applications/dynamicProps/DynamicPropsCmd.cpp

/*
  File autogenerated by gengetopt version 2.15
  generated with the following command:
  gengetopt -i DynamicProps.ggo --file-name=DynamicPropsCmd 

  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>

#include "getopt.h"

#include "DynamicPropsCmd.h"

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);

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->sele1_given = 0 ;
  args_info->sele2_given = 0 ;
  args_info->order_given = 0 ;
  args_info->rcorr_given = 0 ;
  args_info->vcorr_given = 0 ;
  args_info->dcorr_given = 0 ;
  args_info->lcorr_given = 0 ;
  args_info->r_rcorr_given = 0 ;
  args_info->dynamicProps_group_counter = 0 ;
}

static
void clear_args (struct gengetopt_args_info *args_info)
{
  args_info->input_arg = NULL;
  args_info->input_orig = NULL;
  args_info->output_arg = NULL;
  args_info->output_orig = NULL;
  args_info->sele1_arg = NULL;
  args_info->sele1_orig = NULL;
  args_info->sele2_arg = NULL;
  args_info->sele2_orig = NULL;
  args_info->order_orig = NULL;
  
}

void
cmdline_parser_print_version (void)
{
  printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
}

void
cmdline_parser_print_help (void)
{
  cmdline_parser_print_version ();
  printf("\nUsage: DynamicProps [OPTIONS]...\n\n");
  printf("%s\n","  -h, --help                    Print help and exit");
  printf("%s\n","  -V, --version                 Print version and exit");
  printf("%s\n","  -i, --input=filename          input dump file");
  printf("%s\n","  -o, --output=filename         output file name");
  printf("%s\n","      --sele1=selection script  select first stuntdouble set");
  printf("%s\n","      --sele2=selection script  select second stuntdouble set (if sele2 is not \n                                  set, use script from sele1)");
  printf("%s\n","      --order=INT               Lengendre Polynomial Order");
  printf("%s\n","\n Group: dynamicProps\n   an option of this group is required");
  printf("%s\n","  -r, --rcorr                   rmsd");
  printf("%s\n","  -v, --vcorr                   velocity correlation function");
  printf("%s\n","  -d, --dcorr                   dipole correlation function");
  printf("%s\n","  -l, --lcorr                   Lengendre correlation function");
  printf("%s\n","      --r_rcorr                 Radial rmsd");
  
}

void
cmdline_parser_init (struct gengetopt_args_info *args_info)
{
  clear_given (args_info);
  clear_args (args_info);
}

static void
cmdline_parser_release (struct gengetopt_args_info *args_info)
{
  
  if (args_info->input_arg)
    {
      free (args_info->input_arg); /* free previous argument */
      args_info->input_arg = 0;
    }
  if (args_info->input_orig)
    {
      free (args_info->input_orig); /* free previous argument */
      args_info->input_orig = 0;
    }
  if (args_info->output_arg)
    {
      free (args_info->output_arg); /* free previous argument */
      args_info->output_arg = 0;
    }
  if (args_info->output_orig)
    {
      free (args_info->output_orig); /* free previous argument */
      args_info->output_orig = 0;
    }
  if (args_info->sele1_arg)
    {
      free (args_info->sele1_arg); /* free previous argument */
      args_info->sele1_arg = 0;
    }
  if (args_info->sele1_orig)
    {
      free (args_info->sele1_orig); /* free previous argument */
      args_info->sele1_orig = 0;
    }
  if (args_info->sele2_arg)
    {
      free (args_info->sele2_arg); /* free previous argument */
      args_info->sele2_arg = 0;
    }
  if (args_info->sele2_orig)
    {
      free (args_info->sele2_orig); /* free previous argument */
      args_info->sele2_orig = 0;
    }
  if (args_info->order_orig)
    {
      free (args_info->order_orig); /* free previous argument */
      args_info->order_orig = 0;
    }
  
