;
726 –        }
727 –        else
728 –          start_ndx = 0;
729 –
730 –        for (k = start_ndx; k < (n_cells + 1) && !done; k++){
731 –          makeElement(i * cellx, j * celly, k * cellz);
732 –          done = (current_mol >= tot_nmol);
733 –
734 –          if (!done && n_per_extra > 1){
735 –            makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
736 –                        k * cellz);
737 –            done = (current_mol >= tot_nmol);
738 –          }
739 –
740 –          if (!done && n_per_extra > 2){
741 –            makeElement(i * cellx, j * celly + 0.5 * celly,
742 –                        k * cellz + 0.5 * cellz);
743 –            done = (current_mol >= tot_nmol);
744 –          }
745 –
746 –          if (!done && n_per_extra > 3){
747 –            makeElement(i * cellx + 0.5 * cellx, j * celly,
748 –                        k * cellz + 0.5 * cellz);
749 –            done = (current_mol >= tot_nmol);
750 –          }
751 –        }
752 –      }
753 –    }
754 –  }
755 –
756 –  for (i = 0; i < info[0].n_atoms; i++){
757 –    info[0].atoms[i]->setVel(vel);
758 –  }
759 – }
760 –
761 – void SimSetup::makeElement(double x, double y, double z){
762 –  int k;
763 –  AtomStamp* current_atom;
764 –  DirectionalAtom* dAtom;
765 –  double rotMat[3][3];
766 –  double pos[3];
767 –
768 –  for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
769 –    current_atom = comp_stamps[current_comp]->getAtom(k);
770 –    if (!current_atom->havePosition()){
771 –      sprintf(painCave.errMsg,
772 –              "SimSetup:initFromBass error.\n"
773 –              "\tComponent %s, atom %s does not have a position specified.\n"
774 –              "\tThe initialization routine is unable to give a start"
775 –              " position.\n",
776 –              comp_stamps[current_comp]->getID(), current_atom->getType());
777 –      painCave.isFatal = 1;
778 –      simError();
779 –    }
780 –
781 –    pos[0] = x + current_atom->getPosX();
782 –    pos[1] = y + current_atom->getPosY();
783 –    pos[2] = z + current_atom->getPosZ();
784 –
785 –    info[0].atoms[current_atom_ndx]->setPos(pos);
786 –
787 –    if (info[0].atoms[current_atom_ndx]->isDirectional()){
788 –      dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
789 –
790 –      rotMat[0][0] = 1.0;
791 –      rotMat[0][1] = 0.0;
792 –      rotMat[0][2] = 0.0;
793 –
794 –      rotMat[1][0] = 0.0;
795 –      rotMat[1][1] = 1.0;
796 –      rotMat[1][2] = 0.0;
797 –
798 –      rotMat[2][0] = 0.0;
799 –      rotMat[2][1] = 0.0;
800 –      rotMat[2][2] = 1.0;
801 –
802 –      dAtom->setA(rotMat);
803 –    }
804 –
805 –    current_atom_ndx++;
806 –  }
807 –
808 –  current_mol++;
809 –  current_comp_mol++;
810 –
811 –  if (current_comp_mol >= components_nmol[current_comp]){
812 –    current_comp_mol = 0;
813 –    current_comp++;
814 –  }
815 – }
816 –
817 –
671   void SimSetup::gatherInfo(void){
672    int i;
673  
# Line 824 | Line 677 | void SimSetup::gatherInfo(void){
677    // set the easy ones first
678  
679    for (i = 0; i < nInfo; i++){
680 <    info[i].target_temp = globals->getTargetTemp();
681 <    info[i].dt = globals->getDt();
682 <    info[i].run_time = globals->getRunTime();
683 <  }
680 >    if (globals->haveTargetTemp()) {
681 >      info[i].target_temp = globals->getTargetTemp();
682 >      info[i].have_target_temp = 1;
683 >    } else {
684 >      info[i].have_target_temp = 0;
685 >    }
686 >    if (globals->haveDt()) {
687 >      info[i].dt = globals->getDt();
688 >    }
689 >    if (globals->haveRunTime()) {
690 >      info[i].run_time = globals->getRunTime();
691 >    }
692 >    }
693    n_components = globals->getNComponents();
694  
695  
# Line 860 | Line 722 | void SimSetup::gatherInfo(void){
722    
723    // get the ensemble
724  
863 –  strcpy(ensemble, globals->getEnsemble());
725  
726 <  if (!strcasecmp(ensemble, "NVE")){
727 <    ensembleCase = NVE_ENS;
728 <  }
729 <  else if (!strcasecmp(ensemble, "NVT")){
730 <    ensembleCase = NVT_ENS;
731 <  }
732 <  else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
