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root/OpenMD/trunk/src/applications/staticProps/StaticPropsCmd.cpp
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Comparing:
branches/development/src/applications/staticProps/StaticPropsCmd.cpp (file contents), Revision 1762 by plouden, Thu Jun 28 20:17:33 2012 UTC vs.
trunk/src/applications/staticProps/StaticPropsCmd.cpp (file contents), Revision 2015 by gezelter, Wed Aug 13 20:42:43 2014 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 -c cpp -F StaticPropsCmd -u
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  
# Line 52 | Line 56 | const char *gengetopt_args_info_help[] = {
56    "      --sele3=selection script  select the third stuntdouble set",
57    "      --refsele=selection script\n                                select reference (use and only use with --gxyz)",
58    "      --comsele=selection script\n                                select stunt doubles for center-of-mass \n                                  reference point",
59 +  "      --seleoffset=INT          global index offset for a second object (used \n                                  to define a vector between sites in molecule)",
60 +  "      --seleoffset2=INT         global index offset for a third object (used to \n                                  define a vector between sites in molecule)",
61    "      --molname=STRING          molecule name",
62    "      --begin=INT               begin internal index",
63    "      --end=INT                 end internal index",
64    "      --radius=DOUBLE           nanoparticle radius",
65 +  "  -v, --voxelSize=DOUBLE        voxel size (angstroms)",
66 +  "      --gaussWidth=DOUBLE       Gaussian width (angstroms)",
67    "\n Group: staticProps\n   an option of this group is required",
68    "      --bo                      bond order parameter (--rcut must be specified)",
69 <  "      --bor                     bond order parameter as a function of radius \n                                  (--rcut must be specified)",
69 >  "      --ior                     icosahedral bond order parameter as a function \n                                  of radius (--rcut must be specified)",
70 >  "      --for                     FCC bond order parameter as a function of \n                                  radius (--rcut must be specified)",
71    "      --bad                     N(theta) bond angle density within (--rcut must \n                                  be specified)",
72    "      --count                   count of molecules matching selection criteria \n                                  (and associated statistics)",
73    "  -g, --gofr                    g(r)",
# Line 74 | Line 83 | const char *gengetopt_args_info_help[] = {
83    "  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)",
84    "  -d, --density                 density plot",
85    "      --slab_density            slab density",
86 <  "      --p_angle                 p(cos(theta))",
86 >  "      --p_angle                 p(cos(theta)) (--sele1 must be specified, \n                                  --sele2 is optional)",
87    "      --hxy                     hxy",
88    "      --rho_r                   rho of R",
89    "      --angle_r                 angle of R",
90    "      --hullvol                 hull volume of nanoparticle",
91    "      --rodlength               length of nanorod",
92 <  "  -Q, --tet_param               tetrahedrality order parameter",
93 <  "      --tet_param_z             tetrahedrality order parameter by zbin(--sele1 \n                                  must be specified)",
92 >  "  -Q, --tet_param               tetrahedrality order parameter (Qk)",
93 >  "      --tet_param_z             spatially-resolved tetrahedrality order \n                                  parameter Qk(z)",
94 >  "      --tet_param_xyz           volume-resolved tetrahedrality order parameter \n                                  Qk(x,y,z).  (voxelSize, rcut, and gaussWidth \n                                  must be specified)",
95 >  "      --rnemdz                  slab-resolved RNEMD statistics (temperature, \n                                  density, velocity)",
