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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 1843 by gezelter, Tue Jan 29 20:58:08 2013 UTC vs.
Revision 2031 by jmichalk, Fri Oct 31 18:40:40 2014 UTC

# Line 1 | Line 1
1   /*
2    File autogenerated by gengetopt version 2.22.4
3    generated with the following command:
4 <  gengetopt --file-name=StaticPropsCmd --unamed-opts
4 >  gengetopt -i StaticProps.ggo -F StaticPropsCmd -c cpp
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 27 | Line 27 | const char *gengetopt_args_info_purpose = "";
27  
28   const char *gengetopt_args_info_purpose = "";
29  
30 < const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]... [FILES]...";
30 > const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]...";
31  
32   const char *gengetopt_args_info_description = "";
33  
# Line 53 | Line 53 | const char *gengetopt_args_info_help[] = {
53    "      --refsele=selection script\n                                select reference (use and only use with --gxyz)",
54    "      --comsele=selection script\n                                select stunt doubles for center-of-mass \n                                  reference point",
55    "      --seleoffset=INT          global index offset for a second object (used \n                                  to define a vector between sites in molecule)",
56 +  "      --seleoffset2=INT         global index offset for a third object (used to \n                                  define a vector between sites in molecule)",
57    "      --molname=STRING          molecule name",
58    "      --begin=INT               begin internal index",
59    "      --end=INT                 end internal index",
60    "      --radius=DOUBLE           nanoparticle radius",
61 +  "  -v, --voxelSize=DOUBLE        voxel size (angstroms)",
62 +  "      --gaussWidth=DOUBLE       Gaussian width (angstroms)",
63    "\n Group: staticProps\n   an option of this group is required",
64    "      --bo                      bond order parameter (--rcut must be specified)",
65 <  "      --bor                     bond order parameter as a function of radius \n                                  (--rcut must be specified)",
65 >  "      --ior                     icosahedral bond order parameter as a function \n                                  of radius (--rcut must be specified)",
66 >  "      --for                     FCC bond order parameter as a function of \n                                  radius (--rcut must be specified)",
67    "      --bad                     N(theta) bond angle density within (--rcut must \n                                  be specified)",
68    "      --count                   count of molecules matching selection criteria \n                                  (and associated statistics)",
69    "  -g, --gofr                    g(r)",
# Line 75 | Line 79 | const char *gengetopt_args_info_help[] = {
79    "  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)",
80    "  -d, --density                 density plot",
81    "      --slab_density            slab density",
82 <  "      --p_angle                 p(cos(theta))",
82 >  "      --p_angle                 p(cos(theta)) (--sele1 must be specified, \n                                  --sele2 is optional)",
83    "      --hxy                     hxy",
84    "      --rho_r                   rho of R",
85    "      --angle_r                 angle of R",
# Line 83 | Line 87 | const char *gengetopt_args_info_help[] = {
87    "      --rodlength               length of nanorod",
88    "  -Q, --tet_param               tetrahedrality order parameter (Qk)",
89    "      --tet_param_z             spatially-resolved tetrahedrality order \n                                  parameter Qk(z)",
