International
Tables for Crystallography Volume D Physical properties of crystals Edited by A. Authier © International Union of Crystallography 2006 |
International Tables for Crystallography (2006). Vol. D. ch. 1.9, pp. 228-242
https://doi.org/10.1107/97809553602060000636 Chapter 1.9. Atomic displacement parameters
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GZG Abt. Kristallographie, Goldschmidtstrasse 1, 37077 Göttingen, Germany The theory of lattice dynamics shows that the atomic thermal Debye–Waller factor is related to the atomic displacements. In the harmonic approximation, these are fully described by a fully symmetric second-order tensor. Anharmonicity and disorder, however, cause deviations from a Gaussian distribution of the atomic displacements around the atomic position. A generalized description of atomic displacements therefore also involves first-, third-, fourth- and even higher-order displacement terms.The description of the properties of these tensors is the purpose of this chapter. The number of independent tensor coefficients depends on the site symmetry of the atom and are given in tables. The symmetry restrictions according to the site symmetry are tabulated for second- to sixth-rank thermal motion tensors. A selection of representation surfaces of higher-rank tensors showing the distribution of anharmonic deformation densities is given at the end of the chapter. Keywords: Gram–Charlier series; atomic displacement; cumulants; invariants; quasimoments; representation surface; site symmetry; site-symmetry restrictions; tensor contraction; tensor expansion. |
Atomic thermal motion and positional disorder is at the origin of a systematic intensity reduction of Bragg reflections as a function of scattering vector Q. The intensity reduction is given as the well known Debye–Waller factor (DWF); the DWF may be of purely thermal origin (thermal DWF or temperature factor) or it may contain contributions of static atomic disorder (static DWF). As atoms of chemically or isotopically different elements behave differently, the individual atomic contributions to the global DWF (describing the weakening of Bragg intensities) vary. Formally, one may split the global DWF into the individual atomic contributions. Crystallographic experiments usually measure the global weakening of Bragg intensities and the individual contributions have to be assessed by adjusting individual atomic parameters in a least-squares refinement.
The theory of lattice dynamics (see e.g. Willis & Pryor, 1975) shows that the atomic thermal DWF Tα is given by an exponential of the formwhere uα are the individual atomic displacement vectors and the brackets symbolize the thermodynamic (time–space) average over all contributions uα. In the harmonic (Gaussian) approximation, (1.9.1.1) reduces to
The thermodynamically averaged atomic mean-square displacements (of thermal origin) are given as , i.e. they are the thermodynamic average of the product of the displacements along the i and j coordinate directions. Thus (1.9.1.2) may be expressed with in a form more familiar to the crystallographer aswhere are the covariant Miller indices, are the reciprocal-cell basis vectors and . Here and in the following, tensor notation is employed; implicit summation over repeated indices is assumed unless stated otherwise. For computational convenience one often writeswith (no summation). Both h and β are dimensionless tensorial quantities; h transforms as a covariant tensor of rank 1, β as a contravariant tensor of rank 2 (for details of the mathematical notion of a tensor, see Chapter 1.1 ).
Similar formulations are found for the static atomic DWF Sα, where the average of the atomic static displacements Δuα may also be approximated [though with weaker theoretical justification, see Kuhs (1992)] by a Gaussian distribution:
As in equation (1.9.1.3), the static atomic DWF may be formulated with the mean-square disorder displacements as
It is usually difficult to separate thermal and static contributions, and it is often wise to use the sum of both and call them simply (mean-square) atomic displacements. A separation may however be achieved by a temperature-dependent study of atomic displacements. A harmonic diagonal tensor component of purely thermal origin extrapolates linearly to zero at 0 K; zero-point motion causes a deviation from this linear behaviour at low temperatures, but an extrapolation from higher temperatures (where the contribution from zero-point motion becomes negligibly small) still yields a zero intercept. Any positive intercept in such extrapolations is then due to a (temperature-independent) static contribution to the total atomic displacements. Care has to be taken in such extrapolations, as pronounced anharmonicity (frequently encountered at temperatures higher than the Debye temperature) will change the slope, thus invalidating the linear extrapolation (see e.g. Willis & Pryor, 1975). Owing to the difficulty in separating thermal and static displacements in a standard crystallographic structure analysis, a subcommittee of the IUCr Commission on Crystallographic Nomenclature has recommended the use of the term atomic displacement parameters (ADPs) for Uij and βij (Trueblood et al., 1996).
