[ViewVC] Diff of: OpenMD/trunk/src/applications/staticProps/StaticPropsCmd.cpp

Comparing trunk/src/applications/staticProps/StaticPropsCmd.c (file contents):
Revision 326 by tim, Sun Feb 13 20:05:42 2005 UTC vs.
Revision 1213 by xsun, Wed Jan 23 21:21:50 2008 UTC

+/*
-<
+  File autogenerated by gengetopt version 2.11
->
+  File autogenerated by gengetopt version 2.19.1
+  generated with the following command:
-<
+  /home/maul/gezelter/tim/bin/gengetopt -F StaticPropsCmd
->
+  gengetopt --file-name=StaticPropsCmd -u
+  The developers of gengetopt consider the fixed text that goes in all
+  gengetopt output files to be in the public domain:
+  we make no copyright claims on it.
+*/
-–
-–
+#include <stdio.h>
-–
+#include <stdlib.h>
-–
+#include <string.h>
-–
+/* 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 "StaticPropsCmd.h"
-+
+const char *gengetopt_args_info_purpose = "";
-+
-+
+const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]... [FILES]...";
-+
-+
+const char *gengetopt_args_info_description = "";
-+
-+
+const char *gengetopt_args_info_help[] = {
-+
+  "  -h, --help                    Print help and exit",
-+
+  "  -V, --version                 Print version and exit",
-+
+  "  -i, --input=filename          input dump file",
-+
+  "  -o, --output=filename         output file name",
-+
+  "  -n, --step=INT                process every n frame  (default=`1')",
-+
+  "  -b, --nbins=INT               number of bins (general purpose)  \n                                  (default=`100')",
-+
+  "  -x, --nbins_x=INT             number of bins in x axis  (default=`100')",
-+
+  "  -y, --nbins_y=INT             number of bins in y axis  (default=`100')",
-+
+  "  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')",
-+
+  "      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
-+
+  "  -c, --rcut=DOUBLE             cutoff radius (rcut)",
-+
+  "  -z, --zoffset=DOUBLE          Where to set the zero for the slab_density \n                                  calculation  (default=`0')",
-+
+  "      --sele1=selection script  select the first stuntdouble set",
-+
+  "      --sele2=selection script  select the second stuntdouble set",
-+
+  "      --sele3=selection script  select the third stuntdouble set",
-+
+  "      --refsele=selection script\n                                select reference (use and only use with --gxyz)",
-+
+  "      --molname=STRING          molecule name",
-+
+  "      --begin=INT               begin internal index",
-+
+  "      --end=INT                 end internal index",
-+
+  "      --radius=DOUBLE           nanoparticle radius",
-+
+  "\n Group: staticProps\n   an option of this group is required",
-+
+  "      --bo                      bond order parameter (--rcut must be specified)",
-+
+  "      --bor                     bond order parameter as a function of radius \n                                  (--rcut must be specified)",
-+
+  "      --bad                     N(theta) bond angle density within (--rcut must \n                                  be specified)",
-+
+  "  -g, --gofr                    g(r)",
-+
+  "      --gofz                    g(z)",
-+
+  "      --r_theta                 g(r, cos(theta))",
-+
+  "      --r_omega                 g(r, cos(omega))",
-+
+  "      --theta_omega             g(cos(theta), cos(omega))",
-+
+  "      --gxyz                    g(x, y, z)",
-+
+  "  -p, --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)",
-+
+  "      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)",
-+
+  "  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)",
-+
+  "  -d, --density                 density plot",
-+
+  "      --slab_density            slab density",
-+
+  "      --hxy                     hxy",
-+
+  "      --rho_r                   rho of R",
-+
+  "      --hullvol                 hull volume of nanoparticle",
-+
-+
+};
-+
-+
+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->step_given = 0 ;
-+
+  args_info->nbins_given = 0 ;
-+
+  args_info->nbins_x_given = 0 ;
-+
+  args_info->nbins_y_given = 0 ;
-+
+  args_info->nanglebins_given = 0 ;
-+
+  args_info->length_given = 0 ;
-+
+  args_info->rcut_given = 0 ;
-+
+  args_info->zoffset_given = 0 ;
-+
+  args_info->sele1_given = 0 ;
-+
+  args_info->sele2_given = 0 ;
-+
+  args_info->sele3_given = 0 ;
-+
+  args_info->refsele_given = 0 ;
-+
+  args_info->molname_given = 0 ;
-+
+  args_info->begin_given = 0 ;
-+
+  args_info->end_given = 0 ;
-+
+  args_info->radius_given = 0 ;
-+
+  args_info->bo_given = 0 ;
-+
+  args_info->bor_given = 0 ;
-+
+  args_info->bad_given = 0 ;
-+
+  args_info->gofr_given = 0 ;
-+
+  args_info->gofz_given = 0 ;
-+
+  args_info->r_theta_given = 0 ;
-+
+  args_info->r_omega_given = 0 ;
-+
+  args_info->theta_omega_given = 0 ;
-+
+  args_info->gxyz_given = 0 ;
-+
+  args_info->p2_given = 0 ;
-+
+  args_info->rp2_given = 0 ;
-+
+  args_info->scd_given = 0 ;
-+
+  args_info->density_given = 0 ;
-+
+  args_info->slab_density_given = 0 ;
-+
+  args_info->hxy_given = 0 ;
-+
+  args_info->rho_r_given = 0 ;
-+
+  args_info->hullvol_given = 0 ;
-+
+  args_info->staticProps_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->step_arg = 1;
-+
+  args_info->step_orig = NULL;
-+
+  args_info->nbins_arg = 100;
-+
+  args_info->nbins_orig = NULL;
-+
+  args_info->nbins_x_arg = 100;
-+
+  args_info->nbins_x_orig = NULL;
-+
+  args_info->nbins_y_arg = 100;
-+
+  args_info->nbins_y_orig = NULL;
-+
+  args_info->nanglebins_arg = 50;
-+
+  args_info->nanglebins_orig = NULL;
-+
+  args_info->length_orig = NULL;
-+
+  args_info->rcut_orig = NULL;
-+
+  args_info->zoffset_arg = 0;
-+
+  args_info->zoffset_orig = NULL;
-+
+  args_info->sele1_arg = NULL;
-+
+  args_info->sele1_orig = NULL;
-+
+  args_info->sele2_arg = NULL;
-+
+  args_info->sele2_orig = NULL;
-+
+  args_info->sele3_arg = NULL;
-+
+  args_info->sele3_orig = NULL;
-+
+  args_info->refsele_arg = NULL;
-+
+  args_info->refsele_orig = NULL;
-+
+  args_info->molname_arg = NULL;
-+
+  args_info->molname_orig = NULL;
-+
+  args_info->begin_orig = NULL;
-+
+  args_info->end_orig = NULL;
-+
+  args_info->radius_orig = NULL;
-+
-+
+}
-+
-+
+static
-+
+void init_args_info(struct gengetopt_args_info *args_info)
-+
+{
-+
+  args_info->help_help = gengetopt_args_info_help[0] ;
-+
+  args_info->version_help = gengetopt_args_info_help[1] ;
-+
+  args_info->input_help = gengetopt_args_info_help[2] ;
-+
+  args_info->output_help = gengetopt_args_info_help[3] ;
-+
+  args_info->step_help = gengetopt_args_info_help[4] ;
-+
+  args_info->nbins_help = gengetopt_args_info_help[5] ;
-+
+  args_info->nbins_x_help = gengetopt_args_info_help[6] ;
-+
+  args_info->nbins_y_help = gengetopt_args_info_help[7] ;
-+
+  args_info->nanglebins_help = gengetopt_args_info_help[8] ;
-+
+  args_info->length_help = gengetopt_args_info_help[9] ;
-+
