INTERNATIONAL SCHOOL

ON FUNDAMENTAL
CRYSTALLOGRAPHY

jueves 6 de diciembre de 12

CRYSTAL-STRUCTURE
TOOLS
BILBAO CRYSTALLOGRAPHIC SERVER
PRACTICAL EXERCISES

Mois I. Aroyo
Universidad del Pais Vasco, Bilbao, Spain

jueves 6 de diciembre de 12

Bilbao Crystallographic Server

http://www.cryst.ehu.es
STRUCTURE UTILITIES

jueves 6 de diciembre de 12

Bilbao Crystallographic Server

http://www.cryst.ehu.es

Structure Data for the Exercises:

http://www.cryst.ehu.es/resources/uberlandia2012

jueves 6 de diciembre de 12

CRYSTAL-STRUCTURE
DESCRIPTIONS
Conventional and ITA settings
of space groups
Non-conventional settings of
space groups
Equivalent structure
descriptions
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Crystal Structure Descriptions

Inorganic
Crystal
Structure
Database

Bilbao
Crystallographic
Server
jueves 6 de diciembre de 12

# Space Group ITA number

141
# Lattice parameters
6.6164 6.6164 6.0150 90 90 90
# Number of independent atoms in the asymmetric unit
3
# [atom type] [number] [WP] [x] [y] [z]
Zr 1 4a 0 0.75 0.125
Si 1 4b 0 0.75 0.625
O 1 16h 0 0.067 0.198

notation

&
transformation (affine transformation) of th
r& " x& a& ( y& bThe
( z&general
c& "
coordinate
system
consists of two parts, a linear part and a sh
are written in the following
Problem:
BASIS
TRANSFORMATION
n this section, the relations
between
the The
primed
and
unprimed
of origin.
!COORDINATE
3$ matrix
P of
the linear part and the #3 !
5.1. TRANSFORMATIONS
OF #3
THE
SYSTEM
uantities are treated.
column matrix p,
containing the components of the shift vector
P ! Q"1 :
transformation uniquely.
It$is represented
by the symb
The general transformation define
(affinethetransformation)
of
the
!
!
$
(a,
b,
c),
origin
O:
y,
z)
'point X(x,
'#
a
a
p). a linear part and a shift '
oordinate system consists of two(P,parts,
# b & ! P # b'# &!
ftors
origin.
The #3
! 3$ matrix P of the
linear
partpart
and implies
the(P,
#3p!
1$ c' of orientation
of direct
space
(i) The
linear
a)change
or length
c'#
olumn
p, containing
of the
shift a,
vector
dices ofmatrix
a plane
(or a set ofthe components
both of the basis
vectors
b, c, p,
i.e.
efine
the transformation
uniquely. It is represented
the
transformation
rules apply also to the quantities
!& These
!by
! symbol
! covarian
! !
ect space
or the coordinates
&
&
' ' '
(a
,
b
,
c
),
origin
O:
point
X(x
,
y
,
z
with
respect
to
the
basis
vectors
a
,
b
,
c
and
contravariant
wit
#a
b
,
c
$
"
#a,
b,
c$P
P,reciprocal
p).
space
respect to a, b, c, which are
# written as column matrices.
& They are th
indices ofora direction
in
direct
are transforme
P12[uvw],Pwhich
P11space,
13
(i)
The
linear
part
implies
a
change
of
orientation
length
or
5.1.3.1. General affine transformation, consisting of a shift of origin by
rices:
$
'
#
om Oof
to Othe
by abasis
shift vector
p with components
p1i.e.
and p2 and
a change
oth
vectors
a,
b,
c,
(i)
linear
part:
change
of
orientation
or
length
" #a, b, c$!
% P$
21 P!22 $P23 (
#
#
basis
from
a,
b
to
a
,
b
.
This
implies
a
change
in
the
coordinates
of
es of a point in# direct
space
#
u
u
#
e point X from x, y to& x , &y . &
# &
# vP
#a , b , space
c $ " #a, b, c$P
31 ! QP#32v &P
! 33
tors of reciprocal
#
&
w
w#
"
#P
a
(
P
b
(
P
flso,
a direction
in
direct
space
11
21
31 c,
P12 P13
11 are
the inverse matrices of P and p are needed.PThey
$
' to allPquantities
nts of a shift vector from
In contrast
mentioned
above,
the components of
"1
a
(
P
b
(
P
c,
12
22
32
Q
!
P
P
P
P
"
#a,
b,
c$
% 21
22
23 ( vector r or the coordinates of a point X in direct spac
position
he new origin O &
x, y, z depend also
ona the
shift
of(the
origin
in direct space. Th
P
(
P
b
P
c$"
13
23
33
P
P
P
31
32
33
nts of an inverse origin
general
(affine) transformation is given by
"1
&
p!
! "P
igin O to originqO,
with
! $
! #$
the
shift vector p is zero and th
" #P11 a (For
P21ab pure
( P31linear
c, transformation,
x
x
matrix q consists of(ii)
the origin
components
of theby
negative
shiftis
vector
shift
a shift
vector
symbol
(P, o).p(p1,p2,p
" %
"3):
%
#
# #
# y # & ! Q# y & $ q
hich refer to the coordinate system a P
, b12, a
c ,(
i.e.P22 b ( P32 c,
n part of a symmetry
The determinant of P, det#P$,
should be positive. If det#P$
#
#
#
#
z
z
q ! q1 a $ q2 b $ q3 c ! negative, a right-handed coordinate
in direct space
into
$
P13 a ( P23 b ( P33the
c$" origin O has ! system is transformed
Q11 x $ Q
$the
Q13 znew
$ q1 basis vecto
12 y
one
"
0,
s,d the
(Q, O
q) is =
the inverse
transformation
of (or vice versa). If det#P$
O
p#
#4 transformation
! 1$ column
matrix
of # +#left-handed
%
coordinates (p1!,p"
2,p
3)x in
Q
$
Q
y
$
Q
z
$
q
p).
Applying
(Q,
q)
to
the
basis
vectors
a
,
b
,
c
and
the
origin
#
23
2 &!coordina
or
aofpure
linear
transformation,
the shift
vector
p is zero
are
linearly
dependent
andanddothe
not21form22 a complete
es
a
point
in
direct
space
he old basis vectors a, b, c with origin O are obtained.
the old coordinateQsystem
31 x $ Q32 y $ Q33 z $ q3
#
#
system.
ymbol is (P, o).

