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root/OpenMD/trunk/src/applications/staticProps/StaticPropsCmd.c
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Comparing trunk/src/applications/staticProps/StaticPropsCmd.c (file contents):
Revision 1454 by gezelter, Wed Jun 23 19:25:02 2010 UTC vs.
Revision 1526 by kstocke1, Wed Nov 24 17:40:12 2010 UTC

# Line 36 | Line 36 | const char *gengetopt_args_info_help[] = {
36    "  -b, --nbins=INT               number of bins (general purpose)  \n                                  (default=`100')",
37    "  -x, --nbins_x=INT             number of bins in x axis  (default=`100')",
38    "  -y, --nbins_y=INT             number of bins in y axis  (default=`100')",
39 –  "      --nbins_z=INT             number of bins in z axis  (default=`100')",
39    "  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')",
40    "  -c, --rcut=DOUBLE             cutoff radius (rcut)",
41    "      --dz=DOUBLE               slab width (dz)",
# Line 56 | Line 55 | const char *gengetopt_args_info_help[] = {
55    "      --bo                      bond order parameter (--rcut must be specified)",
56    "      --bor                     bond order parameter as a function of radius \n                                  (--rcut must be specified)",
57    "      --bad                     N(theta) bond angle density within (--rcut must \n                                  be specified)",
58 +  "      --count                   count of molecules matching selection criteria \n                                  (and associated statistics)",
59    "  -g, --gofr                    g(r)",
60    "      --gofz                    g(z)",
61    "      --r_theta                 g(r, cos(theta))",
62    "      --r_omega                 g(r, cos(omega))",
63 –  "      --r_z                     g(r, z)",
63    "      --theta_omega             g(cos(theta), cos(omega))",
64    "      --gxyz                    g(x, y, z)",
65    "      --twodgofr                2D g(r) (Slab width --dz must be specified)",
# Line 72 | Line 71 | const char *gengetopt_args_info_help[] = {
71    "      --p_angle                 p(cos(theta))",
72    "      --hxy                     hxy",
73    "      --rho_r                   rho of R",
74 +  "      --angle_r                 angle of R",
75    "      --hullvol                 hull volume of nanoparticle",
76      0
77   };
# Line 108 | Line 108 | void clear_given (struct gengetopt_args_info *args_inf
108    args_info->nbins_given = 0 ;
109    args_info->nbins_x_given = 0 ;
110    args_info->nbins_y_given = 0 ;
111 –  args_info->nbins_z_given = 0 ;
111    args_info->nanglebins_given = 0 ;
112    args_info->rcut_given = 0 ;
113    args_info->dz_given = 0 ;
# Line 127 | Line 126 | void clear_given (struct gengetopt_args_info *args_inf
126    args_info->bo_given = 0 ;
127    args_info->bor_given = 0 ;
128    args_info->bad_given = 0 ;
129 +  args_info->count_given = 0 ;
130    args_info->gofr_given = 0 ;
131    args_info->gofz_given = 0 ;
132    args_info->r_theta_given = 0 ;
133    args_info->r_omega_given = 0 ;
134 –  args_info->r_z_given = 0 ;
134    args_info->theta_omega_given = 0 ;
135    args_info->gxyz_given = 0 ;
136    args_info->twodgofr_given = 0 ;
# Line 143 | Line 142 | void clear_given (struct gengetopt_args_info *args_inf
142    args_info->p_angle_given = 0 ;
143    args_info->hxy_given = 0 ;
144    args_info->rho_r_given = 0 ;
145 +  args_info->angle_r_given = 0 ;
146    args_info->hullvol_given = 0 ;
147    args_info->staticProps_group_counter = 0 ;
148   }
# Line 162 | Line 162 | void clear_args (struct gengetopt_args_info *args_info
162    args_info->nbins_x_orig = NULL;
163    args_info->nbins_y_arg = 100;
164    args_info->nbins_y_orig = NULL;
165 –  args_info->nbins_z_arg = 100;
166 –  args_info->nbins_z_orig = NULL;
165    args_info->nanglebins_arg = 50;
166    args_info->nanglebins_orig = NULL;
167    args_info->rcut_orig = NULL;
# Line 222 | Line 220 | void init_args_info(struct gengetopt_args_info *args_i
220    args_info->bo_help = gengetopt_args_info_help[25] ;
