applications/staticProps/StaticPropsCmd.cpp

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

  The developers of gengetopt consider the fixed text that goes in all
  gengetopt output files to be in the public domain:
  we make no copyright claims on it.
*/

/* If we use autoconf.  */
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif

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

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

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

#include "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')",
  "      --nbins_z=INT             number of bins in z axis  (default=`100')",
  "  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')",
  "  -c, --rcut=DOUBLE             cutoff radius (rcut)",
  "      --thetacut=DOUBLE         cutoff angle (thetacut)",
  "      --dz=DOUBLE               slab width (dz)",
  "      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
  "      --zlength=DOUBLE          maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
  "  -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)",
  "      --comsele=selection script\n                                select stunt doubles for center-of-mass \n                                  reference point",
  "      --seleoffset=INT          global index offset for a second object (used \n                                  to define a vector between sites in molecule)",
  "      --seleoffset2=INT         global index offset for a third object (used to \n                                  define a vector between sites in molecule)",
  "      --molname=STRING          molecule name",
  "      --begin=INT               begin internal index",
  "      --end=INT                 end internal index",
  "      --radius=DOUBLE           nanoparticle radius",
  "  -v, --voxelSize=DOUBLE        voxel size (angstroms)",
  "      --gaussWidth=DOUBLE       Gaussian width (angstroms)",
  "\n Group: staticProps\n   an option of this group is required",
  "      --bo                      bond order parameter (--rcut must be specified)",
  "      --ior                     icosahedral bond order parameter as a function \n                                  of radius (--rcut must be specified)",
  "      --for                     FCC bond order parameter as a function of \n                                  radius (--rcut must be specified)",
  "      --bad                     N(theta) bond angle density within (--rcut must \n                                  be specified)",
  "      --count                   count of molecules matching selection criteria \n                                  (and associated statistics)",
  "  -g, --gofr                    g(r)",
  "      --gofz                    g(z)",
  "      --r_theta                 g(r, cos(theta))",
  "      --r_omega                 g(r, cos(omega))",
  "      --r_z                     g(r, z)",
  "      --theta_omega             g(cos(theta), cos(omega))",
  "      --gxyz                    g(x, y, z)",
  "      --twodgofr                2D g(r) (Slab width --dz must be specified)",
  "  -p, --p2                      p2 order parameter (--sele1 must be specified, \n                                  --sele2 is optional)",
  "      --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",
  "      --p_angle                 p(cos(theta)) (--sele1 must be specified, \n                                  --sele2 is optional)",
  "      --hxy                     hxy",
  "      --rho_r                   rho of R",
  "      --angle_r                 angle of R",
  "      --hullvol                 hull volume of nanoparticle",
  "      --rodlength               length of nanorod",
  "  -Q, --tet_param               tetrahedrality order parameter (Qk)",
  "      --tet_param_z             spatially-resolved tetrahedrality order \n                                  parameter Qk(z)",
  "      --tet_param_xyz           volume-resolved tetrahedrality order parameter \n                                  Qk(x,y,z).  (voxelSize, rcut, and gaussWidth \n                                  must be specified)",
  "      --rnemdz                  slab-resolved RNEMD statistics (temperature, \n                                  density, velocity)",
  "      --rnemdr                  shell-resolved RNEMD statistics (temperature, \n                                  density, angular velocity)",
  "      --rnemdrt                 shell and angle-resolved RNEMD statistics \n                                  (temperature, density, angular velocity)",
  "      --nitrile                 electrostatic potential to frequency map based \n                                  on the Cho nitrile fits",
  "  -m, --multipole               average multipole moments contained within \n                                  cutoff spheres as a function of radius",
  "      --surfDiffusion           X, Y, and R (surface diffusion if Z exposed and \n                                  bulk immobile) diffusion",
  "      --hbond                   Hydrogen Bonding statistics using geometric \n                                  criteria (rcut and thetacut must be \n                                  specified)",
    0
};

typedef enum {ARG_NO
  , ARG_STRING
  , ARG_INT
  , ARG_DOUBLE
} cmdline_parser_arg_type;

static
void clear_given (struct gengetopt_args_info *args_info);
static
void clear_args (struct gengetopt_args_info *args_info);

static int
cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info,
                        struct cmdline_parser_params *params, const char *additional_error);

static int
cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);

static char *
gengetopt_strdup (const char *s);

static
void clear_given (struct gengetopt_args_info *args_info)
{
  args_info->help_given = 0 ;
  args_info->version_given = 0 ;
  args_info->input_given = 0 ;
  args_info->output_given = 0 ;
  args_info->step_given = 0 ;
  args_info->nbins_given = 0 ;
  args_info->nbins_x_given = 0 ;
  args_info->nbins_y_given = 0 ;
  args_info->nbins_z_given = 0 ;
  args_info->nanglebins_given = 0 ;
  args_info->rcut_given = 0 ;
  args_info->thetacut_given = 0 ;
  args_info->dz_given = 0 ;
  args_info->length_given = 0 ;
  args_info->zlength_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->comsele_given = 0 ;
  args_info->seleoffset_given = 0 ;
  args_info->seleoffset2_given = 0 ;
  args_info->molname_given = 0 ;
  args_info->begin_given = 0 ;
  args_info->end_given = 0 ;
  args_info->radius_given = 0 ;
  args_info->voxelSize_given = 0 ;
  args_info->gaussWidth_given = 0 ;
  args_info->bo_given = 0 ;
  args_info->ior_given = 0 ;
  args_info->for_given = 0 ;
  args_info->bad_given = 0 ;
  args_info->count_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->r_z_given = 0 ;
  args_info->theta_omega_given = 0 ;
  args_info->gxyz_given = 0 ;
  args_info->twodgofr_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->p_angle_given = 0 ;
  args_info->hxy_given = 0 ;
  args_info->rho_r_given = 0 ;
  args_info->angle_r_given = 0 ;
  args_info->hullvol_given = 0 ;
  args_info->rodlength_given = 0 ;
  args_info->tet_param_given = 0 ;
  args_info->tet_param_z_given = 0 ;
  args_info->tet_param_xyz_given = 0 ;
  args_info->rnemdz_given = 0 ;
  args_info->rnemdr_given = 0 ;
  args_info->rnemdrt_given = 0 ;
  args_info->nitrile_given = 0 ;
  args_info->multipole_given = 0 ;
  args_info->surfDiffusion_given = 0 ;
  args_info->hbond_given = 0 ;
  args_info->staticProps_group_counter = 0 ;
}

