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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 2048 by jmichalk, Fri Oct 31 18:40:40 2014 UTC vs.
Revision 2049 by gezelter, Tue Jan 6 21:44:10 2015 UTC

# Line 1 | Line 1
1   /*
2    File autogenerated by gengetopt version 2.22.4
3    generated with the following command:
4 <  gengetopt -i StaticProps.ggo -F StaticPropsCmd -c cpp
4 >  gengetopt --file-name=StaticPropsCmd --unamed-opts
5  
6    The developers of gengetopt consider the fixed text that goes in all
7    gengetopt output files to be in the public domain:
# Line 21 | Line 21
21   #define FIX_UNUSED(X) (void) (X) /* avoid warnings for unused params */
22   #endif
23  
24 + #ifdef WIN32
25 + #include "utils/wingetopt.h"
26 + #else
27   #include <getopt.h>
28 + #endif
29  
30   #include "StaticPropsCmd.h"
31  
32   const char *gengetopt_args_info_purpose = "";
33  
34 < const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]...";
34 > const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]... [FILES]...";
35  
36   const char *gengetopt_args_info_description = "";
37  
# Line 43 | Line 47 | const char *gengetopt_args_info_help[] = {
47    "      --nbins_z=INT             number of bins in z axis  (default=`100')",
48    "  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')",
49    "  -c, --rcut=DOUBLE             cutoff radius (rcut)",
50 +  "      --thetacut=DOUBLE         cutoff angle (thetacut)",
51    "      --dz=DOUBLE               slab width (dz)",
52    "      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
53    "      --zlength=DOUBLE          maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
# Line 94 | Line 99 | const char *gengetopt_args_info_help[] = {
99    "      --nitrile                 electrostatic potential to frequency map based \n                                  on the Cho nitrile fits",
100    "  -m, --multipole               average multipole moments contained within \n                                  cutoff spheres as a function of radius",
101    "      --surfDiffusion           X, Y, and R (surface diffusion if Z exposed and \n                                  bulk immobile) diffusion",
102 +  "      --hbond                   Hydrogen Bonding statistics using geometric \n                                  criteria (rcut and thetacut must be \n                                  specified)",
103      0
104   };
105  
# Line 132 | Line 138 | void clear_given (struct gengetopt_args_info *args_inf
138    args_info->nbins_z_given = 0 ;
139    args_info->nanglebins_given = 0 ;
140    args_info->rcut_given = 0 ;
141 +  args_info->thetacut_given = 0 ;
142    args_info->dz_given = 0 ;
143    args_info->length_given = 0 ;
144    args_info->zlength_given = 0 ;
# Line 182 | Line 189 | void clear_given (struct gengetopt_args_info *args_inf
189    args_info->nitrile_given = 0 ;
190    args_info->multipole_given = 0 ;
191    args_info->surfDiffusion_given = 0 ;
192 +  args_info->hbond_given = 0 ;
193    args_info->staticProps_group_counter = 0 ;
194   }
195  
# Line 206 | Line 214 | void clear_args (struct gengetopt_args_info *args_info
214    args_info->nanglebins_arg = 50;
215    args_info->nanglebins_orig = NULL;
216    args_info->rcut_orig = NULL;
217 +  args_info->thetacut_orig = NULL;
218    args_info->dz_orig = NULL;
219    args_info->length_orig = NULL;
220    args_info->zlength_orig = NULL;
# Line 249 | Line 258 | void init_args_info(struct gengetopt_args_info *args_i
258    args_info->nbins_z_help = gengetopt_args_info_help[8] ;
259    args_info->nanglebins_help = gengetopt_args_info_help[9] ;
260    args_info->rcut_help = gengetopt_args_info_help[10] ;
261 <  args_info->dz_help = gengetopt_args_info_help[11] ;
262 <  args_info->length_help = gengetopt_args_info_help[12] ;
263 <  args_info->zlength_help = gengetopt_args_info_help[13] ;
264 <  args_info->zoffset_help = gengetopt_args_info_help[14] ;
265 <  args_info->sele1_help = gengetopt_args_info_help[15] ;
266 <  args_info->sele2_help = gengetopt_args_info_help[16] ;
267 <  args_info->sele3_help = gengetopt_args_info_help[17] ;
