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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 1451 by chrisfen, Mon Aug 9 14:50:35 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 74 | Line 96 | SimSetup::~SimSetup(){
96   }
97  
98   SimSetup::~SimSetup(){
99 +  // clean up the forcefield
100 +  the_ff->cleanMe();
101 +
102    delete stamps;
103    delete globals;
104   }
# Line 92 | Line 117 | void SimSetup::parseFile(char* fileName){
117   #endif // is_mpi
118  
119      inFileName = fileName;
120 +
121 +    globals->initalize();
122      set_interface_stamps(stamps, globals);
123  
124   #ifdef IS_MPI
# Line 122 | Line 149 | void SimSetup::createSim(void){
149  
150   void SimSetup::createSim(void){
151  
152 <  // gather all of the information from the Bass file
152 >  // gather all of the information from the meta-data file
153  
154    gatherInfo();
155  
# Line 643 | Line 670 | void SimSetup::makeMolecules(void){
670    sprintf(checkPointMsg, "all molecules initialized succesfully");
671    MPIcheckPoint();
672   #endif // is_mpi
646 –
647 – }
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;
662 –
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 –    }
673  
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 –  }
674   }
675  
817 –
676   void SimSetup::gatherInfo(void){
677    int i;
678  
# Line 824 | Line 682 | void SimSetup::gatherInfo(void){
682    // set the easy ones first
683  
684    for (i = 0; i < nInfo; i++){
685 <    info[i].target_temp = globals->getTargetTemp();
686 <    info[i].dt = globals->getDt();
687 <    info[i].run_time = globals->getRunTime();
688 <  }
685 >    if (globals->haveTargetTemp()) {
686 >      info[i].target_temp = globals->getTargetTemp();
687 >      info[i].have_target_temp = 1;
688 >    } else {
689 >      info[i].have_target_temp = 0;
690 >    }
691 >    if (globals->haveDt()) {
692 >      info[i].dt = globals->getDt();
693 >    }
694 >    if (globals->haveRunTime()) {
695 >      info[i].run_time = globals->getRunTime();
696 >    }
697 >    }
698    n_components = globals->getNComponents();
699  
700  
# Line 860 | Line 727 | void SimSetup::gatherInfo(void){
727    
728    // get the ensemble
729  
863 –  strcpy(ensemble, globals->getEnsemble());
730  
731 <  if (!strcasecmp(ensemble, "NVE")){
732 <    ensembleCase = NVE_ENS;
733 <  }
734 <  else if (!strcasecmp(ensemble, "NVT")){
735 <    ensembleCase = NVT_ENS;
736 <  }
737 <  else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
738 <    ensembleCase = NPTi_ENS;
739 <  }
740 <  else if (!strcasecmp(ensemble, "NPTf")){
741 <    ensembleCase = NPTf_ENS;
742 <  }
743 <  else if (!strcasecmp(ensemble, "NPTxyz")){
744 <    ensembleCase = NPTxyz_ENS;
745 <  }
746 <  else{
747 <    sprintf(painCave.errMsg,
748 <            "SimSetup Warning. Unrecognized Ensemble -> %s \n"
749 <            "\treverting to NVE for this simulation.\n",
750 <            ensemble);
751 <         painCave.isFatal = 0;
752 <         simError();
753 <         strcpy(ensemble, "NVE");
754 <         ensembleCase = NVE_ENS;
755 <  }  
731 >  if (globals->haveEnsemble()) {
732 >    
733 >    strcpy(ensemble, globals->getEnsemble());
734 >    
735 >    if (!strcasecmp(ensemble, "NVE")){
736 >      ensembleCase = NVE_ENS;
737 >    }
738 >    else if (!strcasecmp(ensemble, "NVT")){
739 >      ensembleCase = NVT_ENS;
740 >    }
741 >    else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
742 >      ensembleCase = NPTi_ENS;
743 >    }
744 >    else if (!strcasecmp(ensemble, "NPTf")){
745 >      ensembleCase = NPTf_ENS;
746 >    }
747 >    else if (!strcasecmp(ensemble, "NPTxyz")){
748 >      ensembleCase = NPTxyz_ENS;
749 >    }
750 >    else{
751 >      sprintf(painCave.errMsg,
752 >              "SimSetup Warning. Unrecognized Ensemble -> %s \n"
753 >              "\treverting to NVE for this simulation.\n",
754 >              ensemble);
755 >      painCave.isFatal = 0;
756 >      simError();
757 >      strcpy(ensemble, "NVE");
758 >      ensembleCase = NVE_ENS;
759 >    }  
760 >    
761 >    for (i = 0; i < nInfo; i++)
762 >      strcpy(info[i].ensemble, ensemble);
763 >      
764 >    
765 >    //check whether sample time, status time, thermal time and reset time are divisble by dt
766 >    if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
767 >      sprintf(painCave.errMsg,
768 >              "Sample time is not divisible by dt.\n"
769 >              "\tThis will result in samples that are not uniformly\n"