90 +  "      --tet_param_xyz           volume-resolved tetrahedrality order parameter \n                                  Qk(x,y,z).  (voxelSize, rcut, and gaussWidth \n                                  must be specified)",
91 +  "      --rnemdz                  slab-resolved RNEMD statistics (temperature, \n                                  density, velocity)",
92 +  "      --rnemdr                  shell-resolved RNEMD statistics (temperature, \n                                  density, angular velocity)",
93 +  "      --rnemdrt                 shell and angle-resolved RNEMD statistics \n                                  (temperature, density, angular velocity)",
94 +  "      --nitrile                 electrostatic potential to frequency map based \n                                  on the Cho nitrile fits",
95 +  "  -m, --multipole               average multipole moments contained within \n                                  cutoff spheres as a function of radius",
96 +  "      --surfDiffusion           X, Y, and R (surface diffusion if Z exposed and \n                                  bulk immobile) diffusion",
97      0
98   };
99  
# Line 131 | Line 142 | void clear_given (struct gengetopt_args_info *args_inf
142    args_info->refsele_given = 0 ;
143    args_info->comsele_given = 0 ;
144    args_info->seleoffset_given = 0 ;
145 +  args_info->seleoffset2_given = 0 ;
146    args_info->molname_given = 0 ;
147    args_info->begin_given = 0 ;
148    args_info->end_given = 0 ;
149    args_info->radius_given = 0 ;
150 +  args_info->voxelSize_given = 0 ;
151 +  args_info->gaussWidth_given = 0 ;
152    args_info->bo_given = 0 ;
153 <  args_info->bor_given = 0 ;
153 >  args_info->ior_given = 0 ;
154 >  args_info->for_given = 0 ;
155    args_info->bad_given = 0 ;
156    args_info->count_given = 0 ;
157    args_info->gofr_given = 0 ;
# Line 160 | Line 175 | void clear_given (struct gengetopt_args_info *args_inf
175    args_info->rodlength_given = 0 ;
176    args_info->tet_param_given = 0 ;
177    args_info->tet_param_z_given = 0 ;
178 +  args_info->tet_param_xyz_given = 0 ;
179 +  args_info->rnemdz_given = 0 ;
180 +  args_info->rnemdr_given = 0 ;
181 +  args_info->rnemdrt_given = 0 ;
182 +  args_info->nitrile_given = 0 ;
183 +  args_info->multipole_given = 0 ;
184 +  args_info->surfDiffusion_given = 0 ;
185    args_info->staticProps_group_counter = 0 ;
186   }
187  
# Line 200 | Line 222 | void clear_args (struct gengetopt_args_info *args_info
222    args_info->comsele_arg = NULL;
223    args_info->comsele_orig = NULL;
224    args_info->seleoffset_orig = NULL;
225 +  args_info->seleoffset2_orig = NULL;
226    args_info->molname_arg = NULL;
227    args_info->molname_orig = NULL;
228    args_info->begin_orig = NULL;
229    args_info->end_orig = NULL;
230    args_info->radius_orig = NULL;
231 +  args_info->voxelSize_orig = NULL;
232 +  args_info->gaussWidth_orig = NULL;
233    
234   }
235  
# Line 234 | Line 259 | void init_args_info(struct gengetopt_args_info *args_i
259    args_info->refsele_help = gengetopt_args_info_help[18] ;
260    args_info->comsele_help = gengetopt_args_info_help[19] ;
261    args_info->seleoffset_help = gengetopt_args_info_help[20] ;
262 <  args_info->molname_help = gengetopt_args_info_help[21] ;
263 <  args_info->begin_help = gengetopt_args_info_help[22] ;
264 <  args_info->end_help = gengetopt_args_info_help[23] ;
265 <  args_info->radius_help = gengetopt_args_info_help[24] ;
266 <  args_info->bo_help = gengetopt_args_info_help[26] ;
267 <  args_info->bor_help = gengetopt_args_info_help[27] ;
268 <  args_info->bad_help = gengetopt_args_info_help[28] ;
269 <  args_info->count_help = gengetopt_args_info_help[29] ;
270 <  args_info->gofr_help = gengetopt_args_info_help[30] ;
271 <  args_info->gofz_help = gengetopt_args_info_help[31] ;
