--- trunk/src/applications/staticProps/StaticPropsCmd.h	2006/04/11 15:33:27	929
+++ trunk/src/applications/staticProps/StaticPropsCmd.h	2014/04/29 17:32:31	1993
@@ -1,7 +1,10 @@
-/* StaticPropsCmd.h */
+/** @file StaticPropsCmd.h
+ *  @brief The header file for the command line option parser
+ *  generated by GNU Gengetopt version 2.22.4
+ *  http://www.gnu.org/software/gengetopt.
+ *  DO NOT modify this file, since it can be overwritten
+ *  @author GNU Gengetopt by Lorenzo Bettini */
 
-/* File autogenerated by gengetopt version 2.16  */
-
 #ifndef STATICPROPSCMD_H
 #define STATICPROPSCMD_H
 
@@ -10,89 +13,315 @@
 #include "config.h"
 #endif
 
+#include <stdio.h> /* for FILE */
+
 #ifdef __cplusplus
 extern "C" {
 #endif /* __cplusplus */
 
 #ifndef CMDLINE_PARSER_PACKAGE
+/** @brief the program name (used for printing errors) */
 #define CMDLINE_PARSER_PACKAGE "StaticProps"
 #endif
 
+#ifndef CMDLINE_PARSER_PACKAGE_NAME
+/** @brief the complete program name (used for help and version) */
+#define CMDLINE_PARSER_PACKAGE_NAME "StaticProps"
+#endif
+
 #ifndef CMDLINE_PARSER_VERSION
+/** @brief the program version */
 #define CMDLINE_PARSER_VERSION "1.00"
 #endif
 