or a two-dimensional transformation of a and b , some

jueves 6 de diciembre de 12

fromthe
O tocomponents
O by a shift of
vector
In contrast to all quantities mentioned above,
a p with components p1 and p2 and a c
basisXfrom
a, b to space
a# , b# . This implies a change in the coordin
position vector r or the coordinates of a ofpoint
in direct
the point
X from
x, y atoThe
x# , y# . X(x,y,z):
x, y, z depend
also on the shift of
of the
the origin
in direct
space.
Transformation
coordinates
of
point
general (affine) transformation is given by Also, the inverse matrices of P and p are needed. They
"1
! $
! #$
Q
!
P
Also, the inverse matrices of P and p are needed. They ar
x
x
" %
" #%
"1
and
$
q
!
Q
y
y
Q
!
P
with
#
&
# &
"1
z
z#
p!
q
!
"P
and
!
$
Q11 x $ Q12 y $ Q13 z $ q1
"1
The
matrix
q
consists
of
the
components
p! of the negative sh
q
!
"P
"
%
#
# #
! # Q21 x $ Q22 y $qQwhich
23 z $ qrefer
2 &! to the coordinate system a , b , c , i.e.
The matrix q consists of the components of the negative shift
Q31 x $ Q32 y $qQwhich
q3 to the coordinate
# q# c# !#
33 z $ refer
q ! q a#system
$ q b#a$
, b , c , i.e.
1

