Crystallography & Symmetry
patterns derived from their groups
Concept

Site symmetry — where it appears

The subgroup of operations fixing a given position, regarded as a point group, which constrains whatever is placed there. A motif more symmetric than its site is harmless; a site more symmetric than the motif intended is where accidental symmetry comes from.

Named by 27 essays across 6 fields — each of them below, with the objects they name alongside it.

The wallpaper group p3m1. A pattern with the symmetry of p3m1, generated by applying the group's 6 operations to an asymmetric motif and repeating across the lattice. The symmetries of the result were then found independently and match the group exactly.

p3m1 and p31m

Two groups with the same lattice, the same point group and the same number of operations, differing only in where the mirrors sit. The pair is the clearest evidence that position is as much a part of a symmetry as presence.

classification · Seventeen A conjugacy class of p4m. One conjugacy class of p4m drawn in place: every copy of the same symmetry that the group can carry onto every other. Conjugation was applied to each of the 8 operations by each of them in turn, and the kind and order of the result was checked to match every time.

The same symmetry, somewhere else

Two mirrors in a pattern can be the same symmetry or two different ones, and looking will not settle it. Conjugation is the operation that decides, and it turns an intuition about sameness into arithmetic.

operations · What symmetry is p4m, displaced and then measured. Every atom of a p4m pattern moved by up to 1.2 per cent of a cell edge, and the resulting positions examined at 26 tolerances. At zero tolerance only the identity survives, so the structure has no exact symmetry whatever. Between 0.021 and 0.094 the count sits at 8, which is the group that was displaced. Above that it climbs to 15, accepting operations no version of this pattern has. The climb is not even steady: at 4 of the 25 steps the count falls as the tolerance is loosened, because operations accepted separately at one threshold merge into one at the next. The correct answer is a step on a staircase and nothing in the coordinates says which step.

Near-symmetry, and the tolerance that is not here

Symmetry decided by integer arithmetic never needs a threshold. Measured coordinates do not arrive that way, and the moment a tolerance is introduced the answer stops being a fact about the structure and becomes a fact about the threshold.

diffraction · Accidental symmetry Special positions in p4m. Every point of a 12×12 grid inside the cell of p4m, drawn at a size set by how many operations fix it. 80 of the 144 are general — nothing but the identity leaves them alone, so their orbit is the full 8 points. The other 64 are special, and fall into 3 kinds: 60 points fixed by 2 operations, with orbits of 4; 2 points fixed by 4 operations, with orbits of 2; 2 points fixed by 8 operations, with orbits of 1.

The points a group treats differently

Almost every point of a cell has an orbit as long as the group. The exceptions are the points some operation leaves alone, and they are where atoms sit, where a structure's formula comes from, and where a careless motif destroys the group it was meant to illustrate.

operations · Fundamental domain 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 Fddd has two published origins. The two conventions, computed from the operations. The International Tables place the origin at the point of highest site symmetry, and also at a centre of inversion, and for this group those are different points — so the group is printed twice, with every coordinate in the second table shifted by (-0.125, 0.125, -0.125) from the first. A structure published on one and read on the other has every atom in the wrong place by that vector, the refinement fails in a way that looks like bad data, and nothing in the symbol says which was used.

Two origins for one group

The International Tables place the origin at the point of highest site symmetry, and also at a centre of inversion. For twenty-four of the two hundred and thirty those are different points, so the group is printed twice with every coordinate shifted — and nothing in the symbol says which table a structure was written against.

space-groups · Settings The symmetry of a cut through Pnma. Every height in one cell, and the number of operations of Pnma that map the plane at that height to itself. The answer is 2 almost everywhere and rises to 4 at the special heights, where the plane group named above the spike is what a reader looking down at that surface would see. The rule is two conditions and no more: the operation must not tilt the plane, and the plane must come back to its own height — so a twofold axis lying in the plane survives at two heights per cell and a screw axis along the normal survives nowhere.

What a cleave leaves

A surface is a crystal that has been cut, and the symmetry it presents is what the space group leaves of itself on that plane. Two conditions decide it — the plane must not tilt, and it must come back to its own height — and the answer changes with where the cut was made.

classification · Subperiodic The most of an icosahedron a crystal can keep. Every subgroup of the sixty rotations of an icosahedron, found by closure, with the crystallographic ones marked — those whose rotation orders are all among the 1, 2, 3, 4 and 6 that a three-dimensional lattice admits. The largest is 23, of order 12, at index 5; everything containing a fivefold axis is refused. So a crystal containing an icosahedral molecule may fix a twelfth of the molecule's own symmetry and no more, and the remaining 5 orientations have to be related by something other than the site's symmetry.

