| 83 | 
  | 
#define G_THERMALTIME       21 | 
| 84 | 
  | 
#define G_USEPBC            22 | 
| 85 | 
  | 
#define G_MIXINGRULE        23 | 
| 86 | 
< | 
#define G_USERF             24 | 
| 87 | 
< | 
#define G_TARGETPRESSURE    25 | 
| 88 | 
< | 
#define G_TAUTHERMOSTAT     26 | 
| 89 | 
< | 
#define G_TAUBAROSTAT       27 | 
| 90 | 
< | 
#define G_ZCONSTIME         28 | 
| 91 | 
< | 
#define G_NZCONSTRAINTS     29 | 
| 92 | 
< | 
#define G_ZCONSTOL          30 | 
| 93 | 
< | 
#define G_ZCONSFORCEPOLICY  31 | 
| 94 | 
< | 
#define G_SEED              32 | 
| 95 | 
< | 
#define G_RESETTIME         33 | 
| 96 | 
< | 
#define G_USEINITTIME       34 | 
| 97 | 
< | 
#define G_USEINIT_XS_STATE  35 | 
| 98 | 
< | 
#define G_ORTHOBOXTOLERANCE 36 | 
| 99 | 
< | 
#define G_MINIMIZER         37 | 
| 100 | 
< | 
#define G_MIN_MAXITER       38 | 
| 101 | 
< | 
#define G_MIN_WRITEFRQ      39 | 
| 102 | 
< | 
#define G_MIN_STEPSIZE      40 | 
| 103 | 
< | 
#define G_MIN_FTOL          41 | 
| 104 | 
< | 
#define G_MIN_GTOL          42 | 
| 105 | 
< | 
#define G_MIN_LSTOL         43 | 
| 106 | 
< | 
#define G_MIN_LSMAXITER     44 | 
| 107 | 
< | 
#define G_ZCONSGAP          45 | 
| 108 | 
< | 
#define G_ZCONSFIXTIME      46 | 
| 109 | 
< | 
#define G_ZCONSUSINGSMD     47 | 
| 110 | 
< | 
#define G_USE_SOLID_THERM_INT     48 | 
| 111 | 
< | 
#define G_USE_LIQUID_THERM_INT    49 | 
| 112 | 
< | 
#define G_THERM_INT_LAMBDA  50 | 
| 113 | 
< | 
#define G_THERM_INT_K       51 | 
| 114 | 
< | 
#define G_FORCEFIELD_VARIANT 52 | 
| 115 | 
< | 
#define G_FORCEFIELD_FILENAME 53 | 
| 116 | 
< | 
#define G_THERM_INT_DIST_SPRING  54 | 
| 117 | 
< | 
#define G_THERM_INT_THETA_SPRING 55 | 
| 118 | 
< | 
#define G_THERM_INT_OMEGA_SPRING 56 | 
| 119 | 
< | 
#define G_SURFACETENSION 57 | 
| 86 | 
> | 
#define G_TARGETPRESSURE    24 | 
| 87 | 
> | 
#define G_TAUTHERMOSTAT     25 | 
| 88 | 
> | 
#define G_TAUBAROSTAT       26 | 
| 89 | 
> | 
#define G_ZCONSTIME         27 | 
| 90 | 
> | 
#define G_NZCONSTRAINTS     28 | 
| 91 | 
> | 
#define G_ZCONSTOL          29 | 
| 92 | 
> | 
#define G_ZCONSFORCEPOLICY  30 | 
| 93 | 
> | 
#define G_SEED              31 | 
| 94 | 
> | 
#define G_RESETTIME         32 | 
| 95 | 
> | 
#define G_USEINITTIME       33 | 
| 96 | 
> | 
#define G_USEINIT_XS_STATE  34 | 
| 97 | 
> | 
#define G_ORTHOBOXTOLERANCE 35 | 
| 98 | 
> | 
#define G_MINIMIZER         36 | 
| 99 | 
> | 
#define G_MIN_MAXITER       37 | 
| 100 | 
> | 
#define G_MIN_WRITEFRQ      38 | 
| 101 | 
> | 
#define G_MIN_STEPSIZE      39 | 
| 102 | 
> | 
#define G_MIN_FTOL          40 | 
| 103 | 
> | 
#define G_MIN_GTOL          41 | 
| 104 | 
> | 
#define G_MIN_LSTOL         42 | 
| 105 | 
> | 
#define G_MIN_LSMAXITER     43 | 
| 106 | 
> | 
#define G_ZCONSGAP          44 | 
| 107 | 
> | 
#define G_ZCONSFIXTIME      45 | 
| 108 | 
> | 
#define G_ZCONSUSINGSMD     46 | 
| 109 | 
> | 
#define G_USE_SOLID_THERM_INT    47 | 
| 110 | 
> | 
#define G_USE_LIQUID_THERM_INT   48 | 
| 111 | 
> | 
