Crystallography & Symmetry
patterns derived from their groups
Concept

Indexing — where it appears

Recovering a unit cell from a list of measured spacings, a problem with many solutions that a figure of merit ranks rather than settles. Every supercell explains the same lines, so the ambiguity is a fact about the arithmetic rather than a shortage of care.

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

168 reflections, 26 rings, one axis. Every reflection of a square lattice out to indices of 6, drawn as a point of the reciprocal lattice with the rings of equal length it lies on. A single crystal gives each point its own place on a detector; a powder is every orientation at once, so what is measured is the ring rather than the point, and the 168 reflections arrive as 26 lines on the single axis at the right, with height the number sharing each. The rings are found by sorting the lengths and grouping equal ones, and every point is checked to sit on the ring it was given. 1 of the rings are marked: they hold reflections that no operation of the lattice's point group relates, so the collapse has added together two genuinely independent measurements and no experiment can take them apart again.

What a powder pattern loses

Grind a crystal up and every orientation is present at once, so a two-dimensional pattern of spots collapses onto a single axis. Reflections that had their own places arrive together, and some of the coincidences are exact and have nothing to do with symmetry.

diffraction · Diffraction The substitution, 6 generations. The rule "every long tile becomes a long and a short, every short tile becomes a long", applied 6 times from a single tile. Each generation is as long as the previous two together, so the tile counts are Fibonacci numbers — 13 long and 8 short at the last row — and their ratio is 1.62500 against the golden ratio's 1.61803. The sequence never repeats and every finite piece of it recurs infinitely often, which is order without periodicity in its smallest form.

The smallest quasicrystal

Two tile lengths on a line, in the golden ratio, in a sequence that never repeats. Three completely different constructions produce it, they are required here to agree, and its diffraction needs two integers per peak where a periodic chain needs one.

aperiodic · Quasicrystals The icosahedral group, counted. The sixty rotations of an icosahedron, found by trying every map that sends one adjacent pair of vertices to another and keeping those that carry the whole vertex set onto itself. They fall into 6 axes of order 5, 10 axes of order 3, 15 axes of order 2 — and the fivefold axes are the reason this group cannot be the point group of any crystal, since no three-dimensional lattice admits a rotation of order five. Quasicrystals have it anyway, which is what made 1982 an argument rather than a measurement.

Icosahedral symmetry

Sixty rotations, six fivefold axes, and no lattice in three dimensions that can hold any of them. It is the point group a crystal is forbidden, and the one the first quasicrystal turned out to have.

aperiodic · Quasicrystals A chain modulated at q = 0.211. The lower row is the lattice: 34 sites, evenly spaced. The upper row is the structure: the same sites displaced by a wave of amplitude 0.12 of a spacing and wavevector 0.211, drawn through them. Because 0.211 is not a ratio of small whole numbers, no cell of any size holds the structure — the displacement pattern never repeats — and yet the atoms are nowhere near random: each one is exactly where a single sine wave says it should be. That is what an incommensurately modulated crystal is, and its diffraction pattern is sharp.

The satellites that need a second integer

A crystal whose atoms are displaced by a wave of the wrong wavelength has no unit cell at all, and diffracts to sharp spots anyway. Indexing them takes two integers per reflection instead of one — and the intensities of the extra spots are Bessel functions, which is a check the arithmetic can be made to pass.

aperiodic · Modulation A quasilattice down a 5-fold axis: 10-fold, from an axis of order 5. 153 points of a three-dimensional quasilattice, made by keeping the points of Z⁶ whose perpendicular image lies inside a window and projecting them into ordinary space, then viewed along one of its 5-fold axes. There is no lattice here and no unit cell, and the symmetry is nevertheless exact: all sixty rotations of the icosahedral group carry the set onto itself, on 153 points of its core, measured by applying them rather than assumed from the construction. Seen down this axis the set comes back to itself under a turn of a 10th and no finer turn, measured over every turn up to a twelfth — twice the order of the axis, and the factor of two is a centre of symmetry: this set equals its own negation, which is what a window centred on the origin produces, and that is checked here rather than assumed. A diffraction experiment would record the same 10 whatever: the measured intensity acquires a centre whether or not the structure has one, so the tenfold photograph of 1982 does not by itself distinguish a structure with a centre from one without.

