SurfaceConfiguration

class SurfaceConfiguration(central_region, electrode, equivalent_electrode_length=None)

A one-probe configuration consisting of a central region coupled to an electrode.

Parameters:
  • central_region (BulkConfiguration) – The surface region.
  • electrode (BulkConfiguration) – The bulk region below the surface.
  • equivalent_electrode_length (PhysicalQuantity of type length
    Default: Length of the actual electrode given.) – The length to use for the equivalent electrode region in the central region.
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.
atomicMasses()
Returns:The masses of the atoms in the configuration.
Return type:PhysicalQuantity of type mass
atomicNumbers()
Returns:The list of atomic numbers associated with the elements.
Return type:list of ints
bonds()
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
bravaisLattice()
Returns:The bravais lattice of the central region.
Return type:BravaisLattice
calculator()
Returns:The calculator attached to the configuration, i.e. the calculator that will be used for both simulation and analysis.
Return type:Calculator
cartesianCoordinates()

The Cartesian coordinates of the atoms in the the central region of the configuration.

Returns:The Cartesian coordinates.
Return type:PhysicalQuantity of type length
centralRegion()

The central region of the surface.

Returns:The central region.
Return type:BulkConfiguration
copy()
Returns:A copy of the current configuration.
Return type:MoleculeConfiguration | BulkConfiguration | DeviceConfiguration | SurfaceConfiguration
copyAndDeleteAtoms(indices)

Create a new configuration by deleting some atoms from this configuration.

Parameters:indices (list of int) – The indices of the atoms to delete.
Returns:The configuration with some atoms deleted.
Return type:|ALL_CONFIGURAITONS|
copyAndMerge(other)

Create a new configuration by merging this configuration with another configuration.

Parameters:other (MoleculeConfiguration | BulkConfiguration | DeviceConfiguration | SurfaceConfiguration) – The other configuration.
Returns:The merged configuration.
Return type:MoleculeConfiguration | BulkConfiguration | DeviceConfiguration | SurfaceConfiguration
copyAndShiftAtoms(displacement, indices=None)

Create a new configuration with some atoms translated.

Parameters:
  • displacement (PhysicalQuantity of type length) – The displacement that should be applied to the atom positions.
  • indices (list of int) – The indices to shift.
    Default: All.
Returns:

The configuration with the translation applied.

Return type:

MoleculeConfiguration | BulkConfiguration | DeviceConfiguration | SurfaceConfiguration

crossSection()

Return the cross-sectional area of the central region.

Returns:The cross-sectional area
Return type:float
deleteAtoms(indices)

Delete the specified atoms.

Parameters:indices (array of int) – The indices to delete.
dielectricRegions()
Returns:The dielectric regions in the central region.
Return type:list of BoxRegion | SphereRegion | TubeRegion
electrodeDisplacement()

The displacement of the BravaisLattice of the electrode in the C-direction in order to match the BravaisLattice of the central_region.

Returns:The electrode displacement.
Return type:PhysicalQuantity of type length
electrodes()

The electrode of the surface as a list.

Returns:The electrode belonging to this configuration.
Return type:list of BulkConfiguration
electrodesDisplacement()

The displacement of the BravaisLattice of the electrode in the C-direction in order to match the BravaisLattice of the central_region.

Returns:The electrode displacement.
Return type:PhysicalQuantity of type length
elements()
Returns:The elements in configuration.
Return type:list of PeriodicTableElement
externalPotential()
Returns:The external potential present in the central region.
Return type:AtomicShift | AtomicCompensationCharge
findBonds(fuzz_factor=1.1, pair_selection=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.
fixedSpinDirections()
Returns:The fixed spin directions for the configuration.
Return type:FixedSpin | None
fractionalCoordinates()
Returns:The fractional coordinates of the central region.
Return type:array of floats
ghostAtoms()
Returns:The list of ghost atoms of the central region.
Return type:list of ints
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
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
merge(other)

Add all atoms from a different configuration.

NOTE: For surface this method shifts the atoms of the other configuration to the lateral center of the cell and to the upper end in z-direction.

Parameters:other (AtomicConfiguration) – A different AtomicConfiguration.
metallicRegions()
Returns:The metallic regions in the central region.
Return type:list of BoxRegion | SphereRegion | TubeRegion
metatext()
Returns:The metatext of the object or None if no metatext is present.
Return type:str | unicode | None
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().
numberOfAtoms()
Returns:The total number of atoms in the configuration.
Return type:int
periodicBoundaries()
Returns:The periodic boundary conditions of the configuration.
Return type:list
primitiveVectors()
Returns:The primitive lattice vectors.
Return type:PhysicalQuantity of type length
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
repeat(na=1, nb=1, nc=1, stack_systems=False)

Repeat the derived class 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 system.

Return type:

DeviceConfiguration | SurfaceConfiguration

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.
  • indices (int(n) | None) – The indices of the atoms to set the list of bonds.
  • skip_checks (bool) – Skip argument type checking and just directly assign the value.
setCalculator(calculator, initial_state=None, initial_spin=None)

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

Parameters:
  • calculator (Calculator) – The calculator object that should be attached to the configuration.
  • initial_state (SurfaceConfiguration with a calculator | None) – The initial state to be used for this configuration.
    Default: No initial state.
  • initial_spin (InitialSpin | None) – The initial InitialSpin object to be used for this configuration.
    Default: No initial spin.
setCartesianCoordinates(cartesian_coordinates, indices=None, skip_checks=False)

Set the Cartesian coordinates of the atoms in the central region. Changes in the coordinates of the electrode extension will be synchronized with the corresponding coordinates in the electrodes.

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
setDielectricRegions(dielectric_regions)

Set the dielectric regions for the central region.

Parameters:dielectric_regions (list of BoxRegion | SphereRegion | TubeRegion) – The list of dielectric regions to set.
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.
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.
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.
setMetallicRegions(metallic_regions)

Set the metallic regions for the central region.

Parameters:metallic_regions (list of BoxRegion | SphereRegion | TubeRegion) – The list of metallic regions to set.
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.
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.
shiftAtoms(displacement, indices=None, skip_checks=False)

Translate some atoms.

Parameters:
  • displacement (PhysicalQuantity of type length) – The displacement that should be applied to the atom positions.
  • indices (list of int) – The indices to shift.
    Default: All.
  • skip_checks (bool) – True, if all consistency checks should be skipped.
symbols()
Returns:The element symbols of the configuration.
Return type:list of str
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
transverseElectrodeRepetitions()
Returns:The transverse electrode repetitions; always [[1, 1]] for a surface.
Return type:list (size 1) of list (size 2) of int
uniqueElements()
Returns:The unique elements contained in the configuration.
Return type:list of PeriodicTableElement
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
velocities()
Returns:The velocities of the atoms. Has the dimensionality nx3.
Return type:PhysicalQuantity of type velocity

Notes

ATK recognizes four types of atomic geometries: