Jean-Guillaume Eon - UFRJ

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Jean-Guillaume Eon - UFRJ
ECM-23, 4-6 August 2006, Leuven Graph theory: fundamentals and applications to crystallographic and crystallochemical problems. The vector method Jean-Guillaume Eon - UFRJ

Summary Motivation Fundamentals of graph theory
Crystallographic nets and their quotient graphs Space group and isomorphism class Topological and geometric properties

Objectives Topology and Geometry: Description and Prevision of Crystal Structures Topological properties: Crystallographic Nets and Quotient Graphs Geometric properties: Crystal Structures as Embeddings of Crystallographic Nets

Crystal structures as topological objects

Example: ReO3 1-Complex = Embedding of the Crystallographic net

Graph theory (Harary 1972) A graph G(V, E, m) is defined by:
a set V of vertices, a set E of edges, an incidence function m from E to V2 u v w V = {u, v, w} E = {e1, e2, e3} e1 e2 e3 m (e1) = (u, v) m (e2) = (v, w) m (e3) = (w, u) e1 = uv e1-1 = vu

Simple graphs and multigraphs
loop Multiple edges Simple graph: graph without loops or multiple edges Multigraph: graph with multiple edges

Some elementary definitions
Order of G: |G| = number of vertices of G Size of G: ||G|| = number of edges of G Adjacency: binary relation between edges or vertices Incidence: binary relation between vertex and edge Degree of a vertex u: d(u) = number of incident edges to u (loops are counted twice) Regular graph of degree r: d(u) = r, for all u in V Adjacent vertices Adjacent edges Incidence relationship

Walks, paths and cycles Walk: alternate sequence of incident vertices and edges Closed walk: the last vertex is equal to the first = the last edge is adjacent to the first one Trail: a walk which traverses only once each edge Path: a walk which traverses only once each vertex Cycle: a closed path Forest: a graph without cycle

b.j.i.b.c walk a.b.j.i trail a.b.j.d path b.j.i.b.j.i closed walk b.j.d.e.f.g.h.i closed trail b.j.i cycle Edges only are enough to define the walk!

Nomenclature Pn path of n edges Cn cycle of n edges
Bn bouquet of n loops Kn complete graph of n vertices Kn(m) complete multigraph of n vertices with all edges of multiplicity m Kn1, n2, ... nr complete r-partite graph with r sets of ni vertices (i=1,..r)

P3 C5 B4

K4 K3(2) K2, 2, 2

Connectivity Connected graph: any two vertices can be linked by a walk
Point connectivity: κ(G), minimum number of vertices that must be withdrawn to get a disconnected graph Line connectivity: λ(G), minimum number of edges that must be withdrawn to get a disconnected graph

G κ(G) = 2 λ(G) = 3 Determine κ(G) and λ(G)

T1 T2 G = T1  T2 Subgraph of a graph
Component = maximum connected subgraph Tree = component of a forest T1 T2 G = T1  T2

Spanning graph = subgraph with the same vertex set as the main graph
T: spanning tree of G

Hamiltonian graph: graph with a spanning cycle
Show that K2, 2, 2 is a hamiltonian graph

Eulerian graph: graph with a closed trail “covering” all edges
Show that K2, 2, 2 is an Eulerian graph

Distances in a graph A---B|=3 |A---B|=4 d(A, B)=3
Length of a walk: ||W|| = number of edges of W Distance between two vertices A and B: d(A, B) length of a shortest path (= a geodesic) A---B|=3 B |A---B|=4 A d(A, B)=3

Morphisms of graphs A morphism between two graphs G(V, E, m) and G’(V’, E’ m’) is a pair of maps fV and fE between the vertex and edge sets that respect the adjacency relationships: for m (e) = (u, v) : m’ {f E (e)} = ( f V (u), f V (v)) or: f(uv) = f(u)f(v) Isomorphism of graphs: 1-1 and onto morphism

