BulkConfiguration

class BulkConfiguration(bravais_lattice, elements, cartesian_coordinates=None, fractional_coordinates=None, ghost_atoms=None, velocities=None, tag_data=None, fast_init=False)

Construction of a bulk configuration from a BravaisLattice object. The additional arguments are the elements, the Cartesian coordinates or fractional coordinates. The Cartesian coordinates and fractional coordinates cannot be given at the same time. The list arguments containing the elements and coordinates must have the same length.

Parameters:
  • bravais_lattice (BravaisLattice) – A lattice of the bulk configuration.
  • elements (PeriodicTableElement) – A sequence containing the elements of the configuration.
  • cartesian_coordinates (PhysicalQuantity of type length | None) – A sequence containing a sequence of atomic coordinates for each element in the configuration. Has the dimensionality nx3.
    Default: None
  • fractional_coordinates (array(n, 3) | None) – A sequence containing sequences of fractional coordinates for each element in the configuration.
    Default: None
  • ghost_atoms (int(n)) – A list of atom indices to treat as ghost atoms.
    Default: None
  • velocities (PhysicalQuantity of type length/time | None) – The velocities of the atoms. Has the dimensionality nx3.
    Default: None
  • tag_data (dict) – A dict of tag data, linking tags to a list of atom indices.
    Default: None
  • fast_init (bool) – Skip checking types and do not copy the arguments (i.e. only store references to them. This is an advanced option that should only be used internally.
    Default: False
class RestartInformation(initial_state, initial_spin, restart_step_length, max_diff)
count(value) → integer -- return number of occurrences of value
index(value[, start[, stop]]) → integer -- return first index of value.

Raises ValueError if the value is not present.

initial_spin

Alias for field number 1

initial_state

Alias for field number 0

max_diff

Alias for field number 3

restart_step_length

Alias for field number 2

BulkConfiguration.addTags(tags, indices=None)

Add a set of tags to atoms matching a collection of indices.

Parameters:
  • tags (list | str) – The list of tags to add to matching atoms.
  • indices (list | int | None) – The list of indices to match atoms against.
    Default: All indices.
BulkConfiguration.atomicMasses()
Returns:The masses of the atoms in the configuration.
Return type:PhysicalQuantity of type mass
BulkConfiguration.atomicNumbers()
Returns:The list of atomic numbers associated with the elements.
Return type:list of ints
BulkConfiguration.bonds()

Get the list of bond connections to can be used for bonded potentials in ATK-ForceField.

Returns:An array with the the two atom indices for each bond along with the vector which periodic images this bond connects.
Return type:array
BulkConfiguration.bravaisLattice()
Returns:The bravais lattice of the configuration.
Return type:BravaisLattice
BulkConfiguration.calculator()
Returns:The calculator attached to the configuration, i.e. the calculator that will be used for both simulation and analysis.
Return type:Calculator
BulkConfiguration.cartesianCoordinates()
Returns:The Cartesian coordinates of the atoms as an nx3 array.
Return type:PhysicalQuantity of type length
BulkConfiguration.center(x_axis=True, y_axis=True, z_axis=True)

Center the BulkConfiguration and the vacuum around the system. The centered system is constructed with a cell of the type UnitCell.

Parameters:
  • x_axis (bool) – Boolean indicating if the system should be centered along the x-axis.
    Default: True
  • y_axis (bool) – Boolean indicating if the system should be centered along the y-axis.
    Default: True
  • z_axis (bool) – Boolean indicating if the system should be centered along the z-axis.
    Default: True
Returns:

The centered bulk system.

Return type:

BulkConfiguration

BulkConfiguration.cleave(h=1, k=0, l=0, max_perpendicular_repeats=100)

Function to cleave the bulk system along the plane given by the Miller indices h, k, and l.

Parameters:
  • h (int) – The first Miller index.
    Default: 1
  • k (int) – The second Miller index.
    Default: 0
  • l (int) – The third Miller index.
    Default: 0
  • max_perpendicular_repeats (int) – The maximum number of times the crystal lattice should be repeated in order to become perpendicular to the surfaces plane. Will thrown and exception if it is not possible.
    Default: 100
Returns:

The cleaved bulk configuration.

