applications/hydrodynamics/HydroCmd.cpp

/*
  File autogenerated by gengetopt version 2.22.4
  generated with the following command:
  gengetopt --file-name=HydroCmd --unamed-opts 

  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 <stdio.h>
#include <stdlib.h>
#include <string.h>

#ifndef FIX_UNUSED
#define FIX_UNUSED(X) (void) (X) /* avoid warnings for unused params */
#endif

#ifdef WIN32
#include "utils/wingetopt.h"
#else
#include <getopt.h>
#endif

#include "HydroCmd.h"

const char *gengetopt_args_info_purpose = "\n+--------------------------------------------------------------------------+\n|    ____                    __  ___ ____                                  |\n|   / __ \\____  ___  ____   /  |/  // __ \\  The Open Molecular Dynamics    |\n|  / / / / __ \\/ _ \\/ __ \\ / /|_/ // / / /  Engine (formerly OOPSE).       |\n| / /_/ / /_/ /  __/ / / // /  / // /_/ /                                  |\n| \\____/ .___/\\___/_/ /_//_/  /_//_____/    Copyright 2004-2013 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, 234107 (2008).              |\n| [4] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).                |\n| [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |\n| [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).                   |\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",
     (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)
{
  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);

  args_info->inputs = 0;
  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
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 = 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 **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, &params, 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)
{
  const char *val = value;
  int found;
  char **string_field;
  FIX_UNUSED (field);

  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 = 0;
  opterr = params->print_errors;
  optopt = '?';

  while (1)
    {
      int option_index = 0;

      static struct option long_options[] = {
        { "help",       0, NULL, 'h' },
        { "version",    0, NULL, 'V' },
        { "input",      1, NULL, 'i' },
        { "output",     1, NULL, 'o' },
        { "model",      1, NULL, 0 },
        { "beads",      0, NULL, 'b' },
        { 0,  0, 0, 0 }
      };

      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.  */
          cmdline_parser_print_help ();
          cmdline_parser_free (&local_args_info);
          exit (EXIT_SUCCESS);

        case 'V':       /* Print version and exit.  */
          cmdline_parser_print_version ();
          cmdline_parser_free (&local_args_info);
          exit (EXIT_SUCCESS);

        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 (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 */
          /* hydrodynamics model (supports RoughShell and BeadModel).  */
          if (strcmp (long_options[option_index].name, "model") == 0)
          {
          
          
            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;
          
          }
          
          break;
        case '?':       /* Invalid option.  */
          /* `getopt_long' already printed an error message.  */
          goto failure;

        default:        /* bug: option not considered.  */
          fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
          abort ();
        } /* switch */
    } /* while */


  if (check_required)
    {
      error += cmdline_parser_required2 (args_info, argv[0], additional_error);
    }