Example

#
#
#
q
!
q
a
$
q
b
$
q
c
!
Thus, the transformation 1(Q, q)2 is the3 inverse
transform

#
# #
(P,
p).
Applying
(Q,
q)
to
the
basis
vectors
a
,
b
, c and t
Transformation
operations
thethetransformation
is the inverse transformati
If no shift of origin
is applied, i.e. p of
!Thus,
q#symmetry
! o,
position
vector(Q, q)(W,w):
theApplying
old basis(Q,
vectors
c with
origin
obtaine
O , p).
(P,
q) to a,
theb,basis
vectors
a# , O
b# ,are
c# and
the
r of point X is transformed by
#
# For a two-dimensional transformation of a and
, the-1old
basis
vectors a, b, c with origin O are obtained.
O
! $
!
$
elements
set as follows:
For a two-dimensional
of a# andQ33b# ,!
x
x# of Q are transformation
Q#13
0. as follows: Q33 ! 1
# &Q31
23 y!
32 ! set
elements
of
are
r# ! %a, b, c&PQ# y & ! %a
, b#!
, c#Q
&#
! Q! Q
which transform in the same way as
Q13The
! Qquantities
23 !
z
z# Q31 ! Q32 ! 0.
vectors
a, b,metric
c arewhich
called
covariant
areaswritt
Transformation
of quantities
the
tensor
G: inquantities
The
transform
the sameand
way
the
matrices.
They
vectors
a, b,
c areare:
called covariant quantities and are written a
#
In this case, r ! r , i.e. the position vector is invariant, although
Theyindices
are:
T Miller
a plane (or a set of planes), (hkl),
the basis vectors and the components matrices.
arethe
transformed.
For a of
pure
#
shift of origin, i.e. P ! Q ! I, the transformed
position
vector
the
Miller
indices
of a rplane
(or a set of planes), (hkl), in
space
and
becomes
space and
the coordinates of a point in reciprocal space, h, k, l.
jueves 6 de diciembre de 12

(W,w)=(P,p) (W,w)(P,p)

G=P (G)P

Bilbao Crystallographic Server

Problem: ITA SETTINGS STRUCTURE

DESCRIPTIONS

SETSTRU

ITA-settings for the space group C2/c (No.15)

initial setting
structure description
Xf=(P,p)-1Xi

final setting
structure description
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EXERCISES

Problem 3.1

Compare the two structure descriptions and check if they

belong to the same structure type.

origin choice 2
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origin choice 1

EXERCISES

Problem 3.1

Structure 1: Space group I41/amd (141) a=6.60

A c=5.88
A
origin choice 1 at
4m2
A
A c=6.015
Structure 2: Space group I41/amd (141) a=6.616
4m2
origin choice 2 at 2/m at 0,-1/4,1/8 from

Compare the two structure descriptions and check if they

belong to the same structure type.
Use the tools of Bilbao Crystallographic server: SETSTRU
Hint: In order to compare the different data, the parameters of

Structure 1 are to be transformed to origin at center 2/m,

i. e. ORIGIN CHOICE 2.

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Problem 3.1

SOLUTION

Structure tools: SETSTRU

Origin 2 description

x = x - p

the rest of oxygen atoms

0, 0.067, 0.198
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Bilbao Crystallographic Server

Problem: UNIT CELL

TRANSFORMATION

CELLTRAN

lattice parameters
hexagonal cell

G=PTGP

lattice parameters
monoclinic cell
jueves 6 de diciembre de 12

(P,p) Transformation
matrix

Bilbao Crystallographic Server

Problem: STRUCTURE

TRANSTRU
TRANSFORMATION

asymmetric
unit

subgroup
basis
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default
settings

arbitrary
transformation

Bilbao Crystallographic Server

Example TRANSTRU: Pb3(VO4)2

Description
R-3m (166)

Validity (P,p)
(P,p)
WP
splittings

Description
P21/c (14)
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Example TRANSTRU: Pb3(VO4)2

R-3m
structure
(P,p)
P21/c
structure

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Pb1(3a) Pb2(6c) PV(6c) O1(6c) O2(18h)

WP
splitting
Pb1(2a) Pb2(4e) PV(4e) O1(4e) O21(4e) O22(4e)

EXERCISES

Problem 3.1(cont.)

