--- trunk/src/applications/nanoparticleBuilder/nanoparticleBuilderCmd.c 2006/10/13 20:16:59 1069 +++ trunk/src/applications/nanoparticleBuilder/nanoparticleBuilderCmd.c 2009/11/25 20:02:06 1390 @@ -1,7 +1,7 @@ /* - File autogenerated by gengetopt version 2.15 + File autogenerated by gengetopt version 2.22 generated with the following command: - gengetopt -u -i nanoparticleBuilder.ggo -F nanoparticleBuilderCmd + gengetopt -u -F nanoparticleBuilderCmd The developers of gengetopt consider the fixed text that goes in all gengetopt output files to be in the public domain: @@ -21,38 +21,43 @@ #include "nanoparticleBuilderCmd.h" +const char *gengetopt_args_info_purpose = "Builds spherical random or core-shell nanoparticles and outputs an OpenMD \nstartup file"; + +const char *gengetopt_args_info_usage = "Usage: nanoparticleBuilder [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", + " -o, --output=STRING Output file name", + " --latticeConstant=DOUBLE Lattice spacing in Angstroms for cubic lattice.", + " --radius=DOUBLE Nanoparticle radius in Angstroms", + " --shellRadius=DOUBLE Radius containing within it only molecules of a \n specific component. Specified for each \n component > 1 in the template file.", + " --molFraction=DOUBLE Builds a multi-component random alloy \n nanoparticle. A mole Fraction must be \n specified for each component > 1 in the \n template file.", + " --vacancyPercent=DOUBLE Percentage of atoms to remove from within \n vacancy range", + " --vacancyInnerRadius=DOUBLE\n Radius arround core-shell where vacancies \n should be located.", + " --vacancyOuterRadius=DOUBLE\n Radius arround core-shell where vacancies \n should be located.", + 0 +}; + +typedef enum {ARG_NO + , ARG_STRING + , 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 * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required, const char *additional_error); +cmdline_parser_internal (int argc, char * const *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); -struct ShellRadius_list -{ - double ShellRadius_arg; - char *ShellRadius_orig; - struct ShellRadius_list * next; -}; - -struct molFraction_list -{ - double molFraction_arg; - char *molFraction_orig; - struct molFraction_list * next; -}; - -struct vacancyRadius_list -{ - double vacancyRadius_arg; - char *vacancyRadius_orig; - struct vacancyRadius_list * next; -}; - static char * gengetopt_strdup (const char *s); @@ -62,12 +67,13 @@ void clear_given (struct gengetopt_args_info *args_inf args_info->help_given = 0 ; args_info->version_given = 0 ; args_info->output_given = 0 ; - args_info->latticeCnst_given = 0 ; + args_info->latticeConstant_given = 0 ; args_info->radius_given = 0 ; - args_info->ShellRadius_given = 0 ; + args_info->shellRadius_given = 0 ; args_info->molFraction_given = 0 ; - args_info->vacancyPCT_given = 0 ; - args_info->vacancyRadius_given = 0 ; + args_info->vacancyPercent_given = 0 ; + args_info->vacancyInnerRadius_given = 0 ; + args_info->vacancyOuterRadius_given = 0 ; } static @@ -75,40 +81,68 @@ void clear_args (struct gengetopt_args_info *args_info { args_info->output_arg = NULL; args_info->output_orig = NULL; - args_info->latticeCnst_orig = NULL; + args_info->latticeConstant_orig = NULL; args_info->radius_orig = NULL; - args_info->ShellRadius_arg = NULL; - args_info->ShellRadius_orig = NULL; + args_info->shellRadius_arg = NULL; + args_info->shellRadius_orig = NULL; args_info->molFraction_arg = NULL; args_info->molFraction_orig = NULL; - args_info->vacancyPCT_orig = NULL; - args_info->vacancyRadius_arg = NULL; - args_info->vacancyRadius_orig = NULL; + args_info->vacancyPercent_orig = NULL; + args_info->vacancyInnerRadius_orig = NULL; + args_info->vacancyOuterRadius_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->output_help = gengetopt_args_info_help[2] ; + args_info->latticeConstant_help = gengetopt_args_info_help[3] ; + args_info->radius_help = gengetopt_args_info_help[4] ; + args_info->shellRadius_help = gengetopt_args_info_help[5] ; + args_info->shellRadius_min = -1; + args_info->shellRadius_max = -1; + args_info->molFraction_help = gengetopt_args_info_help[6] ; + args_info->molFraction_min = -1; + args_info->molFraction_max = -1; + args_info->vacancyPercent_help = gengetopt_args_info_help[7] ; + args_info->vacancyInnerRadius_help = gengetopt_args_info_help[8] ; + args_info->vacancyOuterRadius_help = gengetopt_args_info_help[9] ; + +} + void cmdline_parser_print_version (void) { printf ("%s %s\n", 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", gengetopt_args_info_description); +} + void cmdline_parser_print_help (void) { - cmdline_parser_print_version (); - printf("\n%s\n", "Builds spherical random or core-shell nanoparticles and outputs a xyz input \nfile"); - printf("\nUsage: nanoparticleBuilder [OPTIONS]... [FILES]...