770 >              "\tdistributed in time.  If this is a problem, change\n"
771 >              "\tyour sampleTime variable.\n");
772 >      painCave.isFatal = 0;
773 >      simError();    
774 >    }
775 >    
776 >    if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
777 >      sprintf(painCave.errMsg,
778 >              "Status time is not divisible by dt.\n"
779 >              "\tThis will result in status reports that are not uniformly\n"
780 >              "\tdistributed in time.  If this is a problem, change \n"
781 >              "\tyour statusTime variable.\n");
782 >      painCave.isFatal = 0;
783 >      simError();    
784 >    }
785 >    
786 >    if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
787 >      sprintf(painCave.errMsg,
788 >              "Thermal time is not divisible by dt.\n"
789 >              "\tThis will result in thermalizations that are not uniformly\n"
790 >              "\tdistributed in time.  If this is a problem, change \n"
791 >              "\tyour thermalTime variable.\n");
792 >      painCave.isFatal = 0;
793 >      simError();    
794 >    }  
795 >    
796 >    if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
797 >      sprintf(painCave.errMsg,
798 >              "Reset time is not divisible by dt.\n"
799 >              "\tThis will result in integrator resets that are not uniformly\n"
800 >              "\tdistributed in time.  If this is a problem, change\n"
801 >              "\tyour resetTime variable.\n");
802 >      painCave.isFatal = 0;
803 >      simError();    
804 >    }
805 >    
806 >    // set the status, sample, and thermal kick times
807 >    
808 >    for (i = 0; i < nInfo; i++){
809 >      if (globals->haveSampleTime()){
810 >        info[i].sampleTime = globals->getSampleTime();
811 >        info[i].statusTime = info[i].sampleTime;
812 >      }
813 >      else{
814 >        info[i].sampleTime = globals->getRunTime();
815 >        info[i].statusTime = info[i].sampleTime;
816 >      }
817 >      
818 >      if (globals->haveStatusTime()){
819 >        info[i].statusTime = globals->getStatusTime();
820 >      }
821 >      
822 >      if (globals->haveThermalTime()){
823 >        info[i].thermalTime = globals->getThermalTime();
824 >      } else {
825 >        info[i].thermalTime = globals->getRunTime();
826 >      }
827 >      
828 >      info[i].resetIntegrator = 0;
829 >      if( globals->haveResetTime() ){
830 >        info[i].resetTime = globals->getResetTime();
831 >        info[i].resetIntegrator = 1;
832 >      }        
833 >    }
834  
835 <  for (i = 0; i < nInfo; i++){
836 <    strcpy(info[i].ensemble, ensemble);
837 <
835 >    for (i=0; i < nInfo; i++) {
836 >      
837 >      // check for the temperature set flag
838 >      
839 >      if (globals->haveTempSet())
840 >        info[i].setTemp = globals->getTempSet();
841 >      
842 >      // check for the extended State init
843 >      
844 >      info[i].useInitXSstate = globals->getUseInitXSstate();
845 >      info[i].orthoTolerance = globals->getOrthoBoxTolerance();
846 >      
847 >      // check for thermodynamic integration
848 >      if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
849 >        if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
850 >          info[i].useSolidThermInt = globals->getUseSolidThermInt();
851 >          info[i].thermIntLambda = globals->getThermIntLambda();
852 >          info[i].thermIntK = globals->getThermIntK();
853 >          
854 >          Restraints *myRestraint = new Restraints(info[i].thermIntLambda, info[i].thermIntK);
855 >          info[i].restraint = myRestraint;
856 >        }
857 >        else {
858 >          sprintf(painCave.errMsg,
859 >                  "SimSetup Error:\n"
860 >                  "\tKeyword useSolidThermInt was set to 'true' but\n"
861 >                  "\tthermodynamicIntegrationLambda (and/or\n"
862 >                  "\tthermodynamicIntegrationK) was not specified.\n"
863 >                  "\tPlease provide a lambda value and k value in your meta-data file.\n");
864 >          painCave.isFatal = 1;
865 >          simError();    
866 >        }
867 >      }
868 >      else if(globals->getUseLiquidThermInt()) {
869 >        if (globals->getUseSolidThermInt()) {
870 >          sprintf( painCave.errMsg,
871 >                   "SimSetup Warning: It appears that you have both solid and\n"
872 >                   "\tliquid thermodynamic integration activated in your meta-data\n"
