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 18 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

Every claim on this site is decided by integer arithmetic, so no threshold is ever chosen. 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

Named alongside it

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

OrbitStabiliserWyckoff positionsSpecial positionSubgroupAverage structureConjugacy classOccupancyConjugationDisorderMultiplicityNormaliser

All concepts