--- trunk/src/applications/staticProps/StaticPropsCmd.cpp 2014/05/31 21:00:46 1999 +++ trunk/src/applications/staticProps/StaticPropsCmd.cpp 2014/08/13 20:42:43 2015 @@ -62,6 +62,8 @@ const char *gengetopt_args_info_help[] = { " --begin=INT begin internal index", " --end=INT end internal index", " --radius=DOUBLE nanoparticle radius", + " -v, --voxelSize=DOUBLE voxel size (angstroms)", + " --gaussWidth=DOUBLE Gaussian width (angstroms)", "\n Group: staticProps\n an option of this group is required", " --bo bond order parameter (--rcut must be specified)", " --ior icosahedral bond order parameter as a function \n of radius (--rcut must be specified)", @@ -89,6 +91,7 @@ const char *gengetopt_args_info_help[] = { " --rodlength length of nanorod", " -Q, --tet_param tetrahedrality order parameter (Qk)", " --tet_param_z spatially-resolved tetrahedrality order \n parameter Qk(z)", + " --tet_param_xyz volume-resolved tetrahedrality order parameter \n Qk(x,y,z). (voxelSize, rcut, and gaussWidth \n must be specified)", " --rnemdz slab-resolved RNEMD statistics (temperature, \n density, velocity)", " --rnemdr shell-resolved RNEMD statistics (temperature, \n density, angular velocity)", " --rnemdrt shell and angle-resolved RNEMD statistics \n (temperature, density, angular velocity)", @@ -147,6 +150,8 @@ void clear_given (struct gengetopt_args_info *args_inf args_info->begin_given = 0 ; args_info->end_given = 0 ; args_info->radius_given = 0 ; + args_info->voxelSize_given = 0 ; + args_info->gaussWidth_given = 0 ; args_info->bo_given = 0 ; args_info->ior_given = 0 ; args_info->for_given = 0 ; @@ -173,6 +178,7 @@ void clear_given (struct gengetopt_args_info *args_inf args_info->rodlength_given = 0 ; args_info->tet_param_given = 0 ; args_info->tet_param_z_given = 0 ; + args_info->tet_param_xyz_given = 0 ; args_info->rnemdz_given = 0 ; args_info->rnemdr_given = 0 ; args_info->rnemdrt_given = 0 ; @@ -224,6 +230,8 @@ void clear_args (struct gengetopt_args_info *args_info args_info->begin_orig = NULL; args_info->end_orig = NULL; args_info->radius_orig = NULL; + args_info->voxelSize_orig = NULL; + args_info->gaussWidth_orig = NULL; } @@ -258,37 +266,40 @@ void init_args_info(struct gengetopt_args_info *args_i args_info->begin_help = gengetopt_args_info_help[23] ; args_info->end_help = gengetopt_args_info_help[24] ; args_info->radius_help = gengetopt_args_info_help[25] ; - args_info->bo_help = gengetopt_args_info_help[27] ; - args_info->ior_help = gengetopt_args_info_help[28] ; - args_info->for_help = gengetopt_args_info_help[29] ; - args_info->bad_help = gengetopt_args_info_help[30] ; - args_info->count_help = gengetopt_args_info_help[31] ; - args_info->gofr_help = gengetopt_args_info_help[32] ; - args_info->gofz_help = gengetopt_args_info_help[33] ; - args_info->r_theta_help = gengetopt_args_info_help[34] ; - args_info->r_omega_help = gengetopt_args_info_help[35] ; - args_info->r_z_help = gengetopt_args_info_help[36] ; - args_info->theta_omega_help = gengetopt_args_info_help[37] ; - args_info->gxyz_help = gengetopt_args_info_help[38] ; - args_info->twodgofr_help = gengetopt_args_info_help[39] ; - args_info->p2_help = gengetopt_args_info_help[40] ; - args_info->rp2_help = gengetopt_args_info_help[41] ; - args_info->scd_help = gengetopt_args_info_help[42] ; - args_info->density_help = gengetopt_args_info_help[43] ; - args_info->slab_density_help = gengetopt_args_info_help[44] ; - args_info->p_angle_help = gengetopt_args_info_help[45] ; - args_info->hxy_help = gengetopt_args_info_help[46] ; - args_info->rho_r_help = gengetopt_args_info_help[47] ; - args_info->angle_r_help = gengetopt_args_info_help[48] ; - args_info->hullvol_help = gengetopt_args_info_help[49] ; - args_info->rodlength_help = gengetopt_args_info_help[50] ; - args_info->tet_param_help = gengetopt_args_info_help[51] ; - args_info->tet_param_z_help = gengetopt_args_info_help[52] ; - args_info->rnemdz_help = gengetopt_args_info_help[53] ; - args_info->rnemdr_help = gengetopt_args_info_help[54] ; - args_info->rnemdrt_help = gengetopt_args_info_help[55] ; - args_info->nitrile_help = gengetopt_args_info_help[56] ; - args_info->multipole_help = gengetopt_args_info_help[57] ; + args_info->voxelSize_help = gengetopt_args_info_help[26] ; + args_info->gaussWidth_help = gengetopt_args_info_help[27] ; + args_info->bo_help = gengetopt_args_info_help[29] ; + args_info->ior_help = gengetopt_args_info_help[30] ; + args_info->for_help = gengetopt_args_info_help[31] ; + args_info->bad_help = gengetopt_args_info_help[32] ; + args_info->count_help = gengetopt_args_info_help[33] ; + args_info->gofr_help = gengetopt_args_info_help[34] ; + args_info->gofz_help = gengetopt_args_info_help[35] ; + args_info->r_theta_help = gengetopt_args_info_help[36] ; + args_info->r_omega_help = gengetopt_args_info_help[37] ; + args_info->r_z_help = gengetopt_args_info_help[38] ; + args_info->theta_omega_help = gengetopt_args_info_help[39] ; + args_info->gxyz_help = gengetopt_args_info_help[40] ; + args_info->twodgofr_help = gengetopt_args_info_help[41] ; + args_info->p2_help = gengetopt_args_info_help[42] ; + args_info->rp2_help = gengetopt_args_info_help[43] ; + args_info->scd_help = gengetopt_args_info_help[44] ; + args_info->density_help = gengetopt_args_info_help[45] ; + args_info->slab_density_help = gengetopt_args_info_help[46] ; + args_info->p_angle_help = gengetopt_args_info_help[47] ; + args_info->hxy_help = gengetopt_args_info_help[48] ; + args_info->rho_r_help = gengetopt_args_info_help[49] ; + args_info->angle_r_help = gengetopt_args_info_help[50] ; + args_info->hullvol_help = gengetopt_args_info_help[51] ; + args_info->rodlength_help = gengetopt_args_info_help[52] ; + args_info->tet_param_help = gengetopt_args_info_help[53] ; + args_info->tet_param_z_help = gengetopt_args_info_help[54] ; + args_info->tet_param_xyz_help = gengetopt_args_info_help[55] ; + args_info->rnemdz_help = gengetopt_args_info_help[56] ; + args_info->rnemdr_help = gengetopt_args_info_help[57] ; + args_info->rnemdrt_help = gengetopt_args_info_help[58] ; + args_info->nitrile_help = gengetopt_args_info_help[59] ; + args_info->multipole_help = gengetopt_args_info_help[60] ; } @@ -404,6 +415,8 @@ cmdline_parser_release (struct gengetopt_args_info *ar free_string_field (&(args_info->begin_orig)); free_string_field (&(args_info->end_orig)); free_string_field (&(args_info->radius_orig)); + free_string_field (&(args_info->voxelSize_orig)); + free_string_field (&(args_info->gaussWidth_orig)); for (i = 0; i < args_info->inputs_num; ++i) @@ -491,6 +504,10 @@ cmdline_parser_dump(FILE *outfile, struct gengetopt_ar write_into_file(outfile, "end", args_info->end_orig, 0); if (args_info->radius_given) write_into_file(outfile, "radius", args_info->radius_orig, 0); + if (args_info->voxelSize_given) + write_into_file(outfile, "voxelSize", args_info->voxelSize_orig, 0); + if (args_info->gaussWidth_given) + write_into_file(outfile, "gaussWidth", args_info->gaussWidth_orig, 