  clear_given (args_info);
}

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;
    }

  if (args_info->help_given) {
    fprintf(outfile, "%s\n", "help");
  }
  if (args_info->version_given) {
    fprintf(outfile, "%s\n", "version");
  }
  if (args_info->input_given) {
    if (args_info->input_orig) {
      fprintf(outfile, "%s=\"%s\"\n", "input", args_info->input_orig);
    } else {
      fprintf(outfile, "%s\n", "input");
    }
  }
  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->sele1_given) {
    if (args_info->sele1_orig) {
      fprintf(outfile, "%s=\"%s\"\n", "sele1", args_info->sele1_orig);
    } else {
      fprintf(outfile, "%s\n", "sele1");
    }
  }
  if (args_info->sele2_given) {
    if (args_info->sele2_orig) {
      fprintf(outfile, "%s=\"%s\"\n", "sele2", args_info->sele2_orig);
    } else {
      fprintf(outfile, "%s\n", "sele2");
    }
  }
  if (args_info->order_given) {
    if (args_info->order_orig) {
      fprintf(outfile, "%s=\"%s\"\n", "order", args_info->order_orig);
    } else {
      fprintf(outfile, "%s\n", "order");
    }
  }
  if (args_info->rcorr_given) {
    fprintf(outfile, "%s\n", "rcorr");
  }
  if (args_info->vcorr_given) {
    fprintf(outfile, "%s\n", "vcorr");
  }
  if (args_info->dcorr_given) {
    fprintf(outfile, "%s\n", "dcorr");
  }
  if (args_info->lcorr_given) {
    fprintf(outfile, "%s\n", "lcorr");
  }
  if (args_info->r_rcorr_given) {
    fprintf(outfile, "%s\n", "r_rcorr");
  }
  
  fclose (outfile);

  i = EXIT_SUCCESS;
  return i;
}

void
cmdline_parser_free (struct gengetopt_args_info *args_info)
{
  cmdline_parser_release (args_info);
}


/* gengetopt_strdup() */
/* strdup.c replacement of strdup, which is not standard */
char *
gengetopt_strdup (const char *s)
{
  char *result = NULL;
  if (!s)
    return result;

  result = (char*)malloc(strlen(s) + 1);
  if (result == (char*)0)
    return (char*)0;
  strcpy(result, s);
  return result;
}

static void
reset_group_dynamicProps(struct gengetopt_args_info *args_info);

static void
reset_group_dynamicProps(struct gengetopt_args_info *args_info)
{
  if (! args_info->dynamicProps_group_counter)
    return;
  
  args_info->rcorr_given = 0 ;
  args_info->vcorr_given = 0 ;
  args_info->dcorr_given = 0 ;
  args_info->lcorr_given = 0 ;
  args_info->r_rcorr_given = 0 ;

  args_info->dynamicProps_group_counter = 0;
}

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_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
{
  int result;

  result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);

  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, NULL) > 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;

  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->dynamicProps_group_counter == 0)
    {
      fprintf (stderr, "%s: %d options of group dynamicProps were given. One is required.%s\n", prog_name, args_info->dynamicProps_group_counter, (additional_error ? additional_error : ""));
      error = 1;
    }
  

  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)
{
  int c;        /* Character of the parsed option.  */

  int error = 0;
  struct gengetopt_args_info local_args_info;

  if (initialize)
    cmdline_parser_init (args_info);

  cmdline_parser_init (&local_args_info);

  optarg = 0;
  optind = 1;
  opterr = 1;
  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' },
        { "sele1",      1, NULL, 0 },
        { "sele2",      1, NULL, 0 },
        { "order",      1, NULL, 0 },
        { "rcorr",      0, NULL, 'r' },
        { "vcorr",      0, NULL, 'v' },
        { "dcorr",      0, NULL, 'd' },
        { "lcorr",      0, NULL, 'l' },
        { "r_rcorr",    0, NULL, 0 },
        { NULL, 0, NULL, 0 }
      };

      stop_char = 0;
      c = getopt_long (argc, argv, "hVi:o:rvdl", 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 dump file.  */
          if (local_args_info.input_given)
            {
              fprintf (stderr, "%s: `--input' (`-i') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->input_given && ! override)
            continue;
          local_args_info.input_given = 1;
          args_info->input_given = 1;
          if (args_info->input_arg)
            free (args_info->input_arg); /* free previous string */
          args_info->input_arg = gengetopt_strdup (optarg);
          if (args_info->input_orig)
            free (args_info->input_orig); /* free previous string */
          args_info->input_orig = gengetopt_strdup (optarg);
          break;

