--- trunk/src/applications/staticProps/StaticPropsCmd.c 2005/05/26 22:45:00 543 +++ branches/development/src/applications/staticProps/StaticPropsCmd.cpp 2011/10/03 20:32:45 1655 @@ -1,123 +1,825 @@ /* - File autogenerated by gengetopt version 2.11 + File autogenerated by gengetopt version 2.22.4 generated with the following command: - /home/maul/gezelter/tim/bin/gengetopt -i StaticProps.ggo -F StaticPropsCmd + gengetopt -F StaticPropsCmd -u The developers of gengetopt consider the fixed text that goes in all gengetopt output files to be in the public domain: we make no copyright claims on it. */ +/* If we use autoconf. */ +#ifdef HAVE_CONFIG_H +#include "config.h" +#endif #include #include #include -/* If we use autoconf. */ -#ifdef HAVE_CONFIG_H -#include "config.h" +#ifndef FIX_UNUSED +#define FIX_UNUSED(X) (void) (X) /* avoid warnings for unused params */ #endif -#include "getopt.h" +#include #include "StaticPropsCmd.h" +const char *gengetopt_args_info_purpose = ""; + +const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]... [FILES]..."; + +const char *gengetopt_args_info_description = ""; + +const char *gengetopt_args_info_help[] = { + " -h, --help Print help and exit", + " -V, --version Print version and exit", + " -i, --input=filename input dump file", + " -o, --output=filename output file name", + " -n, --step=INT process every n frame (default=`1')", + " -b, --nbins=INT number of bins (general purpose) \n (default=`100')", + " -x, --nbins_x=INT number of bins in x axis (default=`100')", + " -y, --nbins_y=INT number of bins in y axis (default=`100')", + " --nbins_z=INT number of bins in z axis (default=`100')", + " -a, --nanglebins=INT number of bins for cos(angle) (default=`50')", + " -c, --rcut=DOUBLE cutoff radius (rcut)", + " --dz=DOUBLE slab width (dz)", + " --length=DOUBLE maximum length (Defaults to 1/2 smallest length \n of first frame)", + " --zlength=DOUBLE maximum length (Defaults to 1/2 smallest length \n of first frame)", + " -z, --zoffset=DOUBLE Where to set the zero for the slab_density \n calculation (default=`0')", + " --sele1=selection script select the first stuntdouble set", + " --sele2=selection script select the second stuntdouble set", + " --sele3=selection script select the third stuntdouble set", + " --refsele=selection script\n select reference (use and only use with --gxyz)", + " --comsele=selection script\n select stunt doubles for center-of-mass \n reference point", + " --molname=STRING molecule name", + " --begin=INT begin internal index", + " --end=INT end internal index", + " --radius=DOUBLE nanoparticle radius", + "\n Group: staticProps\n an option of this group is required", + " --bo bond order parameter (--rcut must be specified)", + " --bor bond order parameter as a function of radius \n (--rcut must be specified)", + " --bad N(theta) bond angle density within (--rcut must \n be specified)", + " --count count of molecules matching selection criteria \n (and associated statistics)", + " -g, --gofr g(r)", + " --gofz g(z)", + " --r_theta g(r, cos(theta))", + " --r_omega g(r, cos(omega))", + " --r_z g(r, z)", + " --theta_omega g(cos(theta), cos(omega))", + " --gxyz g(x, y, z)", + " --twodgofr 2D g(r) (Slab width --dz must be specified)", + " -p, --p2 p2 order parameter (--sele1 must be specified, \n --sele2 is optional)", + " --rp2 rp2 order parameter (--sele1 and --sele2 must \n be specified)", + " -s, --scd scd order parameter (either --sele1, --sele2, \n --sele3 are specified or --molname, --begin, \n --end are specified)", + " -d, --density density plot", + " --slab_density slab density", + " --p_angle p(cos(theta))", + " --hxy hxy", + " --rho_r rho of R", + " --angle_r angle of R", + " --hullvol hull volume of nanoparticle", + " --rodlength length of nanorod", + " -Q, --tet_param tetrahedrality order parameter", + 0 +}; + +typedef enum {ARG_NO + , ARG_STRING + , ARG_INT + , ARG_DOUBLE +} cmdline_parser_arg_type; + +static +void clear_given (struct gengetopt_args_info *args_info); +static +void clear_args (struct gengetopt_args_info *args_info); + +static int +cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info, + struct cmdline_parser_params *params, const char *additional_error); + +static int +cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error); + +static char * +gengetopt_strdup (const char *s); + +static +void clear_given (struct gengetopt_args_info *args_info) +{ + args_info->help_given = 0 ; + args_info->version_given = 0 ; + args_info->input_given = 0 ; + args_info->output_given = 0 ; + args_info->step_given = 0 ; + args_info->nbins_given = 0 ; + args_info->nbins_x_given = 0 ; + args_info->nbins_y_given = 0 ; + args_info->nbins_z_given = 0 ; + args_info->nanglebins_given = 0 ; + args_info->rcut_given = 0 ; + args_info->dz_given = 0 ; + args_info->length_given = 0 ; + args_info->zlength_given = 0 ; + args_info->zoffset_given = 0 ; + args_info->sele1_given = 0 ; + args_info->sele2_given = 0 ; + args_info->sele3_given = 0 ; + args_info->refsele_given = 0 ; + args_info->comsele_given = 0 ; + args_info->molname_given = 0 ; + args_info->begin_given = 0 ; + args_info->end_given = 0 ; + args_info->radius_given = 0 ; + args_info->bo_given = 0 ; + args_info->bor_given = 0 ; + args_info->bad_given = 0 ; + args_info->count_given = 0 ; + args_info->gofr_given = 0 ; + args_info->gofz_given = 0 ; + args_info->r_theta_given = 0 ; + args_info->r_omega_given = 0 ; + args_info->r_z_given = 0 ; + args_info->theta_omega_given = 0 ; + args_info->gxyz_given = 0 ; + args_info->twodgofr_given = 0 ; + args_info->p2_given = 0 ; + args_info->rp2_given = 0 ; + args_info->scd_given = 0 ; + args_info->density_given = 0 ; + args_info->slab_density_given = 0 ; + args_info->p_angle_given = 0 ; + args_info->hxy_given = 0 ; + args_info->rho_r_given = 0 ; + args_info->angle_r_given = 0 ; + args_info->hullvol_given = 0 ; + args_info->rodlength_given = 0 ; + args_info->tet_param_given = 0 ; + args_info->staticProps_group_counter = 0 ; +} + +static +void clear_args (struct gengetopt_args_info *args_info) +{ + FIX_UNUSED (args_info); + args_info->input_arg = NULL; + args_info->input_orig = NULL; + args_info->output_arg = NULL; + args_info->output_orig = NULL; + args_info->step_arg = 1; + args_info->step_orig = NULL; + args_info->nbins_arg = 100; + args_info->nbins_orig = NULL; + args_info->nbins_x_arg = 100; + args_info->nbins_x_orig = NULL; + args_info->nbins_y_arg = 100; + args_info->nbins_y_orig = NULL; + args_info->nbins_z_arg = 100; + args_info->nbins_z_orig = NULL; + args_info->nanglebins_arg = 50; + args_info->nanglebins_orig = NULL; + args_info->rcut_orig = NULL; + args_info->dz_orig = NULL; + args_info->length_orig = NULL; + args_info->zlength_orig = NULL; + args_info->zoffset_arg = 0; + args_info->zoffset_orig = NULL; + args_info->sele1_arg = NULL; + args_info->sele1_orig = NULL; + args_info->sele2_arg = NULL; + args_info->sele2_orig = NULL; + args_info->sele3_arg = NULL; + args_info->sele3_orig = NULL; + args_info->refsele_arg = NULL; + args_info->refsele_orig = NULL; + args_info->comsele_arg = NULL; + args_info->comsele_orig = NULL; + args_info->molname_arg = NULL; + args_info->molname_orig = NULL; + args_info->begin_orig = NULL; + args_info->end_orig = NULL; + args_info->radius_orig = NULL; + +} + +static +void init_args_info(struct gengetopt_args_info *args_info) +{ + + + args_info->help_help = gengetopt_args_info_help[0] ; + args_info->version_help = gengetopt_args_info_help[1] ; + args_info->input_help = gengetopt_args_info_help[2] ; + args_info->output_help = gengetopt_args_info_help[3] ; + args_info->step_help = gengetopt_args_info_help[4] ; + args_info->nbins_help = gengetopt_args_info_help[5] ; + args_info->nbins_x_help = gengetopt_args_info_help[6] ; + args_info->nbins_y_help = gengetopt_args_info_help[7] ; + args_info->nbins_z_help = gengetopt_args_info_help[8] ; + args_info->nanglebins_help = gengetopt_args_info_help[9] ; + args_info->rcut_help = gengetopt_args_info_help[10] ; + args_info->dz_help = gengetopt_args_info_help[11] ; + args_info->length_help = gengetopt_args_info_help[12] ; + args_info->zlength_help = gengetopt_args_info_help[13] ; + args_info->zoffset_help = gengetopt_args_info_help[14] ; + args_info->sele1_help = gengetopt_args_info_help[15] ; + args_info->sele2_help = gengetopt_args_info_help[16] ; + args_info->sele3_help = gengetopt_args_info_help[17] ; + args_info->refsele_help = gengetopt_args_info_help[18] ; + args_info->comsele_help = gengetopt_args_info_help[19] ; + args_info->molname_help = gengetopt_args_info_help[20] ; + args_info->begin_help = gengetopt_args_info_help[21] ; + args_info->end_help = gengetopt_args_info_help[22] ; + args_info->radius_help = gengetopt_args_info_help[23] ; + args_info->bo_help = gengetopt_args_info_help[25] ; + args_info->bor_help = gengetopt_args_info_help[26] ; + args_info->bad_help = gengetopt_args_info_help[27] ; + args_info->count_help = gengetopt_args_info_help[28] ; + args_info->gofr_help = gengetopt_args_info_help[29] ; + args_info->gofz_help = gengetopt_args_info_help[30] ; + args_info->r_theta_help = gengetopt_args_info_help[31] ; + args_info->r_omega_help = gengetopt_args_info_help[32] ; + args_info->r_z_help = gengetopt_args_info_help[33] ; + args_info->theta_omega_help = gengetopt_args_info_help[34] ; + args_info->gxyz_help = gengetopt_args_info_help[35] ; + args_info->twodgofr_help = gengetopt_args_info_help[36] ; + args_info->p2_help = gengetopt_args_info_help[37] ; + args_info->rp2_help = gengetopt_args_info_help[38] ; + args_info->scd_help = gengetopt_args_info_help[39] ; + args_info->density_help = gengetopt_args_info_help[40] ; + args_info->slab_density_help = gengetopt_args_info_help[41] ; + args_info->p_angle_help = gengetopt_args_info_help[42] ; + args_info->hxy_help = gengetopt_args_info_help[43] ; + args_info->rho_r_help = gengetopt_args_info_help[44] ; + args_info->angle_r_help = gengetopt_args_info_help[45] ; + args_info->hullvol_help = gengetopt_args_info_help[46] ; + args_info->rodlength_help = gengetopt_args_info_help[47] ; + args_info->tet_param_help = gengetopt_args_info_help[48] ; + +} + void cmdline_parser_print_version (void) { - printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION); + printf ("%s %s\n", + (strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE), + CMDLINE_PARSER_VERSION); } +static void print_help_common(void) { + cmdline_parser_print_version (); + + if (strlen(gengetopt_args_info_purpose) > 0) + printf("\n%s\n", gengetopt_args_info_purpose); + + if (strlen(gengetopt_args_info_usage) > 0) + printf("\n%s\n", gengetopt_args_info_usage); + + printf("\n"); + + if (strlen(gengetopt_args_info_description) > 0) + printf("%s\n\n", gengetopt_args_info_description); +} + void cmdline_parser_print_help (void) { - cmdline_parser_print_version (); - printf("\n" - "Usage: %s [OPTIONS]...\n", CMDLINE_PARSER_PACKAGE); - printf("\n"); - printf(" -h, --help Print help and exit\n"); - printf(" -V, --version Print version and exit\n"); - printf(" -i, --input=filename input dump file\n"); - printf(" -o, --output=filename output file name\n"); - printf(" -n, --step=INT process every n frame (default=`1')\n"); - printf(" -r, --nrbins=INT number of bins for distance (default=`100')\n"); - printf(" -a, --nanglebins=INT number of bins for cos(angle) (default=\n `50')\n"); - printf(" -l, --length=DOUBLE maximum length (Defaults to 1/2 smallest \n length of first frame)\n"); - printf(" --sele1=selection script select first stuntdouble set\n"); - printf(" --sele2=selection script select second stuntdouble set\n"); - printf(" --refsele=selection script select reference (use and only use with \n --gxyz)\n"); - printf("\n"); - printf(" Group: staticProps an option of this group is required\n"); - printf(" --gofr g(r)\n"); - printf(" --r_theta g(r, cos(theta))\n"); - printf(" --r_omega g(r, cos(omega))\n"); - printf(" --theta_omega g(cos(theta), cos(omega))\n"); - printf(" --gxyz g(x, y, z)\n"); - printf(" --p2 p2 order parameter\n"); + int i = 0; + print_help_common(); + while (gengetopt_args_info_help[i]) + printf("%s\n", gengetopt_args_info_help[i++]); } +void +cmdline_parser_init (struct gengetopt_args_info *args_info) +{ + clear_given (args_info); + clear_args (args_info); + init_args_info (args_info); -static char *gengetopt_strdup (const char *s); + args_info->inputs = 0; + args_info->inputs_num = 0; +} -/* gengetopt_strdup() */ -/* strdup.c replacement of strdup, which is not standard */ +void +cmdline_parser_params_init(struct cmdline_parser_params *params) +{ + if (params) + { + params->override = 0; + params->initialize = 1; + params->check_required = 1; + params->check_ambiguity = 