221    args_info->bor_help = gengetopt_args_info_help[26] ;
222    args_info->bad_help = gengetopt_args_info_help[27] ;
223 <  args_info->gofr_help = gengetopt_args_info_help[28] ;
224 <  args_info->gofz_help = gengetopt_args_info_help[29] ;
225 <  args_info->r_theta_help = gengetopt_args_info_help[30] ;
226 <  args_info->r_omega_help = gengetopt_args_info_help[31] ;
227 <  args_info->r_z_help = gengetopt_args_info_help[32] ;
228 <  args_info->theta_omega_help = gengetopt_args_info_help[33] ;
229 <  args_info->gxyz_help = gengetopt_args_info_help[34] ;
230 <  args_info->twodgofr_help = gengetopt_args_info_help[35] ;
231 <  args_info->p2_help = gengetopt_args_info_help[36] ;
232 <  args_info->rp2_help = gengetopt_args_info_help[37] ;
233 <  args_info->scd_help = gengetopt_args_info_help[38] ;
234 <  args_info->density_help = gengetopt_args_info_help[39] ;
235 <  args_info->slab_density_help = gengetopt_args_info_help[40] ;
236 <  args_info->p_angle_help = gengetopt_args_info_help[41] ;
237 <  args_info->hxy_help = gengetopt_args_info_help[42] ;
238 <  args_info->rho_r_help = gengetopt_args_info_help[43] ;
239 <  args_info->hullvol_help = gengetopt_args_info_help[44] ;
223 >  args_info->count_help = gengetopt_args_info_help[28] ;
224 >  args_info->gofr_help = gengetopt_args_info_help[29] ;
225 >  args_info->gofz_help = gengetopt_args_info_help[30] ;
226 >  args_info->r_theta_help = gengetopt_args_info_help[31] ;
227 >  args_info->r_omega_help = gengetopt_args_info_help[32] ;
228 >  args_info->r_z_help = gengetopt_args_info_help[33] ;
229 >  args_info->theta_omega_help = gengetopt_args_info_help[34] ;
230 >  args_info->gxyz_help = gengetopt_args_info_help[35] ;
231 >  args_info->twodgofr_help = gengetopt_args_info_help[36] ;
232 >  args_info->p2_help = gengetopt_args_info_help[37] ;
233 >  args_info->rp2_help = gengetopt_args_info_help[38] ;
234 >  args_info->scd_help = gengetopt_args_info_help[39] ;
235 >  args_info->density_help = gengetopt_args_info_help[40] ;
236 >  args_info->slab_density_help = gengetopt_args_info_help[41] ;
237 >  args_info->p_angle_help = gengetopt_args_info_help[42] ;
238 >  args_info->hxy_help = gengetopt_args_info_help[43] ;
239 >  args_info->rho_r_help = gengetopt_args_info_help[44] ;
240 >  args_info->hullvol_help = gengetopt_args_info_help[45] ;
241    
242   }
243  
# Line 328 | Line 327 | cmdline_parser_release (struct gengetopt_args_info *ar
327    free_string_field (&(args_info->nbins_orig));
328    free_string_field (&(args_info->nbins_x_orig));
329    free_string_field (&(args_info->nbins_y_orig));
331 –  free_string_field (&(args_info->nbins_z_orig));
330    free_string_field (&(args_info->nanglebins_orig));
331    free_string_field (&(args_info->rcut_orig));
332    free_string_field (&(args_info->dz_orig));
# Line 400 | Line 398 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
398      write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0);
399    if (args_info->nbins_y_given)
400      write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0);
403 –  if (args_info->nbins_z_given)
404 –    write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0);
401    if (args_info->nanglebins_given)
402      write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
403    if (args_info->rcut_given)
# Line 438 | Line 434 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
434      write_into_file(outfile, "bor", 0, 0 );
435    if (args_info->bad_given)
436      write_into_file(outfile, "bad", 0, 0 );
437 +  if (args_info->count_given)
438 +    write_into_file(outfile, "count", 0, 0 );
439    if (args_info->gofr_given)
440      write_into_file(outfile, "gofr", 0, 0 );
441    if (args_info->gofz_given)
# Line 446 | Line 444 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
444      write_into_file(outfile, "r_theta", 0, 0 );
445    if (args_info->r_omega_given)
446      write_into_file(outfile, "r_omega", 0, 0 );
449 –  if (args_info->r_z_given)
450 –    write_into_file(outfile, "r_z", 0, 0 );
447    if (args_info->theta_omega_given)