Example: an onto morphism in non-oriented graphs
w b e5 f e3 e2 a C3 u v e4 e1 f(u) = f(v) = a f(w) = b f(e1) = e f(e2) = f(e3) = e5 f(vw) = f(v)f(w)

Aut(G): group of automorphisms
Automorphism: isomorphism of a graph on itself. Aut(G): group of automorphisms by the usual law of composition, noted as a permutation of the (oriented) edges. v u w e1 e2 e3 C3 Generators for Aut(C3) order 6 (e1, e2, e3) order 3 (e1, e3-1) (e2, e2-1) order 2 {

Quotient graphs Let G(V, E, m) be a graph and R < Aut(G)
V/R = orbits [u]R of V by R E/R = orbits [uv]R of E by R G/R = G(V/R, E/R, m*) quotient graph, with m* ([uv]R) = ([u]R, [v]R) The quotient map: qR(x) = [x]R (for x in V or E), defines a graph homomorphism.

e3 e1 e2 u v w R: generated by (e1, e2, e3) ( noted R = <(e1, e2, e3)> ) C3 [u]R [e1]R B1 = C3/R qR

[e3]R e3 x w qR [x]R e4 e2 C4 [e2]R [u]R u v e1 [e1]R R = <(u, v)(x, w)> Find the quotient graph C4/R

Cycle and cocycle spaces on Z
0-chains: L0={∑λiui for ui  V and λi in Z} 1-chains: L1={∑λiei for ei  E and λi in Z} Boundary operator: ∂e = v – u for e = uv Coboundary operator: δu = ∑ei for all ei = uvi Cycle space: C = Ker(∂) (cycle-vector e : ∂e = 0) Cocycle space: C* = Im(δ) (cocycle-vector c = δu) dim(cycle space):  = ||G|| - |G| +1 (cyclomatic number)

Cycle and cocycle vectors
∂e1 = A - D 1 4 2 Cycle-vector: e1+e2-e3 Cocycle-vector: δA = -e1+e2+e4 C 6 5 D 3 B

Cycle and cut spaces on F2 = {0, 1} (non oriented graphs)
The cycle space is generated by the cycles of G Cut vector of G = edge set separating G in disconnected subgraphs The cut space is generated by δu (u in V)

u v w Find δ(u + v + w)

u v w δu

u v w

u v w δu + δv

u v w δu + δv

u v w

δu + δv + δw u v w

u v w

Complementarity: L1 = C  C*
Scalar product in L1: ei.ej = ij dim(C*) = |G|-1 dim(C) + dim(C*) = ||G|| C  C* u C6 C6 . u = 0

} Example: K2(3) e1 e2 A B e3 L1: e1, e2, e3 Natural basis (E)
C: e2 – e1, e3 – e2 Cycle-cocycle basis (CC) C*: e1 + e2 + e3 CC = M.E M =

Write the cycle-cocycle matrix for the graph below
e1 e4 e2 e3 B e5 C

Periodic graphs (G, T) is a periodic graph if:
G is simple and connected, T < Aut(G), is free abelian of rank n, T acts freely on G (no fixed point or edge), The number of (vertex and edge) orbits in G by T is finite.

Example: the square net
V = Z2 E = {pq | q-p = ± a, ± b} a = (1,0), b = (0,1) T = {tr: tr (p) = p+r, r in Z2}

Invariants in perodic graphs: 1. rings
Topological invariants are conserved by graph automorphisms A ring is a cycle that is not the sum of two smaller cycles A strong ring is a cycle that is not the sum of (an arbitrary number of) smaller cycles

Example 1: the square net
A cycle (with shortcuts) Sum of three strong rings A strong ring

Example 2: the cubic net Strong rings: Cz = ABCDA Cx = BEFCB
Cy = CFGDC B C G E F

A cycle that is not a ring: CBEFGDC = Cx + Cy
CF = shortcut G E F

A ring that is not a strong ring: ABEFGDA
= Cx + Cy + Cz A D B C No shortcut! G E F

Invariants in periodic graphs: 2. Infinite geodesic paths
Given a graph G, a geodesic L is an infinite, connected subgraph of degree 2, for which, given two arbitrary vertices A and B of L, the path AB in L is a geodesic path between A and B in G. L is a strong geodesic if the path AB in L is the unique geodesic between A and B in G.