One notes that in the Gaussian approximation, the mean-square atomic displacements (composed of thermal and static contributions) are fully described by six coefficients βij, which transform on a change of the direct-lattice base (according to ) as
This is the transformation law of a tensor (see Section 1.1.3.2 ); the mean-square atomic displacements are thus tensorial properties of an atom α. As the tensor is contravariant and in general is described in a (non-Cartesian) crystallographic basis system, its indices are written as superscripts. It is convenient for comparison purposes to quote the dimensionless coefficients βij as their dimensioned representations Uij.
In the harmonic approximation, the atomic displacements are fully described by the fully symmetric second-order tensor given in (1.9.2.1). Anharmonicity and disorder, however, cause deviations from a Gaussian distribution of the atomic displacements around the atomic position. In fact, anharmonicity in the thermal motion also provokes a shift of the atomic position as a function of temperature. A generalized description of atomic displacements therefore also involves first-, third-, fourth- and even higher-order displacement terms. These terms are defined by a moment-generating function M(Q) which expresses in terms of an infinite number of moments; for a Gaussian distribution of displacement vectors, all moments of order are identically equal to zero. Thus
The moments of order N may be expressed in terms of cumulants by the identity
Separating the powers of Q and u in (1.9.2.2) and (1.9.2.3), one may obtain expressions involving moments μ and cumulants k explicitly asand the cumulant-generating function K(Q) asThe indices run in three-dimensional space from 1 to 3 and refer to the crystallographic basis system. Moments may be expressed in terms of cumulants (and vice versa); the transformation laws are given in IT B (2001), equation (1.2.12.9 ) and more completely in Kuhs (1988, 1992). The moment- and cumulant-generating functions are two ways of expressing the Fourier transform of the atomic probability density function (p.d.f.). If all terms up to infinity are taken into account, M(Q) and K(Q) are [by virtue of the identity ] identical. For a finite series, however, the cumulants of order N carry implicit information on contributions of order N2, N3 etc. in contrast to the moments. Equations (1.9.2.4) and (1.9.2.5) are useful, as they can be entered directly in a structure-factor equation (see Chapter 1.2 in IT B); however, the moments (and thus the cumulants) may also be calculated directly from the atomic p.d.f. as
The real-space expression of the p.d.f. obtained from a Fourier transform of (1.9.2.5) is called an Edgeworth series expansion. If one assumes that the underlying atomic p.d.f. is close to a Gaussian distribution, one may separate out the Gaussian contributions to the moment-generating function as suggested by Kuznetsov et al. (1960) and formulate a generating function for quasimoments asThese quasimoments are especially useful in crystallographic structure-factor equations, as they just modify the harmonic case. The real-space expression of the p.d.f. obtained from a Fourier transformation of (1.9.2.7) is called a Gram–Charlier series expansion. Discussions of its merits as compared to the Edgeworth series are given in Zucker & Schulz (1982a,b), Kuhs (1983, 1988, 1992) and Scheringer (1985).
By separating the powers of Q and u, one obtains in equations (1.9.2.4), (1.9.2.5) and (1.9.2.7) the higher-order displacement tensors in the form of moments, cumulants or quasimoments, which we shall denote in a general way as ; note that bij is identical to βij. They transform on a change of the direct-lattice base according to
The higher-order displacement tensors are fully symmetric with respect to the interchange of any of their indices; in the nomenclature of Jahn (1949), their tensor symmetry thus is [bN]. The number of independent tensor coefficients depends on the site symmetry of the atom and is tabulated in Sirotin (1960) as well as in Tables 1.9.3.1–1.9.3.6. For triclinic site symmetry, the numbers of independent tensor coefficients are 1, 3, 6, 10, 15, 21 and 28 for the zeroth to sixth order. Symmetry may further reduce the number of independent coefficients, as discussed in Section 1.9.3.