+  args_info->rcut_help = gengetopt_args_info_help[10] ;
-+
+  args_info->zoffset_help = gengetopt_args_info_help[11] ;
-+
+  args_info->sele1_help = gengetopt_args_info_help[12] ;
-+
+  args_info->sele2_help = gengetopt_args_info_help[13] ;
-+
+  args_info->sele3_help = gengetopt_args_info_help[14] ;
-+
+  args_info->refsele_help = gengetopt_args_info_help[15] ;
-+
+  args_info->molname_help = gengetopt_args_info_help[16] ;
-+
+  args_info->begin_help = gengetopt_args_info_help[17] ;
-+
+  args_info->end_help = gengetopt_args_info_help[18] ;
-+
+  args_info->radius_help = gengetopt_args_info_help[19] ;
-+
+  args_info->bo_help = gengetopt_args_info_help[20] ;
-+
+  args_info->bor_help = gengetopt_args_info_help[21] ;
-+
+  args_info->bad_help = gengetopt_args_info_help[22] ;
-+
+  args_info->gofr_help = gengetopt_args_info_help[23] ;
-+
+  args_info->gofz_help = gengetopt_args_info_help[24] ;
-+
+  args_info->r_theta_help = gengetopt_args_info_help[25] ;
-+
+  args_info->r_omega_help = gengetopt_args_info_help[26] ;
-+
+  args_info->theta_omega_help = gengetopt_args_info_help[27] ;
-+
+  args_info->gxyz_help = gengetopt_args_info_help[28] ;
-+
+  args_info->p2_help = gengetopt_args_info_help[29] ;
-+
+  args_info->rp2_help = gengetopt_args_info_help[30] ;
-+
+  args_info->scd_help = gengetopt_args_info_help[31] ;
-+
+  args_info->density_help = gengetopt_args_info_help[32] ;
-+
+  args_info->slab_density_help = gengetopt_args_info_help[33] ;
-+
+  args_info->hxy_help = gengetopt_args_info_help[34] ;
-+
+  args_info->rho_r_help = gengetopt_args_info_help[35] ;
-+
+  args_info->hullvol_help = gengetopt_args_info_help[36] ;
-+
-+
+}
-+
+void
+cmdline_parser_print_version (void)
+void
+cmdline_parser_print_help (void)
-+
+  int i = 0;
+  cmdline_parser_print_version ();
-<
+  printf("\n"
-<
+  "Usage: %s [OPTIONS]...\n", CMDLINE_PARSER_PACKAGE);
-<
+  printf("\n");
-<
+  printf("  -h, --help                    Print help and exit\n");
-<
+  printf("  -V, --version                 Print version and exit\n");
-<
+  printf("  -i, --input=filename          input dump file\n");
-<
+  printf("  -o, --output=filename         output file name\n");
-<
+  printf("  -n, --step=INT                process every n frame  (default=`1')\n");
-<
+  printf("  -r, --nrbins=INT              number of bins for distance  (default=`50')\n");
-<
+  printf("  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')\n");
-<
+  printf("  -l, --length=DOUBLE           maximum length (Defaults to cutoff radius)\n");
-<
+  printf("      --sele1=selection script  select first stuntdouble set\n");
-<
+  printf("      --sele2=selection script  select second stuntdouble set\n");
-<
+  printf("\n");
-<
+  printf(" Group: staticProps  an option of this group is required\n");
-<
+  printf("      --gofr                    g(r)\n");
-<
+  printf("      --r_theta                 g(r, cos(theta))\n");
-<
+  printf("      --r_omega                 g(r, cos(omega))\n");
-<
+  printf("      --theta_omega             g(cos(theta), cos(omega))\n");
-<
+  printf("      --xyz                     g(x, y, z)\n");
->
->
+  if (strlen(gengetopt_args_info_purpose) > 0)
->
+    printf("\n%s\n", gengetopt_args_info_purpose);
->
->
+  printf("\n%s\n\n", gengetopt_args_info_usage);
->
->
+  if (strlen(gengetopt_args_info_description) > 0)
->
+    printf("%s\n", gengetopt_args_info_description);
->
->
+  while (gengetopt_args_info_help[i])
->
+    printf("%s\n", gengetopt_args_info_help[i++]);
-+
+void
-+
+cmdline_parser_init (struct gengetopt_args_info *args_info)
-+
+{
-+
+  clear_given (args_info);
-+
+  clear_args (args_info);
-+
+  init_args_info (args_info);
-<
+static char *gengetopt_strdup (const char *s);
->
+  args_info->inputs = NULL;
->
+  args_info->inputs_num = 0;
->
+}
-+
+static void
-+
+cmdline_parser_release (struct gengetopt_args_info *args_info)
-+
+{
-+
-+
+  unsigned int i;
-+
+  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->step_orig)
-+
+    {
-+
+      free (args_info->step_orig); /* free previous argument */
-+
+      args_info->step_orig = 0;
-+
+    }
-+
+  if (args_info->nbins_orig)
-+
+    {
-+
+      free (args_info->nbins_orig); /* free previous argument */
-+
+      args_info->nbins_orig = 0;
-+
+    }
-+
+  if (args_info->nbins_x_orig)
-+
+    {
-+
+      free (args_info->nbins_x_orig); /* free previous argument */
-+
+      args_info->nbins_x_orig = 0;
-+
+    }
-+
+  if (args_info->nbins_y_orig)
-+
+    {
-+
+      free (args_info->nbins_y_orig); /* free previous argument */
-+
+      args_info->nbins_y_orig = 0;
-+
+    }
-+
+  if (args_info->nanglebins_orig)
-+
+    {
-+
+      free (args_info->nanglebins_orig); /* free previous argument */
-+
+      args_info->nanglebins_orig = 0;
-+
+    }
-+
+  if (args_info->length_orig)
-+
+    {
-+
+      free (args_info->length_orig); /* free previous argument */
-+
+      args_info->length_orig = 0;
-+
+    }
-+
+  if (args_info->rcut_orig)
-+
+    {
-+
+      free (args_info->rcut_orig); /* free previous argument */
-+
+      args_info->rcut_orig = 0;
-+
+    }
-+
+  if (args_info->zoffset_orig)
-+
+    {
-+
+      free (args_info->zoffset_orig); /* free previous argument */
-+
+      args_info->zoffset_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->sele3_arg)
-+
+    {
-+
+      free (args_info->sele3_arg); /* free previous argument */
-+
+      args_info->sele3_arg = 0;
-+
+    }
-+
+  if (args_info->sele3_orig)
-+
+    {
-+
+      free (args_info->sele3_orig); /* free previous argument */
-+
+      args_info->sele3_orig = 0;
-+
+    }
-+
+  if (args_info->refsele_arg)
-+
+    {
-+
+      free (args_info->refsele_arg); /* free previous argument */
-+
+      args_info->refsele_arg = 0;
-+
+    }
-+
+  if (args_info->refsele_orig)
-+
+    {
-+
+      free (args_info->refsele_orig); /* free previous argument */
-+
+      args_info->refsele_orig = 0;
-+
+    }
-+
+  if (args_info->molname_arg)
-+
+    {
-+
+      free (args_info->molname_arg); /* free previous argument */
-+
+      args_info->molname_arg = 0;
-+
+    }
-+
+  if (args_info->molname_orig)
-+
+    {
-+
+      free (args_info->molname_orig); /* free previous argument */
-+
+      args_info->molname_orig = 0;
-+
+    }
-+
+  if (args_info->begin_orig)
-+
+    {
-+
+      free (args_info->begin_orig); /* free previous argument */
-+
+      args_info->begin_orig = 0;
-+
+    }
-+
+  if (args_info->end_orig)
-+
+    {
-+
+      free (args_info->end_orig); /* free previous argument */
-+
+      args_info->end_orig = 0;
-+
+    }
-+
+  if (args_info->radius_orig)
-+
+    {
-+
+      free (args_info->radius_orig); /* free previous argument */
-+
+      args_info->radius_orig = 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);
-+
+}
-+
-+
+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->step_given) {
-+
+    if (args_info->step_orig) {
-+
