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root/OpenMD/trunk/src/applications/staticProps/StaticPropsCmd.h
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Comparing trunk/src/applications/staticProps/StaticPropsCmd.h (file contents):
Revision 1531 by kstocke1, Wed Dec 29 16:48:19 2010 UTC vs.
Revision 2049 by gezelter, Tue Jan 6 21:44:10 2015 UTC

# Line 66 | Line 66 | struct gengetopt_args_info
66    double rcut_arg;      /**< @brief cutoff radius (rcut).  */
67    char * rcut_orig;     /**< @brief cutoff radius (rcut) original value given at command line.  */
68    const char *rcut_help; /**< @brief cutoff radius (rcut) help description.  */
69 +  double thetacut_arg;  /**< @brief cutoff angle (thetacut).  */
70 +  char * thetacut_orig; /**< @brief cutoff angle (thetacut) original value given at command line.  */
71 +  const char *thetacut_help; /**< @brief cutoff angle (thetacut) help description.  */
72    double dz_arg;        /**< @brief slab width (dz).  */
73    char * dz_orig;       /**< @brief slab width (dz) original value given at command line.  */
74    const char *dz_help; /**< @brief slab width (dz) help description.  */
# Line 93 | Line 96 | struct gengetopt_args_info
96    char * comsele_arg;   /**< @brief select stunt doubles for center-of-mass reference point.  */
97    char * comsele_orig;  /**< @brief select stunt doubles for center-of-mass reference point original value given at command line.  */
98    const char *comsele_help; /**< @brief select stunt doubles for center-of-mass reference point help description.  */
99 +  int seleoffset_arg;   /**< @brief global index offset for a second object (used to define a vector between sites in molecule).  */
100 +  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.  */
101 +  const char *seleoffset_help; /**< @brief global index offset for a second object (used to define a vector between sites in molecule) help description.  */
102 +  int seleoffset2_arg;  /**< @brief global index offset for a third object (used to define a vector between sites in molecule).  */
103 +  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.  */
104 +  const char *seleoffset2_help; /**< @brief global index offset for a third object (used to define a vector between sites in molecule) help description.  */
105    char * molname_arg;   /**< @brief molecule name.  */
106    char * molname_orig;  /**< @brief molecule name original value given at command line.  */
107    const char *molname_help; /**< @brief molecule name help description.  */
# Line 105 | Line 114 | struct gengetopt_args_info
114    double radius_arg;    /**< @brief nanoparticle radius.  */
115    char * radius_orig;   /**< @brief nanoparticle radius original value given at command line.  */
116    const char *radius_help; /**< @brief nanoparticle radius help description.  */
117 +  double voxelSize_arg; /**< @brief voxel size (angstroms).  */
118 +  char * voxelSize_orig;        /**< @brief voxel size (angstroms) original value given at command line.  */
119 +  const char *voxelSize_help; /**< @brief voxel size (angstroms) help description.  */
120 +  double gaussWidth_arg;        /**< @brief Gaussian width (angstroms).  */
121 +  char * gaussWidth_orig;       /**< @brief Gaussian width (angstroms) original value given at command line.  */
122 +  const char *gaussWidth_help; /**< @brief Gaussian width (angstroms) help description.  */
123    const char *bo_help; /**< @brief bond order parameter (--rcut must be specified) help description.  */
124 <  const char *bor_help; /**< @brief bond order parameter as a function of radius (--rcut must be specified) help description.  */
124 >  const char *ior_help; /**< @brief icosahedral bond order parameter as a function of radius (--rcut must be specified) help description.  */
125 >  const char *for_help; /**< @brief FCC bond order parameter as a function of radius (--rcut must be specified) help description.  */
126    const char *bad_help; /**< @brief N(theta) bond angle density within (--rcut must be specified) help description.  */
127    const char *count_help; /**< @brief count of molecules matching selection criteria (and associated statistics) help description.  */
128    const char *gofr_help; /**< @brief g(r) help description.  */
# Line 117 | Line 133 | struct gengetopt_args_info
133    const char *theta_omega_help; /**< @brief g(cos(theta), cos(omega)) help description.  */
134    const char *gxyz_help; /**< @brief g(x, y, z) help description.  */
135    const char *twodgofr_help; /**< @brief 2D g(r) (Slab width --dz must be specified) help description.  */
136 <  const char *p2_help; /**< @brief p2 order parameter (--sele1 and --sele2 must be specified) help description.  */
136 >  const char *p2_help; /**< @brief p2 order parameter (--sele1 must be specified, --sele2 is optional) help description.  */
137    const char *rp2_help; /**< @brief rp2 order parameter (--sele1 and --sele2 must be specified) help description.  */
138    const char *scd_help; /**< @brief scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified) help description.  */
139    const char *density_help; /**< @brief density plot help description.  */
140    const char *slab_density_help; /**< @brief slab density help description.  */
141 <  const char *p_angle_help; /**< @brief p(cos(theta)) help description.  */
141 >  const char *p_angle_help; /**< @brief p(cos(theta)) (--sele1 must be specified, --sele2 is optional) help description.  */
142    const char *hxy_help; /**< @brief hxy help description.  */