268 <  args_info->refsele_help = gengetopt_args_info_help[18] ;
269 <  args_info->comsele_help = gengetopt_args_info_help[19] ;
270 <  args_info->seleoffset_help = gengetopt_args_info_help[20] ;
271 <  args_info->seleoffset2_help = gengetopt_args_info_help[21] ;
272 <  args_info->molname_help = gengetopt_args_info_help[22] ;
273 <  args_info->begin_help = gengetopt_args_info_help[23] ;
274 <  args_info->end_help = gengetopt_args_info_help[24] ;
275 <  args_info->radius_help = gengetopt_args_info_help[25] ;
276 <  args_info->voxelSize_help = gengetopt_args_info_help[26] ;
277 <  args_info->gaussWidth_help = gengetopt_args_info_help[27] ;
278 <  args_info->bo_help = gengetopt_args_info_help[29] ;
279 <  args_info->ior_help = gengetopt_args_info_help[30] ;
280 <  args_info->for_help = gengetopt_args_info_help[31] ;
281 <  args_info->bad_help = gengetopt_args_info_help[32] ;
282 <  args_info->count_help = gengetopt_args_info_help[33] ;
283 <  args_info->gofr_help = gengetopt_args_info_help[34] ;
284 <  args_info->gofz_help = gengetopt_args_info_help[35] ;
285 <  args_info->r_theta_help = gengetopt_args_info_help[36] ;
286 <  args_info->r_omega_help = gengetopt_args_info_help[37] ;
287 <  args_info->r_z_help = gengetopt_args_info_help[38] ;
288 <  args_info->theta_omega_help = gengetopt_args_info_help[39] ;
289 <  args_info->gxyz_help = gengetopt_args_info_help[40] ;
290 <  args_info->twodgofr_help = gengetopt_args_info_help[41] ;
291 <  args_info->p2_help = gengetopt_args_info_help[42] ;
292 <  args_info->rp2_help = gengetopt_args_info_help[43] ;
293 <  args_info->scd_help = gengetopt_args_info_help[44] ;
294 <  args_info->density_help = gengetopt_args_info_help[45] ;
295 <  args_info->slab_density_help = gengetopt_args_info_help[46] ;
296 <  args_info->p_angle_help = gengetopt_args_info_help[47] ;
297 <  args_info->hxy_help = gengetopt_args_info_help[48] ;
298 <  args_info->rho_r_help = gengetopt_args_info_help[49] ;
299 <  args_info->angle_r_help = gengetopt_args_info_help[50] ;
300 <  args_info->hullvol_help = gengetopt_args_info_help[51] ;
301 <  args_info->rodlength_help = gengetopt_args_info_help[52] ;
302 <  args_info->tet_param_help = gengetopt_args_info_help[53] ;
303 <  args_info->tet_param_z_help = gengetopt_args_info_help[54] ;
304 <  args_info->tet_param_xyz_help = gengetopt_args_info_help[55] ;
305 <  args_info->rnemdz_help = gengetopt_args_info_help[56] ;
306 <  args_info->rnemdr_help = gengetopt_args_info_help[57] ;
307 <  args_info->rnemdrt_help = gengetopt_args_info_help[58] ;
308 <  args_info->nitrile_help = gengetopt_args_info_help[59] ;
309 <  args_info->multipole_help = gengetopt_args_info_help[60] ;
310 <  args_info->surfDiffusion_help = gengetopt_args_info_help[61] ;
261 >  args_info->thetacut_help = gengetopt_args_info_help[11] ;
262 >  args_info->dz_help = gengetopt_args_info_help[12] ;
263 >  args_info->length_help = gengetopt_args_info_help[13] ;
264 >  args_info->zlength_help = gengetopt_args_info_help[14] ;
265 >  args_info->zoffset_help = gengetopt_args_info_help[15] ;
266 >  args_info->sele1_help = gengetopt_args_info_help[16] ;
267 >  args_info->sele2_help = gengetopt_args_info_help[17] ;
268 >  args_info->sele3_help = gengetopt_args_info_help[18] ;
269 >  args_info->refsele_help = gengetopt_args_info_help[19] ;
270 >  args_info->comsele_help = gengetopt_args_info_help[20] ;
271 >  args_info->seleoffset_help = gengetopt_args_info_help[21] ;
272 >  args_info->seleoffset2_help = gengetopt_args_info_help[22] ;
273 >  args_info->molname_help = gengetopt_args_info_help[23] ;
274 >  args_info->begin_help = gengetopt_args_info_help[24] ;
275 >  args_info->end_help = gengetopt_args_info_help[25] ;
276 >  args_info->radius_help = gengetopt_args_info_help[26] ;
277 >  args_info->voxelSize_help = gengetopt_args_info_help[27] ;
278 >  args_info->gaussWidth_help = gengetopt_args_info_help[28] ;
279 >  args_info->bo_help = gengetopt_args_info_help[30] ;
280 >  args_info->ior_help = gengetopt_args_info_help[31] ;
281 >  args_info->for_help = gengetopt_args_info_help[32] ;
282 >  args_info->bad_help = gengetopt_args_info_help[33] ;