272 <  args_info->r_theta_help = gengetopt_args_info_help[32] ;
273 <  args_info->r_omega_help = gengetopt_args_info_help[33] ;
274 <  args_info->r_z_help = gengetopt_args_info_help[34] ;
275 <  args_info->theta_omega_help = gengetopt_args_info_help[35] ;
276 <  args_info->gxyz_help = gengetopt_args_info_help[36] ;
277 <  args_info->twodgofr_help = gengetopt_args_info_help[37] ;
278 <  args_info->p2_help = gengetopt_args_info_help[38] ;
279 <  args_info->rp2_help = gengetopt_args_info_help[39] ;
280 <  args_info->scd_help = gengetopt_args_info_help[40] ;
281 <  args_info->density_help = gengetopt_args_info_help[41] ;
282 <  args_info->slab_density_help = gengetopt_args_info_help[42] ;
283 <  args_info->p_angle_help = gengetopt_args_info_help[43] ;
284 <  args_info->hxy_help = gengetopt_args_info_help[44] ;
285 <  args_info->rho_r_help = gengetopt_args_info_help[45] ;
286 <  args_info->angle_r_help = gengetopt_args_info_help[46] ;
287 <  args_info->hullvol_help = gengetopt_args_info_help[47] ;
288 <  args_info->rodlength_help = gengetopt_args_info_help[48] ;
289 <  args_info->tet_param_help = gengetopt_args_info_help[49] ;
290 <  args_info->tet_param_z_help = gengetopt_args_info_help[50] ;
262 >  args_info->seleoffset2_help = gengetopt_args_info_help[21] ;
263 >  args_info->molname_help = gengetopt_args_info_help[22] ;
264 >  args_info->begin_help = gengetopt_args_info_help[23] ;
265 >  args_info->end_help = gengetopt_args_info_help[24] ;
266 >  args_info->radius_help = gengetopt_args_info_help[25] ;
267 >  args_info->voxelSize_help = gengetopt_args_info_help[26] ;
268 >  args_info->gaussWidth_help = gengetopt_args_info_help[27] ;
269 >  args_info->bo_help = gengetopt_args_info_help[29] ;
270 >  args_info->ior_help = gengetopt_args_info_help[30] ;
271 >  args_info->for_help = gengetopt_args_info_help[31] ;
272 >  args_info->bad_help = gengetopt_args_info_help[32] ;
273 >  args_info->count_help = gengetopt_args_info_help[33] ;
274 >  args_info->gofr_help = gengetopt_args_info_help[34] ;
275 >  args_info->gofz_help = gengetopt_args_info_help[35] ;
276 >  args_info->r_theta_help = gengetopt_args_info_help[36] ;
277 >  args_info->r_omega_help = gengetopt_args_info_help[37] ;
278 >  args_info->r_z_help = gengetopt_args_info_help[38] ;
279 >  args_info->theta_omega_help = gengetopt_args_info_help[39] ;
280 >  args_info->gxyz_help = gengetopt_args_info_help[40] ;
281 >  args_info->twodgofr_help = gengetopt_args_info_help[41] ;
282 >  args_info->p2_help = gengetopt_args_info_help[42] ;
283 >  args_info->rp2_help = gengetopt_args_info_help[43] ;
284 >  args_info->scd_help = gengetopt_args_info_help[44] ;
285 >  args_info->density_help = gengetopt_args_info_help[45] ;
286 >  args_info->slab_density_help = gengetopt_args_info_help[46] ;
287 >  args_info->p_angle_help = gengetopt_args_info_help[47] ;
288 >  args_info->hxy_help = gengetopt_args_info_help[48] ;
289 >  args_info->rho_r_help = gengetopt_args_info_help[49] ;
290 >  args_info->angle_r_help = gengetopt_args_info_help[50] ;
291 >  args_info->hullvol_help = gengetopt_args_info_help[51] ;
292 >  args_info->rodlength_help = gengetopt_args_info_help[52] ;
293 >  args_info->tet_param_help = gengetopt_args_info_help[53] ;
294 >  args_info->tet_param_z_help = gengetopt_args_info_help[54] ;
295 >  args_info->tet_param_xyz_help = gengetopt_args_info_help[55] ;
296 >  args_info->rnemdz_help = gengetopt_args_info_help[56] ;
297 >  args_info->rnemdr_help = gengetopt_args_info_help[57] ;
298 >  args_info->rnemdrt_help = gengetopt_args_info_help[58] ;
299 >  args_info->nitrile_help = gengetopt_args_info_help[59] ;
300 >  args_info->multipole_help = gengetopt_args_info_help[60] ;
301 >  args_info->surfDiffusion_help = gengetopt_args_info_help[61] ;
302    
303   }
304  
# Line 304 | Line 340 | cmdline_parser_init (struct gengetopt_args_info *args_
340    clear_given (args_info);
