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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 1795 by gezelter, Fri Sep 7 18:13:55 2012 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 -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 47 | 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 56 | Line 57 | const char *gengetopt_args_info_help[] = {
57    "      --sele3=selection script  select the third stuntdouble set",
58    "      --refsele=selection script\n                                select reference (use and only use with --gxyz)",
59    "      --comsele=selection script\n                                select stunt doubles for center-of-mass \n                                  reference point",
60 +  "      --seleoffset=INT          global index offset for a second object (used \n                                  to define a vector between sites in molecule)",
61 +  "      --seleoffset2=INT         global index offset for a third object (used to \n                                  define a vector between sites in molecule)",
62    "      --molname=STRING          molecule name",
63    "      --begin=INT               begin internal index",
64    "      --end=INT                 end internal index",
65    "      --radius=DOUBLE           nanoparticle radius",
66 +  "  -v, --voxelSize=DOUBLE        voxel size (angstroms)",
67 +  "      --gaussWidth=DOUBLE       Gaussian width (angstroms)",
68    "\n Group: staticProps\n   an option of this group is required",
69    "      --bo                      bond order parameter (--rcut must be specified)",
70 <  "      --bor                     bond order parameter as a function of radius \n                                  (--rcut must be specified)",
70 >  "      --ior                     icosahedral bond order parameter as a function \n                                  of radius (--rcut must be specified)",
71 >  "      --for                     FCC bond order parameter as a function of \n                                  radius (--rcut must be specified)",
72    "      --bad                     N(theta) bond angle density within (--rcut must \n                                  be specified)",
73    "      --count                   count of molecules matching selection criteria \n                                  (and associated statistics)",
74    "  -g, --gofr                    g(r)",
# Line 78 | Line 84 | const char *gengetopt_args_info_help[] = {
84    "  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)",
85    "  -d, --density                 density plot",
86    "      --slab_density            slab density",
87 <  "      --p_angle                 p(cos(theta))",
87 >  "      --p_angle                 p(cos(theta)) (--sele1 must be specified, \n                                  --sele2 is optional)",
88    "      --hxy                     hxy",
89    "      --rho_r                   rho of R",
90    "      --angle_r                 angle of R",
91    "      --hullvol                 hull volume of nanoparticle",
92    "      --rodlength               length of nanorod",
93 <  "  -Q, --tet_param               tetrahedrality order parameter",
94 <  "      --tet_param_z             tetrahedrality order parameter by zbin(--sele1 \n                                  must be specified)",
93 >  "  -Q, --tet_param               tetrahedrality order parameter (Qk)",
94 >  "      --tet_param_z             spatially-resolved tetrahedrality order \n                                  parameter Qk(z)",
95 >  "      --tet_param_xyz           volume-resolved tetrahedrality order parameter \n                                  Qk(x,y,z).  (voxelSize, rcut, and gaussWidth \n                                  must be specified)",
96 >  "      --rnemdz                  slab-resolved RNEMD statistics (temperature, \n                                  density, velocity)",
97 >  "      --rnemdr                  shell-resolved RNEMD statistics (temperature, \n                                  density, angular velocity)",
98 >  "      --rnemdrt                 shell and angle-resolved RNEMD statistics \n                                  (temperature, density, angular velocity)",
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 124 | 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 133 | Line 148 | void clear_given (struct gengetopt_args_info *args_inf
148    args_info->sele3_given = 0 ;
