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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 1415 by gezelter, Mon Jul 26 17:50:57 2004 UTC

# Line 824 | Line 824 | void SimSetup::gatherInfo(void){
824    // set the easy ones first
825  
826    for (i = 0; i < nInfo; i++){
827 <    info[i].target_temp = globals->getTargetTemp();
828 <    info[i].dt = globals->getDt();
829 <    info[i].run_time = globals->getRunTime();
830 <  }
827 >    if (globals->haveTargetTemp()) {
828 >      info[i].target_temp = globals->getTargetTemp();
829 >      info[i].have_target_temp = 1;
830 >    } else {
831 >      info[i].have_target_temp = 0;
832 >    }
833 >    if (globals->haveDt()) {
834 >      info[i].dt = globals->getDt();
835 >    }
836 >    if (globals->haveRunTime()) {
837 >      info[i].run_time = globals->getRunTime();
838 >    }
839 >    }
840    n_components = globals->getNComponents();
841  
842  
# Line 860 | Line 869 | void SimSetup::gatherInfo(void){
869    
870    // get the ensemble
871  
863 –  strcpy(ensemble, globals->getEnsemble());
872  
873 <  if (!strcasecmp(ensemble, "NVE")){
874 <    ensembleCase = NVE_ENS;
875 <  }
876 <  else if (!strcasecmp(ensemble, "NVT")){
877 <    ensembleCase = NVT_ENS;
878 <  }
879 <  else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
880 <    ensembleCase = NPTi_ENS;
881 <  }
882 <  else if (!strcasecmp(ensemble, "NPTf")){
883 <    ensembleCase = NPTf_ENS;
884 <  }
885 <  else if (!strcasecmp(ensemble, "NPTxyz")){
886 <    ensembleCase = NPTxyz_ENS;
887 <  }
888 <  else{
889 <    sprintf(painCave.errMsg,
890 <            "SimSetup Warning. Unrecognized Ensemble -> %s \n"
891 <            "\treverting to NVE for this simulation.\n",
892 <            ensemble);
893 <         painCave.isFatal = 0;
894 <         simError();
895 <         strcpy(ensemble, "NVE");
896 <         ensembleCase = NVE_ENS;
897 <  }  
898 <
899 <  for (i = 0; i < nInfo; i++){
900 <    strcpy(info[i].ensemble, ensemble);
873 >  if (globals->haveEnsemble()) {
874 >    
875 >    strcpy(ensemble, globals->getEnsemble());
876 >    
877 >    if (!strcasecmp(ensemble, "NVE")){
878 >      ensembleCase = NVE_ENS;
879 >    }
880 >    else if (!strcasecmp(ensemble, "NVT")){
881 >      ensembleCase = NVT_ENS;
882 >    }
883 >    else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
884 >      ensembleCase = NPTi_ENS;
885 >    }
886 >    else if (!strcasecmp(ensemble, "NPTf")){
887 >      ensembleCase = NPTf_ENS;
888 >    }
889 >    else if (!strcasecmp(ensemble, "NPTxyz")){
890 >      ensembleCase = NPTxyz_ENS;
891 >    }
892 >    else{
893 >      sprintf(painCave.errMsg,
894 >              "SimSetup Warning. Unrecognized Ensemble -> %s \n"
895 >              "\treverting to NVE for this simulation.\n",
896 >              ensemble);
897 >      painCave.isFatal = 0;
898 >      simError();
899 >      strcpy(ensemble, "NVE");
900 >      ensembleCase = NVE_ENS;
901 >    }  
902 >    
903 >    for (i = 0; i < nInfo; i++)
904 >      strcpy(info[i].ensemble, ensemble);
905 >      
906 >    
907 >    //check whether sample time, status time, thermal time and reset time are divisble by dt
908 >    if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
909 >      sprintf(painCave.errMsg,
910 >              "Sample time is not divisible by dt.\n"
911 >              "\tThis will result in samples that are not uniformly\n"
912 >              "\tdistributed in time.  If this is a problem, change\n"
913 >              "\tyour sampleTime variable.\n");
914 >      painCave.isFatal = 0;
915 >      simError();    
916 >    }
917 >    
918 >    if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
919 >      sprintf(painCave.errMsg,
920 >              "Status time is not divisible by dt.\n"
921 >              "\tThis will result in status reports that are not uniformly\n"
922 >              "\tdistributed in time.  If this is a problem, change \n"
923 >              "\tyour statusTime variable.\n");
924 >      painCave.isFatal = 0;
925 >      simError();    
926 >    }
927 >    
928 >    if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
929 >      sprintf(painCave.errMsg,
930 >              "Thermal time is not divisible by dt.\n"
931 >              "\tThis will result in thermalizations that are not uniformly\n"
932 >              "\tdistributed in time.  If this is a problem, change \n"
933 >              "\tyour thermalTime variable.\n");
934 >      painCave.isFatal = 0;
935 >      simError();    
936 >    }  
937 >    
938 >    if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