+/** @brief Where the command line options are stored */
 struct gengetopt_args_info
 {
-  char * input_arg;	/* input dump file.  */
-  char * input_orig;	/* input dump file original value given at command line.  */
-  char * output_arg;	/* output file name.  */
-  char * output_orig;	/* output file name original value given at command line.  */
-  int step_arg;	/* process every n frame (default='1').  */
-  char * step_orig;	/* process every n frame original value given at command line.  */
-  int nrbins_arg;	/* number of bins for distance (default='100').  */
-  char * nrbins_orig;	/* number of bins for distance original value given at command line.  */
-  int nanglebins_arg;	/* number of bins for cos(angle) (default='50').  */
-  char * nanglebins_orig;	/* number of bins for cos(angle) original value given at command line.  */
-  double length_arg;	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
-  char * length_orig;	/* maximum length (Defaults to 1/2 smallest length of first frame) original value given at command line.  */
-  double zoffset_arg;	/* Where to set the zero for the slab_density calculation (default='0').  */
-  char * zoffset_orig;	/* Where to set the zero for the slab_density calculation original value given at command line.  */
-  char * sele1_arg;	/* select the first stuntdouble set.  */
-  char * sele1_orig;	/* select the first stuntdouble set original value given at command line.  */
-  char * sele2_arg;	/* select the second stuntdouble set.  */
-  char * sele2_orig;	/* select the second stuntdouble set original value given at command line.  */
-  char * sele3_arg;	/* select the third stuntdouble set.  */
-  char * sele3_orig;	/* select the third stuntdouble set original value given at command line.  */
-  char * refsele_arg;	/* select reference (use and only use with --gxyz).  */
-  char * refsele_orig;	/* select reference (use and only use with --gxyz) original value given at command line.  */
-  char * molname_arg;	/* molecule name.  */
-  char * molname_orig;	/* molecule name original value given at command line.  */
-  int begin_arg;	/* begin interanl index.  */
-  char * begin_orig;	/* begin interanl index original value given at command line.  */
-  int end_arg;	/* end internal index.  */
-  char * end_orig;	/* end internal index original value given at command line.  */
+  const char *help_help; /**< @brief Print help and exit help description.  */
+  const char *version_help; /**< @brief Print version and exit help description.  */
+  char * input_arg;	/**< @brief input dump file.  */
+  char * input_orig;	/**< @brief input dump file original value given at command line.  */
+  const char *input_help; /**< @brief input dump file help description.  */
+  char * output_arg;	/**< @brief output file name.  */
+  char * output_orig;	/**< @brief output file name original value given at command line.  */
+  const char *output_help; /**< @brief output file name help description.  */
+  int step_arg;	/**< @brief process every n frame (default='1').  */
+  char * step_orig;	/**< @brief process every n frame original value given at command line.  */
+  const char *step_help; /**< @brief process every n frame help description.  */
+  int nbins_arg;	/**< @brief number of bins (general purpose) (default='100').  */
+  char * nbins_orig;	/**< @brief number of bins (general purpose) original value given at command line.  */
+  const char *nbins_help; /**< @brief number of bins (general purpose) help description.  */
+  int nbins_x_arg;	/**< @brief number of bins in x axis (default='100').  */
+  char * nbins_x_orig;	/**< @brief number of bins in x axis original value given at command line.  */
+  const char *nbins_x_help; /**< @brief number of bins in x axis help description.  */
+  int nbins_y_arg;	/**< @brief number of bins in y axis (default='100').  */
+  char * nbins_y_orig;	/**< @brief number of bins in y axis original value given at command line.  */
+  const char *nbins_y_help; /**< @brief number of bins in y axis help description.  */
+  int nbins_z_arg;	/**< @brief number of bins in z axis (default='100').  */
+  char * nbins_z_orig;	/**< @brief number of bins in z axis original value given at command line.  */
