Octahedra motif

• Octahedra motif: The sorbate element sit at the center of an octahedra, of which six corners are occupied by coordinated atoms (usually O atom). To ease the following description, let's make the following definitions. sorbate atom: the atom that occupy the center of the tetrahedra motif; foreign coordinated atoms: the coordinated atoms that are not from substrate slab; surface binding site atoms: the coordinated atoms that are from the substrate slab. Pick the right item in the two comboBox (Motif type and predefined subMotifs) in the sorbate tab, then click the button [Extract settings]. A tableview will show up underneath with initialized values. You should modify these init values accordingly.

  • BD_CASE_OH: bidentate binding mode (two of coordinated atoms are provided by substrate surface atoms). The items in the setting table:

    • sorbate: index of sorbate,same as the spinBox value. You can define multiple sorbates on the same surface substrate by simply changing the sorbate index.
    • motif: BD_CASE_OH (don't change this)
    • ids: five-item list, which you define the id of the sorbate atom and the foreign coordinated atoms. You can define the name in your own style as long as they are not used in the substrate and bulk unit cell.
    • els: five item list, element symbols for the constituent atoms.
    • anchor_id: the id of sorbate atom (one of the ids defined above)
    • substrate_domain: the object name of substrate domain. This name has to be unique if there are multiple surface domains. You can name it like surface_1 for domain 1, surface_2 for domain 2 and so on. Keep this simple.
    • attach_atm_ids: the ids of two binding site atoms. It is a good place where you should switch to the surface tab to check the molecular structure and get the surface atoms that you want to consider for surface complexation.
    • offset: x, y translation symmetry tag (either None, '+x', '-x', '+y'or '-y') of the surface binding site atoms. This tag info can be read out from the molecular structure view as well.
    • anchor_ref: id for the anchor atom. This anchor ref is used to define a reference such that when the rotation angle phi = 0 (see below for definition of phi), this anchor atom is coplaner with the sorbate atom and two binding site atoms. You can set the associated metal center that form a substrate structural motif containing two binding site atoms (eg the Fe atom in the above figure). If those two binding site atoms are of a same height, you can just set it to None.
    • anchor_offset: x, y translation symmetry tag for anchor_ref atom as described in aforementioned offset.
    • mode: BD, means bidentate. Should not change it.
    • mirror: bool, define the handedness of the foriegn coordinated atom in reference to the sorbate atom. The effect you will see is the atom will be placed either left (mirror = True) or right (mirror = False) side of the plane formed by sorbate atom and two surface binding site atoms (see the figure above).
    • switch: bool, just change the order of attach_atm_ids. If you see the sorbate atoms are burried inside the surface substrate, then you don't have set the switch right. In this case, just set the switch to the other possible case (either True or False).
    • top_angle_offset: offset (positive or negative values in degree) from the ideal angle of O1-M-O2 (109.5 degree) in a tetrahedra geometry.
    • phi: rotation angel in degree (φ shown in the figure above). The surface complex motif rote about the axis (defined by the surface binding site atoms) by this degree. When phi = 0, sorbate atom, two surface binding site atoms and the anchor atom will be coplanar.
    • dr1, dr2, dr3: defining the offsets (in Å) of three M-O bonds(O from substrate surface).
    • angle_offset: angle offset in degreee (list of two items) to apply extra bond length offset to two foriegn coordinated atoms.
    • lat_pars: lattice parameters you already defined above.

  • TD_CASE_OH: tridentate binding mode (all three coordinated atoms are provided by substrate surface atoms). Refer to case of TD_CASE_TP for how to compute the dummpy point.

    • sorbate: sorbate index, same definition as in BD_CASE_TP
    • motif: always TD_CASE_OH
    • ids: four item list, id for the sorbate atom and three foreign coordinated atom.
    • els: four item list, element symbols for the sorbate atom and foreign coordinated atom.
    • anchor_id: id for the sorbate atom.
    • substrate_domain: the object name of substrate domain. See more details in the case of BD_CASE_TP.
    • attach_atm_ids: the ids of three binding site atoms.
    • offset: x, y translation symmetry tag (either None, '+x', '-x', '+y'or '-y') of the surface binding site atoms.
    • mode: TD, means tridentate. Should not change it.
    • mirror: bool, define the handedness of the sorbate atom. If sorbate atom is burried in the substrate, then you should set mirror to the other bool value.
    • dr1,dr2,dr3: edge offset of three M-O bonds (O is one of the foreign coordinated atoms).
    • lat_pars: lattice parameters you already defined above.

  • OS_CASE_OH: outer-sphere binding mode (no coordinated atoms are provided by substrate surface atoms).

    • sorbate: sorbate index, same definition as in BD_CASE_TP
    • motif: always OS_CASE_OH
    • ids: seven item list, ids for the sorbate atom and four foreign coordinated atoms.
    • els: seven item list, element symbols for the constituent atoms.
    • anchor_id: id for the sorbate atom.
    • substrate_domain: the object name of substrate domain. See more details in the case of BD_CASE_TP.
    • attach_atm_ids: one item list containing the id of surface binding site atom. This is a dummpy site, which will not be anchored by sorbate atoms in the outer-sphere binding mode. This atom serves as a reference for setting the height offset of surface complex species. The height of sorbate atom will be set relative to the height of this atom.
    • offset: x, y translation symmetry tag (either None, '+x', '-x', '+y'or '-y') of the surface binding site atoms.
    • mode: OS, means outher-sphere binding mode. Should not change it.
    • r_sorbate_O: the bond length of covalent bond of sorbate-O.
    • phi: rotation angle along z axis (alias to the rotation_z defined below)
    • rotation_x: rotation angle along x axis (a basis vector)
    • rotation_y: rotation angle along y axis (b basis vector)
    • rotation_z: rotation angle along z axis (c basis vector)
    • lat_pars: lattice parameters you already defined above.