733 <    ensembleCase = NPTi_ENS;
734 <  }
735 <  else if (!strcasecmp(ensemble, "NPTf")){
736 <    ensembleCase = NPTf_ENS;
737 <  }
738 <  else if (!strcasecmp(ensemble, "NPTxyz")){
739 <    ensembleCase = NPTxyz_ENS;
740 <  }
741 <  else{
742 <    sprintf(painCave.errMsg,
743 <            "SimSetup Warning. Unrecognized Ensemble -> %s \n"
744 <            "\treverting to NVE for this simulation.\n",
745 <            ensemble);
746 <         painCave.isFatal = 0;
747 <         simError();
748 <         strcpy(ensemble, "NVE");
749 <         ensembleCase = NVE_ENS;
750 <  }  
726 >  if (globals->haveEnsemble()) {
727 >    
728 >    strcpy(ensemble, globals->getEnsemble());
729 >    
730 >    if (!strcasecmp(ensemble, "NVE")){
731 >      ensembleCase = NVE_ENS;
732 >    }
733 >    else if (!strcasecmp(ensemble, "NVT")){
734 >      ensembleCase = NVT_ENS;
735 >    }
736 >    else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
737 >      ensembleCase = NPTi_ENS;
738 >    }
739 >    else if (!strcasecmp(ensemble, "NPTf")){
740 >      ensembleCase = NPTf_ENS;
741 >    }
742 >    else if (!strcasecmp(ensemble, "NPTxyz")){
743 >      ensembleCase = NPTxyz_ENS;
744 >    }
745 >    else{
746 >      sprintf(painCave.errMsg,
747 >              "SimSetup Warning. Unrecognized Ensemble -> %s \n"
748 >              "\treverting to NVE for this simulation.\n",
749 >              ensemble);
750 >      painCave.isFatal = 0;
751 >      simError();
752 >      strcpy(ensemble, "NVE");
753 >      ensembleCase = NVE_ENS;
754 >    }  
755 >    
756 >    for (i = 0; i < nInfo; i++)
757 >      strcpy(info[i].ensemble, ensemble);
758 >      
759 >    
760 >    //check whether sample time, status time, thermal time and reset time are divisble by dt
761 >    if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
762 >      sprintf(painCave.errMsg,
763 >              "Sample time is not divisible by dt.\n"
764 >              "\tThis will result in samples that are not uniformly\n"
765 >              "\tdistributed in time.  If this is a problem, change\n"
766 >              "\tyour sampleTime variable.\n");
767 >      painCave.isFatal = 0;
768 >      simError();    
769 >    }
770 >    
771 >    if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
772 >      sprintf(painCave.errMsg,
773 >              "Status time is not divisible by dt.\n"
774 >              "\tThis will result in status reports that are not uniformly\n"
775 >              "\tdistributed in time.  If this is a problem, change \n"
776 >              "\tyour statusTime variable.\n");
777 >      painCave.isFatal = 0;
778 >      simError();    
779 >    }
780 >    
781 >    if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
782 >      sprintf(painCave.errMsg,
783 >              "Thermal time is not divisible by dt.\n"
784 >              "\tThis will result in thermalizations that are not uniformly\n"
785 >              "\tdistributed in time.  If this is a problem, change \n"
786 >              "\tyour thermalTime variable.\n");
787 >      painCave.isFatal = 0;
788 >      simError();    
789 >    }  
790 >    
791 >    if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
792 >      sprintf(painCave.errMsg,
793 >              "Reset time is not divisible by dt.\n"
794 >              "\tThis will result in integrator resets that are not uniformly\n"
795 >              "\tdistributed in time.  If this is a problem, change\n"
796 >              "\tyour resetTime variable.\n");
797 >      painCave.isFatal = 0;
798 >      simError();    
799 >    }
800 >    
801 >    // set the status, sample, and thermal kick times
802 >    
803 >    for (i = 0; i < nInfo; i++){
804 >      if (globals->haveSampleTime()){
805 >        info[i].sampleTime = globals->getSampleTime();
806 >        info[i].statusTime = info[i].sampleTime;
807 >      }
808 >      else{
809 >        info[i].sampleTime = globals->getRunTime();
810 >        info[i].statusTime = info[i].sampleTime;
811 >      }
812 >      