+  const char *nbins_z_help; /**< @brief number of bins in z axis help description.  */
+  int nanglebins_arg;	/**< @brief number of bins for cos(angle) (default='50').  */
+  char * nanglebins_orig;	/**< @brief number of bins for cos(angle) original value given at command line.  */
+  const char *nanglebins_help; /**< @brief number of bins for cos(angle) help description.  */
+  double rcut_arg;	/**< @brief cutoff radius (rcut).  */
+  char * rcut_orig;	/**< @brief cutoff radius (rcut) original value given at command line.  */
+  const char *rcut_help; /**< @brief cutoff radius (rcut) help description.  */
+  double dz_arg;	/**< @brief slab width (dz).  */
+  char * dz_orig;	/**< @brief slab width (dz) original value given at command line.  */
+  const char *dz_help; /**< @brief slab width (dz) help description.  */
+  double length_arg;	/**< @brief maximum length (Defaults to 1/2 smallest length of first frame).  */
+  char * length_orig;	/**< @brief maximum length (Defaults to 1/2 smallest length of first frame) original value given at command line.  */
+  const char *length_help; /**< @brief maximum length (Defaults to 1/2 smallest length of first frame) help description.  */
+  double zlength_arg;	/**< @brief maximum length (Defaults to 1/2 smallest length of first frame).  */
+  char * zlength_orig;	/**< @brief maximum length (Defaults to 1/2 smallest length of first frame) original value given at command line.  */
+  const char *zlength_help; /**< @brief maximum length (Defaults to 1/2 smallest length of first frame) help description.  */
+  double zoffset_arg;	/**< @brief Where to set the zero for the slab_density calculation (default='0').  */
+  char * zoffset_orig;	/**< @brief Where to set the zero for the slab_density calculation original value given at command line.  */
+  const char *zoffset_help; /**< @brief Where to set the zero for the slab_density calculation help description.  */
+  char * sele1_arg;	/**< @brief select the first stuntdouble set.  */
+  char * sele1_orig;	/**< @brief select the first stuntdouble set original value given at command line.  */
+  const char *sele1_help; /**< @brief select the first stuntdouble set help description.  */
+  char * sele2_arg;	/**< @brief select the second stuntdouble set.  */
+  char * sele2_orig;	/**< @brief select the second stuntdouble set original value given at command line.  */
+  const char *sele2_help; /**< @brief select the second stuntdouble set help description.  */
+  char * sele3_arg;	/**< @brief select the third stuntdouble set.  */
+  char * sele3_orig;	/**< @brief select the third stuntdouble set original value given at command line.  */
+  const char *sele3_help; /**< @brief select the third stuntdouble set help description.  */
+  char * refsele_arg;	/**< @brief select reference (use and only use with --gxyz).  */
+  char * refsele_orig;	/**< @brief select reference (use and only use with --gxyz) original value given at command line.  */
+  const char *refsele_help; /**< @brief select reference (use and only use with --gxyz) help description.  */
+  char * comsele_arg;	/**< @brief select stunt doubles for center-of-mass reference point.  */
+  char * comsele_orig;	/**< @brief select stunt doubles for center-of-mass reference point original value given at command line.  */
+  const char *comsele_help; /**< @brief select stunt doubles for center-of-mass reference point help description.  */
+  int seleoffset_arg;	/**< @brief global index offset for a second object (used to define a vector between sites in molecule).  */
+  char * seleoffset_orig;	/**< @brief global index offset for a second object (used to define a vector between sites in molecule) original value given at command line.  */
+  const char *seleoffset_help; /**< @brief global index offset for a second object (used to define a vector between sites in molecule) help description.  */
+  int seleoffset2_arg;	/**< @brief global index offset for a third object (used to define a vector between sites in molecule).  */
+  char * seleoffset2_orig;	/**< @brief global index offset for a third object (used to define a vector between sites in molecule) original value given at command line.  */