#define G_THERM_INT_LAMBDA  49 | 
| 112 | 
> | 
#define G_THERM_INT_K       50 | 
| 113 | 
> | 
#define G_FORCEFIELD_VARIANT     51 | 
| 114 | 
> | 
#define G_FORCEFIELD_FILENAME    52 | 
| 115 | 
> | 
#define G_THERM_INT_DIST_SPRING  53 | 
| 116 | 
> | 
#define G_THERM_INT_THETA_SPRING 54 | 
| 117 | 
> | 
#define G_THERM_INT_OMEGA_SPRING 55 | 
| 118 | 
> | 
#define G_SURFACETENSION    56 | 
| 119 | 
> | 
#define G_PRINTPRESSURETENSOR    57 | 
| 120 | 
> | 
#define G_ELECTRO_SUM_METHOD     58 | 
| 121 | 
> | 
#define G_DAMPING_ALPHA     59 | 
| 122 | 
> | 
#define G_CUTOFFPOLICY      60 | 
| 123 | 
> | 
#define G_COMPRESSDUMPFILE  61 | 
| 124 | 
  | 
 | 
| 125 | 
  | 
Globals::Globals(){ | 
| 126 | 
  | 
  initalize(); | 
| 163 | 
  | 
  command_table.insert(CommandMapType::value_type("thermalTime", G_THERMALTIME)); | 
| 164 | 
  | 
  command_table.insert(CommandMapType::value_type("mixingRule", G_MIXINGRULE)); | 
| 165 | 
  | 
  command_table.insert(CommandMapType::value_type("usePeriodicBoundaryConditions", G_USEPBC)); | 
| 162 | 
– | 
  command_table.insert(CommandMapType::value_type("useReactionField", G_USERF)); | 
| 166 | 
  | 
  command_table.insert(CommandMapType::value_type("targetPressure", G_TARGETPRESSURE)); | 
| 167 | 
  | 
  command_table.insert(CommandMapType::value_type("tauThermostat", G_TAUTHERMOSTAT)); | 
| 168 | 
  | 
  command_table.insert(CommandMapType::value_type("tauBarostat", G_TAUBAROSTAT)); | 
| 195 | 
  | 
  command_table.insert(CommandMapType::value_type("thermIntThetaSpringConst", G_THERM_INT_THETA_SPRING)); | 
| 196 | 
  | 
  command_table.insert(CommandMapType::value_type("thermIntOmegaSpringConst", G_THERM_INT_OMEGA_SPRING)); | 
| 197 | 
  | 
  command_table.insert(CommandMapType::value_type("surfaceTension", G_SURFACETENSION)); | 
| 198 | 
< | 
 | 
| 198 | 
> | 
  command_table.insert(CommandMapType::value_type("printPressureTensor", G_PRINTPRESSURETENSOR)); | 
| 199 | 
> | 
  command_table.insert(CommandMapType::value_type("electrostaticSummationMethod", G_ELECTRO_SUM_METHOD)); | 
| 200 | 
> | 
  command_table.insert(CommandMapType::value_type("dampingAlpha", G_DAMPING_ALPHA)); | 
| 201 | 
> | 
  command_table.insert(CommandMapType::value_type("cutoffPolicy", G_CUTOFFPOLICY)); | 
| 202 | 
> | 
  command_table.insert(CommandMapType::value_type("compressDumpFile", G_COMPRESSDUMPFILE)); | 
| 203 | 
  | 
 | 
| 204 | 
  | 
  strcpy( mixingRule,"standard");  //default mixing rules to standard. | 
| 205 | 
  | 
  usePBC = 1; //default  periodic boundry conditions to on | 
| 199 | 
– | 
  useRF  = 0; | 
| 206 | 
  | 
  useInitTime = 0; // default to pull init time from the init file | 
| 207 | 
  | 
  useInitXSstate = 0; // default to pull the extended state from the init file | 
| 208 | 
  | 
  orthoBoxTolerance = 1E-6; | 
| 209 | 
  | 
  useSolidThermInt = 0; // default solid-state thermodynamic integration to off | 
| 210 | 
  | 
  useLiquidThermInt = 0; // default liquid thermodynamic integration to off | 
| 211 | 
+ | 