Apply the program TRANSTRU in order to check

if the two structure descriptions belong to the same
structure type.
A c=5.88
Structure 1: Space group I41/amd (141) a=6.60
A
origin choice 1 at
4m2
A
A c=6.015
Structure 2: Space group I41/amd (141) a=6.616
origin choice 2 at 2/m at 0,-1/4,1/8 from
4m2

Coordinate
Origin choice 2
transformation

p=0,1/4,-1/8

jueves 6 de diciembre de 12

Origin choice 1

Problem: EQUIVALENT

EQUIVSTRU
DESCRIPTIONS

CsCl
Pm-3m (221)

1a (0,0,0)

1b (1/2,1/2,1/2)

1b (1/2,1/2,1/2)

1a (0,0,0)

How to find all possible equivalent

descriptions of a crystal structure?
Number of equivalent descriptions= |N(G)|/|G|
index of the group in its Euclidean normalizer
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Problem 3.2a

Bilbao Crystallographic Server

Equivalent descriptions: CsCl

EQUIVSTRU

space group in
default setting

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Example EQUIVSTRU: CsCl

jueves 6 de diciembre de 12

Symmetry-equivalent
Wyckoff positions

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WYCKOFF SETS

EXERCISES
Problem 3.2b

Equivalent structure
descriptions
Space group: P4/n

N(P4/n) = P4/mmm (a,b,1/2c)

a=1/2(a-b), b=1/2(a+b)
jueves 6 de diciembre de 12

EXERCISES

Problem 3.3
EQUIVSTRU

KAsF6

BaIrF6

BaSnF6

Space-group symmetry: R-3

Euclidean normalizer: R-3m(-a,-b, 1/2c)
Coset representatives: x,y,z; x,y,z+1/2; -y,-x,z; -y,-x,z+1/2;
jueves 6 de diciembre de 12

Structure tools: EQUIVSTRU

SOLUTION
KAsF6

BaIrF6

-y,-x,z

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BaSnF6

SOLUTION
KAsF6

Structure tools: EQUIVSTRU

BaIrF6

BaSnF6

x,y,z+1/2

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CRYSTAL-STRUCTURE
RELATIONSHIPS
Comparison of crystal
structures
Phase transitions
Symmetry relations between
crystal structures
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Crystal-structure relationships

COMPARISON OF
CRYSTAL STRUCTURES

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Different descriptions of
the same structure
PROBLEM:

Two descriptions of the same structure with respect to the

same space group, specified by unit-cell parameters and
atomic coordinates data.
Search for a mapping of the two descriptions such that the
global distortion accompanying the mapping is tolerably small.

symmetry
controlled
mapping

standard

most similar
configuration

(Description 2)1

Description 2

global
distortion of
the mapping

affine
normalizer

standard

Lattice deformation
Atomic displacement
field

COMPSTRU
jueves 6 de diciembre de 12

Description 1

standard

Problem: Similarity of the descriptions

Description 1

a1,b1,c1
(x1,y1,z1)

How to measure the similarity

between two descriptions ?

degree of lattice
distortion

average atomic
displacements

maximal atomic
displacements
jueves 6 de diciembre de 12

S=

dav

sX
1

1
=
n

2
i

sX

Description 2

a2,b2,c2
(x2,y2,z2)

i-eigenvalues of
the Lagrangian
strain tensor

mi u2i

maximal displacements of
the paired atoms

ui-atomic

displacements

Problem: Similarity of the descriptions

Description 1

a1,b1,c1
(x1,y1,z1)

How to measure the similarity

between two descriptions ?

Description 2

a2,b2,c2
(x2,y2,z2)

Bergerhoff et al. Acta Cryst.(1999), B55, 147

structural
descriptor

weighted mean
difference between
atomic coordinates
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relation between
axial ratios

Problem: COMPARISON OF
STRUCTURES

structure 1

default
settings

structure 2

tolerances
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COMPSTRU

Example COMPSTRU: Pb3(PO4)2

affine
normalizer

structural
descriptor

= 0.066

maximal
displacement
dmax=0.34
jueves 6 de diciembre de 12

Problem: COMPARISON OF
STRUCTURE
DESCRIPTIONS

COMPSTRU

Problem 3.4
In ICSD can be found several structure data sets
of -Fe2O3, all of them of symmetry Pna21(No.33).
Compare the following two descriptions and
check if they belong to the same structure type.