96 >  "      --rnemdr                  shell-resolved RNEMD statistics (temperature, \n                                  density, angular velocity)",
97 >  "      --rnemdrt                 shell and angle-resolved RNEMD statistics \n                                  (temperature, density, angular velocity)",
98 >  "      --nitrile                 electrostatic potential to frequency map based \n                                  on the Cho nitrile fits",
99 >  "  -m, --multipole               average multipole moments contained within \n                                  cutoff spheres as a function of radius",
100      0
101   };
102  
# Line 129 | Line 144 | void clear_given (struct gengetopt_args_info *args_inf
144    args_info->sele3_given = 0 ;
145    args_info->refsele_given = 0 ;
146    args_info->comsele_given = 0 ;
147 +  args_info->seleoffset_given = 0 ;
148 +  args_info->seleoffset2_given = 0 ;
149    args_info->molname_given = 0 ;
150    args_info->begin_given = 0 ;
151    args_info->end_given = 0 ;
152    args_info->radius_given = 0 ;
153 +  args_info->voxelSize_given = 0 ;
154 +  args_info->gaussWidth_given = 0 ;
155    args_info->bo_given = 0 ;
156 <  args_info->bor_given = 0 ;
156 >  args_info->ior_given = 0 ;
157 >  args_info->for_given = 0 ;
158    args_info->bad_given = 0 ;
159    args_info->count_given = 0 ;
160    args_info->gofr_given = 0 ;
# Line 158 | Line 178 | void clear_given (struct gengetopt_args_info *args_inf
178    args_info->rodlength_given = 0 ;
179    args_info->tet_param_given = 0 ;
180    args_info->tet_param_z_given = 0 ;
181 +  args_info->tet_param_xyz_given = 0 ;
182 +  args_info->rnemdz_given = 0 ;
183 +  args_info->rnemdr_given = 0 ;
184 +  args_info->rnemdrt_given = 0 ;
185 +  args_info->nitrile_given = 0 ;
186 +  args_info->multipole_given = 0 ;
187    args_info->staticProps_group_counter = 0 ;
188   }
189  
# Line 197 | Line 223 | void clear_args (struct gengetopt_args_info *args_info
223    args_info->refsele_orig = NULL;
224    args_info->comsele_arg = NULL;
225    args_info->comsele_orig = NULL;
226 +  args_info->seleoffset_orig = NULL;
227 +  args_info->seleoffset2_orig = NULL;
228    args_info->molname_arg = NULL;
229    args_info->molname_orig = NULL;
230    args_info->begin_orig = NULL;
231    args_info->end_orig = NULL;
232    args_info->radius_orig = NULL;
233 +  args_info->voxelSize_orig = NULL;
234 +  args_info->gaussWidth_orig = NULL;
235    
236   }
237  
# Line 230 | Line 260 | void init_args_info(struct gengetopt_args_info *args_i
260    args_info->sele3_help = gengetopt_args_info_help[17] ;
261    args_info->refsele_help = gengetopt_args_info_help[18] ;
262    args_info->comsele_help = gengetopt_args_info_help[19] ;
263 <  args_info->molname_help = gengetopt_args_info_help[20] ;
264 <  args_info->begin_help = gengetopt_args_info_help[21] ;
265 <  args_info->end_help = gengetopt_args_info_help[22] ;
266 <  args_info->radius_help = gengetopt_args_info_help[23] ;
267 <  args_info->bo_help = gengetopt_args_info_help[25] ;
268 <  args_info->bor_help = gengetopt_args_info_help[26] ;
269 <  args_info->bad_help = gengetopt_args_info_help[27] ;
270 <  args_info->count_help = gengetopt_args_info_help[28] ;
271 <  args_info->gofr_help = gengetopt_args_info_help[29] ;
272 <  args_info->gofz_help = gengetopt_args_info_help[30] ;
273 <  args_info->r_theta_help = gengetopt_args_info_help[31] ;
274 <  args_info->r_omega_help = gengetopt_args_info_help[32] ;
275 <  args_info->r_z_help = gengetopt_args_info_help[33] ;
276 <  args_info->theta_omega_help = gengetopt_args_info_help[34] ;
277 <  args_info->gxyz_help = gengetopt_args_info_help[35] ;
278 <  args_info->twodgofr_help = gengetopt_args_info_help[36] ;
279 <  args_info->p2_help = gengetopt_args_info_help[37] ;
280 <  args_info->rp2_help = gengetopt_args_info_help[38] ;
281 <  args_info->scd_help = gengetopt_args_info_help[39] ;
282 <  args_info->density_help = gengetopt_args_info_help[40] ;
283 <  args_info->slab_density_help = gengetopt_args_info_help[41] ;
284 <  args_info->p_angle_help = gengetopt_args_info_help[42] ;
285 <  args_info->hxy_help = gengetopt_args_info_help[43] ;