448      write_into_file(outfile, "theta_omega", 0, 0 );
449    if (args_info->gxyz_given)
# Line 470 | Line 466 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
466      write_into_file(outfile, "hxy", 0, 0 );
467    if (args_info->rho_r_given)
468      write_into_file(outfile, "rho_r", 0, 0 );
469 +  if (args_info->angle_r_given)
470 +    write_into_file(outfile, "angle_r", 0, 0 );
471    if (args_info->hullvol_given)
472      write_into_file(outfile, "hullvol", 0, 0 );
473    
# Line 528 | Line 526 | reset_group_staticProps(struct gengetopt_args_info *ar
526    args_info->bo_given = 0 ;
527    args_info->bor_given = 0 ;
528    args_info->bad_given = 0 ;
529 +  args_info->count_given = 0 ;
530    args_info->gofr_given = 0 ;
531    args_info->gofz_given = 0 ;
532    args_info->r_theta_given = 0 ;
533    args_info->r_omega_given = 0 ;
535 –  args_info->r_z_given = 0 ;
534    args_info->theta_omega_given = 0 ;
535    args_info->gxyz_given = 0 ;
536    args_info->twodgofr_given = 0 ;
# Line 544 | Line 542 | reset_group_staticProps(struct gengetopt_args_info *ar
542    args_info->p_angle_given = 0 ;
543    args_info->hxy_given = 0 ;
544    args_info->rho_r_given = 0 ;
545 +  args_info->angle_r_given = 0 ;
546    args_info->hullvol_given = 0 ;
547  
548    args_info->staticProps_group_counter = 0;
# Line 793 | Line 792 | cmdline_parser_internal (int argc, char * const *argv,
792          { "nbins",      1, NULL, 'b' },
793          { "nbins_x",    1, NULL, 'x' },
794          { "nbins_y",    1, NULL, 'y' },
796 –        { "nbins_z",    1, NULL, 0 },
795          { "nanglebins", 1, NULL, 'a' },
796          { "rcut",       1, NULL, 'c' },
797          { "dz", 1, NULL, 0 },
# Line 812 | Line 810 | cmdline_parser_internal (int argc, char * const *argv,
810          { "bo", 0, NULL, 0 },
811          { "bor",        0, NULL, 0 },
812          { "bad",        0, NULL, 0 },
813 +        { "count",      0, NULL, 0 },
814          { "gofr",       0, NULL, 'g' },
815          { "gofz",       0, NULL, 0 },
816          { "r_theta",    0, NULL, 0 },
817          { "r_omega",    0, NULL, 0 },
819 –        { "r_z",        0, NULL, 0 },
818          { "theta_omega",        0, NULL, 0 },
819          { "gxyz",       0, NULL, 0 },
820          { "twodgofr",   0, NULL, 0 },
# Line 828 | Line 826 | cmdline_parser_internal (int argc, char * const *argv,
826          { "p_angle",    0, NULL, 0 },
827          { "hxy",        0, NULL, 0 },
828          { "rho_r",      0, NULL, 0 },
829 +        { "angle_r",    0, NULL, 0 },
830          { "hullvol",    0, NULL, 0 },
831          { NULL, 0, NULL, 0 }
832        };
# Line 906 | Line 905 | cmdline_parser_internal (int argc, char * const *argv,
905                "nbins_x", 'x',
906                additional_error))
907              goto failure;
908 <        
908 >        
909            break;
910          case 'y':       /* number of bins in y axis.  */
911          
# Line 1018 | Line 1017 | cmdline_parser_internal (int argc, char * const *argv,
1017            break;
1018  
1019          case 0: /* Long option with no short option */
1020 <          /* number of bins in z axis.  */
1021 <          if (strcmp (long_options[option_index].name, "nbins_z") == 0)
1022 <          {
1023 <          
1024 <          
1025 <            if (update_arg( (void *)&(args_info->nbins_z_arg),
1026 <                 &(args_info->nbins_z_orig), &(args_info->nbins_z_given),
1027 <                &(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT,
1028 <                check_ambiguity, override, 0, 0,
1029 <                "nbins_z", '-',
1030 <                additional_error))
1031 <              goto failure;
1032 <          
1033 <          }
1020 >          /* number of bins in z axis.  */
1021 >          if (strcmp (long_options[option_index].name, "nbins_z") == 0)
1022 >          {        
1023 >                  
1024 >            if (update_arg( (void *)&(args_info->nbins_z_arg),
1025 >                &(args_info->nbins_z_orig), &(args_info->nbins_z_given),