149    args_info->refsele_given = 0 ;
150    args_info->comsele_given = 0 ;
151 +  args_info->seleoffset_given = 0 ;
152 +  args_info->seleoffset2_given = 0 ;
153    args_info->molname_given = 0 ;
154    args_info->begin_given = 0 ;
155    args_info->end_given = 0 ;
156    args_info->radius_given = 0 ;
157 +  args_info->voxelSize_given = 0 ;
158 +  args_info->gaussWidth_given = 0 ;
159    args_info->bo_given = 0 ;
160 <  args_info->bor_given = 0 ;
160 >  args_info->ior_given = 0 ;
161 >  args_info->for_given = 0 ;
162    args_info->bad_given = 0 ;
163    args_info->count_given = 0 ;
164    args_info->gofr_given = 0 ;
# Line 162 | Line 182 | void clear_given (struct gengetopt_args_info *args_inf
182    args_info->rodlength_given = 0 ;
183    args_info->tet_param_given = 0 ;
184    args_info->tet_param_z_given = 0 ;
185 +  args_info->tet_param_xyz_given = 0 ;
186 +  args_info->rnemdz_given = 0 ;
187 +  args_info->rnemdr_given = 0 ;
188 +  args_info->rnemdrt_given = 0 ;
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 186 | 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 201 | Line 230 | void clear_args (struct gengetopt_args_info *args_info
230    args_info->refsele_orig = NULL;
231    args_info->comsele_arg = NULL;
232    args_info->comsele_orig = NULL;
233 +  args_info->seleoffset_orig = NULL;
234 +  args_info->seleoffset2_orig = NULL;
235    args_info->molname_arg = NULL;
236    args_info->molname_orig = NULL;
237    args_info->begin_orig = NULL;
238    args_info->end_orig = NULL;
239    args_info->radius_orig = NULL;
240 +  args_info->voxelSize_orig = NULL;
241 +  args_info->gaussWidth_orig = NULL;
242    
243   }
244  
# Line 225 | 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->molname_help = gengetopt_args_info_help[20] ;
271 <  args_info->begin_help = gengetopt_args_info_help[21] ;
272 <  args_info->end_help = gengetopt_args_info_help[22] ;
273 <  args_info->radius_help = gengetopt_args_info_help[23] ;
274 <  args_info->bo_help = gengetopt_args_info_help[25] ;
275 <  args_info->bor_help = gengetopt_args_info_help[26] ;
276 <  args_info->bad_help = gengetopt_args_info_help[27] ;
277 <  args_info->count_help = gengetopt_args_info_help[28] ;
278 <  args_info->gofr_help = gengetopt_args_info_help[29] ;
279 <  args_info->gofz_help = gengetopt_args_info_help[30] ;
280 <  args_info->r_theta_help = gengetopt_args_info_help[31] ;
281 <  args_info->r_omega_help = gengetopt_args_info_help[32] ;
282 <  args_info->r_z_help = gengetopt_args_info_help[33] ;
283 <  args_info->theta_omega_help = gengetopt_args_info_help[34] ;
284 <  args_info->gxyz_help = gengetopt_args_info_help[35] ;
285 <  args_info->twodgofr_help = gengetopt_args_info_help[36] ;
286 <  args_info->p2_help = gengetopt_args_info_help[37] ;
287 <  args_info->rp2_help = gengetopt_args_info_help[38] ;
288 <  args_info->scd_help = gengetopt_args_info_help[39] ;
289 <  args_info->density_help = gengetopt_args_info_help[40] ;
290 <  args_info->slab_density_help = gengetopt_args_info_help[41] ;
291 <  args_info->p_angle_help = gengetopt_args_info_help[42] ;
292 <  args_info->hxy_help = gengetopt_args_info_help[43] ;
293 <  args_info->rho_r_help = gengetopt_args_info_help[44] ;
294 <  args_info->angle_r_help = gengetopt_args_info_help[45] ;
295 <  args_info->hullvol_help = gengetopt_args_info_help[46] ;
296 <  args_info->rodlength_help = gengetopt_args_info_help[47] ;
297 <  args_info->tet_param_help = gengetopt_args_info_help[48] ;
298 <  args_info->tet_param_z_help = gengetopt_args_info_help[49] ;
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 357 | 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 371 | Line 419 | cmdline_parser_release (struct gengetopt_args_info *ar
419    free_string_field (&(args_info->refsele_orig));
420    free_string_field (&(args_info->comsele_arg));
421    free_string_field (&(args_info->comsele_orig));
422 +  free_string_field (&(args_info->seleoffset_orig));
423 +  free_string_field (&(args_info->seleoffset2_orig));
424    free_string_field (&(args_info->molname_arg));
425    free_string_field (&(args_info->molname_orig));
426    free_string_field (&(args_info->begin_orig));
427    free_string_field (&(args_info->end_orig));
428    free_string_field (&(args_info->radius_orig));
429 +  free_string_field (&(args_info->voxelSize_orig));
430 +  free_string_field (&(args_info->gaussWidth_orig));
431    
432    
