coordinateGeometry.py
This class calculates distances, angles, and orientational order parameters for atoms coordinated to a central atom
CoordinateGeometry(center, neighbors)[source]¶Bases: object
A coordinate geoetry class that calcualtes distances angles and orientational order parameters.
Attributes
| center | (list) coordinates of the center atom |
| neighbors | (list) coordinates of neighbor atoms |
Methods
get_angles() |
Returns all pairwise angles between a center and pairs of neighbor atoms. |
get_distance() |
Returns an array of distances from the coordination center to the neighbor atoms. |
q3() |
Returns a normalized trigonal orientational order parameter q3. |
q4() |
Returns a normalized tetrahedral orientational order parameter q4. |
q5() |
Returns a normalized trigonal bipyramidal orientational order parameter q5. |
q6() |
Returns a normalized octahedra orientational order parameter q6. |
get_angles()[source]¶Returns all pairwise angles between a center and pairs of neighbor atoms.
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get_distance()[source]¶Returns an array of distances from the coordination center to the neighbor atoms.
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q3()[source]¶Returns a normalized trigonal orientational order parameter q3. The orientational order parameter q3 measures the extent to which a molecule and its three nearest neighbors adopt a trigonal arrangement. It is equal to 0 for a random arrangement and equals 1 in a perfectly trigonal arrangement.
| Returns: | float
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References
q4()[source]¶Returns a normalized tetrahedral orientational order parameter q4. The orientational order parameter q4 measures the extent to which a central atom and its four nearest neighbors adopt a tetrahedral arrangement. It is equal to 0 for a random arrangement and equals 1 in a perfectly tetrahedral arrangement. It can reach a minimum value of -3 for unusual arrangements.
| Returns: | float
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References
Jeffrey R. Errington & Pablo G. Debenedetti (2001) Relationship between structural order and the anomalies of liquid water, Nature 409, 318-321. <a href=”https://dx.doi.org/10.1038/35053024”>doi:10.1038/35053024</a>
P.-L. Chau & A. J. Hardwick (1998) A new order parameter for tetrahedral configurations, Molecular Physics, 93:3, 511-518. <a href”https://dx.doi.org/10.1080/002689798169195”>doi:10.1080/002689798169195</a>
q5()[source]¶Returns a normalized trigonal bipyramidal orientational order parameter q5. The first three nearest atoms to the center atom are used to define the equatorial positions. The next two nearest atoms are used to specify the axial positions. The orientational order parameter q5 measures the extent to which the five nearest atoms adopt a trigonal bipyramidal arrangement. It is equal to 0 for a random arrangement and equals 1 in a perfectly trigonal bipyramidal arrangement. It can reach negative values for certain arrangements.
| Returns: | float
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References
Note, the summations in equation (3) in this paper is incorrect. This method uses the corrected version (R. Henchman, personal communication).
q6()[source]¶Returns a normalized octahedra orientational order parameter q6. The orientational order parameter q6 measures the extent to which a central atom and its six nearest neighbors adopt an octahedral arrangement. It is equal to 0 for a random arrangement and equals 1 in a perfectly octahedralhedral arrangement. It can reach negative values for certain arrangements.
| Returns: | float
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References
The same method as described in this paper was used to derive the q6 parameter (R. Henchman, personal communication).