        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);
          break;

        case 'r':       /* rmsd.  */
          if (local_args_info.rcorr_given)
            {
              fprintf (stderr, "%s: `--rcorr' (`-r') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->rcorr_given && ! override)
            continue;
          local_args_info.rcorr_given = 1;
          args_info->rcorr_given = 1;
          if (args_info->dynamicProps_group_counter && override)
            reset_group_dynamicProps (args_info);
          args_info->dynamicProps_group_counter += 1;
          break;

        case 'v':       /* velocity correlation function.  */
          if (local_args_info.vcorr_given)
            {
              fprintf (stderr, "%s: `--vcorr' (`-v') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->vcorr_given && ! override)
            continue;
          local_args_info.vcorr_given = 1;
          args_info->vcorr_given = 1;
          if (args_info->dynamicProps_group_counter && override)
            reset_group_dynamicProps (args_info);
          args_info->dynamicProps_group_counter += 1;
          break;

        case 'd':       /* dipole correlation function.  */
          if (local_args_info.dcorr_given)
            {
              fprintf (stderr, "%s: `--dcorr' (`-d') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->dcorr_given && ! override)
            continue;
          local_args_info.dcorr_given = 1;
          args_info->dcorr_given = 1;
          if (args_info->dynamicProps_group_counter && override)
            reset_group_dynamicProps (args_info);
          args_info->dynamicProps_group_counter += 1;
          break;

        case 'l':       /* Lengendre correlation function.  */
          if (local_args_info.lcorr_given)
            {
              fprintf (stderr, "%s: `--lcorr' (`-l') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->lcorr_given && ! override)
            continue;
          local_args_info.lcorr_given = 1;
          args_info->lcorr_given = 1;
          if (args_info->dynamicProps_group_counter && override)
            reset_group_dynamicProps (args_info);
          args_info->dynamicProps_group_counter += 1;
          break;


        case 0: /* Long option with no short option */
          /* select first stuntdouble set.  */
          if (strcmp (long_options[option_index].name, "sele1") == 0)
          {
            if (local_args_info.sele1_given)
              {
                fprintf (stderr, "%s: `--sele1' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->sele1_given && ! override)
              continue;
            local_args_info.sele1_given = 1;
            args_info->sele1_given = 1;
            if (args_info->sele1_arg)
              free (args_info->sele1_arg); /* free previous string */
            args_info->sele1_arg = gengetopt_strdup (optarg);
            if (args_info->sele1_orig)
              free (args_info->sele1_orig); /* free previous string */
            args_info->sele1_orig = gengetopt_strdup (optarg);
          }
          /* select second stuntdouble set (if sele2 is not set, use script from sele1).  */
          else if (strcmp (long_options[option_index].name, "sele2") == 0)
          {
            if (local_args_info.sele2_given)
              {
                fprintf (stderr, "%s: `--sele2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->sele2_given && ! override)
              continue;
            local_args_info.sele2_given = 1;
            args_info->sele2_given = 1;
            if (args_info->sele2_arg)
              free (args_info->sele2_arg); /* free previous string */
            args_info->sele2_arg = gengetopt_strdup (optarg);
            if (args_info->sele2_orig)
              free (args_info->sele2_orig); /* free previous string */
            args_info->sele2_orig = gengetopt_strdup (optarg);
          }
          /* Lengendre Polynomial Order.  */
          else if (strcmp (long_options[option_index].name, "order") == 0)
          {
            if (local_args_info.order_given)
              {
                fprintf (stderr, "%s: `--order' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->order_given && ! override)
              continue;
            local_args_info.order_given = 1;
            args_info->order_given = 1;
            args_info->order_arg = strtol (optarg, &stop_char, 0);
            if (!(stop_char && *stop_char == '\0')) {
              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
              goto failure;
            }
            if (args_info->order_orig)
              free (args_info->order_orig); /* free previous string */
            args_info->order_orig = gengetopt_strdup (optarg);
          }
          /* Radial rmsd.  */
          else if (strcmp (long_options[option_index].name, "r_rcorr") == 0)
          {
            if (local_args_info.r_rcorr_given)
              {
                fprintf (stderr, "%s: `--r_rcorr' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->r_rcorr_given && ! override)
              continue;
            local_args_info.r_rcorr_given = 1;
            args_info->r_rcorr_given = 1;
            if (args_info->dynamicProps_group_counter && override)
              reset_group_dynamicProps (args_info);
            args_info->dynamicProps_group_counter += 1;
            break;
          }
          
          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 (args_info->dynamicProps_group_counter > 1)
    {
      fprintf (stderr, "%s: %d options of group dynamicProps were given. One is required.%s\n", argv[0], args_info->dynamicProps_group_counter, (additional_error ? additional_error : ""));
      error = 1;
    }
  

