applications/nanoparticleBuilder/nanoparticleBuilderCmd.c

/*
  File autogenerated by gengetopt version 2.13
  generated with the following command:
  gengetopt -u -F nanoparticleBuilderCmd 

  The developers of gengetopt consider the fixed text that goes in all
  gengetopt output files to be in the public domain:
  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 "nanoparticleBuilderCmd.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);

struct ShellRadius_list
{
  double ShellRadius_arg;
  struct ShellRadius_list * next;
};

struct molFraction_list
{
  double molFraction_arg;
  struct molFraction_list * next;
};

struct vacancyRadius_list
{
  double vacancyRadius_arg;
  struct vacancyRadius_list * next;
};

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->output_given = 0 ;
  args_info->latticetype_given = 0 ;
  args_info->latticeCnst_given = 0 ;
  args_info->radius_given = 0 ;
  args_info->ShellRadius_given = 0 ;
  args_info->molFraction_given = 0 ;
  args_info->vacancyPCT_given = 0 ;
  args_info->vacancyRadius_given = 0 ;
}

static
void clear_args (struct gengetopt_args_info *args_info)
{
  args_info->output_arg = NULL;
  args_info->latticetype_arg = gengetopt_strdup ("fcc");
  args_info->ShellRadius_arg = NULL;
  args_info->molFraction_arg = NULL;
  args_info->vacancyRadius_arg = 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("\n%s\n", "Builds spherical random or core-shell nanoparticles and outputs a xyz input \nfile");
  printf("\nUsage: nanoparticleBuilder [OPTIONS]... [FILES]...\n\n");
  printf("%s\n","  -h, --help                  Print help and exit");
  printf("%s\n","  -V, --version               Print version and exit");
  printf("%s\n","  -o, --output=STRING         Output file name");
  printf("%s\n","      --latticetype=STRING    Lattice type string. Valid types are fcc,hcp,bcc. \n                                 (default=`fcc')");
  printf("%s\n","      --latticeCnst=DOUBLE    Lattice spacing in Angstroms for cubic lattice.");
  printf("%s\n","      --radius=DOUBLE         Nanoparticle radius in Angstroms");
  printf("%s\n","      --ShellRadius=DOUBLE    Radius from the center of the particle to start a \n                                new shell in multi-component core-shell \n                                particle. Specified for each component > 1 in \n                                md file.");
  printf("%s\n","      --molFraction=DOUBLE    (Default) Builds a multi-component random mixed \n                                nanoparticle. Mole Fraction must be specified \n                                for each componet > 1 in MD file.");
  printf("%s\n","      --vacancyPCT=DOUBLE     Percentage of vacancies to build");
  printf("%s\n","      --vacancyRadius=DOUBLE  Radius arround core-shell where vacancies should \n                                be located.");
  
}

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

  args_info->inputs = NULL;
  args_info->inputs_num = 0;
}

void
cmdline_parser_free (struct gengetopt_args_info *args_info)
{
  
  unsigned int i;
  if (args_info->output_arg)
    {
      free (args_info->output_arg); /* free previous argument */
      args_info->output_arg = 0;
    }
  if (args_info->latticetype_arg)
    {
      free (args_info->latticetype_arg); /* free previous argument */
      args_info->latticetype_arg = 0;
    }
  if (args_info->ShellRadius_arg)
    {
      free (args_info->ShellRadius_arg); /* free previous argument */
      args_info->ShellRadius_arg = 0;
    }
  if (args_info->molFraction_arg)
    {
      free (args_info->molFraction_arg); /* free previous argument */
      args_info->molFraction_arg = 0;
    }
  if (args_info->vacancyRadius_arg)
    {
      free (args_info->vacancyRadius_arg); /* free previous argument */
      args_info->vacancyRadius_arg = 0;
    }
  
  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);
}

/* 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 char *
get_multiple_arg_token(const char *arg)
{
  char *tok, *ret;
  size_t len;

  if (!arg)
    return NULL;

  tok = strchr (arg, ',');

  if (tok)
    len = (size_t)(tok - arg + 1);
  else
    len = strlen (arg) + 1;

  ret = (char *) malloc (len);
  strncpy (ret, arg, len-1);
  ret[len-1] = '\0';

  return ret;
}

static char *
get_multiple_arg_token_next(const char *arg)
{
  char *tok;

  if (!arg)
    return NULL;

  tok = strchr (arg, ',');

  if (! tok || strlen(tok) == 1)
    return 0;

  return tok+1;
}

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->latticeCnst_given)
    {
      fprintf (stderr, "%s: '--latticeCnst' option required%s\n", prog_name, (additional_error ? additional_error : ""));
      error = 1;
    }
  if (! args_info->radius_given)
    {
      fprintf (stderr, "%s: '--radius' option required%s\n", prog_name, (additional_error ? additional_error : ""));
      error = 1;
    }

