 Atomic displacement ellipsoid

An atomic displacement ellipsoid visualizes the directional positional spread represented by an anisotropic atomic displacement parameter. For a centered three-dimensional normal distribution with positive-definite Cartesian covariance matrix $U$, its probability surfaces have the formThe eigenvectors of $U$ give the principal directions; if its eigenvalues are ${\lambda }_i$, the semiaxis lengths are $\sqrt{c{\lambda }_i}$. The atomic displacement probability level specifies how much modeled probability is enclosed.^[ref]

The squared Mahalanobis distance ${\mathbf{u}}^T{U}^{-1}\mathbf{u}$ has a chi-squared distribution with3 degrees of freedom in this Gaussian model. A50% ellipsoid uses $c\simeq 2.36597$. Taking $c=1$ instead encloses only about19.9%, so a three-dimensional probability ellipsoid cannot be read as a one-dimensional one-standard-deviation interval.

For an original example, $U=\mathrm{diag}(0.01,0.04,0.09){\mathring{\mathrm{A}}}^2$ gives50% semiaxes approximately0.154,0.308 and0.461 angstroms. An isotropic matrix with the same equivalent isotropic atomic displacement parameter, $U_{\mathrm{eq}}=0.14/3{\mathring{\mathrm{A}}}^2$, instead gives a sphere of radius about0.332 angstroms.

The ellipsoid represents modeled positional spread, including possible static disorder, rather than the atom's physical surface or a confidence region for its refined mean position. Its interpretation depends on the displacement model; the Gaussian probability construction requires a positive-definite covariance and does not turn a negative fitted eigenvalue into a physically meaningful radius.^[ref]