+      fprintf(outfile, "%s=\"%s\"\n", "step", args_info->step_orig);
-+
+    } else {
-+
+      fprintf(outfile, "%s\n", "step");
-+
+    }
-+
+  }
-+
+  if (args_info->nbins_given) {
-+
+    if (args_info->nbins_orig) {
-+
+      fprintf(outfile, "%s=\"%s\"\n", "nbins", args_info->nbins_orig);
-+
+    } else {
-+
+      fprintf(outfile, "%s\n", "nbins");
-+
+    }
-+
+  }
-+
+  if (args_info->nbins_x_given) {
-+
+    if (args_info->nbins_x_orig) {
-+
+      fprintf(outfile, "%s=\"%s\"\n", "nbins_x", args_info->nbins_x_orig);
-+
+    } else {
-+
+      fprintf(outfile, "%s\n", "nbins_x");
-+
+    }
-+
+  }
-+
+  if (args_info->nbins_y_given) {
-+
+    if (args_info->nbins_y_orig) {
-+
+      fprintf(outfile, "%s=\"%s\"\n", "nbins_y", args_info->nbins_y_orig);
-+
+    } else {
-+
+      fprintf(outfile, "%s\n", "nbins_y");
-+
+    }
-+
+  }
-+
+  if (args_info->nanglebins_given) {
-+
+    if (args_info->nanglebins_orig) {
-+
+      fprintf(outfile, "%s=\"%s\"\n", "nanglebins", args_info->nanglebins_orig);
-+
+    } else {
-+
+      fprintf(outfile, "%s\n", "nanglebins");
-+
+    }
-+
+  }
-+
+  if (args_info->length_given) {
-+
+    if (args_info->length_orig) {
-+
+      fprintf(outfile, "%s=\"%s\"\n", "length", args_info->length_orig);
-+
+    } else {
-+
+      fprintf(outfile, "%s\n", "length");
-+
+    }
-+
+  }
-+
+  if (args_info->rcut_given) {
-+
+    if (args_info->rcut_orig) {
-+
+      fprintf(outfile, "%s=\"%s\"\n", "rcut", args_info->rcut_orig);
-+
+    } else {
-+
+      fprintf(outfile, "%s\n", "rcut");
-+
+    }
-+
+  }
-+
+  if (args_info->zoffset_given) {
-+
+    if (args_info->zoffset_orig) {
-+
+      fprintf(outfile, "%s=\"%s\"\n", "zoffset", args_info->zoffset_orig);
-+
+    } else {
-+
+      fprintf(outfile, "%s\n", "zoffset");
-+
+    }
-+
+  }
-+
+  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->sele3_given) {
-+
+    if (args_info->sele3_orig) {
-+
+      fprintf(outfile, "%s=\"%s\"\n", "sele3", args_info->sele3_orig);
-+
+    } else {
-+
+      fprintf(outfile, "%s\n", "sele3");
-+
+    }
-+
+  }
-+
+  if (args_info->refsele_given) {
-+
+    if (args_info->refsele_orig) {
-+
+      fprintf(outfile, "%s=\"%s\"\n", "refsele", args_info->refsele_orig);
-+
+    } else {
-+
+      fprintf(outfile, "%s\n", "refsele");
-+
+    }
-+
+  }
-+
+  if (args_info->molname_given) {
-+
+    if (args_info->molname_orig) {
-+
+      fprintf(outfile, "%s=\"%s\"\n", "molname", args_info->molname_orig);
-+
+    } else {
-+
+      fprintf(outfile, "%s\n", "molname");
-+
+    }
-+
+  }
-+
+  if (args_info->begin_given) {
-+
+    if (args_info->begin_orig) {
-+
+      fprintf(outfile, "%s=\"%s\"\n", "begin", args_info->begin_orig);
-+
+    } else {
-+
+      fprintf(outfile, "%s\n", "begin");
-+
+    }
-+
+  }
-+
+  if (args_info->end_given) {
-+
+    if (args_info->end_orig) {
-+
+      fprintf(outfile, "%s=\"%s\"\n", "end", args_info->end_orig);
-+
+    } else {
-+
+      fprintf(outfile, "%s\n", "end");
-+
+    }
-+
+  }
-+
+  if (args_info->radius_given) {
-+
+    if (args_info->radius_orig) {
-+
+      fprintf(outfile, "%s=\"%s\"\n", "radius", args_info->radius_orig);
-+
+    } else {
-+
+      fprintf(outfile, "%s\n", "radius");
-+
+    }
-+
+  }
-+
+  if (args_info->bo_given) {
-+
+    fprintf(outfile, "%s\n", "bo");
-+
+  }
-+
+  if (args_info->bor_given) {
-+
+    fprintf(outfile, "%s\n", "bor");
-+
+  }
-+
+  if (args_info->bad_given) {
-+
+    fprintf(outfile, "%s\n", "bad");
-+
+  }
-+
+  if (args_info->gofr_given) {
-+
+    fprintf(outfile, "%s\n", "gofr");
-+
+  }
-+
+  if (args_info->gofz_given) {
-+
+    fprintf(outfile, "%s\n", "gofz");
-+
+  }
-+
+  if (args_info->r_theta_given) {
-+
+    fprintf(outfile, "%s\n", "r_theta");
-+
+  }
-+
+  if (args_info->r_omega_given) {
-+
+    fprintf(outfile, "%s\n", "r_omega");
-+
+  }
-+
+  if (args_info->theta_omega_given) {
-+
+    fprintf(outfile, "%s\n", "theta_omega");
-+
+  }
-+
+  if (args_info->gxyz_given) {
-+
+    fprintf(outfile, "%s\n", "gxyz");
-+
+  }
-+
+  if (args_info->p2_given) {
-+
+    fprintf(outfile, "%s\n", "p2");
-+
+  }
-+
+  if (args_info->rp2_given) {
-+
+    fprintf(outfile, "%s\n", "rp2");
-+
+  }
-+
+  if (args_info->scd_given) {
-+
+    fprintf(outfile, "%s\n", "scd");
-+
+  }
-+
+  if (args_info->density_given) {
-+
+    fprintf(outfile, "%s\n", "density");
-+
+  }
-+
+  if (args_info->slab_density_given) {
-+
+    fprintf(outfile, "%s\n", "slab_density");
-+
+  }
-+
+  if (args_info->hxy_given) {
-+
+    fprintf(outfile, "%s\n", "hxy");
-+
+  }
-+
+  if (args_info->rho_r_given) {
-+
+    fprintf(outfile, "%s\n", "rho_r");
-+
+  }
-+
+  if (args_info->hullvol_given) {
-+
+    fprintf(outfile, "%s\n", "hullvol");
-+
+  }
-+
-+
+  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 = (char*)malloc(strlen(s) + 1);
->
+  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;
-<
+int
-<
+cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
->
+static void
->
+reset_group_staticProps(struct gengetopt_args_info *args_info);
->
->
+static void
->
+reset_group_staticProps(struct gengetopt_args_info *args_info)
-<
+  int c;        /* Character of the parsed option.  */
-<
+  int missing_required_options = 0;
-<
+  int staticProps_group_counter = 0;
->
+  if (! args_info->staticProps_group_counter)
->
+    return;
-<
-<
+  args_info->help_given = 0 ;
-<
+  args_info->version_given = 0 ;
-<
+  args_info->input_given = 0 ;
-<
+  args_info->output_given = 0 ;
-<
+  args_info->step_given = 0 ;
-<
+  args_info->nrbins_given = 0 ;
-<
+  args_info->nanglebins_given = 0 ;
-<
+  args_info->length_given = 0 ;
-<
+  args_info->sele1_given = 0 ;
-<
+  args_info->sele2_given = 0 ;
->
+  args_info->bo_given = 0 ;
->
+  args_info->bor_given = 0 ;
->
+  args_info->bad_given = 0 ;
+  args_info->gofr_given = 0 ;
-+
+  args_info->gofz_given = 0 ;
+  args_info->r_theta_given = 0 ;
+  args_info->r_omega_given = 0 ;
+  args_info->theta_omega_given = 0 ;
-<
+  args_info->xyz_given = 0 ;
-<
+#define clear_args() { \
-<
+  args_info->input_arg = NULL; \
-<
+  args_info->output_arg = NULL; \
-<
+  args_info->step_arg = 1 ;\
-<
+  args_info->nrbins_arg = 50 ;\
-<
+  args_info->nanglebins_arg = 50 ;\
-<
+  args_info->sele1_arg = NULL; \
-<
+  args_info->sele2_arg = NULL; \
->
+  args_info->gxyz_given = 0 ;
->
+  args_info->p2_given = 0 ;
->
+  args_info->rp2_given = 0 ;
->
+  args_info->scd_given = 0 ;
->
+  args_info->density_given = 0 ;
->
+  args_info->slab_density_given = 0 ;
->
+  args_info->hxy_given = 0 ;
->
+  args_info->rho_r_given = 0 ;
->
+  args_info->hullvol_given = 0 ;
->
->
+  args_info->staticProps_group_counter = 0;
-<
+  clear_args();
->
+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;
-+
-+
+  /* checks for required options */
-+
+  if (! args_info->input_given)
-+
+    {
-+
+      fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
-+
+      error = 1;
-+
+    }
-+
-+