  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.  */
  char *multi_token, *multi_next; /* for multiple options */

  int i;        /* Counter */

  struct ShellRadius_list * ShellRadius_list = NULL,* ShellRadius_new = NULL;
  struct molFraction_list * molFraction_list = NULL,* molFraction_new = NULL;
  struct vacancyRadius_list * vacancyRadius_list = NULL,* vacancyRadius_new = NULL;
  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' },
        { "output",     1, NULL, 'o' },
        { "latticetype",        1, NULL, 0 },
        { "latticeCnst",        1, NULL, 0 },
        { "radius",     1, NULL, 0 },
        { "ShellRadius",        1, NULL, 0 },
        { "molFraction",        1, NULL, 0 },
        { "vacancyPCT", 1, NULL, 0 },
        { "vacancyRadius",      1, NULL, 0 },
        { NULL, 0, NULL, 0 }
      };

      stop_char = 0;
      c = getopt_long (argc, argv, "hVo:", long_options, &option_index);

      if (c == -1) break;       /* Exit from `while (1)' loop.  */

      switch (c)
        {
        case 'h':       /* Print help and exit.  */
          cmdline_parser_print_help ();
          exit (EXIT_SUCCESS);

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

        case 'o':       /* Output file name.  */
          if (local_args_info.output_given)
            {
              fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->output_given && ! override)
            continue;
          local_args_info.output_given = 1;
          args_info->output_given = 1;
          if (args_info->output_arg)
            free (args_info->output_arg); /* free previous string */
          args_info->output_arg = gengetopt_strdup (optarg);
          break;


        case 0: /* Long option with no short option */
          /* Lattice type string. Valid types are fcc,hcp,bcc..  */
          if (strcmp (long_options[option_index].name, "latticetype") == 0)
          {
            if (local_args_info.latticetype_given)
              {
                fprintf (stderr, "%s: `--latticetype' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->latticetype_given && ! override)
              continue;
            local_args_info.latticetype_given = 1;
            args_info->latticetype_given = 1;
            if (args_info->latticetype_arg)
              free (args_info->latticetype_arg); /* free previous string */
            args_info->latticetype_arg = gengetopt_strdup (optarg);
          }
          /* Lattice spacing in Angstroms for cubic lattice..  */
          else if (strcmp (long_options[option_index].name, "latticeCnst") == 0)
          {
            if (local_args_info.latticeCnst_given)
              {
                fprintf (stderr, "%s: `--latticeCnst' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->latticeCnst_given && ! override)
              continue;
            local_args_info.latticeCnst_given = 1;
            args_info->latticeCnst_given = 1;
            args_info->latticeCnst_arg = strtod (optarg, NULL);
          }
          /* Nanoparticle radius in Angstroms.  */
          else if (strcmp (long_options[option_index].name, "radius") == 0)
          {
            if (local_args_info.radius_given)
              {
                fprintf (stderr, "%s: `--radius' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->radius_given && ! override)
              continue;
            local_args_info.radius_given = 1;
            args_info->radius_given = 1;
            args_info->radius_arg = strtod (optarg, NULL);
          }
          /* Radius from the center of the particle to start a new shell in multi-component core-shell particle. Specified for each component > 1 in md file..  */
          else if (strcmp (long_options[option_index].name, "ShellRadius") == 0)
          {
            local_args_info.ShellRadius_given++;
          
            multi_token = get_multiple_arg_token(optarg);
            multi_next = get_multiple_arg_token_next (optarg);
          
            while (1)
              {
                ShellRadius_new = (struct ShellRadius_list *) malloc (sizeof (struct ShellRadius_list));
                ShellRadius_new->next = ShellRadius_list;
                ShellRadius_list = ShellRadius_new;
                ShellRadius_new->ShellRadius_arg = strtod (multi_token, NULL);
                free (multi_token);
          
