applications/nanoparticleBuilder/nanoparticleBuilderCmd.cpp

/*
  File autogenerated by gengetopt version 2.13.1
  generated with the following command:
  gengetopt -F nanoparticleBuilderCmd --unamed-opts --no-handle-error 

  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;
};

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->latticeConstant_given = 0 ;
  args_info->radius_given = 0 ;
  args_info->shellRadius_given = 0 ;
  args_info->molFraction_given = 0 ;
  args_info->vacancyPercent_given = 0 ;
  args_info->vacancyInnerRadius_given = 0 ;
  args_info->vacancyOuterRadius_given = 0 ;
}

static
void clear_args (struct gengetopt_args_info *args_info)
{
  args_info->output_arg = NULL;
  args_info->shellRadius_arg = NULL;
  args_info->molFraction_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 an OOPSE \nstartup file");
  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","      --latticeConstant=DOUBLE  Lattice spacing in Angstroms for cubic lattice.");
  printf("%s\n","      --radius=DOUBLE           Nanoparticle radius in Angstroms");
  printf("%s\n","      --shellRadius=DOUBLE      Radius containing within it only molecules of a \n                                  specific component. Specified for each \n                                  component > 1 in the template file.");
  printf("%s\n","      --molFraction=DOUBLE      Builds a multi-component random alloy \n                                  nanoparticle. A mole Fraction must be \n                                  specified for each component > 1 in the \n                                  template file.");
  printf("%s\n","      --vacancyPercent=DOUBLE   Percentage of atoms to remove from within \n                                  vacancy range");
  printf("%s\n","      --vacancyInnerRadius=DOUBLE\n                                Radius arround core-shell where vacancies \n                                  should be located.");
  printf("%s\n","      --vacancyOuterRadius=DOUBLE\n                                Radius arround core-shell where vacancies \n                                  should 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->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;
    }
  
  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);

  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;

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

  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;
  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' },
        { "latticeConstant",    1, NULL, 0 },
        { "radius",     1, NULL, 0 },
        { "shellRadius",        1, NULL, 0 },
        { "molFraction",        1, NULL, 0 },
        { "vacancyPercent",     1, NULL, 0 },
        { "vacancyInnerRadius", 1, NULL, 0 },
        { "vacancyOuterRadius", 1, NULL, 0 },
        { NULL, 0, NULL, 0 }
      };

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

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

      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 '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 spacing in Angstroms for cubic lattice..  */
          if (strcmp (long_options[option_index].name, "latticeConstant") == 0)
          {
            if (local_args_info.latticeConstant_given)
              {
                fprintf (stderr, "%s: `--latticeConstant' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->latticeConstant_given && ! override)
              continue;
            local_args_info.latticeConstant_given = 1;
            args_info->latticeConstant_given = 1;
            args_info->latticeConstant_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 containing within it only molecules of a specific component. Specified for each component > 1 in the template file..  */
          else if (strcmp (long_options[option_index].name, "shellRadius") == 0)
          {
            local_args_info.shellRadius_given++;
          
            multi_token = get_multiple_arg_token(optarg);
            multi_next = get_multiple_arg_token_next (optarg);
          
            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;
          }
          /* Builds a multi-component random alloy nanoparticle. A mole Fraction must be specified for each component > 1 in the template file..  */
          else if (strcmp (long_options[option_index].name, "molFraction") == 0)
          {
            local_args_info.molFraction_given++;
          
            multi_token = get_multiple_arg_token(optarg);
            multi_next = get_multiple_arg_token_next (optarg);
          