286 <  args_info->rho_r_help = gengetopt_args_info_help[44] ;
287 <  args_info->angle_r_help = gengetopt_args_info_help[45] ;
288 <  args_info->hullvol_help = gengetopt_args_info_help[46] ;
289 <  args_info->rodlength_help = gengetopt_args_info_help[47] ;
290 <  args_info->tet_param_help = gengetopt_args_info_help[48] ;
291 <  args_info->tet_param_z_help = gengetopt_args_info_help[49] ;
263 >  args_info->seleoffset_help = gengetopt_args_info_help[20] ;
264 >  args_info->seleoffset2_help = gengetopt_args_info_help[21] ;
265 >  args_info->molname_help = gengetopt_args_info_help[22] ;
266 >  args_info->begin_help = gengetopt_args_info_help[23] ;
267 >  args_info->end_help = gengetopt_args_info_help[24] ;
268 >  args_info->radius_help = gengetopt_args_info_help[25] ;
269 >  args_info->voxelSize_help = gengetopt_args_info_help[26] ;
270 >  args_info->gaussWidth_help = gengetopt_args_info_help[27] ;
271 >  args_info->bo_help = gengetopt_args_info_help[29] ;
272 >  args_info->ior_help = gengetopt_args_info_help[30] ;
273 >  args_info->for_help = gengetopt_args_info_help[31] ;
274 >  args_info->bad_help = gengetopt_args_info_help[32] ;
275 >  args_info->count_help = gengetopt_args_info_help[33] ;
276 >  args_info->gofr_help = gengetopt_args_info_help[34] ;
277 >  args_info->gofz_help = gengetopt_args_info_help[35] ;
278 >  args_info->r_theta_help = gengetopt_args_info_help[36] ;
279 >  args_info->r_omega_help = gengetopt_args_info_help[37] ;
280 >  args_info->r_z_help = gengetopt_args_info_help[38] ;
281 >  args_info->theta_omega_help = gengetopt_args_info_help[39] ;
282 >  args_info->gxyz_help = gengetopt_args_info_help[40] ;
283 >  args_info->twodgofr_help = gengetopt_args_info_help[41] ;
284 >  args_info->p2_help = gengetopt_args_info_help[42] ;
285 >  args_info->rp2_help = gengetopt_args_info_help[43] ;
286 >  args_info->scd_help = gengetopt_args_info_help[44] ;
287 >  args_info->density_help = gengetopt_args_info_help[45] ;
288 >  args_info->slab_density_help = gengetopt_args_info_help[46] ;
289 >  args_info->p_angle_help = gengetopt_args_info_help[47] ;
290 >  args_info->hxy_help = gengetopt_args_info_help[48] ;
291 >  args_info->rho_r_help = gengetopt_args_info_help[49] ;
292 >  args_info->angle_r_help = gengetopt_args_info_help[50] ;
293 >  args_info->hullvol_help = gengetopt_args_info_help[51] ;
294 >  args_info->rodlength_help = gengetopt_args_info_help[52] ;
295 >  args_info->tet_param_help = gengetopt_args_info_help[53] ;
296 >  args_info->tet_param_z_help = gengetopt_args_info_help[54] ;
297 >  args_info->tet_param_xyz_help = gengetopt_args_info_help[55] ;
298 >  args_info->rnemdz_help = gengetopt_args_info_help[56] ;
299 >  args_info->rnemdr_help = gengetopt_args_info_help[57] ;
300 >  args_info->rnemdrt_help = gengetopt_args_info_help[58] ;
301 >  args_info->nitrile_help = gengetopt_args_info_help[59] ;
302 >  args_info->multipole_help = gengetopt_args_info_help[60] ;
303    
304   }
305  
# Line 367 | Line 408 | cmdline_parser_release (struct gengetopt_args_info *ar
408    free_string_field (&(args_info->refsele_orig));
409    free_string_field (&(args_info->comsele_arg));
410    free_string_field (&(args_info->comsele_orig));
411 +  free_string_field (&(args_info->seleoffset_orig));
412 +  free_string_field (&(args_info->seleoffset2_orig));
413    free_string_field (&(args_info->molname_arg));
414    free_string_field (&(args_info->molname_orig));
415    free_string_field (&(args_info->begin_orig));
416    free_string_field (&(args_info->end_orig));
417    free_string_field (&(args_info->radius_orig));
418 +  free_string_field (&(args_info->voxelSize_orig));
419 +  free_string_field (&(args_info->gaussWidth_orig));
420    
421    
422    for (i = 0; i < args_info->inputs_num; ++i)
# Line 447 | Line 492 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
492      write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
493    if (args_info->comsele_given)
494      write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
495 +  if (args_info->seleoffset_given)
496 +    write_into_file(outfile, "seleoffset", args_info->seleoffset_orig, 0);
497 +  if (args_info->seleoffset2_given)