                if (multi_next)
                  {
                    multi_token = get_multiple_arg_token(multi_next);
                    multi_next = get_multiple_arg_token_next (multi_next);
                    local_args_info.ShellRadius_given++;
                  }
                else
                  break;
              }
            break;
          }
          /* (Default) Builds a multi-component random mixed nanoparticle. Mole Fraction must be specified for each componet > 1 in MD file..  */
          else if (strcmp (long_options[option_index].name, "molFraction") == 0)
          {
            local_args_info.molFraction_given++;
          
            multi_token = get_multiple_arg_token(optarg);
            multi_next = get_multiple_arg_token_next (optarg);
          
            while (1)
              {
                molFraction_new = (struct molFraction_list *) malloc (sizeof (struct molFraction_list));
                molFraction_new->next = molFraction_list;
                molFraction_list = molFraction_new;
                molFraction_new->molFraction_arg = strtod (multi_token, NULL);
                free (multi_token);
          
                if (multi_next)
                  {
                    multi_token = get_multiple_arg_token(multi_next);
                    multi_next = get_multiple_arg_token_next (multi_next);
                    local_args_info.molFraction_given++;
                  }
                else
                  break;
              }
            break;
          }
          /* Percentage of vacancies to build.  */
          else if (strcmp (long_options[option_index].name, "vacancyPCT") == 0)
          {
            if (local_args_info.vacancyPCT_given)
              {
                fprintf (stderr, "%s: `--vacancyPCT' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->vacancyPCT_given && ! override)
              continue;
            local_args_info.vacancyPCT_given = 1;
            args_info->vacancyPCT_given = 1;
            args_info->vacancyPCT_arg = strtod (optarg, NULL);
          }
          /* Radius arround core-shell where vacancies should be located..  */
          else if (strcmp (long_options[option_index].name, "vacancyRadius") == 0)
          {
            local_args_info.vacancyRadius_given++;
          
            multi_token = get_multiple_arg_token(optarg);
            multi_next = get_multiple_arg_token_next (optarg);
          
            while (1)
              {
                vacancyRadius_new = (struct vacancyRadius_list *) malloc (sizeof (struct vacancyRadius_list));
                vacancyRadius_new->next = vacancyRadius_list;
                vacancyRadius_list = vacancyRadius_new;
                vacancyRadius_new->vacancyRadius_arg = strtod (multi_token, NULL);
                free (multi_token);
          
                if (multi_next)
                  {
                    multi_token = get_multiple_arg_token(multi_next);
                    multi_next = get_multiple_arg_token_next (multi_next);
                    local_args_info.vacancyRadius_given++;
                  }
                else
                  break;
              }
            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 (local_args_info.ShellRadius_given && ShellRadius_list)
    {
      struct ShellRadius_list *tmp;
      args_info->ShellRadius_arg = (double *) realloc (args_info->ShellRadius_arg, (args_info->ShellRadius_given + local_args_info.ShellRadius_given) * sizeof (double));
      for (i = (local_args_info.ShellRadius_given - 1); i >= 0; --i)
        {
          tmp = ShellRadius_list;
          args_info->ShellRadius_arg [i + args_info->ShellRadius_given] = ShellRadius_list->ShellRadius_arg;
          ShellRadius_list = ShellRadius_list->next;
          free (tmp);
        }
    }
  
  if (local_args_info.molFraction_given && molFraction_list)
    {
      struct molFraction_list *tmp;
      args_info->molFraction_arg = (double *) realloc (args_info->molFraction_arg, (args_info->molFraction_given + local_args_info.molFraction_given) * sizeof (double));
      for (i = (local_args_info.molFraction_given - 1); i >= 0; --i)
        {
          tmp = molFraction_list;
          args_info->molFraction_arg [i + args_info->molFraction_given] = molFraction_list->molFraction_arg;
          molFraction_list = molFraction_list->next;
          free (tmp);
        }
    }
  
  if (local_args_info.vacancyRadius_given && vacancyRadius_list)
    {
      struct vacancyRadius_list *tmp;
      args_info->vacancyRadius_arg = (double *) realloc (args_info->vacancyRadius_arg, (args_info->vacancyRadius_given + local_args_info.vacancyRadius_given) * sizeof (double));
      for (i = (local_args_info.vacancyRadius_given - 1); i >= 0; --i)
        {
          tmp = vacancyRadius_list;
          args_info->vacancyRadius_arg [i + args_info->vacancyRadius_given] = vacancyRadius_list->vacancyRadius_arg;
          vacancyRadius_list = vacancyRadius_list->next;
          free (tmp);
        }
    }
  