static
void clear_args (struct gengetopt_args_info *args_info)
{
  FIX_UNUSED (args_info);
  args_info->input_arg = NULL;
  args_info->input_orig = NULL;
  args_info->output_arg = 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->nbins_z_arg = 100;
  args_info->nbins_z_orig = NULL;
  args_info->nanglebins_arg = 50;
  args_info->nanglebins_orig = NULL;
  args_info->rcut_orig = NULL;
  args_info->thetacut_orig = NULL;
  args_info->dz_orig = NULL;
  args_info->length_orig = NULL;
  args_info->zlength_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->comsele_arg = NULL;
  args_info->comsele_orig = NULL;
  args_info->seleoffset_orig = NULL;
  args_info->seleoffset2_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;
  args_info->voxelSize_orig = NULL;
  args_info->gaussWidth_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->nbins_z_help = gengetopt_args_info_help[8] ;
  args_info->nanglebins_help = gengetopt_args_info_help[9] ;
  args_info->rcut_help = gengetopt_args_info_help[10] ;
  args_info->thetacut_help = gengetopt_args_info_help[11] ;
  args_info->dz_help = gengetopt_args_info_help[12] ;
  args_info->length_help = gengetopt_args_info_help[13] ;
  args_info->zlength_help = gengetopt_args_info_help[14] ;
  args_info->zoffset_help = gengetopt_args_info_help[15] ;
  args_info->sele1_help = gengetopt_args_info_help[16] ;
  args_info->sele2_help = gengetopt_args_info_help[17] ;
  args_info->sele3_help = gengetopt_args_info_help[18] ;
  args_info->refsele_help = gengetopt_args_info_help[19] ;
  args_info->comsele_help = gengetopt_args_info_help[20] ;
  args_info->seleoffset_help = gengetopt_args_info_help[21] ;
  args_info->seleoffset2_help = gengetopt_args_info_help[22] ;
  args_info->molname_help = gengetopt_args_info_help[23] ;
  args_info->begin_help = gengetopt_args_info_help[24] ;
  args_info->end_help = gengetopt_args_info_help[25] ;
  args_info->radius_help = gengetopt_args_info_help[26] ;
  args_info->voxelSize_help = gengetopt_args_info_help[27] ;
  args_info->gaussWidth_help = gengetopt_args_info_help[28] ;
  args_info->bo_help = gengetopt_args_info_help[30] ;
  args_info->ior_help = gengetopt_args_info_help[31] ;
  args_info->for_help = gengetopt_args_info_help[32] ;
  args_info->bad_help = gengetopt_args_info_help[33] ;
  args_info->count_help = gengetopt_args_info_help[34] ;
  args_info->gofr_help = gengetopt_args_info_help[35] ;
  args_info->gofz_help = gengetopt_args_info_help[36] ;
  args_info->r_theta_help = gengetopt_args_info_help[37] ;
  args_info->r_omega_help = gengetopt_args_info_help[38] ;
  args_info->r_z_help = gengetopt_args_info_help[39] ;
  args_info->theta_omega_help = gengetopt_args_info_help[40] ;
  args_info->gxyz_help = gengetopt_args_info_help[41] ;
  args_info->twodgofr_help = gengetopt_args_info_help[42] ;
  args_info->p2_help = gengetopt_args_info_help[43] ;
  args_info->rp2_help = gengetopt_args_info_help[44] ;
  args_info->scd_help = gengetopt_args_info_help[45] ;
  args_info->density_help = gengetopt_args_info_help[46] ;
  args_info->slab_density_help = gengetopt_args_info_help[47] ;
  args_info->p_angle_help = gengetopt_args_info_help[48] ;
  args_info->hxy_help = gengetopt_args_info_help[49] ;
  args_info->rho_r_help = gengetopt_args_info_help[50] ;
  args_info->angle_r_help = gengetopt_args_info_help[51] ;
  args_info->hullvol_help = gengetopt_args_info_help[52] ;
  args_info->rodlength_help = gengetopt_args_info_help[53] ;
  args_info->tet_param_help = gengetopt_args_info_help[54] ;
  args_info->tet_param_z_help = gengetopt_args_info_help[55] ;
  args_info->tet_param_xyz_help = gengetopt_args_info_help[56] ;
  args_info->rnemdz_help = gengetopt_args_info_help[57] ;
  args_info->rnemdr_help = gengetopt_args_info_help[58] ;
  args_info->rnemdrt_help = gengetopt_args_info_help[59] ;
  args_info->nitrile_help = gengetopt_args_info_help[60] ;
  args_info->multipole_help = gengetopt_args_info_help[61] ;
  args_info->surfDiffusion_help = gengetopt_args_info_help[62] ;
  args_info->hbond_help = gengetopt_args_info_help[63] ;
  
}

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

static void print_help_common(void) {
  cmdline_parser_print_version ();

  if (strlen(gengetopt_args_info_purpose) > 0)
    printf("\n%s\n", gengetopt_args_info_purpose);

  if (strlen(gengetopt_args_info_usage) > 0)
    printf("\n%s\n", gengetopt_args_info_usage);

  printf("\n");

  if (strlen(gengetopt_args_info_description) > 0)
    printf("%s\n\n", gengetopt_args_info_description);
}

void
cmdline_parser_print_help (void)
{
  int i = 0;
  print_help_common();
  while (gengetopt_args_info_help[i])
    printf("%s\n", gengetopt_args_info_help[i++]);
}

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

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

void
cmdline_parser_params_init(struct cmdline_parser_params *params)
{
  if (params)
    { 
      params->override = 0;
      params->initialize = 1;
      params->check_required = 1;
      params->check_ambiguity = 0;
      params->print_errors = 1;
    }
}

struct cmdline_parser_params *
cmdline_parser_params_create(void)
{
  struct cmdline_parser_params *params = 
    (struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
  cmdline_parser_params_init(params);  
  return params;
}

static void
free_string_field (char **s)
{
  if (*s)
    {
      free (*s);
      *s = 0;
    }
}


static void
cmdline_parser_release (struct gengetopt_args_info *args_info)
{
  unsigned int i;
  free_string_field (&(args_info->input_arg));
  free_string_field (&(args_info->input_orig));
  free_string_field (&(args_info->output_arg));
  free_string_field (&(args_info->output_orig));
  free_string_field (&(args_info->step_orig));
  free_string_field (&(args_info->nbins_orig));
  free_string_field (&(args_info->nbins_x_orig));
  free_string_field (&(args_info->nbins_y_orig));
  free_string_field (&(args_info->nbins_z_orig));
  free_string_field (&(args_info->nanglebins_orig));
  free_string_field (&(args_info->rcut_orig));
  free_string_field (&(args_info->thetacut_orig));
  free_string_field (&(args_info->dz_orig));
  free_string_field (&(args_info->length_orig));
  free_string_field (&(args_info->zlength_orig));
  free_string_field (&(args_info->zoffset_orig));
  free_string_field (&(args_info->sele1_arg));
  free_string_field (&(args_info->sele1_orig));
  free_string_field (&(args_info->sele2_arg));
  free_string_field (&(args_info->sele2_orig));
  free_string_field (&(args_info->sele3_arg));
  free_string_field (&(args_info->sele3_orig));
  free_string_field (&(args_info->refsele_arg));
  free_string_field (&(args_info->refsele_orig));
  free_string_field (&(args_info->comsele_arg));
  free_string_field (&(args_info->comsele_orig));
  free_string_field (&(args_info->seleoffset_orig));
  free_string_field (&(args_info->seleoffset2_orig));
  free_string_field (&(args_info->molname_arg));
  free_string_field (&(args_info->molname_orig));
  free_string_field (&(args_info->begin_orig));
  free_string_field (&(args_info->end_orig));
  free_string_field (&(args_info->radius_orig));
  free_string_field (&(args_info->voxelSize_orig));
  free_string_field (&(args_info->gaussWidth_orig));
  
  
  for (i = 0; i < args_info->inputs_num; ++i)
    free (args_info->inputs [i]);

  if (args_info->inputs_num)
    free (args_info->inputs);

  clear_given (args_info);
}


static void
write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
{
  FIX_UNUSED (values);
  if (arg) {
    fprintf(outfile, "%s=\"%s\"\n", opt, arg);
  } else {
    fprintf(outfile, "%s\n", opt);
  }
}


int
cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
{
  int i = 0;

  if (!outfile)
    {
      fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
      return EXIT_FAILURE;
    }