341    clear_args (args_info);
342    init_args_info (args_info);
307 –
308 –  args_info->inputs = 0;
309 –  args_info->inputs_num = 0;
343   }
344  
345   void
# Line 345 | Line 378 | cmdline_parser_release (struct gengetopt_args_info *ar
378   static void
379   cmdline_parser_release (struct gengetopt_args_info *args_info)
380   {
381 <  unsigned int i;
381 >
382    free_string_field (&(args_info->input_arg));
383    free_string_field (&(args_info->input_orig));
384    free_string_field (&(args_info->output_arg));
# Line 372 | Line 405 | cmdline_parser_release (struct gengetopt_args_info *ar
405    free_string_field (&(args_info->comsele_arg));
406    free_string_field (&(args_info->comsele_orig));
407    free_string_field (&(args_info->seleoffset_orig));
408 +  free_string_field (&(args_info->seleoffset2_orig));
409    free_string_field (&(args_info->molname_arg));
410    free_string_field (&(args_info->molname_orig));
411    free_string_field (&(args_info->begin_orig));
412    free_string_field (&(args_info->end_orig));
413    free_string_field (&(args_info->radius_orig));
414 +  free_string_field (&(args_info->voxelSize_orig));
415 +  free_string_field (&(args_info->gaussWidth_orig));
416    
417    
382 –  for (i = 0; i < args_info->inputs_num; ++i)
383 –    free (args_info->inputs [i]);
418  
385 –  if (args_info->inputs_num)
386 –    free (args_info->inputs);
387 –
419    clear_given (args_info);
420   }
421  
# Line 454 | Line 485 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
485      write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
486    if (args_info->seleoffset_given)
487      write_into_file(outfile, "seleoffset", args_info->seleoffset_orig, 0);
488 +  if (args_info->seleoffset2_given)
489 +    write_into_file(outfile, "seleoffset2", args_info->seleoffset2_orig, 0);
490    if (args_info->molname_given)
491      write_into_file(outfile, "molname", args_info->molname_orig, 0);
492    if (args_info->begin_given)
# Line 462 | Line 495 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
495      write_into_file(outfile, "end", args_info->end_orig, 0);
496    if (args_info->radius_given)
497      write_into_file(outfile, "radius", args_info->radius_orig, 0);
498 +  if (args_info->voxelSize_given)
499 +    write_into_file(outfile, "voxelSize", args_info->voxelSize_orig, 0);
500 +  if (args_info->gaussWidth_given)
501 +    write_into_file(outfile, "gaussWidth", args_info->gaussWidth_orig, 0);
502    if (args_info->bo_given)
503      write_into_file(outfile, "bo", 0, 0 );
504 <  if (args_info->bor_given)
505 <    write_into_file(outfile, "bor", 0, 0 );
504 >  if (args_info->ior_given)
505 >    write_into_file(outfile, "ior", 0, 0 );
506 >  if (args_info->for_given)
507 >    write_into_file(outfile, "for", 0, 0 );
508    if (args_info->bad_given)
509      write_into_file(outfile, "bad", 0, 0 );
510    if (args_info->count_given)
# Line 512 | Line 551 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
551      write_into_file(outfile, "tet_param", 0, 0 );
552    if (args_info->tet_param_z_given)
553      write_into_file(outfile, "tet_param_z", 0, 0 );
554 +  if (args_info->tet_param_xyz_given)
555 +    write_into_file(outfile, "tet_param_xyz", 0, 0 );
556 +  if (args_info->rnemdz_given)
557 +    write_into_file(outfile, "rnemdz", 0, 0 );
558 +  if (args_info->rnemdr_given)
559 +    write_into_file(outfile, "rnemdr", 0, 0 );
560 +  if (args_info->rnemdrt_given)
561 +    write_into_file(outfile, "rnemdrt", 0, 0 );
562 +  if (args_info->nitrile_given)
563 +    write_into_file(outfile, "nitrile", 0, 0 );
564 +  if (args_info->multipole_given)
565 +    write_into_file(outfile, "multipole", 0, 0 );
566 +  if (args_info->surfDiffusion_given)
567 +    write_into_file(outfile, "surfDiffusion", 0, 0 );
