Crystallography & Symmetry
patterns derived from their groups
Concept

Systematic absence — where it appears

A reflection whose intensity is exactly zero for every possible arrangement of atoms, deleted by a screw, a glide or a centring. The most informative part of a diffraction pattern is the part that is not there, because a translation part leaves no other mark on it.

Named by 19 essays across 5 fields — each of them below, with the objects they name alongside it.

What pg scatters. The diffraction pattern computed from the atom positions alone. Where a glide plane is present, alternate reflections along a row cancel exactly — and those missing spots are how the glide is identified in an experiment, since the glide itself is never seen.

Systematic absences

The most informative part of a diffraction pattern is the part that is not there. A glide plane cancels alternate reflections along a row, exactly, and those missing spots are how a symmetry nobody can see is identified.

diffraction · Diffraction One lattice, two cells, and the absences the choice creates. The same set of points described on a centred rectangular cell and on its primitive rhombic cell, with what the centred description scatters. Half the reflections vanish, and they vanish because of how the cell was drawn rather than because of anything the crystal does.

Centring, and why cm is not pm

A centred cell has a lattice point in the middle and twice the area it needs, and crystallography prefers it anyway. The preference has a price, and the price is paid in reflections that vanish for reasons that have nothing to do with the crystal.

lattices · Centring One lattice, two cells, and the absences the choice creates. The same set of points described on a centred rectangular cell and on its primitive rhombic cell, with what the centred description scatters. Half the reflections vanish, and they vanish because of how the cell was drawn rather than because of anything the crystal does.

Why the bigger cell wins

A centred cell has twice the area it needs and crystallography prefers it anyway. The preference is not conservatism — it buys operations that read as whole numbers along the axes, and the price is a set of reflections that vanish for reasons having nothing to do with the crystal.

lattices · Centring The h0l layer of P2₁/c. The h0l reflections of P2₁/c out to 4 in each index, with each spot decided by summing the structure factor over the group's operations: 44 survive and 36 vanish identically, whatever the atoms are. The pattern of holes is the condition h0l: l even, read back off the spots rather than imposed on them.

The reflections that are not there

A screw axis and a glide plane leave no mark on the intensity of any reflection. What they do is delete some, exactly, for every possible arrangement of atoms — and the pattern of deletions is computed here from the sum a crystallographer writes down, rather than read from a table.

diffraction · Diffraction p3, single and twinned. Left, the diffraction pattern of a single crystal of p3. Right, the same crystal twinned, with 50 per cent of it in one orientation. Not one spot has moved — the twin law is a symmetry of the lattice, so the two reciprocal lattices lie exactly on top of one another — and 72 of the 81 reflections drawn have changed intensity. At a fifty-fifty twin the pattern acquires the full symmetry of the lattice's point group and is indistinguishable from a crystal that genuinely has it.

A merohedral twin moves no spot at all

The twin law is a symmetry of the lattice, so the two individuals have reciprocal lattices lying exactly on top of one another. Nothing splits, nothing appears in a new place, and the only thing that changes is that pairs of intensities which were different have been averaged — which produces a diffraction pattern with a symmetry the crystal does not have and no sign that anything is wrong.

applied · Twinning What each group extinguishes. The extinction conditions of 9 space groups, each derived by summing the structure factor over that group's own operations and reading the surviving rule off the result: P1 — nothing; P1̅ — nothing; P2 — nothing; Pm — nothing; P2/m — nothing; P222 — nothing; Pmm2 — nothing; P4 — nothing; P23 — nothing. 9 of the 9 extinguish nothing at all, and diffraction alone cannot distinguish those from each other.

Where the experiment runs out

Absences narrow the space group down and often not to one. Two groups can extinguish exactly the same reflections and scatter with exactly the same symmetry, and telling them apart needs something the diffraction pattern does not contain.

diffraction · Diffraction Two species on one lattice, ordered at index 2. Every position is a lattice point of the parent and none of them has moved. What has changed is which atom sits where: the larger marks are a sublattice of index 2, the smaller ones its other 1 coset, and the outlined cell is the new repeat. The lattice of positions is untouched and the repeat of the contents is 2 times as large, which is the whole of what an ordering transition does and the reason its signature is in reciprocal space rather than in the positions.

The reflections a superlattice adds

Centring a lattice makes reflections vanish. Ordering two kinds of atom onto a sublattice makes new ones appear, exactly n − 1 of them per parent cell, and their intensity is a difference rather than a sum — which is why an ordered alloy of two neighbouring elements can be invisible to X-rays and obvious to neutrons.

lattices · Sublattices Three lattices at 2 forms each: 6, 14, 12 faces. The shape each cubic lattice predicts, built as the solid bounded by its top 2 forms, with each face's distance from the centre inversely proportional to its interplanar spacing. The three lattices have the same metric and the same list of indices; every difference between these solids comes from which reflections are systematically absent. Pm-3m leads on {100} and comes out with 6 faces; Fm-3m leads on {111} and comes out with 14 faces; Im-3m leads on {110} and comes out with 12 faces. Taking more than the leading form matters only where the extinction correction has moved something: in a cubic metric a form's planes are placed at a distance proportional to the root of the sum of the squares of its indices, which is exactly where the corresponding corner of the cube already is, so an uncorrected second form arrives tangent and cuts nothing off.

Which faces a crystal shows

Rock salt grows as cubes, fluorite as octahedra, garnet as dodecahedra. All three have cubic lattices and the same list of possible faces, and what separates them is which reflections are systematically absent — a rule about diffraction predicting a shape a mineralogist can hold.

applied · Growth pg scatters as pmm. The orbit of a motif under pg, and the set of all ordered differences between its points brought to a common origin. The vector set was handed to the detector with no indication of where it came from, and came back as pmm: 31 peaks from 6 atoms, on the same lattice.

