| 120 | 
  | 
#define G_ELECTRO_SUM_METHOD     58 | 
| 121 | 
  | 
#define G_DAMPING_ALPHA     59 | 
| 122 | 
  | 
#define G_CUTOFFPOLICY      60 | 
| 123 | 
+ | 
#define G_COMPRESSDUMPFILE  61 | 
| 124 | 
+ | 
#define G_SKINTHICKNESS     62 | 
| 125 | 
  | 
 | 
| 126 | 
  | 
Globals::Globals(){ | 
| 127 | 
  | 
  initalize(); | 
| 200 | 
  | 
  command_table.insert(CommandMapType::value_type("electrostaticSummationMethod", G_ELECTRO_SUM_METHOD)); | 
| 201 | 
  | 
  command_table.insert(CommandMapType::value_type("dampingAlpha", G_DAMPING_ALPHA)); | 
| 202 | 
  | 
  command_table.insert(CommandMapType::value_type("cutoffPolicy", G_CUTOFFPOLICY)); | 
| 203 | 
+ | 
  command_table.insert(CommandMapType::value_type("compressDumpFile", G_COMPRESSDUMPFILE)); | 
| 204 | 
+ | 
  command_table.insert(CommandMapType::value_type("skinThickness", G_SKINTHICKNESS)); | 
| 205 | 
  | 
 | 
| 206 | 
  | 
  strcpy( mixingRule,"standard");  //default mixing rules to standard. | 
| 207 | 
  | 
  usePBC = 1; //default  periodic boundry conditions to on | 
| 211 | 
  | 
  useSolidThermInt = 0; // default solid-state thermodynamic integration to off | 
| 212 | 
  | 
  useLiquidThermInt = 0; // default liquid thermodynamic integration to off | 
| 213 | 
  | 
  dampingAlpha = 1.5; // default damping parameter in Wolf Electrostatics | 
| 214 | 
+ | 
  compressDumpFile = 0; // default compressDumpFile set to off | 
| 215 | 
+ | 
  skinThickness = 1.0; // default neighborlist skin thickness is one angstrom | 
| 216 | 
  | 
 | 
| 217 | 
  | 
  have_force_field =  0; | 
| 218 | 
  | 
  have_n_components = 0; | 
| 221 | 
  | 
  have_dt =           0; | 
| 222 | 
  | 
  have_run_time =     0; | 
| 223 | 
  | 
   | 
| 224 | 
+ | 
  have_skin_thickness = 0; | 
| 225 | 
  | 
  have_initial_config = 0; | 
| 226 | 
  | 
  have_final_config =   0; | 
| 227 | 
  | 
  have_n_mol =          0; | 
| 271 | 
  | 
  have_electro_sum_method = 0; | 
| 272 | 
  | 
  have_damping_alpha = 0; | 
| 273 | 
  | 
  have_cutoff_policy = 0; | 
| 274 | 
+ | 
  have_compress_dumpfile = 0; | 
| 275 | 
  | 
} | 
| 276 | 
  | 
 | 
| 277 | 
  | 
int Globals::newComponent( event* the_event ){ | 
| 997 | 
  | 
        break; | 
| 998 | 
  | 
      } | 
| 999 | 
  | 
      break; | 
| 1000 | 
+ | 
 | 
| 1001 | 
+ | 
 | 
| 1002 | 
+ | 
    case G_SKINTHICKNESS: | 
| 1003 | 
+ | 
      switch( the_type ){ | 
| 1004 | 
+ | 
         | 
| 1005 | 
+ | 
      case STRING: | 
| 1006 | 
+ | 
        the_event->err_msg =  | 
| 1007 | 
+ | 
          strdup( "Error in parsing meta-data file!\n\tskinThickness is not a double or int.\n" ); | 
| 1008 | 
+ | 
        return 0; | 
| 1009 | 
+ | 
        break; | 
| 1010 | 
+ | 
         | 
| 1011 | 
+ | 
      case DOUBLE: | 
| 1012 | 
+ | 
        skinThickness = the_event->evt.asmt.rhs.dval; | 
| 1013 | 
+ | 
        have_skin_thickness = 1; | 
| 1014 | 
+ | 
        return 1; | 
| 1015 | 
+ | 
        break; | 
| 1016 | 
+ | 
         | 
| 1017 | 
+ | 
      case INT: | 
| 1018 | 
+ | 
        skinThickness = (double)the_event->evt.asmt.rhs.ival; | 
| 1019 | 
+ | 
        have_skin_thickness = 1; | 
| 1020 | 
+ | 
        return 1; | 
| 1021 | 
+ | 
        break; | 
| 1022 | 
+ | 
         | 
| 1023 | 
+ | 
      default: | 
| 1024 | 
+ | 
        the_event->err_msg =  | 
| 1025 | 
+ | 
          strdup( "Error in parsing meta-data file!\n\tskinThickness unrecognized.\n" ); | 
| 1026 | 
+ | 
        return 0; | 
| 1027 | 
+ | 
        break; | 
| 1028 | 
+ | 
      } | 
| 1029 | 
+ | 
      break; | 
| 1030 | 
+ | 
 | 
| 1031 | 
+ | 
 | 
| 1032 | 
  | 
       | 
| 1033 | 
  | 
    case G_DIELECTRIC: | 
| 1034 | 
  | 
      switch( the_type ){ | 
| 1924 | 
  | 
          return 0; | 
| 1925 | 
  | 
          break; | 
| 1926 | 
  | 
 | 
| 1927 | 
+ | 
    case G_COMPRESSDUMPFILE: | 
| 1928 | 
+ | 
       if( the_type == STRING ){ | 
| 1929 | 
+ | 
           | 
| 1930 | 
+ | 
          if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) { | 
| 1931 | 
+ | 
             have_compress_dumpfile = 1; | 
| 1932 | 
+ | 
             compressDumpFile = 1; | 
| 1933 | 
+ | 
          } else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) { | 
| 1934 | 
+ | 
             have_compress_dumpfile= 1; | 
| 1935 | 
+ | 
             compressDumpFile = 0; | 
| 1936 | 
+ | 
          } else{ | 
| 1937 | 
+ | 
             the_event->err_msg =  | 
| 1938 | 
+ | 
             strdup( "Error in parsing meta-data file!\n\tcompressDumpFile was not \"true\" or \"false\".\n" ); | 
| 1939 | 
+ | 
             return 0; | 
| 1940 | 
+ | 
          } | 
| 1941 | 
+ | 
          return 1; | 
| 1942 | 
+ | 
       } | 
| 1943 | 
+ | 
        | 
| 1944 | 
+ | 
       the_event->err_msg =  | 
| 1945 | 
+ | 
       strdup( "Error in parsing meta-data file!\n\tcompressDumpFile was not \"true\" or \"false\".\n" ); | 
| 1946 | 
+ | 
       return 0; | 
| 1947 | 
+ | 
       break; | 
| 1948 | 
+ | 
        | 
| 1949 | 
+ | 
        | 
| 1950 | 
  | 
    case G_ELECTRO_SUM_METHOD: | 
| 1951 | 
  | 
      switch( the_type ){ | 
| 1952 | 
  | 
         |