  if (args_info->help_given)
    write_into_file(outfile, "help", 0, 0 );
  if (args_info->version_given)
    write_into_file(outfile, "version", 0, 0 );
  if (args_info->input_given)
    write_into_file(outfile, "input", args_info->input_orig, 0);
  if (args_info->output_given)
    write_into_file(outfile, "output", args_info->output_orig, 0);
  if (args_info->step_given)
    write_into_file(outfile, "step", args_info->step_orig, 0);
  if (args_info->nbins_given)
    write_into_file(outfile, "nbins", args_info->nbins_orig, 0);
  if (args_info->nbins_x_given)
    write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0);
  if (args_info->nbins_y_given)
    write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0);
  if (args_info->nbins_z_given)
    write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0);
  if (args_info->nanglebins_given)
    write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
  if (args_info->rcut_given)
    write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
  if (args_info->thetacut_given)
    write_into_file(outfile, "thetacut", args_info->thetacut_orig, 0);
  if (args_info->dz_given)
    write_into_file(outfile, "dz", args_info->dz_orig, 0);
  if (args_info->length_given)
    write_into_file(outfile, "length", args_info->length_orig, 0);
  if (args_info->zlength_given)
    write_into_file(outfile, "zlength", args_info->zlength_orig, 0);
  if (args_info->zoffset_given)
    write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0);
  if (args_info->sele1_given)
    write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
  if (args_info->sele2_given)
    write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
  if (args_info->sele3_given)
    write_into_file(outfile, "sele3", args_info->sele3_orig, 0);
  if (args_info->refsele_given)
    write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
  if (args_info->comsele_given)
    write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
  if (args_info->seleoffset_given)
    write_into_file(outfile, "seleoffset", args_info->seleoffset_orig, 0);
  if (args_info->seleoffset2_given)
    write_into_file(outfile, "seleoffset2", args_info->seleoffset2_orig, 0);
  if (args_info->molname_given)
    write_into_file(outfile, "molname", args_info->molname_orig, 0);
  if (args_info->begin_given)
    write_into_file(outfile, "begin", args_info->begin_orig, 0);
  if (args_info->end_given)
    write_into_file(outfile, "end", args_info->end_orig, 0);
  if (args_info->radius_given)
    write_into_file(outfile, "radius", args_info->radius_orig, 0);
  if (args_info->voxelSize_given)
    write_into_file(outfile, "voxelSize", args_info->voxelSize_orig, 0);
  if (args_info->gaussWidth_given)
    write_into_file(outfile, "gaussWidth", args_info->gaussWidth_orig, 0);
  if (args_info->bo_given)
    write_into_file(outfile, "bo", 0, 0 );
  if (args_info->ior_given)
    write_into_file(outfile, "ior", 0, 0 );
  if (args_info->for_given)
    write_into_file(outfile, "for", 0, 0 );
  if (args_info->bad_given)
    write_into_file(outfile, "bad", 0, 0 );
  if (args_info->count_given)
    write_into_file(outfile, "count", 0, 0 );
  if (args_info->gofr_given)
    write_into_file(outfile, "gofr", 0, 0 );
  if (args_info->gofz_given)
    write_into_file(outfile, "gofz", 0, 0 );
  if (args_info->r_theta_given)
    write_into_file(outfile, "r_theta", 0, 0 );
  if (args_info->r_omega_given)
    write_into_file(outfile, "r_omega", 0, 0 );
  if (args_info->r_z_given)
    write_into_file(outfile, "r_z", 0, 0 );
  if (args_info->theta_omega_given)
    write_into_file(outfile, "theta_omega", 0, 0 );
  if (args_info->gxyz_given)
    write_into_file(outfile, "gxyz", 0, 0 );
  if (args_info->twodgofr_given)
    write_into_file(outfile, "twodgofr", 0, 0 );
  if (args_info->p2_given)
    write_into_file(outfile, "p2", 0, 0 );
  if (args_info->rp2_given)
    write_into_file(outfile, "rp2", 0, 0 );
  if (args_info->scd_given)
    write_into_file(outfile, "scd", 0, 0 );
  if (args_info->density_given)
    write_into_file(outfile, "density", 0, 0 );
  if (args_info->slab_density_given)
    write_into_file(outfile, "slab_density", 0, 0 );
  if (args_info->p_angle_given)
    write_into_file(outfile, "p_angle", 0, 0 );
  if (args_info->hxy_given)
    write_into_file(outfile, "hxy", 0, 0 );
  if (args_info->rho_r_given)
    write_into_file(outfile, "rho_r", 0, 0 );
  if (args_info->angle_r_given)
    write_into_file(outfile, "angle_r", 0, 0 );
  if (args_info->hullvol_given)
    write_into_file(outfile, "hullvol", 0, 0 );
  if (args_info->rodlength_given)
    write_into_file(outfile, "rodlength", 0, 0 );
  if (args_info->tet_param_given)
    write_into_file(outfile, "tet_param", 0, 0 );
  if (args_info->tet_param_z_given)
    write_into_file(outfile, "tet_param_z", 0, 0 );
  if (args_info->tet_param_xyz_given)
    write_into_file(outfile, "tet_param_xyz", 0, 0 );
  if (args_info->rnemdz_given)
    write_into_file(outfile, "rnemdz", 0, 0 );
  if (args_info->rnemdr_given)
    write_into_file(outfile, "rnemdr", 0, 0 );
  if (args_info->rnemdrt_given)
    write_into_file(outfile, "rnemdrt", 0, 0 );
  if (args_info->nitrile_given)
    write_into_file(outfile, "nitrile", 0, 0 );
  if (args_info->multipole_given)
    write_into_file(outfile, "multipole", 0, 0 );
  if (args_info->surfDiffusion_given)
    write_into_file(outfile, "surfDiffusion", 0, 0 );
  if (args_info->hbond_given)
    write_into_file(outfile, "hbond", 0, 0 );
  

  i = EXIT_SUCCESS;
  return i;
}

int
cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
{
  FILE *outfile;
  int i = 0;

  outfile = fopen(filename, "w");

  if (!outfile)
    {
      fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
      return EXIT_FAILURE;
    }

  i = cmdline_parser_dump(outfile, args_info);
  fclose (outfile);

  return i;
}

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

/** @brief replacement of strdup, which is not standard */
char *
gengetopt_strdup (const char *s)
{
  char *result = 0;
  if (!s)
    return result;

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

static void
reset_group_staticProps(struct gengetopt_args_info *args_info)
{
  if (! args_info->staticProps_group_counter)
    return;
  
  args_info->bo_given = 0 ;
  args_info->ior_given = 0 ;
  args_info->for_given = 0 ;
  args_info->bad_given = 0 ;
  args_info->count_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->r_z_given = 0 ;
  args_info->theta_omega_given = 0 ;
  args_info->gxyz_given = 0 ;
  args_info->twodgofr_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->p_angle_given = 0 ;
  args_info->hxy_given = 0 ;
  args_info->rho_r_given = 0 ;
  args_info->angle_r_given = 0 ;
  args_info->hullvol_given = 0 ;
  args_info->rodlength_given = 0 ;
  args_info->tet_param_given = 0 ;
  args_info->tet_param_z_given = 0 ;
  args_info->tet_param_xyz_given = 0 ;
  args_info->rnemdz_given = 0 ;
  args_info->rnemdr_given = 0 ;
  args_info->rnemdrt_given = 0 ;
  args_info->nitrile_given = 0 ;
  args_info->multipole_given = 0 ;
  args_info->surfDiffusion_given = 0 ;
  args_info->hbond_given = 0 ;

  args_info->staticProps_group_counter = 0;
}

int
cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info)
{
  return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
}

int
cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info,
                   struct cmdline_parser_params *params)
{
  int result;
  result = cmdline_parser_internal (argc, argv, args_info, params, 0);

  if (result == EXIT_FAILURE)
    {
      cmdline_parser_free (args_info);
      exit (EXIT_FAILURE);
    }
  
  return result;
}

int
cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
{
  int result;
  struct cmdline_parser_params params;
  
  params.override = override;
  params.initialize = initialize;
  params.check_required = check_required;
  params.check_ambiguity = 0;
  params.print_errors = 1;

  result = cmdline_parser_internal (argc, argv, args_info, &params, 0);

  if (result == EXIT_FAILURE)
    {
      cmdline_parser_free (args_info);
      exit (EXIT_FAILURE);
    }
  
  return result;
}

int
cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name)
{
  int result = EXIT_SUCCESS;

  if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
    result = EXIT_FAILURE;

  if (result == EXIT_FAILURE)
    {
      cmdline_parser_free (args_info);
      exit (EXIT_FAILURE);
    }
  
  return result;
}

int
cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
{
  int error = 0;
  FIX_UNUSED (additional_error);