Return type:

BulkConfiguration

BulkConfiguration.copy()
Returns:A copy of the current configuration.
Return type:MoleculeConfiguration | BulkConfiguration | DeviceConfiguration | SurfaceConfiguration
BulkConfiguration.dielectricRegions()
Returns:The dielectric regions in the configuration.
Return type:list of BoxRegion | SphereRegion | TubeRegion
BulkConfiguration.elements()
Returns:The elements in configuration.
Return type:list of PeriodicTableElement
BulkConfiguration.externalPotential()
Returns:The external potential present on the configuration.
Return type:AtomicShift | AtomicCompensationCharge | None
BulkConfiguration.findBonds(fuzz_factor=1.1, pair_selection=None, periodic_boundaries=None)

Find bonds in the configuration according to the combined covalent radii of the element pairs, multiplied with a fuzz factor. Optionally, find bonds only between two specified sub-groups of atoms. The bonds are primarily used in to set the topology of bonded potentials in the TremoloX-calculator.

Parameters:
  • fuzz_factor (float) – The factor by which the covalent radii are multiplied to determine the cutoff distance for a bond.
  • pair_selection (list(2) of type PeriodicTableElement, list of int, or str.) – Specifies two groups between which bonds are detected. Selectable groups are elements, index lists, tag names, or None (all atoms). By default bonds between all atoms in the configuration are taken into account.
BulkConfiguration.fixedSpinDirections()
Returns:The fixed spin directions for the configuration.
Return type:FixedSpin | None
BulkConfiguration.fractionalCoordinates()
Returns:The fractional coordinates of the bulk configuration as a nx3 array.
Return type:array of floats
BulkConfiguration.ghostAtoms()
Returns:The list of ghost atoms.
Return type:list of ints
BulkConfiguration.improperDihedralIndices()
Returns:The list of atom indices for each improper dihedral or None if no improper dihedrals are defined. Improper dihedrals are mainly used in bonded force fields.
Return type:numpy array | None
BulkConfiguration.indicesFromTags(tags=None)

List the indices associated with a given collection of tags.

Parameters:tags (list | str) – A list of tags for which all matching indices should be extracted.
Returns:The list of indices corresponding to the specified tag name(s).
Return type:list of ints
BulkConfiguration.massDensity()
Returns:The mass density.
Return type:PhysicalQuantity of type mass per volume
BulkConfiguration.metallicRegions()
Returns:The metallic regions for the configuration.
Return type:list of BoxRegion | SphereRegion | TubeRegion
BulkConfiguration.metatext()
Returns:The metatext of the object or None if no metatext is present.
Return type:str | unicode | None
BulkConfiguration.nlprint(stream=None)

Print a string containing an ASCII table useful for plotting the AtomicConfiguration object.

Parameters:stream (python stream) – The stream the table should be written to.
Default: NLPrintLogger()
BulkConfiguration.numberOfAtoms()
Returns:The total number of atoms in the configuration.
Return type:int
static BulkConfiguration.periodicBoundaries()
Returns:The periodic boundary conditions of the configuration.
Return type:list
BulkConfiguration.primitiveVectors()
Returns:The primitive lattice vectors.
Return type:PhysicalQuantity of type length
BulkConfiguration.reduce(na=1, nb=1, nc=1, stack_systems=True)

Reduce the BulkConfiguration with the integer values na, nb, and nc along the three primitive unit cell vectors. The reduced system is constructed with a cell of the type UnitCell.

Parameters:
  • na (int) – The repetition along the a-axis.
    Default: 1
  • nb (int) – The repetition along the b-axis.
    Default: 1
  • nc (int) – The repetition along the c-axis.
    Default: 1
  • stack_systems (bool) – If True the basis atoms are reduced as a unit, i.e. a0 and b0 are reduced as: a0,b0,a1,b1, ... If False the basis atom are reduced individually, i.e. a0 and b0 are reduced as: a0,a1,..., b0,b1,...
    Default: True
Returns:

The reduced bulk system.

Return type:

BulkConfiguration

BulkConfiguration.removeTags(tags=None, indices=None, purge=False)

Remove a set of tags from atoms matching a collection of indices.

