--- trunk/src/applications/hydrodynamics/HydroCmd.c 2006/02/23 23:16:43 892 +++ branches/development/src/applications/hydrodynamics/HydroCmd.cpp 2011/11/22 20:38:56 1665 @@ -1,59 +1,279 @@ /* - File autogenerated by gengetopt version 2.11 + File autogenerated by gengetopt version 2.22.4 generated with the following command: - /home/maul/gezelter/tim/program/gengetopt-2.11/src/gengetopt -F HydroCmd + gengetopt -F HydroCmd -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 "HydroCmd.h" +const char *gengetopt_args_info_purpose = "\n +-----------------------------------------------------------------------+\n | ____ __ ___ ____ |\n | / __ \\____ ___ ____ / |/ // __ \\ The Open Molecular Dynamics |\n | / / / / __ \\/ _ \\/ __ \\ / /|_/ // / / / Engine (formerly OOPSE). |\n | / /_/ / /_/ / __/ / / // / / // /_/ / |\n | \\____/ .___/\\___/_/ /_//_/ /_//_____/ Copyright 2004-2009 by the |\n | /_/ University of Notre Dame. |\n | |\n | http://www.openmd.net |\n | |\n | OpenMD is an OpenScience project. All source code is available for |\n | any use whatsoever under a BSD-style license. |\n | |\n | Support OpenScience! If you use OpenMD or its source code in your |\n | research, please cite the appropriate papers when you publish your |\n | work. Good starting points are: |\n | |\n | [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |\n | [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |\n | [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |\n | [4] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |\n +-----------------------------------------------------------------------+"; + +const char *gengetopt_args_info_usage = "Usage: Hydro [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 MetaData (md) file", + " -o, --output=STRING output file prefix (default=`hydro')", + " --model=STRING hydrodynamics model (supports RoughShell and BeadModel)", + " -b, --beads generate the beads only, hydrodynamics will be \n performed (default=off)", + 0 +}; + +typedef enum {ARG_NO + , ARG_FLAG + , ARG_STRING +} 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->model_given = 0 ; + args_info->beads_given = 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 = gengetopt_strdup ("hydro"); + args_info->output_orig = NULL; + args_info->model_arg = NULL; + args_info->model_orig = NULL; + args_info->beads_flag = 0; + +} + +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->model_help = gengetopt_args_info_help[4] ; + args_info->beads_help = gengetopt_args_info_help[5] ; + +} + 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=STRING output file prefix (default=`hydro')\n"); - printf(" --viscosity=DOUBLE viscosity of solvent\n"); - printf(" --temperature=DOUBLE temperature of the system\n"); - printf(" --sigma=DOUBLE diameter of beads(use with rough shell model)\n"); - printf(" --model=STRING hydrodynamics model (support RoughShell and \n BeadModel)\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->model_arg)); + free_string_field (&(args_info->model_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->model_given) + write_into_file(outfile, "model", args_info->model_orig, 0); + if (args_info->beads_given) + write_into_file(outfile, "beads", 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); @@ -61,182 +281,359 @@ int } int -cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info) +cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info) { - int c; /* Character of the parsed option. */ - int missing_required_options = 0; + return cmdline_parser2 (argc, argv, args_info, 0, 1, 1); +} - args_info->help_given = 0 ; - args_info->version_given = 0 ; - args_info->input_given = 0 ; - args_info->output_given = 0 ; - args_info->viscosity_given = 0 ; - args_info->temperature_given = 0 ; - args_info->sigma_given = 0 ; - args_info->model_given = 0 ; -#define clear_args() { \ - args_info->input_arg = NULL; \ - args_info->output_arg = gengetopt_strdup("hydro") ;\ - args_info->model_arg = NULL; \ +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; } - clear_args(); +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->model_given) + { + fprintf (stderr, "%s: '--model' option required%s\n", prog_name, (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_FLAG: + *((int *)field) = !