  dampingAlpha = 1.5; // default damping parameter in Wolf Electrostatics | 
| 212 | 
+ | 
  compressDumpFile = 0; // default compressDumpFile set to off | 
| 213 | 
  | 
 | 
| 214 | 
  | 
  have_force_field =  0; | 
| 215 | 
  | 
  have_n_components = 0; | 
| 263 | 
  | 
  have_theta_spring_constant = 0; | 
| 264 | 
  | 
  have_omega_spring_constant = 0; | 
| 265 | 
  | 
  have_surface_tension = 0; | 
| 266 | 
+ | 
  have_print_pressure_tensor = 0; | 
| 267 | 
+ | 
  have_electro_sum_method = 0; | 
| 268 | 
+ | 
  have_damping_alpha = 0; | 
| 269 | 
+ | 
  have_cutoff_policy = 0; | 
| 270 | 
+ | 
  have_compress_dumpfile = 0; | 
| 271 | 
  | 
} | 
| 272 | 
  | 
 | 
| 273 | 
  | 
int Globals::newComponent( event* the_event ){ | 
| 1098 | 
  | 
      return 0; | 
| 1099 | 
  | 
      break; | 
| 1100 | 
  | 
 | 
| 1088 | 
– | 
    case G_USERF: | 
| 1089 | 
– | 
      if( the_type == STRING ){ | 
| 1090 | 
– | 
         | 
| 1091 | 
– | 
        if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) useRF = 1; | 
| 1092 | 
– | 
        else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) useRF = 0; | 
| 1093 | 
– | 
        else{ | 
| 1094 | 
– | 
          the_event->err_msg =  | 
| 1095 | 
– | 
            strdup( "Error in parsing meta-data file!\n\tuseReactionField was not \"true\" or \"false\".\n" ); | 
| 1096 | 
– | 
          return 0; | 
| 1097 | 
– | 
        } | 
| 1098 | 
– | 
        return 1; | 
| 1099 | 
– | 
      } | 
| 1100 | 
– | 
       | 
| 1101 | 
– | 
      the_event->err_msg =  | 
| 1102 | 
– | 
        strdup( "Error in parsing meta-data file!\n\tuseReactionField was not \"true\" or \"false\".\n" ); | 
| 1103 | 
– | 
      return 0; | 
| 1104 | 
– | 
      break; | 
| 1105 | 
– | 
 | 
| 1101 | 
  | 
    case G_TARGETPRESSURE: | 
| 1102 | 
  | 
      switch( the_type ){ | 
| 1103 | 
  | 
         | 
| 1863 | 
  | 
            strdup( "Error in parsing meta-data file!\n\tsurfaceTension unrecognized.\n" ); | 
| 1864 | 
  | 
          return 0; | 
| 1865 | 
  | 
          break; | 
| 1866 | 
+ | 
        } | 
| 1867 | 
+ | 
        break; | 
| 1868 | 
+ | 
 | 
| 1869 | 
+ | 
    case G_PRINTPRESSURETENSOR: | 
| 1870 | 
+ | 
      if( the_type == STRING ){ | 
| 1871 | 
+ | 
         | 
| 1872 | 
+ | 
        if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) { | 
| 1873 | 
+ | 
            have_print_pressure_tensor= 1; | 
| 1874 | 
+ | 
            print_pressure_tensor = 1; | 
| 1875 | 
+ | 
        } else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) { | 
| 1876 | 
+ | 
            have_print_pressure_tensor= 1; | 
| 1877 | 
+ | 
            print_pressure_tensor = 0; | 
| 1878 | 
+ | 
        } else{ | 
| 1879 | 
+ | 
          the_event->err_msg =  | 
| 1880 | 
+ | 
            strdup( "Error in parsing meta-data file!\n\tprintPressureTensor was not \"true\" or \"false\".\n" ); | 
| 1881 | 
+ | 
          return 0; | 
| 1882 | 
  | 
        } | 
| 1883 | 
+ | 
        return 1; | 
| 1884 | 
+ | 
          } | 
| 1885 | 
