Input Tags

abinitio_code

The first-principles code being used in conjunction with some PM calculation.
  • type: string
  • dimension:
  • scripts:
    • abinitio_code
    • file_hive
    • abinitio_output

acoustic_first

If set, the acoustic mode will be at the beginning of the irrep stack. Otherwise, it is last.
  • type: bool
  • dimension:
  • scripts:
    • phonons_via_irr_derivatives
    • displaced_crystal

add_boundary_atoms

Translate atoms on boundary of supercell by all supercell translations.
  • type: bool
  • dimension:
  • scripts:
    • crystal_viewer

all_in_cell

Translate all atoms within the supercell.
  • type: bool
  • dimension:
  • scripts:
    • crystal_viewer

amplitude


  • type: float-array
  • dimension:
  • scripts:
    • crystal_variables

basis_atoms

Basis atoms of the crystal structure.
  • type: dict-string-to-float-array
  • dimension: scalar \( \leftrightarrow N_{j}\times3\) where \(j\) labels species of atom.
  • scripts:
    • cluster
    • crystal
    • crystal_ftg
    • orbit_qrep
    • disp_qrep
    • phonons_via_irr_derivatives
    • crystal_attributes
    • crystal_viewer
    • displaced_crystal

call_viewer

Perform a system call to start the viewer.
  • type: bool
  • dimension:
  • scripts:
    • crystal_viewer

construct_irr_basis


  • type: bool
  • dimension:
  • scripts:
    • irr_rep_product
    • irr_rep_symmetric_product
    • orbit_qrep
    • disp_qrep
    • tensor_irr_rep

convert_to_supercell

Create a supercell using the provided supercell matrix.
  • type: int-array
  • dimension:
  • scripts:
    • crystal
    • crystal_ftg
    • orbit_qrep
    • disp_qrep
    • phonons_via_irr_derivatives
    • crystal_attributes
    • crystal_viewer
    • displaced_crystal

degub

Defines the verbosity of error handling and may invoke basic tests.
  • type: bool
  • dimension:
  • scripts:
    • All scripts.

displaced_basis_atoms

Displaced basis atoms of the crystal structure.
  • type: dict-string-to-float-array
  • dimension: scalar \( \leftrightarrow N_{j}\times3\) where \(j\) labels species of atom.
  • scripts:
    • displaced_crystal

displaced_lattice_vectors

Distorted lattice vectors in three dimensions, stored in a matrix.
  • type: float-array
  • dimension: \(3\times3\)
  • scripts:
    • displaced_crystal

draw_primitive_cell

Draw the primitive unit cell.
  • type: bool
  • dimension:
  • scripts:
    • crystal_viewer

draw_super_cell

Draw the super cell.
  • type: bool
  • dimension:
  • scripts:
    • crystal_viewer

frequency_units


  • type: string
  • dimension:
  • scripts:
    • phonons_via_irr_derivatives

hdf5_name

Name of the irreducible_derivative hdf5 file produced by main branch.
  • type: string
  • dimension:
  • scripts:
    • convert_id_main_to_dev

hive_attributes

A list of attributes which are to be extracted from first-principles input and output files.
  • type: string-list
  • dimension:
  • scripts:
    • file_hive

hive_files

A list of files within each subdirectory to be archived.
  • type: string-list
  • dimension:
  • scripts:
    • file_hive

hive_path_identifiers

A list a files that will be searched for to identify which directories will be included in the file hive.
  • type: string-list
  • dimension:
  • scripts:
    • file_hive

input_crystal_format

Convention for crystal structure input (e.g. vasp, QE, abinit, etc).
  • type: string
  • dimension:
  • scripts:
    • crystal_format

input_files

Name of yaml files containing input tags which will be read.
  • type: string-list
  • dimension: N, where N is the number of files provided.
  • scripts:
    • All scripts.