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Problem 3.4

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ICSD data for -Fe2O3,

Isoconfigurational
Problem: Structure Types

COMPSTRU

Lima-de Faria et al. Acta Cryst.(1990), A46, 1

Isoconfigurational
structure types

Isopointal
structure types

Isopointal
similar

Space group
Wyckoff position
sequence
Pearson symbol

Allmann, Hinek. Acta Cryst.(2007), A63, 412

Inorganic Crystal Structure Database (2009)
http://icsdweb.fiz-karlsruhe.de

isoconfigurational
structure types?
jueves 6 de diciembre de 12

Crystallographic orbits
Geometrical interrelationships

Composition type
(ANX formula)
Range of c/a ratio
-range
Atomic coordinates
Chemical properties

Isoconfigurational Structure Types

(configurationally isotypic)
PROBLEM:

Consider two isopointal structures specified by their spacegroup symmetry, unit-cell parameters and atomic
coordinates data.
We search for a mapping of the two structures such that
the global distortion accompanying the mapping is tolerably
small.
symmetry
controlled
mapping

most similar
configuration

global
distortion of
the mapping

(Structure 2)1

Structure 2

atomic species standard

standard correspondence
scheme

Lattice deformation
Atomic displacement
field

COMPSTRU
jueves 6 de diciembre de 12

Structure 1

standard

Isoconfigurational
Problem: Structure Types
Structure1
a1,b1,c1
(x1,x2,x3)

COMPSTRU

How to measure the similarity

between two isopointal structures ?

isoconfigurational

degree of lattice
distortion
average atomic
displacements

S=

dav

sX
1

1
=
n

2
i

sX

mi u2i

Structure2
a2,b2,c2
(y1,y2,y3)

i-eigenvalues of
the Lagrangian
strain tensor

ui-atomic

displacements

structural
descriptor
Bergerhoff et al. Acta Cryst.(1999), B55, 147
jueves 6 de diciembre de 12

Problem: Isoconfigurational
StructureTypes
EXERCISES

COMPSTRU

Problem 3.3(cont.)

Do these compounds belong to the

same structure type ?
KAsF6

BaIrF6

BaSnF6

Koch, Fischer. MathCryst Satell., ECM22, Budapest 2004

jueves 6 de diciembre de 12

COMPSTRU
Problem 3.3

structure 1

default
settings

structure 2
tolerances
jueves 6 de diciembre de 12

SOLUTION

Problem 3.3

COMPSTRU

SOLUTION

option 1
correspondence
scheme proposed
by the program

option 2
correspondence
scheme based on
Wyckoff sets

jueves 6 de diciembre de 12

Problem 3.3
KAsF6

SOLUTION

COMPSTRU

BaIrF6

affine
normalizer

structural
descriptor

= 0.051
maximal
displacement
dmax=0.27

jueves 6 de diciembre de 12

Example:

STRUCTURE TYPES

COMPSTRU

STUDY OF THE FAMILY ABF6

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Example:

STRUCTURE TYPES

COMPSTRU

STUDY OF THE FAMILY ABF6

Reference structure:
CaCrF6
maximal
distance []

MnPtF6

0.1282

NiPtF6

0.1802

NiRhF6

Type: LiSbF6
jueves 6 de diciembre de 12

Type: KOsF6

0.2005

CsBrF6

CsUF6

BrIrF6

1.0731

1.1397

1.4067

STUDY OF THE FAMILY ABX3

R-3 (148);WP sequence: fc2; Pearson: hR10

ICSD (c/a)
FeTiO3
FePSe3
jueves 6 de diciembre de 12

Bergerhoff
(structure descriptor)

Bilbao Server
(global distortion)

0.3 FeTiO3 (NaSbO3)

0.4 FePSe3

Crystal-structure relationships

STRUCTURAL PHASE
TRANSITIONS

jueves 6 de diciembre de 12

Structure Relationships
PROBLEM:

Highsymmetry
phase

Consider two phases of the same compound (specified by

their unit-cell parameters and atomic coordinates) with
group-subgroup related symmetry groups G>H
Search for a mapping of the two structures such that the
global distortion accompanying the mapping is tolerably small.
symmetry
controlled
mapping

most similar
configuration

affine
transformation

(High-symmetry
phase)Low

G> H
relationship
Wyckoff positions
schemes

(G)H

global
distortion of
the mapping
Lattice deformation
Atomic displacement
field

STRUCTURE RELATIONS
jueves 6 de diciembre de 12

Lowsymmetry
phase

Given the high- and low-symmetry phases:

1. Characterize the symmetry reduction between
the high- and low-symmetry phases
-index of the group-subgroup pair: INDEX
-group-subgroup graph, (P,p): SUBGROUPGRAPH
2. Domain-structure analysis
3. Determine the so-called reference structure, i.e.
high-symmetry structure in the low-symmetry basis
-lattice parameters: CELLTRANS
-atomic coordinates: TRANSTRU or WYCKSPLIT
4. Evaluate the lattice strain and the atomic
displacements accompanying the phase transitions:
STRAIN, COMPSTRU
jueves 6 de diciembre de 12

Problem 3.5

Cristobalite phase transitions

At low temperatures, the space-group symmetry of cristobalite is

given by the space group is P41212 (92) with lattice parameters
a=4.9586, c=6.9074. The four silicon atoms are located in Wyckoff
position 4(a) ..2 with the coordinates x, x, 0; -x, -x, 1/2; 1/2-x,1/2+x,
1/4; 1/2+x,1/2-x,3/4, x = 0.3028.
During the phase transition, the tetragonal structure is transformed
into a cubic one with space group Fd-3m (227), a=7.147. It is listed
in the space-group tables with two different origins. If Origin choice
2 setting is used (with point symmetry -3m at the origin), then the
silicon atoms occupy the position 8(a) -43m with the coordinates
1/8, 1/8, 1/8; 7/8, 3/8, 3/8 and those related by the face-centring
translations.

Describe the structural distortion from the cubic to the
tetragonal phase by the determination of (i) the displacements if the
Si atoms in relative and absolute units, and (ii) the changes on the
lattice parameters during the transition.
jueves 6 de diciembre de 12

Example: -Cristobalite -Cristobalite

Origin choice 2:
Si 8a 1/8,1/8,1/8 7/8,3/8,3/8
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Problem 3.6

SOLUTION

1. Characterize the symmetry break between the

high- and low-symmetry phases
-index of the group-subgroup pair: INDEX
-transformation matrix: SUBGROUPGRAPH
2. Calculate the lattice parameters of the lowsymmetry phase: CELLTRANS
3. Calculate the atomic coordinates of the lowsymmetry phase: TRANSFORM (or WYCKSPLIT)
4. Evaluate the lattice strain and the atomic
displacements accompanying the phase
transitions: STRAIN, COMPSTRU
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Step 1. Determination of the index of

the group-subgroup pair

INDEX

space-group
identification

formula units

lattice
parameters

[iL]=2
[iP]=6
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[i]=12

Step 2. Study of the group-subgroup symmetry break

SUBGROUPGRAPH

Which of the three matrices corresponds to

the cristobalite case?
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Step 3. Lattice parameters of the reference structure

CELLTRANS
Highsymmetry
phase

G> H
relationship

5.053 5.053 7.147 90 90 90

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(High-symmetry
phase)Low

(G)H

lattice parameters of the

reference structure

Step 3. Atomic coordinates of the reference structure

Highsymmetry
phase

G> H

(High-symmetry
phase)Low
relationship

TRANSTRU

(G)H

(P,p)

atomic coordinates of
the reference structure
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Step 4. Characterization of the global distortion

Symmetry break:
Fd-3mP41212, index 12
at=1/2(ac-bc), bt=1/2(ac+bc),ct=cc
origin shift: (5/8,3/8,3/8)

Experiment:
Cubic phase:
a=7.147

(P,p)

Si 8a 1/8 1/8 1/8

7/8 3/8 3/8

Tetragonal phase:
a=4.9586 , c=6.9074
Si 4a 0.3028 0.3028 0
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Calculated:
Reference structure:
a=5.053 , c=7.147
Si 4a 0.75 0.25 0.75
0.25 0.25 0

affine deformation ?
atomic
displacements ?