0; + params->print_errors = 1; + } +} + +struct cmdline_parser_params * +cmdline_parser_params_create(void) +{ + struct cmdline_parser_params *params = + (struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params)); + cmdline_parser_params_init(params); + return params; +} + +static void +free_string_field (char **s) +{ + if (*s) + { + free (*s); + *s = 0; + } +} + + +static void +cmdline_parser_release (struct gengetopt_args_info *args_info) +{ + unsigned int i; + free_string_field (&(args_info->input_arg)); + free_string_field (&(args_info->input_orig)); + free_string_field (&(args_info->output_arg)); + free_string_field (&(args_info->output_orig)); + free_string_field (&(args_info->step_orig)); + free_string_field (&(args_info->nbins_orig)); + free_string_field (&(args_info->nbins_x_orig)); + free_string_field (&(args_info->nbins_y_orig)); + free_string_field (&(args_info->nbins_z_orig)); + free_string_field (&(args_info->nanglebins_orig)); + free_string_field (&(args_info->rcut_orig)); + free_string_field (&(args_info->dz_orig)); + free_string_field (&(args_info->length_orig)); + free_string_field (&(args_info->zlength_orig)); + free_string_field (&(args_info->zoffset_orig)); + free_string_field (&(args_info->sele1_arg)); + free_string_field (&(args_info->sele1_orig)); + free_string_field (&(args_info->sele2_arg)); + free_string_field (&(args_info->sele2_orig)); + free_string_field (&(args_info->sele3_arg)); + free_string_field (&(args_info->sele3_orig)); + free_string_field (&(args_info->refsele_arg)); + free_string_field (&(args_info->refsele_orig)); + free_string_field (&(args_info->comsele_arg)); + free_string_field (&(args_info->comsele_orig)); + free_string_field (&(args_info->molname_arg)); + free_string_field (&(args_info->molname_orig)); + free_string_field (&(args_info->begin_orig)); + free_string_field (&(args_info->end_orig)); + free_string_field (&(args_info->radius_orig)); + + + for (i = 0; i < args_info->inputs_num; ++i) + free (args_info->inputs [i]); + + if (args_info->inputs_num) + free (args_info->inputs); + + clear_given (args_info); +} + + +static void +write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[]) +{ + FIX_UNUSED (values); + if (arg) { + fprintf(outfile, "%s=\"%s\"\n", opt, arg); + } else { + fprintf(outfile, "%s\n", opt); + } +} + + +int +cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info) +{ + int i = 0; + + if (!outfile) + { + fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE); + return EXIT_FAILURE; + } + + if (args_info->help_given) + write_into_file(outfile, "help", 0, 0 ); + if (args_info->version_given) + write_into_file(outfile, "version", 0, 0 ); + if (args_info->input_given) + write_into_file(outfile, "input", args_info->input_orig, 0); + if (args_info->output_given) + write_into_file(outfile, "output", args_info->output_orig, 0); + if (args_info->step_given) + write_into_file(outfile, "step", args_info->step_orig, 0); + if (args_info->nbins_given) + write_into_file(outfile, "nbins", args_info->nbins_orig, 0); + if (args_info->nbins_x_given) + write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0); + if (args_info->nbins_y_given) + write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0); + if (args_info->nbins_z_given) + write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0); + if (args_info->nanglebins_given) + write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0); + if (args_info->rcut_given) + write_into_file(outfile, "rcut", args_info->rcut_orig, 0); + if (args_info->dz_given) + write_into_file(outfile, "dz", args_info->dz_orig, 0); + if (args_info->length_given) + write_into_file(outfile, "length", args_info->length_orig, 0); + if (args_info->zlength_given) + write_into_file(outfile, "zlength", args_info->zlength_orig, 0); + if (args_info->zoffset_given) + write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0); + if (args_info->sele1_given) + write_into_file(outfile, "sele1", args_info->sele1_orig, 0); + if (args_info->sele2_given) + write_into_file(outfile, "sele2", args_info->sele2_orig, 0); + if (args_info->sele3_given) + write_into_file(outfile, "sele3", args_info->sele3_orig, 0); + if (args_info->refsele_given) + write_into_file(outfile, "refsele", args_info->refsele_orig, 0); + if (args_info->comsele_given) + write_into_file(outfile, "comsele", args_info->comsele_orig, 0); + if (args_info->molname_given) + write_into_file(outfile, "molname", args_info->molname_orig, 0); + if (args_info->begin_given) + write_into_file(outfile, "begin", args_info->begin_orig, 0); + if (args_info->end_given) + 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->bo_given) + write_into_file(outfile, "bo", 0, 0 ); + if (args_info->bor_given) + write_into_file(outfile, "bor", 0, 0 ); + if (args_info->bad_given) + write_into_file(outfile, "bad", 0, 0 ); + if (args_info->count_given) + write_into_file(outfile, "count", 0, 0 ); + if (args_info->gofr_given) + write_into_file(outfile, "gofr", 0, 0 ); + if (args_info->gofz_given) + write_into_file(outfile, "gofz", 0, 0 ); + if (args_info->r_theta_given) + write_into_file(outfile, "r_theta", 0, 0 ); + if (args_info->r_omega_given) + write_into_file(outfile, "r_omega", 0, 0 ); + if (args_info->r_z_given) + write_into_file(outfile, "r_z", 0, 0 ); + if (args_info->theta_omega_given) + write_into_file(outfile, "theta_omega", 0, 0 ); + if (args_info->gxyz_given) + write_into_file(outfile, "gxyz", 0, 0 ); + if (args_info->twodgofr_given) + write_into_file(outfile, "twodgofr", 0, 0 ); + if (args_info->p2_given) + write_into_file(outfile, "p2", 0, 0 ); + if (args_info->rp2_given) + write_into_file(outfile, "rp2", 0, 0 ); + if (args_info->scd_given) + write_into_file(outfile, "scd", 0, 0 ); + if (args_info->density_given) + write_into_file(outfile, "density", 0, 0 ); + if (args_info->slab_density_given) + write_into_file(outfile, "slab_density", 0, 0 ); + if (args_info->p_angle_given) + write_into_file(outfile, "p_angle", 0, 0 ); + if (args_info->hxy_given) + write_into_file(outfile, "hxy", 0, 0 ); + if (args_info->rho_r_given) + write_into_file(outfile, "rho_r", 0, 0 ); + if (args_info->angle_r_given) + write_into_file(outfile, "angle_r", 0, 0 ); + if (args_info->hullvol_given) + write_into_file(outfile, "hullvol", 0, 0 ); + if (args_info->rodlength_given) + write_into_file(outfile, "rodlength", 0, 0 ); + if (args_info->tet_param_given) + write_into_file(outfile, "tet_param", 0, 0 ); + + + i = EXIT_SUCCESS; + return i; +} + +int +cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info) +{ + FILE *outfile; + int i = 0; + + outfile = fopen(filename, "w"); + + if (!outfile) + { + fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename); + return EXIT_FAILURE; + } + + i = cmdline_parser_dump(outfile, args_info); + fclose (outfile); + + return i; +} + +void +cmdline_parser_free (struct gengetopt_args_info *args_info) +{ + cmdline_parser_release (args_info); +} + +/** @brief replacement of strdup, which is not standard */ char * gengetopt_strdup (const char *s) { - char *result = (char*)malloc(strlen(s) + 1); + char *result = 0; + if (!s) + return result; + + result = (char*)malloc(strlen(s) + 1); if (result == (char*)0) return (char*)0; strcpy(result, s); return result; } -int -cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info) +static void +reset_group_staticProps(struct gengetopt_args_info *args_info) { - int c; /* Character of the parsed option. */ - int missing_required_options = 0; - int staticProps_group_counter = 0; + if (! args_info->staticProps_group_counter) + return; - - args_info->help_given = 0 ; - args_info->version_given = 0 ; - args_info->input_given = 0 ; - args_info->output_given = 0 ; - args_info->step_given = 0 ; - args_info->nrbins_given = 0 ; - args_info->nanglebins_given = 0 ; - args_info->length_given = 0 ; - args_info->sele1_given = 0 ; - args_info->sele2_given = 0 ; - args_info->refsele_given = 0 ; + args_info->bo_given = 0 ; + args_info->bor_given = 0 ; + args_info->bad_given = 0 ; + args_info->count_given = 0 ; args_info->gofr_given = 0 ; + args_info->gofz_given = 0 ; args_info->r_theta_given = 0 ; args_info->r_omega_given = 0 ; + args_info->r_z_given = 0 ; args_info->theta_omega_given = 0 ; args_info->gxyz_given = 0 ; + args_info->twodgofr_given = 0 ; args_info->p2_given = 0 ; -#define clear_args() { \ - args_info->input_arg = NULL; \ - args_info->output_arg = NULL; \ - args_info->step_arg = 1 ;\ - args_info->nrbins_arg = 100 ;\ - args_info->nanglebins_arg = 50 ;\ - args_info->sele1_arg = NULL; \ - args_info->sele2_arg = NULL; \ - args_info->refsele_arg = NULL; \ + args_info->rp2_given = 0 ; + args_info->scd_given = 0 ; + args_info->density_given = 0 ; + args_info->slab_density_given = 0 ; + args_info->p_angle_given = 0 ; + args_info->hxy_given = 0 ; + args_info->rho_r_given = 0 ; + args_info->angle_r_given = 0 ; + args_info->hullvol_given = 0 ; + args_info->rodlength_given = 0 ; + args_info->tet_param_given = 0 ; + + args_info->staticProps_group_counter = 0; } - clear_args(); +int +cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info) +{ + return cmdline_parser2 (argc, argv, args_info, 0, 1, 1); +} + +int +cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info, + struct cmdline_parser_params *params) +{ + int result; + result = cmdline_parser_internal (argc, argv, args_info, params, 0); + + if (result == EXIT_FAILURE) + { + cmdline_parser_free (args_info); + exit (EXIT_FAILURE); + } + + return result; +} + +int +cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required) +{ + int result; + struct cmdline_parser_params params; + + params.override = override; + params.initialize = initialize; + params.check_required = check_required; + params.check_ambiguity = 0; + params.print_errors = 1; + + result = cmdline_parser_internal (argc, argv, args_info, ¶ms, 0); + + if (result == EXIT_FAILURE) + { + cmdline_parser_free (args_info); + exit (EXIT_FAILURE); + } + + return result; +} + +int +cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name) +{ + int result = EXIT_SUCCESS; + + if (cmdline_parser_required2(args_info, prog_name, 0) > 0) + result = EXIT_FAILURE; + + if (result == EXIT_FAILURE) + { + cmdline_parser_free (args_info); + exit (EXIT_FAILURE); + } + + return result; +} + +int +cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error) +{ + int error = 0; + FIX_UNUSED (additional_error); + + /* checks for required options */ + if (! args_info->input_given) + { + fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : "")); + error = 1; + } + + if (args_info->staticProps_group_counter == 0) + { + fprintf (stderr, "%s: %d options of group staticProps were given. One is required%s.\n", prog_name, args_info->staticProps_group_counter, (additional_error ? additional_error : "")); + error = 1; + } + + /* checks for dependences among options */ + + return error; +} + + +static char *package_name = 0; + +/** + * @brief updates an option + * @param field the generic pointer to the field to update + * @param orig_field the pointer to the orig field + * @param field_given the pointer to the number of occurrence of this option + * @param prev_given the pointer to the number of occurrence already seen + * @param value the argument for this option (if null no arg was specified) + * @param possible_values the possible values for this option (if specified) + * @param default_value the default value (in case the option only accepts fixed values) + * @param arg_type the type of this option + * @param check_ambiguity @see cmdline_parser_params.check_ambiguity + * @param override @see cmdline_parser_params.override + * @param no_free whether to free a possible previous value + * @param multiple_option whether this is a multiple option + * @param long_opt the corresponding long option + * @param short_opt the corresponding short option (or '-' if none) + * @param additional_error possible further error specification + */ +static +int update_arg(void *field, char **orig_field, + unsigned int *field_given, unsigned int *prev_given, + char *value, const char *possible_values[], + const char *default_value, + cmdline_parser_arg_type arg_type, + int check_ambiguity, int override, + int no_free, int multiple_option, + const char *long_opt, char short_opt, + const char *additional_error) +{ + char *stop_char = 0; + const char *val = value; + int found; + char **string_field; + FIX_UNUSED (field); + + stop_char = 0; + found = 0; + + if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given))) + { + if (short_opt != '-') + fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n", + package_name, long_opt, short_opt, + (additional_error ? additional_error : "")); + else + fprintf (stderr, "%s: `--%s' option given more than once%s\n", + package_name, long_opt, + (additional_error ? additional_error : "")); + return 1; /* failure */ + } + + FIX_UNUSED (default_value); + + if (field_given && *field_given && ! override) + return 0; + if (prev_given) + (*prev_given)++; + if (field_given) + (*field_given)++; + if (possible_values) + val = possible_values[found]; + + switch(arg_type) { + case ARG_INT: + if (val) *((int *)field) = strtol (val, &stop_char, 0); + break; + case ARG_DOUBLE: + if (val) *((double *)field) = strtod (val, &stop_char); + break; + case ARG_STRING: + if (val) { + string_field = (char **)field; + if (!no_free && *string_field) + free (*string_field); /* free previous string */ + *string_field = gengetopt_strdup (val); + } + break; + default: + break; + }; + + /* check numeric conversion */ + switch(arg_type) { + case ARG_INT: + case ARG_DOUBLE: + if (val && !