75 lines
3.0 KiB
ReStructuredText
75 lines
3.0 KiB
ReStructuredText
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.. _hemispherical_cluster_faq:
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The hemispherical_cluster function
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----------------------------------
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A the :py:func:`hemispherical_cluster` takes one mandatory argument and 4 keyword arguments.
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The first required argument is an ASE Atoms object. This object will be the base pattern used to create a cluster.
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It is usually a primitive cell of a structure. The 4 keywords arguments describe the dimensions of the cluster and
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the location of the emitter atom:
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- emitter_tag: is an integer which is the tag of the emitter atom
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- emitter_plane: is an integer to tell in which plane to put the emitter
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- diameter: is the diameter of the hemispherically shaped cluster (in angströms)
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- planes: is the total number of planes
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Three simple example are shown in the figure 1 below. These are cut view in the (xOz) plane of the clusters. the
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clusters were created with those commands:
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.. code-block:: python
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from msspec.utils import hemispherical_cluster
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from ase.build import bulk
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iron = bulk('Fe', cubic=True) # The base cell to be repeated to shape a cluster
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# The cluster 1a, with an emitter on the surface
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cluster1a = hemispherical_cluster(iron, diameter=25, emitter_plane=0)
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# The cluster 1c, with an emitter in the second plane
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cluster1b = hemispherical_cluster(iron, diameter=25, emitter_plane=1)
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# The cluster 1c, with an emitter in the third plane and with just one plane below
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# the emitter
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cluster1c = hemispherical_cluster(iron, diameter=25, emitter_plane=2, planes=4)
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.. figure:: Fe_clusters.png
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:align: center
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:width: 80%
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Figure 1.
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The *emitter_tag* keyword is used to specify the emitter in a multielemental structure or if two atoms of the same
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kind exist in the primitive cell with different chemical or geometrical environment. For example, the CsCl structure
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is also *bcc* like the iron above, but the chlorine atom is at the center of a cube with 4 Caesium atoms on the apex.
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To get a Cl emitter in the desired plane, we should first tag it in the cell:
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.. code-block:: python
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from msspec.utils import hemispherical_cluster
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from ase.spacegroup import crystal
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# Definition of this cubic cell
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a0 = 2.05
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a = b = c = a0
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alpha = beta = gamma = 90
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cellpar = [a, b, c, alpha, beta, gamma]
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# Create the CsCl structure with the crystal function
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CsCl = crystal(['Cs', 'Cl'], basis=[(0,0,0),(0.5,0.5,0.5)], spacegroup=221, cellpar=cellpar)
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# by default, all atoms tags are 0
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# set the Cl tag to 1
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CsCl[1].tag = 1
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# Create a cluster with the Cl emitter
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cluster = hemispherical_cluster(CsCl, emitter_tag=1, emitter_plane=3, diameter=25)
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The resulting cluster is shown in the figure 2 below
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.. figure:: CsCl_cluster.png
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:align: center
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:width: 80%
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Figure 2. A cut view in the (xOz) plane of a CsCl cluster with a Cl emitter atom in the third plane
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