  args_info->ShellRadius_given += local_args_info.ShellRadius_given;
  local_args_info.ShellRadius_given = 0;
  args_info->molFraction_given += local_args_info.molFraction_given;
  local_args_info.molFraction_given = 0;
  args_info->vacancyRadius_given += local_args_info.vacancyRadius_given;
  local_args_info.vacancyRadius_given = 0;
  
  if (check_required)
    {
      error += cmdline_parser_required2 (args_info, argv[0], additional_error);
    }

  cmdline_parser_free (&local_args_info);

  if ( error )
    return (EXIT_FAILURE);

  if (optind < argc)
    {
      int i = 0 ;

      args_info->inputs_num = argc - optind ;
      args_info->inputs =
        (char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
      while (optind < argc)
        args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind++]) ;
    }

  return 0;

failure:
  if (ShellRadius_list)
    {
      struct ShellRadius_list *tmp;
      while (ShellRadius_list)
        {
          tmp = ShellRadius_list;
          ShellRadius_list = ShellRadius_list->next;
          free (tmp);
        }
    }
  if (molFraction_list)
    {
      struct molFraction_list *tmp;
      while (molFraction_list)
        {
          tmp = molFraction_list;
          molFraction_list = molFraction_list->next;
          free (tmp);
        }
    }
  if (vacancyRadius_list)
    {
      struct vacancyRadius_list *tmp;
      while (vacancyRadius_list)
        {
          tmp = vacancyRadius_list;
          vacancyRadius_list = vacancyRadius_list->next;
          free (tmp);
        }
    }
  