433    for (i = 0; i < args_info->inputs_num; ++i)
# Line 433 | 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 451 | Line 505 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
505      write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
506    if (args_info->comsele_given)
507      write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
508 +  if (args_info->seleoffset_given)
509 +    write_into_file(outfile, "seleoffset", args_info->seleoffset_orig, 0);
510 +  if (args_info->seleoffset2_given)
511 +    write_into_file(outfile, "seleoffset2", args_info->seleoffset2_orig, 0);
512    if (args_info->molname_given)
513      write_into_file(outfile, "molname", args_info->molname_orig, 0);
514    if (args_info->begin_given)
# Line 459 | Line 517 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
517      write_into_file(outfile, "end", args_info->end_orig, 0);
518    if (args_info->radius_given)
519      write_into_file(outfile, "radius", args_info->radius_orig, 0);
520 +  if (args_info->voxelSize_given)
521 +    write_into_file(outfile, "voxelSize", args_info->voxelSize_orig, 0);
522 +  if (args_info->gaussWidth_given)
523 +    write_into_file(outfile, "gaussWidth", args_info->gaussWidth_orig, 0);
524    if (args_info->bo_given)
525      write_into_file(outfile, "bo", 0, 0 );
526 <  if (args_info->bor_given)
527 <    write_into_file(outfile, "bor", 0, 0 );
526 >  if (args_info->ior_given)
527 >    write_into_file(outfile, "ior", 0, 0 );
528 >  if (args_info->for_given)
529 >    write_into_file(outfile, "for", 0, 0 );
530    if (args_info->bad_given)
531      write_into_file(outfile, "bad", 0, 0 );
532    if (args_info->count_given)
# Line 509 | Line 573 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
573      write_into_file(outfile, "tet_param", 0, 0 );
574    if (args_info->tet_param_z_given)
575      write_into_file(outfile, "tet_param_z", 0, 0 );
576 +  if (args_info->tet_param_xyz_given)
577 +    write_into_file(outfile, "tet_param_xyz", 0, 0 );
578 +  if (args_info->rnemdz_given)
579 +    write_into_file(outfile, "rnemdz", 0, 0 );
580 +  if (args_info->rnemdr_given)
581 +    write_into_file(outfile, "rnemdr", 0, 0 );
582 +  if (args_info->rnemdrt_given)
583 +    write_into_file(outfile, "rnemdrt", 0, 0 );
584 +  if (args_info->nitrile_given)
585 +    write_into_file(outfile, "nitrile", 0, 0 );
586 +  if (args_info->multipole_given)
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 563 | Line 643 | reset_group_staticProps(struct gengetopt_args_info *ar
643      return;
644    
645    args_info->bo_given = 0 ;
646 <  args_info->bor_given = 0 ;
646 >  args_info->ior_given = 0 ;
647 >  args_info->for_given = 0 ;
648    args_info->bad_given = 0 ;
649    args_info->count_given = 0 ;
650    args_info->gofr_given = 0 ;
# Line 587 | Line 668 | reset_group_staticProps(struct gengetopt_args_info *ar
668    args_info->rodlength_given = 0 ;
669    args_info->tet_param_given = 0 ;
670    args_info->tet_param_z_given = 0 ;
671 +  args_info->tet_param_xyz_given = 0 ;
672 +  args_info->rnemdz_given = 0 ;
673 +  args_info->rnemdr_given = 0 ;
674 +  args_info->rnemdrt_given = 0 ;
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 843 | 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 852 | Line 942 | cmdline_parser_internal (
942          { "sele3",      1, NULL, 0 },
943          { "refsele",    1, NULL, 0 },
944          { "comsele",    1, NULL, 0 },
945 +        { "seleoffset", 1, NULL, 0 },
946 +        { "seleoffset2",        1, NULL, 0 },
947          { "molname",    1, NULL, 0 },
948          { "begin",      1, NULL, 0 },
949          { "end",        1, NULL, 0 },
950          { "radius",     1, NULL, 0 },
951 +        { "voxelSize",  1, NULL, 'v' },
952 +        { "gaussWidth", 1, NULL, 0 },
953          { "bo", 0, NULL, 0 },
954 <        { "bor",        0, NULL, 0 },
954 >        { "ior",        0, NULL, 0 },
955 >        { "for",        0, NULL, 0 },
956          { "bad",        0, NULL, 0 },
957          { "count",      0, NULL, 0 },
958          { "gofr",       0, NULL, 'g' },
# Line 881 | Line 976 | cmdline_parser_internal (
976          { "rodlength",  0, NULL, 0 },
977          { "tet_param",  0, NULL, 'Q' },
978          { "tet_param_z",        0, NULL, 0 },
979 +        { "tet_param_xyz",      0, NULL, 0 },
980 +        { "rnemdz",     0, NULL, 0 },
981 +        { "rnemdr",     0, NULL, 0 },