939 >      sprintf(painCave.errMsg,
940 >              "Reset time is not divisible by dt.\n"
941 >              "\tThis will result in integrator resets that are not uniformly\n"
942 >              "\tdistributed in time.  If this is a problem, change\n"
943 >              "\tyour resetTime variable.\n");
944 >      painCave.isFatal = 0;
945 >      simError();    
946 >    }
947 >    
948 >    // set the status, sample, and thermal kick times
949 >    
950 >    for (i = 0; i < nInfo; i++){
951 >      if (globals->haveSampleTime()){
952 >        info[i].sampleTime = globals->getSampleTime();
953 >        info[i].statusTime = info[i].sampleTime;
954 >      }
955 >      else{
956 >        info[i].sampleTime = globals->getRunTime();
957 >        info[i].statusTime = info[i].sampleTime;
958 >      }
959 >      
960 >      if (globals->haveStatusTime()){
961 >        info[i].statusTime = globals->getStatusTime();
962 >      }
963 >      
964 >      if (globals->haveThermalTime()){
965 >        info[i].thermalTime = globals->getThermalTime();
966 >      } else {
967 >        info[i].thermalTime = globals->getRunTime();
968 >      }
969 >      
970 >      info[i].resetIntegrator = 0;
971 >      if( globals->haveResetTime() ){
972 >        info[i].resetTime = globals->getResetTime();
973 >        info[i].resetIntegrator = 1;
974 >      }        
975 >    }
976  
977 +    
978 +    for (i=0; i < nInfo; i++) {
979 +      
980 +      // check for the temperature set flag
981 +      
982 +      if (globals->haveTempSet())
983 +        info[i].setTemp = globals->getTempSet();
984 +      
985 +      // check for the extended State init
986 +      
987 +      info[i].useInitXSstate = globals->getUseInitXSstate();
988 +      info[i].orthoTolerance = globals->getOrthoBoxTolerance();
989 +      
990 +      // check for thermodynamic integration
991 +      if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
992 +        if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
993 +          info[i].useSolidThermInt = globals->getUseSolidThermInt();
994 +          info[i].thermIntLambda = globals->getThermIntLambda();
995 +          info[i].thermIntK = globals->getThermIntK();
996 +          
997 +          Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
998 +          info[i].restraint = myRestraint;
999 +        }
1000 +        else {
1001 +          sprintf(painCave.errMsg,
1002 +                  "SimSetup Error:\n"
1003 +                  "\tKeyword useSolidThermInt was set to 'true' but\n"
1004 +                  "\tthermodynamicIntegrationLambda (and/or\n"
1005 +                  "\tthermodynamicIntegrationK) was not specified.\n"
1006 +                  "\tPlease provide a lambda value and k value in your .bass file.\n");
1007 +          painCave.isFatal = 1;
1008 +          simError();    
1009 +        }
1010 +      }
1011 +      else if(globals->getUseLiquidThermInt()) {
1012 +        if (globals->getUseSolidThermInt()) {
1013 +          sprintf( painCave.errMsg,
1014 +                   "SimSetup Warning: It appears that you have both solid and\n"
1015 +                   "\tliquid thermodynamic integration activated in your .bass\n"
1016 +                   "\tfile. To avoid confusion, specify only one technique in\n"
1017 +                   "\tyour .bass file. Liquid-state thermodynamic integration\n"
1018 +                   "\twill be assumed for the current simulation. If this is not\n"
1019 +                   "\twhat you desire, set useSolidThermInt to 'true' and\n"
1020 +                   "\tuseLiquidThermInt to 'false' in your .bass file.\n");
1021 +          painCave.isFatal = 0;
1022 +          simError();
1023 +        }
1024 +        if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1025 +          info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1026 +          info[i].thermIntLambda = globals->getThermIntLambda();
1027 +          info[i].thermIntK = globals->getThermIntK();
1028 +        }
1029 +        else {
1030 +          sprintf(painCave.errMsg,
1031 +                  "SimSetup Error:\n"
1032 +                  "\tKeyword useLiquidThermInt was set to 'true' but\n"
1033 +                  "\tthermodynamicIntegrationLambda (and/or\n"
1034 +                  "\tthermodynamicIntegrationK) was not specified.\n"
1035 +                  "\tPlease provide a lambda value and k value in your .bass file.\n");
1036 +          painCave.isFatal = 1;
1037 +          simError();    
1038 +        }
1039 +      }
1040 +      else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