+  if (args_info->staticProps_group_counter == 0)
-+
+    {
-+
+      fprintf (stderr, "%s: %d options of group staticProps were given. One is required.%s\n", prog_name, args_info->staticProps_group_counter, (additional_error ? additional_error : ""));
-+
+      error = 1;
-+
+    }
-+
-+
-+
+  /* checks for dependences among options */
-+
-+
+  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;
->
+  optind = 0;
+  opterr = 1;
+  optopt = '?';
+        { "input",      1, NULL, 'i' },
+        { "output",     1, NULL, 'o' },
+        { "step",       1, NULL, 'n' },
-<
+        { "nrbins",     1, NULL, 'r' },
->
+        { "nbins",      1, NULL, 'b' },
->
+        { "nbins_x",    1, NULL, 'x' },
->
+        { "nbins_y",    1, NULL, 'y' },
+        { "nanglebins", 1, NULL, 'a' },
-<
+        { "length",     1, NULL, 'l' },
->
+        { "length",     1, NULL, 0 },
->
+        { "rcut",       1, NULL, 'c' },
->
+        { "zoffset",    1, NULL, 'z' },
+        { "sele1",      1, NULL, 0 },
+        { "sele2",      1, NULL, 0 },
-<
+        { "gofr",       0, NULL, 0 },
->
+        { "sele3",      1, NULL, 0 },
->
+        { "refsele",    1, NULL, 0 },
->
+        { "molname",    1, NULL, 0 },
->
+        { "begin",      1, NULL, 0 },
->
+        { "end",        1, NULL, 0 },
->
+        { "radius",     1, NULL, 0 },
->
+        { "bo", 0, NULL, 0 },
->
+        { "bor",        0, NULL, 0 },
->
+        { "bad",        0, NULL, 0 },
->
+        { "gofr",       0, NULL, 'g' },
->
+        { "gofz",       0, NULL, 0 },
+        { "r_theta",    0, NULL, 0 },
+        { "r_omega",    0, NULL, 0 },
+        { "theta_omega",        0, NULL, 0 },
-<
+        { "xyz",        0, NULL, 0 },
->
+        { "gxyz",       0, NULL, 0 },
->
+        { "p2", 0, NULL, 'p' },
->
+        { "rp2",        0, NULL, 0 },
->
+        { "scd",        0, NULL, 's' },
->
+        { "density",    0, NULL, 'd' },
->
+        { "slab_density",       0, NULL, 0 },
->
+        { "hxy",        0, NULL, 0 },
->
+        { "rho_r",      0, NULL, 0 },
->
+        { "hullvol",    0, NULL, 0 },
+        { NULL, 0, NULL, 0 }
+      };
+      stop_char = 0;
-<
+      c = getopt_long (argc, argv, "hVi:o:n:r:a:l:", long_options, &option_index);
->
+      c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index);
+      if (c == -1) break;       /* Exit from `while (1)' loop.  */
+      switch (c)
+        case 'h':       /* Print help and exit.  */
-–
+          clear_args ();
+          cmdline_parser_print_help ();
-+
+          cmdline_parser_free (&local_args_info);
+          exit (EXIT_SUCCESS);
+        case 'V':       /* Print version and exit.  */
-–
+          clear_args ();
+          cmdline_parser_print_version ();
-+
+          cmdline_parser_free (&local_args_info);
+          exit (EXIT_SUCCESS);
+        case 'i':       /* input dump file.  */
-<
+          if (args_info->input_given)
->
+          if (local_args_info.input_given)
-<
+              fprintf (stderr, "%s: `--input' (`-i') option given more than once\n", CMDLINE_PARSER_PACKAGE);
-<
+              clear_args ();
-<
+              exit (EXIT_FAILURE);
->
+              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 (args_info->output_given)
->
+          if (local_args_info.output_given)
-<
+              fprintf (stderr, "%s: `--output' (`-o') option given more than once\n", CMDLINE_PARSER_PACKAGE);
-<
+              clear_args ();
-<
+              exit (EXIT_FAILURE);
->
+              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 'n':       /* process every n frame.  */
-<
+          if (args_info->step_given)
->
+          if (local_args_info.step_given)
-<
+              fprintf (stderr, "%s: `--step' (`-n') option given more than once\n", CMDLINE_PARSER_PACKAGE);
-<
+              clear_args ();
-<
+              exit (EXIT_FAILURE);
->
+              fprintf (stderr, "%s: `--step' (`-n') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
->
+              goto failure;
-+
+          if (args_info->step_given && ! override)
-+
+            continue;
-+
+          local_args_info.step_given = 1;
+          args_info->step_given = 1;
-<
+          args_info->step_arg = strtol (optarg,&stop_char,0);
->
+          args_info->step_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->step_orig)
->
+            free (args_info->step_orig); /* free previous string */
->
+          args_info->step_orig = gengetopt_strdup (optarg);
+          break;
-<
+        case 'r':       /* number of bins for distance.  */
-<
+          if (args_info->nrbins_given)
->
+        case 'b':       /* number of bins (general purpose).  */
->
+          if (local_args_info.nbins_given)
-<
+              fprintf (stderr, "%s: `--nrbins' (`-r') option given more than once\n", CMDLINE_PARSER_PACKAGE);
-<
+              clear_args ();
-<
+              exit (EXIT_FAILURE);
->
+              fprintf (stderr, "%s: `--nbins' (`-b') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
->
+              goto failure;
-<
+          args_info->nrbins_given = 1;
-<
+          args_info->nrbins_arg = strtol (optarg,&stop_char,0);
->
+          if (args_info->nbins_given && ! override)
->
+            continue;
->
+          local_args_info.nbins_given = 1;
->
+          args_info->nbins_given = 1;
->
+          args_info->nbins_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->nbins_orig)
->
+            free (args_info->nbins_orig); /* free previous string */
->
+          args_info->nbins_orig = gengetopt_strdup (optarg);
+          break;
-+
+        case 'x':       /* number of bins in x axis.  */
-+
+          if (local_args_info.nbins_x_given)
-+
+            {
-+
+              fprintf (stderr, "%s: `--nbins_x' (`-x') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-+
+              goto failure;
-+
+            }
-+
+          if (args_info->nbins_x_given && ! override)
-+
+            continue;
-+
+          local_args_info.nbins_x_given = 1;
-+
+          args_info->nbins_x_given = 1;
-+
+          args_info->nbins_x_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->nbins_x_orig)
-+
+            free (args_info->nbins_x_orig); /* free previous string */
-+
+          args_info->nbins_x_orig = gengetopt_strdup (optarg);
-+
+          break;
-+
-+
+        case 'y':       /* number of bins in y axis.  */
-+
+          if (local_args_info.nbins_y_given)
-+
+            {
-+
+              fprintf (stderr, "%s: `--nbins_y' (`-y') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-+
+              goto failure;
-+
+            }
-+
+          if (args_info->nbins_y_given && ! override)
-+
+            continue;
-+
+          local_args_info.nbins_y_given = 1;
-+
+          args_info->nbins_y_given = 1;
-+
+          args_info->nbins_y_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->nbins_y_orig)
-+
