Crystallography & Symmetry
patterns derived from their groups
Concept

Average structure — where it appears

The periodic structure obtained by putting the mean occupation at every site of a disordered crystal. It is what the Bragg intensities alone report, it need not be anything a crystal could be, and everything about the arrangement is in the diffuse scattering instead.

Named by 12 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 The diffuse intensity of an alloy with α₁ = -0.46. The diffuse part of the scattering across the wavevectors an 12 × 12 block can be asked about, one square per wavevector with darkness the intensity. The marked squares are where the average structure scatters — the sharp part, which is what a Bragg reflection is. The diffuse maximum here is at (0.50, 0.50), which is the zone boundary: the alloy is trying to alternate, and a crystal that succeeded would put a sharp reflection exactly there. Summed over every wavevector, the intensity is exactly one per site whatever the correlations are — order moves scattering about, it does not create it.

The average scatters sharply and the rest does not

A crystal whose lattice is perfect and whose occupation is not scatters in two parts: the average structure gives Bragg reflections, and the variance is spread over everything between them. The split is exact, the total is one unit per site whatever the disorder does, and an ensemble of n arrangements mislays exactly a fraction 1/n of 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 Which sites a smooth error can mislead. For the eighteen pairs of disorder models at three site symmetries, under a smooth scale error of degree two (five molecule sizes) and of degree four (three sizes): how many verdicts of perfect counting go the wrong way, how many pairs no data can decide, the largest correlation between the error and the two models' difference, and how many harmonics of the error's degree the site's group leaves unchanged. At the cubic site the degree-two error correlates with nothing, to rounding, and decides no pair wrongly; the degree-four error, which the cubic site keeps one harmonic of, reaches it.

A cubic site is blind to a degree-two error

A smooth scale error left uncorrected made perfect counting choose the wrong disorder model for eight of ninety pairs and sizes, and the obvious way to predict which is to correlate the error with the two models' difference before refining anything. That correlation predicts none of them. What it does predict, exactly, is which pairs can never go wrong: at a cubic site a scale error of degree two correlates with nothing and is absorbed by nothing, because a cubic group keeps no harmonic of degree two. A degree-four error, which it keeps one of, reaches the cubic site at once.

restriction · Local symmetry The first-order prediction against the actual verdict, for every pair and size. The 85 decidable pairs of disorder models at five molecule sizes, each placed by the first-order prediction of the wrong model's misfit minus the right model's, made from the two error-free refinements and their Jacobians, and by the actual difference after refining against data with a 3% smooth error. Shaded quadrants are agreement. 77 agree. Of the 8 wrong verdicts, ringed, 4 are predicted; 4 right verdicts are predicted wrong.

The wrong model moves too far for first order

Which disorder models a smooth error will turn the wrong way was left as a calculation to make before any data exist: project the error onto the directions each refinement's parameters can move. Made, it gets the sign of the verdict right in seventy-seven of eighty-five cases, catches four of the eight wrong verdicts and raises four false alarms. Every case it gets wrong is either a near-tie or a refinement that absorbed more than twice, or less than half, of what its first-order directions allow.

restriction · Local symmetry Diffuse scattering gathered under every Bragg peak. The one-phonon thermal diffuse scattering of a square lattice with springs to nearest and next-nearest neighbours, over the reciprocal plane from minus 2.5 to 2.5 in each index, with the Bragg reflections marked. The intensity rises as one over the squared distance to every reflection, because the acoustic phonons' frequencies vanish there, and it grows with the square of the scattering vector, so the lobes are strongest far from the origin. The lobes are not round: a small step from (1,0) along k gives 2.7 times the intensity of the same step along h, because it probes transverse phonons, which are softer, and that ratio is what an experiment reads the elastic constants from.

A warm plane crystal has no Bragg peaks

Thermal motion is disorder that moves, and in space it costs a crystal a little of each Bragg peak and gathers it into diffuse scattering underneath. In a plane it costs more than a little. Computed exactly from the phonons of a harmonic square lattice, an atom's mean-square wandering grows by the same amount every time the crystal doubles in size, so no Debye–Waller factor survives, and every Bragg peak fades as a power of the crystal's size — a power proportional to the temperature times the square of the reflection's distance from the origin.

diffraction · Disorder The error in the count, against tiles chosen at random. For clusters from about twenty-five hats to nearly two trillion, the distance of the reflected count from the exact share of all hats. For the hat it stays under one half. For independent random choice at the same share the expected error grows as the square root of the size, past 400,000 at the largest cluster.

The count of reflected hats is never one out

In a hat tiling one tile in about eight is reflected, and that ratio was only ever quoted here. Four clusters and a table of small integers give it exactly: seven plus three root five over two, the fourth power of the golden ratio. The same table says something the ratio does not. Grow a cluster to two trillion hats and its reflected count is still within half a tile of the exact share, where the same share chosen at random would be out by nearly half a million.

aperiodic · Monotile

Named alongside it

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

DisorderSite symmetryOccupancyStructure factorLeast squaresSpecial positionBragg peakDiffuse scatteringOrbitResolutionStabiliserAperiodicity

All concepts