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tim |
310 |
# Input file for gengetopt --generates cmdline.c and cmdline.h |
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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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gezelter |
1819 |
# invoke with: |
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# gengetopt < StaticProps.ggo --file-name=StaticPropsCmd --unamed-opts |
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tim |
311 |
package "StaticProps" |
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tim |
310 |
version "1.00" |
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# Options |
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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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tim |
311 |
option "step" n "process every n frame" int default="1" no |
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gezelter |
1041 |
option "nbins" b "number of bins (general purpose)" int default="100" no |
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xsun |
967 |
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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gezelter |
1440 |
option "nbins_z" - "number of bins in z axis" int default="100" no |
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tim |
310 |
option "nanglebins" a "number of bins for cos(angle)" int default="50" no |
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chuckv |
1445 |
option "rcut" c "cutoff radius (rcut)" double no |
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gezelter |
1454 |
option "dz" - "slab width (dz)" double no |
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gezelter |
1039 |
option "length" - "maximum length (Defaults to 1/2 smallest length of first frame)" double no |
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chuckv |
1445 |
option "zlength" - "maximum length (Defaults to 1/2 smallest length of first frame)" double no |
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gezelter |
929 |
option "zoffset" z "Where to set the zero for the slab_density calculation" double default="0" no |
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tim |
544 |
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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gezelter |
1282 |
option "comsele" - "select stunt doubles for center-of-mass reference point" string typestr="selection script" no |
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gezelter |
1819 |
option "seleoffset" - "global index offset for a second object (used to define a vector between sites in molecule)" int no |
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gezelter |
1991 |
option "seleoffset2" - "global index offset for a third object (used to define a vector between sites in molecule)" int no |
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tim |
544 |
option "molname" - "molecule name" string no |
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gezelter |
1039 |
option "begin" - "begin internal index" int no |
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tim |
544 |
option "end" - "end internal index" int no |
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chuckv |
1091 |
option "radius" - "nanoparticle radius" double no |
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gezelter |
2015 |
option "voxelSize" v "voxel size (angstroms)" double no |
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option "gaussWidth" - "Gaussian width (angstroms)" double no |
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tim |
310 |
defgroup "staticProps" groupdesc=" an option of this group is required" yes |
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chuckv |
1128 |
groupoption "bo" - "bond order parameter (--rcut must be specified)" group="staticProps" |
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gezelter |
1992 |
groupoption "ior" - "icosahedral bond order parameter as a function of radius (--rcut must be specified)" group="staticProps" |
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groupoption "for" - "FCC bond order parameter as a function of radius (--rcut must be specified)" group="staticProps" |
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chuckv |
1180 |
groupoption "bad" - "N(theta) bond angle density within (--rcut must be specified)" group="staticProps" |
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gezelter |
1513 |
groupoption "count" - "count of molecules matching selection criteria (and associated statistics)" group="staticProps" |
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gezelter |
1039 |
groupoption "gofr" g "g(r)" group="staticProps" |
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xsun |
1213 |
groupoption "gofz" - "g(z)" group="staticProps" |
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gezelter |
1039 |
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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gezelter |
1440 |
groupoption "r_z" - "g(r, z)" group="staticProps" |
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gezelter |
1039 |
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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gezelter |
1454 |
groupoption "twodgofr" - "2D g(r) (Slab width --dz must be specified)" group="staticProps" |
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gezelter |
1542 |
groupoption "p2" p "p2 order parameter (--sele1 must be specified, --sele2 is optional)" group="staticProps" |
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gezelter |
1039 |
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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gezelter |
1979 |
groupoption "p_angle" - "p(cos(theta)) (--sele1 must be specified, --sele2 is optional)" group="staticProps" |
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gezelter |
1039 |
groupoption "hxy" - "hxy" group="staticProps" |
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gezelter |
1413 |
groupoption "rho_r" - "rho of R" group="staticProps" |
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kstocke1 |
1522 |
groupoption "angle_r" - "angle of R" group="staticProps" |
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gezelter |
1413 |
groupoption "hullvol" - "hull volume of nanoparticle" group="staticProps" |
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gezelter |
1843 |
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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gezelter |
2015 |
groupoption "tet_param_xyz" - "volume-resolved tetrahedrality order parameter Qk(x,y,z). (voxelSize, rcut, and gaussWidth must be specified)" group="staticProps" |
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gezelter |
1879 |
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" |
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gezelter |
1953 |
groupoption "rnemdrt" - "shell and angle-resolved RNEMD statistics (temperature, density, angular velocity)" group="staticProps" |
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gezelter |
1994 |
groupoption "nitrile" - "electrostatic potential to frequency map based on the Cho nitrile fits" group="staticProps" |
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gezelter |
1999 |
groupoption "multipole" m "average multipole moments contained within cutoff spheres as a function of radius" group="staticProps" |
