Crystallography & Symmetry
patterns derived from their groups
Concept

Disorder — where it appears

The presence of many arrangements consistent with one average structure, so that a diffraction experiment reports occupancies rather than positions. The count of arrangements is an entropy, and the correlations between them go into diffuse scattering rather than into the Bragg peaks.

Named by 15 essays across 4 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 Arrangements per site, falling towards the exact value. The number of configurations of an L × L torus obeying the ice rule, taken to the power of one over the number of sites. The largest computed here is 4,484,823,396 configurations on a 7 × 7 torus. The values fall towards Lieb's exact 1.54 from above, and every one of them is above Pauling's estimate of 1.5 — which undercounts, because it treats the vertices as independent and they are not.

The arrangements a crystal keeps at absolute zero

Ice has a residual entropy, and the number a calorimeter measures is the logarithm of a count of arrangements. Pauling's one-line estimate of that count is out by two and a half per cent; the exact count in two dimensions is available, falls towards its limit from above, and the whole disorder is invisible to a diffraction experiment, which sees only the average.

aperiodic · Entropy One crystal, two rows: one streaks and one does not. Two rows of reflections from the same faulted crystal, at a fault rate of 0.05, each drawn against the same row from a perfect one. The upper row has h − k not divisible by three, so each layer contributes a different cube root of unity and the sequence of layers enters the sum: the sharp peaks collapse into a streak. The lower row has h − k divisible by three, the phase factor is one, every layer scatters in step, and the peaks are exactly as sharp as in the perfect crystal. The sorting is an integer condition — a reflection either can see the stacking or cannot, decided by h − k modulo three — which is the most direct evidence there is that the disorder is in the stacking and not in the layers. The profiles are averaged over 16 independently faulted crystals, because one crystal gives speckle rather than a diffuse profile.

The streaks a faulted stack makes

Close packing settles two directions and leaves the third to chance. A crystal that chooses wrongly now and then has a lattice in the plane of its layers and none across them — and its diffraction pattern says so, with some rows of spots as sharp as ever and others smeared into streaks, sorted by an integer condition.

diffraction · Diffraction One local configuration, and a number of structures that doubles. How many kinds of adjacent pair a close-packed stack has, how many kinds of triple, and how many stackings of each period there are. The first column never moves: every pair of layers is congruent to every other, at every period, which is what an order-disorder family is. The last two agree with 2ⁿ + 2(−1)ⁿ, which is the chromatic polynomial of a ring of n layers at three colours, because a stacking of period n is exactly a proper three-colouring of that ring. The gap between the first column and the last is the whole subject.

A stack with no space group

Every pair of layers in a close-packed stack is congruent to every other pair, and the number of stacks doubles with every layer added. A family whose local configuration is completely determined and whose global structure is not determined at all has no single symmetry group — what it has is a set of operations that compose only when their ends match, which is a groupoid.

applied · Packing 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 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 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 Every arrangement on a torus 4 across, sorted by defects. The transfer matrix that counts ice arrangements chooses, at each vertex, the one horizontal arrow the rule permits. Enumerating both choices instead and carrying a polynomial that records how many vertices end up with three arrows in or three out gives the number of arrangements at every defect count at once. The first column, drawn solid, is the ice count — 2970 arrangements with no defect at all, which is the number the earlier transfer matrix gives and is checked against it. The second column is empty: no arrangement has exactly one defective vertex, because a defect carries a charge and the charges on a closed surface must cancel. The columns together add to two raised to the number of edges, which is every assignment of arrows whatever.

What a defect costs the count

Each broken vertex relaxes the rule and so adds arrangements — the question left standing was whether each adds a fixed amount or the cloud around it costs some back. The exact count at every defect number at once answers the first half outright: almost all of the rise is the freedom to choose which vertices break, and what is left once that is taken out exactly is small, uneven, and lowest at the first count that needs a four.

aperiodic · Entropy 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 Along the rod above a reflection, a free sheet loses its peak. The Bragg intensity per site squared of a warm square-lattice sheet at the in-plane reflection (1, 0) and at heights 0.1, 0.2 and 0.3 along the rod above it, against the sheet's size, on logarithmic axes. In the plane the peak falls as a power of the size whatever the sheet does out of it. Above the plane a free sheet's peak collapses faster and faster, to 2.3e-2 at size 128 and height 0.3; under tension every height falls as a power, to 0.38.

A flapping sheet keeps its peaks in the plane

A warm sheet one atom thick wanders out of its plane far more than within it: a free sheet with only bending stiffness has a mean-square height that grows with its area. That wandering cannot touch a reflection whose scattering vector lies in the plane, which fades exactly as it would if the sheet were held flat. Every reflection with a component along the normal loses its peak faster than any power of the size. Tension puts it back on a power law.

diffraction · Disorder Every stacking reflection of a warm stack of sheets falls as a power of its size. The Bragg peak per site squared per layer squared of the stacking reflections (0, 0, l), l = 1 to 5, of a stack of flapping square-lattice sheets with bending stiffness 1 and coupling 0.1 between neighbouring layers, at kT/k₁ = 0.02, against the stack's width, with the number of layers growing as the width squared. Each order falls as a fixed power of the size, and the powers grow as the square of the order: 0.20, 0.80, 1.79 and 3.18 for the first four. The fifth falls as the fourth power, as fast as the crystal's volume grows, which is what a reflection with no peak at all does.

A stack lends each sheet a tension

A single warm sheet wanders so far out of its plane that every reflection with a component along its normal is lost. Stack the sheets and couple each to its neighbours, and inside the stack each sheet wanders only as a sheet under tension does, logarithmically. The stacking reflections survive as peaks that fall as powers of the crystal's size, and the power grows as the square of the order, so the fifth order of the stack computed here has no peak at all. A stack of finitely many sheets keeps even the first only out to a width growing as the square root of its thickness.

diffraction · Disorder

Named alongside it

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

Average structureSite symmetryStructure factorOccupancyLeast squaresLong-range orderBragg peakOrbitResolutionSpecial positionClose packingCounting

All concepts