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

  cmdline_parser_release (&local_args_info);

  if ( error )
    return (EXIT_FAILURE);

  return 0;

failure:
  
  cmdline_parser_release (&local_args_info);
  return (EXIT_FAILURE);
}
Revision:	1098
Committed:	Thu Dec 14 19:38:56 2006 UTC (18 years, 4 months ago) by chuckv
Content type:	text/plain
Original Path:	*trunk/src/applications/dynamicProps/DynamicPropsCmd.c*
File size:	19133 byte(s)
Log Message:	Code to run radial rcorr.
#	User	Rev	Content
1	tim	320	/*
2	chuckv	1098	File autogenerated by gengetopt version 2.15
3	tim	320	generated with the following command:
4	chuckv	1098	gengetopt -i DynamicProps.ggo --file-name=DynamicPropsCmd
5	tim	320
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	chuckv	1098	/* If we use autoconf. */
12			#ifdef HAVE_CONFIG_H
13			#include "config.h"
14			#endif
15	tim	320
16			#include <stdio.h>
17			#include <stdlib.h>
18			#include <string.h>
19
20			#include "getopt.h"
21
22			#include "DynamicPropsCmd.h"
23
24	chuckv	1098	static
25			void clear_given (struct gengetopt_args_info *args_info);
26			static
27			void clear_args (struct gengetopt_args_info *args_info);
28
29			static int
30			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);
31
32			static int
33			cmdline_parser_required2 (struct gengetopt_args_info args_info, const char prog_name, const char *additional_error);
34
35			static char *
36			gengetopt_strdup (const char *s);
37
38			static
39			void clear_given (struct gengetopt_args_info *args_info)
40			{
41			args_info->help_given = 0 ;
42			args_info->version_given = 0 ;
43			args_info->input_given = 0 ;
44			args_info->output_given = 0 ;
45			args_info->sele1_given = 0 ;
46			args_info->sele2_given = 0 ;
47			args_info->order_given = 0 ;
48			args_info->rcorr_given = 0 ;
49			args_info->vcorr_given = 0 ;
50			args_info->dcorr_given = 0 ;
51			args_info->lcorr_given = 0 ;
52			args_info->r_rcorr_given = 0 ;
53			args_info->dynamicProps_group_counter = 0 ;
54			}
55
56			static
57			void clear_args (struct gengetopt_args_info *args_info)
58			{
59			args_info->input_arg = NULL;
60			args_info->input_orig = NULL;
61			args_info->output_arg = NULL;
62			args_info->output_orig = NULL;
63			args_info->sele1_arg = NULL;
64			args_info->sele1_orig = NULL;
65			args_info->sele2_arg = NULL;
66			args_info->sele2_orig = NULL;
67			args_info->order_orig = NULL;
68
69			}
70
71	tim	320	void
72			cmdline_parser_print_version (void)
73			{
74			printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
75			}
76
77			void
78			cmdline_parser_print_help (void)
79			{
80			cmdline_parser_print_version ();
81	chuckv	1098	printf("\nUsage: DynamicProps [OPTIONS]...\n\n");
82			printf("%s\n"," -h, --help Print help and exit");
83			printf("%s\n"," -V, --version Print version and exit");
84			printf("%s\n"," -i, --input=filename input dump file");
85			printf("%s\n"," -o, --output=filename output file name");
86			printf("%s\n"," --sele1=selection script select first stuntdouble set");
87			printf("%s\n"," --sele2=selection script select second stuntdouble set (if sele2 is not \n set, use script from sele1)");
88			printf("%s\n"," --order=INT Lengendre Polynomial Order");
89			printf("%s\n","\n Group: dynamicProps\n an option of this group is required");
90			printf("%s\n"," -r, --rcorr rmsd");
91			printf("%s\n"," -v, --vcorr velocity correlation function");
92			printf("%s\n"," -d, --dcorr dipole correlation function");
93			printf("%s\n"," -l, --lcorr Lengendre correlation function");
94			printf("%s\n"," --r_rcorr Radial rmsd");
95
96	tim	320	}
97
98	chuckv	1098	void
99			cmdline_parser_init (struct gengetopt_args_info *args_info)
100			{
101			clear_given (args_info);
102			clear_args (args_info);
103			}
104	tim	320
105	chuckv	1098	static void
106			cmdline_parser_release (struct gengetopt_args_info *args_info)
107			{
108
109			if (args_info->input_arg)
110			{
