--- trunk/src/applications/staticProps/StaticPropsCmd.h 2014/04/05 20:56:01 1979 +++ trunk/src/applications/staticProps/StaticPropsCmd.h 2015/01/06 21:44:10 2049 @@ -66,6 +66,9 @@ struct gengetopt_args_info 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 thetacut_arg; /**< @brief cutoff angle (thetacut). */ + char * thetacut_orig; /**< @brief cutoff angle (thetacut) original value given at command line. */ + const char *thetacut_help; /**< @brief cutoff angle (thetacut) 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. */ @@ -96,6 +99,9 @@ struct gengetopt_args_info 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. */ @@ -108,8 +114,15 @@ struct gengetopt_args_info 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. */ + double voxelSize_arg; /**< @brief voxel size (angstroms). */ + char * voxelSize_orig; /**< @brief voxel size (angstroms) original value given at command line. */ + const char *voxelSize_help; /**< @brief voxel size (angstroms) help description. */ + double gaussWidth_arg; /**< @brief Gaussian width (angstroms). */ + char * gaussWidth_orig; /**< @brief Gaussian width (angstroms) original value given at command line. */ + const char *gaussWidth_help; /**< @brief Gaussian width (angstroms) help description. */ const char *bo_help; /**< @brief bond order parameter (--rcut must be specified) help description. */ - const char *bor_help; /**< @brief bond order parameter as a function of radius (--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. */ @@ -133,9 +146,14 @@ struct gengetopt_args_info 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 *tet_param_xyz_help; /**< @brief volume-resolved tetrahedrality order parameter Qk(x,y,z). (voxelSize, rcut, and gaussWidth must be specified) 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 *nitrile_help; /**< @brief electrostatic potential to frequency map based on the Cho nitrile fits help description. */ + const char *multipole_help; /**< @brief average multipole moments contained within cutoff spheres as a function of radius help description. */ + const char *surfDiffusion_help; /**< @brief X, Y, and R (surface diffusion if Z exposed and bulk immobile) diffusion help description. */ + const char *hbond_help; /**< @brief Hydrogen Bonding statistics using geometric criteria (rcut and thetacut must be specified) help description. */ unsigned int help_given ; /**< @brief Whether help was given. */ unsigned int version_given ; /**< @brief Whether version was given. */ @@ -148,6 +166,7 @@ struct gengetopt_args_info 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 thetacut_given ; /**< @brief Whether thetacut 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. */ @@ -158,12 +177,16 @@ struct gengetopt_args_info 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 voxelSize_given ; /**< @brief Whether voxelSize was given. */ + unsigned int gaussWidth_given ; /**< @brief Whether gaussWidth was given. */ unsigned int bo_given ; /**< @brief Whether bo was given. */ - unsigned int bor_given ; /**< @brief Whether bor 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. */ @@ -187,9 +210,14 @@ struct gengetopt_args_info 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 tet_param_xyz_given ; /**< @brief Whether tet_param_xyz 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 nitrile_given ; /**< @brief Whether nitrile was given. */ + unsigned int multipole_given ; /**< @brief Whether multipole was given. */ + unsigned int surfDiffusion_given ; /**< @brief Whether surfDiffusion was given. */ + unsigned int hbond_given ; /**< @brief Whether hbond was given. */ char **inputs ; /**< @brief unamed options (options without names) */ unsigned inputs_num ; /**< @brief unamed options number */