813 >      if (globals->haveStatusTime()){
814 >        info[i].statusTime = globals->getStatusTime();
815 >      }
816 >      
817 >      if (globals->haveThermalTime()){
818 >        info[i].thermalTime = globals->getThermalTime();
819 >      } else {
820 >        info[i].thermalTime = globals->getRunTime();
821 >      }
822 >      
823 >      info[i].resetIntegrator = 0;
824 >      if( globals->haveResetTime() ){
825 >        info[i].resetTime = globals->getResetTime();
826 >        info[i].resetIntegrator = 1;
827 >      }        
828 >    }
829  
830 <  for (i = 0; i < nInfo; i++){
831 <    strcpy(info[i].ensemble, ensemble);
832 <
830 >    
831 >    for (i=0; i < nInfo; i++) {
832 >      
833 >      // check for the temperature set flag
834 >      
835 >      if (globals->haveTempSet())
836 >        info[i].setTemp = globals->getTempSet();
837 >      
838 >      // check for the extended State init
839 >      
840 >      info[i].useInitXSstate = globals->getUseInitXSstate();
841 >      info[i].orthoTolerance = globals->getOrthoBoxTolerance();
842 >      
843 >      // check for thermodynamic integration
844 >      if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
845 >        if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
846 >          info[i].useSolidThermInt = globals->getUseSolidThermInt();
847 >          info[i].thermIntLambda = globals->getThermIntLambda();
848 >          info[i].thermIntK = globals->getThermIntK();
849 >          
850 >          Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
851 >          info[i].restraint = myRestraint;
852 >        }
853 >        else {
854 >          sprintf(painCave.errMsg,
855 >                  "SimSetup Error:\n"
856 >                  "\tKeyword useSolidThermInt was set to 'true' but\n"
857 >                  "\tthermodynamicIntegrationLambda (and/or\n"
858 >                  "\tthermodynamicIntegrationK) was not specified.\n"
859 >                  "\tPlease provide a lambda value and k value in your meta-data file.\n");
860 >          painCave.isFatal = 1;
861 >          simError();    
862 >        }
863 >      }
864 >      else if(globals->getUseLiquidThermInt()) {
865 >        if (globals->getUseSolidThermInt()) {
866 >          sprintf( painCave.errMsg,
867 >                   "SimSetup Warning: It appears that you have both solid and\n"
868 >                   "\tliquid thermodynamic integration activated in your meta-data\n"
869 >                   "\tfile. To avoid confusion, specify only one technique in\n"
870 >                   "\tyour meta-data file. Liquid-state thermodynamic integration\n"
871 >                   "\twill be assumed for the current simulation. If this is not\n"
872 >                   "\twhat you desire, set useSolidThermInt to 'true' and\n"
873 >                   "\tuseLiquidThermInt to 'false' in your meta-data file.\n");
874 >          painCave.isFatal = 0;
875 >          simError();
876 >        }
877 >        if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
878 >          info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
879 >          info[i].thermIntLambda = globals->getThermIntLambda();
880 >          info[i].thermIntK = globals->getThermIntK();
881 >        }
882 >        else {
883 >          sprintf(painCave.errMsg,
884 >                  "SimSetup Error:\n"
885 >                  "\tKeyword useLiquidThermInt was set to 'true' but\n"
886 >                  "\tthermodynamicIntegrationLambda (and/or\n"
887 >                  "\tthermodynamicIntegrationK) was not specified.\n"
888 >                  "\tPlease provide a lambda value and k value in your meta-data file.\n");
889 >          painCave.isFatal = 1;
890 >          simError();    
891 >        }
892 >      }
893 >      else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
894 >        sprintf(painCave.errMsg,
895 >                "SimSetup Warning: If you want to use Thermodynamic\n"
896 >                "\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
897 >                "\t'true' in your meta-data file.  These keywords are set to\n"
