\(\newcommand{\AA}{\text{Å}}\)
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)#
Write input file. Any coordinate types specified are ignored, only those in the input are used.
If one wants to benefit from the automatic search, they may run lmodea-k with the desired --coord-types specified and the --no-reduce and --no-complete flags. This will output a text file listing all internal coordinates of the specified type found in the structure, based on default or custom bonding cutoffs. The user may then select the desired coordinates from the list and include them in the input file.
If the user wants to preserve all specified internal coordinates, they should use the --no-reduce flag. By default, B matrix augmentation is implemented to ensure that the internal coordinate set spans all of the system’s degrees of freedom. If this is not desired, the user should specify the --no-complete flag.
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, ensuring no linear dependencies and augmenting the B matrix to full-rank if necessary.