+  const char *seleoffset2_help; /**< @brief global index offset for a third object (used to define a vector between sites in molecule) help description.  */
+  char * molname_arg;	/**< @brief molecule name.  */
+  char * molname_orig;	/**< @brief molecule name original value given at command line.  */
+  const char *molname_help; /**< @brief molecule name help description.  */
+  int begin_arg;	/**< @brief begin internal index.  */
+  char * begin_orig;	/**< @brief begin internal index original value given at command line.  */
+  const char *begin_help; /**< @brief begin internal index help description.  */
+  int end_arg;	/**< @brief end internal index.  */
+  char * end_orig;	/**< @brief end internal index original value given at command line.  */
+  const char *end_help; /**< @brief end internal index help description.  */
+  double radius_arg;	/**< @brief nanoparticle radius.  */
+  char * radius_orig;	/**< @brief nanoparticle radius original value given at command line.  */
+  const char *radius_help; /**< @brief nanoparticle radius help description.  */
+  const char *bo_help; /**< @brief bond order parameter (--rcut must be specified) help description.  */
+  const char *ior_help; /**< @brief icosahedral bond order parameter as a function of radius (--rcut must be specified) help description.  */
+  const char *for_help; /**< @brief FCC bond order parameter as a function of radius (--rcut must be specified) help description.  */
+  const char *bad_help; /**< @brief N(theta) bond angle density within (--rcut must be specified) help description.  */
+  const char *count_help; /**< @brief count of molecules matching selection criteria (and associated statistics) help description.  */
+  const char *gofr_help; /**< @brief g(r) help description.  */
+  const char *gofz_help; /**< @brief g(z) help description.  */
+  const char *r_theta_help; /**< @brief g(r, cos(theta)) help description.  */
+  const char *r_omega_help; /**< @brief g(r, cos(omega)) help description.  */
+  const char *r_z_help; /**< @brief g(r, z) help description.  */
+  const char *theta_omega_help; /**< @brief g(cos(theta), cos(omega)) help description.  */
+  const char *gxyz_help; /**< @brief g(x, y, z) help description.  */
+  const char *twodgofr_help; /**< @brief 2D g(r) (Slab width --dz must be specified) help description.  */
+  const char *p2_help; /**< @brief p2 order parameter (--sele1 must be specified, --sele2 is optional) help description.  */
+  const char *rp2_help; /**< @brief rp2 order parameter (--sele1 and --sele2 must be specified) help description.  */
+  const char *scd_help; /**< @brief scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified) help description.  */
+  const char *density_help; /**< @brief density plot help description.  */
+  const char *slab_density_help; /**< @brief slab density help description.  */
+  const char *p_angle_help; /**< @brief p(cos(theta)) (--sele1 must be specified, --sele2 is optional) help description.  */
+  const char *hxy_help; /**< @brief hxy help description.  */
+  const char *rho_r_help; /**< @brief rho of R help description.  */
+  const char *angle_r_help; /**< @brief angle of R help description.  */
+  const char *hullvol_help; /**< @brief hull volume of nanoparticle help description.  */
+  const char *rodlength_help; /**< @brief length of nanorod help description.  */
+  const char *tet_param_help; /**< @brief tetrahedrality order parameter (Qk) help description.  */
+  const char *tet_param_z_help; /**< @brief spatially-resolved tetrahedrality order parameter Qk(z) help description.  */
+  const char *rnemdz_help; /**< @brief slab-resolved RNEMD statistics (temperature, density, velocity) help description.  */
+  const char *rnemdr_help; /**< @brief shell-resolved RNEMD statistics (temperature, density, angular velocity) help description.  */
+  const char *rnemdrt_help; /**< @brief shell and angle-resolved RNEMD statistics (temperature, density, angular velocity) help description.  */
+  const char *uFreqMap_help; /**< @brief electrostatic potential to frequency map based on the Cho nitrile fits help description.  */
   