898 >                "\t'false' by default, so your lambda and/or k values are\n"
899 >                "\tbeing ignored.\n");
900 >        painCave.isFatal = 0;
901 >        simError();  
902 >      }
903 >    }        
904 >  }
905 >  
906 >  for (i = 0; i < nInfo; i++) {
907      // get the mixing rule
908 <
908 >    
909      strcpy(info[i].mixingRule, globals->getMixingRule());
910      info[i].usePBC = globals->getPBC();
911    }
912 <
912 >  
913    // get the components and calculate the tot_nMol and indvidual n_mol
914 <
914 >  
915    the_components = globals->getComponents();
916    components_nmol = new int[n_components];
917 <
905 <
917 >  
918    if (!globals->haveNMol()){
919      // we don't have the total number of molecules, so we assume it is
920      // given in each component
# Line 932 | Line 944 | void SimSetup::gatherInfo(void){
944      painCave.isFatal = 1;
945      simError();
946    }
947 +  
948  
936 –  //check whether sample time, status time, thermal time and reset time are divisble by dt
937 –  if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
938 –    sprintf(painCave.errMsg,
939 –            "Sample time is not divisible by dt.\n"
940 –            "\tThis will result in samples that are not uniformly\n"
941 –            "\tdistributed in time.  If this is a problem, change\n"
942 –            "\tyour sampleTime variable.\n");
943 –    painCave.isFatal = 0;
944 –    simError();    
945 –  }
949  
947 –  if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
948 –    sprintf(painCave.errMsg,
949 –            "Status time is not divisible by dt.\n"
950 –            "\tThis will result in status reports that are not uniformly\n"
951 –            "\tdistributed in time.  If this is a problem, change \n"
952 –            "\tyour statusTime variable.\n");
953 –    painCave.isFatal = 0;
954 –    simError();    
955 –  }
956 –
957 –  if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
958 –    sprintf(painCave.errMsg,
959 –            "Thermal time is not divisible by dt.\n"
960 –            "\tThis will result in thermalizations that are not uniformly\n"
961 –            "\tdistributed in time.  If this is a problem, change \n"
962 –            "\tyour thermalTime variable.\n");
963 –    painCave.isFatal = 0;
964 –    simError();    
965 –  }  
966 –
967 –  if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
968 –    sprintf(painCave.errMsg,
969 –            "Reset time is not divisible by dt.\n"
970 –            "\tThis will result in integrator resets that are not uniformly\n"
971 –            "\tdistributed in time.  If this is a problem, change\n"
972 –            "\tyour resetTime variable.\n");
973 –    painCave.isFatal = 0;
974 –    simError();    
975 –  }
976 –
977 –  // set the status, sample, and thermal kick times
978 –
979 –  for (i = 0; i < nInfo; i++){
980 –    if (globals->haveSampleTime()){
981 –      info[i].sampleTime = globals->getSampleTime();
982 –      info[i].statusTime = info[i].sampleTime;
983 –    }
984 –    else{
985 –      info[i].sampleTime = globals->getRunTime();
986 –      info[i].statusTime = info[i].sampleTime;
987 –    }
988 –
989 –    if (globals->haveStatusTime()){
990 –      info[i].statusTime = globals->getStatusTime();
991 –    }
992 –
993 –    if (globals->haveThermalTime()){
994 –      info[i].thermalTime = globals->getThermalTime();
995 –    } else {
996 –      info[i].thermalTime = globals->getRunTime();
997 –    }
998 –
999 –    info[i].resetIntegrator = 0;
1000 –    if( globals->haveResetTime() ){
1001 –      info[i].resetTime = globals->getResetTime();
1002 –      info[i].resetIntegrator = 1;
1003 –    }
1004 –
1005 –    // check for the temperature set flag
1006 –    
1007 –    if (globals->haveTempSet())
1008 –      info[i].setTemp = globals->getTempSet();
1009 –
1010 –    // check for the extended State init
1011 –
1012 –    info[i].useInitXSstate = globals->getUseInitXSstate();
1013 –    info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1014 –