(stop_char && *stop_char == '\0')) { + fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val); + return 1; /* failure */ + } + break; + default: + ; + }; + + /* store the original value */ + switch(arg_type) { + case ARG_NO: + break; + default: + if (value && orig_field) { + if (no_free) { + *orig_field = value; + } else { + if (*orig_field) + free (*orig_field); /* free previous string */ + *orig_field = gengetopt_strdup (value); + } + } + }; + + return 0; /* OK */ +} + + +int +cmdline_parser_internal ( + int argc, char **argv, struct gengetopt_args_info *args_info, + struct cmdline_parser_params *params, const char *additional_error) +{ + int c; /* Character of the parsed option. */ + + int error = 0; + struct gengetopt_args_info local_args_info; + + int override; + int initialize; + int check_required; + int check_ambiguity; + + package_name = argv[0]; + + override = params->override; + initialize = params->initialize; + check_required = params->check_required; + check_ambiguity = params->check_ambiguity; + + if (initialize) + cmdline_parser_init (args_info); + + cmdline_parser_init (&local_args_info); + optarg = 0; - optind = 1; - opterr = 1; + optind = 0; + opterr = params->print_errors; optopt = '?'; while (1) { int option_index = 0; - char *stop_char; static struct option long_options[] = { { "help", 0, NULL, 'h' }, @@ -125,257 +827,816 @@ cmdline_parser (int argc, char * const *argv, struct g { "input", 1, NULL, 'i' }, { "output", 1, NULL, 'o' }, { "step", 1, NULL, 'n' }, - { "nrbins", 1, NULL, 'r' }, + { "nbins", 1, NULL, 'b' }, + { "nbins_x", 1, NULL, 'x' }, + { "nbins_y", 1, NULL, 'y' }, + { "nbins_z", 1, NULL, 0 }, { "nanglebins", 1, NULL, 'a' }, - { "length", 1, NULL, 'l' }, + { "rcut", 1, NULL, 'c' }, + { "dz", 1, NULL, 0 }, + { "length", 1, NULL, 0 }, + { "zlength", 1, NULL, 0 }, + { "zoffset", 1, NULL, 'z' }, { "sele1", 1, NULL, 0 }, { "sele2", 1, NULL, 0 }, + { "sele3", 1, NULL, 0 }, { "refsele", 1, NULL, 0 }, - { "gofr", 0, NULL, 0 }, + { "comsele", 1, NULL, 0 }, + { "molname", 1, NULL, 0 }, + { "begin", 1, NULL, 0 }, + { "end", 1, NULL, 0 }, + { "radius", 1, NULL, 0 }, + { "bo", 0, NULL, 0 }, + { "bor", 0, NULL, 0 }, + { "bad", 0, NULL, 0 }, + { "count", 0, NULL, 0 }, + { "gofr", 0, NULL, 'g' }, + { "gofz", 0, NULL, 0 }, { "r_theta", 0, NULL, 0 }, { "r_omega", 0, NULL, 0 }, + { "r_z", 0, NULL, 0 }, { "theta_omega", 0, NULL, 0 }, { "gxyz", 0, NULL, 0 }, - { "p2", 0, NULL, 0 }, - { NULL, 0, NULL, 0 } + { "twodgofr", 0, NULL, 0 }, + { "p2", 0, NULL, 'p' }, + { "rp2", 0, NULL, 0 }, + { "scd", 0, NULL, 's' }, + { "density", 0, NULL, 'd' }, + { "slab_density", 0, NULL, 0 }, + { "p_angle", 0, NULL, 0 }, + { "hxy", 0, NULL, 0 }, + { "rho_r", 0, NULL, 0 }, + { "angle_r", 0, NULL, 0 }, + { "hullvol", 0, NULL, 0 }, + { "rodlength", 0, NULL, 0 }, + { "tet_param", 0, NULL, 'Q' }, + { 0, 0, 0, 0 } }; - stop_char = 0; - c = getopt_long (argc, argv, "hVi:o:n:r:a:l:", long_options, &option_index); + c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsdQ", long_options, &option_index); if (c == -1) break; /* Exit from `while (1)' loop. */ switch (c) { case 'h': /* Print help and exit. */ - clear_args (); cmdline_parser_print_help (); + cmdline_parser_free (&local_args_info); exit (EXIT_SUCCESS); case 'V': /* Print version and exit. */ - clear_args (); cmdline_parser_print_version (); + cmdline_parser_free (&local_args_info); exit (EXIT_SUCCESS); case 'i': /* input dump file. */ - if (args_info->input_given) - { - fprintf (stderr, "%s: `--input' (`-i') option given more than once\n", CMDLINE_PARSER_PACKAGE); - clear_args (); - exit (EXIT_FAILURE); - } - args_info->input_given = 1; - args_info->input_arg = gengetopt_strdup (optarg); + + + if (update_arg( (void *)&(args_info->input_arg), + &(args_info->input_orig), &(args_info->input_given), + &(local_args_info.input_given), optarg, 0, 0, ARG_STRING, + check_ambiguity, override, 0, 0, + "input", 'i', + additional_error)) + goto failure; + break; - case 'o': /* output file name. */ - if (args_info->output_given) - { - fprintf (stderr, "%s: `--output' (`-o') option given more than once\n", CMDLINE_PARSER_PACKAGE); - clear_args (); - exit (EXIT_FAILURE); - } - args_info->output_given = 1; - args_info->output_arg = gengetopt_strdup (optarg); + + + if (update_arg( (void *)&(args_info->output_arg), + &(args_info->output_orig), &(args_info->output_given), + &(local_args_info.output_given), optarg, 0, 0, ARG_STRING, + check_ambiguity, override, 0, 0, + "output", 'o', + additional_error)) + goto failure; + break; - case 'n': /* process every n frame. */ - if (args_info->step_given) - { - fprintf (stderr, "%s: `--step' (`-n') option given more than once\n", CMDLINE_PARSER_PACKAGE); - clear_args (); - exit (EXIT_FAILURE); - } - args_info->step_given = 1; - args_info->step_arg = strtol (optarg,&stop_char,0); + + + if (update_arg( (void *)&(args_info->step_arg), + &(args_info->step_orig), &(args_info->step_given), + &(local_args_info.step_given), optarg, 0, "1", ARG_INT, + check_ambiguity, override, 0, 0, + "step", 'n', + additional_error)) + goto failure; + break; - - case 'r': /* number of bins for distance. */ - if (args_info->nrbins_given) - { - fprintf (stderr, "%s: `--nrbins' (`-r') option given more than once\n", CMDLINE_PARSER_PACKAGE); - clear_args (); - exit (EXIT_FAILURE); - } - args_info->nrbins_given = 1; - args_info->nrbins_arg = strtol (optarg,&stop_char,0); + case 'b': /* number