-  int help_given ;	/* Whether help was given.  */
-  int version_given ;	/* Whether version was given.  */
-  int input_given ;	/* Whether input was given.  */
-  int output_given ;	/* Whether output was given.  */
-  int step_given ;	/* Whether step was given.  */
-  int nrbins_given ;	/* Whether nrbins was given.  */
-  int nanglebins_given ;	/* Whether nanglebins was given.  */
-  int length_given ;	/* Whether length was given.  */
-  int zoffset_given ;	/* Whether zoffset was given.  */
-  int sele1_given ;	/* Whether sele1 was given.  */
-  int sele2_given ;	/* Whether sele2 was given.  */
-  int sele3_given ;	/* Whether sele3 was given.  */
-  int refsele_given ;	/* Whether refsele was given.  */
-  int molname_given ;	/* Whether molname was given.  */
-  int begin_given ;	/* Whether begin was given.  */
-  int end_given ;	/* Whether end was given.  */
-  int gofr_given ;	/* Whether gofr was given.  */
-  int r_theta_given ;	/* Whether r_theta was given.  */
-  int r_omega_given ;	/* Whether r_omega was given.  */
-  int theta_omega_given ;	/* Whether theta_omega was given.  */
-  int gxyz_given ;	/* Whether gxyz was given.  */
-  int p2_given ;	/* Whether p2 was given.  */
-  int scd_given ;	/* Whether scd was given.  */
-  int density_given ;	/* Whether density was given.  */
-  int slab_density_given ;	/* Whether slab_density was given.  */
+  unsigned int help_given ;	/**< @brief Whether help was given.  */
+  unsigned int version_given ;	/**< @brief Whether version was given.  */
+  unsigned int input_given ;	/**< @brief Whether input was given.  */
+  unsigned int output_given ;	/**< @brief Whether output was given.  */
+  unsigned int step_given ;	/**< @brief Whether step was given.  */
+  unsigned int nbins_given ;	/**< @brief Whether nbins was given.  */
+  unsigned int nbins_x_given ;	/**< @brief Whether nbins_x was given.  */
+  unsigned int nbins_y_given ;	/**< @brief Whether nbins_y was given.  */
+  unsigned int nbins_z_given ;	/**< @brief Whether nbins_z was given.  */
+  unsigned int nanglebins_given ;	/**< @brief Whether nanglebins was given.  */
+  unsigned int rcut_given ;	/**< @brief Whether rcut was given.  */
+  unsigned int dz_given ;	/**< @brief Whether dz was given.  */
+  unsigned int length_given ;	/**< @brief Whether length was given.  */
+  unsigned int zlength_given ;	/**< @brief Whether zlength was given.  */
+  unsigned int zoffset_given ;	/**< @brief Whether zoffset was given.  */
+  unsigned int sele1_given ;	/**< @brief Whether sele1 was given.  */
+  unsigned int sele2_given ;	/**< @brief Whether sele2 was given.  */
+  unsigned int sele3_given ;	/**< @brief Whether sele3 was given.  */
+  unsigned int refsele_given ;	/**< @brief Whether refsele was given.  */
+  unsigned int comsele_given ;	/**< @brief Whether comsele was given.  */
+  unsigned int seleoffset_given ;	/**< @brief Whether seleoffset was given.  */
+  unsigned int seleoffset2_given ;	/**< @brief Whether seleoffset2 was given.  */
+  unsigned int molname_given ;	/**< @brief Whether molname was given.  */
+  unsigned int begin_given ;	/**< @brief Whether begin was given.  */
+  unsigned int end_given ;	/**< @brief Whether end was given.  */
+  unsigned int radius_given ;	/**< @brief Whether radius was given.  */
+  unsigned int bo_given ;	/**< @brief Whether bo was given.  */
+  unsigned int ior_given ;	/**< @brief Whether ior was given.  */
+  unsigned int for_given ;	/**< @brief Whether for was given.  */
+  unsigned int bad_given ;	/**< @brief Whether bad was given.  */
+  unsigned int count_given ;	/**< @brief Whether count was given.  */
+  unsigned int gofr_given ;	/**< @brief Whether gofr was given.  */
+  unsigned int gofz_given ;	/**< @brief Whether gofz was given.  */
+  unsigned int r_theta_given ;	/**< @brief Whether r_theta was given.  */
+  unsigned int r_omega_given ;	/**< @brief Whether r_omega was given.  */
+  unsigned int r_z_given ;	/**< @brief Whether r_z was given.  */
+  unsigned int theta_omega_given ;	/**< @brief Whether theta_omega was given.  */
+  unsigned int gxyz_given ;	/**< @brief Whether gxyz was given.  */
+  unsigned int twodgofr_given ;	/**< @brief Whether twodgofr was given.  */
+  unsigned int p2_given ;	/**< @brief Whether p2 was given.  */
+  unsigned int rp2_given ;	/**< @brief Whether rp2 was given.  */
+  unsigned int scd_given ;	/**< @brief Whether scd was given.  */
+  unsigned int density_given ;	/**< @brief Whether density was given.  */
+  unsigned int slab_density_given ;	/**< @brief Whether slab_density was given.  */
+  unsigned int p_angle_given ;	/**< @brief Whether p_angle was given.  */
+  unsigned int hxy_given ;	/**< @brief Whether hxy was given.  */
+  unsigned int rho_r_given ;	/**< @brief Whether rho_r was given.  */
+  unsigned int angle_r_given ;	/**< @brief Whether angle_r was given.  */
+  unsigned int hullvol_given ;	/**< @brief Whether hullvol was given.  */
+  unsigned int rodlength_given ;	/**< @brief Whether rodlength was given.  */
+  unsigned int tet_param_given ;	/**< @brief Whether tet_param was given.  */
+  unsigned int tet_param_z_given ;	/**< @brief Whether tet_param_z was given.  */
+  unsigned int rnemdz_given ;	/**< @brief Whether rnemdz was given.  */
+  unsigned int rnemdr_given ;	/**< @brief Whether rnemdr was given.  */
+  unsigned int rnemdrt_given ;	/**< @brief Whether rnemdrt was given.  */
+  unsigned int uFreqMap_given ;	/**< @brief Whether uFreqMap was given.  */
 