982 +        { "rnemdrt",    0, NULL, 0 },
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  
990 <      c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsdQ", long_options, &option_index);
990 >      c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:v:gpsdQm", long_options, &option_index);
991  
992        if (c == -1) break;       /* Exit from `while (1)' loop.  */
993  
# Line 1008 | Line 1111 | cmdline_parser_internal (
1111              goto failure;
1112          
1113            break;
1114 +        case 'v':       /* voxel size (angstroms).  */
1115 +        
1116 +        
1117 +          if (update_arg( (void *)&(args_info->voxelSize_arg),
1118 +               &(args_info->voxelSize_orig), &(args_info->voxelSize_given),
1119 +              &(local_args_info.voxelSize_given), optarg, 0, 0, ARG_DOUBLE,
1120 +              check_ambiguity, override, 0, 0,
1121 +              "voxelSize", 'v',
1122 +              additional_error))
1123 +            goto failure;
1124 +        
1125 +          break;
1126          case 'g':       /* g(r).  */
1127          
1128            if (args_info->staticProps_group_counter && override)
# Line 1068 | Line 1183 | cmdline_parser_internal (
1183              goto failure;
1184          
1185            break;
1186 <        case 'Q':       /* tetrahedrality order parameter.  */
1186 >        case 'Q':       /* tetrahedrality order parameter (Qk).  */
1187          
1188            if (args_info->staticProps_group_counter && override)
1189              reset_group_staticProps (args_info);
# Line 1079 | Line 1194 | cmdline_parser_internal (
1194                &(local_args_info.tet_param_given), optarg, 0, 0, ARG_NO,
1195                check_ambiguity, override, 0, 0,
1196                "tet_param", 'Q',
1197 +              additional_error))
1198 +            goto failure;
1199 +        
1200 +          break;
1201 +        case 'm':       /* average multipole moments contained within cutoff spheres as a function of radius.  */
1202 +        
1203 +          if (args_info->staticProps_group_counter && override)
1204 +            reset_group_staticProps (args_info);
1205 +          args_info->staticProps_group_counter += 1;
1206 +        
1207 +          if (update_arg( 0 ,
1208 +               0 , &(args_info->multipole_given),
1209 +              &(local_args_info.multipole_given), optarg, 0, 0, ARG_NO,
1210 +              check_ambiguity, override, 0, 0,
1211 +              "multipole", 'm',
1212                additional_error))
1213              goto failure;
1214          
# Line 1099 | 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 1211 | Line 1355 | cmdline_parser_internal (
1355                goto failure;
1356            
1357            }
1358 +          /* global index offset for a second object (used to define a vector between sites in molecule).  */
1359 +          else if (strcmp (long_options[option_index].name, "seleoffset") == 0)
1360 +          {
1361 +          
1362 +          
1363 +            if (update_arg( (void *)&(args_info->seleoffset_arg),
1364 +                 &(args_info->seleoffset_orig), &(args_info->seleoffset_given),
1365 +                &(local_args_info.seleoffset_given), optarg, 0, 0, ARG_INT,
1366 +                check_ambiguity, override, 0, 0,
1367 +                "seleoffset", '-',
1368 +                additional_error))
1369 +              goto failure;
1370 +          
1371 +          }
1372 +          /* global index offset for a third object (used to define a vector between sites in molecule).  */
1373 +          else if (strcmp (long_options[option_index].name, "seleoffset2") == 0)
1374 +          {
1375 +          
1376 +          
1377 +            if (update_arg( (void *)&(args_info->seleoffset2_arg),
1378 +                 &(args_info->seleoffset2_orig), &(args_info->seleoffset2_given),
1379 +                &(local_args_info.seleoffset2_given), optarg, 0, 0, ARG_INT,
1380 +                check_ambiguity, override, 0, 0,
1381 +                "seleoffset2", '-',
1382 +                additional_error))
1383 +              goto failure;
1384 +          
1385 +          }
1386            /* molecule name.  */
1387            else if (strcmp (long_options[option_index].name, "molname") == 0)
1388            {
# Line 1263 | Line 1435 | cmdline_parser_internal (
1435                  &(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