568    
569  
570    i = EXIT_SUCCESS;
# Line 566 | Line 619 | reset_group_staticProps(struct gengetopt_args_info *ar
619      return;
620    
621    args_info->bo_given = 0 ;
622 <  args_info->bor_given = 0 ;
622 >  args_info->ior_given = 0 ;
623 >  args_info->for_given = 0 ;
624    args_info->bad_given = 0 ;
625    args_info->count_given = 0 ;
626    args_info->gofr_given = 0 ;
# Line 590 | Line 644 | reset_group_staticProps(struct gengetopt_args_info *ar
644    args_info->rodlength_given = 0 ;
645    args_info->tet_param_given = 0 ;
646    args_info->tet_param_z_given = 0 ;
647 +  args_info->tet_param_xyz_given = 0 ;
648 +  args_info->rnemdz_given = 0 ;
649 +  args_info->rnemdr_given = 0 ;
650 +  args_info->rnemdrt_given = 0 ;
651 +  args_info->nitrile_given = 0 ;
652 +  args_info->multipole_given = 0 ;
653 +  args_info->surfDiffusion_given = 0 ;
654  
655    args_info->staticProps_group_counter = 0;
656   }
# Line 856 | Line 917 | cmdline_parser_internal (
917          { "refsele",    1, NULL, 0 },
918          { "comsele",    1, NULL, 0 },
919          { "seleoffset", 1, NULL, 0 },
920 +        { "seleoffset2",        1, NULL, 0 },
921          { "molname",    1, NULL, 0 },
922          { "begin",      1, NULL, 0 },
923          { "end",        1, NULL, 0 },
924          { "radius",     1, NULL, 0 },
925 +        { "voxelSize",  1, NULL, 'v' },
926 +        { "gaussWidth", 1, NULL, 0 },
927          { "bo", 0, NULL, 0 },
928 <        { "bor",        0, NULL, 0 },
928 >        { "ior",        0, NULL, 0 },
929 >        { "for",        0, NULL, 0 },
930          { "bad",        0, NULL, 0 },
931          { "count",      0, NULL, 0 },
932          { "gofr",       0, NULL, 'g' },
# Line 885 | Line 950 | cmdline_parser_internal (
950          { "rodlength",  0, NULL, 0 },
951          { "tet_param",  0, NULL, 'Q' },
952          { "tet_param_z",        0, NULL, 0 },
953 +        { "tet_param_xyz",      0, NULL, 0 },
954 +        { "rnemdz",     0, NULL, 0 },
955 +        { "rnemdr",     0, NULL, 0 },
956 +        { "rnemdrt",    0, NULL, 0 },
957 +        { "nitrile",    0, NULL, 0 },
958 +        { "multipole",  0, NULL, 'm' },
959 +        { "surfDiffusion",      0, NULL, 0 },
960          { 0,  0, 0, 0 }
961        };
962  
963 <      c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsdQ", long_options, &option_index);
963 >      c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:v:gpsdQm", long_options, &option_index);
964  
965        if (c == -1) break;       /* Exit from `while (1)' loop.  */
966  
# Line 1012 | Line 1084 | cmdline_parser_internal (
1084              goto failure;
1085          
1086            break;
1087 +        case 'v':       /* voxel size (angstroms).  */
1088 +        
1089 +        
1090 +          if (update_arg( (void *)&(args_info->voxelSize_arg),
1091 +               &(args_info->voxelSize_orig), &(args_info->voxelSize_given),
1092 +              &(local_args_info.voxelSize_given), optarg, 0, 0, ARG_DOUBLE,
1093 +              check_ambiguity, override, 0, 0,
1094 +              "voxelSize", 'v',
1095 +              additional_error))
1096 +            goto failure;
1097 +        
1098 +          break;
1099          case 'g':       /* g(r).  */
1100          
1101            if (args_info->staticProps_group_counter && override)
# Line 1083 | Line 1167 | cmdline_parser_internal (
1167                &(local_args_info.tet_param_given), optarg, 0, 0, ARG_NO,
1168                check_ambiguity, override, 0, 0,
1169                "tet_param", 'Q',
1170 +              additional_error))
1171 +            goto failure;
1172 +        
1173 +          break;
1174 +        case 'm':       /* average multipole moments contained within cutoff spheres as a function of radius.  */
1175 +        
