| 93 |
|
char * comsele_arg; /**< @brief select stunt doubles for center-of-mass reference point. */ |
| 94 |
|
char * comsele_orig; /**< @brief select stunt doubles for center-of-mass reference point original value given at command line. */ |
| 95 |
|
const char *comsele_help; /**< @brief select stunt doubles for center-of-mass reference point help description. */ |
| 96 |
+ |
int seleoffset_arg; /**< @brief global index offset for a second object (used to define a vector between sites in molecule). */ |
| 97 |
+ |
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. */ |
| 98 |
+ |
const char *seleoffset_help; /**< @brief global index offset for a second object (used to define a vector between sites in molecule) help description. */ |
| 99 |
+ |
int seleoffset2_arg; /**< @brief global index offset for a third object (used to define a vector between sites in molecule). */ |
| 100 |
+ |
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. */ |
| 101 |
+ |
const char *seleoffset2_help; /**< @brief global index offset for a third object (used to define a vector between sites in molecule) help description. */ |
| 102 |
|
char * molname_arg; /**< @brief molecule name. */ |
| 103 |
|
char * molname_orig; /**< @brief molecule name original value given at command line. */ |
| 104 |
|
const char *molname_help; /**< @brief molecule name help description. */ |
| 111 |
|
double radius_arg; /**< @brief nanoparticle radius. */ |
| 112 |
|
char * radius_orig; /**< @brief nanoparticle radius original value given at command line. */ |
| 113 |
|
const char *radius_help; /**< @brief nanoparticle radius help description. */ |
| 114 |
+ |
double voxelSize_arg; /**< @brief voxel size (angstroms). */ |
| 115 |
+ |
char * voxelSize_orig; /**< @brief voxel size (angstroms) original value given at command line. */ |
| 116 |
+ |
const char *voxelSize_help; /**< @brief voxel size (angstroms) help description. */ |
| 117 |
+ |
double gaussWidth_arg; /**< @brief Gaussian width (angstroms). */ |
| 118 |
+ |
char * gaussWidth_orig; /**< @brief Gaussian width (angstroms) original value given at command line. */ |
| 119 |
+ |
const char *gaussWidth_help; /**< @brief Gaussian width (angstroms) help description. */ |
| 120 |
|
const char *bo_help; /**< @brief bond order parameter (--rcut must be specified) help description. */ |
| 121 |
< |
const char *bor_help; /**< @brief bond order parameter as a function of radius (--rcut must be specified) help description. */ |
| 121 |
> |
const char *ior_help; /**< @brief icosahedral bond order parameter as a function of radius (--rcut must be specified) help description. */ |
| 122 |
> |
const char *for_help; /**< @brief FCC bond order parameter as a function of radius (--rcut must be specified) help description. */ |
| 123 |
|
const char *bad_help; /**< @brief N(theta) bond angle density within (--rcut must be specified) help description. */ |
| 124 |
|
const char *count_help; /**< @brief count of molecules matching selection criteria (and associated statistics) help description. */ |
| 125 |
|
const char *gofr_help; /**< @brief g(r) help description. */ |
| 130 |
|
const char *theta_omega_help; /**< @brief g(cos(theta), cos(omega)) help description. */ |
| 131 |
|
const char *gxyz_help; /**< @brief g(x, y, z) help description. */ |
| 132 |
|
const char *twodgofr_help; /**< @brief 2D g(r) (Slab width --dz must be specified) help description. */ |
| 133 |
< |
const char *p2_help; /**< @brief p2 order parameter (--sele1 and --sele2 must be specified) help description. */ |
| 133 |
> |
const char *p2_help; /**< @brief p2 order parameter (--sele1 must be specified, --sele2 is optional) help description. */ |
| 134 |
|
const char *rp2_help; /**< @brief rp2 order parameter (--sele1 and --sele2 must be specified) help description. */ |
| 135 |
|
const char *scd_help; /**< @brief scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified) help description. */ |
| 136 |
|
const char *density_help; /**< @brief density plot help description. */ |
| 137 |
|
const char *slab_density_help; /**< @brief slab density help description. */ |
| 138 |
< |
const char *p_angle_help; /**< @brief p(cos(theta)) help description. */ |
| 138 |
> |
const char *p_angle_help; /**< @brief p(cos(theta)) (--sele1 must be specified, --sele2 is optional) help description. */ |
| 139 |
|
const char *hxy_help; /**< @brief hxy help description. */ |