1015 –    // check for thermodynamic integration
1016 –    if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
1017 –      if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1018 –        info[i].useSolidThermInt = globals->getUseSolidThermInt();
1019 –        info[i].thermIntLambda = globals->getThermIntLambda();
1020 –        info[i].thermIntK = globals->getThermIntK();
1021 –        
1022 –        Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
1023 –        info[i].restraint = myRestraint;
1024 –      }
1025 –      else {
1026 –        sprintf(painCave.errMsg,
1027 –                "SimSetup Error:\n"
1028 –                "\tKeyword useSolidThermInt was set to 'true' but\n"
1029 –                "\tthermodynamicIntegrationLambda (and/or\n"
1030 –                "\tthermodynamicIntegrationK) was not specified.\n"
1031 –                "\tPlease provide a lambda value and k value in your .bass file.\n");
1032 –        painCave.isFatal = 1;
1033 –        simError();    
1034 –      }
1035 –    }
1036 –    else if(globals->getUseLiquidThermInt()) {
1037 –      if (globals->getUseSolidThermInt()) {
1038 –        sprintf( painCave.errMsg,
1039 –                 "SimSetup Warning: It appears that you have both solid and\n"
1040 –                 "\tliquid thermodynamic integration activated in your .bass\n"
1041 –                 "\tfile. To avoid confusion, specify only one technique in\n"
1042 –                 "\tyour .bass file. Liquid-state thermodynamic integration\n"
1043 –                 "\twill be assumed for the current simulation. If this is not\n"
1044 –                 "\twhat you desire, set useSolidThermInt to 'true' and\n"
1045 –                 "\tuseLiquidThermInt to 'false' in your .bass file.\n");
1046 –        painCave.isFatal = 0;
1047 –        simError();
1048 –      }
1049 –      if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1050 –        info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1051 –        info[i].thermIntLambda = globals->getThermIntLambda();
1052 –        info[i].thermIntK = globals->getThermIntK();
1053 –      }
1054 –      else {
1055 –        sprintf(painCave.errMsg,
1056 –                "SimSetup Error:\n"
1057 –                "\tKeyword useLiquidThermInt was set to 'true' but\n"
1058 –                "\tthermodynamicIntegrationLambda (and/or\n"
1059 –                "\tthermodynamicIntegrationK) was not specified.\n"
1060 –                "\tPlease provide a lambda value and k value in your .bass file.\n");
1061 –        painCave.isFatal = 1;
1062 –        simError();    
1063 –      }
1064 –    }
1065 –    else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
1066 –        sprintf(painCave.errMsg,
1067 –                "SimSetup Warning: If you want to use Thermodynamic\n"
1068 –                "\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1069 –                "\t'true' in your .bass file.  These keywords are set to\n"
1070 –                "\t'false' by default, so your lambda and/or k values are\n"
1071 –                "\tbeing ignored.\n");
1072 –        painCave.isFatal = 0;
1073 –        simError();  
1074 –    }
1075 –  }
950    
951    //setup seed for random number generator
952    int seedValue;
# Line 1115 | Line 989 | void SimSetup::gatherInfo(void){
989    }
990    
991   #ifdef IS_MPI
992 <  strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
992 >  strcpy(checkPointMsg, "Successfully gathered all information from meta-data file\n");
993    MPIcheckPoint();
994   #endif // is_mpi
995   }
# Line 1284 | Line 1158 | void SimSetup::initSystemCoords(void){
1158    }
1159    else{
1160      
1161 <    // no init from bass
1161 >    // no init from md file
1162      
1163      sprintf(painCave.errMsg,
1164              "Cannot intialize a simulation without an initial configuration file.\n");
# Line 1302 | Line 1176 | void SimSetup::makeOutNames(void){
1176  
1177   void SimSetup::makeOutNames(void){
1178    int k;
1179 +  string prefix;
1180  
1306 –
1181    for (k = 0; k < nInfo; k++){