  cmdline_parser_free (&local_args_info);
  return (EXIT_FAILURE);
}
Revision:	2352
Committed:	Tue Oct 11 21:57:22 2005 UTC (18 years, 9 months ago) by chuckv
Content type:	text/plain
File size:	19606 byte(s)
Log Message:	Added code for nanoparticle builder to cvs.
#	User	Rev	Content
1	chuckv	2352	/*
2			File autogenerated by gengetopt version 2.13
3			generated with the following command:
4			gengetopt -u -F nanoparticleBuilderCmd
5
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			/* If we use autoconf. */
12			#ifdef HAVE_CONFIG_H
13			#include "config.h"
14			#endif
15
16			#include <stdio.h>
17			#include <stdlib.h>
18			#include <string.h>
19
20			#include "getopt.h"
21
22			#include "nanoparticleBuilderCmd.h"
23
24			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			struct ShellRadius_list
36			{
37			double ShellRadius_arg;
38			struct ShellRadius_list * next;
39			};
40
41			struct molFraction_list
42			{
43			double molFraction_arg;
44			struct molFraction_list * next;
45			};
46
47			struct vacancyRadius_list
48			{
49			double vacancyRadius_arg;
50			struct vacancyRadius_list * next;
51			};
52
53			static char *
54			gengetopt_strdup (const char *s);
55
56			static
57			void clear_given (struct gengetopt_args_info *args_info)
58			{
59			args_info->help_given = 0 ;
60			args_info->version_given = 0 ;
61			args_info->output_given = 0 ;
62			args_info->latticetype_given = 0 ;
63			args_info->latticeCnst_given = 0 ;
64			args_info->radius_given = 0 ;
65			args_info->ShellRadius_given = 0 ;
66			args_info->molFraction_given = 0 ;
67			args_info->vacancyPCT_given = 0 ;
68			args_info->vacancyRadius_given = 0 ;
69			}
70
71			static
72			void clear_args (struct gengetopt_args_info *args_info)
73			{
74			args_info->output_arg = NULL;
75			args_info->latticetype_arg = gengetopt_strdup ("fcc");
76			args_info->ShellRadius_arg = NULL;
77			args_info->molFraction_arg = NULL;
78			args_info->vacancyRadius_arg = NULL;
79			}
80
81			void
82			cmdline_parser_print_version (void)
83			{
84			printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
85			}
86
87			void
88			cmdline_parser_print_help (void)
89			{
90			cmdline_parser_print_version ();
91			printf("\n%s\n", "Builds spherical random or core-shell nanoparticles and outputs a xyz input \nfile");
92			printf("\nUsage: nanoparticleBuilder [OPTIONS]... [FILES]...\n\n");
93			printf("%s\n"," -h, --help Print help and exit");
94			printf("%s\n"," -V, --version Print version and exit");
95			printf("%s\n"," -o, --output=STRING Output file name");
96			printf("%s\n"," --latticetype=STRING Lattice type string. Valid types are fcc,hcp,bcc. \n (default=`fcc')");
97			printf("%s\n"," --latticeCnst=DOUBLE Lattice spacing in Angstroms for cubic lattice.");
98			printf("%s\n"," --radius=DOUBLE Nanoparticle radius in Angstroms");
99			printf("%s\n"," --ShellRadius=DOUBLE Radius from the center of the particle to start a \n new shell in multi-component core-shell \n particle. Specified for each component > 1 in \n md file.");
100			printf("%s\n"," --molFraction=DOUBLE (Default) Builds a multi-component random mixed \n nanoparticle. Mole Fraction must be specified \n for each componet > 1 in MD file.");
101			printf("%s\n"," --vacancyPCT=DOUBLE Percentage of vacancies to build");
102			printf("%s\n"," --vacancyRadius=DOUBLE Radius arround core-shell where vacancies should \n be located.");
103
104			}
105
106			void
107			cmdline_parser_init (struct gengetopt_args_info *args_info)
108			{
109			clear_given (args_info);
110			clear_args (args_info);
111
112			args_info->inputs = NULL;
113			args_info->inputs_num = 0;
114			}
115
116			void
117			cmdline_parser_free (struct gengetopt_args_info *args_info)
118			{
119
120			unsigned int i;
121			if (args_info->output_arg)
122			{
123			free (args_info->output_arg); /* free previous argument */
124			args_info->output_arg = 0;
125			}
126			if (args_info->latticetype_arg)
127			{
128			free (args_info->latticetype_arg); /* free previous argument */
129			args_info->latticetype_arg = 0;
130			}
131			if (args_info->ShellRadius_arg)
132			{
133			free (args_info->ShellRadius_arg); /* free previous argument */
134			args_info->ShellRadius_arg = 0;
135			}
136			if (args_info->molFraction_arg)
137			{
138			free (args_info->molFraction_arg); /* free previous argument */
139			args_info->molFraction_arg = 0;
140			}
141			if (args_info->vacancyRadius_arg)
142			{
143			free (args_info->vacancyRadius_arg); /* free previous argument */
144			args_info->vacancyRadius_arg = 0;
145			}
146
147			for (i = 0; i < args_info->inputs_num; ++i)
