Crystallography & Symmetry
patterns derived from their groups
Concept

Occupancy — where it appears

The fraction of a crystallographic site that is actually filled, averaged over the crystal. A refinement reports it as a number between zero and one, and questions about connectivity, conduction and rigidity depend on the arrangement it averages over rather than on the number itself.

Named by 10 essays across 3 fields — each of them below, with the objects they name alongside it.

p2 in one cell, p4 on average. On the left, a molecule in one orientation at a site whose symmetry is larger than its own: the arrangement has 2 operations and the detector says p2. On the right, the average over the 2 orientations the site offers, which is what a diffraction experiment measures because different cells choose differently and nothing prefers one choice. The average has 4 operations — it is p4 — and every atom in it is present in half of the cells. Both groups are detected from the point sets rather than assumed, and the difference between them is the reason a refined structure can have symmetry no molecule in the crystal has.

The symmetry of an average

A diffraction experiment measures an average over some 10²⁰ unit cells, and the average of several orientations is more symmetric than any of them. So a refined structure can carry symmetry that no molecule in the crystal has — including, in the worst case, a centre of inversion in a crystal built entirely of one hand.

restriction · Local symmetry One crossing or the other, and never both. Two events on a square patch of lattice: a path of occupied sites crossing from left to right, and a path of vacant sites crossing from top to bottom. On the triangular lattice exactly one of them happens in every configuration tested — the claim is combinatorial rather than statistical, so one counterexample would end it. On the square lattice both can fail at once, and do, in more than a quarter of the configurations. That difference is the whole of what follows.

The threshold a symmetry pins down

Occupy sites at random and somewhere the occupied ones first join up across the crystal. For almost every lattice that occupancy is known only to a few digits. For the triangular lattice it is exactly a half, and the reason is that on a lattice whose faces are all triangles an occupied path and a vacant path cannot slip past each other — a statement about one configuration at a time, with no probability in it.

diffraction · Disorder 19 site symmetries, and the counts each can impose. Every distinct site symmetry across the space groups this site builds, named by the multiset of its operation types, with the orientation counts a disordered molecule there may take. The counts are the indices of the site group's subgroups, computed by closing subsets under multiplication rather than looked up. Nearly every row offers every divisor of its order. One does not: a site of order twelve whose group is the tetrahedral rotation group refuses an orientation count of two, because that group has no subgroup of order six.

How many orientations a disorder needs

A molecule at a site with more symmetry than it has resolves the contradiction by occupying several orientations at once. How many is not fitted: it is the index of the molecule's symmetry in the site's, so the occupancy is the reciprocal of a whole number — and one site in the census refuses a divisor of its own order.

restriction · Local symmetry Disorder models against occupancies, site by site. Every distinct site symmetry in the space groups built here — 19 of them — with its order, its number of subgroups, the number of distinct disorder models, which are the subgroups up to conjugacy by the operations of the site symmetry, and the number of different occupancies those models can have. The last column is the largest number of models that share one occupancy. In all, 162 models share far fewer occupancies; the most crowded is 4/mmm, where 11 different models all give an occupancy of 1/4. At every site, the classes of operation a model keeps separate it from every other model with the same occupancy.

The occupancy does not name the disorder

A molecule disordered on a special position takes a number of orientations fixed by a group index, and its occupancy is the reciprocal. Many different disorders share one occupancy — eleven at a single kind of tetragonal site — and what separates them is which of the site's operations the molecule keeps, which the averaged structure records and the occupancy does not.

restriction · Local symmetry A patch of hats scatters a pattern that repeats. The diffracted intensity of the 1217 points of a patch of 183 tiles laid out as the hat, over 2 by 2 cells of the kite grid's reciprocal lattice, whose edges are the faint lines. Every local maximum above a hundredth of the central peak is a disc with area proportional to its intensity; 12 reach the central peak's full height. 72 maxima are drawn. Adding a reciprocal lattice vector to the scattering vector changes the intensity by at most 1.1e-15 of the central peak, so each cell holds the same pattern.

How much of the hat is a crystal

Put a scatterer on every corner of a patch of hats and the diffraction pattern repeats exactly, because every corner sits on a lattice. Inside each repeat the strongest reflections are those of an ordinary crystal with partly filled sites, and by Parseval's identity they carry sixty-three per cent of what the pattern holds. The aperiodicity the hat is famous for lives in the remaining third, in reflections a hundred times weaker.

aperiodic · Monotile The average is the site's orbit, with occupancies. A molecule at a site of symmetry mmm keeping a subgroup of order two takes four orientations, and the average over them is the site group's orbit of each of the molecule's atoms, every image at one over the length of its own orbit. Atoms in general positions give eight images at an eighth each, and give the same eight whichever subgroup the molecule keeps. Atoms on a locus the model keeps give a shorter orbit at a higher occupancy, drawn larger and darker, and those are the only atoms that differ between models. The total scattering is the same for every model, so all of them agree exactly at zero scattering angle.