Parameters:
  • tags (list | str) – The list of tags to add to matching atoms.
    Default: All tags.
  • indices (list | int) – The list of indices to match atoms against.
    Default: All indices.
  • purge (bool) – When removing tags from the configuration, delete the tag completely when not associated with any atoms anymore.
    Default: False
BulkConfiguration.repeat(na=1, nb=1, nc=1, stack_systems=True)

Repeat the BulkConfiguration with the integer values na, nb, and nc along the three primitive unit cell vectors. The repeated system is constructed with a cell of the type UnitCell.

Parameters:
  • na (int) – The repetition along the a-axis.
    Default: 1
  • nb (int) – The repetition along the b-axis.
    Default: 1
  • nc (int) – The repetition along the c-axis.
    Default: 1
  • stack_systems (bool) – If True the basis atoms are repeated as a unit, i.e. a0 and b0 are repeated as: a0,b0,a1,b1, ... If False the basis atom are repeated individually, i.e. a0 and b0 are repeated as: a0,a1,..., b0,b1,...
    Default: True
Returns:

The repeated bulk system.

Return type:

BulkConfiguration

BulkConfiguration.scalePrimitiveVectors(scale_a=None, scale_b=None, scale_c=None)

Scale the length of each lattice vector. The fractional coordinates of the atoms and the Bravais lattice type will be remain unchanged if possible.

Parameters:
  • scale_a (float) – The scaling factor for the a-axis to apply.
    Default: 1.0
  • scale_b (float) – The scaling factor for the b-axis to apply.
    Default: 1.0
  • scale_c (float) – The scaling factor for the c-axis to apply.
    Default: 1.0
BulkConfiguration.scaleVolume(scaling_factor)

Scale the volume of the crystal by an isotropic expansion of the lattice vectors. The fractional coordinates of the atoms and the Bravais lattice type will be unchanged.

Parameters:scaling_factor (float) – The scaling factor to apply. A value of 1.01 leads to a 1% increase in the volume.
BulkConfiguration.setBonds(bond_list, skip_checks=False)

Set the bonds on the configuration. The bonds are primarily used in to set the topology of bonded potentials in the TremoloX-calculator.

Parameters:
  • bond_list (list(n, 2) | list(n, 5) | None.) – A list which contains for each bond the indices of the two connected atoms. Optionally, three more integers can be specified for each bond, which must be between -1 and 1, and which denote to which neighboring image cell the bond is connected. Without these additional indices, the minimum image convention is obeyed.
  • skip_checks (bool) – Skip argument type checking and just directly assign the value.
    Default: False
BulkConfiguration.setBravaisLattice(bravais_lattice, conserve_coordinates=<class 'NL.ComputerScienceUtilities.NLFlag._NLFlag.Cartesian'>)

Change the bravais lattice.

Parameters:
  • bravais_lattice (BravaisLattice) – The new lattice.
  • conserve_coordinates (Cartesian | Fractional) – The type of coordinates to conserve..
    Default: Cartesian
BulkConfiguration.setCalculator(calculator, initial_state=None, initial_spin=None)

Attach a Calculator to the configuration which will be used in calculations involving the configuration.

Parameters:
BulkConfiguration.setCartesianCoordinates(cartesian_coordinates, indices=None, skip_checks=False)

Set the Cartesian coordinates of the atoms.

Parameters:
  • cartesian_coordinates (PhysicalQuantity of type length) – The new coordinates of the atoms in each image.
  • indices (list) – The indices of the atoms to set the positions of.
    Default: All indices.
  • skip_checks (bool) – Skip argument type checking and just directly assign the value.
    Default: False
BulkConfiguration.setDielectricRegions(dielectric_regions)

Set the dielectric regions for the configuration.

Parameters:dielectric_regions (list of BoxRegion | SphereRegion | TubeRegion) – The list of dielectric regions to set.
BulkConfiguration.setExternalPotential(external_potential)

Set an external potential on the configuration that will be used in calculations involving the configuration.

Parameters:external_potential (AtomicShift | AtomicCompensationCharge) – The external potential to apply.
BulkConfiguration.setFractionalCoordinates(fractional_coordinates, indices=None)

Set the Cartesian coordinates of the atoms.

Parameters:
  • fractional_coordinates (array of floats) – The new coordinates of the atoms as a nx3 array.
  • indices (array of ints | None) – The indices of the atoms to set the positions of.
    Default: All indices.
BulkConfiguration.setImproperDihedralIndices(improper_dihedral_indices)

Set the list of atom indices for each improper dihedral in bonded force fields.