148			free (args_info->inputs [i]);
149
150			if (args_info->inputs_num)
151			free (args_info->inputs);
152
153			clear_given (args_info);
154			}
155
156			/* gengetopt_strdup() */
157			/* strdup.c replacement of strdup, which is not standard */
158			char *
159			gengetopt_strdup (const char *s)
160			{
161			char *result = NULL;
162			if (!s)
163			return result;
164
165			result = (char*)malloc(strlen(s) + 1);
166			if (result == (char*)0)
167			return (char*)0;
168			strcpy(result, s);
169			return result;
170			}
171
172			static char *
173			get_multiple_arg_token(const char *arg)
174			{
175			char tok, ret;
176			size_t len;
177
178			if (!arg)
179			return NULL;
180
181			tok = strchr (arg, ',');
182
183			if (tok)
184			len = (size_t)(tok - arg + 1);
185			else
186			len = strlen (arg) + 1;
187
188			ret = (char *) malloc (len);
189			strncpy (ret, arg, len-1);
190			ret[len-1] = '\0';
191
192			return ret;
193			}
194
195			static char *
196			get_multiple_arg_token_next(const char *arg)
197			{
198			char *tok;
199
200			if (!arg)
201			return NULL;
202
203			tok = strchr (arg, ',');
204
205			if (! tok \|\| strlen(tok) == 1)
206			return 0;
207
208			return tok+1;
209			}
210
211			int
212			cmdline_parser (int argc, char * const argv, struct gengetopt_args_info args_info)
213			{
214			return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
215			}
216
217			int
218			cmdline_parser2 (int argc, char * const argv, struct gengetopt_args_info args_info, int override, int initialize, int check_required)
219			{
220			int result;
221
222			result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
223
224			if (result == EXIT_FAILURE)
225			{
226			cmdline_parser_free (args_info);
227			exit (EXIT_FAILURE);
228			}
229
230			return result;
231			}
232
233			int
234			cmdline_parser_required (struct gengetopt_args_info args_info, const char prog_name)
235			{
236			int result = EXIT_SUCCESS;
237
238			if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
239			result = EXIT_FAILURE;
240
241			if (result == EXIT_FAILURE)
242			{
243			cmdline_parser_free (args_info);
244			exit (EXIT_FAILURE);
245			}
246
247			return result;
248			}
249
250			int
251			cmdline_parser_required2 (struct gengetopt_args_info args_info, const char prog_name, const char *additional_error)
252			{
253			int error = 0;
254
255			if (! args_info->latticeCnst_given)
256			{
257			fprintf (stderr, "%s: '--latticeCnst' option required%s\n", prog_name, (additional_error ? additional_error : ""));
258			error = 1;
259			}
260			if (! args_info->radius_given)
261			{
262			fprintf (stderr, "%s: '--radius' option required%s\n", prog_name, (additional_error ? additional_error : ""));
263			error = 1;
264			}
265
266			return error;
267			}
268
269			int
270			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)
271			{
272			int c; /* Character of the parsed option. */
273			char multi_token, multi_next; /* for multiple options */
274
275			int i; /* Counter */
276
277			struct ShellRadius_list * ShellRadius_list = NULL,* ShellRadius_new = NULL;
278			struct molFraction_list * molFraction_list = NULL,* molFraction_new = NULL;
279			struct vacancyRadius_list * vacancyRadius_list = NULL,* vacancyRadius_new = NULL;
280			int error = 0;
281			struct gengetopt_args_info local_args_info;
282
283			if (initialize)
284			cmdline_parser_init (args_info);
285
286			cmdline_parser_init (&local_args_info);
287
288			optarg = 0;
289			optind = 1;
290			opterr = 1;
291			optopt = '?';
292
293			while (1)
294			{
295			int option_index = 0;
296			char *stop_char;
297
298			static struct option long_options[] = {
299			{ "help", 0, NULL, 'h' },
300			{ "version", 0, NULL, 'V' },
301			{ "output", 1, NULL, 'o' },
302			{ "latticetype", 1, NULL, 0 },
303			{ "latticeCnst", 1, NULL, 0 },
304			{ "radius", 1, NULL, 0 },
305			{ "ShellRadius", 1, NULL, 0 },
306			{ "molFraction", 1, NULL, 0 },
307			{ "vacancyPCT", 1, NULL, 0 },
308			{ "vacancyRadius", 1, NULL, 0 },
309			{ NULL, 0, NULL, 0 }
310			};
311
312			stop_char = 0;
313			c = getopt_long (argc, argv, "hVo:", long_options, &option_index);
314
315			if (c == -1) break; /* Exit from `while (1)' loop. */
316
317			switch (c)
318			{
319			case 'h': /* Print help and exit. */
320			cmdline_parser_print_help ();
321			exit (EXIT_SUCCESS);
322
323			case 'V': /* Print version and exit. */
324			cmdline_parser_print_version ();
325			exit (EXIT_SUCCESS);
326
327			case 'o': /* Output file name. */
328			if (local_args_info.output_given)
329			{
330			fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