of bins (general purpose). */ + + + if (update_arg( (void *)&(args_info->nbins_arg), + &(args_info->nbins_orig), &(args_info->nbins_given), + &(local_args_info.nbins_given), optarg, 0, "100", ARG_INT, + check_ambiguity, override, 0, 0, + "nbins", 'b', + additional_error)) + goto failure; + break; - + case 'x': /* number of bins in x axis. */ + + + if (update_arg( (void *)&(args_info->nbins_x_arg), + &(args_info->nbins_x_orig), &(args_info->nbins_x_given), + &(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT, + check_ambiguity, override, 0, 0, + "nbins_x", 'x', + additional_error)) + goto failure; + + break; + case 'y': /* number of bins in y axis. */ + + + if (update_arg( (void *)&(args_info->nbins_y_arg), + &(args_info->nbins_y_orig), &(args_info->nbins_y_given), + &(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT, + check_ambiguity, override, 0, 0, + "nbins_y", 'y', + additional_error)) + goto failure; + + break; case 'a': /* number of bins for cos(angle). */ - if (args_info->nanglebins_given) - { - fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once\n", CMDLINE_PARSER_PACKAGE); - clear_args (); - exit (EXIT_FAILURE); - } - args_info->nanglebins_given = 1; - args_info->nanglebins_arg = strtol (optarg,&stop_char,0); + + + if (update_arg( (void *)&(args_info->nanglebins_arg), + &(args_info->nanglebins_orig), &(args_info->nanglebins_given), + &(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT, + check_ambiguity, override, 0, 0, + "nanglebins", 'a', + additional_error)) + goto failure; + break; - - case 'l': /* maximum length (Defaults to 1/2 smallest length of first frame). */ - if (args_info->length_given) - { - fprintf (stderr, "%s: `--length' (`-l') option given more than once\n", CMDLINE_PARSER_PACKAGE); - clear_args (); - exit (EXIT_FAILURE); - } - args_info->length_given = 1; - args_info->length_arg = strtod (optarg, NULL); + case 'c': /* cutoff radius (rcut). */ + + + if (update_arg( (void *)&(args_info->rcut_arg), + &(args_info->rcut_orig), &(args_info->rcut_given), + &(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE, + check_ambiguity, override, 0, 0, + "rcut", 'c', + additional_error)) + goto failure; + break; + case 'z': /* Where to set the zero for the slab_density calculation. */ + + + if (update_arg( (void *)&(args_info->zoffset_arg), + &(args_info->zoffset_orig), &(args_info->zoffset_given), + &(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE, + check_ambiguity, override, 0, 0, + "zoffset", 'z', + additional_error)) + goto failure; + + break; + case 'g': /* g(r). */ + + 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->gofr_given), + &(local_args_info.gofr_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "gofr", 'g', + additional_error)) + goto failure; + + break; + case 'p': /* p2 order parameter (--sele1 must be specified, --sele2 is optional). */ + + 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->p2_given), + &(local_args_info.p2_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "p2", 'p', + additional_error)) + goto failure; + + break; + case 's': /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified). */ + + 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->scd_given), + &(local_args_info.scd_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "scd", 's', + additional_error)) + goto failure; + + break; + case 'd': /* density plot. */ + + 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->density_given), + &(local_args_info.density_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "density", 'd', + additional_error)) + goto failure; + + break; + case 'Q': /* tetrahedrality order parameter. */ + + 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_given), + &(local_args_info.tet_param_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "tet_param", 'Q', + additional_error)) + goto failure; + + break; - case 0: /* Long option with no short option */ - /* select first stuntdouble set. */ - if (strcmp (long_options[option_index].name, "sele1") == 0) + /* number of bins in z axis. */ + if (strcmp (long_options[option_index].name, "nbins_z") == 0) { - if (args_info->sele1_given) - { - fprintf (stderr, "%s: `--sele1' option given more than once\n", CMDLINE_PARSER_PACKAGE); - clear_args (); - exit (EXIT_FAILURE); - } - args_info->sele1_given = 1; - args_info->sele1_arg = gengetopt_strdup (optarg); - break; + + + if (update_arg( (void *)&(args_info->nbins_z_arg), + &(args_info->nbins_z_orig), &(args_info->nbins_z_given), + &(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT, + check_ambiguity, override, 0, 0, + "nbins_z", '-', + additional_error)) + goto failure; + } + /* slab width (dz). */ + else if (strcmp (long_options[option_index].name, "dz") == 0) + { - /* select second stuntdouble set. */ + + if (update_arg( (void *)&(args_info->dz_arg), + &(args_info->dz_orig), &(args_info->dz_given), + &(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE, + check_ambiguity, override, 0, 0, + "dz", '-', + additional_error)) + goto failure; + + } + /* maximum length (Defaults to 1/2 smallest length of first frame). */ + else if (strcmp (long_options[option_index].name, "length") == 0) + { + + + if (update_arg( (void *)&(args_info->length_arg), + &(args_info->length_orig), &(args_info->length_given), + &(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE, + check_ambiguity, override, 0, 0, + "length", '-', + additional_error)) + goto failure; + + } + /* maximum length (Defaults to 1/2 smallest length of first frame). */ + else if (strcmp (long_options[option_index].name, "zlength") == 0) + { + + + if (update_arg( (void *)&(args_info->zlength_arg), + &(args_info->zlength_orig), &(args_info->zlength_given), + &(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE, + check_ambiguity, override, 0, 0, + "zlength", '-', + additional_error)) + goto failure; + + } + /* select the first stuntdouble set. */ + else if (strcmp (long_options[option_index].name, "sele1") == 0) + { + + + if (update_arg( (void *)&(args_info->sele1_arg), + &(args_info->sele1_orig), &(args_info->sele1_given), + &(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING, + check_ambiguity, override, 0, 0, + "sele1", '-', + additional_error)) + goto failure; + + } + /* select the second stuntdouble set. */ else if (strcmp (long_options[option_index].name, "sele2") == 