Step 4a. Determination of the affine deformation

Symmetry break:
Fd-3mP41212, index 12
at=1/2(ac-bc), bt=1/2(ac+bc),ct=cc
origin shift: (5/8,3/8,3/8)

Experiment:
Calculated:
Cubic phase:
Reference structure:
CELLTRANS
a=7.147
a=5.053 , c=7.147
P=

1/2 1/2

-1/2 1/2

STRAIN

Tetragonal phase:
a=4.9586 , c=6.9074
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affine
deformation

Step 4a. Determination of the affine deformation

(High-symmetry
phase)Low

Low-symmetry
phase

(G)H

H
STRAIN

Strain
tensor

S=1/3(i2)1/2
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Problem: LATTICE STRAIN

CALCULATION

Finite Lagrangian strain tensor:

Degree of lattice distortion:

Valid for linear and non-linear strains!
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S=1/3(i2)1/2

STRAIN

Step 4b. Atomic displacement field

Symmetry break:
Fd-3mP41212, index 12

Experiment:
Cubic phase:
a=7.147
Si 8a 1/8 1/8 1/8
7/8 3/8 3/8

TRANSTRU

Calculated:
Reference structure:

1/2 1/2

5/8

-1/2 1/2

3/8

3/8

a=5.053 , c=7.147
Si 4a 0.75 0.25 0.75
0.25 0.25 0

U
R

T
S

Tetragonal phase:
a=4.9586 , c=6.9074

Si 4a 0.3028 0.3028 0
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O
C

atomic
displacement
field

Step 4b. Atomic displacement field

Reference structure

COMPSTRU

Experimental data

affine
normalizer

Most similar configuration

structural
descriptor

= 0.122
maximal
displacement
dmax=0.377

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PROBLEM:

Structural Relationship between two

structures with group-subgroup related
symmetry groups G H

High-symmetry phase: G
symmetry
reduction

Group-subgroup
relation G>H
Wyckoff positions
splittings

Reference structure: (G)H

affine lattice deformation
transformation atomic
displacement field

Low-symmetry phase: H
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INDEX
SUBGROUPGRAPH
RE

U
T
S
C
HERMANN
N
U
R
O
I
T AT
SWYCKSPLIT
L
E
R
STRAIN
COMPSTRU

STRUCTURE RELATIONS

Problem 3.5
SOLUTION
highsymmetry
structure

Cristobalite
phase transition

lowsymmetry
structure

tolerances
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SOLUTION

Problem 3.5

STRUCTURE RELATIONS

Cristobalite phase transition

Fd-3m High-symmetry phase
(P,p)=
Symmetry-controlled mapping

(High-symmetry phase)P41212
Global distortion
Lattice deformation
Atomic displacement field

P41212 Low-symmetry phase

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Problem 3.5

STRUCTURE RELATIONS

SOLUTION

Cristobalite phase transition

Fd-3m High-symmetry phase
(P,p)=
alternative
transformation matrices

structural
descriptor

average
distance
dav

1
=
n

sX

mi u2i

Global
distortion

(P,p)1=

lattice
3
deformation
S=

(P,p)2=

P41212 low-symmetry phase

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sX
1

2
i

maximal distance

Problem 3.5
SOLUTION
highsymmetry
structure
Origin choice 1

Cristobalite
phase transition
lowsymmetry
structure

tolerances
NON-standard settings
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STRUCTURE RELATIONS
NON-STANDARD settings

Problem 3.5

SOLUTION

STRUCTURE RELATIONS
NON-STANDARD settings

highsymmetry
structure
Origin choice 1

lowsymmetry
structure

Cristobalite
phase transition
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Problem 3.6(a)

Lead phosphate phase transition

Lead phosphate Pb3(PO4)2 shows a phase transition from a

paraelastic high-temperature phase with symmetry R-3m (No.
166) to a ferroelastic phase of symmetry C2/c (No.15).

Using the structure data given in the ExerciseData file and
the tools of the Bilbao Crystallographic Server:
(i)characterize the symmetry reduction between the high- and
low-symmetry phases (index, graph of maximal subgroups,
etc.);
(ii)describe the structural distortion from the rhombohedral
to the monoclinic phase by the evaluation of the lattice strain
and the atomic displacements accompanying the phase
transition.
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STRUCTURE RELATIONS

Problem 3.6
SOLUTION
highsymmetry
structure

Pb3(PO4)2
ferroelastic
phase transition
lowsymmetry
structure

tolerances
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Problem 3.6

SOLUTION

STRUCTURE RELATIONS

Ferroelastic phase transition Pb3(PO4)2

R-3m High-symmetry phase

Symmetry-controlled mapping

(High-symmetry phase)C2/c
Global distortion
Lattice deformation
Atomic displacement field

