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MoleculeConfiguration |  |
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| Core NanoLanguage elements | BulkConfiguration |
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MoleculeConfiguration | |
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| Core NanoLanguage elements | BulkConfiguration |
Construction of an atomic configuration from its elements and the corresponding Cartesian coordinates. The input can be given in two ways: (i) Either by supplying the elements and Cartesian coordinates as two separate lists of the same length, or (ii) by supplying a formatted XYZ string as input.
A sequence containing the elements of the configuration.
Type: A list or tuple containing objects of the type PeriodicTable, e.g. [Carbon, Oxygen].
A sequence containing a sequence of atomic coordinates for each element in the configuration,
Type: A list of 3-d coordinates given as a PhysicalQuantity of the type length, e.g. [[0,0,0], [1,1,1]]*Angstrom.
A XYZ formatted string representing the configuration. When the xyz_format argument is used, the arguments elements and cartesian_coordinates cannot be used.
Type: A description of the XYZ format can be found at http://openbabel.org/wiki/XYZ_(format).
A list of atom indices to treat as ghost atoms.
Type: A list of integer numbers.
Default:
None
Length of additional vacuum put around the molecule configuration when inscribed in a calculational box.
Type: Physical Quantity with unit length
Default:
0.0*Angstrom
Type: A list of PhysicalQuantity with velocity units, with the same dimensions as the coordinates, or None for no velocities.
Default:
None
A MoleculeConfiguration object provides the following methods:
addTags(tags, indices): Add a set of tags to atoms matching a collection of indices.
calculator(): Return the calculator attached to the configuration, i.e. the calculator that will
be used for both simulation and analysis.
cartesianCoordinates(): The Cartesian coordinates of the atoms.
dielectricRegions(): Get the dielectric regions for the configuration.
elements(): The elements of the configuration.
externalPotential(): Obtain the external potential present on the configuration.
ghostAtoms(): Return list of ghost_atoms.
indicesFromTags(tags): List the indices associated with a given collection of tags.
metallicRegions(): Get the metallic regions for the configuration.
nlprint(stream, name): Print a string containing an XYZ representation of the MoleculeConfiguration.
paddingLength(): Return the padding length for the molecule configuration
removeTags(tags, indices, purge): Remove a set of tags from atoms matching a collection of indices.
The list, tuple or set of tags to remove from matching atoms. If None, then all tags are removed.
The list, tuple or set of indices to match atoms against. A numpy array of integers may be provided, as well as single integers. If None, then all atoms are matched.
When removing tags from the configuration, delete the tag completely when not associated with any atoms anymore.
setCalculator(calculator, initial_state, initial_spin): Attach a Calculator class to the configuration which will be used in calculations
involving the configuration.
The calculator object that should be attached to the configuration.
Type: A calculator compatible with the configuration.
Default:
None
The initial state to be used for this configuration.
Type: A Configuration with an attached calculator.
Default:
None
The initial InitialSpin object to be used for this configuration.
Type: InitialSpin | None
Default:
None for calculators not supporting spin. Maximally spin-polarized InitialSpin for calculators supporting spin.
setDielectricRegions(dielectric_regions): Set the dielectric regions for the configuration.
setExternalPotential(external_potential): Set an external potential on the configuration that will be used
in calculations involving the configuration.
The external potential to apply.
Type: AtomicShift
Default:
None
setMetallicRegions(metallic_regions): Set the metallic regions for the configuration.
setVelocities(velocities): Function to set velocities on the configuration.
symbols(): The element symbols of the configuration.
tags(indices): 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
is returned.
update(force_restart): Using the configurations set calculator, a self-consistent solution is generated.
velocities(): The velocities of the atoms.
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)
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""")
A molecule is considered to be a system isolated in space. The ATK 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.
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| Core NanoLanguage elements |
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BulkConfiguration |