1026 >                &(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT,
1027 >                check_ambiguity, override, 0, 0,
1028 >                "nbins_z", '-',
1029 >                 additional_error))
1030 >               goto failure;
1031 >                  
1032 >          }
1033 >
1034 >
1035            /* slab width (dz).  */
1036            else if (strcmp (long_options[option_index].name, "dz") == 0)
1037            {
# Line 1047 | Line 1047 | cmdline_parser_internal (int argc, char * const *argv,
1047            
1048            }
1049            /* maximum length (Defaults to 1/2 smallest length of first frame).  */
1050 <          else if (strcmp (long_options[option_index].name, "length") == 0)
1050 >          if (strcmp (long_options[option_index].name, "length") == 0)
1051            {
1052            
1053            
# Line 1247 | Line 1247 | cmdline_parser_internal (int argc, char * const *argv,
1247                  &(local_args_info.bad_given), optarg, 0, 0, ARG_NO,
1248                  check_ambiguity, override, 0, 0,
1249                  "bad", '-',
1250 +                additional_error))
1251 +              goto failure;
1252 +          
1253 +          }
1254 +          /* count of molecules matching selection criteria (and associated statistics).  */
1255 +          else if (strcmp (long_options[option_index].name, "count") == 0)
1256 +          {
1257 +          
1258 +            if (args_info->staticProps_group_counter && override)
1259 +              reset_group_staticProps (args_info);
1260 +            args_info->staticProps_group_counter += 1;
1261 +          
1262 +            if (update_arg( 0 ,
1263 +                 0 , &(args_info->count_given),
1264 +                &(local_args_info.count_given), optarg, 0, 0, ARG_NO,
1265 +                check_ambiguity, override, 0, 0,
1266 +                "count", '-',
1267                  additional_error))
1268                goto failure;
1269            
# Line 1302 | Line 1319 | cmdline_parser_internal (int argc, char * const *argv,
1319                goto failure;
1320            
1321            }
1305 –          /* g(r, z).  */
1306 –          else if (strcmp (long_options[option_index].name, "r_z") == 0)
1307 –          {
1308 –          
1309 –            if (args_info->staticProps_group_counter && override)
1310 –              reset_group_staticProps (args_info);
1311 –            args_info->staticProps_group_counter += 1;
1312 –          
1313 –            if (update_arg( 0 ,
1314 –                 0 , &(args_info->r_z_given),
1315 –                &(local_args_info.r_z_given), optarg, 0, 0, ARG_NO,
1316 –                check_ambiguity, override, 0, 0,
1317 –                "r_z", '-',
1318 –                additional_error))
1319 –              goto failure;
1320 –          
1321 –          }
1322            /* g(cos(theta), cos(omega)).  */
1323            else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1324            {
# Line 1455 | Line 1455 | cmdline_parser_internal (int argc, char * const *argv,
1455                goto failure;
1456            
1457            }
1458 +          /* angle of R.  */
1459 +          else if (strcmp (long_options[option_index].name, "angle_r") == 0)
1460 +          {
1461 +          
1462 +            if (args_info->staticProps_group_counter && override)
1463 +              reset_group_staticProps (args_info);
1464 +            args_info->staticProps_group_counter += 1;
1465 +          
1466 +            if (update_arg( 0 ,
1467 +                 0 , &(args_info->angle_r_given),
1468 +                &(local_args_info.angle_r_given), optarg, 0, 0, ARG_NO,
1469 +                check_ambiguity, override, 0, 0,
1470 +                "angle_r", '-',
1471 +                additional_error))
1472 +              goto failure;
1473 +          
1474 +          }
1475            /* hull volume of nanoparticle.  */
1476            else if (strcmp (long_options[option_index].name, "hullvol") == 0)
1477            {

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