  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);
}
Revision:	1879
Committed:	Sun Jun 16 15:15:42 2013 UTC (11 years, 10 months ago) by gezelter
File size:	18795 byte(s)
Log Message:	MERGE OpenMD development 1783:1878 into trunk
#	User	Rev	Content
1	tim	891	/*
2	gezelter	1630	File autogenerated by gengetopt version 2.22.4
3	tim	891	generated with the following command:
4	gezelter	1879	gengetopt --file-name=HydroCmd --unamed-opts
5	tim	891
6			The developers of gengetopt consider the fixed text that goes in all
7			gengetopt output files to be in the public domain:
8			we make no copyright claims on it.
9			*/
10
11	gezelter	938	/* If we use autoconf. */
12			#ifdef HAVE_CONFIG_H
13			#include "config.h"
14			#endif
15	tim	891
16			#include <stdio.h>
17			#include <stdlib.h>
18			#include <string.h>
19
20	gezelter	1630	#ifndef FIX_UNUSED
21			#define FIX_UNUSED(X) (void) (X) /* avoid warnings for unused params */
22			#endif
23	tim	891
24	gezelter	1795	#ifdef WIN32
25			#include "utils/wingetopt.h"
26			#else
27	gezelter	1630	#include <getopt.h>
28	gezelter	1795	#endif
29	gezelter	1630
30	tim	891	#include "HydroCmd.h"
31
32	gezelter	1879	const char *gengetopt_args_info_purpose = "\n+--------------------------------------------------------------------------+\n\| ____ __ ___ ____ \|\n\| / __ \\____ ___ ____ / \|/ // __ \\ The Open Molecular Dynamics \|\n\| / / / / __ \\/ _ \\/ __ \\ / /\|_/ // / / / Engine (formerly OOPSE). \|\n\| / /_/ / /_/ / __/ / / // / / // /_/ / \|\n\| \\____/ .___/\\___/_/ /_//_/ /_//_____/ Copyright 2004-2013 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, 234107 (2008). \|\n\| [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). \|\n\| [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). \|\n\| [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012). \|\n+--------------------------------------------------------------------------+";
33	gezelter	1390
34	gezelter	1630	const char *gengetopt_args_info_usage = "Usage: Hydro [OPTIONS]... [FILES]...";
35	gezelter	1390
36			const char *gengetopt_args_info_description = "";
37
38			const char *gengetopt_args_info_help[] = {
39			" -h, --help Print help and exit",
40			" -V, --version Print version and exit",
41			" -i, --input=filename input MetaData (md) file",
42			" -o, --output=STRING output file prefix (default=`hydro')",
43			" --model=STRING hydrodynamics model (supports RoughShell and BeadModel)",
44			" -b, --beads generate the beads only, hydrodynamics will be \n performed (default=off)",
45			0
46			};
47
48			typedef enum {ARG_NO
49			, ARG_FLAG
50			, ARG_STRING
51			} cmdline_parser_arg_type;
52
53	gezelter	938	static
54			void clear_given (struct gengetopt_args_info *args_info);
55			static
56			void clear_args (struct gengetopt_args_info *args_info);
57
58			static int
59	gezelter	1630	cmdline_parser_internal (int argc, char *argv, struct gengetopt_args_info args_info,
60	gezelter	1390	struct cmdline_parser_params params, const char additional_error);
61	gezelter	938
62			static int
63			cmdline_parser_required2 (struct gengetopt_args_info args_info, const char prog_name, const char *additional_error);
64
65			static char *
66			gengetopt_strdup (const char *s);
67
68			static
69			void clear_given (struct gengetopt_args_info *args_info)
70			{
71			args_info->help_given = 0 ;
72			args_info->version_given = 0 ;
73			args_info->input_given = 0 ;
74			args_info->output_given = 0 ;
75			args_info->model_given = 0 ;
76			args_info->beads_given = 0 ;
77			}
78
79			static
80			void clear_args (struct gengetopt_args_info *args_info)
81			{
82	gezelter	1630	FIX_UNUSED (args_info);
83	gezelter	938	args_info->input_arg = NULL;
84			args_info->input_orig = NULL;
85			args_info->output_arg = gengetopt_strdup ("hydro");
86			args_info->output_orig = NULL;
87			args_info->model_arg = NULL;
88			args_info->model_orig = NULL;
89			args_info->beads_flag = 0;
90
91			}
92
93	gezelter	1390	static
94			void init_args_info(struct gengetopt_args_info *args_info)
95			{
96
97
98			args_info->help_help = gengetopt_args_info_help[0] ;