            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 atoms to remove from within vacancy range.  */
          else if (strcmp (long_options[option_index].name, "vacancyPercent") == 0)
          {
            if (local_args_info.vacancyPercent_given)
              {
                fprintf (stderr, "%s: `--vacancyPercent' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->vacancyPercent_given && ! override)
              continue;
            local_args_info.vacancyPercent_given = 1;
            args_info->vacancyPercent_given = 1;
            args_info->vacancyPercent_arg = strtod (optarg, NULL);
          }
          /* Radius arround core-shell where vacancies should be located..  */
          else if (strcmp (long_options[option_index].name, "vacancyInnerRadius") == 0)
          {
            if (local_args_info.vacancyInnerRadius_given)
              {
                fprintf (stderr, "%s: `--vacancyInnerRadius' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->vacancyInnerRadius_given && ! override)
              continue;
            local_args_info.vacancyInnerRadius_given = 1;
            args_info->vacancyInnerRadius_given = 1;
            args_info->vacancyInnerRadius_arg = strtod (optarg, NULL);
          }
          /* Radius arround core-shell where vacancies should be located..  */
          else if (strcmp (long_options[option_index].name, "vacancyOuterRadius") == 0)
          {
            if (local_args_info.vacancyOuterRadius_given)
              {
                fprintf (stderr, "%s: `--vacancyOuterRadius' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->vacancyOuterRadius_given && ! override)
              continue;
            local_args_info.vacancyOuterRadius_given = 1;
            args_info->vacancyOuterRadius_given = 1;
            args_info->vacancyOuterRadius_arg = strtod (optarg, NULL);
          }
          
          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);
        }
    }
  

  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;
  