Example 1: the square net
Yi Infinite path (shortcut) Geodesics Xj Strong geodesics

Example 2: the β-W net Strong geodesic
Are the following infinite paths geodesics or strong geodesics?

Strong geodesic

Geodesic

Example 3: the 34.6 net Not every periodic graph has strong geodesics!

Geodesic fiber 1-periodic subgraph F of a periodic graph G, such that:
for any pair of vertices x and y, F contains all geodesic lines xy of G, and F is minimal, in the sense that no subgraph satisfies the above conditions.

Example: the β-W net

The 34.6 net

Crystallographic nets
Crystallographic net: simple 3-connected graph whose automorphism group is isomorphic to a crystallographic space group. n-Dimensional crystallographic space group: a group Γ with a free abelian group T of rank n which is normal in Γ, has finite factor group Γ/T and whose centralizer coincides with T.

Local automorphisms Automorphism f with an upper bound b for the distance between a vertex and its image: d{u, f (u)} < b for all u The set L(N) of local automorphisms of an infinite graph N forms a normal subgroup of Aut(N) A net is a crystallographic net iff the group of local automorphisms L(N) is free abelian and admits a finite number of (vertex and edge) orbits

Automorphisms and geodesics
Graph automorphisms map (strong) geodesics on (strong) geodesics. A strong geodesic is said to be along f if it is invariant by the local automorphism f. Two strong geodesics are parallel if they are invariant by the same local automorphism. Local automorphisms map strong geodesics on parallel ones.

Example: the square net
T={ti,j: ti,j (m, n) = (m+i, n+j)} : T  L(N) Y0 Yi Y0 invariant by t0,1 as Yi Xj X0 invariant by t1,0 as Xj (i, j)  fixes X0 and Y0  fixes the whole net L(N) = T X0 (0,0) Conversely: Let f be any local automorphism with f(0,0) = (i,j); then, we will see that   ti, j-1. f = 1

Example: the square net
Simple, 4-connected L(N) = T free abelian One vertex orbit Two edge orbits Every automorphism of the infinite graph can be associated to an isometry of the plane Crystallographic net

Quotient graph of a periodic graph: the square net
Q = G/T, T translation subgroup T of the automorphism group

Example: the β-W net at bt ct t in Z2, i=(1,0), j=(0,1)
V = {at , bt , ct} E = {atbt , atct , btct , atbt+j , atct+j , ctbt+i} at bt ct Show that β-W is a crystallographic net and Find its quotient graph

β-W net: quotient graph
c b

ReO3: vertex and edge lattices

Quotient graph: ReO3 K1,3(2)

Simple structure types

Symmetry : Space group of the crystal structure
T: Normal subgroup of translations /T: Factor group Aut(G): Group of automorphism of the quotient graph G /T is isomorphic to a subgroup of Aut(G)

ReO3: /T  Aut(G)  m3m C4 Rotation: (e1, e3, e2, e4)
C3 Rotation: (e1, e3, e5) (e2, e4, e6) Mirror: (e1, e2)

Drawbacks of the quotient graph
Non-isomorphic nets can have isomorphic quotient graphs Different 1-complexes with isomorphic nets can have non-isomorphic quotient graphs Different 1-complexes can have both isomorphic nets and isomorphic quotient graph!