143    const char *rho_r_help; /**< @brief rho of R help description.  */
144    const char *angle_r_help; /**< @brief angle of R help description.  */
145    const char *hullvol_help; /**< @brief hull volume of nanoparticle help description.  */
146 <  const char *tet_param_help; /**< @brief tetrahedrality order parameter help description.  */
146 >  const char *rodlength_help; /**< @brief length of nanorod help description.  */
147 >  const char *tet_param_help; /**< @brief tetrahedrality order parameter (Qk) help description.  */
148 >  const char *tet_param_z_help; /**< @brief spatially-resolved tetrahedrality order parameter Qk(z) help description.  */
149 >  const char *tet_param_xyz_help; /**< @brief volume-resolved tetrahedrality order parameter Qk(x,y,z).  (voxelSize, rcut, and gaussWidth must be specified) help description.  */
150 >  const char *rnemdz_help; /**< @brief slab-resolved RNEMD statistics (temperature, density, velocity) help description.  */
151 >  const char *rnemdr_help; /**< @brief shell-resolved RNEMD statistics (temperature, density, angular velocity) help description.  */
152 >  const char *rnemdrt_help; /**< @brief shell and angle-resolved RNEMD statistics (temperature, density, angular velocity) help description.  */
153 >  const char *nitrile_help; /**< @brief electrostatic potential to frequency map based on the Cho nitrile fits help description.  */
154 >  const char *multipole_help; /**< @brief average multipole moments contained within cutoff spheres as a function of radius help description.  */
155 >  const char *surfDiffusion_help; /**< @brief X, Y, and R (surface diffusion if Z exposed and bulk immobile) diffusion help description.  */
156 >  const char *hbond_help; /**< @brief Hydrogen Bonding statistics using geometric criteria (rcut and thetacut must be specified) help description.  */
157    
158    unsigned int help_given ;     /**< @brief Whether help was given.  */
159    unsigned int version_given ;  /**< @brief Whether version was given.  */
# Line 140 | Line 166 | struct gengetopt_args_info
166    unsigned int nbins_z_given ;  /**< @brief Whether nbins_z was given.  */
167    unsigned int nanglebins_given ;       /**< @brief Whether nanglebins was given.  */
168    unsigned int rcut_given ;     /**< @brief Whether rcut was given.  */
169 +  unsigned int thetacut_given ; /**< @brief Whether thetacut was given.  */
170    unsigned int dz_given ;       /**< @brief Whether dz was given.  */
171    unsigned int length_given ;   /**< @brief Whether length was given.  */
172    unsigned int zlength_given ;  /**< @brief Whether zlength was given.  */
# Line 149 | Line 176 | struct gengetopt_args_info
176    unsigned int sele3_given ;    /**< @brief Whether sele3 was given.  */
177    unsigned int refsele_given ;  /**< @brief Whether refsele was given.  */
178    unsigned int comsele_given ;  /**< @brief Whether comsele was given.  */
179 +  unsigned int seleoffset_given ;       /**< @brief Whether seleoffset was given.  */
180 +  unsigned int seleoffset2_given ;      /**< @brief Whether seleoffset2 was given.  */
181    unsigned int molname_given ;  /**< @brief Whether molname was given.  */
182    unsigned int begin_given ;    /**< @brief Whether begin was given.  */
183    unsigned int end_given ;      /**< @brief Whether end was given.  */
184    unsigned int radius_given ;   /**< @brief Whether radius was given.  */
185 +  unsigned int voxelSize_given ;        /**< @brief Whether voxelSize was given.  */
186 +  unsigned int gaussWidth_given ;       /**< @brief Whether gaussWidth was given.  */
187    unsigned int bo_given ;       /**< @brief Whether bo was given.  */
188 <  unsigned int bor_given ;      /**< @brief Whether bor was given.  */
188 >  unsigned int ior_given ;      /**< @brief Whether ior was given.  */
189 >  unsigned int for_given ;      /**< @brief Whether for was given.  */
190    unsigned int bad_given ;      /**< @brief Whether bad was given.  */
191    unsigned int count_given ;    /**< @brief Whether count was given.  */
192    unsigned int gofr_given ;     /**< @brief Whether gofr was given.  */
# Line 175 | Line 207 | struct gengetopt_args_info
207    unsigned int rho_r_given ;    /**< @brief Whether rho_r was given.  */
208    unsigned int angle_r_given ;  /**< @brief Whether angle_r was given.  */
209    unsigned int hullvol_given ;  /**< @brief Whether hullvol was given.  */
210 +  unsigned int rodlength_given ;        /**< @brief Whether rodlength was given.  */
211    unsigned int tet_param_given ;        /**< @brief Whether tet_param was given.  */
212 +  unsigned int tet_param_z_given ;      /**< @brief Whether tet_param_z was given.  */
213 +  unsigned int tet_param_xyz_given ;    /**< @brief Whether tet_param_xyz was given.  */
214 +  unsigned int rnemdz_given ;   /**< @brief Whether rnemdz was given.  */
215 +  unsigned int rnemdr_given ;   /**< @brief Whether rnemdr was given.  */
216 +  unsigned int rnemdrt_given ;  /**< @brief Whether rnemdrt was given.  */
217 +  unsigned int nitrile_given ;  /**< @brief Whether nitrile was given.  */
218 +  unsigned int multipole_given ;        /**< @brief Whether multipole was given.  */
219 +  unsigned int surfDiffusion_given ;    /**< @brief Whether surfDiffusion was given.  */
220 +  unsigned int hbond_given ;    /**< @brief Whether hbond was given.  */
221  
222    char **inputs ; /**< @brief unamed options (options without names) */
223    unsigned inputs_num ; /**< @brief unamed options number */

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