+            free (args_info->nbins_y_orig); /* free previous string */
-+
+          args_info->nbins_y_orig = gengetopt_strdup (optarg);
-+
+          break;
-+
+        case 'a':       /* number of bins for cos(angle).  */
-<
+          if (args_info->nanglebins_given)
->
+          if (local_args_info.nanglebins_given)
-<
+              fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once\n", CMDLINE_PARSER_PACKAGE);
-<
+              clear_args ();
-<
+              exit (EXIT_FAILURE);
->
+              fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
->
+              goto failure;
-+
+          if (args_info->nanglebins_given && ! override)
-+
+            continue;
-+
+          local_args_info.nanglebins_given = 1;
+          args_info->nanglebins_given = 1;
-<
+          args_info->nanglebins_arg = strtol (optarg,&stop_char,0);
->
+          args_info->nanglebins_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->nanglebins_orig)
->
+            free (args_info->nanglebins_orig); /* free previous string */
->
+          args_info->nanglebins_orig = gengetopt_strdup (optarg);
+          break;
-<
+        case 'l':       /* maximum length (Defaults to cutoff radius).  */
-<
+          if (args_info->length_given)
->
+        case 'c':       /* cutoff radius (rcut).  */
->
+          if (local_args_info.rcut_given)
-<
+              fprintf (stderr, "%s: `--length' (`-l') option given more than once\n", CMDLINE_PARSER_PACKAGE);
-<
+              clear_args ();
-<
+              exit (EXIT_FAILURE);
->
+              fprintf (stderr, "%s: `--rcut' (`-c') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
->
+              goto failure;
-<
+          args_info->length_given = 1;
-<
+          args_info->length_arg = strtod (optarg, NULL);
->
+          if (args_info->rcut_given && ! override)
->
+            continue;
->
+          local_args_info.rcut_given = 1;
->
+          args_info->rcut_given = 1;
->
+          args_info->rcut_arg = strtod (optarg, &stop_char);
->
+          if (!(stop_char && *stop_char == '\0')) {
->
+            fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
->
+            goto failure;
->
+          }
->
+          if (args_info->rcut_orig)
->
+            free (args_info->rcut_orig); /* free previous string */
->
+          args_info->rcut_orig = gengetopt_strdup (optarg);
+          break;
-+
+        case 'z':       /* Where to set the zero for the slab_density calculation.  */
-+
+          if (local_args_info.zoffset_given)
-+
+            {
-+
+              fprintf (stderr, "%s: `--zoffset' (`-z') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-+
+              goto failure;
-+
+            }
-+
+          if (args_info->zoffset_given && ! override)
-+
+            continue;
-+
+          local_args_info.zoffset_given = 1;
-+
+          args_info->zoffset_given = 1;
-+
+          args_info->zoffset_arg = strtod (optarg, &stop_char);
-+
+          if (!(stop_char && *stop_char == '\0')) {
-+
+            fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
-+
+            goto failure;
-+
+          }
-+
+          if (args_info->zoffset_orig)
-+
+            free (args_info->zoffset_orig); /* free previous string */
-+
+          args_info->zoffset_orig = gengetopt_strdup (optarg);
-+
+          break;
-+
+        case 'g':       /* g(r).  */
-+
+          if (local_args_info.gofr_given)
-+
+            {
-+
+              fprintf (stderr, "%s: `--gofr' (`-g') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-+
+              goto failure;
-+
+            }
-+
+          if (args_info->gofr_given && ! override)
-+
+            continue;
-+
+          local_args_info.gofr_given = 1;
-+
+          args_info->gofr_given = 1;
-+
+          if (args_info->staticProps_group_counter && override)
-+
+            reset_group_staticProps (args_info);
-+
+          args_info->staticProps_group_counter += 1;
-+
+          break;
-+
-+
+        case 'p':       /* p2 order parameter (--sele1 and --sele2 must be specified).  */
-+
+          if (local_args_info.p2_given)
-+
+            {
-+
+              fprintf (stderr, "%s: `--p2' (`-p') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-+
+              goto failure;
-+
+            }
-+
+          if (args_info->p2_given && ! override)
-+
+            continue;
-+
+          local_args_info.p2_given = 1;
-+
+          args_info->p2_given = 1;
-+
+          if (args_info->staticProps_group_counter && override)
-+
+            reset_group_staticProps (args_info);
-+
+          args_info->staticProps_group_counter += 1;
-+
+          break;
-+
-+
+        case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
-+
+          if (local_args_info.scd_given)
-+
+            {
-+
+              fprintf (stderr, "%s: `--scd' (`-s') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-+
+              goto failure;
-+
+            }
-+
+          if (args_info->scd_given && ! override)
-+
+            continue;
-+
+          local_args_info.scd_given = 1;
-+
+          args_info->scd_given = 1;
-+
+          if (args_info->staticProps_group_counter && override)
-+
+            reset_group_staticProps (args_info);
-+
+          args_info->staticProps_group_counter += 1;
-+
+          break;
-+
-+
+        case 'd':       /* density plot.  */
-+
+          if (local_args_info.density_given)
-+
+            {
-+
+              fprintf (stderr, "%s: `--density' (`-d') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-+
+              goto failure;
-+
+            }
-+
+          if (args_info->density_given && ! override)
-+
+            continue;
-+
+          local_args_info.density_given = 1;
-+
+          args_info->density_given = 1;
-+
+          if (args_info->staticProps_group_counter && override)
-+
+            reset_group_staticProps (args_info);
-+
+          args_info->staticProps_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)
->
+          /* maximum length (Defaults to 1/2 smallest length of first frame).  */
->
+          if (strcmp (long_options[option_index].name, "length") == 0)
-<
+            if (args_info->sele1_given)
->
+            if (local_args_info.length_given)
-<
+                fprintf (stderr, "%s: `--sele1' option given more than once\n", CMDLINE_PARSER_PACKAGE);
-<
+                clear_args ();
-<
+                exit (EXIT_FAILURE);
->
+                fprintf (stderr, "%s: `--length' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
->
+                goto failure;
-+
+            if (args_info->length_given && ! override)
-+
+              continue;
-+
+            local_args_info.length_given = 1;
-+
+            args_info->length_given = 1;
-+
+            args_info->length_arg = strtod (optarg, &stop_char);
-+
+            if (!(stop_char && *stop_char == '\0')) {
-+