  /* checks for required options */
  if (! args_info->input_given)
    {
      fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
      error = 1;
    }
  
  if (args_info->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;
}


static char *package_name = 0;

/**
 * @brief updates an option
 * @param field the generic pointer to the field to update
 * @param orig_field the pointer to the orig field
 * @param field_given the pointer to the number of occurrence of this option
 * @param prev_given the pointer to the number of occurrence already seen
 * @param value the argument for this option (if null no arg was specified)
 * @param possible_values the possible values for this option (if specified)
 * @param default_value the default value (in case the option only accepts fixed values)
 * @param arg_type the type of this option
 * @param check_ambiguity @see cmdline_parser_params.check_ambiguity
 * @param override @see cmdline_parser_params.override
 * @param no_free whether to free a possible previous value
 * @param multiple_option whether this is a multiple option
 * @param long_opt the corresponding long option
 * @param short_opt the corresponding short option (or '-' if none)
 * @param additional_error possible further error specification
 */
static
int update_arg(void *field, char **orig_field,
               unsigned int *field_given, unsigned int *prev_given, 
               char *value, const char *possible_values[],
               const char *default_value,
               cmdline_parser_arg_type arg_type,
               int check_ambiguity, int override,
               int no_free, int multiple_option,
               const char *long_opt, char short_opt,
               const char *additional_error)
{
  char *stop_char = 0;
  const char *val = value;
  int found;
  char **string_field;
  FIX_UNUSED (field);

  stop_char = 0;
  found = 0;

  if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
    {
      if (short_opt != '-')
        fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n", 
               package_name, long_opt, short_opt,
               (additional_error ? additional_error : ""));
      else
        fprintf (stderr, "%s: `--%s' option given more than once%s\n", 
               package_name, long_opt,
               (additional_error ? additional_error : ""));
      return 1; /* failure */
    }

  FIX_UNUSED (default_value);
    
  if (field_given && *field_given && ! override)
    return 0;
  if (prev_given)
    (*prev_given)++;
  if (field_given)
    (*field_given)++;
  if (possible_values)
    val = possible_values[found];

  switch(arg_type) {
  case ARG_INT:
    if (val) *((int *)field) = strtol (val, &stop_char, 0);
    break;
  case ARG_DOUBLE:
    if (val) *((double *)field) = strtod (val, &stop_char);
    break;
  case ARG_STRING:
    if (val) {
      string_field = (char **)field;
      if (!no_free && *string_field)
        free (*string_field); /* free previous string */
      *string_field = gengetopt_strdup (val);
    }
    break;
  default:
    break;
  };

  /* check numeric conversion */
  switch(arg_type) {
  case ARG_INT:
  case ARG_DOUBLE:
    if (val && !(stop_char && *stop_char == '\0')) {
      fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
      return 1; /* failure */
    }
    break;
  default:
    ;
  };

  /* store the original value */
  switch(arg_type) {
  case ARG_NO:
    break;
  default:
    if (value && orig_field) {
      if (no_free) {
        *orig_field = value;
      } else {
        if (*orig_field)
          free (*orig_field); /* free previous string */
        *orig_field = gengetopt_strdup (value);
      }
    }
  };

  return 0; /* OK */
}


int
cmdline_parser_internal (
  int argc, char **argv, struct gengetopt_args_info *args_info,
                        struct cmdline_parser_params *params, const char *additional_error)
{
  int c;        /* Character of the parsed option.  */

  int error = 0;
  struct gengetopt_args_info local_args_info;
  
  int override;
  int initialize;
  int check_required;
  int check_ambiguity;
  
  package_name = argv[0];
  
  override = params->override;
  initialize = params->initialize;
  check_required = params->check_required;
  check_ambiguity = params->check_ambiguity;

  if (initialize)
    cmdline_parser_init (args_info);

  cmdline_parser_init (&local_args_info);

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

  while (1)
    {
      int option_index = 0;

      static struct option long_options[] = {
        { "help",       0, NULL, 'h' },
        { "version",    0, NULL, 'V' },
        { "input",      1, NULL, 'i' },
        { "output",     1, NULL, 'o' },
        { "step",       1, NULL, 'n' },
        { "nbins",      1, NULL, 'b' },
        { "nbins_x",    1, NULL, 'x' },
        { "nbins_y",    1, NULL, 'y' },
        { "nbins_z",    1, NULL, 0 },
        { "nanglebins", 1, NULL, 'a' },
        { "rcut",       1, NULL, 'c' },
        { "thetacut",   1, NULL, 0 },
        { "dz", 1, NULL, 0 },
        { "length",     1, NULL, 0 },
        { "zlength",    1, NULL, 0 },
        { "zoffset",    1, NULL, 'z' },
        { "sele1",      1, NULL, 0 },
        { "sele2",      1, NULL, 0 },
        { "sele3",      1, NULL, 0 },
        { "refsele",    1, NULL, 0 },
        { "comsele",    1, NULL, 0 },
        { "seleoffset", 1, NULL, 0 },
        { "seleoffset2",        1, NULL, 0 },
        { "molname",    1, NULL, 0 },
        { "begin",      1, NULL, 0 },
        { "end",        1, NULL, 0 },
        { "radius",     1, NULL, 0 },
        { "voxelSize",  1, NULL, 'v' },
        { "gaussWidth", 1, NULL, 0 },
        { "bo", 0, NULL, 0 },
        { "ior",        0, NULL, 0 },
        { "for",        0, NULL, 0 },
        { "bad",        0, NULL, 0 },
        { "count",      0, NULL, 0 },
        { "gofr",       0, NULL, 'g' },
        { "gofz",       0, NULL, 0 },
        { "r_theta",    0, NULL, 0 },
        { "r_omega",    0, NULL, 0 },
        { "r_z",        0, NULL, 0 },
        { "theta_omega",        0, NULL, 0 },
        { "gxyz",       0, NULL, 0 },
        { "twodgofr",   0, NULL, 0 },
        { "p2", 0, NULL, 'p' },
        { "rp2",        0, NULL, 0 },
        { "scd",        0, NULL, 's' },
        { "density",    0, NULL, 'd' },
        { "slab_density",       0, NULL, 0 },
        { "p_angle",    0, NULL, 0 },
        { "hxy",        0, NULL, 0 },
        { "rho_r",      0, NULL, 0 },
        { "angle_r",    0, NULL, 0 },
        { "hullvol",    0, NULL, 0 },
        { "rodlength",  0, NULL, 0 },
        { "tet_param",  0, NULL, 'Q' },
        { "tet_param_z",        0, NULL, 0 },
        { "tet_param_xyz",      0, NULL, 0 },
        { "rnemdz",     0, NULL, 0 },
        { "rnemdr",     0, NULL, 0 },
        { "rnemdrt",    0, NULL, 0 },
        { "nitrile",    0, NULL, 0 },
        { "multipole",  0, NULL, 'm' },
        { "surfDiffusion",      0, NULL, 0 },
        { "hbond",      0, NULL, 0 },
        { 0,  0, 0, 0 }
      };

      c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:v:gpsdQm", long_options, &option_index);