1041 +        sprintf(painCave.errMsg,
1042 +                "SimSetup Warning: If you want to use Thermodynamic\n"
1043 +                "\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1044 +                "\t'true' in your .bass file.  These keywords are set to\n"
1045 +                "\t'false' by default, so your lambda and/or k values are\n"
1046 +                "\tbeing ignored.\n");
1047 +        painCave.isFatal = 0;
1048 +        simError();  
1049 +      }
1050 +    }        
1051 +  }
1052 +  
1053 +  for (i = 0; i < nInfo; i++) {
1054      // get the mixing rule
1055 <
1055 >    
1056      strcpy(info[i].mixingRule, globals->getMixingRule());
1057      info[i].usePBC = globals->getPBC();
1058    }
1059 <
1059 >  
1060    // get the components and calculate the tot_nMol and indvidual n_mol
1061 <
1061 >  
1062    the_components = globals->getComponents();
1063    components_nmol = new int[n_components];
1064 <
905 <
1064 >  
1065    if (!globals->haveNMol()){
1066      // we don't have the total number of molecules, so we assume it is
1067      // given in each component
# Line 932 | Line 1091 | void SimSetup::gatherInfo(void){
1091      painCave.isFatal = 1;
1092      simError();
1093    }
1094 +  
1095  
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 –  }
946 –
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();
1096  
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 –  }
1097    
1098    //setup seed for random number generator
1099    int seedValue;
# Line 1785 | Line 1806 | void SimSetup::makeIntegrator(void){
1806          else
1807            myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1808  
1809 <        myNVT->setTargetTemp(globals->getTargetTemp());
1809 >        
1810 >        if (globals->haveTargetTemp())
1811 >          myNVT->setTargetTemp(globals->getTargetTemp());
1812 >        else{
1813 >          sprintf(painCave.errMsg,
1814 >                  "SimSetup error: If you use the NVT\n"
1815 >                  "\tensemble, you must set targetTemp.\n");
1816 >          painCave.isFatal = 1;
1817 >          simError();
1818 >        }
1819  
1820          if (globals->haveTauThermostat())
1821            myNVT->setTauThermostat(globals->getTauThermostat());
# Line 1808 | Line 1838 | void SimSetup::makeIntegrator(void){
1838          else
1839            myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1840  
1841 <        myNPTi->setTargetTemp(globals->getTargetTemp());
1841 >        if (globals->haveTargetTemp())
1842 >          myNPTi->setTargetTemp(globals->getTargetTemp());
1843 >        else{
1844 >          sprintf(painCave.errMsg,
1845 >                  "SimSetup error: If you use a constant pressure\n"
1846 >                  "\tensemble, you must set targetTemp.\n");
1847 >          painCave.isFatal = 1;
1848 >          simError();
1849 >        }
1850  
1851          if (globals->haveTargetPressure())
1852            myNPTi->setTargetPressure(globals->getTargetPressure());
# Line 1851 | Line 1889 | void SimSetup::makeIntegrator(void){
1889          else
1890            myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1891  
1892 <        myNPTf->setTargetTemp(globals->getTargetTemp());
1892 >        if (globals->haveTargetTemp())
1893 >          myNPTf->setTargetTemp(globals->getTargetTemp());
1894 >        else{
1895 >          sprintf(painCave.errMsg,
1896 >                  "SimSetup error: If you use a constant pressure\n"
1897 >                  "\tensemble, you must set targetTemp.\n");
1898 >          painCave.isFatal = 1;
1899 >          simError();
1900 >        }
1901  
1902          if (globals->haveTargetPressure())
1903            myNPTf->setTargetPressure(globals->getTargetPressure());
# Line 1896 | Line 1942 | void SimSetup::makeIntegrator(void){
1942          else
1943            myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1944  
1945 <        myNPTxyz->setTargetTemp(globals->getTargetTemp());
1945 >        if (globals->haveTargetTemp())
1946 >          myNPTxyz->setTargetTemp(globals->getTargetTemp());
1947 >        else{
1948 >          sprintf(painCave.errMsg,
1949 >                  "SimSetup error: If you use a constant pressure\n"
1950 >                  "\tensemble, you must set targetTemp.\n");
1951 >          painCave.isFatal = 1;
1952 >          simError();
1953 >        }
1954  
1955          if (globals->haveTargetPressure())
1956            myNPTxyz->setTargetPressure(globals->getTargetPressure());

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