498 +    write_into_file(outfile, "seleoffset2", args_info->seleoffset2_orig, 0);
499    if (args_info->molname_given)
500      write_into_file(outfile, "molname", args_info->molname_orig, 0);
501    if (args_info->begin_given)
# Line 455 | Line 504 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
504      write_into_file(outfile, "end", args_info->end_orig, 0);
505    if (args_info->radius_given)
506      write_into_file(outfile, "radius", args_info->radius_orig, 0);
507 +  if (args_info->voxelSize_given)
508 +    write_into_file(outfile, "voxelSize", args_info->voxelSize_orig, 0);
509 +  if (args_info->gaussWidth_given)
510 +    write_into_file(outfile, "gaussWidth", args_info->gaussWidth_orig, 0);
511    if (args_info->bo_given)
512      write_into_file(outfile, "bo", 0, 0 );
513 <  if (args_info->bor_given)
514 <    write_into_file(outfile, "bor", 0, 0 );
513 >  if (args_info->ior_given)
514 >    write_into_file(outfile, "ior", 0, 0 );
515 >  if (args_info->for_given)
516 >    write_into_file(outfile, "for", 0, 0 );
517    if (args_info->bad_given)
518      write_into_file(outfile, "bad", 0, 0 );
519    if (args_info->count_given)
# Line 505 | Line 560 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
560      write_into_file(outfile, "tet_param", 0, 0 );
561    if (args_info->tet_param_z_given)
562      write_into_file(outfile, "tet_param_z", 0, 0 );
563 +  if (args_info->tet_param_xyz_given)
564 +    write_into_file(outfile, "tet_param_xyz", 0, 0 );
565 +  if (args_info->rnemdz_given)
566 +    write_into_file(outfile, "rnemdz", 0, 0 );
567 +  if (args_info->rnemdr_given)
568 +    write_into_file(outfile, "rnemdr", 0, 0 );
569 +  if (args_info->rnemdrt_given)
570 +    write_into_file(outfile, "rnemdrt", 0, 0 );
571 +  if (args_info->nitrile_given)
572 +    write_into_file(outfile, "nitrile", 0, 0 );
573 +  if (args_info->multipole_given)
574 +    write_into_file(outfile, "multipole", 0, 0 );
575    
576  
577    i = EXIT_SUCCESS;
# Line 559 | Line 626 | reset_group_staticProps(struct gengetopt_args_info *ar
626      return;
627    
628    args_info->bo_given = 0 ;
629 <  args_info->bor_given = 0 ;
629 >  args_info->ior_given = 0 ;
630 >  args_info->for_given = 0 ;
631    args_info->bad_given = 0 ;
632    args_info->count_given = 0 ;
633    args_info->gofr_given = 0 ;
# Line 583 | Line 651 | reset_group_staticProps(struct gengetopt_args_info *ar
651    args_info->rodlength_given = 0 ;
652    args_info->tet_param_given = 0 ;
653    args_info->tet_param_z_given = 0 ;
654 +  args_info->tet_param_xyz_given = 0 ;
655 +  args_info->rnemdz_given = 0 ;
656 +  args_info->rnemdr_given = 0 ;
657 +  args_info->rnemdrt_given = 0 ;
658 +  args_info->nitrile_given = 0 ;
659 +  args_info->multipole_given = 0 ;
660  
661    args_info->staticProps_group_counter = 0;
662   }
# Line 848 | Line 922 | cmdline_parser_internal (
922          { "sele3",      1, NULL, 0 },
923          { "refsele",    1, NULL, 0 },
924          { "comsele",    1, NULL, 0 },
925 +        { "seleoffset", 1, NULL, 0 },
926 +        { "seleoffset2",        1, NULL, 0 },
927          { "molname",    1, NULL, 0 },
928          { "begin",      1, NULL, 0 },
929          { "end",        1, NULL, 0 },
930          { "radius",     1, NULL, 0 },
931 +        { "voxelSize",  1, NULL, 'v' },
932 +        { "gaussWidth", 1, NULL, 0 },
933          { "bo", 0, NULL, 0 },
934 <        { "bor",        0, NULL, 0 },
934 >        { "ior",        0, NULL, 0 },
935 >        { "for",        0, NULL, 0 },
936          { "bad",        0, NULL, 0 },
937          { "count",      0, NULL, 0 },
938          { "gofr",       0, NULL, 'g' },
# Line 877 | Line 956 | cmdline_parser_internal (
956          { "rodlength",  0, NULL, 0 },
957          { "tet_param",  0, NULL, 'Q' },
958          { "tet_param_z",        0, NULL, 0 },
959 +        { "tet_param_xyz",      0, NULL, 0 },
960 +        { "rnemdz",     0, NULL, 0 },
961 +        { "rnemdr",     0, NULL, 0 },
962 +        { "rnemdrt",    0, NULL, 0 },
963 +        { "nitrile",    0, NULL, 0 },
964 +        { "multipole",  0, NULL, 'm' },
965          { 0,  0, 0, 0 }
966        };