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

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

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

        case 'i':       /* input dump file.  */
        
        
          if (update_arg( (void *)&(args_info->input_arg), 
               &(args_info->input_orig), &(args_info->input_given),
              &(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
              check_ambiguity, override, 0, 0,
              "input", 'i',
              additional_error))
            goto failure;
        
          break;
        case 'o':       /* output file name.  */
        
        
          if (update_arg( (void *)&(args_info->output_arg), 
               &(args_info->output_orig), &(args_info->output_given),
              &(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
              check_ambiguity, override, 0, 0,
              "output", 'o',
              additional_error))
            goto failure;
        
          break;
        case 'n':       /* process every n frame.  */
        
        
          if (update_arg( (void *)&(args_info->step_arg), 
               &(args_info->step_orig), &(args_info->step_given),
              &(local_args_info.step_given), optarg, 0, "1", ARG_INT,
              check_ambiguity, override, 0, 0,
              "step", 'n',
              additional_error))
            goto failure;
        
          break;
        case 'b':       /* number of bins (general purpose).  */
        
        
          if (update_arg( (void *)&(args_info->nbins_arg), 
               &(args_info->nbins_orig), &(args_info->nbins_given),
              &(local_args_info.nbins_given), optarg, 0, "100", ARG_INT,
              check_ambiguity, override, 0, 0,
              "nbins", 'b',
              additional_error))
            goto failure;
        
          break;
        case 'x':       /* number of bins in x axis.  */
        
        
          if (update_arg( (void *)&(args_info->nbins_x_arg), 
               &(args_info->nbins_x_orig), &(args_info->nbins_x_given),
              &(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT,
              check_ambiguity, override, 0, 0,
              "nbins_x", 'x',
              additional_error))
            goto failure;
        
          break;
        case 'y':       /* number of bins in y axis.  */
        
        
          if (update_arg( (void *)&(args_info->nbins_y_arg), 
               &(args_info->nbins_y_orig), &(args_info->nbins_y_given),
              &(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT,
              check_ambiguity, override, 0, 0,
              "nbins_y", 'y',
              additional_error))
            goto failure;
        
          break;
        case 'a':       /* number of bins for cos(angle).  */
        
        
          if (update_arg( (void *)&(args_info->nanglebins_arg), 
               &(args_info->nanglebins_orig), &(args_info->nanglebins_given),
              &(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT,
              check_ambiguity, override, 0, 0,
              "nanglebins", 'a',
              additional_error))
            goto failure;
        
          break;
        case 'c':       /* cutoff radius (rcut).  */
        
        
          if (update_arg( (void *)&(args_info->rcut_arg), 
               &(args_info->rcut_orig), &(args_info->rcut_given),
              &(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE,
              check_ambiguity, override, 0, 0,
              "rcut", 'c',
              additional_error))
            goto failure;
        
          break;
        case 'z':       /* Where to set the zero for the slab_density calculation.  */
        
        
          if (update_arg( (void *)&(args_info->zoffset_arg), 
               &(args_info->zoffset_orig), &(args_info->zoffset_given),
              &(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE,
              check_ambiguity, override, 0, 0,
              "zoffset", 'z',
              additional_error))
            goto failure;
        
          break;
        case 'v':       /* voxel size (angstroms).  */
        
        
          if (update_arg( (void *)&(args_info->voxelSize_arg), 
               &(args_info->voxelSize_orig), &(args_info->voxelSize_given),
              &(local_args_info.voxelSize_given), optarg, 0, 0, ARG_DOUBLE,
              check_ambiguity, override, 0, 0,
              "voxelSize", 'v',
              additional_error))
            goto failure;
        
          break;
        case 'g':       /* g(r).  */
        
          if (args_info->staticProps_group_counter && override)
            reset_group_staticProps (args_info);
          args_info->staticProps_group_counter += 1;
        
          if (update_arg( 0 , 
               0 , &(args_info->gofr_given),
              &(local_args_info.gofr_given), optarg, 0, 0, ARG_NO,
              check_ambiguity, override, 0, 0,
              "gofr", 'g',
              additional_error))
            goto failure;
        
          break;
        case 'p':       /* p2 order parameter (--sele1 must be specified, --sele2 is optional).  */
        
          if (args_info->staticProps_group_counter && override)
            reset_group_staticProps (args_info);
          args_info->staticProps_group_counter += 1;
        
          if (update_arg( 0 , 
               0 , &(args_info->p2_given),
              &(local_args_info.p2_given), optarg, 0, 0, ARG_NO,
              check_ambiguity, override, 0, 0,
              "p2", 'p',
              additional_error))
            goto failure;
        
          break;
        case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
        
          if (args_info->staticProps_group_counter && override)
            reset_group_staticProps (args_info);
          args_info->staticProps_group_counter += 1;
        
          if (update_arg( 0 , 
               0 , &(args_info->scd_given),
              &(local_args_info.scd_given), optarg, 0, 0, ARG_NO,
              check_ambiguity, override, 0, 0,
              "scd", 's',
              additional_error))
            goto failure;
        
          break;
        case 'd':       /* density plot.  */
        
          if (args_info->staticProps_group_counter && override)
            reset_group_staticProps (args_info);
          args_info->staticProps_group_counter += 1;
        
          if (update_arg( 0 , 
               0 , &(args_info->density_given),
              &(local_args_info.density_given), optarg, 0, 0, ARG_NO,
              check_ambiguity, override, 0, 0,
              "density", 'd',
              additional_error))
            goto failure;
        
          break;
        case 'Q':       /* tetrahedrality order parameter (Qk).  */
        
          if (args_info->staticProps_group_counter && override)
            reset_group_staticProps (args_info);
          args_info->staticProps_group_counter += 1;
        
          if (update_arg( 0 , 
               0 , &(args_info->tet_param_given),
              &(local_args_info.tet_param_given), optarg, 0, 0, ARG_NO,
              check_ambiguity, override, 0, 0,
              "tet_param", 'Q',
              additional_error))
            goto failure;
        
          break;
        case 'm':       /* average multipole moments contained within cutoff spheres as a function of radius.  */
        
          if (args_info->staticProps_group_counter && override)
            reset_group_staticProps (args_info);
          args_info->staticProps_group_counter += 1;
        
          if (update_arg( 0 , 
               0 , &(args_info->multipole_given),
              &(local_args_info.multipole_given), optarg, 0, 0, ARG_NO,
              check_ambiguity, override, 0, 0,
              "multipole", 'm',
              additional_error))
            goto failure;
        
          break;

        case 0: /* Long option with no short option */
          /* number of bins in z axis.  */
          if (strcmp (long_options[option_index].name, "nbins_z") == 0)
          {
          
          
            if (update_arg( (void *)&(args_info->nbins_z_arg), 
                 &(args_info->nbins_z_orig), &(args_info->nbins_z_given),
                &(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT,
                check_ambiguity, override, 0, 0,
                "nbins_z", '-',
                additional_error))
              goto failure;
          
          }
          /* cutoff angle (thetacut).  */
          else if (strcmp (long_options[option_index].name, "thetacut") == 0)
          {
          
          
            if (update_arg( (void *)&(args_info->thetacut_arg), 
                 &(args_info->thetacut_orig), &(args_info->thetacut_given),
                &(local_args_info.thetacut_given), optarg, 0, 0, ARG_DOUBLE,
                check_ambiguity, override, 0, 0,
                "thetacut", '-',
                additional_error))
              goto failure;
          