1436                  check_ambiguity, override, 0, 0,
1437                  "radius", '-',
1438 +                additional_error))
1439 +              goto failure;
1440 +          
1441 +          }
1442 +          /* Gaussian width (angstroms).  */
1443 +          else if (strcmp (long_options[option_index].name, "gaussWidth") == 0)
1444 +          {
1445 +          
1446 +          
1447 +            if (update_arg( (void *)&(args_info->gaussWidth_arg),
1448 +                 &(args_info->gaussWidth_orig), &(args_info->gaussWidth_given),
1449 +                &(local_args_info.gaussWidth_given), optarg, 0, 0, ARG_DOUBLE,
1450 +                check_ambiguity, override, 0, 0,
1451 +                "gaussWidth", '-',
1452                  additional_error))
1453                goto failure;
1454            
# Line 1284 | Line 1470 | cmdline_parser_internal (
1470                goto failure;
1471            
1472            }
1473 <          /* bond order parameter as a function of radius (--rcut must be specified).  */
1474 <          else if (strcmp (long_options[option_index].name, "bor") == 0)
1473 >          /* icosahedral bond order parameter as a function of radius (--rcut must be specified).  */
1474 >          else if (strcmp (long_options[option_index].name, "ior") == 0)
1475            {
1476            
1477              if (args_info->staticProps_group_counter && override)
# Line 1293 | Line 1479 | cmdline_parser_internal (
1479              args_info->staticProps_group_counter += 1;
1480            
1481              if (update_arg( 0 ,
1482 <                 0 , &(args_info->bor_given),
1483 <                &(local_args_info.bor_given), optarg, 0, 0, ARG_NO,
1482 >                 0 , &(args_info->ior_given),
1483 >                &(local_args_info.ior_given), optarg, 0, 0, ARG_NO,
1484                  check_ambiguity, override, 0, 0,
1485 <                "bor", '-',
1485 >                "ior", '-',
1486 >                additional_error))
1487 >              goto failure;
1488 >          
1489 >          }
1490 >          /* FCC bond order parameter as a function of radius (--rcut must be specified).  */
1491 >          else if (strcmp (long_options[option_index].name, "for") == 0)
1492 >          {
1493 >          
1494 >            if (args_info->staticProps_group_counter && override)
1495 >              reset_group_staticProps (args_info);
1496 >            args_info->staticProps_group_counter += 1;
1497 >          
1498 >            if (update_arg( 0 ,
1499 >                 0 , &(args_info->for_given),
1500 >                &(local_args_info.for_given), optarg, 0, 0, ARG_NO,
1501 >                check_ambiguity, override, 0, 0,
1502 >                "for", '-',
1503                  additional_error))
1504                goto failure;
1505            
# Line 1488 | Line 1691 | cmdline_parser_internal (
1691                goto failure;
1692            
1693            }
1694 <          /* p(cos(theta)).  */
1694 >          /* p(cos(theta)) (--sele1 must be specified, --sele2 is optional).  */
1695            else if (strcmp (long_options[option_index].name, "p_angle") == 0)
1696            {
1697            
# Line 1590 | Line 1793 | cmdline_parser_internal (
1793                goto failure;
1794            
1795            }
1796 <          /* tetrahedrality order parameter by zbin(--sele1 must be specified).  */
1796 >          /* spatially-resolved tetrahedrality order parameter Qk(z).  */
1797            else if (strcmp (long_options[option_index].name, "tet_param_z") == 0)
1798            {
1799            
# Line 1603 | Line 1806 | cmdline_parser_internal (
1806                  &(local_args_info.tet_param_z_given), optarg, 0, 0, ARG_NO,
1807                  check_ambiguity, override, 0, 0,
1808                  "tet_param_z", '-',
1809 +                additional_error))
1810 +              goto failure;
1811 +          
1812 +          }
1813 +          /* volume-resolved tetrahedrality order parameter Qk(x,y,z).  (voxelSize, rcut, and gaussWidth must be specified).  */
1814 +          else if (strcmp (long_options[option_index].name, "tet_param_xyz") == 0)
1815 +          {
1816 +          
1817 +            if (args_info->staticProps_group_counter && override)
1818 +              reset_group_staticProps (args_info);
1819 +            args_info->staticProps_group_counter += 1;
1820 +          