1176 +          if (args_info->staticProps_group_counter && override)
1177 +            reset_group_staticProps (args_info);
1178 +          args_info->staticProps_group_counter += 1;
1179 +        
1180 +          if (update_arg( 0 ,
1181 +               0 , &(args_info->multipole_given),
1182 +              &(local_args_info.multipole_given), optarg, 0, 0, ARG_NO,
1183 +              check_ambiguity, override, 0, 0,
1184 +              "multipole", 'm',
1185                additional_error))
1186              goto failure;
1187          
# Line 1229 | Line 1328 | cmdline_parser_internal (
1328                goto failure;
1329            
1330            }
1331 +          /* global index offset for a third object (used to define a vector between sites in molecule).  */
1332 +          else if (strcmp (long_options[option_index].name, "seleoffset2") == 0)
1333 +          {
1334 +          
1335 +          
1336 +            if (update_arg( (void *)&(args_info->seleoffset2_arg),
1337 +                 &(args_info->seleoffset2_orig), &(args_info->seleoffset2_given),
1338 +                &(local_args_info.seleoffset2_given), optarg, 0, 0, ARG_INT,
1339 +                check_ambiguity, override, 0, 0,
1340 +                "seleoffset2", '-',
1341 +                additional_error))
1342 +              goto failure;
1343 +          
1344 +          }
1345            /* molecule name.  */
1346            else if (strcmp (long_options[option_index].name, "molname") == 0)
1347            {
# Line 1285 | Line 1398 | cmdline_parser_internal (
1398                goto failure;
1399            
1400            }
1401 +          /* Gaussian width (angstroms).  */
1402 +          else if (strcmp (long_options[option_index].name, "gaussWidth") == 0)
1403 +          {
1404 +          
1405 +          
1406 +            if (update_arg( (void *)&(args_info->gaussWidth_arg),
1407 +                 &(args_info->gaussWidth_orig), &(args_info->gaussWidth_given),
1408 +                &(local_args_info.gaussWidth_given), optarg, 0, 0, ARG_DOUBLE,
1409 +                check_ambiguity, override, 0, 0,
1410 +                "gaussWidth", '-',
1411 +                additional_error))
1412 +              goto failure;
1413 +          
1414 +          }
1415            /* bond order parameter (--rcut must be specified).  */
1416            else if (strcmp (long_options[option_index].name, "bo") == 0)
1417            {
# Line 1302 | Line 1429 | cmdline_parser_internal (
1429                goto failure;
1430            
1431            }
1432 <          /* bond order parameter as a function of radius (--rcut must be specified).  */
1433 <          else if (strcmp (long_options[option_index].name, "bor") == 0)
1432 >          /* icosahedral bond order parameter as a function of radius (--rcut must be specified).  */
1433 >          else if (strcmp (long_options[option_index].name, "ior") == 0)
1434            {
1435            
1436              if (args_info->staticProps_group_counter && override)
# Line 1311 | Line 1438 | cmdline_parser_internal (
1438              args_info->staticProps_group_counter += 1;
1439            
1440              if (update_arg( 0 ,
1441 <                 0 , &(args_info->bor_given),
1442 <                &(local_args_info.bor_given), optarg, 0, 0, ARG_NO,
1441 >                 0 , &(args_info->ior_given),
1442 >                &(local_args_info.ior_given), optarg, 0, 0, ARG_NO,
1443                  check_ambiguity, override, 0, 0,
1444 <                "bor", '-',
1444 >                "ior", '-',
1445                  additional_error))
1446                goto failure;
1447            
1448            }
1449 +          /* FCC bond order parameter as a function of radius (--rcut must be specified).  */