Parameters:improper_dihedral_indices (list or array with shape (m, 4) | None) – The list of the 4 indices defining the connectivity for each improper dihedral or None to delete the current dihedral connectivity.
BulkConfiguration.setMagneticField(magnetic_field)

Set local magnetic field. The spins will be forced to point in the directions given by the magnetic_field object. The magnetic field can be defined for each atom. This only has an effect for Noncollinear or Spinorbit calculations.

Parameters:magnetic_field (FixedSpin) – The magnetic field to be applied.
BulkConfiguration.setMetallicRegions(metallic_regions)

Set the metallic regions for the configuration.

Parameters:metallic_regions (list of BoxRegion | SphereRegion | TubeRegion) – The list of metallic regions to set.
BulkConfiguration.setMetatext(metatext)

Set a given metatext string on the object.

Parameters:metatext (str | unicode | None) – The metatext string that should be set. A value of “None” can be given to remove the current metatext.
BulkConfiguration.setPrimitiveVectors(a, b, c, conserve_coordinates=<class 'NL.ComputerScienceUtilities.NLFlag._NLFlag.Cartesian'>)

Set the primitive lattice vectors for the configuration. This will change the BravaisLattice to a UnitCell. By default the Cartesian coordinates are not changed, which means that the relative positions of the atoms will change when the lattice vectors change.

Parameters:
  • a (PhysicalQuantity of type length) – The first lattice vector.
  • b (PhysicalQuantity of type length) – The second lattice vector.
  • c (PhysicalQuantity of type length) – The third lattice vector.
  • conserve_coordinates (Cartesian | Fractional) – The type of coordinates to conserve.
    Default: Cartesian
BulkConfiguration.setVelocities(velocities=None, skip_checks=False)

Function to set velocities on the configuration.

Parameters:
  • velocities (PhysicalQuantity of type velocity | None) – The velocities to set on the configuration. Has the dimensionality nx3.
    Default: None
  • skip_checks (bool) – Skip argument type checking and just directly assign the value.
    Default: False
BulkConfiguration.sortAlongC()

Method for sorting the atoms along C.

BulkConfiguration.symbols()
Returns:The element symbols of the configuration.
Return type:list of str
BulkConfiguration.tags(indices=None)

List the tags associated with a given collection of indices. The list returned is the set union of tags associated with the given indices. If no collection of indices is provided, then all tags on the configuration are returned.

Parameters:indices (list | int) – The indices to check.
Default: All indices.
Returns:The set union of tags present on the provided indices.
Return type:set
BulkConfiguration.uniqueElements()
Returns:The unique elements contained in the configuration.
Return type:list of PeriodicTableElement
BulkConfiguration.update(force_restart=False)

A self-consistent solution is generated, using the currently set calculator.

Parameters:force_restart (bool) – Force the self-consistent calculation to restart.
Default: False
BulkConfiguration.velocities()
Returns:The velocities of the atoms. Has the dimensionality nx3.
Return type:PhysicalQuantity of type velocity

Usage Examples

Define the geometry of a lithium BCC crystal:

lattice = BodyCenteredCubic( 3.509 * Ang)
li_bcc_bulk = BulkConfiguration(
    lattice,
    [Lithium],
    [ ( 0.0, 0.0, 0.0 ) * Ang ]
    )

li_bcc.py

Specify the geometry of a diamond crystal:

elements = [ Carbon ] * 2
coordinates = [
    ( 0.00, 0.00, 0.00 ),
    ( 0.25, 0.25, 0.25 )
    ]
diamond_lattice = FaceCenteredCubic( 3.567 * Ang )
diamond = BulkConfiguration(
    diamond_lattice,
    elements,
    fractional_coordinates = coordinates
    )

si_diamond.py

Notes

ATK recognizes four types of atomic geometries:

1D or 2D periodic geometries, such as nanotubes, slabs, and atomic chains must be represented as a BulkConfiguration with sufficient vacuum to isolate the system in the non-periodic directions.

It is possible to specify vacuum basis sets (ghost atoms) by adding an additional atom and include the index of that atom in the ghost_atom list. In this case the valence basis set of the atom is included in the orbital list, but there will be no atomic potential at the site.