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root/group/trunk/OOPSE-2.0/src/io/Globals.cpp
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Comparing trunk/OOPSE-2.0/src/io/Globals.cpp (file contents):
Revision 2297 by chrisfen, Thu Sep 15 00:14:35 2005 UTC vs.
Revision 2328 by chuckv, Mon Sep 26 15:58:17 2005 UTC

# Line 83 | Line 83
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
120 < #define G_PRINTPRESSURETENSOR   58
121 < #define G_COULOMBIC_CORRECTION  59
122 < #define G_DAMPING_ALPHA     60
123 < #define G_CUTOFFPOLICY      61
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 > #define G_SKINTHICKNESS     62
125  
126   Globals::Globals(){
127    initalize();
# Line 163 | Line 164 | void Globals::initalize(){
164    command_table.insert(CommandMapType::value_type("thermalTime", G_THERMALTIME));
165    command_table.insert(CommandMapType::value_type("mixingRule", G_MIXINGRULE));
166    command_table.insert(CommandMapType::value_type("usePeriodicBoundaryConditions", G_USEPBC));
166 –  command_table.insert(CommandMapType::value_type("useReactionField", G_USERF));
167    command_table.insert(CommandMapType::value_type("targetPressure", G_TARGETPRESSURE));
168    command_table.insert(CommandMapType::value_type("tauThermostat", G_TAUTHERMOSTAT));
169    command_table.insert(CommandMapType::value_type("tauBarostat", G_TAUBAROSTAT));
# Line 197 | Line 197 | void Globals::initalize(){
197    command_table.insert(CommandMapType::value_type("thermIntOmegaSpringConst", G_THERM_INT_OMEGA_SPRING));
198    command_table.insert(CommandMapType::value_type("surfaceTension", G_SURFACETENSION));
199    command_table.insert(CommandMapType::value_type("printPressureTensor", G_PRINTPRESSURETENSOR));
200 <  command_table.insert(CommandMapType::value_type("coulombicCorrection", G_COULOMBIC_CORRECTION));
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
206 –  useRF  = 0;
208    useInitTime = 0; // default to pull init time from the init file
209    useInitXSstate = 0; // default to pull the extended state from the init file
210    orthoBoxTolerance = 1E-6;
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;
# Line 218 | Line 221 | void Globals::initalize(){
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;
# Line 264 | Line 268 | void Globals::initalize(){
268    have_omega_spring_constant = 0;
269    have_surface_tension = 0;
270    have_print_pressure_tensor = 0;
271 <  have_coulombic_correction = 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 ){
# Line 988 | Line 993 | int Globals::globalAssign( event* the_event ){
993        default:
994          the_event->err_msg =
995            strdup( "Error in parsing meta-data file!\n\tswitchingRadius unrecognized.\n" );
996 +        return 0;
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 ){
# Line 1097 | Line 1134 | int Globals::globalAssign( event* the_event ){
1134        return 0;
1135        break;
1136  
1100 –    case G_USERF:
1101 –      if( the_type == STRING ){
1102 –        
1103 –        if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) useRF = 1;
1104 –        else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) useRF = 0;
1105 –        else{
1106 –          the_event->err_msg =
1107 –            strdup( "Error in parsing meta-data file!\n\tuseReactionField was not \"true\" or \"false\".\n" );
1108 –          return 0;
1109 –        }
1110 –        return 1;
1111 –      }
1112 –      
1113 –      the_event->err_msg =
1114 –        strdup( "Error in parsing meta-data file!\n\tuseReactionField was not \"true\" or \"false\".\n" );
1115 –      return 0;
1116 –      break;
1117 –
1137      case G_TARGETPRESSURE:
1138        switch( the_type ){
1139          
# Line 1905 | Line 1924 | int Globals::globalAssign( event* the_event ){
1924            return 0;
1925            break;
1926  
1927 <    case G_COULOMBIC_CORRECTION:
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          
1953        case STRING:
1954 <        strcpy(coulombicCorrection, the_event->evt.asmt.rhs.sval);
1954 >        strcpy(electrostaticSummationMethod, the_event->evt.asmt.rhs.sval);
1955  
1956 <        for(int i = 0; coulombicCorrection[i] != '\0'; i++)
1956 >        for(int i = 0; electrostaticSummationMethod[i] != '\0'; i++)
1957            {
1958 <            coulombicCorrection[i] = toupper(coulombicCorrection[i]);
1958 >            electrostaticSummationMethod[i] = toupper(electrostaticSummationMethod[i]);
1959            }
1960 <        have_coulombic_correction = 1;
1960 >        have_electro_sum_method = 1;
1961          return 1;
1962          break;
1963          
1964        case DOUBLE:
1965          the_event->err_msg =
1966 <          strdup( "Error in parsing meta-data file!\n\tcoulombicCorrection should be a string!\n" );
1966 >          strdup( "Error in parsing meta-data file!\n\telectrostaticSummationMethod should be a string!\n" );
1967          return 0;
1968          break;
1969          
1970        case INT:
1971          the_event->err_msg =
1972 <          strdup( "Error in parsing meta-data file!\n\tcoulombicCorrection should be a string!\n" );
1972 >          strdup( "Error in parsing meta-data file!\n\telectrostaticSummationMethod should be a string!\n" );
1973          return 0;
1974          break;
1975          
1976        default:
1977          the_event->err_msg =
1978 <          strdup( "Error in parsing meta-data file!\n\tcoulombicCorrection unrecognized.\n" );
1978 >          strdup( "Error in parsing meta-data file!\n\telectrostaticSummationMethod unrecognized.\n" );
1979          return 0;
1980          break;
1981        }

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