*((int *)field); + 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; + }; + + + /* store the original value */ + switch(arg_type) { + case ARG_NO: + case ARG_FLAG: + 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' }, { "version", 0, NULL, 'V' }, { "input", 1, NULL, 'i' }, { "output", 1, NULL, 'o' }, - { "viscosity", 1, NULL, 0 }, - { "temperature", 1, NULL, 0 }, - { "sigma", 1, NULL, 0 }, { "model", 1, NULL, 0 }, - { NULL, 0, NULL, 0 } + { "beads", 0, NULL, 'b' }, + { 0, 0, 0, 0 } }; - stop_char = 0; - c = getopt_long (argc, argv, "hVi:o:", long_options, &option_index); + c = getopt_long (argc, argv, "hVi:o:b", 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); + case 'i': /* input MetaData (md) file. */ + + + 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 prefix. */ - 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; - if (args_info->output_arg) - free (args_info->output_arg); /* free default string */ - 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, "hydro", ARG_STRING, + check_ambiguity, override, 0, 0, + "output", 'o', + additional_error)) + goto failure; + break; + case 'b': /* generate the beads only, hydrodynamics will be performed. */ + + + if (update_arg((void *)&(args_info->beads_flag), 0, &(args_info->beads_given), + &(local_args_info.beads_given), optarg, 0, 0, ARG_FLAG, + check_ambiguity, override, 1, 0, "beads", 'b', + additional_error)) + goto failure; + + break; - case 0: /* Long option with no short option */ - /* viscosity of solvent. */ - if (strcmp (long_options[option_index].name, "viscosity") == 0) + /* hydrodynamics model (supports RoughShell and BeadModel). */ + if (strcmp (long_options[option_index].name, "model") == 0) { - if (args_info->viscosity_given) - { - fprintf (stderr, "%s: `--viscosity' option given more than once\n", CMDLINE_PARSER_PACKAGE); - clear_args (); - exit (EXIT_FAILURE); - } - args_info->viscosity_given = 1; - args_info->viscosity_arg = strtod (optarg, NULL); - break; - } - /* temperature of the system. */ - else if (strcmp (long_options[option_index].name, "temperature") == 0) - { - if (args_info->temperature_given) - { - fprintf (stderr, "%s: `--temperature' option given more than once\n", CMDLINE_PARSER_PACKAGE); - clear_args (); - exit (EXIT_FAILURE); - } - args_info->temperature_given = 1; - args_info->temperature_arg = strtod (optarg, NULL); - break; - } - /* diameter of beads(use with rough shell model). */ - else if (strcmp (long_options[option_index].name, "sigma") == 0) - { - if (args_info->sigma_given) - { - fprintf (stderr, "%s: `--sigma' option given more than once\n", CMDLINE_PARSER_PACKAGE); - clear_args (); - exit (EXIT_FAILURE); - } - args_info->sigma_given = 1; - args_info->sigma_arg = strtod (optarg, NULL); - break; - } + if (update_arg( (void *)&(args_info->model_arg), + &(args_info->model_orig), &(args_info->model_given), + &(local_args_info.model_given), optarg, 0, 0, ARG_STRING, + check_ambiguity, override, 0, 0, + "model", '-', + additional_error)) + goto failure; - /* hydrodynamics model (support RoughShell and BeadModel). */ - else if (strcmp (long_options[option_index].name, "model") == 0) - { - if (args_info->model_given) - { - fprintf (stderr, "%s: `--model' option given more than once\n", CMDLINE_PARSER_PACKAGE); - clear_args (); - exit (EXIT_FAILURE); - } - args_info->model_given = 1; - args_info->model_arg = gengetopt_strdup (optarg); - break; } - + 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 (! 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 (! args_info->viscosity_given) + + cmdline_parser_release (&local_args_info); + + if ( error ) + return (EXIT_FAILURE); + + if (optind < argc) { - fprintf (stderr, "%s: '--viscosity' option required\n", CMDLINE_PARSER_PACKAGE); - missing_required_options = 1; + 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]) ; } - if (! args_info->temperature_given) - { - fprintf (stderr, "%s: '--temperature' option required\n", CMDLINE_PARSER_PACKAGE); - missing_required_options = 1; - } - if (! args_info->model_given) - { - fprintf (stderr, "%s: '--model' option required\n", CMDLINE_PARSER_PACKAGE); - missing_required_options = 1; - } - if ( missing_required_options ) - exit (EXIT_FAILURE); return 0; + +failure: + + cmdline_parser_release (&local_args_info); + return (EXIT_FAILURE); }