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root/OpenMD/trunk/src/applications/staticProps/StaticPropsCmd.cpp
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Comparing trunk/src/applications/staticProps/StaticPropsCmd.cpp (file contents):
Revision 1991 by gezelter, Wed Apr 23 20:34:17 2014 UTC vs.
Revision 1994 by gezelter, Wed Apr 30 18:50:45 2014 UTC

# Line 64 | Line 64 | const char *gengetopt_args_info_help[] = {
64    "      --radius=DOUBLE           nanoparticle radius",
65    "\n Group: staticProps\n   an option of this group is required",
66    "      --bo                      bond order parameter (--rcut must be specified)",
67 <  "      --bor                     bond order parameter as a function of radius \n                                  (--rcut must be specified)",
67 >  "      --ior                     icosahedral bond order parameter as a function \n                                  of radius (--rcut must be specified)",
68 >  "      --for                     FCC bond order parameter as a function of \n                                  radius (--rcut must be specified)",
69    "      --bad                     N(theta) bond angle density within (--rcut must \n                                  be specified)",
70    "      --count                   count of molecules matching selection criteria \n                                  (and associated statistics)",
71    "  -g, --gofr                    g(r)",
# Line 91 | Line 92 | const char *gengetopt_args_info_help[] = {
92    "      --rnemdz                  slab-resolved RNEMD statistics (temperature, \n                                  density, velocity)",
93    "      --rnemdr                  shell-resolved RNEMD statistics (temperature, \n                                  density, angular velocity)",
94    "      --rnemdrt                 shell and angle-resolved RNEMD statistics \n                                  (temperature, density, angular velocity)",
95 +  "      --nitrile                 electrostatic potential to frequency map based \n                                  on the Cho nitrile fits",
96      0
97   };
98  
# Line 145 | Line 147 | void clear_given (struct gengetopt_args_info *args_inf
147    args_info->end_given = 0 ;
148    args_info->radius_given = 0 ;
149    args_info->bo_given = 0 ;
150 <  args_info->bor_given = 0 ;
150 >  args_info->ior_given = 0 ;
151 >  args_info->for_given = 0 ;
152    args_info->bad_given = 0 ;
153    args_info->count_given = 0 ;
154    args_info->gofr_given = 0 ;
# Line 172 | Line 175 | void clear_given (struct gengetopt_args_info *args_inf
175    args_info->rnemdz_given = 0 ;
176    args_info->rnemdr_given = 0 ;
177    args_info->rnemdrt_given = 0 ;
178 +  args_info->nitrile_given = 0 ;
179    args_info->staticProps_group_counter = 0 ;
180   }
181  
# Line 253 | Line 257 | void init_args_info(struct gengetopt_args_info *args_i
257    args_info->end_help = gengetopt_args_info_help[24] ;
258    args_info->radius_help = gengetopt_args_info_help[25] ;
259    args_info->bo_help = gengetopt_args_info_help[27] ;
260 <  args_info->bor_help = gengetopt_args_info_help[28] ;
261 <  args_info->bad_help = gengetopt_args_info_help[29] ;
262 <  args_info->count_help = gengetopt_args_info_help[30] ;
263 <  args_info->gofr_help = gengetopt_args_info_help[31] ;
264 <  args_info->gofz_help = gengetopt_args_info_help[32] ;
265 <  args_info->r_theta_help = gengetopt_args_info_help[33] ;
266 <  args_info->r_omega_help = gengetopt_args_info_help[34] ;
267 <  args_info->r_z_help = gengetopt_args_info_help[35] ;
268 <  args_info->theta_omega_help = gengetopt_args_info_help[36] ;
269 <  args_info->gxyz_help = gengetopt_args_info_help[37] ;
270 <  args_info->twodgofr_help = gengetopt_args_info_help[38] ;
271 <  args_info->p2_help = gengetopt_args_info_help[39] ;
272 <  args_info->rp2_help = gengetopt_args_info_help[40] ;
273 <  args_info->scd_help = gengetopt_args_info_help[41] ;
274 <  args_info->density_help = gengetopt_args_info_help[42] ;