The most of an icosahedron a crystal can keep

C₆₀ sits in crystals and virus capsids sit in crystals, and neither of them stops being icosahedral. What a lattice can fix is a subgroup — and the largest crystallographic subgroup of the sixty rotations has order twelve, at index five. The five are Kepler's five cubes.

restriction · Local symmetry orders 5 and 7 reach a site of symmetry 1 and no more. A molecule whose only symmetry is one n-fold axis, and the highest site symmetry it may occupy in any of the 45 space groups this site builds. The site's symmetry has to be a subgroup of the molecule's, so the site's order must divide n and the site group must be cyclic. Orders 1, 2, 3, 4 and 6 reach a site of their own order. Orders 5 and 7 reach one, because no site symmetry in any space group contains an operation of order five or seven — the orders available are 1, 2, 3, 4, 6, computed by asking every operation of every group whether it moves a point. A five-fold molecule keeps its axis; the crystal simply has no use for it.

What a molecule gives up to sit in a crystal

A molecule brings its own symmetry. A crystal offers sites with symmetries of their own, and the two have to be compatible — the site's symmetry must be a subgroup of the molecule's. So a molecule may always keep more than its site offers, and a molecule with a five-fold axis may sit only where the crystal offers nothing at all.

restriction · Local symmetry p4m: which distortions the atoms of each position can make. Every Wyckoff position of p4m, with the number of independent displacement patterns of each symmetry its atoms supply. A zero is a distortion those atoms cannot make however their amplitudes are chosen — an atom pinned at a rotation centre cannot move in a way that keeps less symmetry than the centre has. The row sums, weighted by the dimensions along the top, come to twice the number of atoms in the cell, which is the check that nothing has been lost. The last column is the number of free coordinates the position has, and it equals the multiplicity of the identity representation in that row: a displacement that keeps every symmetry is exactly a move of the position within its own Wyckoff set.

Which modes a site can carry

An atom on a mirror cannot move in a way that breaks the mirror while its images move with it: the displacements of a Wyckoff orbit carry a representation, and some of its pieces have multiplicity zero. The count of those pieces is a character, and the one that breaks nothing is the position's own freedom.

operations · Fundamental domain One orbit of p4m, two of p4. The general position of p4m — 8 points in a cell, all equivalent under that group — with each point coloured by which orbit of p4 it belongs to. Losing half the operations does not move a single point; it changes which of them are related, and the one orbit becomes 2. An atom sitting on this position in the parent becomes 2 crystallographically distinct atoms in the child, which may then be different elements, or move independently, or order.

What a position becomes on the way down

Cool a crystal through a transition and it loses operations. Nothing moves — and one crystallographic site becomes two, which is how an ordering transition finds somewhere to put a second kind of atom.

operations · Fundamental domain The table of marks of 4mm. Every conjugacy class of subgroup of 4mm, against every other. The entry is the number of cosets of the column's subgroup that the row's subgroup holds still. The first row is the identity, which fixes everything, so it is the size of each coset space; the last column is the whole group, whose only coset is fixed by everybody.

The table that decides every action

Burnside's lemma counts orbits and stops there — two completely different actions with the same orbit count are indistinguishable to it. The object that settles the whole question is a square table whose entries count fixed cosets: lower triangular because a subgroup fixes no coset of anything smaller, positive on the diagonal because it fixes its own, and therefore invertible. Inverting it turns a list of fixed-point counts back into the orbits themselves.

point-groups · Counting Five strains, and which of them move the atoms. A honeycomb of harmonic bonds, strained five ways, with the internal coordinate minimised at fixed cell each time. The shuffle is how far the second atom moves away from where the strain alone would have put it. Which strains produce one is decided before any energy is computed: a strain that leaves the site's three-fold axis intact forces the shuffle to vanish, because the only vector a three-fold rotation of the plane fixes is the zero vector. The prediction and the measurement are in adjacent columns.

The strain the atoms do not follow

The rule that makes an elastic constant computable — deform the cell and move every atom by the same map — is exact for a lattice with one atom in it and wrong for every other, and the reason is a site symmetry rather than a mechanical one. Which strains move the atoms inside the cell is decided by what survives of the site's own group, and a wrong answer here is a constant that is too stiff by a third.

point-groups · Properties 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 Seventy-two positions and the sets they fall into. Every plane group with the number of its Wyckoff positions, and the number of sets those positions fall into when the positions a normaliser exchanges are counted once: on the cell the group requires, on the most symmetric cell it may sit on, and under every change of basis carrying the group onto itself. 72 positions become 53 sets on the required cells and 51 on the best ones, and the last column never goes lower. The two groups a special cell changes are pmm and cmm.

The same site under two names

A structure report puts each atom on a Wyckoff position, and two correct reports of one crystal can name different positions. The positions that can trade places are exactly the ones the normaliser exchanges — and which those are depends on the cell as measured, not only on the group.

operations · Normalisers 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 p2's symmetries, sorted into classes by the group itself. A pattern with the symmetry of p2 over 2 by 2 cells, with its rotation centres and mirror lines marked in the International Tables' shapes and coloured by conjugacy class in the infinite group: two marks share a colour exactly when some operation of the group carries one element onto the other. Where rotations of several orders share a centre, the mark is the highest order's and so is its colour. Glides are not drawn. Classes counted: half-turns: 1 in the quotient, 4 in the group.