In many least-squares programs for structure refinement, the atomic displacement parameters are used in a dimensionless form [as given in (1.9.1.4) for the harmonic case]. These dimensionless quantities may be transformed according to(no summation) into quantities of units ÅN (or pmN); ai etc. are reciprocal-lattice vectors. Nowadays, the published structural results usually quote Uij for the second-order terms; it would be good practice to publish only dimensioned atomic displacements for the higher-order terms as well.
Anisotropic or higher-order atomic displacement tensors may contain a wealth of information. However, this information content is not always worth publishing in full, either because the physical meaning is not of importance or the significance is only marginal. Quantities of higher significance or better clarity are obtained by an operation known as tensor contraction. Likewise, lower-order terms may be expanded to higher order to impose certain (chemically implied) symmetries on the displacement tensors or to provide initial parameters for least-squares refinements. A contraction is obtained by multiplying the contravariant tensor components (referring to the real-space basis vectors) with the covariant components of the real-space metric tensor gij; for further details on tensor contraction, see Section 1.1.3.3.3 . In the general case of atomic displacement tensors of (even) rank N, one obtains is called the trace of a tensor of rank N and is a scalar invariant; it is given in units of lengthN and provides an easily interpretable quantity: In the case of , a positive sign indicates that the corresponding (real-space) p.d.f. is peaked, a negative sign indicates flatness of the p.d.f. The larger , the stronger the deviation from a Gaussian p.d.f. provoked by the atomic displacements of order N. The frequently quoted isotropic equivalent U value Ueq is also obtained by this contraction process. Noting that Uij may be expressed in terms of bij (= βij) according to (1.9.2.9) and that the trace of the matrix U is given as , one obtainsNote that in all non-orthogonal bases, . In older literature, the isotropic equivalent displacement parameter is often quoted as Beq, which is related to Ueq through the identity . The use of Beq is now discouraged (Trueblood et al., 1996). Higher atomic displacement tensors of odd rank N may be reduced to simple vectors v by the following contraction:where v1 is the 23 trace etc. Nvi is sometimes called a vector invariant, as it can be uniquely assigned to the tensor in question (Pach & Frey, 1964) and its units are lengthN − 1. The vector v is oriented along the line of maximum projected asymmetry for a given atom and vanishes for atoms with positional parameters fixed by symmetry; Johnson (1970) has named a vector closely related to 3v the vector of skew divergence. The calculation of v is useful as it gives the direction of the largest antisymmetric displacements contained in odd-rank higher-order thermal-motion tensors.
Atomic displacement tensors may also be partially contracted or expanded; rules for these operations are found in Kuhs (1992).