331			goto failure;
332			}
333			if (args_info->output_given && ! override)
334			continue;
335			local_args_info.output_given = 1;
336			args_info->output_given = 1;
337			if (args_info->output_arg)
338			free (args_info->output_arg); /* free previous string */
339			args_info->output_arg = gengetopt_strdup (optarg);
340			break;
341
342
343			case 0: /* Long option with no short option */
344			/* Lattice type string. Valid types are fcc,hcp,bcc.. */
345			if (strcmp (long_options[option_index].name, "latticetype") == 0)
346			{
347			if (local_args_info.latticetype_given)
348			{
349			fprintf (stderr, "%s: `--latticetype' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
350			goto failure;
351			}
352			if (args_info->latticetype_given && ! override)
353			continue;
354			local_args_info.latticetype_given = 1;
355			args_info->latticetype_given = 1;
356			if (args_info->latticetype_arg)
357			free (args_info->latticetype_arg); /* free previous string */
358			args_info->latticetype_arg = gengetopt_strdup (optarg);
359			}
360			/* Lattice spacing in Angstroms for cubic lattice.. */
361			else if (strcmp (long_options[option_index].name, "latticeCnst") == 0)
362			{
363			if (local_args_info.latticeCnst_given)
364			{
365			fprintf (stderr, "%s: `--latticeCnst' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
366			goto failure;
367			}
368			if (args_info->latticeCnst_given && ! override)
369			continue;
370			local_args_info.latticeCnst_given = 1;
371			args_info->latticeCnst_given = 1;
372			args_info->latticeCnst_arg = strtod (optarg, NULL);
373			}
374			/* Nanoparticle radius in Angstroms. */
375			else if (strcmp (long_options[option_index].name, "radius") == 0)
376			{
377			if (local_args_info.radius_given)
378			{
379			fprintf (stderr, "%s: `--radius' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
380			goto failure;
381			}
382			if (args_info->radius_given && ! override)
383			continue;
384			local_args_info.radius_given = 1;
385			args_info->radius_given = 1;
386			args_info->radius_arg = strtod (optarg, NULL);
387			}
388			/* Radius from the center of the particle to start a new shell in multi-component core-shell particle. Specified for each component > 1 in md file.. */
389			else if (strcmp (long_options[option_index].name, "ShellRadius") == 0)
390			{
391			local_args_info.ShellRadius_given++;
392
393			multi_token = get_multiple_arg_token(optarg);
394			multi_next = get_multiple_arg_token_next (optarg);
395
396			while (1)
397			{
398			ShellRadius_new = (struct ShellRadius_list *) malloc (sizeof (struct ShellRadius_list));
399			ShellRadius_new->next = ShellRadius_list;
400			ShellRadius_list = ShellRadius_new;
401			ShellRadius_new->ShellRadius_arg = strtod (multi_token, NULL);
402			free (multi_token);
403
404			if (multi_next)
405			{
406			multi_token = get_multiple_arg_token(multi_next);
407			multi_next = get_multiple_arg_token_next (multi_next);
408			local_args_info.ShellRadius_given++;
409			}
410			else
411			break;
412			}
413			break;
414			}
415			/* (Default) Builds a multi-component random mixed nanoparticle. Mole Fraction must be specified for each componet > 1 in MD file.. */
416			else if (strcmp (long_options[option_index].name, "molFraction") == 0)
417			{
418			local_args_info.molFraction_given++;
419
420			multi_token = get_multiple_arg_token(optarg);
421			multi_next = get_multiple_arg_token_next (optarg);
422
423			while (1)
424			{
425			molFraction_new = (struct molFraction_list *) malloc (sizeof (struct molFraction_list));
426			molFraction_new->next = molFraction_list;
427			molFraction_list = molFraction_new;
428			molFraction_new->molFraction_arg = strtod (multi_token, NULL);
429			free (multi_token);
430
431			if (multi_next)
432			{
433			multi_token = get_multiple_arg_token(multi_next);
434			multi_next = get_multiple_arg_token_next (multi_next);
435			local_args_info.molFraction_given++;
436			}
437			else
438			break;
439			}
440			break;
441			}
442			/* Percentage of vacancies to build. */
443			else if (strcmp (long_options[option_index].name, "vacancyPCT") == 0)
444			{
445			if (local_args_info.vacancyPCT_given)
446			{
447			fprintf (stderr, "%s: `--vacancyPCT' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
448			goto failure;
449			}
450			if (args_info->vacancyPCT_given && ! override)
451			continue;
452			local_args_info.vacancyPCT_given = 1;
453			args_info->vacancyPCT_given = 1;
454			args_info->vacancyPCT_arg = strtod (optarg, NULL);
455			}
456			/* Radius arround core-shell where vacancies should be located.. */