+              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
-+
+              goto failure;
-+
+            }
-+
+            if (args_info->length_orig)
-+
+              free (args_info->length_orig); /* free previous string */
-+
+            args_info->length_orig = gengetopt_strdup (optarg);
-+
+          }
-+
+          /* select the first stuntdouble set.  */
-+
+          else 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);
-<
+            break;
->
+            if (args_info->sele1_orig)
->
+              free (args_info->sele1_orig); /* free previous string */
->
+            args_info->sele1_orig = gengetopt_strdup (optarg);
-<
-<
+          /* select second stuntdouble set.  */
->
+          /* select the second stuntdouble set.  */
+          else if (strcmp (long_options[option_index].name, "sele2") == 0)
-<
+            if (args_info->sele2_given)
->
+            if (local_args_info.sele2_given)
-<
+                fprintf (stderr, "%s: `--sele2' option given more than once\n", CMDLINE_PARSER_PACKAGE);
-<
+                clear_args ();
-<
+                exit (EXIT_FAILURE);
->
+                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);
-<
+            break;
->
+            if (args_info->sele2_orig)
->
+              free (args_info->sele2_orig); /* free previous string */
->
+            args_info->sele2_orig = gengetopt_strdup (optarg);
-<
-<
+          /* g(r).  */
-<
+          else if (strcmp (long_options[option_index].name, "gofr") == 0)
->
+          /* select the third stuntdouble set.  */
->
+          else if (strcmp (long_options[option_index].name, "sele3") == 0)
-<
+            if (args_info->gofr_given)
->
+            if (local_args_info.sele3_given)
-<
+                fprintf (stderr, "%s: `--gofr' option given more than once\n", CMDLINE_PARSER_PACKAGE);
-<
+                clear_args ();
-<
+                exit (EXIT_FAILURE);
->
+                fprintf (stderr, "%s: `--sele3' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
->
+                goto failure;
-<
+            args_info->gofr_given = 1; staticProps_group_counter += 1;
-<
->
+            if (args_info->sele3_given && ! override)
->
+              continue;
->
+            local_args_info.sele3_given = 1;
->
+            args_info->sele3_given = 1;
->
+            if (args_info->sele3_arg)
->
+              free (args_info->sele3_arg); /* free previous string */
->
+            args_info->sele3_arg = gengetopt_strdup (optarg);
->
+            if (args_info->sele3_orig)
->
+              free (args_info->sele3_orig); /* free previous string */
->
+            args_info->sele3_orig = gengetopt_strdup (optarg);
->
+          }
->
+          /* select reference (use and only use with --gxyz).  */
->
+          else if (strcmp (long_options[option_index].name, "refsele") == 0)
->
+          {
->
+            if (local_args_info.refsele_given)
->
+              {
->
+                fprintf (stderr, "%s: `--refsele' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
->
+                goto failure;
->
+              }
->
+            if (args_info->refsele_given && ! override)
->
+              continue;
->
+            local_args_info.refsele_given = 1;
->
+            args_info->refsele_given = 1;
->
+            if (args_info->refsele_arg)
->
+              free (args_info->refsele_arg); /* free previous string */
->
+            args_info->refsele_arg = gengetopt_strdup (optarg);
->
+            if (args_info->refsele_orig)
->
+              free (args_info->refsele_orig); /* free previous string */
->
+            args_info->refsele_orig = gengetopt_strdup (optarg);
->
+          }
->
+          /* molecule name.  */
->
+          else if (strcmp (long_options[option_index].name, "molname") == 0)
->
+          {
->
+            if (local_args_info.molname_given)
->
+              {
->
+                fprintf (stderr, "%s: `--molname' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
->
+                goto failure;
->
+              }
->
+            if (args_info->molname_given && ! override)
->
+              continue;
->
+            local_args_info.molname_given = 1;
->
+            args_info->molname_given = 1;
->
+            if (args_info->molname_arg)
->
+              free (args_info->molname_arg); /* free previous string */
->
+            args_info->molname_arg = gengetopt_strdup (optarg);
->
+            if (args_info->molname_orig)
->
+              free (args_info->molname_orig); /* free previous string */
->
+            args_info->molname_orig = gengetopt_strdup (optarg);
->
+          }
->
+          /* begin internal index.  */
->
+          else if (strcmp (long_options[option_index].name, "begin") == 0)
->
+          {
->
+            if (local_args_info.begin_given)
->
+              {
->
+                fprintf (stderr, "%s: `--begin' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
->
+                goto failure;
->
+              }
->
+            if (args_info->begin_given && ! override)
->
+              continue;
->
+            local_args_info.begin_given = 1;
->
+            args_info->begin_given = 1;
->
+            args_info->begin_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->begin_orig)
->
+              free (args_info->begin_orig); /* free previous string */
->
+            args_info->begin_orig = gengetopt_strdup (optarg);
->
+          }
->
+          /* end internal index.  */
->
+          else if (strcmp (long_options[option_index].name, "end") == 0)
->
+          {
->
+            if (local_args_info.end_given)
->
+              {
->
+                fprintf (stderr, "%s: `--end' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
->
+                goto failure;
->
+              }
->
+            if (args_info->end_given && ! override)
->
+              continue;
->
+            local_args_info.end_given = 1;
->
+            args_info->end_given = 1;
->
+            args_info->end_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->end_orig)
->
+              free (args_info->end_orig); /* free previous string */
->
+            args_info->end_orig = gengetopt_strdup (optarg);
->
+          }
->
+          /* nanoparticle radius.  */
->
+          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, &stop_char);
->
+            if (!(stop_char && *stop_char == '\0')) {
->
+              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
->
+              goto failure;
->
+            }
->
+            if (args_info->radius_orig)
->
+              free (args_info->radius_orig); /* free previous string */
->
+            args_info->radius_orig = gengetopt_strdup (optarg);
->
+          }
->
+          /* bond order parameter (--rcut must be specified).  */
->
+          else if (strcmp (long_options[option_index].name, "bo") == 0)
->
+          {
->