-  int staticProps_group_counter; /* counter for group staticProps */
+  char **inputs ; /**< @brief unamed options (options without names) */
+  unsigned inputs_num ; /**< @brief unamed options number */
+  int staticProps_group_counter; /**< @brief Counter for group staticProps */
 } ;
 
-int cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info);
-int cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required);
-int cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info);
+/** @brief The additional parameters to pass to parser functions */
+struct cmdline_parser_params
+{
+  int override; /**< @brief whether to override possibly already present options (default 0) */
+  int initialize; /**< @brief whether to initialize the option structure gengetopt_args_info (default 1) */
+  int check_required; /**< @brief whether to check that all required options were provided (default 1) */
+  int check_ambiguity; /**< @brief whether to check for options already specified in the option structure gengetopt_args_info (default 0) */
+  int print_errors; /**< @brief whether getopt_long should print an error message for a bad option (default 1) */
+} ;
 
+/** @brief the purpose string of the program */
+extern const char *gengetopt_args_info_purpose;
+/** @brief the usage string of the program */
+extern const char *gengetopt_args_info_usage;
+/** @brief all the lines making the help output */
+extern const char *gengetopt_args_info_help[];
+
+/**
+ * The command line parser
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser (int argc, char **argv,
+  struct gengetopt_args_info *args_info);
+
+/**
+ * The command line parser (version with additional parameters - deprecated)
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @param override whether to override possibly already present options
+ * @param initialize whether to initialize the option structure my_args_info
+ * @param check_required whether to check that all required options were provided
+ * @return 0 if everything went fine, NON 0 if an error took place
+ * @deprecated use cmdline_parser_ext() instead
+ */
+int cmdline_parser2 (int argc, char **argv,
+  struct gengetopt_args_info *args_info,
+  int override, int initialize, int check_required);
+
+/**
+ * The command line parser (version with additional parameters)
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @param params additional parameters for the parser
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_ext (int argc, char **argv,
+  struct gengetopt_args_info *args_info,
+  struct cmdline_parser_params *params);
+
+/**
+ * Save the contents of the option struct into an already open FILE stream.
+ * @param outfile the stream where to dump options
+ * @param args_info the option struct to dump
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_dump(FILE *outfile,
+  struct gengetopt_args_info *args_info);
+
+/**
+ * Save the contents of the option struct into a (text) file.
+ * This file can be read by the config file parser (if generated by gengetopt)
+ * @param filename the file where to save
+ * @param args_info the option struct to save
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_file_save(const char *filename,
+  struct gengetopt_args_info *args_info);
+
+/**
+ * Print the help
+ */
 void cmdline_parser_print_help(void);
+/**
+ * Print the version
+ */
 void cmdline_parser_print_version(void);
 
+/**
+ * Initializes all the fields a cmdline_parser_params structure 
+ * to their default values
+ * @param params the structure to initialize
+ */
+void cmdline_parser_params_init(struct cmdline_parser_params *params);
+
+/**
+ * Allocates dynamically a cmdline_parser_params structure and initializes
+ * all its fields to their default values
+ * @return the created and initialized cmdline_parser_params structure
+ */
+struct cmdline_parser_params *cmdline_parser_params_create(void);
+
+/**
+ * Initializes the passed gengetopt_args_info structure's fields
+ * (also set default values for options that have a default)
+ * @param args_info the structure to initialize
+ */
 void cmdline_parser_init (struct gengetopt_args_info *args_info);
+/**
+ * Deallocates the string fields of the gengetopt_args_info structure
+ * (but does not deallocate the structure itself)
+ * @param args_info the structure to deallocate
+ */
 void cmdline_parser_free (struct gengetopt_args_info *args_info);
 
-int cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name);
+/**
+ * Checks that all the required options were specified
+ * @param args_info the structure to check
+ * @param prog_name the name of the program that will be used to print
+ *   possible errors
+ * @return
+ */
+int cmdline_parser_required (struct gengetopt_args_info *args_info,
+  const char *prog_name);
 
 
 #ifdef __cplusplus