Atoms (or molecules) situated on special positions of a space group exhibit (time–space averaged) probability distributions with a symmetry corresponding to the site symmetry. The p.d.f.'s describing these distributions contain the atomic displacement tensors. The displacement tensors enter into the structure-factor equation, which is the Fourier transform of the scattering density of the unit cell, via the atomic Debye–Waller factor, which is the Fourier transform of the atomic p.d.f. (see Chapter 1.2 of IT B). As discussed above, the tensor is fully symmetric with respect to the interchange of indices (inner symmetry). The site-symmetry restrictions (outer symmetry) of atomic displacement tensors of rank 2 are given in Chapter 8.3 of IT C (2004), where the tabulation of the constraints on the tensor coefficients are quoted for every Wyckoff position in each space group. Here the constraints for atomic displacement tensors of ranks 2, 3, 4, 5 and 6 for any crystallographic site symmetry are tabulated; some restrictions for tensors of rank 7 and 8 can be found in Kuhs (1984). To use these tables, first the site symmetry has to be identified. The site symmetries are given in IT A (2005) for the first equipoint of every Wyckoff position in each space group. The tabulated constraints may be introduced in least-squares refinements (some programs have the constraints of second-order displacement tensor components already imbedded). It should also be remembered that, due to arbitrary phase shifts in the structure-factor equation in a least-squares refinement of a noncentrosymmetric structure, for all odd-order tensors one coefficient corresponding to a nonzero entry for the corresponding acentric space group has to be kept fixed (in very much the same way as for positional parameters); e.g. the term b123 has to be kept fixed for one atom for all refinements in all space groups belonging to the point groups or 23, while all other terms bijk are allowed to vary freely for all atoms (Hazell & Willis, 1978). Even if this is strictly true only for the Edgeworth-series expansion, it also holds in practice for the Gram–Charlier case (Kuhs, 1992).
Levy (1956) and Peterse & Palm (1966) have given algorithms for determining the constraints on anisotropic displacement tensor coefficients, which are also applicable to higher-order tensors. The basic idea is that a tensor transformation according to the symmetry operation of the site symmetry under consideration (represented by the point-group generators) should leave the tensor unchanged. For symmetries higher than the identity 1, this only holds true if some of the tensor coefficients are either zero or interrelated. The constraints may be obtained explicitly from solving the homogeneous system of equations of tensor transformations (with one equation for each coefficient).
After identification of the site symmetry of the atomic site under consideration, the entry point (cross-reference) for the tabulation of the displacement tensors of a given rank (Tables 1.9.3.2–1.9.3.6) needs to be looked up in Table 1.9.3.1. The line entry corresponding to the cross-reference number in Tables 1.9.3.2–1.9.3.6 holds the information on the constraints imposed by the outer symmetry on the tensor coefficients. The order of assignment of independency of the coefficients is as for increasing indices of the coefficients (first 1, then 2, then 3, where 1, 2 and 3 refer to the three crystallographic axes), except for the unmixed coefficients, which have highest priority in every case; this order of priority is the same as the order in the tables reading from left to right. For better readability, each coefficent is assigned a letter (or 0 if the component is equal to zero by symmetry). Constraints thus read as algebraic relations between letter variables. Some more complicated constraint relations are quoted as footnotes to the tables.
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(1) −2A/5 + D; (2) −3A/5 + B/10 + 3D/2; (3) −3A/5 + D; (4) −D + 2F; (5) −A/4 + 3F/2; (6) −2A/5 + B/5 + D; (7) −A + D; (8) −A/5 + 2B/5 + F; (9) −D + 2I; (10) −2G + 3J; (11) −E/4 + 3J/2; (12) −2H + 3K; (13) −H + K; (14) −G + 2N; (15) −4G + 6J; (16) −H/4 + 3P/2; (17) −4H + 6K.
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(1) −A/4 + F/2; (2) A/2 − 3D/2 + 3F/2; (3) B/20 − 3D/5 + 3F/2; (4) −2E/5 + G; (5) A − 2D + F; (6) B/5 − 2D/5 + F; (7) −3E/5 + G; (8) 2E − 5G + 4J; (9) −G + 2J; (10) −E/4 + 3J/2; (11) A − D; (12) A/2 − 5F/2 + 5M/2; (13) −E + G; (14) 6E − 15G + 10J; (15) −G + 2N; (16) −2K + 3P; (17) −H/4 + 3P/2; (18) −L + Q; (19) −2L + 3Q; (20) 12E − 30G + 20J; (21) E/2 − 5J/2 + 5T/2; (22) −4K + 6P; (23) −4L + 6Q; (24) −L/4 + 3V/2.
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Atomic displacement tensors (ADTs) described by their tensor coefficients may be represented graphically to clarify their physical meaning. Different graphical representations exist and will be discussed separately for second- and higher-order tensors in the following.
