csg_partial_rdf1

Usage

Overview

Calculate spatially confined rdfs

Options

Allowed options:

-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
--top arg atomistic topology file

Mapping options:

--cg arg [OPTIONAL] coarse graining mapping and bond
definitions
(xml-file). If no file is given, program acts on
original trajectory
--map-ignore arg list of molecules to ignore if mapping is done
separated by ;

Specific options:

--options arg options file defining the rdfs
--subvolume_radius arg Rdf calc. in spherical subvolume of this radius (from
center of box)
--do-vol-corr Correct for subvolume truncation in rdf
--write-every arg (UNIMPLEMENTED) write after every block of this
length, if --blocking is set, the averages are
cleared after every output
--do-blocks write output for blocking analysis

Threading options:

--nt arg (=1) number of threads

Trajectory options:

--trj arg atomistic trajectory file
--begin arg (=0) skip frames before this time (only works for
Gromacs files)
--first-frame arg (=0) start with this frame
--nframes arg process the given number of frames