| 140 |
|
const char *rho_r_help; /**< @brief rho of R help description. */ |
| 141 |
|
const char *angle_r_help; /**< @brief angle of R help description. */ |
| 142 |
|
const char *hullvol_help; /**< @brief hull volume of nanoparticle help description. */ |
| 143 |
< |
const char *tet_param_help; /**< @brief tetrahedrality order parameter help description. */ |
| 143 |
> |
const char *rodlength_help; /**< @brief length of nanorod help description. */ |
| 144 |
> |
const char *tet_param_help; /**< @brief tetrahedrality order parameter (Qk) help description. */ |
| 145 |
> |
const char *tet_param_z_help; /**< @brief spatially-resolved tetrahedrality order parameter Qk(z) help description. */ |
| 146 |
> |
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. */ |
| 147 |
> |
const char *rnemdz_help; /**< @brief slab-resolved RNEMD statistics (temperature, density, velocity) help description. */ |
| 148 |
> |
const char *rnemdr_help; /**< @brief shell-resolved RNEMD statistics (temperature, density, angular velocity) help description. */ |
| 149 |
> |
const char *rnemdrt_help; /**< @brief shell and angle-resolved RNEMD statistics (temperature, density, angular velocity) help description. */ |
| 150 |
> |
const char *nitrile_help; /**< @brief electrostatic potential to frequency map based on the Cho nitrile fits help description. */ |
| 151 |
> |
const char *multipole_help; /**< @brief average multipole moments contained within cutoff spheres as a function of radius help description. */ |
| 152 |
|
|
| 153 |
|
unsigned int help_given ; /**< @brief Whether help was given. */ |
| 154 |
|
unsigned int version_given ; /**< @brief Whether version was given. */ |
| 170 |
|
unsigned int sele3_given ; /**< @brief Whether sele3 was given. */ |
| 171 |
|
unsigned int refsele_given ; /**< @brief Whether refsele was given. */ |
| 172 |
|
unsigned int comsele_given ; /**< @brief Whether comsele was given. */ |
| 173 |
+ |
unsigned int seleoffset_given ; /**< @brief Whether seleoffset was given. */ |
| 174 |
+ |
unsigned int seleoffset2_given ; /**< @brief Whether seleoffset2 was given. */ |
| 175 |
|
unsigned int molname_given ; /**< @brief Whether molname was given. */ |
| 176 |
|
unsigned int begin_given ; /**< @brief Whether begin was given. */ |
| 177 |
|
unsigned int end_given ; /**< @brief Whether end was given. */ |
| 178 |
|
unsigned int radius_given ; /**< @brief Whether radius was given. */ |
| 179 |
+ |
unsigned int voxelSize_given ; /**< @brief Whether voxelSize was given. */ |
| 180 |
+ |
unsigned int gaussWidth_given ; /**< @brief Whether gaussWidth was given. */ |
| 181 |
|
unsigned int bo_given ; /**< @brief Whether bo was given. */ |
| 182 |
< |
unsigned int bor_given ; /**< @brief Whether bor was given. */ |
| 182 |
> |
unsigned int ior_given ; /**< @brief Whether ior was given. */ |
| 183 |
> |
unsigned int for_given ; /**< @brief Whether for was given. */ |
| 184 |
|
unsigned int bad_given ; /**< @brief Whether bad was given. */ |
| 185 |
|
unsigned int count_given ; /**< @brief Whether count was given. */ |
| 186 |
|
unsigned int gofr_given ; /**< @brief Whether gofr was given. */ |
| 201 |
|
unsigned int rho_r_given ; /**< @brief Whether rho_r was given. */ |
| 202 |
|
unsigned int angle_r_given ; /**< @brief Whether angle_r was given. */ |
| 203 |
|
unsigned int hullvol_given ; /**< @brief Whether hullvol was given. */ |
| 204 |
+ |
unsigned int rodlength_given ; /**< @brief Whether rodlength was given. */ |
| 205 |
|
unsigned int tet_param_given ; /**< @brief Whether tet_param was given. */ |
| 206 |
+ |
unsigned int tet_param_z_given ; /**< @brief Whether tet_param_z was given. */ |
| 207 |
+ |
unsigned int tet_param_xyz_given ; /**< @brief Whether tet_param_xyz was given. */ |
| 208 |
+ |
unsigned int rnemdz_given ; /**< @brief Whether rnemdz was given. */ |
| 209 |
+ |
unsigned int rnemdr_given ; /**< @brief Whether rnemdr was given. */ |
| 210 |
+ |
unsigned int rnemdrt_given ; /**< @brief Whether rnemdrt was given. */ |
| 211 |
+ |
unsigned int nitrile_given ; /**< @brief Whether nitrile was given. */ |
| 212 |
+ |
unsigned int multipole_given ; /**< @brief Whether multipole was given. */ |
| 213 |
|
|
| 214 |
|
char **inputs ; /**< @brief unamed options (options without names) */ |
| 215 |
|
unsigned inputs_num ; /**< @brief unamed options number */ |