+            if (local_args_info.bo_given)
->
+              {
->
+                fprintf (stderr, "%s: `--bo' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
->
+                goto failure;
->
+              }
->
+            if (args_info->bo_given && ! override)
->
+              continue;
->
+            local_args_info.bo_given = 1;
->
+            args_info->bo_given = 1;
->
+            if (args_info->staticProps_group_counter && override)
->
+              reset_group_staticProps (args_info);
->
+            args_info->staticProps_group_counter += 1;
+            break;
-<
->
+          /* bond order parameter as a function of radius (--rcut must be specified).  */
->
+          else if (strcmp (long_options[option_index].name, "bor") == 0)
->
+          {
->
+            if (local_args_info.bor_given)
->
+              {
->
+                fprintf (stderr, "%s: `--bor' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
->
+                goto failure;
->
+              }
->
+            if (args_info->bor_given && ! override)
->
+              continue;
->
+            local_args_info.bor_given = 1;
->
+            args_info->bor_given = 1;
->
+            if (args_info->staticProps_group_counter && override)
->
+              reset_group_staticProps (args_info);
->
+            args_info->staticProps_group_counter += 1;
->
+            break;
->
+          }
->
+          /* N(theta) bond angle density within (--rcut must be specified).  */
->
+          else if (strcmp (long_options[option_index].name, "bad") == 0)
->
+          {
->
+            if (local_args_info.bad_given)
->
+              {
->
+                fprintf (stderr, "%s: `--bad' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
->
+                goto failure;
->
+              }
->
+            if (args_info->bad_given && ! override)
->
+              continue;
->
+            local_args_info.bad_given = 1;
->
+            args_info->bad_given = 1;
->
+            if (args_info->staticProps_group_counter && override)
->
+              reset_group_staticProps (args_info);
->
+            args_info->staticProps_group_counter += 1;
->
+            break;
->
+          }
->
+          /* g(z).  */
->
+          else if (strcmp (long_options[option_index].name, "gofz") == 0)
->
+          {
->
+            if (local_args_info.gofz_given)
->
+              {
->
+                fprintf (stderr, "%s: `--gofz' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
->
+                goto failure;
->
+              }
->
+            if (args_info->gofz_given && ! override)
->
+              continue;
->
+            local_args_info.gofz_given = 1;
->
+            args_info->gofz_given = 1;
->
+            if (args_info->staticProps_group_counter && override)
->
+              reset_group_staticProps (args_info);
->
+            args_info->staticProps_group_counter += 1;
->
+            break;
->
+          }
+          /* g(r, cos(theta)).  */
+          else if (strcmp (long_options[option_index].name, "r_theta") == 0)
-<
+            if (args_info->r_theta_given)
->
+            if (local_args_info.r_theta_given)
-<
+                fprintf (stderr, "%s: `--r_theta' option given more than once\n", CMDLINE_PARSER_PACKAGE);
-<
+                clear_args ();
-<
+                exit (EXIT_FAILURE);
->
+                fprintf (stderr, "%s: `--r_theta' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
->
+                goto failure;
-<
+            args_info->r_theta_given = 1; staticProps_group_counter += 1;
-<
->
+            if (args_info->r_theta_given && ! override)
->
+              continue;
->
+            local_args_info.r_theta_given = 1;
->
+            args_info->r_theta_given = 1;
->
+            if (args_info->staticProps_group_counter && override)
->
+              reset_group_staticProps (args_info);
->
+            args_info->staticProps_group_counter += 1;
+            break;
-–
+          /* g(r, cos(omega)).  */
+          else if (strcmp (long_options[option_index].name, "r_omega") == 0)
-<
+            if (args_info->r_omega_given)
->
+            if (local_args_info.r_omega_given)
-<
+                fprintf (stderr, "%s: `--r_omega' option given more than once\n", CMDLINE_PARSER_PACKAGE);
-<
+                clear_args ();
-<
+                exit (EXIT_FAILURE);
->
+                fprintf (stderr, "%s: `--r_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
->
+                goto failure;
-<
+            args_info->r_omega_given = 1; staticProps_group_counter += 1;
-<
->
+            if (args_info->r_omega_given && ! override)
->
+              continue;
->
+            local_args_info.r_omega_given = 1;
->
+            args_info->r_omega_given = 1;
->
+            if (args_info->staticProps_group_counter && override)
->
+              reset_group_staticProps (args_info);
->
+            args_info->staticProps_group_counter += 1;
+            break;
-–
+          /* g(cos(theta), cos(omega)).  */
+          else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
-<
+            if (args_info->theta_omega_given)
->
+            if (local_args_info.theta_omega_given)
-<
+                fprintf (stderr, "%s: `--theta_omega' option given more than once\n", CMDLINE_PARSER_PACKAGE);
-<
+                clear_args ();
-<
+                exit (EXIT_FAILURE);
->
+                fprintf (stderr, "%s: `--theta_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
->
+                goto failure;
-<
+            args_info->theta_omega_given = 1; staticProps_group_counter += 1;
-<
->
+            if (args_info->theta_omega_given && ! override)
->
+              continue;
->
+            local_args_info.theta_omega_given = 1;
->
+            args_info->theta_omega_given = 1;
->
+            if (args_info->staticProps_group_counter && override)
->
+              reset_group_staticProps (args_info);
->
+            args_info->staticProps_group_counter += 1;
+            break;
-–
+          /* g(x, y, z).  */
-<
+          else if (strcmp (long_options[option_index].name, "xyz") == 0)
->
+          else if (strcmp (long_options[option_index].name, "gxyz") == 0)
-<
+            if (args_info->xyz_given)
->
+            if (local_args_info.gxyz_given)
-<
+                fprintf (stderr, "%s: `--xyz' option given more than once\n", CMDLINE_PARSER_PACKAGE);
-<
+                clear_args ();
-<
+                exit (EXIT_FAILURE);
->
+                fprintf (stderr, "%s: `--gxyz' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
->
+                goto failure;
-<
+            args_info->xyz_given = 1; staticProps_group_counter += 1;
-<
->
+            if (args_info->gxyz_given && ! override)
->
+              continue;
->
+            local_args_info.gxyz_given = 1;
->
+            args_info->gxyz_given = 1;
->