          }
          /* slab width (dz).  */
          else if (strcmp (long_options[option_index].name, "dz") == 0)
          {
          
          
            if (update_arg( (void *)&(args_info->dz_arg), 
                 &(args_info->dz_orig), &(args_info->dz_given),
                &(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE,
                check_ambiguity, override, 0, 0,
                "dz", '-',
                additional_error))
              goto failure;
          
          }
          /* maximum length (Defaults to 1/2 smallest length of first frame).  */
          else if (strcmp (long_options[option_index].name, "length") == 0)
          {
          
          
            if (update_arg( (void *)&(args_info->length_arg), 
                 &(args_info->length_orig), &(args_info->length_given),
                &(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE,
                check_ambiguity, override, 0, 0,
                "length", '-',
                additional_error))
              goto failure;
          
          }
          /* maximum length (Defaults to 1/2 smallest length of first frame).  */
          else if (strcmp (long_options[option_index].name, "zlength") == 0)
          {
          
          
            if (update_arg( (void *)&(args_info->zlength_arg), 
                 &(args_info->zlength_orig), &(args_info->zlength_given),
                &(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE,
                check_ambiguity, override, 0, 0,
                "zlength", '-',
                additional_error))
              goto failure;
          
          }
          /* select the first stuntdouble set.  */
          else if (strcmp (long_options[option_index].name, "sele1") == 0)
          {
          
          
            if (update_arg( (void *)&(args_info->sele1_arg), 
                 &(args_info->sele1_orig), &(args_info->sele1_given),
                &(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
                check_ambiguity, override, 0, 0,
                "sele1", '-',
                additional_error))
              goto failure;
          
          }
          /* select the second stuntdouble set.  */
          else if (strcmp (long_options[option_index].name, "sele2") == 0)
          {
          
          
            if (update_arg( (void *)&(args_info->sele2_arg), 
                 &(args_info->sele2_orig), &(args_info->sele2_given),
                &(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
                check_ambiguity, override, 0, 0,
                "sele2", '-',
                additional_error))
              goto failure;
          
          }
          /* select the third stuntdouble set.  */
          else if (strcmp (long_options[option_index].name, "sele3") == 0)
          {
          
          
            if (update_arg( (void *)&(args_info->sele3_arg), 
                 &(args_info->sele3_orig), &(args_info->sele3_given),
                &(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING,
                check_ambiguity, override, 0, 0,
                "sele3", '-',
                additional_error))
              goto failure;
          
          }
          /* select reference (use and only use with --gxyz).  */
          else if (strcmp (long_options[option_index].name, "refsele") == 0)
          {
          
          
            if (update_arg( (void *)&(args_info->refsele_arg), 
                 &(args_info->refsele_orig), &(args_info->refsele_given),
                &(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
                check_ambiguity, override, 0, 0,
                "refsele", '-',
                additional_error))
              goto failure;
          
          }
          /* select stunt doubles for center-of-mass reference point.  */
          else if (strcmp (long_options[option_index].name, "comsele") == 0)
          {
          
          
            if (update_arg( (void *)&(args_info->comsele_arg), 
                 &(args_info->comsele_orig), &(args_info->comsele_given),
                &(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING,
                check_ambiguity, override, 0, 0,
                "comsele", '-',
                additional_error))
              goto failure;
          
          }
          /* global index offset for a second object (used to define a vector between sites in molecule).  */
          else if (strcmp (long_options[option_index].name, "seleoffset") == 0)
          {
          
          
            if (update_arg( (void *)&(args_info->seleoffset_arg), 
                 &(args_info->seleoffset_orig), &(args_info->seleoffset_given),
                &(local_args_info.seleoffset_given), optarg, 0, 0, ARG_INT,
                check_ambiguity, override, 0, 0,
                "seleoffset", '-',
                additional_error))
              goto failure;
          
          }
          /* global index offset for a third object (used to define a vector between sites in molecule).  */
          else if (strcmp (long_options[option_index].name, "seleoffset2") == 0)
          {
          
          
            if (update_arg( (void *)&(args_info->seleoffset2_arg), 
                 &(args_info->seleoffset2_orig), &(args_info->seleoffset2_given),
                &(local_args_info.seleoffset2_given), optarg, 0, 0, ARG_INT,
                check_ambiguity, override, 0, 0,
                "seleoffset2", '-',
                additional_error))
              goto failure;
          
          }
          /* molecule name.  */
          else if (strcmp (long_options[option_index].name, "molname") == 0)
          {
          
          
            if (update_arg( (void *)&(args_info->molname_arg), 
                 &(args_info->molname_orig), &(args_info->molname_given),
                &(local_args_info.molname_given), optarg, 0, 0, ARG_STRING,
                check_ambiguity, override, 0, 0,
                "molname", '-',
                additional_error))
              goto failure;
          
          }
          /* begin internal index.  */
          else if (strcmp (long_options[option_index].name, "begin") == 0)
          {
          
          
            if (update_arg( (void *)&(args_info->begin_arg), 
                 &(args_info->begin_orig), &(args_info->begin_given),
                &(local_args_info.begin_given), optarg, 0, 0, ARG_INT,
                check_ambiguity, override, 0, 0,
                "begin", '-',
                additional_error))
              goto failure;
          
          }
          /* end internal index.  */
          else if (strcmp (long_options[option_index].name, "end") == 0)
          {
          
          
            if (update_arg( (void *)&(args_info->end_arg), 
                 &(args_info->end_orig), &(args_info->end_given),
                &(local_args_info.end_given), optarg, 0, 0, ARG_INT,
                check_ambiguity, override, 0, 0,
                "end", '-',
                additional_error))
              goto failure;
          
          }
          /* nanoparticle radius.  */
          else if (strcmp (long_options[option_index].name, "radius") == 0)
          {
          
          
            if (update_arg( (void *)&(args_info->radius_arg), 
                 &(args_info->radius_orig), &(args_info->radius_given),
                &(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
                check_ambiguity, override, 0, 0,
                "radius", '-',
                additional_error))
              goto failure;
          
          }
          /* Gaussian width (angstroms).  */
          else if (strcmp (long_options[option_index].name, "gaussWidth") == 0)
          {
          
          
            if (update_arg( (void *)&(args_info->gaussWidth_arg), 
                 &(args_info->gaussWidth_orig), &(args_info->gaussWidth_given),
                &(local_args_info.gaussWidth_given), optarg, 0, 0, ARG_DOUBLE,
                check_ambiguity, override, 0, 0,
                "gaussWidth", '-',
                additional_error))
              goto failure;
          
          }
          /* bond order parameter (--rcut must be specified).  */
          else if (strcmp (long_options[option_index].name, "bo") == 0)
          {
          
            if (args_info->staticProps_group_counter && override)
              reset_group_staticProps (args_info);
            args_info->staticProps_group_counter += 1;
          
            if (update_arg( 0 , 
                 0 , &(args_info->bo_given),
                &(local_args_info.bo_given), optarg, 0, 0, ARG_NO,
                check_ambiguity, override, 0, 0,
                "bo", '-',
                additional_error))
              goto failure;
          
          }
          /* icosahedral bond order parameter as a function of radius (--rcut must be specified).  */
          else if (strcmp (long_options[option_index].name, "ior") == 0)
          {
          
            if (args_info->staticProps_group_counter && override)
              reset_group_staticProps (args_info);
            args_info->staticProps_group_counter += 1;
          
            if (update_arg( 0 , 
                 0 , &(args_info->ior_given),
                &(local_args_info.ior_given), optarg, 0, 0, ARG_NO,
                check_ambiguity, override, 0, 0,
                "ior", '-',
                additional_error))
              goto failure;
          
