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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 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC vs.
Revision 1993 by gezelter, Tue Apr 29 17:32:31 2014 UTC

# Line 57 | Line 57 | const char *gengetopt_args_info_help[] = {
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    "\n Group: staticProps\n   an option of this group is required",
66    "      --bo                      bond order parameter (--rcut must be specified)",
67 <  "      --bor                     bond order parameter as a function of radius \n                                  (--rcut must be specified)",
67 >  "      --ior                     icosahedral bond order parameter as a function \n                                  of radius (--rcut must be specified)",
68 >  "      --for                     FCC bond order parameter as a function of \n                                  radius (--rcut must be specified)",
69    "      --bad                     N(theta) bond angle density within (--rcut must \n                                  be specified)",
70    "      --count                   count of molecules matching selection criteria \n                                  (and associated statistics)",
71    "  -g, --gofr                    g(r)",
# Line 79 | Line 81 | const char *gengetopt_args_info_help[] = {
81    "  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)",
82    "  -d, --density                 density plot",
83    "      --slab_density            slab density",
84 <  "      --p_angle                 p(cos(theta))",
84 >  "      --p_angle                 p(cos(theta)) (--sele1 must be specified, \n                                  --sele2 is optional)",
85    "      --hxy                     hxy",
86    "      --rho_r                   rho of R",
87    "      --angle_r                 angle of R",
# Line 89 | Line 91 | const char *gengetopt_args_info_help[] = {
91    "      --tet_param_z             spatially-resolved tetrahedrality order \n                                  parameter Qk(z)",
92    "      --rnemdz                  slab-resolved RNEMD statistics (temperature, \n                                  density, velocity)",
93    "      --rnemdr                  shell-resolved RNEMD statistics (temperature, \n                                  density, angular velocity)",
94 +  "      --rnemdrt                 shell and angle-resolved RNEMD statistics \n                                  (temperature, density, angular velocity)",
95 +  "      --uFreqMap                electrostatic potential to frequency map based \n                                  on the Cho nitrile fits",
96      0
97   };
98  
# Line 137 | Line 141 | void clear_given (struct gengetopt_args_info *args_inf
141    args_info->refsele_given = 0 ;
142    args_info->comsele_given = 0 ;
143    args_info->seleoffset_given = 0 ;
144 +  args_info->seleoffset2_given = 0 ;
145    args_info->molname_given = 0 ;
146    args_info->begin_given = 0 ;
147    args_info->end_given = 0 ;
148    args_info->radius_given = 0 ;
149    args_info->bo_given = 0 ;
150 <  args_info->bor_given = 0 ;
150 >  args_info->ior_given = 0 ;
151 >  args_info->for_given = 0 ;
152    args_info->bad_given = 0 ;
153    args_info->count_given = 0 ;
154    args_info->gofr_given = 0 ;
# Line 168 | Line 174 | void clear_given (struct gengetopt_args_info *args_inf
174    args_info->tet_param_z_given = 0 ;
175    args_info->rnemdz_given = 0 ;
176    args_info->rnemdr_given = 0 ;
177 +  args_info->rnemdrt_given = 0 ;
178 +  args_info->uFreqMap_given = 0 ;
179    args_info->staticProps_group_counter = 0 ;
180   }
181  
# Line 208 | Line 216 | void clear_args (struct gengetopt_args_info *args_info
216    args_info->comsele_arg = NULL;
217    args_info->comsele_orig = NULL;
218    args_info->seleoffset_orig = NULL;
219 +  args_info->seleoffset2_orig = NULL;
220    args_info->molname_arg = NULL;
221    args_info->molname_orig = NULL;
222    args_info->begin_orig = NULL;
# Line 242 | Line 251 | void init_args_info(struct gengetopt_args_info *args_i
251    args_info->refsele_help = gengetopt_args_info_help[18] ;
252    args_info->comsele_help = gengetopt_args_info_help[19] ;
253    args_info->seleoffset_help = gengetopt_args_info_help[20] ;
254 <  args_info->molname_help = gengetopt_args_info_help[21] ;
255 <  args_info->begin_help = gengetopt_args_info_help[22] ;
256 <  args_info->end_help = gengetopt_args_info_help[23] ;