Different nets with isomorphic quotient graphs

Vector method: the labeled quotient graph as a voltage graph

β-W net: Find the labeled quotient graph
C 10 01 at bt ct t in Z2, i=(1,0), j=(0,1) V = {at , bt , ct} E = {atbt , atct , btct , atbt+j , atct+j , ctbt+i}

The minimal net Translation subgroup isomorphic to the cycle space of the quotient graph G (dimension equal to the cyclomatic number) Factor group: isomorphic to Aut(G) Unique embedding of maximum symmetry: the archetype (barycentric embedding for stable nets)

Example 1: graphite layer - K2(3)
B e1 2 a b e2 3 e3 1-chain space: 3-dimensional Two independent cycles: a = e1-e2, b = e2-e3 One independent cocycle vector: e1+ e2+e3

p6mm 1 Generators of Aut[K2(3)]: (e1, e2, e3) (ei , -ei)(A, B)
(e1, -e3)(e2, -e2)(A, B) A B 2 3 Linear operations in the cycle space (point symmetry): (a, b) = (e1 – e2, e2 – e3) → (e2 – e3, e3 – e1) = (b, - a - b) In matrix form: γ{(e1, e2, e3)} = p6mm γ{(e1, -e3)( e2, -e2)} = γ{(ei, -ei)} =

Embedding in E3 Inversion of the cycle-cocycle Matrix a = e1 – e2
b = e2 – e3 c = e1 + e2 + e3 a e1 b = x e2 c e3 e a e2 = 1/ x b e c Barycentric embedding: c = 0 e1 = 1/3 (2a + b) e2 = 1/3 (-a + b) e3 = 1/3 (-a – 2b)

Atomic positions p6mm Generator 0 -1 -1 0 0 1 1 -1 0 -1 1 0
Translation ( ) ( ) ( ) A: x + T B: x + e1 + T A: 2a/3 + b/3 + T B: a/3 + 2b/3 + T After inversion: A → -x + T = B = x + 2a/3 + b/3 + T -2x = 2a/3 + b/3 + T With t = b , x = -a/3 -2b/3 = 2a/3 + b/3

Example 2: hyper-quartz
Archetype: 4-dimensional Tetrahedral coordenation Cubic-orthogonal family: (e1-e4), (e2-e5), (e3-e6), ∑ei Lengths: √2, √2, √2, √6 Space group: 25/08/03/003 1 3 4 6 5 2

Nets as quotients of the minimal net
100 a b 010 N/<111> N (T = Z3) 001 <111> = translation subgroup generated by 111 N/<111>: T = <{100, 010}>

(Periodic) voltage net
 = 1 1 1 010 100 a b

Embeddings as projections of the archetype
3-d archetype, 2-d structures: 1-d kernel 1 4 2 3-cycle: 3.92, 93 C 6 5 4-cycle: 4.82 D 3 B

Check the space group of 4.82
Kernel: c = e4 + e6 + e3 – e2 A Generators: (e4,e6,e3,-e2)(e1,-e5,-e1,e5)(A,B,C,D) (e4,-e6)(e2,e3)(e1,-e1)(A,C) 1 4 2 Cycle basis: a = e1 + e4 + e5 – e3 b = e1 + e2 - e5 + e6 Notice: a ┴ b ┴ c B 6 5 C D 3

Point symmetry (a, b) → (-e5 + e6 + e1 + e2, -e5 – e4 – e1 + e3) = (b, -a) (a, b) → (-e1 – e6 + e5 – e2, -e1 + e3 - e5 – e4) = (-b, -a) p4mm Generator Translation ( ) ( ) e e e e2 Walk: A → B → C → D → A Final translation : c = 0

Find the space group of quartz
a = 1000 = e1 - e4 b = 0100 = e2 - e5 c = 0010 = e3 - e6 d = 0001 = e4 + e5 + e6 1 3 4 6 Hyper quartz = N[K3(2)] Quartz = N[K3(2)]/<1110> 5 B C 2

Point symmetry Generators:  (1,4)(2,5)(3,6) order 2
 (1,2,3)(4,5,6)(A,B,C) order 3  (1,6)(2,5)(3,4)(B,C) order 2 (e1 + e2 + e3 - e4 - e5 - e6 = 0 ) Basis: (a, b, d) order 12 : (a, b, d) (-a, -b, d) C2 rotation  d : (a, b, d)  (b, -a-b, d) C3 rotation  d : (a, b, d)  (-a-b, b, -d) C2 rotation  d C6 rotation