1821 +            if (update_arg( 0 ,
1822 +                 0 , &(args_info->tet_param_xyz_given),
1823 +                &(local_args_info.tet_param_xyz_given), optarg, 0, 0, ARG_NO,
1824 +                check_ambiguity, override, 0, 0,
1825 +                "tet_param_xyz", '-',
1826                  additional_error))
1827                goto failure;
1828            
1829            }
1830 +          /* slab-resolved RNEMD statistics (temperature, density, velocity).  */
1831 +          else if (strcmp (long_options[option_index].name, "rnemdz") == 0)
1832 +          {
1833            
1834 +            if (args_info->staticProps_group_counter && override)
1835 +              reset_group_staticProps (args_info);
1836 +            args_info->staticProps_group_counter += 1;
1837 +          
1838 +            if (update_arg( 0 ,
1839 +                 0 , &(args_info->rnemdz_given),
1840 +                &(local_args_info.rnemdz_given), optarg, 0, 0, ARG_NO,
1841 +                check_ambiguity, override, 0, 0,
1842 +                "rnemdz", '-',
1843 +                additional_error))
1844 +              goto failure;
1845 +          
1846 +          }
1847 +          /* shell-resolved RNEMD statistics (temperature, density, angular velocity).  */
1848 +          else if (strcmp (long_options[option_index].name, "rnemdr") == 0)
1849 +          {
1850 +          
1851 +            if (args_info->staticProps_group_counter && override)
1852 +              reset_group_staticProps (args_info);
1853 +            args_info->staticProps_group_counter += 1;
1854 +          
1855 +            if (update_arg( 0 ,
1856 +                 0 , &(args_info->rnemdr_given),
1857 +                &(local_args_info.rnemdr_given), optarg, 0, 0, ARG_NO,
1858 +                check_ambiguity, override, 0, 0,
1859 +                "rnemdr", '-',
1860 +                additional_error))
1861 +              goto failure;
1862 +          
1863 +          }
1864 +          /* shell and angle-resolved RNEMD statistics (temperature, density, angular velocity).  */
1865 +          else if (strcmp (long_options[option_index].name, "rnemdrt") == 0)
1866 +          {
1867 +          
1868 +            if (args_info->staticProps_group_counter && override)
1869 +              reset_group_staticProps (args_info);
1870 +            args_info->staticProps_group_counter += 1;
1871 +          
1872 +            if (update_arg( 0 ,
1873 +                 0 , &(args_info->rnemdrt_given),
1874 +                &(local_args_info.rnemdrt_given), optarg, 0, 0, ARG_NO,
1875 +                check_ambiguity, override, 0, 0,
1876 +                "rnemdrt", '-',
1877 +                additional_error))
1878 +              goto failure;
1879 +          
1880 +          }
1881 +          /* electrostatic potential to frequency map based on the Cho nitrile fits.  */
1882 +          else if (strcmp (long_options[option_index].name, "nitrile") == 0)
1883 +          {
1884 +          
1885 +            if (args_info->staticProps_group_counter && override)
1886 +              reset_group_staticProps (args_info);
1887 +            args_info->staticProps_group_counter += 1;
1888 +          
1889 +            if (update_arg( 0 ,
1890 +                 0 , &(args_info->nitrile_given),
1891 +                &(local_args_info.nitrile_given), optarg, 0, 0, ARG_NO,
1892 +                check_ambiguity, override, 0, 0,
1893 +                "nitrile", '-',
1894 +                additional_error))
1895 +              goto failure;
1896 +          
1897 +          }
1898 +          /* X, Y, and R (surface diffusion if Z exposed and bulk immobile) diffusion.  */
1899 +          else if (strcmp (long_options[option_index].name, "surfDiffusion") == 0)
1900 +          {
1901 +          
1902 +            if (args_info->staticProps_group_counter && override)
1903 +              reset_group_staticProps (args_info);
1904 +            args_info->staticProps_group_counter += 1;
1905 +          
1906 +            if (update_arg( 0 ,
1907 +                 0 , &(args_info->surfDiffusion_given),
1908 +                &(local_args_info.surfDiffusion_given), optarg, 0, 0, ARG_NO,
1909 +                check_ambiguity, override, 0, 0,
1910 +                "surfDiffusion", '-',
1911 +                additional_error))
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.  */

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