Six integers, and the lattice that holds them

A fivefold rotation is not an integer matrix in three dimensions and is one in six. The icosahedral group permutes its own six fivefold axes, so in coordinates along those axes every one of its sixty rotations is a signed permutation — and Z⁶ is a lattice it maps onto itself.

aperiodic · Quasicrystals 7 cells explain the lines; one of them is right. A line list from a face-centred cubic cell of 5.64 Å, with a realistic error added, handed to a sweep over every cubic cell between 2 and 12 Å in all three centrings. 7 distinct cells explain every line within the tolerance, and each is a genuine solution rather than a numerical accident. The true cell comes top by de Wolff's figure of merit — the last Q over twice the mean discrepancy times the number of lines the candidate says should have been visible — which punishes a candidate for predicting lines nobody saw. That is the whole of what makes indexing decidable in practice: not the arithmetic, which has many answers, but a criterion for preferring one.

Indexing a powder pattern

A powder pattern is a list of numbers and a cell is six. Getting the second from the first is the first step of every powder study and the one that fails — because the arithmetic has many answers, and choosing between them is a ranking rather than a deduction.

applied · Indexing two chains, periods 1 and 1.62. Two interpenetrating chains of atoms with periods 1 and 1.62, whose ratio is irrational, so no length is a whole number of both. Each chain is displaced from its own lattice by a wave with the other's period — the short ticks show each atom's displacement from where an unmodulated chain would put it — which is what makes this one crystal rather than two side by side. Nothing here is a unit cell: any length chosen contains a whole number of one chain's atoms and a fractional number of the other's.

Two lattices, one crystal, and no cell at all

A modulated crystal has a lattice and a wave running through it. A composite has neither host nor guest: two interpenetrating substructures with periods that share no common multiple, each modulating the other. Every reflection needs an index from both, and the unit cell a diffractometer reports belongs to whichever half scattered harder.

aperiodic · Modulation 342 unlabelled spots, cell volume 52. A bag of 342 reflection positions with no indices on them, collected out to a bound of 3 on each index. Their pairwise differences generate the reciprocal lattice; a basis of that is taken by integer elimination and then reduced, and the reduced basis is printed. Its determinant is 52, which is the volume of the cell the reflections were computed from — so the cell has been recovered from positions alone, with no intensity used anywhere.

A cell from a bag of spots

A single-crystal experiment returns a list of directions with no labels on them. Recovering the cell is recovering the lattice those directions generate, and the whole of it is take differences, reduce, read the answer. What no quantity of data settles is whether the lattice found is the true one or a sublattice of it.

applied · Indexing The figure of merit a supercell always beats. One line list, indexed on the true cell and on five multiples of it. The mean discrepancy is not merely similar down the column, it is identical to every digit: the supercell's grid of allowed Q values contains the true cell's grid exactly, so each line lands on precisely the same place and misses by precisely the same amount. Any figure of merit built on agreement alone therefore returns one number for the whole family, and cannot prefer the true cell. What falls is the last column, and the only thing in it that the fit does not already contain is the count of lines the cell says should have been seen.

The figure of merit a supercell always beats

Indexing a powder pattern returns a ranked list rather than an answer, and the ranking needs a number. The obvious number — how well the cell accounts for the lines — is exactly the number a supercell cannot lose on, because the supercell's grid contains the true cell's grid and the discrepancies are identical to every digit. What has to be paid for is the lines nobody saw.

applied · Indexing The alias accounts for every line and predicts more. The observed lines above, and below them the grid of a supercell that explains all of them. The full ticks are the observed lines, which the alias reproduces exactly; the faint ones are lines the alias predicts and nobody saw. That second set is the only thing that separates the two cells, and it is why an indexing criterion has to charge for unobserved lines rather than measure agreement.

Every alias is a supercell

A cell that explains every line of a powder pattern is not a near miss and not a coincidence: its reciprocal grid contains the true one, which means its own cell is a superlattice of the true cell. So the ambiguity of indexing is the arithmetic of superlattices, and it can be counted — two cells with one unknown, sixteen with two, sixty-two with three, all of them accounting for the same twenty lines exactly.

applied · Indexing

Named alongside it

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

Figure of meritPowder diffractionSystematic absenceAccidental overlapCut-and-projectGolden ratioHigher-dimensional latticeIncommensurateLong-range orderMeasurementQuasicrystalQuasiperiodic

All concepts