111			free (args_info->input_arg); /* free previous argument */
112			args_info->input_arg = 0;
113			}
114			if (args_info->input_orig)
115			{
116			free (args_info->input_orig); /* free previous argument */
117			args_info->input_orig = 0;
118			}
119			if (args_info->output_arg)
120			{
121			free (args_info->output_arg); /* free previous argument */
122			args_info->output_arg = 0;
123			}
124			if (args_info->output_orig)
125			{
126			free (args_info->output_orig); /* free previous argument */
127			args_info->output_orig = 0;
128			}
129			if (args_info->sele1_arg)
130			{
131			free (args_info->sele1_arg); /* free previous argument */
132			args_info->sele1_arg = 0;
133			}
134			if (args_info->sele1_orig)
135			{
136			free (args_info->sele1_orig); /* free previous argument */
137			args_info->sele1_orig = 0;
138			}
139			if (args_info->sele2_arg)
140			{
141			free (args_info->sele2_arg); /* free previous argument */
142			args_info->sele2_arg = 0;
143			}
144			if (args_info->sele2_orig)
145			{
146			free (args_info->sele2_orig); /* free previous argument */
147			args_info->sele2_orig = 0;
148			}
149			if (args_info->order_orig)
150			{
151			free (args_info->order_orig); /* free previous argument */
152			args_info->order_orig = 0;
153			}
154
155			clear_given (args_info);
156			}
157	tim	320
158	chuckv	1098	int
159			cmdline_parser_file_save(const char filename, struct gengetopt_args_info args_info)
160			{
161			FILE *outfile;
162			int i = 0;
163
164			outfile = fopen(filename, "w");
165
166			if (!outfile)
167			{
168			fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
169			return EXIT_FAILURE;
170			}
171
172			if (args_info->help_given) {
173			fprintf(outfile, "%s\n", "help");
174			}
175			if (args_info->version_given) {
176			fprintf(outfile, "%s\n", "version");
177			}
178			if (args_info->input_given) {
179			if (args_info->input_orig) {
180			fprintf(outfile, "%s=\"%s\"\n", "input", args_info->input_orig);
181			} else {
182			fprintf(outfile, "%s\n", "input");
183			}
184			}
185			if (args_info->output_given) {
186			if (args_info->output_orig) {
187			fprintf(outfile, "%s=\"%s\"\n", "output", args_info->output_orig);
188			} else {
189			fprintf(outfile, "%s\n", "output");
190			}
191			}
192			if (args_info->sele1_given) {
193			if (args_info->sele1_orig) {
194			fprintf(outfile, "%s=\"%s\"\n", "sele1", args_info->sele1_orig);
195			} else {
196			fprintf(outfile, "%s\n", "sele1");
197			}
198			}
199			if (args_info->sele2_given) {
200			if (args_info->sele2_orig) {
201			fprintf(outfile, "%s=\"%s\"\n", "sele2", args_info->sele2_orig);
202			} else {
203			fprintf(outfile, "%s\n", "sele2");
204			}
205			}
206			if (args_info->order_given) {
207			if (args_info->order_orig) {
208			fprintf(outfile, "%s=\"%s\"\n", "order", args_info->order_orig);
209			} else {
210			fprintf(outfile, "%s\n", "order");
211			}
212			}
213			if (args_info->rcorr_given) {
214			fprintf(outfile, "%s\n", "rcorr");
215			}
216			if (args_info->vcorr_given) {
217			fprintf(outfile, "%s\n", "vcorr");
218			}
219			if (args_info->dcorr_given) {
220			fprintf(outfile, "%s\n", "dcorr");
221			}
222			if (args_info->lcorr_given) {
223			fprintf(outfile, "%s\n", "lcorr");
224			}
225			if (args_info->r_rcorr_given) {
226			fprintf(outfile, "%s\n", "r_rcorr");
227			}
228
229			fclose (outfile);
230
231			i = EXIT_SUCCESS;
232			return i;
233			}
234
235			void
236			cmdline_parser_free (struct gengetopt_args_info *args_info)
237			{
238			cmdline_parser_release (args_info);
239			}
240
241
242	tim	320	/* gengetopt_strdup() */
243			/* strdup.c replacement of strdup, which is not standard */
244			char *
245			gengetopt_strdup (const char *s)
246			{
247	chuckv	1098	char *result = NULL;
248			if (!s)
249			return result;
250
251			result = (char*)malloc(strlen(s) + 1);
252	tim	320	if (result == (char*)0)
253			return (char*)0;
254			strcpy(result, s);
255			return result;
256			}
257
258	chuckv	1098	static void