+ | 
           | 
| 1886 | 
+ | 
          the_event->err_msg =  | 
| 1887 | 
+ | 
        strdup( "Error in parsing meta-data file!\n\tprintPressureTensor was not \"true\" or \"false\".\n" ); | 
| 1888 | 
+ | 
          return 0; | 
| 1889 | 
+ | 
          break; | 
| 1890 | 
+ | 
 | 
| 1891 | 
+ | 
    case G_COMPRESSDUMPFILE: | 
| 1892 | 
+ | 
       if( the_type == STRING ){ | 
| 1893 | 
+ | 
           | 
| 1894 | 
+ | 
          if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) { | 
| 1895 | 
+ | 
             have_compress_dumpfile = 1; | 
| 1896 | 
+ | 
             compressDumpFile = 1; | 
| 1897 | 
+ | 
          } else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) { | 
| 1898 | 
+ | 
             have_compress_dumpfile= 1; | 
| 1899 | 
+ | 
             compressDumpFile = 0; | 
| 1900 | 
+ | 
          } else{ | 
| 1901 | 
+ | 
             the_event->err_msg =  | 
| 1902 | 
+ | 
             strdup( "Error in parsing meta-data file!\n\tcompressDumpFile was not \"true\" or \"false\".\n" ); | 
| 1903 | 
+ | 
             return 0; | 
| 1904 | 
+ | 
          } | 
| 1905 | 
+ | 
          return 1; | 
| 1906 | 
+ | 
       } | 
| 1907 | 
+ | 
        | 
| 1908 | 
+ | 
       the_event->err_msg =  | 
| 1909 | 
+ | 
       strdup( "Error in parsing meta-data file!\n\tcompressDumpFile was not \"true\" or \"false\".\n" ); | 
| 1910 | 
+ | 
       return 0; | 
| 1911 | 
+ | 
       break; | 
| 1912 | 
+ | 
        | 
| 1913 | 
+ | 
        | 
| 1914 | 
+ | 
    case G_ELECTRO_SUM_METHOD: | 
| 1915 | 
+ | 
      switch( the_type ){ | 
| 1916 | 
+ | 
         | 
| 1917 | 
+ | 
      case STRING: | 
| 1918 | 
+ | 
        strcpy(electrostaticSummationMethod, the_event->evt.asmt.rhs.sval); | 
| 1919 | 
+ | 
 | 
| 1920 | 
+ | 
        for(int i = 0; electrostaticSummationMethod[i] != '\0'; i++) | 
| 1921 | 
+ | 
          { | 
| 1922 | 
+ | 
            electrostaticSummationMethod[i] = toupper(electrostaticSummationMethod[i]); | 
| 1923 | 
+ | 
          } | 
| 1924 | 
+ | 
        have_electro_sum_method = 1; | 
| 1925 | 
+ | 
        return 1; | 
| 1926 | 
+ | 
        break; | 
| 1927 | 
+ | 
         | 
| 1928 | 
+ | 
      case DOUBLE: | 
| 1929 | 
+ | 
        the_event->err_msg =  | 
| 1930 | 
+ | 
          strdup( "Error in parsing meta-data file!\n\telectrostaticSummationMethod should be a string!\n" ); | 
| 1931 | 
+ | 
        return 0; | 
| 1932 | 
+ | 
        break; | 
| 1933 | 
+ | 
         | 
| 1934 | 
+ | 
      case INT: | 
| 1935 | 
+ | 
        the_event->err_msg =  | 
| 1936 | 
+ | 
          strdup( "Error in parsing meta-data file!\n\telectrostaticSummationMethod should be a string!\n" ); | 
| 1937 | 
+ | 
        return 0; | 
| 1938 | 
+ | 
        break; | 
| 1939 | 
+ | 
         | 
| 1940 | 
+ | 
      default: | 
| 1941 | 
+ | 
        the_event->err_msg =  | 
| 1942 | 
+ | 
          strdup( "Error in parsing meta-data file!\n\telectrostaticSummationMethod unrecognized.\n" ); | 
| 1943 | 
+ | 