  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);
        }
    }
  
  cmdline_parser_free (&local_args_info);
  return (EXIT_FAILURE);
}
Revision:	1077
Committed:	Wed Oct 18 19:35:07 2006 UTC (18 years, 6 months ago) by gezelter
Content type:	text/plain
Original Path:	*trunk/src/applications/nanoparticleBuilder/nanoparticleBuilderCmd.c*
File size:	17918 byte(s)
Log Message:	bug fixes for vacancies
#	User	Rev	Content
1	chuckv	653	/*
2	gezelter	1077	File autogenerated by gengetopt version 2.13.1
3	chuckv	653	generated with the following command:
4	gezelter	1077	gengetopt -F nanoparticleBuilderCmd --unamed-opts --no-handle-error
5	chuckv	653
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	gezelter	1077	struct shellRadius_list
36	chuckv	653	{
37	gezelter	1077	double shellRadius_arg;
38			struct shellRadius_list * next;
39	chuckv	653	};
40
41			struct molFraction_list
42			{
43			double molFraction_arg;
44			struct molFraction_list * next;
45			};
46
47			static char *
48			gengetopt_strdup (const char *s);
49
50			static
51			void clear_given (struct gengetopt_args_info *args_info)
52			{
53			args_info->help_given = 0 ;
54			args_info->version_given = 0 ;
55			args_info->output_given = 0 ;
56	gezelter	1077	args_info->latticeConstant_given = 0 ;
57	chuckv	653	args_info->radius_given = 0 ;
58	gezelter	1077	args_info->shellRadius_given = 0 ;
59	chuckv	653	args_info->molFraction_given = 0 ;
60	gezelter	1077	args_info->vacancyPercent_given = 0 ;
61			args_info->vacancyInnerRadius_given = 0 ;
62			args_info->vacancyOuterRadius_given = 0 ;
63	chuckv	653	}
64
65			static
66			void clear_args (struct gengetopt_args_info *args_info)
67			{
68			args_info->output_arg = NULL;
69	gezelter	1077	args_info->shellRadius_arg = NULL;
70	chuckv	653	args_info->molFraction_arg = NULL;
71			}
72
73			void
74			cmdline_parser_print_version (void)
75			{
76			printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
77			}
78
79			void
80			cmdline_parser_print_help (void)
81			{
82			cmdline_parser_print_version ();
83	gezelter	1077	printf("\n%s\n", "Builds spherical random or core-shell nanoparticles and outputs an OOPSE \nstartup file");
84	chuckv	653	printf("\nUsage: nanoparticleBuilder [OPTIONS]... [FILES]...\n\n");
85	gezelter	1077	printf("%s\n"," -h, --help Print help and exit");
86			printf("%s\n"," -V, --version Print version and exit");
87			printf("%s\n"," -o, --output=STRING Output file name");
88			printf("%s\n"," --latticeConstant=DOUBLE Lattice spacing in Angstroms for cubic lattice.");
89			printf("%s\n"," --radius=DOUBLE Nanoparticle radius in Angstroms");
90			printf("%s\n"," --shellRadius=DOUBLE Radius containing within it only molecules of a \n specific component. Specified for each \n component > 1 in the template file.");
91			printf("%s\n"," --molFraction=DOUBLE Builds a multi-component random alloy \n nanoparticle. A mole Fraction must be \n specified for each component > 1 in the \n template file.");
92			printf("%s\n"," --vacancyPercent=DOUBLE Percentage of atoms to remove from within \n vacancy range");
93			printf("%s\n"," --vacancyInnerRadius=DOUBLE\n Radius arround core-shell where vacancies \n should be located.");
94			printf("%s\n"," --vacancyOuterRadius=DOUBLE\n Radius arround core-shell where vacancies \n should be located.");
95	chuckv	653
96			}
97
98			void
99			cmdline_parser_init (struct gengetopt_args_info *args_info)
100			{
101			clear_given (args_info);
102			clear_args (args_info);
103
104			args_info->inputs = NULL;
105			args_info->inputs_num = 0;
106			}
107
108	gezelter	1077	void
109			cmdline_parser_free (struct gengetopt_args_info *args_info)
110	chuckv	653	{
111
112			unsigned int i;
113			if (args_info->output_arg)
114			{
115			free (args_info->output_arg); /* free previous argument */
116			args_info->output_arg = 0;
117			}
118	gezelter	1077	if (args_info->shellRadius_arg)
119	chuckv	653	{
120	gezelter	1077	free (args_info->shellRadius_arg); /* free previous argument */
121			args_info->shellRadius_arg = 0;
122	chuckv	653	}
123			if (args_info->molFraction_arg)
124			{
125			free (args_info->molFraction_arg); /* free previous argument */
126			args_info->molFraction_arg = 0;
127			}
128
129			for (i = 0; i < args_info->inputs_num; ++i)
130			free (args_info->inputs [i]);
131
132			if (args_info->inputs_num)
133			free (args_info->inputs);
134
135			clear_given (args_info);
136			}
137