99			args_info->version_help = gengetopt_args_info_help[1] ;
100			args_info->input_help = gengetopt_args_info_help[2] ;
101			args_info->output_help = gengetopt_args_info_help[3] ;
102			args_info->model_help = gengetopt_args_info_help[4] ;
103			args_info->beads_help = gengetopt_args_info_help[5] ;
104
105			}
106
107	tim	891	void
108			cmdline_parser_print_version (void)
109			{
110	gezelter	1630	printf ("%s %s\n",
111			(strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE),
112			CMDLINE_PARSER_VERSION);
113	tim	891	}
114
115	gezelter	1390	static void print_help_common(void) {
116			cmdline_parser_print_version ();
117
118			if (strlen(gengetopt_args_info_purpose) > 0)
119			printf("\n%s\n", gengetopt_args_info_purpose);
120
121			if (strlen(gengetopt_args_info_usage) > 0)
122			printf("\n%s\n", gengetopt_args_info_usage);
123
124			printf("\n");
125
126			if (strlen(gengetopt_args_info_description) > 0)
127	gezelter	1630	printf("%s\n\n", gengetopt_args_info_description);
128	gezelter	1390	}
129
130	tim	891	void
131			cmdline_parser_print_help (void)
132			{
133	gezelter	1390	int i = 0;
134			print_help_common();
135			while (gengetopt_args_info_help[i])
136			printf("%s\n", gengetopt_args_info_help[i++]);
137	tim	891	}
138
139	gezelter	938	void
140			cmdline_parser_init (struct gengetopt_args_info *args_info)
141			{
142			clear_given (args_info);
143			clear_args (args_info);
144	gezelter	1390	init_args_info (args_info);
145	gezelter	1630
146			args_info->inputs = 0;
147			args_info->inputs_num = 0;
148	gezelter	938	}
149	tim	891
150	gezelter	1390	void
151			cmdline_parser_params_init(struct cmdline_parser_params *params)
152			{
153			if (params)
154			{
155			params->override = 0;
156			params->initialize = 1;
157			params->check_required = 1;
158			params->check_ambiguity = 0;
159			params->print_errors = 1;
160			}
161			}
162
163			struct cmdline_parser_params *
164			cmdline_parser_params_create(void)
165			{
166			struct cmdline_parser_params *params =
167			(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
168			cmdline_parser_params_init(params);
169			return params;
170			}
171
172	gezelter	938	static void
173	gezelter	1390	free_string_field (char **s)
174			{
175			if (*s)
176			{
177			free (*s);
178			*s = 0;
179			}
180			}
181
182
183			static void
184	gezelter	938	cmdline_parser_release (struct gengetopt_args_info *args_info)
185			{
186	gezelter	1630	unsigned int i;
187	gezelter	1390	free_string_field (&(args_info->input_arg));
188			free_string_field (&(args_info->input_orig));
189			free_string_field (&(args_info->output_arg));
190			free_string_field (&(args_info->output_orig));
191			free_string_field (&(args_info->model_arg));
192			free_string_field (&(args_info->model_orig));
193	gezelter	938
194	gezelter	1390
195	gezelter	1630	for (i = 0; i < args_info->inputs_num; ++i)
196			free (args_info->inputs [i]);
197	gezelter	1390
198	gezelter	1630	if (args_info->inputs_num)
199			free (args_info->inputs);
200
201	gezelter	1390	clear_given (args_info);
202			}
203
204
205			static void
206	gezelter	1630	write_into_file(FILE outfile, const char opt, const char arg, const char values[])
207	gezelter	1390	{
208	gezelter	1630	FIX_UNUSED (values);
209	gezelter	1390	if (arg) {
210			fprintf(outfile, "%s=\"%s\"\n", opt, arg);
211			} else {
212			fprintf(outfile, "%s\n", opt);
213			}
214			}
215
216
217			int
218			cmdline_parser_dump(FILE outfile, struct gengetopt_args_info args_info)
219			{
220			int i = 0;
221
222			if (!outfile)
223	gezelter	938	{
224	gezelter	1390	fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
225			return EXIT_FAILURE;
226	gezelter	938	}
227	gezelter	1390
228			if (args_info->help_given)
229			write_into_file(outfile, "help", 0, 0 );
230			if (args_info->version_given)
231			write_into_file(outfile, "version", 0, 0 );
232			if (args_info->input_given)
233			write_into_file(outfile, "input", args_info->input_orig, 0);
234			if (args_info->output_given)
235			write_into_file(outfile, "output", args_info->output_orig, 0);