1450 +          else if (strcmp (long_options[option_index].name, "for") == 0)
1451 +          {
1452 +          
1453 +            if (args_info->staticProps_group_counter && override)
1454 +              reset_group_staticProps (args_info);
1455 +            args_info->staticProps_group_counter += 1;
1456 +          
1457 +            if (update_arg( 0 ,
1458 +                 0 , &(args_info->for_given),
1459 +                &(local_args_info.for_given), optarg, 0, 0, ARG_NO,
1460 +                check_ambiguity, override, 0, 0,
1461 +                "for", '-',
1462 +                additional_error))
1463 +              goto failure;
1464 +          
1465 +          }
1466            /* N(theta) bond angle density within (--rcut must be specified).  */
1467            else if (strcmp (long_options[option_index].name, "bad") == 0)
1468            {
# Line 1506 | Line 1650 | cmdline_parser_internal (
1650                goto failure;
1651            
1652            }
1653 <          /* p(cos(theta)).  */
1653 >          /* p(cos(theta)) (--sele1 must be specified, --sele2 is optional).  */
1654            else if (strcmp (long_options[option_index].name, "p_angle") == 0)
1655            {
1656            
# Line 1621 | Line 1765 | cmdline_parser_internal (
1765                  &(local_args_info.tet_param_z_given), optarg, 0, 0, ARG_NO,
1766                  check_ambiguity, override, 0, 0,
1767                  "tet_param_z", '-',
1768 +                additional_error))
1769 +              goto failure;
1770 +          
1771 +          }
1772 +          /* volume-resolved tetrahedrality order parameter Qk(x,y,z).  (voxelSize, rcut, and gaussWidth must be specified).  */
1773 +          else if (strcmp (long_options[option_index].name, "tet_param_xyz") == 0)
1774 +          {
1775 +          
1776 +            if (args_info->staticProps_group_counter && override)
1777 +              reset_group_staticProps (args_info);
1778 +            args_info->staticProps_group_counter += 1;
1779 +          
1780 +            if (update_arg( 0 ,
1781 +                 0 , &(args_info->tet_param_xyz_given),
1782 +                &(local_args_info.tet_param_xyz_given), optarg, 0, 0, ARG_NO,
1783 +                check_ambiguity, override, 0, 0,
1784 +                "tet_param_xyz", '-',
1785                  additional_error))
1786                goto failure;
1787            
1788            }
1789 +          /* slab-resolved RNEMD statistics (temperature, density, velocity).  */
1790 +          else if (strcmp (long_options[option_index].name, "rnemdz") == 0)
1791 +          {
1792            
1793 +            if (args_info->staticProps_group_counter && override)
1794 +              reset_group_staticProps (args_info);
1795 +            args_info->staticProps_group_counter += 1;
1796 +          
1797 +            if (update_arg( 0 ,
1798 +                 0 , &(args_info->rnemdz_given),
1799 +                &(local_args_info.rnemdz_given), optarg, 0, 0, ARG_NO,
1800 +                check_ambiguity, override, 0, 0,
1801 +                "rnemdz", '-',
1802 +                additional_error))
1803 +              goto failure;
1804 +          
1805 +          }
1806 +          /* shell-resolved RNEMD statistics (temperature, density, angular velocity).  */
1807 +          else if (strcmp (long_options[option_index].name, "rnemdr") == 0)
1808 +          {
1809 +          
1810 +            if (args_info->staticProps_group_counter && override)
1811 +              reset_group_staticProps (args_info);
1812 +            args_info->staticProps_group_counter += 1;
1813 +          
1814 +            if (update_arg( 0 ,
1815 +                 0 , &(args_info->rnemdr_given),
1816 +                &(local_args_info.rnemdr_given), optarg, 0, 0, ARG_NO,
1817 +                check_ambiguity, override, 0, 0,
