Utils

twod_materials.utils.add_vacuum(delta, cut=0.9)

Adds vacuum to a POSCAR.

Parameters:

• delta (float) – vacuum thickness in Angstroms
• cut (delta) – fractional height above which atoms will need to be fixed. Defaults to 0.9.

twod_materials.utils.align_c_axis_along_001(structure)

Given a structure with a c-axis not along [001], returns the same structure rotated so that the c-axis is along the [001] direction. This is useful for vasp compiled with no z-axis relaxation.

Parameters:structure (structure) – Pymatgen Structure object to rotate. Returns:structure. Rotated to align c-axis along [001].

twod_materials.utils.get_magmom_string()

Based on a POSCAR, returns the string required for the MAGMOM setting in the INCAR. Initializes transition metals with 6.0 bohr magneton and all others with 0.5.

Returns:string. e.g. ‘1*6.0 3*0.5’

twod_materials.utils.get_markovian_path(points)

Calculates the shortest path connecting an array of 2D points.

Parameters:points (list) – list/array of points of the format [[x_1, y_1, z_1], [x_2, y_2, z_2], ...] Returns:A sorted list of the points in order on the markovian path.

twod_materials.utils.get_rotation_matrix(axis, theta)

Find the rotation matrix associated with counterclockwise rotation about the given axis by theta radians. Credit: http://stackoverflow.com/users/190597/unutbu

Parameters:

• axis (list) – rotation axis of the form [x, y, z]
• theta (float) – rotational angle in radians

Returns:

array. Rotation matrix.

twod_materials.utils.get_spacing(filename=u'POSCAR', cut=0.9)

Returns the interlayer spacing for a 2D material.

Parameters:

• filename (str) – ‘CONTCAR’ or ‘POSCAR’, whichever file to check.
• cut (float) – a fractional z-coordinate that must be within the vacuum region.

Returns:

float. Spacing in Angstroms.

twod_materials.utils.get_status(directory)

Return the state of job in a directory. Designed for use on Slurm systems.

Parameters:directory (str) – absolute path to the directory to check. Returns:

string version of SLURM job status.

‘None’ = No running job in this directory

twod_materials.utils.get_structure_type(structure, write_poscar_from_cluster=False)

This is a topology-scaling algorithm used to describe the periodicity of bonded clusters in a bulk structure.

Parameters:

• structure (structure) – Pymatgen structure object to classify.
• write_poscar_from_cluster (bool) – Set to True to write a POSCAR from the sites in the cluster.

Returns:

string. ‘molecular’ (0D), ‘chain’, ‘layered’, ‘heterogeneous’

(intercalated 3D), or ‘conventional’ (3D)

twod_materials.utils.is_converged(directory)

Check if a relaxation has converged.

Parameters:directory (str) – path to directory to check. Returns:boolean. Whether or not the job is converged.

twod_materials.utils.remove_z_kpoints()

Strips all linemode k-points from the KPOINTS file that include a z-component, since these are not relevant for 2D materials.

twod_materials.utils.write_circle_mesh_kpoints(center=[0, 0, 0], radius=0.1, resolution=20)

Create a circular mesh of k-points centered around a specific k-point and write it to the KPOINTS file. Non-circular meshes are not supported, but shouldn’t be too hard to code. All k-point weights are 1.

Parameters:

• center (list) – x, y, and z coordinates of mesh center. Defaults to Gamma.
• radius (float) – Size of the mesh in inverse Angstroms.
• resolution (int) – Number of mesh divisions along the radius in the 3 primary directions.

twod_materials.utils.write_pbs_runjob(name, nnodes, nprocessors, pmem, walltime, binary)

writes a runjob based on a name, nnodes, nprocessors, walltime, and binary. Designed for runjobs on the Hennig group_list on HiperGator 1 (PBS).

Parameters:

• name (str) – job name.
• nnodes (int) – number of requested nodes.
• nprocessors (int) – number of requested processors.
• pmem (str) – requested memory including units, e.g. ‘1600mb’.
• walltime (str) – requested wall time, hh:mm:ss e.g. ‘2:00:00’.
• binary (str) – absolute path to binary to run.

twod_materials.utils.write_potcar(pot_path='/path/to/POTCAR/files', types=u'None')

Writes a POTCAR file based on a list of types.

Parameters:

• pot_path (str) – can be changed to override default location of POTCAR files.
• types (list) – list of same length as number of elements containing specifications for the kind of potential desired for each element. If left as ‘None’, uses the defaults in the ‘potcar_symbols.yaml’ file in the package root.

twod_materials.utils.write_slurm_runjob(name, ntasks, pmem, walltime, binary)

writes a runjob based on a name, nnodes, nprocessors, walltime, and binary. Designed for runjobs on the Hennig group_list on HiperGator 2 (SLURM).

Parameters:

• name (str) – job name.
• ntasks (int) – total number of requested processors.
• pmem (str) – requested memory including units, e.g. ‘1600mb’.
• walltime (str) – requested wall time, hh:mm:ss e.g. ‘2:00:00’.
• binary (str) – absolute path to binary to run.