Translation part Associated to the C3 rotation: Walk: A → B → C → A
Final translation : e1+e2+e3 = d  or 62 e e e3 For  and , t=0 (fixed points)  P6222

Isomorphism class of a net
b b a b Find the labeled quotient graph for the double cell

Isomorphism class of a net
Kernel: e1-e2 b b : (e1, e2)(e3, e4) 3 1 2 Automorphisms  of the quotient graph G, which leave the quotient group of the cycle space by its kernel invariant, can be used to extend the translation group if they act freely: t(o.q-1o [W]) = o.q-1o [.(W)] , where δ is a path in G from O to (O)

Isomorphism class of a net
t(o. q-1o [W]) = o.q-1o [.(W)] t: new translation o: arbitrary origin in N : boundary operator q: N  G = N/T W: walk in G starting at O=q(o) q-1o [W]: walk in N starting at o and projecting on W o. q-1o [W]: defines a vertex of N δ: a fixed, arbitrary path in G from O to (O) : (extension) automorphism of the quotient graph G W = OO (path nul): t(o) = o.q-1o []

Isomorphism class of a net
t(o. q-1o [W]) = o.q-1o [.(W)] 4, a Kernel: e1-e2 b b Extension by  = (e1, e2)(e3, e4) A B 3 1 2 a b a b t: {e1, e2} {e3, e4} b t ? t2 = a {A, B} With o in q-1(A) and  = e3 : t (o) = o.q-1o [e3] t 2 (o) = t (o.q-1o [e3]) = o.q-1o [e3.(e3)] = o.q-1o [e3.e4] = a(o)

Show that cristobalite has the diamond net
{A,D} {B,C} {1,8} {2,7}, 100 e1 e8 e7 e6 e5 e4 e3 e2 A C B D {4,5}, k {3,6}, l 100 010 010 Kernel: e2 – e1 = e7 – e8 e3 – e4 = e6 – e5 101 (1,8)(2,7)(3,6)(4,5)(A,D)(B,C) 001 e8 – e4 + e1 – e5 = 001 → e1 – e5 + e8 – e4 = 001 2k = e4 – e8 + e5 – e1 = {3,6}-{4,5} =  l = k

Non-crystallographic nets
σ b T = <t: t (xm) = xm+1 , x = a, b> Local automorphisms = T x {I, σ} : abelian but not free! e t t σ: (e, -e) A B

Non-crystallographic nets
σ b T’ = <t’: t’ (am) = bm+1 , t (bm) = am+1 > Local automorphisms = T’ x {I, σ} t’ -t’

tfc and derived nets A 100 010 B C 001

tfc/<(001)> A 10 01 B C

tfc / < (001), (110) > b0 c0 A B C T
Local automorphisms = not abelian But : (b0, c0) ↔ (b, c) 1 1 The 1-periodic graph is a geodesic fiber B C

Projection of a geodesic fiber on the quotient graph: the β-W net
G/T F 01 01 at bt ct B C 10 01 F/<01> is a subgraph of G/T

The 34.6 net (G/T = K6) G 21 G 10 10 10 11 21 10 (Counterclockwise
-1 0 (Counterclockwise oriented cycles)

b a c d Determine the quotient graph G/T of the 32.4.3.4 net,
list all the cycles of G/T; find the strong geodesic lines of and its geodesic fibers.