967  
968 <      c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsdQ", long_options, &option_index);
968 >      c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:v:gpsdQm", long_options, &option_index);
969  
970        if (c == -1) break;       /* Exit from `while (1)' loop.  */
971  
# Line 1000 | Line 1085 | cmdline_parser_internal (
1085                &(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE,
1086                check_ambiguity, override, 0, 0,
1087                "zoffset", 'z',
1088 +              additional_error))
1089 +            goto failure;
1090 +        
1091 +          break;
1092 +        case 'v':       /* voxel size (angstroms).  */
1093 +        
1094 +        
1095 +          if (update_arg( (void *)&(args_info->voxelSize_arg),
1096 +               &(args_info->voxelSize_orig), &(args_info->voxelSize_given),
1097 +              &(local_args_info.voxelSize_given), optarg, 0, 0, ARG_DOUBLE,
1098 +              check_ambiguity, override, 0, 0,
1099 +              "voxelSize", 'v',
1100                additional_error))
1101              goto failure;
1102          
# Line 1064 | Line 1161 | cmdline_parser_internal (
1161              goto failure;
1162          
1163            break;
1164 <        case 'Q':       /* tetrahedrality order parameter.  */
1164 >        case 'Q':       /* tetrahedrality order parameter (Qk).  */
1165          
1166            if (args_info->staticProps_group_counter && override)
1167              reset_group_staticProps (args_info);
# Line 1079 | Line 1176 | cmdline_parser_internal (
1176              goto failure;
1177          
1178            break;
1179 +        case 'm':       /* average multipole moments contained within cutoff spheres as a function of radius.  */
1180 +        
1181 +          if (args_info->staticProps_group_counter && override)
1182 +            reset_group_staticProps (args_info);
1183 +          args_info->staticProps_group_counter += 1;
1184 +        
1185 +          if (update_arg( 0 ,
1186 +               0 , &(args_info->multipole_given),
1187 +              &(local_args_info.multipole_given), optarg, 0, 0, ARG_NO,
1188 +              check_ambiguity, override, 0, 0,
1189 +              "multipole", 'm',
1190 +              additional_error))
1191 +            goto failure;
1192 +        
1193 +          break;
1194  
1195          case 0: /* Long option with no short option */
1196            /* number of bins in z axis.  */
# Line 1203 | Line 1315 | cmdline_parser_internal (
1315                  &(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING,
1316                  check_ambiguity, override, 0, 0,
1317                  "comsele", '-',
1318 +                additional_error))
1319 +              goto failure;
1320 +          
1321 +          }
1322 +          /* global index offset for a second object (used to define a vector between sites in molecule).  */
1323 +          else if (strcmp (long_options[option_index].name, "seleoffset") == 0)
1324 +          {
1325 +          
1326 +          
1327 +            if (update_arg( (void *)&(args_info->seleoffset_arg),
1328 +                 &(args_info->seleoffset_orig), &(args_info->seleoffset_given),
1329 +                &(local_args_info.seleoffset_given), optarg, 0, 0, ARG_INT,
1330 +                check_ambiguity, override, 0, 0,
1331 +                "seleoffset", '-',
1332 +                additional_error))
1333 +              goto failure;
1334 +          
1335 +          }
1336 +          /* global index offset for a third object (used to define a vector between sites in molecule).  */
1337 +          else if (strcmp (long_options[option_index].name, "seleoffset2") == 0)
1338 +          {
1339 +          
1340 +          
1341 +            if (update_arg( (void *)&(args_info->seleoffset2_arg),
1342 +                 &(args_info->seleoffset2_orig), &(args_info->seleoffset2_given),
1343 +                &(local_args_info.seleoffset2_given), optarg, 0, 0, ARG_INT,
1344 +                check_ambiguity, override, 0, 0,
1345 +                "seleoffset2", '-',
1346                  additional_error))