259			reset_group_dynamicProps(struct gengetopt_args_info *args_info);
260
261			static void
262			reset_group_dynamicProps(struct gengetopt_args_info *args_info)
263	tim	320	{
264	chuckv	1098	if (! args_info->dynamicProps_group_counter)
265			return;
266	tim	320
267			args_info->rcorr_given = 0 ;
268			args_info->vcorr_given = 0 ;
269			args_info->dcorr_given = 0 ;
270	tim	876	args_info->lcorr_given = 0 ;
271	chuckv	1098	args_info->r_rcorr_given = 0 ;
272
273			args_info->dynamicProps_group_counter = 0;
274	tim	876	}
275	tim	320
276	chuckv	1098	int
277			cmdline_parser (int argc, char * const argv, struct gengetopt_args_info args_info)
278			{
279			return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
280			}
281	tim	320
282	chuckv	1098	int
283			cmdline_parser2 (int argc, char * const argv, struct gengetopt_args_info args_info, int override, int initialize, int check_required)
284			{
285			int result;
286
287			result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
288
289			if (result == EXIT_FAILURE)
290			{
291			cmdline_parser_free (args_info);
292			exit (EXIT_FAILURE);
293			}
294
295			return result;
296			}
297
298			int
299			cmdline_parser_required (struct gengetopt_args_info args_info, const char prog_name)
300			{
301			int result = EXIT_SUCCESS;
302
303			if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
304			result = EXIT_FAILURE;
305
306			if (result == EXIT_FAILURE)
307			{
308			cmdline_parser_free (args_info);
309			exit (EXIT_FAILURE);
310			}
311
312			return result;
313			}
314
315			int
316			cmdline_parser_required2 (struct gengetopt_args_info args_info, const char prog_name, const char *additional_error)
317			{
318			int error = 0;
319
320			if (! args_info->input_given)
321			{
322			fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
323			error = 1;
324			}
325			if (args_info->dynamicProps_group_counter == 0)
326			{
327			fprintf (stderr, "%s: %d options of group dynamicProps were given. One is required.%s\n", prog_name, args_info->dynamicProps_group_counter, (additional_error ? additional_error : ""));
328			error = 1;
329			}
330
331
332			return error;
333			}
334
335			int
336			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)
337			{
338			int c; /* Character of the parsed option. */
339
340			int error = 0;
341			struct gengetopt_args_info local_args_info;
342
343			if (initialize)
344			cmdline_parser_init (args_info);
345
346			cmdline_parser_init (&local_args_info);
347
348	tim	320	optarg = 0;
349			optind = 1;
350			opterr = 1;
351			optopt = '?';
352
353			while (1)
354			{
355			int option_index = 0;
356			char *stop_char;
357
358			static struct option long_options[] = {
359			{ "help", 0, NULL, 'h' },
360			{ "version", 0, NULL, 'V' },
361			{ "input", 1, NULL, 'i' },
362			{ "output", 1, NULL, 'o' },
363			{ "sele1", 1, NULL, 0 },
364			{ "sele2", 1, NULL, 0 },
365	tim	876	{ "order", 1, NULL, 0 },
366	tim	320	{ "rcorr", 0, NULL, 'r' },
367			{ "vcorr", 0, NULL, 'v' },
368			{ "dcorr", 0, NULL, 'd' },
369	tim	876	{ "lcorr", 0, NULL, 'l' },
370	chuckv	1098	{ "r_rcorr", 0, NULL, 0 },
371	tim	320	{ NULL, 0, NULL, 0 }
372			};
373
374			stop_char = 0;
375	tim	917	c = getopt_long (argc, argv, "hVi:o:rvdl", long_options, &option_index);
376	tim	320
377			if (c == -1) break; /* Exit from `while (1)' loop. */
378
379			switch (c)
380			{
381			case 'h': /* Print help and exit. */
382			cmdline_parser_print_help ();
383	chuckv	1098	cmdline_parser_free (&local_args_info);
384	tim	320	exit (EXIT_SUCCESS);
385
386			case 'V': /* Print version and exit. */
387			cmdline_parser_print_version ();
388	chuckv	1098	cmdline_parser_free (&local_args_info);
389	tim	320	exit (EXIT_SUCCESS);
390
391			case 'i': /* input dump file. */
392	chuckv	1098	if (local_args_info.input_given)
393	tim	320	{
394	chuckv	1098	fprintf (stderr, "%s: `--input' (`-i') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
395			goto failure;
396	tim	320	}