0); if (args_info->bo_given) write_into_file(outfile, "bo", 0, 0 ); if (args_info->ior_given) @@ -543,6 +560,8 @@ cmdline_parser_dump(FILE *outfile, struct gengetopt_ar write_into_file(outfile, "tet_param", 0, 0 ); if (args_info->tet_param_z_given) write_into_file(outfile, "tet_param_z", 0, 0 ); + if (args_info->tet_param_xyz_given) + write_into_file(outfile, "tet_param_xyz", 0, 0 ); if (args_info->rnemdz_given) write_into_file(outfile, "rnemdz", 0, 0 ); if (args_info->rnemdr_given) @@ -632,6 +651,7 @@ reset_group_staticProps(struct gengetopt_args_info *ar args_info->rodlength_given = 0 ; args_info->tet_param_given = 0 ; args_info->tet_param_z_given = 0 ; + args_info->tet_param_xyz_given = 0 ; args_info->rnemdz_given = 0 ; args_info->rnemdr_given = 0 ; args_info->rnemdrt_given = 0 ; @@ -908,6 +928,8 @@ cmdline_parser_internal ( { "begin", 1, NULL, 0 }, { "end", 1, NULL, 0 }, { "radius", 1, NULL, 0 }, + { "voxelSize", 1, NULL, 'v' }, + { "gaussWidth", 1, NULL, 0 }, { "bo", 0, NULL, 0 }, { "ior", 0, NULL, 0 }, { "for", 0, NULL, 0 }, @@ -934,6 +956,7 @@ cmdline_parser_internal ( { "rodlength", 0, NULL, 0 }, { "tet_param", 0, NULL, 'Q' }, { "tet_param_z", 0, NULL, 0 }, + { "tet_param_xyz", 0, NULL, 0 }, { "rnemdz", 0, NULL, 0 }, { "rnemdr", 0, NULL, 0 }, { "rnemdrt", 0, NULL, 0 }, @@ -942,7 +965,7 @@ cmdline_parser_internal ( { 0, 0, 0, 0 } }; - c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsdQm", long_options, &option_index); + c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:v:gpsdQm", long_options, &option_index); if (c == -1) break; /* Exit from `while (1)' loop. */ @@ -1062,6 +1085,18 @@ cmdline_parser_internal ( &(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE, check_ambiguity, override, 0, 0, "zoffset", 'z', + additional_error)) + goto failure; + + break; + case 'v': /* voxel size (angstroms). */ + + + if (update_arg( (void *)&(args_info->voxelSize_arg), + &(args_info->voxelSize_orig), &(args_info->voxelSize_given), + &(local_args_info.voxelSize_given), optarg, 0, 0, ARG_DOUBLE, + check_ambiguity, override, 0, 0, + "voxelSize", 'v', additional_error)) goto failure; @@ -1368,6 +1403,20 @@ cmdline_parser_internal ( goto failure; } + /* Gaussian width (angstroms). */ + else if (strcmp (long_options[option_index].name, "gaussWidth") == 0) + { + + + if (update_arg( (void *)&(args_info->gaussWidth_arg), + &(args_info->gaussWidth_orig), &(args_info->gaussWidth_given), + &(local_args_info.gaussWidth_given), optarg, 0, 0, ARG_DOUBLE, + check_ambiguity, override, 0, 0, + "gaussWidth", '-', + additional_error)) + goto failure; + + } /* bond order parameter (--rcut must be specified). */ else if (strcmp (long_options[option_index].name, "bo") == 0) { @@ -1725,6 +1774,23 @@ cmdline_parser_internal ( goto failure; } + /* volume-resolved tetrahedrality order parameter Qk(x,y,z). (voxelSize, rcut, and gaussWidth must be specified). */ + else if (strcmp (long_options[option_index].name, "tet_param_xyz") == 0) + { + + if (args_info->staticProps_group_counter && override) + reset_group_staticProps (args_info); + args_info->staticProps_group_counter += 1; + + if (update_arg( 0 , + 0 , &(args_info->tet_param_xyz_given), + &(local_args_info.tet_param_xyz_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "tet_param_xyz", '-', + additional_error)) + goto failure; + + } /* slab-resolved RNEMD statistics (temperature, density, velocity). */ else if (strcmp (long_options[option_index].name, "rnemdz") == 0) {