Two mirrors a coset cannot tell apart

Taken modulo its lattice a wallpaper group is finite, and its conjugacy classes are easy to list. But a coset holds every mirror of one direction at once, and the group itself keeps apart mirrors the list merges: pm has two classes of mirror, p2 four classes of half-turn, p3 six classes of rotation. Deciding which is which is Dehn's conjugacy problem, and for these groups it comes down to whether one vector lies in one lattice.

operations · What symmetry is 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 Every group a symmetric motif can lift a plane group to. The seventeen plane groups arranged by lattice, with an arrow from each group to every group a motif of higher symmetry, placed at some position, turns it into, on the generic lattice of the first. Dashed arrows mark the lifts that also halve the cell, two of which return the same type on the smaller cell. p1 lifts only to p2, the rectangular groups to pmm, pmg and cmm, the square ones to p4g and p4m, and p3 to four different groups. Three groups, outlined, cannot be lifted at all without a special metric: p2, pmm and p6m.

Where a symmetric motif lifts the group

A motif with more symmetry than its site asks for can raise the group of the whole pattern — or not, and which one is decided by the site, not the motif. The criterion is one line: a symmetry of the motif survives into the pattern exactly when it normalises the group. Run over every Wyckoff position of the seventeen, it finds twenty-nine of seventy-two where a motif can lift the group, general positions only in the four groups with a direction to slide along, two sites where the same motif gives different groups depending on how it is turned, and seven lifts between groups that halve the cell.

classification · Accidental symmetry Where the four-fold screws of one crystal cross a plane. A space group of the body-centred class I4/m that has a centre of symmetry, seen along the direction of its four-fold axes: the points where the special lines along that direction cross a plane, over four cells of the projection. A rod cut along the large filled lines is p4₃, a four-fold screw of one hand; along the other large lines, p4₁, its mirror image. The crystal's centre of symmetry carries each kind onto the other, so both are there and neither hand is favoured.

A crystal with no hand holds rods of both hands

Rolling a flat pattern into a tube reaches fifty-four of the seventy-five rod groups and never a screw that comes in a pair of hands. Cutting a column out of a crystal reaches all seventy-five. Sixteen of them are handed screws, and half of those can be cut from a crystal that has a centre of symmetry, from a line that happens to be a screw of one hand, with its mirror image a short distance away. A handed thread does not need a handed crystal, only a handed place in one.

space-groups · Chirality Every special position of the seventeen plane groups, with its regular subgroups. The 55 special Wyckoff positions of the seventeen plane groups, one chip each, labelled by site symmetry and points to a cell and carrying the number of subgroups that act on the position regularly. None is zero. 26 positions have one point to a cell and are reached by the lattice alone; 12 can be reached only by subgroups containing rotations; four, the positions of three points to a cell in p3m1, p31m, p6 and p6m, are reached by exactly one subgroup each.

No Petersen graph in the plane

A finite graph can look the same from every vertex and still be the picture of no group; the Petersen graph is the smallest that does. A periodic net in the plane cannot. Whether one is a Cayley graph depends only on where its vertices sit, and they sit on one of the fifty-five special positions of the seventeen plane groups or on a general one. Every one of the fifty-five has a subgroup that carries any of its points to any other in exactly one way, and four of them have exactly one.

operations · Presentations 1,694 positions, 1,182 sets on the general cell, and 1,128 on the best. Every affine type of space group by crystal system: its Wyckoff positions, the sets those fall into under the normaliser on the cell the group requires, on the best cell it may sit on, and under the whole affine normaliser. The total is 1694 positions, 1731 with enantiomorphs counted twice, 1182 sets on the general cell and 1128 on the best, which equals the affine 1128 in every system. The two columns differ only in the orthorhombic system and in one monoclinic type.

One cell reaches every Wyckoff set

In the plane, every identification the affine normaliser makes between two positions is made by an isometry of some cell, and the essay that found this warned against carrying it into space, where changes of basis can mix axes without limit. It carries. The 1,731 positions of the 230 groups were found from stabilisers and the sets from normalisers, and on one cell for each type the two partitions agree. Past the monoclinic system that is a one-line average. Below it, the infinite normaliser turns out to have nothing left to join.

operations · Normalisers Two positions in three can be lifted, and more than one in three can lose their cell. All 1694 Wyckoff positions of the 219 affine types by crystal system. On 1132 a motif with more symmetry than its site can raise the group of the crystal, and on 606 of those, across 126 types, some such motif makes the true cell smaller than the group's.

In space a motif can lift two positions in three

A molecule with more symmetry than its site can raise the group of the whole crystal, or not, and which one is decided by the site. In the plane twenty-nine positions of seventy-two allow it. In space it is 1,132 of 1,694, and 606 of them allow a lift that shrinks the cell, the case a structure solution meets as a warning. General positions can be lifted only in polar groups, as predicted, but eleven polar groups refuse: a mirror turns their screws over.

classification · Accidental symmetry

Named alongside it

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

Wyckoff positionsAverage structureDisorderOrbitSpecial positionStabiliserNormaliserOccupancyStructure factorSubgroupAccidental symmetryConjugacy class

All concepts