1347                goto failure;
1348            
# Line 1263 | Line 1403 | cmdline_parser_internal (
1403                goto failure;
1404            
1405            }
1406 +          /* Gaussian width (angstroms).  */
1407 +          else if (strcmp (long_options[option_index].name, "gaussWidth") == 0)
1408 +          {
1409 +          
1410 +          
1411 +            if (update_arg( (void *)&(args_info->gaussWidth_arg),
1412 +                 &(args_info->gaussWidth_orig), &(args_info->gaussWidth_given),
1413 +                &(local_args_info.gaussWidth_given), optarg, 0, 0, ARG_DOUBLE,
1414 +                check_ambiguity, override, 0, 0,
1415 +                "gaussWidth", '-',
1416 +                additional_error))
1417 +              goto failure;
1418 +          
1419 +          }
1420            /* bond order parameter (--rcut must be specified).  */
1421            else if (strcmp (long_options[option_index].name, "bo") == 0)
1422            {
# Line 1280 | Line 1434 | cmdline_parser_internal (
1434                goto failure;
1435            
1436            }
1437 <          /* bond order parameter as a function of radius (--rcut must be specified).  */
1438 <          else if (strcmp (long_options[option_index].name, "bor") == 0)
1437 >          /* icosahedral bond order parameter as a function of radius (--rcut must be specified).  */
1438 >          else if (strcmp (long_options[option_index].name, "ior") == 0)
1439            {
1440            
1441              if (args_info->staticProps_group_counter && override)
# Line 1289 | Line 1443 | cmdline_parser_internal (
1443              args_info->staticProps_group_counter += 1;
1444            
1445              if (update_arg( 0 ,
1446 <                 0 , &(args_info->bor_given),
1447 <                &(local_args_info.bor_given), optarg, 0, 0, ARG_NO,
1446 >                 0 , &(args_info->ior_given),
1447 >                &(local_args_info.ior_given), optarg, 0, 0, ARG_NO,
1448                  check_ambiguity, override, 0, 0,
1449 <                "bor", '-',
1449 >                "ior", '-',
1450                  additional_error))
1451                goto failure;
1452            
1453            }
1454 +          /* FCC bond order parameter as a function of radius (--rcut must be specified).  */
1455 +          else if (strcmp (long_options[option_index].name, "for") == 0)
1456 +          {
1457 +          
1458 +            if (args_info->staticProps_group_counter && override)
1459 +              reset_group_staticProps (args_info);
1460 +            args_info->staticProps_group_counter += 1;
1461 +          
1462 +            if (update_arg( 0 ,
1463 +                 0 , &(args_info->for_given),
1464 +                &(local_args_info.for_given), optarg, 0, 0, ARG_NO,
1465 +                check_ambiguity, override, 0, 0,
1466 +                "for", '-',
1467 +                additional_error))
1468 +              goto failure;
1469 +          
1470 +          }
1471            /* N(theta) bond angle density within (--rcut must be specified).  */
1472            else if (strcmp (long_options[option_index].name, "bad") == 0)
1473            {
# Line 1484 | Line 1655 | cmdline_parser_internal (
1655                goto failure;
1656            
1657            }
1658 <          /* p(cos(theta)).  */
1658 >          /* p(cos(theta)) (--sele1 must be specified, --sele2 is optional).  */
1659            else if (strcmp (long_options[option_index].name, "p_angle") == 0)
1660            {
1661            
# Line 1586 | Line 1757 | cmdline_parser_internal (
1757                goto failure;
1758            
1759            }
1760 <          /* tetrahedrality order parameter by zbin(--sele1 must be specified).  */
1760 >          /* spatially-resolved tetrahedrality order parameter Qk(z).  */
1761            else if (strcmp (long_options[option_index].name, "tet_param_z") == 0)
1762            {
1763            
# Line 1603 | Line 1774 | cmdline_parser_internal (
1774                goto failure;
1775            
1776            }
1777 +          /* volume-resolved tetrahedrality order parameter Qk(x,y,z).  (voxelSize, rcut, and gaussWidth must be specified).  */