138			/* gengetopt_strdup() */
139			/* strdup.c replacement of strdup, which is not standard */
140			char *
141			gengetopt_strdup (const char *s)
142			{
143			char *result = NULL;
144			if (!s)
145			return result;
146
147			result = (char*)malloc(strlen(s) + 1);
148			if (result == (char*)0)
149			return (char*)0;
150			strcpy(result, s);
151			return result;
152			}
153
154			static char *
155			get_multiple_arg_token(const char *arg)
156			{
157			char tok, ret;
158			size_t len;
159
160			if (!arg)
161			return NULL;
162
163			tok = strchr (arg, ',');
164
165			if (tok)
166			len = (size_t)(tok - arg + 1);
167			else
168			len = strlen (arg) + 1;
169
170			ret = (char *) malloc (len);
171			strncpy (ret, arg, len-1);
172			ret[len-1] = '\0';
173
174			return ret;
175			}
176
177			static char *
178			get_multiple_arg_token_next(const char *arg)
179			{
180			char *tok;
181
182			if (!arg)
183			return NULL;
184
185			tok = strchr (arg, ',');
186
187			if (! tok \|\| strlen(tok) == 1)
188			return 0;
189
190			return tok+1;
191			}
192
193			int
194			cmdline_parser (int argc, char * const argv, struct gengetopt_args_info args_info)
195			{
196			return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
197			}
198
199			int
200			cmdline_parser2 (int argc, char * const argv, struct gengetopt_args_info args_info, int override, int initialize, int check_required)
201			{
202			int result;
203
204			result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
205
206			return result;
207			}
208
209			int
210			cmdline_parser_required (struct gengetopt_args_info args_info, const char prog_name)
211			{
212			int result = EXIT_SUCCESS;
213
214			if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
215			result = EXIT_FAILURE;
216
217			return result;
218			}
219
220			int
221			cmdline_parser_required2 (struct gengetopt_args_info args_info, const char prog_name, const char *additional_error)
222			{
223			int error = 0;
224
225	gezelter	1077	if (! args_info->output_given)
226	chuckv	653	{
227	gezelter	1077	fprintf (stderr, "%s: '--output' ('-o') option required%s\n", prog_name, (additional_error ? additional_error : ""));
228	chuckv	653	error = 1;
229			}
230	gezelter	1077	if (! args_info->latticeConstant_given)
231			{
232			fprintf (stderr, "%s: '--latticeConstant' option required%s\n", prog_name, (additional_error ? additional_error : ""));
233			error = 1;
234			}
235	chuckv	653	if (! args_info->radius_given)
236			{
237			fprintf (stderr, "%s: '--radius' option required%s\n", prog_name, (additional_error ? additional_error : ""));
238			error = 1;
239			}
240
241			return error;
242			}
243
244			int
245			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)
246			{
247			int c; /* Character of the parsed option. */
248			char multi_token, multi_next; /* for multiple options */
249
250			int i; /* Counter */
251
252	gezelter	1077	struct shellRadius_list * shellRadius_list = NULL,* shellRadius_new = NULL;
253	chuckv	653	struct molFraction_list * molFraction_list = NULL,* molFraction_new = NULL;
254			int error = 0;
255			struct gengetopt_args_info local_args_info;
256
257			if (initialize)
258			cmdline_parser_init (args_info);
259
260			cmdline_parser_init (&local_args_info);
261
262			optarg = 0;
263			optind = 1;
264			opterr = 1;
265			optopt = '?';
266
267			while (1)
268			{
269			int option_index = 0;
270			char *stop_char;
271
272			static struct option long_options[] = {
273			{ "help", 0, NULL, 'h' },
274			{ "version", 0, NULL, 'V' },
275			{ "output", 1, NULL, 'o' },
276	gezelter	1077	{ "latticeConstant", 1, NULL, 0 },
277	chuckv	653	{ "radius", 1, NULL, 0 },
278	gezelter	1077	{ "shellRadius", 1, NULL, 0 },
279	chuckv	653	{ "molFraction", 1, NULL, 0 },
280	gezelter	1077	{ "vacancyPercent", 1, NULL, 0 },
281			{ "vacancyInnerRadius", 1, NULL, 0 },
282			{ "vacancyOuterRadius", 1, NULL, 0 },
283	chuckv	653	{ NULL, 0, NULL, 0 }
284			};
285
286			stop_char = 0;
287			c = getopt_long (argc, argv, "hVo:", long_options, &option_index);
288
289			if (c == -1) break; /* Exit from `while (1)' loop. */
290
291			switch (c)
292			{
293			case 'h': /* Print help and exit. */
294			cmdline_parser_print_help ();
295	chuckv	1069	cmdline_parser_free (&local_args_info);
296	chuckv	653	exit (EXIT_SUCCESS);
297
298			case 'V': /* Print version and exit. */
299			cmdline_parser_print_version ();
300	chuckv	1069	cmdline_parser_free (&local_args_info);