873 >                   "\tfile. To avoid confusion, specify only one technique in\n"
874 >                   "\tyour meta-data file. Liquid-state thermodynamic integration\n"
875 >                   "\twill be assumed for the current simulation. If this is not\n"
876 >                   "\twhat you desire, set useSolidThermInt to 'true' and\n"
877 >                   "\tuseLiquidThermInt to 'false' in your meta-data file.\n");
878 >          painCave.isFatal = 0;
879 >          simError();
880 >        }
881 >        if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
882 >          info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
883 >          info[i].thermIntLambda = globals->getThermIntLambda();
884 >          info[i].thermIntK = globals->getThermIntK();
885 >        }
886 >        else {
887 >          sprintf(painCave.errMsg,
888 >                  "SimSetup Error:\n"
889 >                  "\tKeyword useLiquidThermInt was set to 'true' but\n"
890 >                  "\tthermodynamicIntegrationLambda (and/or\n"
891 >                  "\tthermodynamicIntegrationK) was not specified.\n"
892 >                  "\tPlease provide a lambda value and k value in your meta-data file.\n");
893 >          painCave.isFatal = 1;
894 >          simError();    
895 >        }
896 >      }
897 >      else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
898 >        sprintf(painCave.errMsg,
899 >                "SimSetup Warning: If you want to use Thermodynamic\n"
900 >                "\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
901 >                "\t'true' in your meta-data file.  These keywords are set to\n"
902 >                "\t'false' by default, so your lambda and/or k values are\n"
903 >                "\tbeing ignored.\n");
904 >        painCave.isFatal = 0;
905 >        simError();  
906 >      }
907 >    }        
908 >  }
909 >  
910 >  for (i = 0; i < nInfo; i++) {
911      // get the mixing rule
912 <
912 >    
913      strcpy(info[i].mixingRule, globals->getMixingRule());
914      info[i].usePBC = globals->getPBC();
915    }
916 <
916 >  
917    // get the components and calculate the tot_nMol and indvidual n_mol
918 <
918 >  
919    the_components = globals->getComponents();
920    components_nmol = new int[n_components];
921 <
905 <
921 >  
922    if (!globals->haveNMol()){
923      // we don't have the total number of molecules, so we assume it is
924      // given in each component
# Line 932 | Line 948 | void SimSetup::gatherInfo(void){
948      painCave.isFatal = 1;
949      simError();
950    }
951 +  
952  
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 –  }
953  
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 –  }
954    
955    //setup seed for random number generator
956    int seedValue;
# Line 1115 | Line 993 | void SimSetup::gatherInfo(void){
993    }
994    
995   #ifdef IS_MPI
996 <  strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
996 >  strcpy(checkPointMsg, "Successfully gathered all information from meta-data file\n");
997    MPIcheckPoint();
998   #endif // is_mpi
999   }
# Line 1252 | Line 1130 | void SimSetup::finalInfoCheck(void){
1130    MPIcheckPoint();
1131   #endif // is_mpi
1132  
1255 –  // clean up the forcefield
1256 –  the_ff->cleanMe();
1133   }
1134    
1135   void SimSetup::initSystemCoords(void){
# Line 1284 | Line 1160 | void SimSetup::initSystemCoords(void){
1160    }
1161    else{
1162      
1163 <    // no init from bass
1163 >    // no init from md file
1164      
1165      sprintf(painCave.errMsg,
1166              "Cannot intialize a simulation without an initial configuration file.\n");
# Line 1302 | Line 1178 | void SimSetup::makeOutNames(void){
1178  
1179   void SimSetup::makeOutNames(void){
1180    int k;
1181 +  string prefix;
1182  
1306 –
1183    for (k = 0; k < nInfo; k++){
1184   #ifdef IS_MPI
1185      if (worldRank == 0){
1186   #endif // is_mpi
1187 <
1188 <      if (globals->haveFinalConfig()){
1189 <        strcpy(info[k].finalName, globals->getFinalConfig());
1190 <      }
1191 <      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 <      }
1187 >      
1188 >      if(globals->haveFinalConfig())
1189 >        prefix = getPrefix(globals->getFinalConfig());  
1190 >      else
1191 >        prefix = getPrefix(inFileName);
1192  
1193 <      // make the sample and status out names
1194 <
1195 <      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 <      }