1778 +          else if (strcmp (long_options[option_index].name, "tet_param_xyz") == 0)
1779 +          {
1780            
1781 +            if (args_info->staticProps_group_counter && override)
1782 +              reset_group_staticProps (args_info);
1783 +            args_info->staticProps_group_counter += 1;
1784 +          
1785 +            if (update_arg( 0 ,
1786 +                 0 , &(args_info->tet_param_xyz_given),
1787 +                &(local_args_info.tet_param_xyz_given), optarg, 0, 0, ARG_NO,
1788 +                check_ambiguity, override, 0, 0,
1789 +                "tet_param_xyz", '-',
1790 +                additional_error))
1791 +              goto failure;
1792 +          
1793 +          }
1794 +          /* slab-resolved RNEMD statistics (temperature, density, velocity).  */
1795 +          else if (strcmp (long_options[option_index].name, "rnemdz") == 0)
1796 +          {
1797 +          
1798 +            if (args_info->staticProps_group_counter && override)
1799 +              reset_group_staticProps (args_info);
1800 +            args_info->staticProps_group_counter += 1;
1801 +          
1802 +            if (update_arg( 0 ,
1803 +                 0 , &(args_info->rnemdz_given),
1804 +                &(local_args_info.rnemdz_given), optarg, 0, 0, ARG_NO,
1805 +                check_ambiguity, override, 0, 0,
1806 +                "rnemdz", '-',
1807 +                additional_error))
1808 +              goto failure;
1809 +          
1810 +          }
1811 +          /* shell-resolved RNEMD statistics (temperature, density, angular velocity).  */
1812 +          else if (strcmp (long_options[option_index].name, "rnemdr") == 0)
1813 +          {
1814 +          
1815 +            if (args_info->staticProps_group_counter && override)
1816 +              reset_group_staticProps (args_info);
1817 +            args_info->staticProps_group_counter += 1;
1818 +          
1819 +            if (update_arg( 0 ,
1820 +                 0 , &(args_info->rnemdr_given),
1821 +                &(local_args_info.rnemdr_given), optarg, 0, 0, ARG_NO,
1822 +                check_ambiguity, override, 0, 0,
1823 +                "rnemdr", '-',
1824 +                additional_error))
1825 +              goto failure;
1826 +          
1827 +          }
1828 +          /* shell and angle-resolved RNEMD statistics (temperature, density, angular velocity).  */
1829 +          else if (strcmp (long_options[option_index].name, "rnemdrt") == 0)
1830 +          {
1831 +          
1832 +            if (args_info->staticProps_group_counter && override)
1833 +              reset_group_staticProps (args_info);
1834 +            args_info->staticProps_group_counter += 1;
1835 +          
1836 +            if (update_arg( 0 ,
1837 +                 0 , &(args_info->rnemdrt_given),
1838 +                &(local_args_info.rnemdrt_given), optarg, 0, 0, ARG_NO,
1839 +                check_ambiguity, override, 0, 0,
1840 +                "rnemdrt", '-',
1841 +                additional_error))
1842 +              goto failure;
1843 +          
1844 +          }
1845 +          /* electrostatic potential to frequency map based on the Cho nitrile fits.  */
1846 +          else if (strcmp (long_options[option_index].name, "nitrile") == 0)
1847 +          {
1848 +          
1849 +            if (args_info->staticProps_group_counter && override)
1850 +              reset_group_staticProps (args_info);
1851 +            args_info->staticProps_group_counter += 1;
1852 +          
1853 +            if (update_arg( 0 ,
1854 +                 0 , &(args_info->nitrile_given),
1855 +                &(local_args_info.nitrile_given), optarg, 0, 0, ARG_NO,
1856 +                check_ambiguity, override, 0, 0,
1857 +                "nitrile", '-',
1858 +                additional_error))
1859 +              goto failure;
1860 +          
1861 +          }
1862 +          
1863            break;
1864          case '?':       /* Invalid option.  */
1865            /* `getopt_long' already printed an error message.  */

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