        return 0; | 
| 1944 | 
+ | 
        break; | 
| 1945 | 
+ | 
      } | 
| 1946 | 
+ | 
      break; | 
| 1947 | 
+ | 
 | 
| 1948 | 
+ | 
    case G_DAMPING_ALPHA: | 
| 1949 | 
+ | 
      switch( the_type ){ | 
| 1950 | 
+ | 
         | 
| 1951 | 
+ | 
      case STRING: | 
| 1952 | 
+ | 
        the_event->err_msg =  | 
| 1953 | 
+ | 
          strdup( "Error in parsing meta-data file!\n\tdampingAlpha is not a double or int.\n" ); | 
| 1954 | 
+ | 
        return 1; | 
| 1955 | 
  | 
        break; | 
| 1956 | 
  | 
         | 
| 1957 | 
+ | 
      case DOUBLE: | 
| 1958 | 
+ | 
        dampingAlpha = the_event->evt.asmt.rhs.dval; | 
| 1959 | 
+ | 
        have_damping_alpha = 1; | 
| 1960 | 
+ | 
        return 1; | 
| 1961 | 
+ | 
        break; | 
| 1962 | 
+ | 
         | 
| 1963 | 
+ | 
      case INT: | 
| 1964 | 
+ | 
        dampingAlpha = (double)the_event->evt.asmt.rhs.dval; | 
| 1965 | 
+ | 
        have_damping_alpha = 1; | 
| 1966 | 
+ | 
        return 1; | 
| 1967 | 
+ | 
        break; | 
| 1968 | 
+ | 
         | 
| 1969 | 
+ | 
      default: | 
| 1970 | 
+ | 
        the_event->err_msg =  | 
| 1971 | 
+ | 
          strdup( "Error in parsing meta-data file!\n\tdampingAlpha unrecognized.\n" ); | 
| 1972 | 
+ | 
        return 0; | 
| 1973 | 
+ | 
        break; | 
| 1974 | 
+ | 
      } | 
| 1975 | 
+ | 
      break;    | 
| 1976 | 
  | 
 | 
| 1977 | 
+ | 
    case G_CUTOFFPOLICY: | 
| 1978 | 
+ | 
      switch( the_type ){ | 
| 1979 | 
+ | 
         | 
| 1980 | 
+ | 
      case STRING: | 
| 1981 | 
+ | 
        strcpy(cutoffPolicy, the_event->evt.asmt.rhs.sval); | 
| 1982 | 
+ | 
 | 
| 1983 | 
+ | 
        for(int i = 0; cutoffPolicy[i] != '\0'; i++) | 
| 1984 | 
+ | 
          { | 
| 1985 | 
+ | 
            cutoffPolicy[i] = toupper(cutoffPolicy[i]); | 
| 1986 | 
+ | 
          } | 
| 1987 | 
+ | 
        have_cutoff_policy = 1; | 
| 1988 | 
+ | 
        return 1; | 
| 1989 | 
+ | 
        break; | 
| 1990 | 
+ | 
         | 
| 1991 | 
+ | 
      case DOUBLE: | 
| 1992 | 
+ | 
        the_event->err_msg =  | 
| 1993 | 
+ | 
          strdup( "Error in parsing meta-data file!\n\tcutoffPolicy should be a string!\n" ); | 
| 1994 | 
+ | 
        return 0; | 
| 1995 | 
+ | 
        break; | 
| 1996 | 
+ | 
         | 
| 1997 | 
+ | 
      case INT: | 
| 1998 | 
+ | 
        the_event->err_msg =  | 
| 1999 | 
+ | 
          strdup( "Error in parsing meta-data file!\n\tcutoffPolicy should be a string!\n" ); | 
| 2000 | 
+ | 
        return 0; | 
| 2001 | 
+ | 
        break; | 
| 2002 | 
+ | 
         | 
| 2003 | 
+ | 
      default: | 
| 2004 | 
+ | 
        the_event->err_msg =  | 
| 2005 | 
+ | 
          strdup( "Error in parsing meta-data file!\n\tcutoffPolicy unrecognized.\n" ); | 
| 2006 | 
+ | 
        return 0; | 
| 2007 | 
+ | 
        break; | 
| 2008 | 
+ | 
      } | 
| 2009 | 
+ | 
      break; | 
| 2010 | 
+ | 
 | 
| 2011 | 
  | 
       | 
| 2012 | 
  | 
      // add more token cases here.       | 
| 2013 | 
  | 
    } |