275 <  args_info->slab_density_help = gengetopt_args_info_help[43] ;
276 <  args_info->p_angle_help = gengetopt_args_info_help[44] ;
277 <  args_info->hxy_help = gengetopt_args_info_help[45] ;
278 <  args_info->rho_r_help = gengetopt_args_info_help[46] ;
279 <  args_info->angle_r_help = gengetopt_args_info_help[47] ;
280 <  args_info->hullvol_help = gengetopt_args_info_help[48] ;
281 <  args_info->rodlength_help = gengetopt_args_info_help[49] ;
282 <  args_info->tet_param_help = gengetopt_args_info_help[50] ;
283 <  args_info->tet_param_z_help = gengetopt_args_info_help[51] ;
284 <  args_info->rnemdz_help = gengetopt_args_info_help[52] ;
285 <  args_info->rnemdr_help = gengetopt_args_info_help[53] ;
286 <  args_info->rnemdrt_help = gengetopt_args_info_help[54] ;
260 >  args_info->ior_help = gengetopt_args_info_help[28] ;
261 >  args_info->for_help = gengetopt_args_info_help[29] ;
262 >  args_info->bad_help = gengetopt_args_info_help[30] ;
263 >  args_info->count_help = gengetopt_args_info_help[31] ;
264 >  args_info->gofr_help = gengetopt_args_info_help[32] ;
265 >  args_info->gofz_help = gengetopt_args_info_help[33] ;
266 >  args_info->r_theta_help = gengetopt_args_info_help[34] ;
267 >  args_info->r_omega_help = gengetopt_args_info_help[35] ;
268 >  args_info->r_z_help = gengetopt_args_info_help[36] ;
269 >  args_info->theta_omega_help = gengetopt_args_info_help[37] ;
270 >  args_info->gxyz_help = gengetopt_args_info_help[38] ;
271 >  args_info->twodgofr_help = gengetopt_args_info_help[39] ;
272 >  args_info->p2_help = gengetopt_args_info_help[40] ;
273 >  args_info->rp2_help = gengetopt_args_info_help[41] ;
274 >  args_info->scd_help = gengetopt_args_info_help[42] ;
275 >  args_info->density_help = gengetopt_args_info_help[43] ;
276 >  args_info->slab_density_help = gengetopt_args_info_help[44] ;
277 >  args_info->p_angle_help = gengetopt_args_info_help[45] ;
278 >  args_info->hxy_help = gengetopt_args_info_help[46] ;
279 >  args_info->rho_r_help = gengetopt_args_info_help[47] ;
280 >  args_info->angle_r_help = gengetopt_args_info_help[48] ;
281 >  args_info->hullvol_help = gengetopt_args_info_help[49] ;
282 >  args_info->rodlength_help = gengetopt_args_info_help[50] ;
283 >  args_info->tet_param_help = gengetopt_args_info_help[51] ;
284 >  args_info->tet_param_z_help = gengetopt_args_info_help[52] ;
285 >  args_info->rnemdz_help = gengetopt_args_info_help[53] ;
286 >  args_info->rnemdr_help = gengetopt_args_info_help[54] ;
287 >  args_info->rnemdrt_help = gengetopt_args_info_help[55] ;
288 >  args_info->nitrile_help = gengetopt_args_info_help[56] ;
289    
290   }
291  
# Line 484 | Line 490 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
490      write_into_file(outfile, "radius", args_info->radius_orig, 0);
491    if (args_info->bo_given)
492      write_into_file(outfile, "bo", 0, 0 );
493 <  if (args_info->bor_given)
494 <    write_into_file(outfile, "bor", 0, 0 );
493 >  if (args_info->ior_given)
494 >    write_into_file(outfile, "ior", 0, 0 );
495 >  if (args_info->for_given)
496 >    write_into_file(outfile, "for", 0, 0 );
497    if (args_info->bad_given)
498      write_into_file(outfile, "bad", 0, 0 );
499    if (args_info->count_given)
# Line 538 | Line 546 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
546      write_into_file(outfile, "rnemdr", 0, 0 );
547    if (args_info->rnemdrt_given)
548      write_into_file(outfile, "rnemdrt", 0, 0 );
549 +  if (args_info->nitrile_given)
550 +    write_into_file(outfile, "nitrile", 0, 0 );
551    
552  
553    i = EXIT_SUCCESS;
# Line 592 | Line 602 | reset_group_staticProps(struct gengetopt_args_info *ar
602      return;
603    
604    args_info->bo_given = 0 ;
605 <  args_info->bor_given = 0 ;
605 >  args_info->ior_given = 0 ;
606 >  args_info->for_given = 0 ;
607    args_info->bad_given = 0 ;
608    args_info->count_given = 0 ;
609    args_info->gofr_given = 0 ;
# Line 619 | Line 630 | reset_group_staticProps(struct gengetopt_args_info *ar
630    args_info->rnemdz_given = 0 ;