257 <  args_info->radius_help = gengetopt_args_info_help[24] ;
258 <  args_info->bo_help = gengetopt_args_info_help[26] ;
259 <  args_info->bor_help = gengetopt_args_info_help[27] ;
260 <  args_info->bad_help = gengetopt_args_info_help[28] ;
261 <  args_info->count_help = gengetopt_args_info_help[29] ;
262 <  args_info->gofr_help = gengetopt_args_info_help[30] ;
263 <  args_info->gofz_help = gengetopt_args_info_help[31] ;
264 <  args_info->r_theta_help = gengetopt_args_info_help[32] ;
265 <  args_info->r_omega_help = gengetopt_args_info_help[33] ;
266 <  args_info->r_z_help = gengetopt_args_info_help[34] ;
267 <  args_info->theta_omega_help = gengetopt_args_info_help[35] ;
268 <  args_info->gxyz_help = gengetopt_args_info_help[36] ;
269 <  args_info->twodgofr_help = gengetopt_args_info_help[37] ;
270 <  args_info->p2_help = gengetopt_args_info_help[38] ;
271 <  args_info->rp2_help = gengetopt_args_info_help[39] ;
272 <  args_info->scd_help = gengetopt_args_info_help[40] ;
273 <  args_info->density_help = gengetopt_args_info_help[41] ;
274 <  args_info->slab_density_help = gengetopt_args_info_help[42] ;
275 <  args_info->p_angle_help = gengetopt_args_info_help[43] ;
276 <  args_info->hxy_help = gengetopt_args_info_help[44] ;
277 <  args_info->rho_r_help = gengetopt_args_info_help[45] ;
278 <  args_info->angle_r_help = gengetopt_args_info_help[46] ;
279 <  args_info->hullvol_help = gengetopt_args_info_help[47] ;
280 <  args_info->rodlength_help = gengetopt_args_info_help[48] ;
281 <  args_info->tet_param_help = gengetopt_args_info_help[49] ;
282 <  args_info->tet_param_z_help = gengetopt_args_info_help[50] ;
283 <  args_info->rnemdz_help = gengetopt_args_info_help[51] ;
284 <  args_info->rnemdr_help = gengetopt_args_info_help[52] ;
254 >  args_info->seleoffset2_help = gengetopt_args_info_help[21] ;
255 >  args_info->molname_help = gengetopt_args_info_help[22] ;
256 >  args_info->begin_help = gengetopt_args_info_help[23] ;
257 >  args_info->end_help = gengetopt_args_info_help[24] ;
258 >  args_info->radius_help = gengetopt_args_info_help[25] ;
259 >  args_info->bo_help = gengetopt_args_info_help[27] ;
260 >  args_info->ior_help = gengetopt_args_info_help[28] ;
261 >  args_info->for_help = gengetopt_args_info_help[29] ;
262 >  args_info->bad_help = gengetopt_args_info_help[30] ;
263 >  args_info->count_help = gengetopt_args_info_help[31] ;
264 >  args_info->gofr_help = gengetopt_args_info_help[32] ;
265 >  args_info->gofz_help = gengetopt_args_info_help[33] ;
266 >  args_info->r_theta_help = gengetopt_args_info_help[34] ;
267 >  args_info->r_omega_help = gengetopt_args_info_help[35] ;
268 >  args_info->r_z_help = gengetopt_args_info_help[36] ;
269 >  args_info->theta_omega_help = gengetopt_args_info_help[37] ;
270 >  args_info->gxyz_help = gengetopt_args_info_help[38] ;
271 >  args_info->twodgofr_help = gengetopt_args_info_help[39] ;
272 >  args_info->p2_help = gengetopt_args_info_help[40] ;
273 >  args_info->rp2_help = gengetopt_args_info_help[41] ;
274 >  args_info->scd_help = gengetopt_args_info_help[42] ;
275 >  args_info->density_help = gengetopt_args_info_help[43] ;
276 >  args_info->slab_density_help = gengetopt_args_info_help[44] ;
277 >  args_info->p_angle_help = gengetopt_args_info_help[45] ;
278 >  args_info->hxy_help = gengetopt_args_info_help[46] ;
279 >  args_info->rho_r_help = gengetopt_args_info_help[47] ;
280 >  args_info->angle_r_help = gengetopt_args_info_help[48] ;
281 >  args_info->hullvol_help = gengetopt_args_info_help[49] ;
282 >  args_info->rodlength_help = gengetopt_args_info_help[50] ;
283 >  args_info->tet_param_help = gengetopt_args_info_help[51] ;
284 >  args_info->tet_param_z_help = gengetopt_args_info_help[52] ;
285 >  args_info->rnemdz_help = gengetopt_args_info_help[53] ;
286 >  args_info->rnemdr_help = gengetopt_args_info_help[54] ;
287 >  args_info->rnemdrt_help = gengetopt_args_info_help[55] ;
288 >  args_info->uFreqMap_help = gengetopt_args_info_help[56] ;
289    
290   }
291  
# Line 382 | Line 395 | cmdline_parser_release (struct gengetopt_args_info *ar
395    free_string_field (&(args_info->comsele_arg));
396    free_string_field (&(args_info->comsele_orig));
397    free_string_field (&(args_info->seleoffset_orig));
398 +  free_string_field (&(args_info->seleoffset2_orig));
399    free_string_field (&(args_info->molname_arg));
400    free_string_field (&(args_info->molname_orig));
401    free_string_field (&(args_info->begin_orig));