          }
          /* FCC bond order parameter as a function of radius (--rcut must be specified).  */
          else if (strcmp (long_options[option_index].name, "for") == 0)
          {
          
            if (args_info->staticProps_group_counter && override)
              reset_group_staticProps (args_info);
            args_info->staticProps_group_counter += 1;
          
            if (update_arg( 0 , 
                 0 , &(args_info->for_given),
                &(local_args_info.for_given), optarg, 0, 0, ARG_NO,
                check_ambiguity, override, 0, 0,
                "for", '-',
                additional_error))
              goto failure;
          
          }
          /* N(theta) bond angle density within (--rcut must be specified).  */
          else if (strcmp (long_options[option_index].name, "bad") == 0)
          {
          
            if (args_info->staticProps_group_counter && override)
              reset_group_staticProps (args_info);
            args_info->staticProps_group_counter += 1;
          
            if (update_arg( 0 , 
                 0 , &(args_info->bad_given),
                &(local_args_info.bad_given), optarg, 0, 0, ARG_NO,
                check_ambiguity, override, 0, 0,
                "bad", '-',
                additional_error))
              goto failure;
          
          }
          /* count of molecules matching selection criteria (and associated statistics).  */
          else if (strcmp (long_options[option_index].name, "count") == 0)
          {
          
            if (args_info->staticProps_group_counter && override)
              reset_group_staticProps (args_info);
            args_info->staticProps_group_counter += 1;
          
            if (update_arg( 0 , 
                 0 , &(args_info->count_given),
                &(local_args_info.count_given), optarg, 0, 0, ARG_NO,
                check_ambiguity, override, 0, 0,
                "count", '-',
                additional_error))
              goto failure;
          
          }
          /* g(z).  */
          else if (strcmp (long_options[option_index].name, "gofz") == 0)
          {
          
            if (args_info->staticProps_group_counter && override)
              reset_group_staticProps (args_info);
            args_info->staticProps_group_counter += 1;
          
            if (update_arg( 0 , 
                 0 , &(args_info->gofz_given),
                &(local_args_info.gofz_given), optarg, 0, 0, ARG_NO,
                check_ambiguity, override, 0, 0,
                "gofz", '-',
                additional_error))
              goto failure;
          
          }
          /* g(r, cos(theta)).  */
          else if (strcmp (long_options[option_index].name, "r_theta") == 0)
          {
          
            if (args_info->staticProps_group_counter && override)
              reset_group_staticProps (args_info);
            args_info->staticProps_group_counter += 1;
          
            if (update_arg( 0 , 
                 0 , &(args_info->r_theta_given),
                &(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO,
                check_ambiguity, override, 0, 0,
                "r_theta", '-',
                additional_error))
              goto failure;
          
          }
          /* g(r, cos(omega)).  */
          else if (strcmp (long_options[option_index].name, "r_omega") == 0)
          {
          
            if (args_info->staticProps_group_counter && override)
              reset_group_staticProps (args_info);
            args_info->staticProps_group_counter += 1;
          
            if (update_arg( 0 , 
                 0 , &(args_info->r_omega_given),
                &(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO,
                check_ambiguity, override, 0, 0,
                "r_omega", '-',
                additional_error))
              goto failure;
          
          }
          /* g(r, z).  */
          else if (strcmp (long_options[option_index].name, "r_z") == 0)
          {
          
            if (args_info->staticProps_group_counter && override)
              reset_group_staticProps (args_info);
            args_info->staticProps_group_counter += 1;
          
            if (update_arg( 0 , 
                 0 , &(args_info->r_z_given),
                &(local_args_info.r_z_given), optarg, 0, 0, ARG_NO,
                check_ambiguity, override, 0, 0,
                "r_z", '-',
                additional_error))
              goto failure;
          
          }
          /* g(cos(theta), cos(omega)).  */
          else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
          {
          
            if (args_info->staticProps_group_counter && override)
              reset_group_staticProps (args_info);
            args_info->staticProps_group_counter += 1;
          
            if (update_arg( 0 , 
                 0 , &(args_info->theta_omega_given),
                &(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO,
                check_ambiguity, override, 0, 0,
                "theta_omega", '-',
                additional_error))
              goto failure;
          
          }
          /* g(x, y, z).  */
          else if (strcmp (long_options[option_index].name, "gxyz") == 0)
          {
          
            if (args_info->staticProps_group_counter && override)
              reset_group_staticProps (args_info);
            args_info->staticProps_group_counter += 1;
          
            if (update_arg( 0 , 
                 0 , &(args_info->gxyz_given),
                &(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO,
                check_ambiguity, override, 0, 0,
                "gxyz", '-',
                additional_error))
              goto failure;
          
          }
          /* 2D g(r) (Slab width --dz must be specified).  */
          else if (strcmp (long_options[option_index].name, "twodgofr") == 0)
          {
          
            if (args_info->staticProps_group_counter && override)
              reset_group_staticProps (args_info);
            args_info->staticProps_group_counter += 1;
          
            if (update_arg( 0 , 
                 0 , &(args_info->twodgofr_given),
                &(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO,
                check_ambiguity, override, 0, 0,
                "twodgofr", '-',
                additional_error))
              goto failure;
          
          }
          /* rp2 order parameter (--sele1 and --sele2 must be specified).  */
          else if (strcmp (long_options[option_index].name, "rp2") == 0)
          {
          
            if (args_info->staticProps_group_counter && override)
              reset_group_staticProps (args_info);
            args_info->staticProps_group_counter += 1;
          
            if (update_arg( 0 , 
                 0 , &(args_info->rp2_given),
                &(local_args_info.rp2_given), optarg, 0, 0, ARG_NO,
                check_ambiguity, override, 0, 0,
                "rp2", '-',
                additional_error))
              goto failure;
          
          }
          /* slab density.  */
          else if (strcmp (long_options[option_index].name, "slab_density") == 0)
          {
          
            if (args_info->staticProps_group_counter && override)
              reset_group_staticProps (args_info);
            args_info->staticProps_group_counter += 1;
          
            if (update_arg( 0 , 
                 0 , &(args_info->slab_density_given),
                &(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO,
                check_ambiguity, override, 0, 0,
                "slab_density", '-',
                additional_error))
              goto failure;
          
          }
          /* p(cos(theta)) (--sele1 must be specified, --sele2 is optional).  */
          else if (strcmp (long_options[option_index].name, "p_angle") == 0)
          {
          
            if (args_info->staticProps_group_counter && override)
              reset_group_staticProps (args_info);
            args_info->staticProps_group_counter += 1;
          
            if (update_arg( 0 , 
                 0 , &(args_info->p_angle_given),
                &(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO,
                check_ambiguity, override, 0, 0,
                "p_angle", '-',
                additional_error))
              goto failure;
          
          }
          /* hxy.  */
          else if (strcmp (long_options[option_index].name, "hxy") == 0)
          {
          
            if (args_info->staticProps_group_counter && override)
              reset_group_staticProps (args_info);
            args_info->staticProps_group_counter += 1;
          
            if (update_arg( 0 , 
                 0 , &(args_info->hxy_given),
                &(local_args_info.hxy_given), optarg, 0, 0, ARG_NO,
                check_ambiguity, override, 0, 0,
                "hxy", '-',
                additional_error))
              goto failure;
          
          }
          /* rho of R.  */
          else if (strcmp (long_options[option_index].name, "rho_r") == 0)
          {
          
            if (args_info->staticProps_group_counter && override)
              reset_group_staticProps (args_info);
            args_info->staticProps_group_counter += 1;
          
            if (update_arg( 0 , 
                 0 , &(args_info->rho_r_given),
                &(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO,
                check_ambiguity, override, 0, 0,
                "rho_r", '-',
                additional_error))
              goto failure;
          