1818 +                "rnemdr", '-',
1819 +                additional_error))
1820 +              goto failure;
1821 +          
1822 +          }
1823 +          /* shell and angle-resolved RNEMD statistics (temperature, density, angular velocity).  */
1824 +          else if (strcmp (long_options[option_index].name, "rnemdrt") == 0)
1825 +          {
1826 +          
1827 +            if (args_info->staticProps_group_counter && override)
1828 +              reset_group_staticProps (args_info);
1829 +            args_info->staticProps_group_counter += 1;
1830 +          
1831 +            if (update_arg( 0 ,
1832 +                 0 , &(args_info->rnemdrt_given),
1833 +                &(local_args_info.rnemdrt_given), optarg, 0, 0, ARG_NO,
1834 +                check_ambiguity, override, 0, 0,
1835 +                "rnemdrt", '-',
1836 +                additional_error))
1837 +              goto failure;
1838 +          
1839 +          }
1840 +          /* electrostatic potential to frequency map based on the Cho nitrile fits.  */
1841 +          else if (strcmp (long_options[option_index].name, "nitrile") == 0)
1842 +          {
1843 +          
1844 +            if (args_info->staticProps_group_counter && override)
1845 +              reset_group_staticProps (args_info);
1846 +            args_info->staticProps_group_counter += 1;
1847 +          
1848 +            if (update_arg( 0 ,
1849 +                 0 , &(args_info->nitrile_given),
1850 +                &(local_args_info.nitrile_given), optarg, 0, 0, ARG_NO,
1851 +                check_ambiguity, override, 0, 0,
1852 +                "nitrile", '-',
1853 +                additional_error))
1854 +              goto failure;
1855 +          
1856 +          }
1857 +          /* X, Y, and R (surface diffusion if Z exposed and bulk immobile) diffusion.  */
1858 +          else if (strcmp (long_options[option_index].name, "surfDiffusion") == 0)
1859 +          {
1860 +          
1861 +            if (args_info->staticProps_group_counter && override)
1862 +              reset_group_staticProps (args_info);
1863 +            args_info->staticProps_group_counter += 1;
1864 +          
1865 +            if (update_arg( 0 ,
1866 +                 0 , &(args_info->surfDiffusion_given),
1867 +                &(local_args_info.surfDiffusion_given), optarg, 0, 0, ARG_NO,
1868 +                check_ambiguity, override, 0, 0,
1869 +                "surfDiffusion", '-',
1870 +                additional_error))
1871 +              goto failure;
1872 +          
1873 +          }
1874 +          
1875            break;
1876          case '?':       /* Invalid option.  */
1877            /* `getopt_long' already printed an error message.  */
# Line 1655 | Line 1901 | cmdline_parser_internal (
1901    if ( error )
1902      return (EXIT_FAILURE);
1903  
1658 –  if (optind < argc)
1659 –    {
1660 –      int i = 0 ;
1661 –      int found_prog_name = 0;
1662 –      /* whether program name, i.e., argv[0], is in the remaining args
1663 –         (this may happen with some implementations of getopt,
1664 –          but surely not with the one included by gengetopt) */
1665 –
1666 –      i = optind;
1667 –      while (i < argc)
1668 –        if (argv[i++] == argv[0]) {
1669 –          found_prog_name = 1;
1670 –          break;
1671 –        }
1672 –      i = 0;
1673 –
1674 –      args_info->inputs_num = argc - optind - found_prog_name;
1675 –      args_info->inputs =
1676 –        (char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
1677 –      while (optind < argc)
1678 –        if (argv[optind++] != argv[0])
1679 –          args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
1680 –    }
1681 –
1904    return 0;
1905  
1906   failure:

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