397	chuckv	1098	if (args_info->input_given && ! override)
398			continue;
399			local_args_info.input_given = 1;
400	tim	320	args_info->input_given = 1;
401	chuckv	1098	if (args_info->input_arg)
402			free (args_info->input_arg); /* free previous string */
403	tim	320	args_info->input_arg = gengetopt_strdup (optarg);
404	chuckv	1098	if (args_info->input_orig)
405			free (args_info->input_orig); /* free previous string */
406			args_info->input_orig = gengetopt_strdup (optarg);
407	tim	320	break;
408
409			case 'o': /* output file name. */
410	chuckv	1098	if (local_args_info.output_given)
411	tim	320	{
412	chuckv	1098	fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
413			goto failure;
414	tim	320	}
415	chuckv	1098	if (args_info->output_given && ! override)
416			continue;
417			local_args_info.output_given = 1;
418	tim	320	args_info->output_given = 1;
419	chuckv	1098	if (args_info->output_arg)
420			free (args_info->output_arg); /* free previous string */
421	tim	320	args_info->output_arg = gengetopt_strdup (optarg);
422	chuckv	1098	if (args_info->output_orig)
423			free (args_info->output_orig); /* free previous string */
424			args_info->output_orig = gengetopt_strdup (optarg);
425	tim	320	break;
426
427	tim	917	case 'r': /* rmsd. */
428	chuckv	1098	if (local_args_info.rcorr_given)
429	tim	320	{
430	chuckv	1098	fprintf (stderr, "%s: `--rcorr' (`-r') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
431			goto failure;
432	tim	320	}
433	chuckv	1098	if (args_info->rcorr_given && ! override)
434			continue;
435			local_args_info.rcorr_given = 1;
436	tim	320	args_info->rcorr_given = 1;
437	chuckv	1098	if (args_info->dynamicProps_group_counter && override)
438			reset_group_dynamicProps (args_info);
439			args_info->dynamicProps_group_counter += 1;
440			break;
441	tim	320
442			case 'v': /* velocity correlation function. */
443	chuckv	1098	if (local_args_info.vcorr_given)
444	tim	320	{
445	chuckv	1098	fprintf (stderr, "%s: `--vcorr' (`-v') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
446			goto failure;
447	tim	320	}
448	chuckv	1098	if (args_info->vcorr_given && ! override)
449			continue;
450			local_args_info.vcorr_given = 1;
451	tim	320	args_info->vcorr_given = 1;
452	chuckv	1098	if (args_info->dynamicProps_group_counter && override)
453			reset_group_dynamicProps (args_info);
454			args_info->dynamicProps_group_counter += 1;
455			break;
456	tim	320
457			case 'd': /* dipole correlation function. */
458	chuckv	1098	if (local_args_info.dcorr_given)
459	tim	320	{
460	chuckv	1098	fprintf (stderr, "%s: `--dcorr' (`-d') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
461			goto failure;
462	tim	320	}
463	chuckv	1098	if (args_info->dcorr_given && ! override)
464			continue;
465			local_args_info.dcorr_given = 1;
466	tim	320	args_info->dcorr_given = 1;
467	chuckv	1098	if (args_info->dynamicProps_group_counter && override)
468			reset_group_dynamicProps (args_info);
469			args_info->dynamicProps_group_counter += 1;
470			break;
471	tim	320
472	tim	876	case 'l': /* Lengendre correlation function. */
473	chuckv	1098	if (local_args_info.lcorr_given)
474	tim	876	{
475	chuckv	1098	fprintf (stderr, "%s: `--lcorr' (`-l') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
476			goto failure;
477	tim	876	}
478	chuckv	1098	if (args_info->lcorr_given && ! override)
479			continue;
480			local_args_info.lcorr_given = 1;
481	tim	876	args_info->lcorr_given = 1;
482	chuckv	1098	if (args_info->dynamicProps_group_counter && override)
483			reset_group_dynamicProps (args_info);
484			args_info->dynamicProps_group_counter += 1;
485			break;
486	tim	320
487	tim	876
488	tim	320	case 0: /* Long option with no short option */
489			/* select first stuntdouble set. */
490			if (strcmp (long_options[option_index].name, "sele1") == 0)
491	tim	876	{
492	chuckv	1098	if (local_args_info.sele1_given)
493	tim	876	{
494	chuckv	1098	fprintf (stderr, "%s: `--sele1' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