1193 >      info[k].finalName = prefix + ".eor";      
1194 >      info[k].sampleName = prefix + ".dump";
1195 >      info[k].statusName = prefix + ".stat";
1196  
1197   #ifdef IS_MPI
1198  
# Line 1785 | Line 1573 | void SimSetup::makeIntegrator(void){
1573          else
1574            myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1575  
1576 <        myNVT->setTargetTemp(globals->getTargetTemp());
1576 >        
1577 >        if (globals->haveTargetTemp())
1578 >          myNVT->setTargetTemp(globals->getTargetTemp());
1579 >        else{
1580 >          sprintf(painCave.errMsg,
1581 >                  "SimSetup error: If you use the NVT\n"
1582 >                  "\tensemble, you must set targetTemp.\n");
1583 >          painCave.isFatal = 1;
1584 >          simError();
1585 >        }
1586  
1587          if (globals->haveTauThermostat())
1588            myNVT->setTauThermostat(globals->getTauThermostat());
# Line 1808 | Line 1605 | void SimSetup::makeIntegrator(void){
1605          else
1606            myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1607  
1608 <        myNPTi->setTargetTemp(globals->getTargetTemp());
1608 >        if (globals->haveTargetTemp())
1609 >          myNPTi->setTargetTemp(globals->getTargetTemp());
1610 >        else{
1611 >          sprintf(painCave.errMsg,
1612 >                  "SimSetup error: If you use a constant pressure\n"
1613 >                  "\tensemble, you must set targetTemp.\n");
1614 >          painCave.isFatal = 1;
1615 >          simError();
1616 >        }
1617  
1618          if (globals->haveTargetPressure())
1619            myNPTi->setTargetPressure(globals->getTargetPressure());
1620          else{
1621            sprintf(painCave.errMsg,
1622                    "SimSetup error: If you use a constant pressure\n"
1623 <                  "\tensemble, you must set targetPressure in the BASS file.\n");
1623 >                  "\tensemble, you must set targetPressure in the meta-data file.\n");
1624            painCave.isFatal = 1;
1625            simError();
1626          }
# Line 1851 | Line 1656 | void SimSetup::makeIntegrator(void){
1656          else
1657            myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1658  
1659 <        myNPTf->setTargetTemp(globals->getTargetTemp());
1659 >        if (globals->haveTargetTemp())
1660 >          myNPTf->setTargetTemp(globals->getTargetTemp());
1661 >        else{
1662 >          sprintf(painCave.errMsg,
1663 >                  "SimSetup error: If you use a constant pressure\n"
1664 >                  "\tensemble, you must set targetTemp.\n");
1665 >          painCave.isFatal = 1;
1666 >          simError();
1667 >        }
1668  
1669          if (globals->haveTargetPressure())
1670            myNPTf->setTargetPressure(globals->getTargetPressure());
1671          else{
1672            sprintf(painCave.errMsg,
1673                    "SimSetup error: If you use a constant pressure\n"
1674 <                  "\tensemble, you must set targetPressure in the BASS file.\n");
1674 >                  "\tensemble, you must set targetPressure in the meta-data file.\n");
1675            painCave.isFatal = 1;
1676            simError();
1677          }    
# Line 1896 | Line 1709 | void SimSetup::makeIntegrator(void){
1709          else
1710            myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1711  
1712 <        myNPTxyz->setTargetTemp(globals->getTargetTemp());
1712 >        if (globals->haveTargetTemp())
1713 >          myNPTxyz->setTargetTemp(globals->getTargetTemp());
1714 >        else{
1715 >          sprintf(painCave.errMsg,
1716 >                  "SimSetup error: If you use a constant pressure\n"
1717 >                  "\tensemble, you must set targetTemp.\n");
1718 >          painCave.isFatal = 1;
1719 >          simError();
1720 >        }
1721  
1722          if (globals->haveTargetPressure())
1723            myNPTxyz->setTargetPressure(globals->getTargetPressure());
1724          else{
1725            sprintf(painCave.errMsg,
1726                    "SimSetup error: If you use a constant pressure\n"
1727 <                  "\tensemble, you must set targetPressure in the BASS file.\n");
1727 >                  "\tensemble, you must set targetPressure in the meta-data file.\n");
1728            painCave.isFatal = 1;
1729            simError();
1730          }    

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