The molecule size that hides a disorder

Two disorder models with the same occupancy leave averaged structures that differ only in a handful of partial atoms. The difference is 20% in structure factors for a ten-atom molecule and 3% for a sixty-atom one — so the data choose between the models for a small molecule and stop choosing for a large one, and seven pairs are identical at any size.

restriction · Local symmetry What refinement takes back from a wrong disorder model. Every directed pair of disorder models sharing an occupancy, 462 in all: data made from one model's averaged structure, the other model refined against them with positions on its own loci, two-component displacement parameters and fixed occupancies. Across is the residual between the two ideal structures; up is the residual after refinement. Points on the dashed line lost nothing to refinement; the median point lost 58 per cent of its residual. Every point on the floor, where the wrong model fits exactly, is one whose loci contain the true model's.

What refinement takes back from a wrong model

Two disorder models sharing an occupancy leave averaged structures typically a sixth apart. Refine the wrong one against the right one's data and it takes back more than half of that — all of it wherever its loci contain the true ones. Yet the data still choose, even for a molecule of sixty-four atoms, because a likelihood summed over every reflection sees what no single reflection can, and the wrong model's partial atoms give it away through the size of their displacement parameters, not their shape.

restriction · Local symmetry Better counting makes an uncorrected smooth error choose the wrong model. Eighteen pairs of disorder models, each decided by the likelihood ratio at the 0.1 per cent level, at sixty-four and a hundred and twenty-eight atoms, as the random error falls from 3% to 1% to 0.3% of the mean amplitude. In each group, the first bar has random error only, the second adds a smooth scale error of 3% across reciprocal space, and the third adds the same error with a degree-two scale surface refined alongside the structure. With random error only, better counting decides more pairs correctly. With the uncorrected smooth error it stops helping and the number decided for the wrong model grows, to three at a hundred and twenty-eight atoms. With the surface refined, the result is the random-only one in every group.

Better counting, and the wrong model

A smooth error across reciprocal space, as large as the random one, hardly changes which disorder model the data choose: it enters both models' residuals and cancels from their difference. What it changes is where better data lead. With random error alone, counting harder decides more pairs correctly. With the smooth error left in, counting harder stops helping and starts deciding pairs for the model that did not make the data — at the 0.1% level, and more of them the better the counting.

restriction · Local symmetry Three ways to fill a lattice with a wave. Three occupation waves at the same irrational wavevector, each drawn as its profile over one period, the occupancy of a site as a function of where the wave stands there, and as the first thirty sites of the chain it produces, each filled in proportion to its occupancy. A cosine fills every site partly. A crenel of width 0.3 fills three sites in ten completely and leaves the rest empty. A crenel of width 1/φ fills sites exactly where the Fibonacci chain has its long letter, so the third row is that chain written as two species on a lattice.

An occupation wave is its own Fourier series

A modulated crystal whose atoms stay put while a wave decides how much of an atom sits on each site diffracts to satellites, and the satellite of each order is simply the matching Fourier coefficient of the wave's profile. A cosine stops at first order and can never exceed a quarter of a site; a step makes satellites of every order, skips exactly the orders its width divides, and makes the strongest first-order satellite any wave can. And a step as wide as its own wavevector is the Fibonacci chain.

aperiodic · Modulation Two waves that are each symmetric enough make a lopsided pair. The first-order satellite amplitudes at h − q and h + q around the main reflections h = 1 to 4, for three chains: an occupation wave on the lattice, whose pairs are equal; the strain wave alone, the displacement the size effect produces with every site equally full, whose satellites are weak and grow with h; and both together. Together the pairs are unequal, the low side stronger, by an amount that grows from one reflection to the next — an imbalance neither wave has on its own, from a displacement of less than a hundredth of a spacing.

The strain wave that tips the satellites

An occupation wave puts equal satellites on both sides of every main reflection, and a strain wave a hundredth of a lattice spacing high is enough to tip them. Real composition waves drag such a strain with them, because atoms of different sizes want different spacings, and the tilt that results is not a nuisance. To first order it does not depend on how strong the occupation wave is at all. It reads the size mismatch directly, and its sign says which species is the larger.

aperiodic · Modulation

Named alongside it

The objects these essays reach for when they reach for this one.

Average structureDisorderSite symmetrySpecial positionStructure factorOrbitResolutionStabiliserCut-and-projectDisplacement parameterThe Fourier transformIncommensurate

All concepts