236			if (args_info->model_given)
237			write_into_file(outfile, "model", args_info->model_orig, 0);
238			if (args_info->beads_given)
239			write_into_file(outfile, "beads", 0, 0 );
240	gezelter	938
241	gezelter	1390
242			i = EXIT_SUCCESS;
243			return i;
244	gezelter	938	}
245	tim	891
246	gezelter	938	int
247			cmdline_parser_file_save(const char filename, struct gengetopt_args_info args_info)
248			{
249			FILE *outfile;
250			int i = 0;
251
252			outfile = fopen(filename, "w");
253
254			if (!outfile)
255			{
256			fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
257			return EXIT_FAILURE;
258			}
259
260	gezelter	1390	i = cmdline_parser_dump(outfile, args_info);
261	gezelter	938	fclose (outfile);
262
263			return i;
264			}
265
266			void
267			cmdline_parser_free (struct gengetopt_args_info *args_info)
268			{
269			cmdline_parser_release (args_info);
270			}
271
272	gezelter	1390	/** @brief replacement of strdup, which is not standard */
273	tim	891	char *
274			gengetopt_strdup (const char *s)
275			{
276	gezelter	1630	char *result = 0;
277	gezelter	938	if (!s)
278			return result;
279
280			result = (char*)malloc(strlen(s) + 1);
281	tim	891	if (result == (char*)0)
282			return (char*)0;
283			strcpy(result, s);
284			return result;
285			}
286
287			int
288	gezelter	1630	cmdline_parser (int argc, char *argv, struct gengetopt_args_info args_info)
289	tim	891	{
290	gezelter	938	return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
291			}
292	tim	891
293	gezelter	938	int
294	gezelter	1630	cmdline_parser_ext (int argc, char *argv, struct gengetopt_args_info args_info,
295	gezelter	1390	struct cmdline_parser_params *params)
296			{
297			int result;
298	gezelter	1630	result = cmdline_parser_internal (argc, argv, args_info, params, 0);
299	gezelter	1390
300			if (result == EXIT_FAILURE)
301			{
302			cmdline_parser_free (args_info);
303			exit (EXIT_FAILURE);
304			}
305
306			return result;
307			}
308
309			int
310	gezelter	1630	cmdline_parser2 (int argc, char *argv, struct gengetopt_args_info args_info, int override, int initialize, int check_required)
311	gezelter	938	{
312			int result;
313	gezelter	1390	struct cmdline_parser_params params;
314
315			params.override = override;
316			params.initialize = initialize;
317			params.check_required = check_required;
318			params.check_ambiguity = 0;
319			params.print_errors = 1;
320	gezelter	938
321	gezelter	1630	result = cmdline_parser_internal (argc, argv, args_info, &params, 0);
322	gezelter	938
323			if (result == EXIT_FAILURE)
324			{
325			cmdline_parser_free (args_info);
326			exit (EXIT_FAILURE);
327			}
328
329			return result;
330	tim	891	}
331
332	gezelter	938	int
333			cmdline_parser_required (struct gengetopt_args_info args_info, const char prog_name)
334			{
335			int result = EXIT_SUCCESS;
336	tim	891
337	gezelter	1630	if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
338	gezelter	938	result = EXIT_FAILURE;
339
340			if (result == EXIT_FAILURE)
341			{
342			cmdline_parser_free (args_info);
343			exit (EXIT_FAILURE);
344			}
345
346			return result;
347			}
348
349			int
350			cmdline_parser_required2 (struct gengetopt_args_info args_info, const char prog_name, const char *additional_error)
351			{
352			int error = 0;
353	gezelter	1630	FIX_UNUSED (additional_error);
354	gezelter	938
355	gezelter	1390	/* checks for required options */
356	gezelter	938	if (! args_info->input_given)
357			{
358			fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
359			error = 1;
360			}
361	gezelter	1390
362	gezelter	938	if (! args_info->model_given)
363			{
364			fprintf (stderr, "%s: '--model' option required%s\n", prog_name, (additional_error ? additional_error : ""));
365			error = 1;
366			}
367	gezelter	1390
368
369			/* checks for dependences among options */
370	gezelter	938
371			return error;
372			}
373
374	gezelter	1390
375			static char *package_name = 0;
376
377			/**
378			* @brief updates an option
379			* @param field the generic pointer to the field to update
380			* @param orig_field the pointer to the orig field
381			* @param field_given the pointer to the number of occurrence of this option
382			* @param prev_given the pointer to the number of occurrence already seen
383			* @param value the argument for this option (if null no arg was specified)
384			* @param possible_values the possible values for this option (if specified)
385			* @param default_value the default value (in case the option only accepts fixed values)
386			* @param arg_type the type of this option
387			* @param check_ambiguity @see cmdline_parser_params.check_ambiguity
388			* @param override @see cmdline_parser_params.override
389			* @param no_free whether to free a possible previous value
390			* @param multiple_option whether this is a multiple option
391			* @param long_opt the corresponding long option
392			* @param short_opt the corresponding short option (or '-' if none)
393			* @param additional_error possible further error specification
394			*/
395			static
396			int update_arg(void field, char *orig_field,
397			unsigned int field_given, unsigned int prev_given,
398	gezelter	1630	char value, const char possible_values[],
399			const char *default_value,
400	gezelter	1390	cmdline_parser_arg_type arg_type,
401			int check_ambiguity, int override,
402			int no_free, int multiple_option,
403			const char *long_opt, char short_opt,
404			const char *additional_error)
405			{
406			const char *val = value;
407			int found;
408			char **string_field;
409	gezelter	1630	FIX_UNUSED (field);
410	gezelter	1390
411			found = 0;
412
413			if (!multiple_option && prev_given && (prev_given \|\| (check_ambiguity && field_given)))
414			{
415			if (short_opt != '-')
416			fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
417			package_name, long_opt, short_opt,
418			(additional_error ? additional_error : ""));
419			else
420			fprintf (stderr, "%s: `--%s' option given more than once%s\n",
421			package_name, long_opt,
422			(additional_error ? additional_error : ""));
423			return 1; /* failure */
424			}
425
426	gezelter	1630	FIX_UNUSED (default_value);
427	gezelter	1390
428			if (field_given && *field_given && ! override)
429			return 0;
430			if (prev_given)
431			(*prev_given)++;
432			if (field_given)
433			(*field_given)++;
434			if (possible_values)
435			val = possible_values[found];
436
437			switch(arg_type) {
438			case ARG_FLAG:
439			((int )field) = !((int )field);
440			break;
441			case ARG_STRING:
442			if (val) {
443			string_field = (char **)field;
444			if (!no_free && *string_field)
445			free (string_field); / free previous string */
446			*string_field = gengetopt_strdup (val);
447			}
448			break;
449			default:
450			break;
451			};
452
453
454			/* store the original value */
455			switch(arg_type) {
456			case ARG_NO:
457			case ARG_FLAG:
458			break;
459			default:
460			if (value && orig_field) {
461			if (no_free) {
462			*orig_field = value;
463			} else {
464			if (*orig_field)
465			free (orig_field); / free previous string */
466			*orig_field = gengetopt_strdup (value);
467			}
468			}
469			};
470
471			return 0; /* OK */
472			}
473
474
475	gezelter	938	int
476	gezelter	1630	cmdline_parser_internal (
477			int argc, char *argv, struct gengetopt_args_info args_info,
478	gezelter	1390	struct cmdline_parser_params params, const char additional_error)
479	gezelter	938	{
480			int c; /* Character of the parsed option. */
481
482			int error = 0;
483			struct gengetopt_args_info local_args_info;
484	gezelter	1390
485			int override;
486			int initialize;
487			int check_required;
488			int check_ambiguity;
489
490			package_name = argv[0];
491
492			override = params->override;
493			initialize = params->initialize;
494			check_required = params->check_required;
495			check_ambiguity = params->check_ambiguity;
496	gezelter	938
497			if (initialize)
498			cmdline_parser_init (args_info);
499
500			cmdline_parser_init (&local_args_info);
501
502	tim	891	optarg = 0;
503	gezelter	938	optind = 0;
504	gezelter	1390	opterr = params->print_errors;
505	tim	891	optopt = '?';
506
507			while (1)
508			{
509			int option_index = 0;
