Class HoneycombUnitCell
object --+
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HoneycombUnitCell
Create a unit cell of a honeycomb lattice. The unit cell will be a
regular hexagon according to the following coordinate system:
----------------------------------------- | Y
| | -------------------- | | / 6 5
\ | | / \ | | /
\ | | / \ | | /
\ | | / \ | | | 1 O
4 | X | | \ / | | \
/ | | \ / | | \
/ | | \ / | | \ 2
3 / | | -------------------- |
-----------------------------------------
The hexagon will be centered on the origin O where vec(X, O) and
vec(Y, O) are the X- and Y-axes and the Z-coordinate is zero. All edge
lengths are equivalent and internal small triangles, i.e. triangle(1, O,
2) are equilateral. The following angles will be important: angle(1, 2,
3) = 120 degrees, angle(1, 2, O) = 60 degrees, and angle(1, 2, 6) = 30
degrees. In general the asymmetric unit will contain two atoms. The
symmetry operation is C3 and thus symmetry equivalent positions fall into
two sets, i.e. [1, 3, 5] and [2, 4, 6]. This unit cell will have single
bonds assigned to pairs of adjacent atoms. Unless disabled by the user
bonds [1, 2], [3, 4], and [5, 6] will be double bonds.
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__init__(self,
element1,
element2,
bondlength,
no_double_bonds)
Create an instance. |
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numpy.array, numpy.array
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schrodinger.structure.Structure
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getStructure(self,
symgroup1,
symgroup2,
no_double_bonds)
Create Structure for the unit cell. |
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setAtomProps(self)
Create structure.atom properties for later use. |
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buildUnitCell(self)
Build the unit cell. |
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Inherited from object:
__delattr__,
__format__,
__getattribute__,
__hash__,
__new__,
__reduce__,
__reduce_ex__,
__repr__,
__setattr__,
__sizeof__,
__str__,
__subclasshook__
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ANGLELARGE = math.radians(120)
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ANGLEMEDIUM = math.radians(60)
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ANGLESMALL = math.radians(30)
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NUMATOMS = 6
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NUM_EQUIV_SETS = 2
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NUM_SYM_ATOMS = NUMATOMS/ NUM_EQUIV_SETS
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SYMATOMS = [[1, 3, 5], [2, 4, 6]]
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UNITCELLINDEX = 'i_matsci_Unit_Cell_Index'
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Inherited from object:
__class__
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__init__(self,
element1,
element2,
bondlength,
no_double_bonds)
(Constructor)
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Create an instance.
- Parameters:
element1 (str) - elemental symbol of the first atomelement2 (str) - elemental symbol of the second atombondlength (float) - bond length between the first and second atoms in Angstromno_double_bonds (bool) - disable the formation of double bonds - Overrides:
object.__init__
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Return two vectors to the atoms in the asymmetric unit.
- Returns: numpy.array, numpy.array
- asupos1, asupos2, positions of the two atoms in the asymmetric
unit
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getStructure(self,
symgroup1,
symgroup2,
no_double_bonds)
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Create Structure for the unit cell.
- Parameters:
symgroup1 (SymmetryEquiv) - first equivalent groupsymgroup2 (SymmetryEquiv) - second equivalent groupno_double_bonds (bool) - disables the formation of double bonds - Returns: schrodinger.structure.Structure
- unitcell, structure for the unit cell
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