irr_rep_inst


  • type: int-array
  • dimension:
  • scripts:
    • crystal_variables

irr_rep_name


  • type: string-array
  • dimension:
  • scripts:
    • crystal_variables

irr_rep_row


  • type: int-array
  • dimension:
  • scripts:
    • crystal_variables

irr_reps


  • type: string-array
  • dimension:
  • scripts:
    • irr_rep_product
    • irr_rep_symmetric_product

lattice_vectors

Lattice vectors in three dimensions, stored in a matrix \(\hat a\).
  • type: float-array
  • dimension: \(3\times3\)
  • scripts:
    • lattice
    • lattice_ftg
    • lattice_fsg
    • kpoints_ftg
    • kpoints_fsg
    • cluster
    • crystal
    • crystal_ftg
    • orbit_qrep
    • disp_qrep
    • phonons_via_irr_derivatives
    • crystal_attributes
    • crystal_viewer
    • star_rep
    • displaced_crystal

only_print_identity


  • type: bool
  • dimension:
  • scripts:
    • irr_rep_product
    • irr_rep_symmetric_product
    • orbit_qrep
    • disp_qrep
    • tensor_irr_rep

output_crystal_format

Convention for crystal structure output (e.g. vasp, QE, abinit, etc).
  • type: string
  • dimension:
  • scripts:
    • crystal_format

output_transpose


  • type: bool
  • dimension:
  • scripts:
    • irr_rep_product
    • irr_rep_symmetric_product
    • orbit_qrep
    • disp_qrep
    • tensor_irr_rep

permute_atoms

Permute the atoms.
  • type: int-array
  • dimension:
  • scripts:
    • cluster
    • crystal
    • crystal_ftg
    • orbit_qrep
    • disp_qrep
    • phonons_via_irr_derivatives
    • crystal_attributes
    • crystal_viewer
    • displaced_crystal

point_group

The name of the point group of the space group.
  • type: str
  • dimension: scalar
  • scripts:
    • lattice_fsg
    • kpoints_fsg
    • point_group
    • irr_rep_product
    • irr_rep_symmetric_product
    • orbit_qrep
    • disp_qrep
    • tensor_irr_rep
    • phonons_via_irr_derivatives
    • star_rep
    • point_group_viewer
    • displaced_crystal

point_group_family


  • type: string
  • dimension:
  • scripts:
    • lattice_fsg
    • kpoints_fsg
    • point_group
    • irr_rep_product
    • irr_rep_symmetric_product
    • orbit_qrep
    • disp_qrep
    • tensor_irr_rep
    • phonons_via_irr_derivatives
    • star_rep
    • point_group_viewer
    • displaced_crystal

point_group_instance


  • type: int
  • dimension: scalar
  • scripts:
    • lattice_fsg
    • kpoints_fsg
    • point_group
    • irr_rep_product
    • irr_rep_symmetric_product
    • orbit_qrep
    • disp_qrep
    • tensor_irr_rep
    • phonons_via_irr_derivatives
    • star_rep
    • point_group_viewer
    • displaced_crystal

precision

Sets the number of decimal places that are retained when testing a floating point equality.
  • type: int
  • dimension:
  • scripts:
    • All scripts.

print_attribute

Print attributes of the underlying class.
  • type: string-list
  • dimension:
  • scripts:
    • All scripts.

print_irr_reps


  • type: bool
  • dimension:
  • scripts:
    • orbit_qrep
    • disp_qrep
    • tensor_irr_rep

print_irr_vector_stack

Print the irreducible representation vectors as a row stacked matrix.
  • type: bool
  • dimension:
  • scripts:
    • disp_qrep

print_irr_vectors


  • type: bool
  • dimension:
  • scripts:
    • irr_rep_product
    • irr_rep_symmetric_product
    • orbit_qrep
    • disp_qrep
    • tensor_irr_rep

print_summary


  • type: bool
  • dimension:
  • scripts:
    • phonons_via_irr_derivatives

project_xtal

A distorted crystal structure that will be projected onto the irreducible representations of displacement.
  • type: string
  • dimension:
  • scripts:
    • disp_qrep

qpoint

A point in reciprocal space when dealing with phonons.
  • type: float-array
  • dimension: 3
  • scripts:
    • qpoint
    • orbit_qrep
    • disp_qrep
    • star_rep
    • crystal_variables

qpoint_type


  • type: int-array
  • dimension:
  • scripts:
    • crystal_variables

quadratic_irr_derivatives

The real part of the irreducible derivatives, given by a dictionary of k-points with values of a dictionary mapping irreducible representations to a list of irreducible derivatives (upper diagonal).
  • type: dict-irr-deriv
  • dimension:
  • scripts:
    • phonons_via_irr_derivatives
    • displaced_crystal