283 >  args_info->count_help = gengetopt_args_info_help[34] ;
284 >  args_info->gofr_help = gengetopt_args_info_help[35] ;
285 >  args_info->gofz_help = gengetopt_args_info_help[36] ;
286 >  args_info->r_theta_help = gengetopt_args_info_help[37] ;
287 >  args_info->r_omega_help = gengetopt_args_info_help[38] ;
288 >  args_info->r_z_help = gengetopt_args_info_help[39] ;
289 >  args_info->theta_omega_help = gengetopt_args_info_help[40] ;
290 >  args_info->gxyz_help = gengetopt_args_info_help[41] ;
291 >  args_info->twodgofr_help = gengetopt_args_info_help[42] ;
292 >  args_info->p2_help = gengetopt_args_info_help[43] ;
293 >  args_info->rp2_help = gengetopt_args_info_help[44] ;
294 >  args_info->scd_help = gengetopt_args_info_help[45] ;
295 >  args_info->density_help = gengetopt_args_info_help[46] ;
296 >  args_info->slab_density_help = gengetopt_args_info_help[47] ;
297 >  args_info->p_angle_help = gengetopt_args_info_help[48] ;
298 >  args_info->hxy_help = gengetopt_args_info_help[49] ;
299 >  args_info->rho_r_help = gengetopt_args_info_help[50] ;
300 >  args_info->angle_r_help = gengetopt_args_info_help[51] ;
301 >  args_info->hullvol_help = gengetopt_args_info_help[52] ;
302 >  args_info->rodlength_help = gengetopt_args_info_help[53] ;
303 >  args_info->tet_param_help = gengetopt_args_info_help[54] ;
304 >  args_info->tet_param_z_help = gengetopt_args_info_help[55] ;
305 >  args_info->tet_param_xyz_help = gengetopt_args_info_help[56] ;
306 >  args_info->rnemdz_help = gengetopt_args_info_help[57] ;
307 >  args_info->rnemdr_help = gengetopt_args_info_help[58] ;
308 >  args_info->rnemdrt_help = gengetopt_args_info_help[59] ;
309 >  args_info->nitrile_help = gengetopt_args_info_help[60] ;
310 >  args_info->multipole_help = gengetopt_args_info_help[61] ;
311 >  args_info->surfDiffusion_help = gengetopt_args_info_help[62] ;
312 >  args_info->hbond_help = gengetopt_args_info_help[63] ;
313    
314   }
315  
# Line 340 | Line 351 | cmdline_parser_init (struct gengetopt_args_info *args_
351    clear_given (args_info);
352    clear_args (args_info);
353    init_args_info (args_info);
354 +
355 +  args_info->inputs = 0;
356 +  args_info->inputs_num = 0;
357   }
358  
359   void
# Line 378 | Line 392 | cmdline_parser_release (struct gengetopt_args_info *ar
392   static void
393   cmdline_parser_release (struct gengetopt_args_info *args_info)
394   {
395 <
395 >  unsigned int i;
396    free_string_field (&(args_info->input_arg));
397    free_string_field (&(args_info->input_orig));
398    free_string_field (&(args_info->output_arg));
# Line 390 | Line 404 | cmdline_parser_release (struct gengetopt_args_info *ar
404    free_string_field (&(args_info->nbins_z_orig));
405    free_string_field (&(args_info->nanglebins_orig));
406    free_string_field (&(args_info->rcut_orig));
407 +  free_string_field (&(args_info->thetacut_orig));
408    free_string_field (&(args_info->dz_orig));
409    free_string_field (&(args_info->length_orig));
410    free_string_field (&(args_info->zlength_orig));
# Line 415 | Line 430 | cmdline_parser_release (struct gengetopt_args_info *ar
430    free_string_field (&(args_info->gaussWidth_orig));
431    
432    
433 +  for (i = 0; i < args_info->inputs_num; ++i)
434 +    free (args_info->inputs [i]);
435  
436 +  if (args_info->inputs_num)
437 +    free (args_info->inputs);
438 +
439    clear_given (args_info);
440   }
441  
# Line 465 | Line 485 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
485      write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
486    if (args_info->rcut_given)
487      write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
488 +  if (args_info->thetacut_given)
489 +    write_into_file(outfile, "thetacut", args_info->thetacut_orig, 0);
490    if (args_info->dz_given)
491      write_into_file(outfile, "dz", args_info->dz_orig, 0);
492    if (args_info->length_given)
# Line 565 | Line 587 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
587      write_into_file(outfile, "multipole", 0, 0 );
588    if (args_info->surfDiffusion_given)
589      write_into_file(outfile, "surfDiffusion", 0, 0 );