# Line 464 | Line 478 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
478      write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
479    if (args_info->seleoffset_given)
480      write_into_file(outfile, "seleoffset", args_info->seleoffset_orig, 0);
481 +  if (args_info->seleoffset2_given)
482 +    write_into_file(outfile, "seleoffset2", args_info->seleoffset2_orig, 0);
483    if (args_info->molname_given)
484      write_into_file(outfile, "molname", args_info->molname_orig, 0);
485    if (args_info->begin_given)
# Line 474 | Line 490 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
490      write_into_file(outfile, "radius", args_info->radius_orig, 0);
491    if (args_info->bo_given)
492      write_into_file(outfile, "bo", 0, 0 );
493 <  if (args_info->bor_given)
494 <    write_into_file(outfile, "bor", 0, 0 );
493 >  if (args_info->ior_given)
494 >    write_into_file(outfile, "ior", 0, 0 );
495 >  if (args_info->for_given)
496 >    write_into_file(outfile, "for", 0, 0 );
497    if (args_info->bad_given)
498      write_into_file(outfile, "bad", 0, 0 );
499    if (args_info->count_given)
# Line 526 | Line 544 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
544      write_into_file(outfile, "rnemdz", 0, 0 );
545    if (args_info->rnemdr_given)
546      write_into_file(outfile, "rnemdr", 0, 0 );
547 +  if (args_info->rnemdrt_given)
548 +    write_into_file(outfile, "rnemdrt", 0, 0 );
549 +  if (args_info->uFreqMap_given)
550 +    write_into_file(outfile, "uFreqMap", 0, 0 );
551    
552  
553    i = EXIT_SUCCESS;
# Line 580 | Line 602 | reset_group_staticProps(struct gengetopt_args_info *ar
602      return;
603    
604    args_info->bo_given = 0 ;
605 <  args_info->bor_given = 0 ;
605 >  args_info->ior_given = 0 ;
606 >  args_info->for_given = 0 ;
607    args_info->bad_given = 0 ;
608    args_info->count_given = 0 ;
609    args_info->gofr_given = 0 ;
# Line 606 | Line 629 | reset_group_staticProps(struct gengetopt_args_info *ar
629    args_info->tet_param_z_given = 0 ;
630    args_info->rnemdz_given = 0 ;
631    args_info->rnemdr_given = 0 ;
632 +  args_info->rnemdrt_given = 0 ;
633 +  args_info->uFreqMap_given = 0 ;
634  
635    args_info->staticProps_group_counter = 0;
636   }
# Line 872 | Line 897 | cmdline_parser_internal (
897          { "refsele",    1, NULL, 0 },
898          { "comsele",    1, NULL, 0 },
899          { "seleoffset", 1, NULL, 0 },
900 +        { "seleoffset2",        1, NULL, 0 },
901          { "molname",    1, NULL, 0 },
902          { "begin",      1, NULL, 0 },
903          { "end",        1, NULL, 0 },
904          { "radius",     1, NULL, 0 },
905          { "bo", 0, NULL, 0 },
906 <        { "bor",        0, NULL, 0 },
906 >        { "ior",        0, NULL, 0 },
907 >        { "for",        0, NULL, 0 },
908          { "bad",        0, NULL, 0 },
909          { "count",      0, NULL, 0 },
910          { "gofr",       0, NULL, 'g' },
# Line 903 | Line 930 | cmdline_parser_internal (
930          { "tet_param_z",        0, NULL, 0 },
931          { "rnemdz",     0, NULL, 0 },
932          { "rnemdr",     0, NULL, 0 },
933 +        { "rnemdrt",    0, NULL, 0 },
934 +        { "uFreqMap",   0, NULL, 0 },
935          { 0,  0, 0, 0 }
936        };
937  
# Line 1243 | Line 1272 | cmdline_parser_internal (
1272                  &(local_args_info.seleoffset_given), optarg, 0, 0, ARG_INT,
1273                  check_ambiguity, override, 0, 0,
1274                  "seleoffset", '-',
1275 +                additional_error))
1276 +              goto failure;
1277 +          
1278 +          }
1279 +          /* global index offset for a third object (used to define a vector between sites in molecule).  */
1280 +          else if (strcmp (long_options[option_index].name, "seleoffset2") == 0)
1281 +          {
1282 +          
1283 +          
1284 +            if (update_arg( (void *)&(args_info->seleoffset2_arg),
1285 +                 &(args_info->seleoffset2_orig), &(args_info->seleoffset2_given),
1286 +                &(local_args_info.seleoffset2_given), optarg, 0, 0, ARG_INT,
1287 +                check_ambiguity, override, 0, 0,
1288 +                "seleoffset2", '-',
1289                  additional_error))
1290                goto failure;
1291            
# Line 1320 | Line 1363 | cmdline_parser_internal (
1363                goto failure;
1364            
1365            }
1366 <          /* bond order parameter as a function of radius (--rcut must be specified).  */