495			goto failure;
496	tim	876	}
497	chuckv	1098	if (args_info->sele1_given && ! override)
498			continue;
499			local_args_info.sele1_given = 1;
500	tim	876	args_info->sele1_given = 1;
501	chuckv	1098	if (args_info->sele1_arg)
502			free (args_info->sele1_arg); /* free previous string */
503	tim	876	args_info->sele1_arg = gengetopt_strdup (optarg);
504	chuckv	1098	if (args_info->sele1_orig)
505			free (args_info->sele1_orig); /* free previous string */
506			args_info->sele1_orig = gengetopt_strdup (optarg);
507	tim	876	}
508	tim	320	/* select second stuntdouble set (if sele2 is not set, use script from sele1). */
509			else if (strcmp (long_options[option_index].name, "sele2") == 0)
510	tim	876	{
511	chuckv	1098	if (local_args_info.sele2_given)
512	tim	876	{
513	chuckv	1098	fprintf (stderr, "%s: `--sele2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
514			goto failure;
515	tim	876	}
516	chuckv	1098	if (args_info->sele2_given && ! override)
517			continue;
518			local_args_info.sele2_given = 1;
519	tim	876	args_info->sele2_given = 1;
520	chuckv	1098	if (args_info->sele2_arg)
521			free (args_info->sele2_arg); /* free previous string */
522	tim	876	args_info->sele2_arg = gengetopt_strdup (optarg);
523	chuckv	1098	if (args_info->sele2_orig)
524			free (args_info->sele2_orig); /* free previous string */
525			args_info->sele2_orig = gengetopt_strdup (optarg);
526	tim	876	}
527			/* Lengendre Polynomial Order. */
528			else if (strcmp (long_options[option_index].name, "order") == 0)
529			{
530	chuckv	1098	if (local_args_info.order_given)
531	tim	876	{
532	chuckv	1098	fprintf (stderr, "%s: `--order' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
533			goto failure;
534	tim	876	}
535	chuckv	1098	if (args_info->order_given && ! override)
536			continue;
537			local_args_info.order_given = 1;
538	tim	876	args_info->order_given = 1;
539	chuckv	1098	args_info->order_arg = strtol (optarg, &stop_char, 0);
540			if (!(stop_char && *stop_char == '\0')) {
541			fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
542			goto failure;
543			}
544			if (args_info->order_orig)
545			free (args_info->order_orig); /* free previous string */
546			args_info->order_orig = gengetopt_strdup (optarg);
547			}
548			/* Radial rmsd. */
549			else if (strcmp (long_options[option_index].name, "r_rcorr") == 0)
550			{
551			if (local_args_info.r_rcorr_given)
552			{
553			fprintf (stderr, "%s: `--r_rcorr' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
554			goto failure;
555			}
556			if (args_info->r_rcorr_given && ! override)
557			continue;
558			local_args_info.r_rcorr_given = 1;
559			args_info->r_rcorr_given = 1;
560			if (args_info->dynamicProps_group_counter && override)
561			reset_group_dynamicProps (args_info);
562			args_info->dynamicProps_group_counter += 1;
563	tim	876	break;
564			}
565
566	chuckv	1098	break;
567	tim	320	case '?': /* Invalid option. */
568			/* `getopt_long' already printed an error message. */
569	chuckv	1098	goto failure;
570	tim	320
571			default: /* bug: option not considered. */
572	chuckv	1098	fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
573	tim	320	abort ();
574			} /* switch */
575			} /* while */
576
577	chuckv	1098	if (args_info->dynamicProps_group_counter > 1)
578	tim	320	{
579	chuckv	1098	fprintf (stderr, "%s: %d options of group dynamicProps were given. One is required.%s\n", argv[0], args_info->dynamicProps_group_counter, (additional_error ? additional_error : ""));
580			error = 1;
581	tim	320	}
582
583
584	chuckv	1098
585			if (check_required)
586	tim	320	{
587	chuckv	1098	error += cmdline_parser_required2 (args_info, argv[0], additional_error);
588	tim	320	}
589
590	chuckv	1098	cmdline_parser_release (&local_args_info);
591
592			if ( error )
593			return (EXIT_FAILURE);
594
595	tim	320	return 0;
596	chuckv	1098
597			failure:
598
599			cmdline_parser_release (&local_args_info);
600			return (EXIT_FAILURE);
601	tim	320	}