0) { - if (args_info->sele2_given) - { - fprintf (stderr, "%s: `--sele2' option given more than once\n", CMDLINE_PARSER_PACKAGE); - clear_args (); - exit (EXIT_FAILURE); - } - args_info->sele2_given = 1; - args_info->sele2_arg = gengetopt_strdup (optarg); - break; + + + if (update_arg( (void *)&(args_info->sele2_arg), + &(args_info->sele2_orig), &(args_info->sele2_given), + &(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING, + check_ambiguity, override, 0, 0, + "sele2", '-', + additional_error)) + goto failure; + } + /* select the third stuntdouble set. */ + else if (strcmp (long_options[option_index].name, "sele3") == 0) + { + + if (update_arg( (void *)&(args_info->sele3_arg), + &(args_info->sele3_orig), &(args_info->sele3_given), + &(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING, + check_ambiguity, override, 0, 0, + "sele3", '-', + additional_error)) + goto failure; + + } /* select reference (use and only use with --gxyz). */ else if (strcmp (long_options[option_index].name, "refsele") == 0) { - if (args_info->refsele_given) - { - fprintf (stderr, "%s: `--refsele' option given more than once\n", CMDLINE_PARSER_PACKAGE); - clear_args (); - exit (EXIT_FAILURE); - } - args_info->refsele_given = 1; - args_info->refsele_arg = gengetopt_strdup (optarg); - break; + + + if (update_arg( (void *)&(args_info->refsele_arg), + &(args_info->refsele_orig), &(args_info->refsele_given), + &(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING, + check_ambiguity, override, 0, 0, + "refsele", '-', + additional_error)) + goto failure; + } + /* select stunt doubles for center-of-mass reference point. */ + else if (strcmp (long_options[option_index].name, "comsele") == 0) + { - /* g(r). */ - else if (strcmp (long_options[option_index].name, "gofr") == 0) + + if (update_arg( (void *)&(args_info->comsele_arg), + &(args_info->comsele_orig), &(args_info->comsele_given), + &(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING, + check_ambiguity, override, 0, 0, + "comsele", '-', + additional_error)) + goto failure; + + } + /* molecule name. */ + else if (strcmp (long_options[option_index].name, "molname") == 0) { - if (args_info->gofr_given) - { - fprintf (stderr, "%s: `--gofr' option given more than once\n", CMDLINE_PARSER_PACKAGE); - clear_args (); - exit (EXIT_FAILURE); - } - args_info->gofr_given = 1; staticProps_group_counter += 1; - break; + + if (update_arg( (void *)&(args_info->molname_arg), + &(args_info->molname_orig), &(args_info->molname_given), + &(local_args_info.molname_given), optarg, 0, 0, ARG_STRING, + check_ambiguity, override, 0, 0, + "molname", '-', + additional_error)) + goto failure; + } + /* begin internal index. */ + else if (strcmp (long_options[option_index].name, "begin") == 0) + { + + if (update_arg( (void *)&(args_info->begin_arg), + &(args_info->begin_orig), &(args_info->begin_given), + &(local_args_info.begin_given), optarg, 0, 0, ARG_INT, + check_ambiguity, override, 0, 0, + "begin", '-', + additional_error)) + goto failure; + + } + /* end internal index. */ + else if (strcmp (long_options[option_index].name, "end") == 0) + { + + + if (update_arg( (void *)&(args_info->end_arg), + &(args_info->end_orig), &(args_info->end_given), + &(local_args_info.end_given), optarg, 0, 0, ARG_INT, + check_ambiguity, override, 0, 0, + "end", '-', + additional_error)) + goto failure; + + } + /* nanoparticle radius. */ + else if (strcmp (long_options[option_index].name, "radius") == 0) + { + + + if (update_arg( (void *)&(args_info->radius_arg), + &(args_info->radius_orig), &(args_info->radius_given), + &(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE, + check_ambiguity, override, 0, 0, + "radius", '-', + additional_error)) + goto failure; + + } + /* bond order parameter (--rcut must be specified). */ + else if (strcmp (long_options[option_index].name, "bo") == 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->bo_given), + &(local_args_info.bo_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "bo", '-', + additional_error)) + goto failure; + + } + /* bond order parameter as a function of radius (--rcut must be specified). */ + else if (strcmp (long_options[option_index].name, "bor") == 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->bor_given), + &(local_args_info.bor_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "bor", '-', + additional_error)) + goto failure; + + } + /* N(theta) bond angle density within (--rcut must be specified). */ + else if (strcmp (long_options[option_index].name, "bad") == 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->bad_given), + &(local_args_info.bad_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "bad", '-', + additional_error)) + goto failure; + + } + /* count of molecules matching selection criteria (and associated statistics). */ + else if (strcmp (long_options[option_index].name, "count") == 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->count_given), + &(local_args_info.count_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "count", '-', + additional_error)) + goto failure; + + } + /* g(z). */ + else if (strcmp (long_options[option_index].name, "gofz") == 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->gofz_given), + &(local_args_info.gofz_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "gofz", '-', + additional_error)) + goto failure; + + } /* g(r, cos(theta)). */ else if (strcmp (long_options[option_index].name, "r_theta") == 0) { - if (args_info->r_theta_given) - { - fprintf (stderr, "%s: `--r_theta' option given more than once\n", CMDLINE_PARSER_PACKAGE); - clear_args (); - exit (EXIT_FAILURE); - } - args_info->r_theta_given = 1; staticProps_group_counter += 1; - break; - } + 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->r_theta_given), + &(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "r_theta", '-', + additional_error)) + goto failure; + + } /* g(r, cos(omega)). */ else if (strcmp (long_options[option_index].name, "r_omega") == 0) { - if (args_info->r_omega_given) - { - fprintf (stderr, "%s: `--r_omega' option given more than once\n", CMDLINE_PARSER_PACKAGE); - clear_args (); - exit (EXIT_FAILURE); - } - args_info->r_omega_given = 1; staticProps_group_counter += 1; - break; + 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->r_omega_given), + &(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "r_omega", '-', + additional_error)) + goto