MoleculeConfiguration

class MoleculeConfiguration(elements=None, cartesian_coordinates=None, xyz_format=None, ghost_atoms=None, padding_length=None, velocities=None, tag_data=None, fast_init=False)

A molecule configuration consisting elements and coordinates.

Parameters:
  • elements (array of PeriodicTableElement) – The elements that should be in the configuration.
  • cartesian_coordinates (PhysicalQuantity of type length) – The Cartesian coordinates of the atoms in the configuration.
  • xyz_format (str) – A XYZ formatted string representing the configuration. The parameter is mutually exclusive to elements and cartesian_coordinates.
  • ghost_atoms (list of ints) – Indices of atoms that should be treated as ghost.
    Default: No ghost atoms.
  • padding_length (PhysicalQuantity of type length) – Length of additional vacuum put around the molecule configuration when inscribed in a calculation box.
    Default: 0.0*Angstrom
  • tag_data (dict) – Mapping between tags and associated indices.
    Default: No tags
  • velocities (PhysicalQuantity of type velocity | None) – The velocities to set on the configuration. Has the dimensionality nx3.
    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

MoleculeConfiguration.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.
MoleculeConfiguration.atomicMasses()
Returns:The masses of the atoms in the configuration.
Return type:PhysicalQuantity of type mass
MoleculeConfiguration.atomicNumbers()
Returns:The list of atomic numbers associated with the elements.
Return type:list of ints
MoleculeConfiguration.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
MoleculeConfiguration.calculator()
Returns:The calculator attached to the configuration, i.e. the calculator that will be used for both simulation and analysis.
Return type:Calculator
MoleculeConfiguration.cartesianCoordinates()
Returns:The Cartesian coordinates of the atoms as an nx3 array.
Return type:PhysicalQuantity of type length
MoleculeConfiguration.copy()
Returns:A copy of the current configuration.
Return type:MoleculeConfiguration | BulkConfiguration | DeviceConfiguration | SurfaceConfiguration
MoleculeConfiguration.dielectricRegions()
Returns:The dielectric regions in the configuration.
Return type:list of BoxRegion | SphereRegion | TubeRegion
MoleculeConfiguration.elements()
Returns:The elements in configuration.
Return type:list of PeriodicTableElement
MoleculeConfiguration.externalPotential()
Returns:The external potential present on the configuration.
Return type:AtomicShift | AtomicCompensationCharge | None
MoleculeConfiguration.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.
MoleculeConfiguration.fixedSpinDirections()
Returns:The fixed spin directions for the configuration.
Return type:FixedSpin | None
MoleculeConfiguration.ghostAtoms()
Returns:The list of ghost atoms.
Return type:list of ints
MoleculeConfiguration.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
MoleculeConfiguration.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
MoleculeConfiguration.metallicRegions()
Returns:The metallic regions for the configuration.
Return type:list of BoxRegion | SphereRegion | TubeRegion
MoleculeConfiguration.metatext()
Returns:The metatext of the object or None if no metatext is present.
Return type:str | unicode | None
MoleculeConfiguration.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()
MoleculeConfiguration.numberOfAtoms()
Returns:The total number of atoms in the configuration.
Return type:int
MoleculeConfiguration.paddingLength()
Returns:The padding length.
Return type:PhysicalQuantity of type length
MoleculeConfiguration.periodicBoundaries()
Returns:The periodic boundary conditions of the configuration.
Return type:list
MoleculeConfiguration.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
MoleculeConfiguration.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) | None.) – A list which contains for each bond the indices of the two connected atoms.
  • skip_checks (bool) – Skip argument type checking and just directly assign the value.
    Default: False
MoleculeConfiguration.setCalculator(calculator, initial_state=None, initial_spin=None)

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

Parameters:
MoleculeConfiguration.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
MoleculeConfiguration.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.
MoleculeConfiguration.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.
MoleculeConfiguration.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.
MoleculeConfiguration.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.
MoleculeConfiguration.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.
MoleculeConfiguration.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.
MoleculeConfiguration.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
MoleculeConfiguration.symbols()
Returns:The element symbols of the configuration.
Return type:list of str
MoleculeConfiguration.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
MoleculeConfiguration.uniqueElements()
Returns:The unique elements contained in the configuration.
Return type:list of PeriodicTableElement
MoleculeConfiguration.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
MoleculeConfiguration.velocities()
Returns:The velocities of the atoms. Has the dimensionality nx3.
Return type:PhysicalQuantity of type velocity

Usage Examples

Define the geometry of and construct a water molecule:

# Set up elements and positions
elm = [ Oxygen, Hydrogen, Hydrogen ]
pos = [[ 0.000, 0.000, 0.0],
       [ 0.757, 0.586, 0.0],
       [-0.757, 0.586, 0.0]]*Angstrom

# Add them to a configuration
h2o = MoleculeConfiguration(elm, pos)

molecule_configuration.py

Alternative way of specification:

# Set up elements and positions using xyz format
h2o = MoleculeConfiguration(xyz_format=
    """3

       O   0.000 0.000 0.0
       H   0.757 0.586 0.0
       H  -0.757 0.586 0.0""")

molecule_configuration_xyz.py

Notes

ATK recognizes four types of atomic geometries:

A molecule is considered to be a system isolated in space. The QuantumATK calculators will place the molecule within an unit cell, in order to obtain a real space grid for describing the effective potential of the system.

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.