1182   #ifdef IS_MPI
1183      if (worldRank == 0){
1184   #endif // is_mpi
1185 <
1186 <      if (globals->haveFinalConfig()){
1187 <        strcpy(info[k].finalName, globals->getFinalConfig());
1188 <      }
1189 <      else{
1316 <        strcpy(info[k].finalName, inFileName);
1317 <        char* endTest;
1318 <        int nameLength = strlen(info[k].finalName);
1319 <        endTest = &(info[k].finalName[nameLength - 5]);
1320 <        if (!strcmp(endTest, ".bass")){
1321 <          strcpy(endTest, ".eor");
1322 <        }
1323 <        else if (!strcmp(endTest, ".BASS")){
1324 <          strcpy(endTest, ".eor");
1325 <        }
1326 <        else{
1327 <          endTest = &(info[k].finalName[nameLength - 4]);
1328 <          if (!strcmp(endTest, ".bss")){
1329 <            strcpy(endTest, ".eor");
1330 <          }
1331 <          else if (!strcmp(endTest, ".mdl")){
1332 <            strcpy(endTest, ".eor");
1333 <          }
1334 <          else{
1335 <            strcat(info[k].finalName, ".eor");
1336 <          }
1337 <        }
1338 <      }
1185 >      
1186 >      if(globals->haveFinalConfig())
1187 >        prefix = getPrefix(globals->getFinalConfig());  
1188 >      else
1189 >        prefix = getPrefix(inFileName);
1190  
1191 <      // make the sample and status out names
1192 <
1193 <      strcpy(info[k].sampleName, inFileName);
1343 <      char* endTest;
1344 <      int nameLength = strlen(info[k].sampleName);
1345 <      endTest = &(info[k].sampleName[nameLength - 5]);
1346 <      if (!strcmp(endTest, ".bass")){
1347 <        strcpy(endTest, ".dump");
1348 <      }
1349 <      else if (!strcmp(endTest, ".BASS")){
1350 <        strcpy(endTest, ".dump");
1351 <      }
1352 <      else{
1353 <        endTest = &(info[k].sampleName[nameLength - 4]);
1354 <        if (!strcmp(endTest, ".bss")){
1355 <          strcpy(endTest, ".dump");
1356 <        }
1357 <        else if (!strcmp(endTest, ".mdl")){
1358 <          strcpy(endTest, ".dump");
1359 <        }
1360 <        else{
1361 <          strcat(info[k].sampleName, ".dump");
1362 <        }
1363 <      }
1364 <
1365 <      strcpy(info[k].statusName, inFileName);
1366 <      nameLength = strlen(info[k].statusName);
1367 <      endTest = &(info[k].statusName[nameLength - 5]);
1368 <      if (!strcmp(endTest, ".bass")){
1369 <        strcpy(endTest, ".stat");
1370 <      }
1371 <      else if (!strcmp(endTest, ".BASS")){
1372 <        strcpy(endTest, ".stat");
1373 <      }
1374 <      else{
1375 <        endTest = &(info[k].statusName[nameLength - 4]);
1376 <        if (!strcmp(endTest, ".bss")){
1377 <          strcpy(endTest, ".stat");
1378 <        }
1379 <        else if (!strcmp(endTest, ".mdl")){
1380 <          strcpy(endTest, ".stat");
1381 <        }
1382 <        else{
1383 <          strcat(info[k].statusName, ".stat");
1384 <        }
1385 <      }
1386 <
1387 <      strcpy(info[k].rawPotName, inFileName);
1388 <      nameLength = strlen(info[k].rawPotName);
1389 <      endTest = &(info[k].rawPotName[nameLength - 5]);
1390 <      if (!strcmp(endTest, ".bass")){
1391 <        strcpy(endTest, ".raw");
1392 <      }
1393 <      else if (!strcmp(endTest, ".BASS")){
1394 <        strcpy(endTest, ".raw");
1395 <      }
1396 <      else{
1397 <        endTest = &(info[k].rawPotName[nameLength - 4]);
1398 <        if (!strcmp(endTest, ".bss")){
1399 <          strcpy(endTest, ".raw");
1400 <        }
1401 <        else if (!strcmp(endTest, ".mdl")){
1402 <          strcpy(endTest, ".raw");
1403 <        }
1404 <        else{
1405 <          strcat(info[k].rawPotName, ".raw");
1406 <        }
1407 <      }
1191 >      info[k].finalName = prefix + ".eor";      
1192 >      info[k].sampleName = prefix + ".dump";
1193 >      info[k].statusName = prefix + ".stat";
1194  
1195   #ifdef IS_MPI
1196  
# Line 1785 | Line 1571 | void SimSetup::makeIntegrator(void){
1571          else
1572            myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1573  
1574 <        myNVT->setTargetTemp(globals->getTargetTemp());
1574 >        
1575 >        if (globals->haveTargetTemp())
1576 >          myNVT->setTargetTemp(globals->getTargetTemp());
1577 >        else{
1578 >          sprintf(painCave.errMsg,
1579 >                  "SimSetup error: If you use the NVT\n"
1580 >                  "\tensemble, you must set targetTemp.\n");
1581 >          painCave.isFatal = 1;
1582 >          simError();
1583 >        }
1584  
1585          if (globals->haveTauThermostat())
1586            myNVT->setTauThermostat(globals->getTauThermostat());
# Line 1808 | Line 1603 | void SimSetup::makeIntegrator(void){
1603          else
1604            myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1605  
1606 <        myNPTi->setTargetTemp(globals->getTargetTemp());
1606 >        if (globals->haveTargetTemp())
1607 >          myNPTi->setTargetTemp(globals->getTargetTemp());
1608 >        else{
1609 >          sprintf(painCave.errMsg,
1610 >                  "SimSetup error: If you use a constant pressure\n"
1611 >                  "\tensemble, you must set targetTemp.\n");
1612 >          painCave.isFatal = 1;
1613 >          simError();
1614 >        }
1615  
1616          if (globals->haveTargetPressure())
1617            myNPTi->setTargetPressure(globals->getTargetPressure());
1618          else{
1619            sprintf(painCave.errMsg,
1620                    "SimSetup error: If you use a constant pressure\n"
1621 <                  "\tensemble, you must set targetPressure in the BASS file.\n");
1621 >                  "\tensemble, you must set targetPressure in the meta-data file.\n");
1622            painCave.isFatal = 1;
1623            simError();
1624          }
# Line 1851 | Line 1654 | void SimSetup::makeIntegrator(void){
1654          else
1655            myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1656  
1657 <        myNPTf->setTargetTemp(globals->getTargetTemp());
1657 >        if (globals->haveTargetTemp())
1658 >          myNPTf->setTargetTemp(globals->getTargetTemp());
1659 >        else{
1660 >          sprintf(painCave.errMsg,
1661 >                  "SimSetup error: If you use a constant pressure\n"
1662 >                  "\tensemble, you must set targetTemp.\n");
1663 >          painCave.isFatal = 1;
1664 >          simError();
1665 >        }
1666  
1667          if (globals->haveTargetPressure())
1668            myNPTf->setTargetPressure(globals->getTargetPressure());
1669          else{
1670            sprintf(painCave.errMsg,
1671                    "SimSetup error: If you use a constant pressure\n"
1672 <                  "\tensemble, you must set targetPressure in the BASS file.\n");
1672 >                  "\tensemble, you must set targetPressure in the meta-data file.\n");
1673            painCave.isFatal = 1;
1674            simError();
1675          }    
# Line 1896 | Line 1707 | void SimSetup::makeIntegrator(void){
1707          else
1708            myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1709  
1710 <        myNPTxyz->setTargetTemp(globals->getTargetTemp());
1710 >        if (globals->haveTargetTemp())
1711 >          myNPTxyz->setTargetTemp(globals->getTargetTemp());
1712 >        else{
1713 >          sprintf(painCave.errMsg,
1714 >                  "SimSetup error: If you use a constant pressure\n"
1715 >                  "\tensemble, you must set targetTemp.\n");
1716 >          painCave.isFatal = 1;
1717 >          simError();
1718 >        }
1719  
1720          if (globals->haveTargetPressure())
1721            myNPTxyz->setTargetPressure(globals->getTargetPressure());
1722          else{
1723            sprintf(painCave.errMsg,
1724                    "SimSetup error: If you use a constant pressure\n"
1725 <                  "\tensemble, you must set targetPressure in the BASS file.\n");
1725 >                  "\tensemble, you must set targetPressure in the meta-data file.\n");
1726            painCave.isFatal = 1;
1727            simError();
1728          }    

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