\(\newcommand{\AA}{\text{Å}}\)
Usage#
\(\mathrm{LModeA\text{-}}\vec{\mathbf{k}}\) can be used in various ways depending on the intended analysis type. This page outlines common uses of the command-line interface, which is expected to cover most use cases. Advanced users can script their own workflows using the \(\mathrm{LModeA\text{-}}\vec{\mathbf{k}}\) API.
Run with user-specified internal coordinates (recommended)#
To run \(\mathrm{LModeA\text{-}}\vec{\mathbf{k}}\) with user-specified internal coordinates, write a coordinate specification file and pass its path to the --coord-spec command-line flag:
lmodea-k input.castep --coord-spec coords.in
If no path is given, --coord-spec defaults to coords.in in the current directory.
The full syntax for the coordinate specification file is described on the Internal coordinates page. An example coords.in file showing several common coordinate types is:
bond 1 4
bond 3[0 0 1] 8
angle 4 6 9
angle 12[1 0 0] 14 17
dihedral 3 5 7 9
group ring1 3 4 5 6 7 8
pucker ring1
group fragA 1 2 3 4
group fragB 5 6 7 8
inter fragA fragB
group mol 2 5 8 4 6
translate mol x y
rotate mol z
translate system x y
rotate system z
complement
When --coord-spec is used, any coordinate types specified via --coord-types are ignored; only the coordinates listed in the specification file are used.
If one wants to benefit from the automatic search, they may run lmodea-k with the desired --coord-types specified and the --write-coords flag. This will output a coords.in listing all internal coordinates of the specified type found in the structure, based on default or custom bonding cutoffs. The user may then edit the file and run \(\mathrm{LModeA\text{-}}\vec{\mathbf{k}}\) as described above.
Run with automatic generation of internal coordinates (default)#
A default run of lmodea-k will automatically generate a set of internal coordinates including bonds, angles, dihedrals and rigid-body system translations.
If the user wants to remove linearly-dependent internal coordinates from the set, they should use the --reduce flag.