\n\n"); - printf("%s\n"," -h, --help Print help and exit"); - printf("%s\n"," -V, --version Print version and exit"); - printf("%s\n"," -o, --output=STRING Output file name"); - printf("%s\n"," --latticeCnst=DOUBLE Lattice spacing in Angstroms for cubic lattice."); - printf("%s\n"," --radius=DOUBLE Nanoparticle radius in Angstroms"); - printf("%s\n"," --ShellRadius=DOUBLE Radius from the center of the particle to start a \n new shell in multi-component core-shell \n particle. Specified for each component > 1 in \n md file."); - printf("%s\n"," --molFraction=DOUBLE (Default) Builds a multi-component random mixed \n nanoparticle. Mole Fraction must be specified \n for each componet > 1 in MD file."); - printf("%s\n"," --vacancyPCT=DOUBLE Percentage of vacancies to build"); - printf("%s\n"," --vacancyRadius=DOUBLE Radius arround core-shell where vacancies should \n be located."); - + int i = 0; + print_help_common(); + while (gengetopt_args_info_help[i]) + printf("%s\n", gengetopt_args_info_help[i++]); } void @@ -116,97 +150,167 @@ cmdline_parser_init (struct gengetopt_args_info *args_ { clear_given (args_info); clear_args (args_info); + init_args_info (args_info); args_info->inputs = NULL; args_info->inputs_num = 0; } +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 -cmdline_parser_release (struct gengetopt_args_info *args_info) +free_string_field (char **s) { - - unsigned int i; - if (args_info->output_arg) + if (*s) { - free (args_info->output_arg); /* free previous argument */ - args_info->output_arg = 0; + free (*s); + *s = 0; } - if (args_info->output_orig) - { - free (args_info->output_orig); /* free previous argument */ - args_info->output_orig = 0; - } - if (args_info->latticeCnst_orig) - { - free (args_info->latticeCnst_orig); /* free previous argument */ - args_info->latticeCnst_orig = 0; - } - if (args_info->radius_orig) - { - free (args_info->radius_orig); /* free previous argument */ - args_info->radius_orig = 0; - } - if (args_info->ShellRadius_arg) - { - for (i = 0; i < args_info->ShellRadius_given; ++i) - { - if (args_info->ShellRadius_orig [i]) - { - free (args_info->ShellRadius_orig [i]); /* free previous argument */ - args_info->ShellRadius_orig [i] = 0; - } - } - free (args_info->ShellRadius_arg); /* free previous argument */ - args_info->ShellRadius_arg = 0; - free (args_info->ShellRadius_orig); /* free previous argument */ - args_info->ShellRadius_orig = 0; - } - if (args_info->molFraction_arg) - { - for (i = 0; i < args_info->molFraction_given; ++i) - { - if (args_info->molFraction_orig [i]) - { - free (args_info->molFraction_orig [i]); /* free previous argument */ - args_info->molFraction_orig [i] = 0; - } - } - free (args_info->molFraction_arg); /* free previous argument */ - args_info->molFraction_arg = 0; - free (args_info->molFraction_orig); /* free previous argument */ - args_info->molFraction_orig = 0; - } - if (args_info->vacancyPCT_orig) - { - free (args_info->vacancyPCT_orig); /* free previous argument */ - args_info->vacancyPCT_orig = 0; - } - if (args_info->vacancyRadius_arg) - { - for (i = 0; i < args_info->vacancyRadius_given; ++i) - { - if (args_info->vacancyRadius_orig [i]) - { - free (args_info->vacancyRadius_orig [i]); /* free previous argument */ - args_info->vacancyRadius_orig [i] = 0; - } - } - free (args_info->vacancyRadius_arg); /* free previous argument */ - args_info->vacancyRadius_arg = 0; - free (args_info->vacancyRadius_orig); /* free previous argument */ - args_info->vacancyRadius_orig = 0; - } +} + +/** @brief generic value variable */ +union generic_value { + double double_arg; + char *string_arg; +}; + +/** @brief holds temporary values for multiple options */ +struct generic_list +{ + union generic_value arg; + char *orig; + struct generic_list *next; +}; + +/** + * @brief add a node at the head of the list + */ +static void add_node(struct generic_list **list) { + struct generic_list *new_node = (struct generic_list *) malloc (sizeof (struct generic_list)); + new_node->next = *list; + *list = new_node; + new_node->arg.string_arg = NULL; + new_node->orig = NULL; +} + +static void +free_multiple_field(unsigned int len, void **arg, char ***orig) +{ + unsigned int i; + if (*arg) { + for (i = 0; i < len; ++i) + { + free_string_field(&((*orig)[i])); + } + + free (*arg); + *arg = 0; + free (*orig); + *orig = 0; + } +} + + +static void +cmdline_parser_release (struct gengetopt_args_info *args_info) +{ + unsigned int i; + free_string_field (&(args_info->output_arg)); + free_string_field (&(args_info->output_orig)); + free_string_field (&(args_info->latticeConstant_orig)); + free_string_field (&(args_info->radius_orig)); + free_multiple_field (args_info->shellRadius_given, (void **)&(args_info->shellRadius_arg), &(args_info->shellRadius_orig)); + free_multiple_field (args_info->molFraction_given, (void **)&(args_info->molFraction_arg), &(args_info->molFraction_orig)); + free_string_field (&(args_info->vacancyPercent_orig)); + free_string_field (&(args_info->vacancyInnerRadius_orig)); + free_string_field (&(args_info->vacancyOuterRadius_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, char *values[]) +{ + if (arg) { + fprintf(outfile, "%s=\"%s\"\n", opt, arg); + } else { + fprintf(outfile, "%s\n", opt); + } +} + +static void +write_multiple_into_file(FILE *outfile, int len, const char *opt, char **arg, char *values[]) +{ + int i; + + for (i = 0; i < len; ++i) + write_into_file(outfile, opt, (arg ? arg[i] : 0), values); +} + 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->output_given) + write_into_file(outfile, "output", args_info->output_orig, 0); + if (args_info->latticeConstant_given) + write_into_file(outfile, "latticeConstant", args_info->latticeConstant_orig, 0); + if (args_info->radius_given) + write_into_file(outfile, "radius", args_info->radius_orig, 0); + write_multiple_into_file(outfile, args_info->shellRadius_given, "shellRadius", args_info->shellRadius_orig, 0); + write_multiple_into_file(outfile, args_info->molFraction_given, "molFraction", args_info->molFraction_orig, 0); + if (args_info->vacancyPercent_given) + write_into_file(outfile, "vacancyPercent", args_info->vacancyPercent_orig, 0); + if (args_info->vacancyInnerRadius_given) + write_into_file(outfile, "vacancyInnerRadius", args_info->vacancyInnerRadius_orig, 0); + if (args_info->vacancyOuterRadius_given) + write_into_file(outfile, "vacancyOuterRadius", args_info->vacancyOuterRadius_orig, 0); + + + i = EXIT_SUCCESS; + return i; +} + +int cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info) { FILE *outfile; @@ -220,74 +324,9 @@ cmdline_parser_file_save(const char *filename, struct return EXIT_FAILURE; } - if (args_info->help_given) { - fprintf(outfile, "%s\n", "help"); - } - if (args_info->version_given) { - fprintf(outfile, "%s\n", "version"); - } - if (args_info->output_given) { - if (args_info->output_orig) { - fprintf(outfile, "%s=\"%s\"\n", "output", args_info->output_orig); - } else { - fprintf(outfile, "%s\n", "output"); - } - } - if (args_info->latticeCnst_given) { - if (args_info->latticeCnst_orig) { - fprintf(outfile, "%s=\"%s\"\n", "latticeCnst", args_info->latticeCnst_orig); - } else { - fprintf(outfile, "%s\n", "latticeCnst"); - } - } - if (args_info->radius_given) { - if (args_info->radius_orig) { - fprintf(outfile, "%s=\"%s\"\n", "radius", args_info->radius_orig); - } else { - fprintf(outfile, "%s\n", "radius"); - } - } - if (args_info->ShellRadius_orig) - { - for (i = 0; i < args_info->ShellRadius_given; ++i) - { - if (args_info->ShellRadius_orig [i]) - { - fprintf(outfile, "%s=\"%s\"\n", "ShellRadius", args_info->ShellRadius_orig [i]); - } - } - } - if (args_info->molFraction_orig) - { - for (i = 0; i < args_info->molFraction_given; ++i) - { - if (args_info->molFraction_orig [i]) - { - fprintf(outfile, "%s=\"%s\"\n", "molFraction", args_info->molFraction_orig [i]); - } - } - } - if (args_info->vacancyPCT_given) { - if (args_info->vacancyPCT_orig) { - fprintf(outfile, "%s=\"%s\"\n", "vacancyPCT", args_info->vacancyPCT_orig); - } else { - fprintf(outfile, "%s\n", "vacancyPCT"); - } - } - if (args_info->vacancyRadius_orig) - { - for (i = 0; i < args_info->vacancyRadius_given; ++i) - { - if (args_info->vacancyRadius_orig [i]) - { - fprintf(outfile, "%s=\"%s\"\n", "vacancyRadius", args_info->vacancyRadius_orig [i]); - } - } - } - + i = cmdline_parser_dump(outfile, args_info); fclose (outfile); - i = EXIT_SUCCESS; return i; } @@ -297,9 +336,7 @@ cmdline_parser_free (struct gengetopt_args_info *args_ cmdline_parser_release (args_info); } - -/* gengetopt_strdup() */ -/* strdup.c replacement of strdup, which is not standard */ +/** @brief replacement of strdup, which is not standard */ char * gengetopt_strdup (const char *s) { @@ -318,20 +355,48 @@ get_multiple_arg_token(const char *arg) get_multiple_arg_token(const char *arg) { char *tok, *ret; - size_t len; + size_t len, num_of_escape, i, j; if (!arg) return NULL; tok = strchr (arg, ','); + num_of_escape = 0; + /* make sure it is not escaped */ + while (tok) + { + if (*(tok-1) == '\\') + { + /* find the next one */ + tok = strchr (tok+1, ','); + ++num_of_escape; + } + else + break; + } + if (tok) len = (size_t)(tok - arg + 1); else len = strlen (arg) + 1; + len -= num_of_escape; + ret = (char *) malloc (len); - strncpy (ret, arg, len-1); + + i = 0; + j = 0; + while (arg[i] && (j < len-1)) + { + if (arg[i] == '\\' && + arg[ i + 1 ] && + arg[ i + 1 ] == ',') + ++i; + + ret[j++] = arg[i++]; + } + ret[len-1] = '\0'; return ret; @@ -347,24 +412,114 @@ get_multiple_arg_token_next(const char *arg) tok = strchr (arg, ','); + /* make sure it is not escaped */ + while (tok) + { + if (*(tok-1) == '\\') + { + /* find the next one */ + tok = strchr (tok+1, ','); + } + else + break; + } + if (! tok || strlen(tok) == 1) return 0; return tok+1; } +static int +check_multiple_option_occurrences(const char *prog_name, unsigned int option_given, int min, int max, const char *option_desc); + int +check_multiple_option_occurrences(const char *prog_name, unsigned int option_given, int min, int max, const char *option_desc) +{ + int error = 0; + + if (option_given && ! (min < 0 && max < 0)) + { + if (min >= 0 && max >= 0) + { + if (min == max) + { + /* specific occurrences */ + if (option_given != min) + { + fprintf (stderr, "%s: %s option occurrences must be %d\n", + prog_name, option_desc, min); + error = 1; + } + } + else if (option_given < min + || option_given > max) + { + /* range occurrences */ + fprintf (stderr, "%s: %s option occurrences must be between %d and %d\n", + prog_name, option_desc, min, max); + error = 1; + } + } + else if (min >= 0) + { + /* at least check */ + if (option_given < min) + { + fprintf (stderr, "%s: %s option occurrences must be at least %d\n", + prog_name, option_desc, min); + error = 1; + } + } + else if (max >= 0) + { + /* at most check */ + if (option_given > max) + { + fprintf (stderr, "%s: %s option occurrences must be at most %d\n", + prog_name, option_desc, max); + error = 1; + } + } + } + + return error; +} +int cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info) { return cmdline_parser2 (argc, argv, args_info, 0, 1, 1); } int +cmdline_parser_ext (int argc, char * const *argv, struct gengetopt_args_info *args_info, + struct cmdline_parser_params *params) +{ + int result; + result = cmdline_parser_internal (argc, argv, args_info, params, NULL); + + if (result == EXIT_FAILURE) + { + cmdline_parser_free (args_info); + exit (EXIT_FAILURE); + } + + return result; +} + +int cmdline_parser2 (int argc, char * const *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, override, initialize, check_required, NULL); + result = cmdline_parser_internal (argc, argv, args_info, ¶ms, NULL); if (result == EXIT_FAILURE) { @@ -397,33 +552,298 @@ cmdline_parser_required2 (struct gengetopt_args_info * { int error = 0; - if (! args_info->latticeCnst_given) + /* checks for required options */ + if (! args_info->output_given) { - fprintf (stderr, "%s: '--latticeCnst' option required%s\n", prog_name, (additional_error ? additional_error : "")); + fprintf (stderr, "%s: '--output' ('-o') option required%s\n", prog_name, (additional_error ? additional_error : "")); error = 1; } + + if (! args_info->latticeConstant_given) + { + fprintf (stderr, "%s: '--latticeConstant' option required%s\n", prog_name, (additional_error ? additional_error : "")); + error = 1; + } + if (! args_info->radius_given) { fprintf (stderr, "%s: '--radius' option required%s\n", prog_name, (additional_error ? additional_error : "")); error = 1; } + + if (check_multiple_option_occurrences(prog_name, args_info->shellRadius_given, args_info->shellRadius_min, args_info->shellRadius_max, "'--shellRadius'")) + error = 1; + + if (check_multiple_option_occurrences(prog_name, args_info->molFraction_given, args_info->molFraction_min, args_info->molFraction_max, "'--molFraction'")) + error = 1; + + + /* checks for dependences among options */ return error; } -int -cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required, const char *additional_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, 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) { - int c; /* Character of the parsed option. */ - char *multi_token, *multi_next; /* for multiple options */ + char *stop_char = 0; + const char *val = value; + int found; + char **string_field; - int i; /* Counter */ + stop_char = 0; + found = 0; - struct ShellRadius_list * ShellRadius_list = NULL,* ShellRadius_new = NULL; - struct molFraction_list * molFraction_list = NULL,* molFraction_new = NULL; - struct vacancyRadius_list * vacancyRadius_list = NULL,* vacancyRadius_new = NULL; + 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 */ + } + + + 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_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_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 */ +} + +/** + * @brief store information about a multiple option in a temporary list + * @param list where to (temporarily) store multiple options + */ +static +int update_multiple_arg_temp(struct generic_list **list, + unsigned int *prev_given, const char *val, + char *possible_values[], const char *default_value, + cmdline_parser_arg_type arg_type, + const char *long_opt, char short_opt, + const char *additional_error) +{ + char *multi_token, *multi_next; /* store single arguments */ + + if (arg_type == ARG_NO) { + (*prev_given)++; + return 0; /* OK */ + } + + multi_token = get_multiple_arg_token(val); + multi_next = get_multiple_arg_token_next (val); + + while (1) + { + add_node (list); + if (update_arg((void *)&((*list)->arg), &((*list)->orig), 0, + prev_given, multi_token, possible_values, default_value, + arg_type, 0, 1, 1, 1, long_opt, short_opt, additional_error)) { + if (multi_token) free(multi_token); + return 1; /* failure */ + } + + if (multi_next) + { + multi_token = get_multiple_arg_token(multi_next); + multi_next = get_multiple_arg_token_next (multi_next); + } + else + break; + } + + return 0; /* OK */ +} + +/** + * @brief free the passed list (including possible string argument) + */ +static +void free_list(struct generic_list *list, short string_arg) +{ + if (list) { + struct generic_list *tmp; + while (list) + { + tmp = list; + if (string_arg && list->arg.string_arg) + free (list->arg.string_arg); + if (list->orig) + free (list->orig); + list = list->next; + free (tmp); + } + } +} + +/** + * @brief updates a multiple option starting from the passed list + */ +static +void update_multiple_arg(void *field, char ***orig_field, + unsigned int field_given, unsigned int prev_given, union generic_value *default_value, + cmdline_parser_arg_type arg_type, + struct generic_list *list) +{ + int i; + struct generic_list *tmp; + + if (prev_given && list) { + *orig_field = (char **) realloc (*orig_field, (field_given + prev_given) * sizeof (char *)); + + switch(arg_type) { + case ARG_DOUBLE: + *((double **)field) = (double *)realloc (*((double **)field), (field_given + prev_given) * sizeof (double)); break; + case ARG_STRING: + *((char ***)field) = (char **)realloc (*((char ***)field), (field_given + prev_given) * sizeof (char *)); break; + default: + break; + }; + + for (i = (prev_given - 1); i >= 0; --i) + { + tmp = list; + + switch(arg_type) { + case ARG_DOUBLE: + (*((double **)field))[i + field_given] = tmp->arg.double_arg; break; + case ARG_STRING: + (*((char ***)field))[i + field_given] = tmp->arg.string_arg; break; + default: + break; + } + (*orig_field) [i + field_given] = list->orig; + list = list->next; + free (tmp); + } + } else { /* set the default value */ + if (default_value && ! field_given) { + switch(arg_type) { + case ARG_DOUBLE: + if (! *((double **)field)) { + *((double **)field) = (double *)malloc (sizeof (double)); + (*((double **)field))[0] = default_value->double_arg; + } + break; + case ARG_STRING: + if (! *((char ***)field)) { + *((char ***)field) = (char **)malloc (sizeof (char *)); + (*((char ***)field))[0] = gengetopt_strdup(default_value->string_arg); + } + break; + default: break; + } + if (!(*orig_field)) { + *orig_field = (char **) malloc (sizeof (char *)); + (*orig_field)[0] = NULL; + } + } + } +} + +int +cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info, + struct cmdline_parser_params *params, const char *additional_error) +{ + int c; /* Character of the parsed option. */ + + struct generic_list * shellRadius_list = NULL; + struct generic_list * molFraction_list = NULL; 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); @@ -431,29 +851,28 @@ cmdline_parser_internal (int argc, char * const *argv, 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' }, { "version", 0, NULL, 'V' }, { "output", 1, NULL, 'o' }, - { "latticeCnst", 1, NULL, 0 }, + { "latticeConstant", 1, NULL, 0 }, { "radius", 1, NULL, 0 }, - { "ShellRadius", 1, NULL, 0 }, + { "shellRadius", 1, NULL, 0 }, { "molFraction", 1, NULL, 0 }, - { "vacancyPCT", 1, NULL, 0 }, - { "vacancyRadius", 1, NULL, 0 }, + { "vacancyPercent", 1, NULL, 0 }, + { "vacancyInnerRadius", 1, NULL, 0 }, + { "vacancyOuterRadius", 1, NULL, 0 }, { NULL, 0, NULL, 0 } }; - stop_char = 0; c = getopt_long (argc, argv, "hVo:", long_options, &option_index); if (c == -1) break; /* Exit from `while (1)' loop. */ @@ -471,180 +890,110 @@ cmdline_parser_internal (int argc, char * const *argv, exit (EXIT_SUCCESS); case 'o': /* Output file name. */ - if (local_args_info.output_given) - { - fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : "")); - goto failure; - } - if (args_info->output_given && ! override) - continue; - local_args_info.output_given = 1; - args_info->output_given = 1; - if (args_info->output_arg) - free (args_info->output_arg); /* free previous string */ - args_info->output_arg = gengetopt_strdup (optarg); - if (args_info->output_orig) - free (args_info->output_orig); /* free previous string */ - args_info->output_orig = 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 0: /* Long option with no short option */ /* Lattice spacing in Angstroms for cubic lattice.. */ - if (strcmp (long_options[option_index].name, "latticeCnst") == 0) + if (strcmp (long_options[option_index].name, "latticeConstant") == 0) { - if (local_args_info.latticeCnst_given) - { - fprintf (stderr, "%s: `--latticeCnst' option given more than once%s\n", argv[0], (additional_error ? additional_error : "")); - goto failure; - } - if (args_info->latticeCnst_given && ! override) - continue; - local_args_info.latticeCnst_given = 1; - args_info->latticeCnst_given = 1; - args_info->latticeCnst_arg = strtod (optarg, &stop_char); - if (!(stop_char && *stop_char == '\0')) { - fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg); + + + if (update_arg( (void *)&(args_info->latticeConstant_arg), + &(args_info->latticeConstant_orig), &(args_info->latticeConstant_given), + &(local_args_info.latticeConstant_given), optarg, 0, 0, ARG_DOUBLE, + check_ambiguity, override, 0, 0, + "latticeConstant", '-', + additional_error)) goto failure; - } - if (args_info->latticeCnst_orig) - free (args_info->latticeCnst_orig); /* free previous string */ - args_info->latticeCnst_orig = gengetopt_strdup (optarg); + } /* Nanoparticle radius in Angstroms. */ else if (strcmp (long_options[option_index].name, "radius") == 0) { - if (local_args_info.radius_given) - { - fprintf (stderr, "%s: `--radius' option given more than once%s\n", argv[0], (additional_error ? additional_error : "")); - goto failure; - } - if (args_info->radius_given && ! override) - continue; - local_args_info.radius_given = 1; - args_info->radius_given = 1; - args_info->radius_arg = strtod (optarg, &stop_char); - if (!(stop_char && *stop_char == '\0')) { - fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg); + + + 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; - } - if (args_info->radius_orig) - free (args_info->radius_orig); /* free previous string */ - args_info->radius_orig = gengetopt_strdup (optarg); + } - /* Radius from the center of the particle to start a new shell in multi-component core-shell particle. Specified for each component > 1 in md file.. */ - else if (strcmp (long_options[option_index].name, "ShellRadius") == 0) + /* Radius containing within it only molecules of a specific component. Specified for each component > 1 in the template file.. */ + else if (strcmp (long_options[option_index].name, "shellRadius") == 0) { - local_args_info.ShellRadius_given++; - multi_token = get_multiple_arg_token(optarg); - multi_next = get_multiple_arg_token_next (optarg); + if (update_multiple_arg_temp(&shellRadius_list, + &(local_args_info.shellRadius_given), optarg, 0, 0, ARG_DOUBLE, + "shellRadius", '-', + additional_error)) + goto failure; - while (1) - { - ShellRadius_new = (struct ShellRadius_list *) malloc (sizeof (struct ShellRadius_list)); - ShellRadius_new->next = ShellRadius_list; - ShellRadius_list = ShellRadius_new; - ShellRadius_new->ShellRadius_arg = strtod (multi_token, &stop_char); - if (!