510
511			static struct option long_options[] = {
512			{ "help", 0, NULL, 'h' },
513			{ "version", 0, NULL, 'V' },
514			{ "input", 1, NULL, 'i' },
515			{ "output", 1, NULL, 'o' },
516			{ "model", 1, NULL, 0 },
517	tim	921	{ "beads", 0, NULL, 'b' },
518	gezelter	1630	{ 0, 0, 0, 0 }
519	tim	891	};
520
521	tim	921	c = getopt_long (argc, argv, "hVi:o:b", long_options, &option_index);
522	tim	891
523			if (c == -1) break; /* Exit from `while (1)' loop. */
524
525			switch (c)
526			{
527			case 'h': /* Print help and exit. */
528			cmdline_parser_print_help ();
529	gezelter	938	cmdline_parser_free (&local_args_info);
530	tim	891	exit (EXIT_SUCCESS);
531
532			case 'V': /* Print version and exit. */
533			cmdline_parser_print_version ();
534	gezelter	938	cmdline_parser_free (&local_args_info);
535	tim	891	exit (EXIT_SUCCESS);
536
537	xsun	1177	case 'i': /* input MetaData (md) file. */
538	gezelter	1390
539
540			if (update_arg( (void *)&(args_info->input_arg),
541			&(args_info->input_orig), &(args_info->input_given),
542			&(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
543			check_ambiguity, override, 0, 0,
544			"input", 'i',
545			additional_error))
546			goto failure;
547
548	tim	891	break;
549			case 'o': /* output file prefix. */
550	gezelter	1390
551
552			if (update_arg( (void *)&(args_info->output_arg),
553			&(args_info->output_orig), &(args_info->output_given),
554			&(local_args_info.output_given), optarg, 0, "hydro", ARG_STRING,
555			check_ambiguity, override, 0, 0,
556			"output", 'o',
557			additional_error))
558			goto failure;
559
560	tim	891	break;
561	tim	921	case 'b': /* generate the beads only, hydrodynamics will be performed. */
562	gezelter	1390
563
564			if (update_arg((void *)&(args_info->beads_flag), 0, &(args_info->beads_given),
565			&(local_args_info.beads_given), optarg, 0, 0, ARG_FLAG,
566			check_ambiguity, override, 1, 0, "beads", 'b',
567			additional_error))
568			goto failure;
569
570	tim	921	break;
571	tim	891
572			case 0: /* Long option with no short option */
573	xsun	1177	/* hydrodynamics model (supports RoughShell and BeadModel). */
574	tim	906	if (strcmp (long_options[option_index].name, "model") == 0)
575	tim	891	{
576	gezelter	1390
577
578			if (update_arg( (void *)&(args_info->model_arg),
579			&(args_info->model_orig), &(args_info->model_given),
580			&(local_args_info.model_given), optarg, 0, 0, ARG_STRING,
581			check_ambiguity, override, 0, 0,
582			"model", '-',
583			additional_error))
584			goto failure;
585
586	tim	891	}
587
588	gezelter	938	break;
589	tim	891	case '?': /* Invalid option. */
590			/* `getopt_long' already printed an error message. */
591	gezelter	938	goto failure;
592	tim	891
593			default: /* bug: option not considered. */
594	gezelter	938	fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
595	tim	891	abort ();
596			} /* switch */
597			} /* while */
598
599
600	gezelter	938
601			if (check_required)
602	tim	891	{
603	gezelter	938	error += cmdline_parser_required2 (args_info, argv[0], additional_error);
604	tim	891	}
605
606	gezelter	938	cmdline_parser_release (&local_args_info);
607
608			if ( error )
609	xsun	1177	return (EXIT_FAILURE);
610	gezelter	938
611	gezelter	1630	if (optind < argc)
612			{
613			int i = 0 ;
614			int found_prog_name = 0;
615			/* whether program name, i.e., argv[0], is in the remaining args
616			(this may happen with some implementations of getopt,
617			but surely not with the one included by gengetopt) */
618
619			i = optind;
620			while (i < argc)
621			if (argv[i++] == argv[0]) {
622			found_prog_name = 1;
623			break;
624			}
625			i = 0;
626
627			args_info->inputs_num = argc - optind - found_prog_name;
628			args_info->inputs =
629			(char *)(malloc ((args_info->inputs_num)sizeof(char *))) ;
630			while (optind < argc)
631			if (argv[optind++] != argv[0])
632			args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
633			}
634
635	tim	891	return 0;
636	gezelter	938
637			failure:
638
639			cmdline_parser_release (&local_args_info);
640			return (EXIT_FAILURE);
641	tim	891	}