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# for parsing command line arguments useing getopt and getoptlong. |
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# gengetopt is available from: |
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# http://www.gnu.org/software/gengetopt/gengetopt.html |
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# invoke with: |
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# gengetopt < StaticProps.ggo --file-name=StaticPropsCmd --unamed-opts |
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package "StaticProps" |
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version "1.00" |
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option "input" i "input dump file" string typestr="filename" yes |
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option "output" o "output file name" string typestr="filename" no |
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option "step" n "process every n frame" int default="1" no |
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option "nrbins" r "number of bins for distance" int default="100" no |
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option "nbins" b "number of bins (general purpose)" int default="100" no |
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option "nbins_x" x "number of bins in x axis" int default="100" no |
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option "nbins_y" y "number of bins in y axis" int default="100" no |
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option "nbins_z" - "number of bins in z axis" int default="100" no |
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option "nanglebins" a "number of bins for cos(angle)" int default="50" no |
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option "length" l "maximum length (Defaults to 1/2 smallest length of first frame)" double no |
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option "sele1" - "select first stuntdouble set" string typestr="selection script" no |
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option "sele2" - "select second stuntdouble set" string typestr="selection script" no |
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option "refsele" - "select reference (use and only use with --gxyz)" string typestr="selection script" no |
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option "rcut" c "cutoff radius (rcut)" double no |
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option "dz" - "slab width (dz)" double no |
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option "length" - "maximum length (Defaults to 1/2 smallest length of first frame)" double no |
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option "zlength" - "maximum length (Defaults to 1/2 smallest length of first frame)" double no |
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option "zoffset" z "Where to set the zero for the slab_density calculation" double default="0" no |
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option "sele1" - "select the first stuntdouble set" string typestr="selection script" no |
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option "sele2" - "select the second stuntdouble set" string typestr="selection script" no |
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option "sele3" - "select the third stuntdouble set" string typestr="selection script" no |
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option "refsele" - "select reference (use and only use with --gxyz)" string typestr="selection script" no |
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option "comsele" - "select stunt doubles for center-of-mass reference point" string typestr="selection script" no |
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option "seleoffset" - "global index offset for a second object (used to define a vector between sites in molecule)" int no |
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option "molname" - "molecule name" string no |
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option "begin" - "begin internal index" int no |
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option "end" - "end internal index" int no |
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option "radius" - "nanoparticle radius" double no |
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defgroup "staticProps" groupdesc=" an option of this group is required" yes |
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groupoption "gofr" - "g(r)" group="staticProps" |
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groupoption "r_theta" - "g(r, cos(theta))" group="staticProps" |
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groupoption "r_omega" - "g(r, cos(omega))" group="staticProps" |
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groupoption "theta_omega" - "g(cos(theta), cos(omega))" group="staticProps" |
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groupoption "gxyz" - "g(x, y, z)" group="staticProps" |
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groupoption "bo" - "bond order parameter (--rcut must be specified)" group="staticProps" |
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groupoption "bor" - "bond order parameter as a function of radius (--rcut must be specified)" group="staticProps" |
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groupoption "bad" - "N(theta) bond angle density within (--rcut must be specified)" group="staticProps" |
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groupoption "count" - "count of molecules matching selection criteria (and associated statistics)" group="staticProps" |
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groupoption "gofr" g "g(r)" group="staticProps" |
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groupoption "gofz" - "g(z)" group="staticProps" |
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groupoption "r_theta" - "g(r, cos(theta))" group="staticProps" |
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groupoption "r_omega" - "g(r, cos(omega))" group="staticProps" |
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groupoption "r_z" - "g(r, z)" group="staticProps" |
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groupoption "theta_omega" - "g(cos(theta), cos(omega))" group="staticProps" |
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groupoption "gxyz" - "g(x, y, z)" group="staticProps" |
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groupoption "twodgofr" - "2D g(r) (Slab width --dz must be specified)" group="staticProps" |
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groupoption "p2" p "p2 order parameter (--sele1 must be specified, --sele2 is optional)" group="staticProps" |
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groupoption "rp2" - "rp2 order parameter (--sele1 and --sele2 must be specified)" group="staticProps" |
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groupoption "scd" s "scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified)" group="staticProps" |
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groupoption "density" d "density plot" group="staticProps" |
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groupoption "slab_density" - "slab density" group="staticProps" |
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groupoption "p_angle" - "p(cos(theta))" group="staticProps" |
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groupoption "hxy" - "hxy" group="staticProps" |
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groupoption "rho_r" - "rho of R" group="staticProps" |
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groupoption "angle_r" - "angle of R" group="staticProps" |
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groupoption "hullvol" - "hull volume of nanoparticle" group="staticProps" |
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groupoption "rodlength" - "length of nanorod" group="staticProps" |
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groupoption "tet_param" Q "tetrahedrality order parameter (Qk)" group="staticProps" |
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groupoption "tet_param_z" - "spatially-resolved tetrahedrality order parameter Qk(z)" group="staticProps" |
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groupoption "rnemdz" - "slab-resolved RNEMD statistics (temperature, density, velocity)" group="staticProps" |
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groupoption "rnemdr" - "shell-resolved RNEMD statistics (temperature, density, angular velocity)" group="staticProps" |