Numerous examples of graphical representations of thermal-motion tensors (or, more generally speaking, atomic displacement tensors) have appeared in the literature since the early days of the computer program ORTEP written by C. K. Johnson (1965), yet the equal-probability surface usually displayed is only one of the possible representations of a second-order atomic displacement tensor. Representation surfaces are usually calculated in a Cartesian coordinate system. Accordingly, one has to transform the second-order ADT b into UC described in a Cartesian frame:The transformation matrix depends on the choice of Cartesian axes ei with respect to the reciprocal-cell axes ai (or equally well with respect to the direct axes ai). Choosing e1 along a1, e2 in the a1a2 plane and e3 completing the right-handed set, one obtains for the transformation matrix F (see also Willis & Pryor, 1975)
Clearly, there is an infinite number of possible choices for relating a Cartesian frame to a crystallographic coordinate system with correspondingly different transformation matrices F (see e.g. Chapter 1.1 of IT B). The most useful representation surface of the second-order atomic displacement tensor UC is the representation quadric defined by the tensor invariantwhere u is a displacement vector; U−1 is often called the variance–covariance matrix and has (in a general axes frame) covariant components. Under the conditions of positive definiteness,the surface of the representation quadric is an ellipsoid whose semi-major axes (for ) are of lengths equal to the root-mean-square displacements (r.m.s.d.'s) along the axes directions. The thermal vibration ellipsoids calculated in ORTEP are related to this surface; considering the discussion in Section 1.9.1, they should more appropriately be called atomic displacement ellipsoids or simply ORTEP ellipsoids. One notes that the Fourier transform of the atomic DWF, the atomic probability density function P(u), is given in the case of a second-order tensor as a trivariate Gaussian distribution,
On comparing (1.9.4.3) and (1.9.4.5), it is evident that (1.9.4.3) defines a surface of constant probability of finding a (displaced) atom. The integral of (1.9.4.5) over the volume inside the ellipsoid is a constant. For with the integration limit (2.5003), the integral is equal to one half (nine tenths), and the ellipsoid is then called a 50 (90) per cent probability ellipsoid.
Other representation surfaces can be defined and are useful for special considerations. The quantities of interest are either the r.m.s.d.'s or the mean-square displacements (m.s.d.'s) defined in direct space. Here a distinction has to be made between the averaged squared displacement along a certain direction and the average for all squared displacements of an atom projected onto a given direction. Representation surfaces may also be calculated in reciprocal space, related to surfaces in direct space by Fourier transformation. For further details, see Nelmes (1969) and Hummel et al. (1990).
Representation surfaces of higher-order tensors may be calculated from their invariants. While for second-order tensors surfaces can be found that fully describe the directional aspects of the tensor involved, higher-order tensors need several different surfaces for a full description (see e.g. Wondratschek, 1958; Sirotin, 1961). This makes the graphical representation of the displacements somewhat cumbersome and it is therefore rarely used. Instead, the probability density functions [given in equations (6.1.1.46 ), (6.1.1.48 ) or (6.1.1.49 ) of IT C] are calculated from the tensor coefficients and displayed in sections or as three-dimensional surfaces. If the higher-order terms are small, it is more appropriate to display only the difference between the total p.d.f. and the related Gaussian p.d.f., which may be calculated from the second-order displacement tensor using equation (1.9.4.5). Here, the second-order terms that were refined together with the higher-order terms are usually used (not the best-fitting second-order terms of a fit in the harmonic approximation):The resulting anharmonic deformation densities (or disorder deformation densities in the case of static disorder) Pdeformation(u) may be displayed in a similar way to the total p.d.f.'s Pgeneral(u). The graphical representations appropriate for displaying those densities are similar to those used for electronic deformation densities (see e.g. Smith et al., 1977). A number of examples of displacement deformation densities of high symmetry are shown in Fig. 1.9.4.1 as three-dimensional contour maps.
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