          }
          /* angle of R.  */
          else if (strcmp (long_options[option_index].name, "angle_r") == 0)
          {
          
            if (args_info->staticProps_group_counter && override)
              reset_group_staticProps (args_info);
            args_info->staticProps_group_counter += 1;
          
            if (update_arg( 0 , 
                 0 , &(args_info->angle_r_given),
                &(local_args_info.angle_r_given), optarg, 0, 0, ARG_NO,
                check_ambiguity, override, 0, 0,
                "angle_r", '-',
                additional_error))
              goto failure;
          
          }
          /* hull volume of nanoparticle.  */
          else if (strcmp (long_options[option_index].name, "hullvol") == 0)
          {
          
            if (args_info->staticProps_group_counter && override)
              reset_group_staticProps (args_info);
            args_info->staticProps_group_counter += 1;
          
            if (update_arg( 0 , 
                 0 , &(args_info->hullvol_given),
                &(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO,
                check_ambiguity, override, 0, 0,
                "hullvol", '-',
                additional_error))
              goto failure;
          
          }
          /* length of nanorod.  */
          else if (strcmp (long_options[option_index].name, "rodlength") == 0)
          {
          
            if (args_info->staticProps_group_counter && override)
              reset_group_staticProps (args_info);
            args_info->staticProps_group_counter += 1;
          
            if (update_arg( 0 , 
                 0 , &(args_info->rodlength_given),
                &(local_args_info.rodlength_given), optarg, 0, 0, ARG_NO,
                check_ambiguity, override, 0, 0,
                "rodlength", '-',
                additional_error))
              goto failure;
          
          }
          /* spatially-resolved tetrahedrality order parameter Qk(z).  */
          else if (strcmp (long_options[option_index].name, "tet_param_z") == 0)
          {
          
            if (args_info->staticProps_group_counter && override)
              reset_group_staticProps (args_info);
            args_info->staticProps_group_counter += 1;
          
            if (update_arg( 0 , 
                 0 , &(args_info->tet_param_z_given),
                &(local_args_info.tet_param_z_given), optarg, 0, 0, ARG_NO,
                check_ambiguity, override, 0, 0,
                "tet_param_z", '-',
                additional_error))
              goto failure;
          
          }
          /* volume-resolved tetrahedrality order parameter Qk(x,y,z).  (voxelSize, rcut, and gaussWidth must be specified).  */
          else if (strcmp (long_options[option_index].name, "tet_param_xyz") == 0)
          {
          
            if (args_info->staticProps_group_counter && override)
              reset_group_staticProps (args_info);
            args_info->staticProps_group_counter += 1;
          
            if (update_arg( 0 , 
                 0 , &(args_info->tet_param_xyz_given),
                &(local_args_info.tet_param_xyz_given), optarg, 0, 0, ARG_NO,
                check_ambiguity, override, 0, 0,
                "tet_param_xyz", '-',
                additional_error))
              goto failure;
          
          }
          /* slab-resolved RNEMD statistics (temperature, density, velocity).  */
          else if (strcmp (long_options[option_index].name, "rnemdz") == 0)
          {
          
            if (args_info->staticProps_group_counter && override)
              reset_group_staticProps (args_info);
            args_info->staticProps_group_counter += 1;
          
            if (update_arg( 0 , 
                 0 , &(args_info->rnemdz_given),
                &(local_args_info.rnemdz_given), optarg, 0, 0, ARG_NO,
                check_ambiguity, override, 0, 0,
                "rnemdz", '-',
                additional_error))
              goto failure;
          
          }
          /* shell-resolved RNEMD statistics (temperature, density, angular velocity).  */
          else if (strcmp (long_options[option_index].name, "rnemdr") == 0)
          {
          
            if (args_info->staticProps_group_counter && override)
              reset_group_staticProps (args_info);
            args_info->staticProps_group_counter += 1;
          
            if (update_arg( 0 , 
                 0 , &(args_info->rnemdr_given),
                &(local_args_info.rnemdr_given), optarg, 0, 0, ARG_NO,
                check_ambiguity, override, 0, 0,
                "rnemdr", '-',
                additional_error))
              goto failure;
          
          }
          /* shell and angle-resolved RNEMD statistics (temperature, density, angular velocity).  */
          else if (strcmp (long_options[option_index].name, "rnemdrt") == 0)
          {
          
            if (args_info->staticProps_group_counter && override)
              reset_group_staticProps (args_info);
            args_info->staticProps_group_counter += 1;
          
            if (update_arg( 0 , 
                 0 , &(args_info->rnemdrt_given),
                &(local_args_info.rnemdrt_given), optarg, 0, 0, ARG_NO,
                check_ambiguity, override, 0, 0,
                "rnemdrt", '-',
                additional_error))
              goto failure;
          
          }
          /* electrostatic potential to frequency map based on the Cho nitrile fits.  */
          else if (strcmp (long_options[option_index].name, "nitrile") == 0)
          {
          
            if (args_info->staticProps_group_counter && override)
              reset_group_staticProps (args_info);
            args_info->staticProps_group_counter += 1;
          
            if (update_arg( 0 , 
                 0 , &(args_info->nitrile_given),
                &(local_args_info.nitrile_given), optarg, 0, 0, ARG_NO,
                check_ambiguity, override, 0, 0,
                "nitrile", '-',
                additional_error))
              goto failure;
          
          }
          /* X, Y, and R (surface diffusion if Z exposed and bulk immobile) diffusion.  */
          else if (strcmp (long_options[option_index].name, "surfDiffusion") == 0)
          {
          
            if (args_info->staticProps_group_counter && override)
              reset_group_staticProps (args_info);
            args_info->staticProps_group_counter += 1;
          
            if (update_arg( 0 , 
                 0 , &(args_info->surfDiffusion_given),
                &(local_args_info.surfDiffusion_given), optarg, 0, 0, ARG_NO,
                check_ambiguity, override, 0, 0,
                "surfDiffusion", '-',
                additional_error))
              goto failure;
          
          }
          /* Hydrogen Bonding statistics using geometric criteria (rcut and thetacut must be specified).  */
          else if (strcmp (long_options[option_index].name, "hbond") == 0)
          {
          
            if (args_info->staticProps_group_counter && override)
              reset_group_staticProps (args_info);
            args_info->staticProps_group_counter += 1;
          
            if (update_arg( 0 , 
                 0 , &(args_info->hbond_given),
                &(local_args_info.hbond_given), optarg, 0, 0, ARG_NO,
                check_ambiguity, override, 0, 0,
                "hbond", '-',
                additional_error))
              goto failure;
          
          }
          
          break;
        case '?':       /* Invalid option.  */
          /* `getopt_long' already printed an error message.  */
          goto failure;

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

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

  cmdline_parser_release (&local_args_info);

  if ( error )
    return (EXIT_FAILURE);

  if (optind < argc)
    {
      int i = 0 ;
      int found_prog_name = 0;
      /* whether program name, i.e., argv[0], is in the remaining args
         (this may happen with some implementations of getopt,
          but surely not with the one included by gengetopt) */

      i = optind;
      while (i < argc)
        if (argv[i++] == argv[0]) {
          found_prog_name = 1;
          break;
        }
      i = 0;

      args_info->inputs_num = argc - optind - found_prog_name;
      args_info->inputs =
        (char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
      while (optind < argc)
        if (argv[optind++] != argv[0])
          args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
    }

  return 0;

failure:
  
  cmdline_parser_release (&local_args_info);
  return (EXIT_FAILURE);
}
Revision:	2049
Committed:	Tue Jan 6 21:44:10 2015 UTC (10 years, 3 months ago) by gezelter
File size:	73483 byte(s)
Log Message:	Added Geometric HBond StaticProps module.