2-cycles AB, CD: 10 AD, BC: 01 10 B disjoint cycles A 10 01 tangent cycles 3-cycles ABC: 00, 01, 11, 10 ABD: 00, 01, -1 0, -1 1 ACD: 00, -1 0, 0 -1, BCD: 00, 0 -1, 1 -1, 10 01 01 C D 10 4-cycles ABCD: 00, 01, 10, 11, 1 -1 ABDC: 01, 11, -1 1 ADBC: 1 -1, 10, 11 Strong geodesic lines: 10, 01 Geodesic fibers: 11, -1 1

10 B A b a c d C D 10 G 10

B A b 10 a 01 01 01 c d C D G 11

A b a 11 B c d C D G 11

Geodesic fibers and local automorphisms
Local automorphisms send geodesic fibers to parallel geodesic fibers. The absence, in 2-connected labeled quotient graphs, of automorphism that leave unchanged the vector labels of any loop or cycle ensures the derived graph is a crystallographic net.

Cycle figure Def: vector star in the direction of geodesic fibers 01
11 10 -1 0 10 0 -1 Graphite layer -1 -1 0 -1 Def: vector star in the direction of geodesic fibers

Topological density ρ = lim ∑k=1,r Ck / rn Ck: kth coordination number
n : dimension of the net r→∞ ρ = Z.{Σσ f(σ)}/ n! Z : order of the quotient graph f(σ) : frequency of the face σ of the cycles figure = inverse product of the lengths of the vertices of the face of the cycles figure

Topological density: graphite layer
01 11 f(σ1) = 1/(2.2) σ1 -1 0 10 ρ = Z.{Σσ f(σ)}/ n! ρ = 2.6.(2.2)-1/2! = 3/2 -1 -1 0 -1

Topological density: net 32.4.3.4
01 -1 1 11 3-cycle -1 0 10 2-cycle ρ = 4.8.(2.3)-1/2! = 8/3 -1 -1 1 -1 0 -1

Find the topological density the β-W net
10 01 0 -1 11 -1 1 -1 -1 1 -1 3-cycle 2-cycle 01 01 B C 10 ρ = 3.8.(2.3)-1/2! = 2

Plane nets A B C Embedding of the quotient graph in the torus
10 01 b b B C a Embedding of the quotient graph in the torus Face boundaries project on oriented trails of the quotient graph

Oriented trails are based on oriented edges
c c10 B C a0-1 a1-1 A b1-1 e1, 10 e2, 01 B C

K4 revisited 3.92, 93 4.82 Two classes of trails: 3-cycles and 4-cycles

A plane net from K3, 3 4.102, 42.10 Kernel : two tangent 4-cycles b a
Cyclomatic number: υ = 9 – = 4 4.102, 42.10 Kernel : two tangent 4-cycles

Topological invariants of nets in projection on the quotient graph
Strong geodesic Geodesic fiber Strong ring Shorter isolated cycle Connected subgraph of shorter cycles (of equal length) with equal or opposite net voltages Set of edge-disjoint cycles with nul net voltage

Non-ambiently isotopic embeddings of the same net
ThSi2 SrSi2

Self-interpenetrated ThSi2

Self-interpenetrated SrSi2

Some references Beukemann A., Klee W.E., Z. Krist. 201, 37-51 (1992)
Carlucci L., Ciani G., Proserpio D.M., Coord. Chem. Rev. 246, (2003) Chung S.J., Hahn Th., Klee W.E., Acta Cryst. A40, (1984) Delgado-Friedrichs O., Lecture Notes Comp. Sci. 2912, (2004) Delgado-Friedrichs O., O´Keeffe M., Acta Cryst. A59, (2003) Blatov V.A., Acta. Cryst. A56, (2000) Eon J.-G., J. Solid State Chem. 138, (1998) Eon J.-G., J. Solid State Chem. 147, (1999) Eon J.-G., Acta Cryst. A58, (2002) Eon J.-G., Acta Cryst, A60, 7-18 (2004) Eon J.-G., Acta Cryst A61, (2005) Harary F., Graph Theory, Addison-Wesley (1972) Klee W.E., Cryst. Res. Technol., 39(11), (2004) Klein H.-J., Mathematical Modeling and Scientific Computing, 6, (1996) Schwarzenberger R.L.E., N-dimensional crystallography, Pitman, London (1980) Gross J.L, Tucker T.W., Topological Graph Theory, Dover (2001)