quadratic_irr_derivatives_imaginary

The imaginary part of the irreducible derivatives, in same format as real part.
  • type: dict-irr-deriv
  • dimension:
  • scripts:
    • phonons_via_irr_derivatives
    • displaced_crystal

remove_acoustic

If the qpoint is the Gamma point, construct the acoustic mode and corresponding orthonormal modes, then remove the acoustic mode.
  • type: bool
  • dimension:
  • scripts:
    • orbit_qrep
    • disp_qrep

rotate_lattice_vectors

Rotate the lattice vectors.
  • type: float-array
  • dimension:
  • scripts:
    • cluster
    • crystal
    • crystal_ftg
    • orbit_qrep
    • disp_qrep
    • phonons_via_irr_derivatives
    • crystal_attributes
    • crystal_viewer
    • displaced_crystal

set_acoustic

If the qpoint is the Gamma point, construct the acoustic mode and correspond orthonormal modes.
  • type: bool
  • dimension:
  • scripts:
    • orbit_qrep
    • disp_qrep

shift_atom

Shift block B, atom n, alpha direction by amp, given as B n alpha amp, which can be delimited by anything compatible with the PM array parser. Multiple shifts can be given as B,n,alpha,amp1;A,m,beta,amp2 etc.
  • type: string-array
  • dimension:
  • scripts:
    • cluster
    • crystal
    • crystal_ftg
    • orbit_qrep
    • disp_qrep
    • phonons_via_irr_derivatives
    • crystal_attributes
    • crystal_viewer
    • displaced_crystal

shift_into_cell

Shift atoms such that they are within the conventional unit cell.
  • type: bool
  • dimension:
  • scripts:
    • crystal
    • crystal_ftg
    • orbit_qrep
    • disp_qrep
    • phonons_via_irr_derivatives
    • crystal_attributes
    • crystal_viewer
    • displaced_crystal

shift_origin

Shift the origin, where the shift is specified in lattice coordinates.
  • type: float-array
  • dimension:
  • scripts:
    • cluster
    • crystal
    • crystal_ftg
    • orbit_qrep
    • disp_qrep
    • phonons_via_irr_derivatives
    • crystal_attributes
    • crystal_viewer
    • displaced_crystal

shift_primitive_cell

When drawing the primitive unit cell, shift by the amount specified in primitive lattice coordinates.
  • type: fraction-array
  • dimension:
  • scripts:
    • crystal_viewer

shift_super_cell

When drawing the super cell, shift by the amount specified in primitive lattice coordinates.
  • type: fraction-array
  • dimension:
  • scripts:
    • crystal_viewer

species_colors

Set the colors for each species of atoms, given as common color names (e.g. red, blue, etc) or as a rgb color [x,y,z].
  • type: string-list
  • dimension:
  • scripts:
    • crystal_viewer

strict_input

If true, the provided input tags must be known to the command line interface.
  • type: bool
  • dimension:
  • scripts:
    • All scripts.

supercell_matrix

A matrix of integers \( \hat S_{BZ}\) that multiplies the lattice vector matrix to yield the supercell lattice vectors, \(\hat S_{BZ}\hat a\).
  • type: int-array
  • dimension: \(3\times3\)
  • scripts:
    • lattice_ftg
    • lattice_fsg
    • kpoints_ftg
    • kpoints_fsg
    • crystal_ftg
    • crystal_attributes
    • crystal_viewer

tensor_rank

The rank of the tensor to be symmetrized.
  • type: int
  • dimension:
  • scripts:
    • tensor_irr_rep

use_cartesian_coordinates

Basis atoms are provided in cartesian coordinates.
  • type: bool
  • dimension:
  • scripts:
    • cluster
    • crystal
    • crystal_ftg
    • orbit_qrep
    • disp_qrep
    • phonons_via_irr_derivatives
    • crystal_attributes
    • crystal_viewer
    • displaced_crystal

verbosity


  • type: string
  • dimension:
  • scripts:
    • phonons_via_irr_derivatives

viewer

Call jmol to visualize xyz file.
  • type: string
  • dimension:
  • scripts:
    • crystal_viewer

wigner_seitz

Use the basis atoms from the Wigner-Seitz cell.
  • type: bool
  • dimension:
  • scripts:
    • crystal_viewer