failure; + } + /* g(r, z). */ + else if (strcmp (long_options[option_index].name, "r_z") == 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->r_z_given), + &(local_args_info.r_z_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "r_z", '-', + additional_error)) + goto failure; + + } /* g(cos(theta), cos(omega)). */ else if (strcmp (long_options[option_index].name, "theta_omega") == 0) { - if (args_info->theta_omega_given) - { - fprintf (stderr, "%s: `--theta_omega' option given more than once\n", CMDLINE_PARSER_PACKAGE); - clear_args (); - exit (EXIT_FAILURE); - } - args_info->theta_omega_given = 1; staticProps_group_counter += 1; - break; - } + 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->theta_omega_given), + &(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "theta_omega", '-', + additional_error)) + goto failure; + + } /* g(x, y, z). */ else if (strcmp (long_options[option_index].name, "gxyz") == 0) { - if (args_info->gxyz_given) - { - fprintf (stderr, "%s: `--gxyz' option given more than once\n", CMDLINE_PARSER_PACKAGE); - clear_args (); - exit (EXIT_FAILURE); - } - args_info->gxyz_given = 1; staticProps_group_counter += 1; - break; + 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->gxyz_given), + &(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "gxyz", '-', + additional_error)) + goto failure; + } + /* 2D g(r) (Slab width --dz must be specified). */ + else if (strcmp (long_options[option_index].name, "twodgofr") == 0) + { - /* p2 order parameter. */ - else if (strcmp (long_options[option_index].name, "p2") == 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->twodgofr_given), + &(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "twodgofr", '-', + additional_error)) + goto failure; + + } + /* rp2 order parameter (--sele1 and --sele2 must be specified). */ + else if (strcmp (long_options[option_index].name, "rp2") == 0) { - if (args_info->p2_given) - { - fprintf (stderr, "%s: `--p2' option given more than once\n", CMDLINE_PARSER_PACKAGE); - clear_args (); - exit (EXIT_FAILURE); - } - args_info->p2_given = 1; staticProps_group_counter += 1; - break; + 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->rp2_given), + &(local_args_info.rp2_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "rp2", '-', + additional_error)) + goto failure; + } + /* slab density. */ + else if (strcmp (long_options[option_index].name, "slab_density") == 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->slab_density_given), + &(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "slab_density", '-', + additional_error)) + goto failure; + + } + /* p(cos(theta)). */ + else if (strcmp (long_options[option_index].name, "p_angle") == 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->p_angle_given), + &(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "p_angle", '-', + additional_error)) + goto failure; + + } + /* hxy. */ + else if (strcmp (long_options[option_index].name, "hxy") == 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->hxy_given), + &(local_args_info.hxy_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "hxy", '-', + additional_error)) + goto failure; + + } + /* rho of R. */ + else if (strcmp (long_options[option_index].name, "rho_r") == 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->rho_r_given), + &(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "rho_r", '-', + additional_error)) + goto failure; + + } + /* angle of R. */ + else if (strcmp (long_options[option_index].name, "angle_r") == 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->angle_r_given), + &(local_args_info.angle_r_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "angle_r", '-', + additional_error)) + goto failure; + + } + /* hull volume of nanoparticle. */ + else if (strcmp (long_options[option_index].name, "hullvol") == 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->hullvol_given), + &(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "hullvol", '-', + additional_error)) + goto failure; + + } + /* length of nanorod. */ + else if (strcmp (long_options[option_index].name, "rodlength") == 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->rodlength_given), + &(local_args_info.rodlength_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "rodlength", '-', + additional_error)) + goto failure; + + } + + break; case '?': /* Invalid option. */ /* `getopt_long' already printed an error message. */ - exit (EXIT_FAILURE); + goto failure; default: /* bug: option not considered. */ - fprintf (stderr, "%s: option unknown: %c\n", CMDLINE_PARSER_PACKAGE, c); + fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : "")); abort (); } /* switch */ } /* while */ - if ( staticProps_group_counter != 1) + if (args_info->staticProps_group_counter > 1) { - fprintf (stderr, "%s: %d options of group staticProps were given. One is required\n", CMDLINE_PARSER_PACKAGE, staticProps_group_counter); - missing_required_options = 1; + fprintf (stderr, "%s: %d options of group staticProps were given. One is required%s.\n", argv[0], args_info->staticProps_group_counter, (additional_error ? additional_error : "")); + error = 1; } - if (! args_info->input_given) + + if (check_required) { - fprintf (stderr, "%s: '--input' ('-i') option required\n", CMDLINE_PARSER_PACKAGE); - missing_required_options = 1; + error += cmdline_parser_required2 (args_info, argv[0], additional_error); } - if ( missing_required_options ) - exit (EXIT_FAILURE); + cmdline_parser_release (&local_args_info); + + if ( error ) + return (EXIT_FAILURE); + + if (optind < argc) + { + int i = 0 ; + int found_prog_name = 0; + /* whether program name, i.e., argv[0], is in the remaining args + (this may happen with some implementations of getopt, + but surely not with the one included by gengetopt) */ + + i = optind; + while (i < argc) + if (argv[i++] == argv[0]) { + found_prog_name = 1; + break; + } + i = 0; + + args_info->inputs_num = argc - optind - found_prog_name; + args_info->inputs = + (char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ; + while (optind < argc) + if (argv[optind++] != argv[0]) + args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ; + } + return 0; + +failure: + + cmdline_parser_release (&local_args_info); + return (EXIT_FAILURE); }