(stop_char && *stop_char == '\0')) { - fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], multi_token); - goto failure; - } - ShellRadius_new->ShellRadius_orig = multi_token; - - if (multi_next) - { - multi_token = get_multiple_arg_token(multi_next); - multi_next = get_multiple_arg_token_next (multi_next); - local_args_info.ShellRadius_given++; - } - else - break; - } - break; } - /* (Default) Builds a multi-component random mixed nanoparticle. Mole Fraction must be specified for each componet > 1 in MD file.. */ + /* Builds a multi-component random alloy nanoparticle. A mole Fraction must be specified for each component > 1 in the template file.. */ else if (strcmp (long_options[option_index].name, "molFraction") == 0) { - local_args_info.molFraction_given++; - multi_token = get_multiple_arg_token(optarg); - multi_next = get_multiple_arg_token_next (optarg); + if (update_multiple_arg_temp(&molFraction_list, + &(local_args_info.molFraction_given), optarg, 0, 0, ARG_DOUBLE, + "molFraction", '-', + additional_error)) + goto failure; - while (1) - { - molFraction_new = (struct molFraction_list *) malloc (sizeof (struct molFraction_list)); - molFraction_new->next = molFraction_list; - molFraction_list = molFraction_new; - molFraction_new->molFraction_arg = strtod (multi_token, &stop_char); - if (!(stop_char && *stop_char == '\0')) { - fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], multi_token); - goto failure; - } - molFraction_new->molFraction_orig = multi_token; + } + /* Percentage of atoms to remove from within vacancy range. */ + else if (strcmp (long_options[option_index].name, "vacancyPercent") == 0) + { - if (multi_next) - { - multi_token = get_multiple_arg_token(multi_next); - multi_next = get_multiple_arg_token_next (multi_next); - local_args_info.molFraction_given++; - } - else - break; - } - break; + + if (update_arg( (void *)&(args_info->vacancyPercent_arg), + &(args_info->vacancyPercent_orig), &(args_info->vacancyPercent_given), + &(local_args_info.vacancyPercent_given), optarg, 0, 0, ARG_DOUBLE, + check_ambiguity, override, 0, 0, + "vacancyPercent", '-', + additional_error)) + goto failure; + } - /* Percentage of vacancies to build. */ - else if (strcmp (long_options[option_index].name, "vacancyPCT") == 0) + /* Radius arround core-shell where vacancies should be located.. */ + else if (strcmp (long_options[option_index].name, "vacancyInnerRadius") == 0) { - if (local_args_info.vacancyPCT_given) - { - fprintf (stderr, "%s: `--vacancyPCT' option given more than once%s\n", argv[0], (additional_error ? additional_error : "")); - goto failure; - } - if (args_info->vacancyPCT_given && ! override) - continue; - local_args_info.vacancyPCT_given = 1; - args_info->vacancyPCT_given = 1; - args_info->vacancyPCT_arg = strtod (optarg, &stop_char); - if (!(stop_char && *stop_char == '\0')) { - fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg); + + + if (update_arg( (void *)&(args_info->vacancyInnerRadius_arg), + &(args_info->vacancyInnerRadius_orig), &(args_info->vacancyInnerRadius_given), + &(local_args_info.vacancyInnerRadius_given), optarg, 0, 0, ARG_DOUBLE, + check_ambiguity, override, 0, 0, + "vacancyInnerRadius", '-', + additional_error)) goto failure; - } - if (args_info->vacancyPCT_orig) - free (args_info->vacancyPCT_orig); /* free previous string */ - args_info->vacancyPCT_orig = gengetopt_strdup (optarg); + } /* Radius arround core-shell where vacancies should be located.. */ - else if (strcmp (long_options[option_index].name, "vacancyRadius") == 0) + else if (strcmp (long_options[option_index].name, "vacancyOuterRadius") == 0) { - local_args_info.vacancyRadius_given++; - multi_token = get_multiple_arg_token(optarg); - multi_next = get_multiple_arg_token_next (optarg); - while (1) - { - vacancyRadius_new = (struct vacancyRadius_list *) malloc (sizeof (struct vacancyRadius_list)); - vacancyRadius_new->next = vacancyRadius_list; - vacancyRadius_list = vacancyRadius_new; - vacancyRadius_new->vacancyRadius_arg = strtod (multi_token, &stop_char); - if (!(stop_char && *stop_char == '\0')) { - fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], multi_token); - goto failure; - } - vacancyRadius_new->vacancyRadius_orig = multi_token; + if (update_arg( (void *)&(args_info->vacancyOuterRadius_arg), + &(args_info->vacancyOuterRadius_orig), &(args_info->vacancyOuterRadius_given), + &(local_args_info.vacancyOuterRadius_given), optarg, 0, 0, ARG_DOUBLE, + check_ambiguity, override, 0, 0, + "vacancyOuterRadius", '-', + additional_error)) + goto failure; - if (multi_next) - { - multi_token = get_multiple_arg_token(multi_next); - multi_next = get_multiple_arg_token_next (multi_next); - local_args_info.vacancyRadius_given++; - } - else - break; - } - break; } break; @@ -659,58 +1008,19 @@ cmdline_parser_internal (int argc, char * const *argv, } /* while */ - if (local_args_info.ShellRadius_given && ShellRadius_list) - { - struct ShellRadius_list *tmp; - args_info->ShellRadius_arg = (double *) realloc (args_info->ShellRadius_arg, (args_info->ShellRadius_given + local_args_info.ShellRadius_given) * sizeof (double)); - args_info->ShellRadius_orig = (char **) realloc (args_info->ShellRadius_orig, (args_info->ShellRadius_given + local_args_info.ShellRadius_given) * sizeof (char *)); - for (i = (local_args_info.ShellRadius_given - 1); i >= 0; --i) - { - tmp = ShellRadius_list; - args_info->ShellRadius_arg [i + args_info->ShellRadius_given] = ShellRadius_list->ShellRadius_arg; - args_info->ShellRadius_orig [i + args_info->ShellRadius_given] = ShellRadius_list->ShellRadius_orig; - ShellRadius_list = ShellRadius_list->next; - free (tmp); - } - } - - if (local_args_info.molFraction_given && molFraction_list) - { - struct molFraction_list *tmp; - args_info->molFraction_arg = (double *) realloc (args_info->molFraction_arg, (args_info->molFraction_given + local_args_info.molFraction_given) * sizeof (double)); - args_info->molFraction_orig = (char **) realloc (args_info->molFraction_orig, (args_info->molFraction_given + local_args_info.molFraction_given) * sizeof (char *)); - for (i = (local_args_info.molFraction_given - 1); i >= 0; --i) - { - tmp = molFraction_list; - args_info->molFraction_arg [i + args_info->molFraction_given] = molFraction_list->molFraction_arg; - args_info->molFraction_orig [i + args_info->molFraction_given] = molFraction_list->molFraction_orig; - molFraction_list = molFraction_list->next; - free (tmp); - } - } - - if (local_args_info.vacancyRadius_given && vacancyRadius_list) - { - struct vacancyRadius_list *tmp; - args_info->vacancyRadius_arg = (double *) realloc (args_info->vacancyRadius_arg, (args_info->vacancyRadius_given + local_args_info.vacancyRadius_given) * sizeof (double)); - args_info->vacancyRadius_orig = (char **) realloc (args_info->vacancyRadius_orig, (args_info->vacancyRadius_given + local_args_info.vacancyRadius_given) * sizeof (char *)); - for (i = (local_args_info.vacancyRadius_given - 1); i >= 0; --i) - { - tmp = vacancyRadius_list; - args_info->vacancyRadius_arg [i + args_info->vacancyRadius_given] = vacancyRadius_list->vacancyRadius_arg; - args_info->vacancyRadius_orig [i + args_info->vacancyRadius_given] = vacancyRadius_list->vacancyRadius_orig; - vacancyRadius_list = vacancyRadius_list->next; - free (tmp); - } - } - + update_multiple_arg((void *)&(args_info->shellRadius_arg), + &(args_info->shellRadius_orig), args_info->shellRadius_given, + local_args_info.shellRadius_given, 0 , + ARG_DOUBLE, shellRadius_list); + update_multiple_arg((void *)&(args_info->molFraction_arg), + &(args_info->molFraction_orig), args_info->molFraction_given, + local_args_info.molFraction_given, 0 , + ARG_DOUBLE, molFraction_list); - args_info->ShellRadius_given += local_args_info.ShellRadius_given; - local_args_info.ShellRadius_given = 0; + args_info->shellRadius_given += local_args_info.shellRadius_given; + local_args_info.shellRadius_given = 0; args_info->molFraction_given += local_args_info.molFraction_given; local_args_info.molFraction_given = 0; - args_info->vacancyRadius_given += local_args_info.vacancyRadius_given; - local_args_info.vacancyRadius_given = 0; if (check_required) { @@ -725,50 +1035,32 @@ cmdline_parser_internal (int argc, char * const *argv, 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) */ - args_info->inputs_num = argc - optind ; + 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) - args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind++]) ; + if (argv[optind++] != argv[0]) + args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ; } return 0; failure: - if (ShellRadius_list) - { - struct ShellRadius_list *tmp; - while (ShellRadius_list) - { - tmp = ShellRadius_list; - free (ShellRadius_list->ShellRadius_orig); - ShellRadius_list = ShellRadius_list->next; - free (tmp); - } - } - if (molFraction_list) - { - struct molFraction_list *tmp; - while (molFraction_list) - { - tmp = molFraction_list; - free (molFraction_list->molFraction_orig); - molFraction_list = molFraction_list->next; - free (tmp); - } - } - if (vacancyRadius_list) - { - struct vacancyRadius_list *tmp; - while (vacancyRadius_list) - { - tmp = vacancyRadius_list; - free (vacancyRadius_list->vacancyRadius_orig); - vacancyRadius_list = vacancyRadius_list->next; - free (tmp); - } - } + free_list (shellRadius_list, 0 ); + free_list (molFraction_list, 0 ); cmdline_parser_release (&local_args_info); return (EXIT_FAILURE);