| 9 |
|
option "input" i "input dump file" string typestr="filename" yes |
| 10 |
|
option "output" o "output file name" string typestr="filename" no |
| 11 |
|
option "step" n "process every n frame" int default="1" no |
| 12 |
< |
option "nrbins" r "number of bins for distance" int default="100" no |
| 12 |
> |
option "nbins" b "number of bins (general purpose)" int default="100" no |
| 13 |
|
option "nbins_x" x "number of bins in x axis" int default="100" no |
| 14 |
|
option "nbins_y" y "number of bins in y axis" int default="100" no |
| 15 |
|
option "nanglebins" a "number of bins for cos(angle)" int default="50" no |
| 16 |
|
option "length" - "maximum length (Defaults to 1/2 smallest length of first frame)" double no |
| 17 |
– |
option "LegendreL" l "Order of Legendre Polynomial (used for Bond Order calculations)" int no |
| 17 |
|
option "rcut" c "cutoff radius (rcut)" double no |
| 18 |
|
option "zoffset" z "Where to set the zero for the slab_density calculation" double default="0" no |
| 19 |
|
option "sele1" - "select the first stuntdouble set" string typestr="selection script" no |
| 20 |
|
option "sele2" - "select the second stuntdouble set" string typestr="selection script" no |
| 21 |
|
option "sele3" - "select the third stuntdouble set" string typestr="selection script" no |
| 22 |
|
option "refsele" - "select reference (use and only use with --gxyz)" string typestr="selection script" no |
| 23 |
+ |
option "comsele" - "select stunt doubles for center-of-mass reference point" string typestr="selection script" no |
| 24 |
|
option "molname" - "molecule name" string no |
| 25 |
|
option "begin" - "begin internal index" int no |
| 26 |
|
option "end" - "end internal index" int no |
| 27 |
+ |
option "radius" - "nanoparticle radius" double no |
| 28 |
|
defgroup "staticProps" groupdesc=" an option of this group is required" yes |
| 29 |
< |
groupoption "bo" b "bond order parameter (--rcut and --LegendreL must be specified" group="staticProps" |
| 29 |
> |
groupoption "bo" - "bond order parameter (--rcut must be specified)" group="staticProps" |
| 30 |
> |
groupoption "bor" - "bond order parameter as a function of radius (--rcut must be specified)" group="staticProps" |
| 31 |
> |
groupoption "bad" - "N(theta) bond angle density within (--rcut must be specified)" group="staticProps" |
| 32 |
|
groupoption "gofr" g "g(r)" group="staticProps" |
| 33 |
+ |
groupoption "gofz" - "g(z)" group="staticProps" |
| 34 |
|
groupoption "r_theta" - "g(r, cos(theta))" group="staticProps" |
| 35 |
|
groupoption "r_omega" - "g(r, cos(omega))" group="staticProps" |
| 36 |
|
groupoption "theta_omega" - "g(cos(theta), cos(omega))" group="staticProps" |
| 41 |
|
groupoption "density" d "density plot" group="staticProps" |
| 42 |
|
groupoption "slab_density" - "slab density" group="staticProps" |
| 43 |
|
groupoption "hxy" - "hxy" group="staticProps" |
| 44 |
+ |
groupoption "rho_r" - "rho of R" group="staticProps" |
| 45 |
+ |
groupoption "hullvol" - "hull volume of nanoparticle" group="staticProps" |