1367 <          else if (strcmp (long_options[option_index].name, "bor") == 0)
1366 >          /* icosahedral bond order parameter as a function of radius (--rcut must be specified).  */
1367 >          else if (strcmp (long_options[option_index].name, "ior") == 0)
1368            {
1369            
1370              if (args_info->staticProps_group_counter && override)
# Line 1329 | Line 1372 | cmdline_parser_internal (
1372              args_info->staticProps_group_counter += 1;
1373            
1374              if (update_arg( 0 ,
1375 <                 0 , &(args_info->bor_given),
1376 <                &(local_args_info.bor_given), optarg, 0, 0, ARG_NO,
1375 >                 0 , &(args_info->ior_given),
1376 >                &(local_args_info.ior_given), optarg, 0, 0, ARG_NO,
1377                  check_ambiguity, override, 0, 0,
1378 <                "bor", '-',
1378 >                "ior", '-',
1379                  additional_error))
1380                goto failure;
1381            
1382            }
1383 +          /* FCC bond order parameter as a function of radius (--rcut must be specified).  */
1384 +          else if (strcmp (long_options[option_index].name, "for") == 0)
1385 +          {
1386 +          
1387 +            if (args_info->staticProps_group_counter && override)
1388 +              reset_group_staticProps (args_info);
1389 +            args_info->staticProps_group_counter += 1;
1390 +          
1391 +            if (update_arg( 0 ,
1392 +                 0 , &(args_info->for_given),
1393 +                &(local_args_info.for_given), optarg, 0, 0, ARG_NO,
1394 +                check_ambiguity, override, 0, 0,
1395 +                "for", '-',
1396 +                additional_error))
1397 +              goto failure;
1398 +          
1399 +          }
1400            /* N(theta) bond angle density within (--rcut must be specified).  */
1401            else if (strcmp (long_options[option_index].name, "bad") == 0)
1402            {
# Line 1524 | Line 1584 | cmdline_parser_internal (
1584                goto failure;
1585            
1586            }
1587 <          /* p(cos(theta)).  */
1587 >          /* p(cos(theta)) (--sele1 must be specified, --sele2 is optional).  */
1588            else if (strcmp (long_options[option_index].name, "p_angle") == 0)
1589            {
1590            
# Line 1673 | Line 1733 | cmdline_parser_internal (
1733                  &(local_args_info.rnemdr_given), optarg, 0, 0, ARG_NO,
1734                  check_ambiguity, override, 0, 0,
1735                  "rnemdr", '-',
1736 +                additional_error))
1737 +              goto failure;
1738 +          
1739 +          }
1740 +          /* shell and angle-resolved RNEMD statistics (temperature, density, angular velocity).  */
1741 +          else if (strcmp (long_options[option_index].name, "rnemdrt") == 0)
1742 +          {
1743 +          
1744 +            if (args_info->staticProps_group_counter && override)
1745 +              reset_group_staticProps (args_info);
1746 +            args_info->staticProps_group_counter += 1;
1747 +          
1748 +            if (update_arg( 0 ,
1749 +                 0 , &(args_info->rnemdrt_given),
1750 +                &(local_args_info.rnemdrt_given), optarg, 0, 0, ARG_NO,
1751 +                check_ambiguity, override, 0, 0,
1752 +                "rnemdrt", '-',
1753                  additional_error))
1754                goto failure;
1755            
1756            }
1757 +          /* electrostatic potential to frequency map based on the Cho nitrile fits.  */
1758 +          else if (strcmp (long_options[option_index].name, "uFreqMap") == 0)
1759 +          {
1760            
1761 +            if (args_info->staticProps_group_counter && override)
1762 +              reset_group_staticProps (args_info);
1763 +            args_info->staticProps_group_counter += 1;
1764 +          
1765 +            if (update_arg( 0 ,
1766 +                 0 , &(args_info->uFreqMap_given),
1767 +                &(local_args_info.uFreqMap_given), optarg, 0, 0, ARG_NO,
1768 +                check_ambiguity, override, 0, 0,
1769 +                "uFreqMap", '-',
1770 +                additional_error))
1771 +              goto failure;
1772 +          
1773 +          }
1774 +          
1775            break;
1776          case '?':       /* Invalid option.  */
1777            /* `getopt_long' already printed an error message.  */

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