301	chuckv	653	exit (EXIT_SUCCESS);
302
303			case 'o': /* Output file name. */
304			if (local_args_info.output_given)
305			{
306			fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
307			goto failure;
308			}
309			if (args_info->output_given && ! override)
310			continue;
311			local_args_info.output_given = 1;
312			args_info->output_given = 1;
313			if (args_info->output_arg)
314			free (args_info->output_arg); /* free previous string */
315			args_info->output_arg = gengetopt_strdup (optarg);
316			break;
317
318
319			case 0: /* Long option with no short option */
320			/* Lattice spacing in Angstroms for cubic lattice.. */
321	gezelter	1077	if (strcmp (long_options[option_index].name, "latticeConstant") == 0)
322	chuckv	653	{
323	gezelter	1077	if (local_args_info.latticeConstant_given)
324	chuckv	653	{
325	gezelter	1077	fprintf (stderr, "%s: `--latticeConstant' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
326	chuckv	653	goto failure;
327			}
328	gezelter	1077	if (args_info->latticeConstant_given && ! override)
329	chuckv	653	continue;
330	gezelter	1077	local_args_info.latticeConstant_given = 1;
331			args_info->latticeConstant_given = 1;
332			args_info->latticeConstant_arg = strtod (optarg, NULL);
333	chuckv	653	}
334			/* Nanoparticle radius in Angstroms. */
335			else if (strcmp (long_options[option_index].name, "radius") == 0)
336			{
337			if (local_args_info.radius_given)
338			{
339			fprintf (stderr, "%s: `--radius' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
340			goto failure;
341			}
342			if (args_info->radius_given && ! override)
343			continue;
344			local_args_info.radius_given = 1;
345			args_info->radius_given = 1;
346	gezelter	1077	args_info->radius_arg = strtod (optarg, NULL);
347	chuckv	653	}
348	gezelter	1077	/* Radius containing within it only molecules of a specific component. Specified for each component > 1 in the template file.. */
349			else if (strcmp (long_options[option_index].name, "shellRadius") == 0)
350	chuckv	653	{
351	gezelter	1077	local_args_info.shellRadius_given++;
352	chuckv	653
353			multi_token = get_multiple_arg_token(optarg);
354			multi_next = get_multiple_arg_token_next (optarg);
355
356			while (1)
357			{
358	gezelter	1077	shellRadius_new = (struct shellRadius_list *) malloc (sizeof (struct shellRadius_list));
359			shellRadius_new->next = shellRadius_list;
360			shellRadius_list = shellRadius_new;
361			shellRadius_new->shellRadius_arg = strtod (multi_token, NULL);
362			free (multi_token);
363	chuckv	653
364			if (multi_next)
365			{
366			multi_token = get_multiple_arg_token(multi_next);
367			multi_next = get_multiple_arg_token_next (multi_next);
368	gezelter	1077	local_args_info.shellRadius_given++;
369	chuckv	653	}
370			else
371			break;
372			}
373			break;
374			}
375	gezelter	1077	/* Builds a multi-component random alloy nanoparticle. A mole Fraction must be specified for each component > 1 in the template file.. */
376	chuckv	653	else if (strcmp (long_options[option_index].name, "molFraction") == 0)
377			{
378			local_args_info.molFraction_given++;
379
380			multi_token = get_multiple_arg_token(optarg);
381			multi_next = get_multiple_arg_token_next (optarg);
382
383			while (1)
384			{
385			molFraction_new = (struct molFraction_list *) malloc (sizeof (struct molFraction_list));
386			molFraction_new->next = molFraction_list;
387			molFraction_list = molFraction_new;
388	gezelter	1077	molFraction_new->molFraction_arg = strtod (multi_token, NULL);
389			free (multi_token);
390	chuckv	653
391			if (multi_next)
392			{
393			multi_token = get_multiple_arg_token(multi_next);
394			multi_next = get_multiple_arg_token_next (multi_next);
395			local_args_info.molFraction_given++;
396			}
397			else
398			break;
399			}
400			break;
401			}
402	gezelter	1077	/* Percentage of atoms to remove from within vacancy range. */
403			else if (strcmp (long_options[option_index].name, "vacancyPercent") == 0)
404	chuckv	653	{
405	gezelter	1077	if (local_args_info.vacancyPercent_given)
406	chuckv	653	{
407	gezelter	1077	fprintf (stderr, "%s: `--vacancyPercent' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
408	chuckv	653	goto failure;
409			}
410	gezelter	1077	if (args_info->vacancyPercent_given && ! override)
411	chuckv	653	continue;
412	gezelter	1077	local_args_info.vacancyPercent_given = 1;
413			args_info->vacancyPercent_given = 1;
