What is multishifter for?

A common technique for investigating dislocations, stacking faults, and slip planes in crystals involves the calculation of $\gamma$-surface energies. The software provided in the multishifter toolbox facilitate the creation of crystal structures for calculations of UBER curves and surface energies along arbitrary slip planes. The multishifter libraries also have tools that aid in the construction of twisted bilayers to create periodic Moiré structures.

Basic usage

The multishift executable is a suite of command line tools that can manipulate and create crystal structures for slab model calculations. Each tool is specialized to complete a particular task, and accepts arguments directly from the command line. Input and output files of crystal structures use the VASP format.

Starting from a primitive structure, several steps must be taken to create the slab models, each accomplished using a multishifter tool. A typical workflow looks like

Slice the primitive structure to expose the desired surface plane (slice).
Specify the thickness of the slabs (stack).
Rigidly translate the basis of the slab, to expose the desired atomic layer/center the rotation axis (translate)
Generate a set of shifted slab structures with shift ($\gamma$-surface), cleave the structure at different intervals with cleave (UBER), or create commensurate structures that have been rotated with twist (Moiré/twisted layers).

Each of these commands takes the form

multishift <command> --args

All available tools and a list on their input parameters can be found with

multishift --help
multhishift <command> --help

Feature overview

multishift comes as a collection of tools, each meant to manipulate crystal structures a particular way.

slice

multishift slice will create a supercell of a primitive cell that exposes a particular slip or surface plane.

Parameters

input: path to starting structure.
output: output file path.
millers: defines slip plane.

stack

multishift stack will concatenate a list of structures together. The stack is created by fusing unit cells together along the $ab$ facet.

Parameters

input: list of structures to stack together.
output: output file path.

translate

multishift translate will rigidly translate all the basis atoms of the given structure.

Parameters

input: path to starting structure.
output: output file path.
value: translation vector to apply to the basis.
floor: index of atom that should end up at the origin after translating the basis.
fractional: if given, “value” will be interpreted as a fractional value relative to the lattice vectors.

align

multishift align will apply a rigid rotation to the structure, aligning the $a$ vector along the $x$ direction, and restricting the $b$ vector to the $xy$-plane.

Parameters

input: path to starting structure.
output: output file path.
prismatic: if given, the $c$ vector will also be rectified to be perpendicular to the $ab$ plane, creating a prismatic slab. This may break the periodicity of your crystal.

mutate

multishift mutate will alter the $c$ vector of the lattice, while retaining all Cartesian values of the basis. Useful for individual stacking fault and surface energy calculations.

Parameters

input: path to starting structure.
output: output file path.
mutation: value to add to the third lattice vector.
fractional: if given, “mutation” will be interpreted as a fractional value relative to the lattice vectors.

cleave

multishift cleave will generate a series of slab structures with a specified amount of vacuum between their periodic images. Useful for Universal Binding Energy Relation (UBER) calculations.

Parameters

input: path to starting structure.
output: output directory.
values: vacuum spacings to insert between the periodic images of the slabs in $\AA$. Negative values will bring periodic slabs closer to each other.

shift

multishift shift will generate a series of slab structures that have been shifted relative to each other along the $ab$-plane. Useful for $\gamma$-surface calculations.

Parameters

input: path to starting structure.
output: output directory.
grid: divisions to make along the $ab$-plane. Each grid point will correspond to a particular shift applied to the slabs. Periodic images are not counted in the grid.

chain

multishift chain combines the shift and chain commands. For each perturbed slab generated by shift, all the values of cleave are applied to it. Useful for $\gamma$-surface calculations.

Parameters

input: path to starting structure.
output: output directory.
grid: divisions to make along the $ab$-plane. Each grid point will correspond to a particular shift applied to the slabs. Periodic images are not counted in the grid.

fourier

multishift fourier reads DFT or UBER parameters that you’ve assigned to each gridpoint from a chain or shift command, and returns an analytical expression for your surface. The expression is printed as python code.

Parameters

data: path to json file that holds the data to interpolate.
cleavage-slice: specifies which cleavage values to read from the data set. Use this when your data set has multiple values per grid point.
key: string used to access the values to interpolate in your json file.
crush: minimum magnitude required for basis function to be included.

twist

multishift twist creates twisted commensurate supercells that can be combined to create Moiré patterns when stacked together.

Parameters

input: path to starting structure.
output: output directory.
angles: rotation angles to apply to the slab. Rotation axis is always perpedicular to the $ab$-plane, and goes through the origin.
max-lattice-sites: determines how large the search space for highly commensurate supercells should be. Larger values will result in less deformation of the final layers.
error-tol: minimum improvement necessary to consider a larger supcercell better.
brillouin-zone: select whether the rotated or the original (aligned) Brillouin zone should be used to map reciprocal vectors back into the first zone.
supercells: determines whether only the best supercell, or supercells of different sizes should be outputted.

Tutorials

Follow this series of tutorials to acquaint yourself with all of the available features. Each tutorial focuses on one or two of the available tools, and build on each other as they progress.

Tutorial I: Slicing a structure
Tutorial II: Stacking structures
Tutorial III: Stacking faults and surfaces
Tutorial IV: Cleaving for UBER
Tutorial V: Shifting for $\gamma$-surfaces
Tutorial VI: Chaining shifting and cleaving
Tutorial VII: Fourier interpolation
Tutorial VIII: Do the twist
Tutorial IX: What’s in a record.json?

Acknowledgements

Initial development of this software package was possible thanks to the financial support from NSF DMREF program under grant DMR-1534264. Subsequent development was made possible by additional grants. The scientific work was supported by the National Science Foundation DMREF grant: DMR-1729166 “DMREF/GOALI: Integrated ComputationalFramework for Designing Dynamically Controlled Alloy-Oxide Heterostructures”. Software development was supported by the National Science Foundation, Grant No. OAC-1642433.