+            if (args_info->staticProps_group_counter && override)
->
+              reset_group_staticProps (args_info);
->
+            args_info->staticProps_group_counter += 1;
+            break;
-+
+          /* rp2 order parameter (--sele1 and --sele2 must be specified).  */
-+
+          else if (strcmp (long_options[option_index].name, "rp2") == 0)
-+
+          {
-+
+            if (local_args_info.rp2_given)
-+
+              {
-+
+                fprintf (stderr, "%s: `--rp2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-+
+                goto failure;
-+
+              }
-+
+            if (args_info->rp2_given && ! override)
-+
+              continue;
-+
+            local_args_info.rp2_given = 1;
-+
+            args_info->rp2_given = 1;
-+
+            if (args_info->staticProps_group_counter && override)
-+
+              reset_group_staticProps (args_info);
-+
+            args_info->staticProps_group_counter += 1;
-+
+            break;
-+
+          }
-+
+          /* slab density.  */
-+
+          else if (strcmp (long_options[option_index].name, "slab_density") == 0)
-+
+          {
-+
+            if (local_args_info.slab_density_given)
-+
+              {
-+
+                fprintf (stderr, "%s: `--slab_density' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-+
+                goto failure;
-+
+              }
-+
+            if (args_info->slab_density_given && ! override)
-+
+              continue;
-+
+            local_args_info.slab_density_given = 1;
-+
+            args_info->slab_density_given = 1;
-+
+            if (args_info->staticProps_group_counter && override)
-+
+              reset_group_staticProps (args_info);
-+
+            args_info->staticProps_group_counter += 1;
-+
+            break;
-+
+          }
-+
+          /* hxy.  */
-+
+          else if (strcmp (long_options[option_index].name, "hxy") == 0)
-+
+          {
-+
+            if (local_args_info.hxy_given)
-+
+              {
-+
+                fprintf (stderr, "%s: `--hxy' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-+
+                goto failure;
-+
+              }
-+
+            if (args_info->hxy_given && ! override)
-+
+              continue;
-+
+            local_args_info.hxy_given = 1;
-+
+            args_info->hxy_given = 1;
-+
+            if (args_info->staticProps_group_counter && override)
-+
+              reset_group_staticProps (args_info);
-+
+            args_info->staticProps_group_counter += 1;
-+
+            break;
-+
+          }
-+
+          /* rho of R.  */
-+
+          else if (strcmp (long_options[option_index].name, "rho_r") == 0)
-+
+          {
-+
+            if (local_args_info.rho_r_given)
-+
+              {
-+
+                fprintf (stderr, "%s: `--rho_r' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-+
+                goto failure;
-+
+              }
-+
+            if (args_info->rho_r_given && ! override)
-+
+              continue;
-+
+            local_args_info.rho_r_given = 1;
-+
+            args_info->rho_r_given = 1;
-+
+            if (args_info->staticProps_group_counter && override)
-+
+              reset_group_staticProps (args_info);
-+
+            args_info->staticProps_group_counter += 1;
-+
+            break;
-+
+          }
-+
+          /* hull volume of nanoparticle.  */
-+
+          else if (strcmp (long_options[option_index].name, "hullvol") == 0)
-+
+          {
-+
+            if (local_args_info.hullvol_given)
-+
+              {
-+
+                fprintf (stderr, "%s: `--hullvol' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-+
+                goto failure;
-+
+              }
-+
+            if (args_info->hullvol_given && ! override)
-+
+              continue;
-+
+            local_args_info.hullvol_given = 1;
-+
+            args_info->hullvol_given = 1;
-+
+            if (args_info->staticProps_group_counter && override)
-+
+              reset_group_staticProps (args_info);
-+
+            args_info->staticProps_group_counter += 1;
-+
+            break;
-+
+          }
-<
->
+          break;
+        case '?':       /* Invalid option.  */
+          /* `getopt_long' already printed an error message.  */
-<
+          exit (EXIT_FAILURE);
->
+          goto failure;
+        default:        /* bug: option not considered.  */
-<
+          fprintf (stderr, "%s: option unknown: %c\n", CMDLINE_PARSER_PACKAGE, c);
->
+          fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
+          abort ();
+        } /* switch */
+    } /* while */
-<
+  if ( staticProps_group_counter != 1)
->
+  if (args_info->staticProps_group_counter > 1)
-<
+      fprintf (stderr, "%s: %d options of group staticProps were given. One is required\n", CMDLINE_PARSER_PACKAGE, staticProps_group_counter);
-<
+      missing_required_options = 1;
->
+      fprintf (stderr, "%s: %d options of group staticProps were given. One is required.%s\n", argv[0], args_info->staticProps_group_counter, (additional_error ? additional_error : ""));
->
+      error = 1;
-<
+  if (! args_info->input_given)
->
->
+  if (check_required)
-<
+      fprintf (stderr, "%s: '--input' ('-i') option required\n", CMDLINE_PARSER_PACKAGE);
-<
+      missing_required_options = 1;
->
+      error += cmdline_parser_required2 (args_info, argv[0], additional_error);
-–
+  if ( missing_required_options )
-–
+    exit (EXIT_FAILURE);
-+
+  cmdline_parser_release (&local_args_info);
-+
-+
+  if ( error )
-+
+    return (EXIT_FAILURE);
-+
-+
+  if (optind < argc)
-+
+    {
-+
+      int i = 0 ;
-+
+      int found_prog_name = 0;
-+
+      /* whether program name, i.e., argv[0], is in the remaining args
-+
+         (this may happen with some implementations of getopt,
-+
+          but surely not with the one included by gengetopt) */
-+
-+
+      i = optind;
-+
+      while (i < argc)
-+
+        if (argv[i++] == argv[0]) {
-+
+          found_prog_name = 1;
-+
+          break;
-+
+        }
-+
+      i = 0;
-+
-+
+      args_info->inputs_num = argc - optind - found_prog_name;
-+
+      args_info->inputs =
-+
+        (char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
-+
+      while (optind < argc)
-+
+        if (argv[optind++] != argv[0])
-+
+          args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
-+
+    }
-+
+  return 0;
-+
-+
+failure:
-+
-+
+  cmdline_parser_release (&local_args_info);
-+
+  return (EXIT_FAILURE);

Diff Legend

-–
+Removed lines
-+
+Added lines
-<
+Changed lines
->
+Changed lines

Comparing trunk/src/applications/staticProps/StaticPropsCmd.c (file contents): Revision 326 by tim, Sun Feb 13 20:05:42 2005 UTC vs. Revision 1213 by xsun, Wed Jan 23 21:21:50 2008 UTC

Diff Legend

Comparing trunk/src/applications/staticProps/StaticPropsCmd.c (file contents):
Revision 326 by tim, Sun Feb 13 20:05:42 2005 UTC vs.
Revision 1213 by xsun, Wed Jan 23 21:21:50 2008 UTC