414			args_info->vacancyPercent_arg = strtod (optarg, NULL);
415	chuckv	653	}
416			/* Radius arround core-shell where vacancies should be located.. */
417	gezelter	1077	else if (strcmp (long_options[option_index].name, "vacancyInnerRadius") == 0)
418	chuckv	653	{
419	gezelter	1077	if (local_args_info.vacancyInnerRadius_given)
420	chuckv	653	{
421	gezelter	1077	fprintf (stderr, "%s: `--vacancyInnerRadius' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
422			goto failure;
423	chuckv	653	}
424	gezelter	1077	if (args_info->vacancyInnerRadius_given && ! override)
425			continue;
426			local_args_info.vacancyInnerRadius_given = 1;
427			args_info->vacancyInnerRadius_given = 1;
428			args_info->vacancyInnerRadius_arg = strtod (optarg, NULL);
429	chuckv	653	}
430	gezelter	1077	/* Radius arround core-shell where vacancies should be located.. */
431			else if (strcmp (long_options[option_index].name, "vacancyOuterRadius") == 0)
432			{
433			if (local_args_info.vacancyOuterRadius_given)
434			{
435			fprintf (stderr, "%s: `--vacancyOuterRadius' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
436			goto failure;
437			}
438			if (args_info->vacancyOuterRadius_given && ! override)
439			continue;
440			local_args_info.vacancyOuterRadius_given = 1;
441			args_info->vacancyOuterRadius_given = 1;
442			args_info->vacancyOuterRadius_arg = strtod (optarg, NULL);
443			}
444	chuckv	653
445			break;
446			case '?': /* Invalid option. */
447			/* `getopt_long' already printed an error message. */
448			goto failure;
449
450			default: /* bug: option not considered. */
451			fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
452			abort ();
453			} /* switch */
454			} /* while */
455
456
457	gezelter	1077	if (local_args_info.shellRadius_given && shellRadius_list)
458	chuckv	653	{
459	gezelter	1077	struct shellRadius_list *tmp;
460			args_info->shellRadius_arg = (double ) realloc (args_info->shellRadius_arg, (args_info->shellRadius_given + local_args_info.shellRadius_given) sizeof (double));
461			for (i = (local_args_info.shellRadius_given - 1); i >= 0; --i)
462	chuckv	653	{
463	gezelter	1077	tmp = shellRadius_list;
464			args_info->shellRadius_arg [i + args_info->shellRadius_given] = shellRadius_list->shellRadius_arg;
465			shellRadius_list = shellRadius_list->next;
466	chuckv	653	free (tmp);
467			}
468			}
469
470			if (local_args_info.molFraction_given && molFraction_list)
471			{
472			struct molFraction_list *tmp;
473			args_info->molFraction_arg = (double ) realloc (args_info->molFraction_arg, (args_info->molFraction_given + local_args_info.molFraction_given) sizeof (double));
474			for (i = (local_args_info.molFraction_given - 1); i >= 0; --i)
475			{
476			tmp = molFraction_list;
477			args_info->molFraction_arg [i + args_info->molFraction_given] = molFraction_list->molFraction_arg;
478			molFraction_list = molFraction_list->next;
479			free (tmp);
480			}
481			}
482
483
484	gezelter	1077	args_info->shellRadius_given += local_args_info.shellRadius_given;
485			local_args_info.shellRadius_given = 0;
486	chuckv	653	args_info->molFraction_given += local_args_info.molFraction_given;
487			local_args_info.molFraction_given = 0;
488
489			if (check_required)
490			{
491			error += cmdline_parser_required2 (args_info, argv[0], additional_error);
492			}
493
494	gezelter	1077	cmdline_parser_free (&local_args_info);
495	chuckv	653
496			if ( error )
497			return (EXIT_FAILURE);
498
499			if (optind < argc)
500			{
501			int i = 0 ;
502
503			args_info->inputs_num = argc - optind ;
504			args_info->inputs =
505			(char *)(malloc ((args_info->inputs_num)sizeof(char *))) ;
506			while (optind < argc)
507			args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind++]) ;
508			}
509
510			return 0;
511
512			failure:
513	gezelter	1077	if (shellRadius_list)
514	chuckv	653	{
515	gezelter	1077	struct shellRadius_list *tmp;
516			while (shellRadius_list)
517	chuckv	653	{
518	gezelter	1077	tmp = shellRadius_list;
519			shellRadius_list = shellRadius_list->next;
520	chuckv	653	free (tmp);
521			}
522			}
523			if (molFraction_list)
524			{
525			struct molFraction_list *tmp;
526			while (molFraction_list)
527			{
528			tmp = molFraction_list;
529			molFraction_list = molFraction_list->next;
530			free (tmp);
531			}
532			}
533
534	gezelter	1077	cmdline_parser_free (&local_args_info);
535	chuckv	653	return (EXIT_FAILURE);
536			}