631    args_info->rnemdr_given = 0 ;
632    args_info->rnemdrt_given = 0 ;
633 +  args_info->nitrile_given = 0 ;
634  
635    args_info->staticProps_group_counter = 0;
636   }
# Line 891 | Line 903 | cmdline_parser_internal (
903          { "end",        1, NULL, 0 },
904          { "radius",     1, NULL, 0 },
905          { "bo", 0, NULL, 0 },
906 <        { "bor",        0, NULL, 0 },
906 >        { "ior",        0, NULL, 0 },
907 >        { "for",        0, NULL, 0 },
908          { "bad",        0, NULL, 0 },
909          { "count",      0, NULL, 0 },
910          { "gofr",       0, NULL, 'g' },
# Line 918 | Line 931 | cmdline_parser_internal (
931          { "rnemdz",     0, NULL, 0 },
932          { "rnemdr",     0, NULL, 0 },
933          { "rnemdrt",    0, NULL, 0 },
934 +        { "nitrile",    0, NULL, 0 },
935          { 0,  0, 0, 0 }
936        };
937  
# Line 1349 | Line 1363 | cmdline_parser_internal (
1363                goto failure;
1364            
1365            }
1366 <          /* bond order parameter as a function of radius (--rcut must be specified).  */
1367 <          else if (strcmp (long_options[option_index].name, "bor") == 0)
1366 >          /* icosahedral bond order parameter as a function of radius (--rcut must be specified).  */
1367 >          else if (strcmp (long_options[option_index].name, "ior") == 0)
1368            {
1369            
1370              if (args_info->staticProps_group_counter && override)
# Line 1358 | Line 1372 | cmdline_parser_internal (
1372              args_info->staticProps_group_counter += 1;
1373            
1374              if (update_arg( 0 ,
1375 <                 0 , &(args_info->bor_given),
1376 <                &(local_args_info.bor_given), optarg, 0, 0, ARG_NO,
1375 >                 0 , &(args_info->ior_given),
1376 >                &(local_args_info.ior_given), optarg, 0, 0, ARG_NO,
1377                  check_ambiguity, override, 0, 0,
1378 <                "bor", '-',
1378 >                "ior", '-',
1379 >                additional_error))
1380 >              goto failure;
1381 >          
1382 >          }
1383 >          /* FCC bond order parameter as a function of radius (--rcut must be specified).  */
1384 >          else if (strcmp (long_options[option_index].name, "for") == 0)
1385 >          {
1386 >          
1387 >            if (args_info->staticProps_group_counter && override)
1388 >              reset_group_staticProps (args_info);
1389 >            args_info->staticProps_group_counter += 1;
1390 >          
1391 >            if (update_arg( 0 ,
1392 >                 0 , &(args_info->for_given),
1393 >                &(local_args_info.for_given), optarg, 0, 0, ARG_NO,
1394 >                check_ambiguity, override, 0, 0,
1395 >                "for", '-',
1396                  additional_error))
1397                goto failure;
1398            
# Line 1723 | Line 1754 | cmdline_parser_internal (
1754                goto failure;
1755            
1756            }
1757 +          /* electrostatic potential to frequency map based on the Cho nitrile fits.  */
1758 +          else if (strcmp (long_options[option_index].name, "nitrile") == 0)
1759 +          {
1760            
1761 +            if (args_info->staticProps_group_counter && override)
1762 +              reset_group_staticProps (args_info);
1763 +            args_info->staticProps_group_counter += 1;
1764 +          
1765 +            if (update_arg( 0 ,
1766 +                 0 , &(args_info->nitrile_given),
1767 +                &(local_args_info.nitrile_given), optarg, 0, 0, ARG_NO,
1768 +                check_ambiguity, override, 0, 0,
1769 +                "nitrile", '-',
1770 +                additional_error))
1771 +              goto failure;
1772 +          
1773 +          }
1774 +          
1775            break;
1776          case '?':       /* Invalid option.  */
1777            /* `getopt_long' already printed an error message.  */

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