590 +  if (args_info->hbond_given)
591 +    write_into_file(outfile, "hbond", 0, 0 );
592    
593  
594    i = EXIT_SUCCESS;
# Line 651 | Line 675 | reset_group_staticProps(struct gengetopt_args_info *ar
675    args_info->nitrile_given = 0 ;
676    args_info->multipole_given = 0 ;
677    args_info->surfDiffusion_given = 0 ;
678 +  args_info->hbond_given = 0 ;
679  
680    args_info->staticProps_group_counter = 0;
681   }
# Line 907 | Line 932 | cmdline_parser_internal (
932          { "nbins_z",    1, NULL, 0 },
933          { "nanglebins", 1, NULL, 'a' },
934          { "rcut",       1, NULL, 'c' },
935 +        { "thetacut",   1, NULL, 0 },
936          { "dz", 1, NULL, 0 },
937          { "length",     1, NULL, 0 },
938          { "zlength",    1, NULL, 0 },
# Line 957 | Line 983 | cmdline_parser_internal (
983          { "nitrile",    0, NULL, 0 },
984          { "multipole",  0, NULL, 'm' },
985          { "surfDiffusion",      0, NULL, 0 },
986 +        { "hbond",      0, NULL, 0 },
987          { 0,  0, 0, 0 }
988        };
989  
# Line 1202 | Line 1229 | cmdline_parser_internal (
1229                goto failure;
1230            
1231            }
1232 +          /* cutoff angle (thetacut).  */
1233 +          else if (strcmp (long_options[option_index].name, "thetacut") == 0)
1234 +          {
1235 +          
1236 +          
1237 +            if (update_arg( (void *)&(args_info->thetacut_arg),
1238 +                 &(args_info->thetacut_orig), &(args_info->thetacut_given),
1239 +                &(local_args_info.thetacut_given), optarg, 0, 0, ARG_DOUBLE,
1240 +                check_ambiguity, override, 0, 0,
1241 +                "thetacut", '-',
1242 +                additional_error))
1243 +              goto failure;
1244 +          
1245 +          }
1246            /* slab width (dz).  */
1247            else if (strcmp (long_options[option_index].name, "dz") == 0)
1248            {
# Line 1871 | Line 1912 | cmdline_parser_internal (
1912                goto failure;
1913            
1914            }
1915 +          /* Hydrogen Bonding statistics using geometric criteria (rcut and thetacut must be specified).  */
1916 +          else if (strcmp (long_options[option_index].name, "hbond") == 0)
1917 +          {
1918            
1919 +            if (args_info->staticProps_group_counter && override)
1920 +              reset_group_staticProps (args_info);
1921 +            args_info->staticProps_group_counter += 1;
1922 +          
1923 +            if (update_arg( 0 ,
1924 +                 0 , &(args_info->hbond_given),
1925 +                &(local_args_info.hbond_given), optarg, 0, 0, ARG_NO,
1926 +                check_ambiguity, override, 0, 0,
1927 +                "hbond", '-',
1928 +                additional_error))
1929 +              goto failure;
1930 +          
1931 +          }
1932 +          
1933            break;
1934          case '?':       /* Invalid option.  */
1935            /* `getopt_long' already printed an error message.  */
# Line 1900 | Line 1958 | cmdline_parser_internal (
1958  
1959    if ( error )
1960      return (EXIT_FAILURE);
1961 +
1962 +  if (optind < argc)
1963 +    {
1964 +      int i = 0 ;
1965 +      int found_prog_name = 0;
1966 +      /* whether program name, i.e., argv[0], is in the remaining args
1967 +         (this may happen with some implementations of getopt,
1968 +          but surely not with the one included by gengetopt) */
1969  
1970 +      i = optind;
1971 +      while (i < argc)
1972 +        if (argv[i++] == argv[0]) {
1973 +          found_prog_name = 1;
1974 +          break;
1975 +        }
1976 +      i = 0;
1977 +
1978 +      args_info->inputs_num = argc - optind - found_prog_name;
1979 +      args_info->inputs =
1980 +        (char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
1981 +      while (optind < argc)
1982 +        if (argv[optind++] != argv[0])
1983 +          args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
1984 +    }
1985 +
1986    return 0;
1987  
1988   failure:

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