Seventeen groups, seven vector sets

A map of interatomic vectors is more symmetric than the structure it came from, twice over: it always acquires a centre, and it loses every translation part. So a glide becomes a mirror, seventeen plane groups collapse onto seven — and the collapse is verified by handing the vectors to a detector that has never heard of Patterson.

diffraction · The Patterson function 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 -2 0 -3 is forbidden and is reached 64 ways. A layer of the reciprocal lattice of Cc: pale spots are reflections the group extinguishes, solid ones are allowed. The path shows a detour — the beam diffracts once at -3 -3 -3 and again at 1 3 0, and the two together send it in exactly the direction a single reflection at -2 0 -3 would. That reflection is forbidden, so intensity arrives where the symmetry said none could. There are 64 such routes to this one spot inside this window alone.

The absence that fills itself in

A systematic absence is the strongest evidence this subject has: a whole zone of reflections cancelling exactly, for reasons of symmetry rather than of arithmetic accident. The exactness belongs to a model — that the beam scatters once. A beam that has already been diffracted can be diffracted again, and the two events together land where the group said nothing could.

diffraction · Diffraction pmg: 80 of 80 restricted. The reflections of pmg inside a window of ±4, with the ones whose phase symmetry restricts to two values picked out. Every solid spot has a structure factor that must be real up to a fixed rotation — a sign, in effect — whatever the atoms turn out to be, and the pale ones have a phase symmetry says nothing about. The 4 palest spots carry two incompatible restrictions at once, which leaves them nothing to be but zero. Which spots these are was computed from the operations, before any structure existed.

The zones that behave as if there were a centre

The phase problem is usually stated as though symmetry had nothing to say about phases. It is true of most reflections and false of some, and which is decidable from the group alone: where an operation carries a reflection onto its own negative, the phase is confined to two values half a turn apart, computed from that operation's translation.

diffraction · Statistics p4m from 3 orbits of waves — detected p4m. A density built as a sum of 3 symmetry-adapted waves of p4m, each of them the average of a plane wave over the group, shaded from light to dark across one cell. The level set of this density — the darkest points of it — was handed to the same detector the pattern figures use, and it reports p4m, which is exactly the group the waves were built from. The waves are invariant by construction, so the density can never have less symmetry than the group; the interesting direction is the other one.

How many waves a group permits

A pattern can be written as a sum of waves instead of as an orbit of a motif, and then the group ties the coefficients together and forbids some outright. Building a density from the permitted ones and handing it back to the detector closes the same loop through a different door — and at low resolution the density has symmetry the crystal has not.

classification · Seventeen 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 Two populations, and neither of them empty. The reflections of a structure in which three quarters of the atoms are paired by a half-cell shift, sorted by the parity of h + k and each class scaled by its own mean. The two histograms have the same shape, which is the point: each class on its own is an ordinary acentric distribution. What differs is the scale — the odd class is a sixth of the even one on average — and no odd reflection is absent, so no extinction rule fires and nothing about the space group is affected.

A translation that is nearly there

Half a structure copied onto the other half by a half-cell shift, with nothing exact about it. No reflection vanishes, so no extinction rule fires — and the test for a centre of symmetry answers yes about a structure that has none.

diffraction · Statistics 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 Cube, octahedron, rhombic dodecahedron — from connectivity alone. Every form of index two or less, classified by how many chains lie inside it: two or more and the face is flat, exactly one and it is stepped, none and it is kinked. The number beside each flat form is how many chains it contains, which is the rule's own tie-break — a face with three chains is flatter than one with two. Nothing about interplanar spacing enters, and the three structures are told apart by their bonds.

Which faces are flat

Bravais ranks a crystal's faces by how far apart their planes lie. Hartman and Perdok classify them by how many uninterrupted chains of bonds run inside them, which uses no spacing at all — and on the three cubic structures the two rules put the same face first every time. Then the second rule's power turns out to live entirely in where the chain list is cut off.

applied · Growth The cross, from the selection rule alone. The layer lines of a helix with the first maximum of each marked on both sides. Nothing here is a picture of a photograph: each mark is at the radius where the Bessel function of the lowest order the selection rule permits on that layer line first peaks, and that radius is proportional to the order. The order rises by one per layer line until the middle of the repeat, so the maxima lie on two straight lines through the origin — the X — and the larger marks are the layer lines that reach the axis.

What a thread scatters

A helix with ten subunits in a turn is not a screw axis a crystal may have, and nothing about its diffraction pattern is lawless. The pattern lies on layer lines, and on each one only certain angular orders may contribute — a selection rule as hard as any extinction condition. The lowest permitted order rises by one per layer line, a Bessel function of order n does nothing until its argument is about n, and the maxima therefore lie on two straight lines through the origin.

classification · Subperiodic One change of setting, four rules. The four things a structure report contains and the rule each obeys under a change of setting with basis change P and origin shift p. The cell and the indices are multiplied by P; a coordinate is multiplied by its inverse, after the origin has been subtracted; and an operation is conjugated and then shifted by (W − I)p, a term the other three have no equivalent of. Applied to Pnma with the change below, the operations still close into 8, the orbit maps point for point, and every |F| is unchanged.

One matrix, four rules

Changing the setting of a structure is one matrix and one origin shift — and the cell, the coordinates, the indices and the operations each obey a different rule under it. Three of the four ways of getting it wrong still leave a closed group of the right order, so closure catches none of them.

space-groups · Settings

Named alongside it

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

Structure factorCentringReciprocal latticeCentrosymmetryFriedel lawGlide planeIndexingInterplanar spacingLaue classMeasurementScrew axisSpace group determination

All concepts