| 2 |
|
# for parsing command line arguments useing getopt and getoptlong. |
| 3 |
|
# gengetopt is available from: |
| 4 |
|
# http://www.gnu.org/software/gengetopt/gengetopt.html |
| 5 |
+ |
# invoke with: |
| 6 |
+ |
# gengetopt < StaticProps.ggo --file-name=StaticPropsCmd --unamed-opts |
| 7 |
+ |
|
| 8 |
|
package "StaticProps" |
| 9 |
|
version "1.00" |
| 10 |
|
|
| 15 |
|
option "nbins" b "number of bins (general purpose)" int default="100" no |
| 16 |
|
option "nbins_x" x "number of bins in x axis" int default="100" no |
| 17 |
|
option "nbins_y" y "number of bins in y axis" int default="100" no |
| 18 |
+ |
option "nbins_z" - "number of bins in z axis" int default="100" no |
| 19 |
|
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 |
| 20 |
|
option "rcut" c "cutoff radius (rcut)" double no |
| 21 |
+ |
option "dz" - "slab width (dz)" double no |
| 22 |
+ |
option "length" - "maximum length (Defaults to 1/2 smallest length of first frame)" double no |
| 23 |
+ |
option "zlength" - "maximum length (Defaults to 1/2 smallest length of first frame)" double no |
| 24 |
|
option "zoffset" z "Where to set the zero for the slab_density calculation" double default="0" no |
| 25 |
|
option "sele1" - "select the first stuntdouble set" string typestr="selection script" no |
| 26 |
|
option "sele2" - "select the second stuntdouble set" string typestr="selection script" no |
| 27 |
|
option "sele3" - "select the third stuntdouble set" string typestr="selection script" no |
| 28 |
|
option "refsele" - "select reference (use and only use with --gxyz)" string typestr="selection script" no |
| 29 |
+ |
option "comsele" - "select stunt doubles for center-of-mass reference point" string typestr="selection script" no |
| 30 |
+ |
option "seleoffset" - "global index offset for a second object (used to define a vector between sites in molecule)" int no |
| 31 |
|
option "molname" - "molecule name" string no |
| 32 |
|
option "begin" - "begin internal index" int no |
| 33 |
|
option "end" - "end internal index" int no |
| 34 |
+ |
option "radius" - "nanoparticle radius" double no |
| 35 |
|
defgroup "staticProps" groupdesc=" an option of this group is required" yes |
| 36 |
< |
groupoption "bo" - "bond order parameter (--rcut must be specified" group="staticProps" |
| 36 |
> |
groupoption "bo" - "bond order parameter (--rcut must be specified)" group="staticProps" |
| 37 |
> |
groupoption "bor" - "bond order parameter as a function of radius (--rcut must be specified)" group="staticProps" |
| 38 |
> |
groupoption "bad" - "N(theta) bond angle density within (--rcut must be specified)" group="staticProps" |
| 39 |
> |
groupoption "count" - "count of molecules matching selection criteria (and associated statistics)" group="staticProps" |
| 40 |
|
groupoption "gofr" g "g(r)" group="staticProps" |
| 41 |
+ |
groupoption "gofz" - "g(z)" group="staticProps" |
| 42 |
|
groupoption "r_theta" - "g(r, cos(theta))" group="staticProps" |
| 43 |
|
groupoption "r_omega" - "g(r, cos(omega))" group="staticProps" |
| 44 |
+ |
groupoption "r_z" - "g(r, z)" group="staticProps" |
| 45 |
|
groupoption "theta_omega" - "g(cos(theta), cos(omega))" group="staticProps" |
| 46 |
|
groupoption "gxyz" - "g(x, y, z)" group="staticProps" |
| 47 |
< |
groupoption "p2" p "p2 order parameter (--sele1 and --sele2 must be specified)" group="staticProps" |
| 47 |
> |
groupoption "twodgofr" - "2D g(r) (Slab width --dz must be specified)" group="staticProps" |
| 48 |
> |
groupoption "p2" p "p2 order parameter (--sele1 must be specified, --sele2 is optional)" group="staticProps" |
| 49 |
|
groupoption "rp2" - "rp2 order parameter (--sele1 and --sele2 must be specified)" group="staticProps" |
| 50 |
|
groupoption "scd" s "scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified)" group="staticProps" |
| 51 |
|
groupoption "density" d "density plot" group="staticProps" |
| 52 |
|
groupoption "slab_density" - "slab density" group="staticProps" |
| 53 |
+ |
groupoption "p_angle" - "p(cos(theta))" group="staticProps" |
| 54 |
|
groupoption "hxy" - "hxy" group="staticProps" |
| 55 |
+ |
groupoption "rho_r" - "rho of R" group="staticProps" |
| 56 |
+ |
groupoption "angle_r" - "angle of R" group="staticProps" |
| 57 |
+ |
groupoption "hullvol" - "hull volume of nanoparticle" group="staticProps" |
| 58 |
+ |
groupoption "rodlength" - "length of nanorod" group="staticProps" |
| 59 |
+ |
groupoption "tet_param" Q "tetrahedrality order parameter (Qk)" group="staticProps" |
| 60 |
+ |
groupoption "tet_param_z" - "spatially-resolved tetrahedrality order parameter Qk(z)" group="staticProps" |
| 61 |
+ |
groupoption "rnemdz" - "slab-resolved RNEMD statistics (temperature, density, velocity)" group="staticProps" |
| 62 |
+ |
groupoption "rnemdr" - "shell-resolved RNEMD statistics (temperature, density, angular velocity)" group="staticProps" |