457			else if (strcmp (long_options[option_index].name, "vacancyRadius") == 0)
458			{
459			local_args_info.vacancyRadius_given++;
460
461			multi_token = get_multiple_arg_token(optarg);
462			multi_next = get_multiple_arg_token_next (optarg);
463
464			while (1)
465			{
466			vacancyRadius_new = (struct vacancyRadius_list *) malloc (sizeof (struct vacancyRadius_list));
467			vacancyRadius_new->next = vacancyRadius_list;
468			vacancyRadius_list = vacancyRadius_new;
469			vacancyRadius_new->vacancyRadius_arg = strtod (multi_token, NULL);
470			free (multi_token);
471
472			if (multi_next)
473			{
474			multi_token = get_multiple_arg_token(multi_next);
475			multi_next = get_multiple_arg_token_next (multi_next);
476			local_args_info.vacancyRadius_given++;
477			}
478			else
479			break;
480			}
481			break;
482			}
483
484			break;
485			case '?': /* Invalid option. */
486			/* `getopt_long' already printed an error message. */
487			goto failure;
488
489			default: /* bug: option not considered. */
490			fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
491			abort ();
492			} /* switch */
493			} /* while */
494
495
496			if (local_args_info.ShellRadius_given && ShellRadius_list)
497			{
498			struct ShellRadius_list *tmp;
499			args_info->ShellRadius_arg = (double ) realloc (args_info->ShellRadius_arg, (args_info->ShellRadius_given + local_args_info.ShellRadius_given) sizeof (double));
500			for (i = (local_args_info.ShellRadius_given - 1); i >= 0; --i)
501			{
502			tmp = ShellRadius_list;
503			args_info->ShellRadius_arg [i + args_info->ShellRadius_given] = ShellRadius_list->ShellRadius_arg;
504			ShellRadius_list = ShellRadius_list->next;
505			free (tmp);
506			}
507			}
508
509			if (local_args_info.molFraction_given && molFraction_list)
510			{
511			struct molFraction_list *tmp;
512			args_info->molFraction_arg = (double ) realloc (args_info->molFraction_arg, (args_info->molFraction_given + local_args_info.molFraction_given) sizeof (double));
513			for (i = (local_args_info.molFraction_given - 1); i >= 0; --i)
514			{
515			tmp = molFraction_list;
516			args_info->molFraction_arg [i + args_info->molFraction_given] = molFraction_list->molFraction_arg;
517			molFraction_list = molFraction_list->next;
518			free (tmp);
519			}
520			}
521
522			if (local_args_info.vacancyRadius_given && vacancyRadius_list)
523			{
524			struct vacancyRadius_list *tmp;
525			args_info->vacancyRadius_arg = (double ) realloc (args_info->vacancyRadius_arg, (args_info->vacancyRadius_given + local_args_info.vacancyRadius_given) sizeof (double));
526			for (i = (local_args_info.vacancyRadius_given - 1); i >= 0; --i)
527			{
528			tmp = vacancyRadius_list;
529			args_info->vacancyRadius_arg [i + args_info->vacancyRadius_given] = vacancyRadius_list->vacancyRadius_arg;
530			vacancyRadius_list = vacancyRadius_list->next;
531			free (tmp);
532			}
533			}
534
535
536			args_info->ShellRadius_given += local_args_info.ShellRadius_given;
537			local_args_info.ShellRadius_given = 0;
538			args_info->molFraction_given += local_args_info.molFraction_given;
539			local_args_info.molFraction_given = 0;
540			args_info->vacancyRadius_given += local_args_info.vacancyRadius_given;
541			local_args_info.vacancyRadius_given = 0;
542
543			if (check_required)
544			{
545			error += cmdline_parser_required2 (args_info, argv[0], additional_error);
546			}
547
548			cmdline_parser_free (&local_args_info);
549
550			if ( error )
551			return (EXIT_FAILURE);
552
553			if (optind < argc)
554			{
555			int i = 0 ;
556
557			args_info->inputs_num = argc - optind ;
558			args_info->inputs =
559			(char *)(malloc ((args_info->inputs_num)sizeof(char *))) ;
560			while (optind < argc)
561			args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind++]) ;
562			}
563
564			return 0;
565
566			failure:
567			if (ShellRadius_list)
568			{
569			struct ShellRadius_list *tmp;
570			while (ShellRadius_list)
571			{
572			tmp = ShellRadius_list;
573			ShellRadius_list = ShellRadius_list->next;
574			free (tmp);
575			}
576			}
577			if (molFraction_list)
578			{
579			struct molFraction_list *tmp;
580			while (molFraction_list)
581			{
582			tmp = molFraction_list;
583			molFraction_list = molFraction_list->next;
584			free (tmp);
585			}
586			}
587			if (vacancyRadius_list)
588			{
589			struct vacancyRadius_list *tmp;
590			while (vacancyRadius_list)
591			{
592			tmp = vacancyRadius_list;
593			vacancyRadius_list = vacancyRadius_list->next;
594			free (tmp);
595			}
596			}
597
598			cmdline_parser_free (&local_args_info);
599			return (EXIT_FAILURE);
600			}