C2/c Low-symmetry phase

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Problem 3.6

SOLUTION

STRUCTURE RELATIONS

Ferroelastic phase transition Pb3(PO4)2

R-3m High-symmetry phase

alternative
transformation matrices

lattice
deformation
s

structural
descriptor

1
S=
3

2
i

Global
distortion

(P,p)1=
(P,p)2=

P21/c low-symmetry phase

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maximal distance

average
distance

dav

1
=
n

sX
i

mi u2i

Study of the group-subgroup symmetry break

[i]=[iP].[iL]

INDEX:

[i]=3.2=6

Input for SUBGROUPGRAPH

Group-subgroup graph for Pb3(PO4)2

R3m

R3c

C2/m

C2/c(3)

C2/c(4)

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C2/c(1)

C2/c(1)

R3c

C2/m

C2/c(4)

C2/c(2)

C2/c(3)

C2/m

C2/c(1)

C2/c(2)

C2/c(2)

C2/c(3)

C2/c(4)

Problem 3.6 (b)

Lead vanadate phase transition

Lead phosphate Pb3(VO4)2 shows a phase transition from a

paraelastic high-temperature phase with symmetry R-3m (No.
166) to a ferroelastic phase of symmetry P21/c (No.14).

Using the structure data given in the ExerciseData file and
the tools of the Bilbao Crystallographic Server:
(i)characterize the symmetry reduction between the high- and
low-symmetry phases (index, graph of maximal subgroups,
etc.);
(ii)describe the structural distortion from the rhombohedral
to the monoclinic phase by the evaluation of the lattice strain
and the atomic displacements accompanying the phase
transition.
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Problem 3.6(b)
SOLUTION

STRUCTURE RELATIONS
formula
units

highsymmetry
structure

Pb3(VO4)2
ferroelastic
phase transition
lowsymmetry
structure

higher
tolerances
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formula
units

STRUCTURE RELATIONS

Problem 3.6(b)
SOLUTION

Ferroelastic phase transition Pb3(VO4)2

R-3m High-symmetry phase

(P,p)=

P21/c low-symmetry phase

alternative transformation matrix
(P,p)=
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Step 1. Determination of the index of

the group-subgroup pair
Example: Pb3(VO4)2

INDEX:

High-symmetry phase

INDEX
[i]=[iP].[iL]
[i]=3.2=6

R-3m
iP=PG/PH=3
Low-symmetry phase

C2/m
iL=ZH/ZG=2
P21/c

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Step 2. Study of the group-subgroup symmetry break

Input for SUBGROUPGRAPH

Group-subgroup graph for Pb3(VO4)2

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Transformation matrix (P,p) for G>H

Subgroups P21/c of R-3m of index 6
(data ITA1)

(P,p)ITA1

Arbitrariness of (P,p)
[(P,p)exp]-1(P,p)ITA1=N(P21/c)
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2/3 0 -2 0
(P,p)exp= 1/3 1 -1 0
1/3 0 0 0

Problem 3.7

Problem: Order-disorder
phase transition

Example: Order-disorder transition in AuCu

1/2(ac2)=1/22 3.83A=0.707 3.83A = 2.708A

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Problem 3.7

Order-disorder
phase transition
CuAu

modified
structure
data

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Example STRUCTURE RELATIONS

Order-disorder phase transition CuAu
Fm-3m

High-symmetry phase
a=3.83

(P,p)=

Reference structure
(Fm-3m)P4/mmm
a=2.83, c=3.66

a=2.71, c=3.83

P4/mmm Low-symmetry phase

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High-symmetry disordered phase

Space group: Fm-3m

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Symmetry break: Fm-3mP4/mmm

at=1/2(ac-bc), bt=1/2(ac+bc),ct=cc

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Low-symmetry ordered phase

Space group: P4/mmm

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Crystal-structure relationships

SYMMETRY RELATIONS
BETWEEN CRYSTAL
STRUCTURES

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Problem:

Symmetry Relations
between Crystal Structures
Baernighausen Trees

Pyrite
Structural family

Aristotype
Basic
structure

Hettotypes
Derivative
structures

U. Mueller, Gargnano 2008

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Baernighausen Trees

Modul design of crystal

symmetry relations

Element symbol
Wyckoff posit.
cite symmetry
coordinates

Element symbol
Wyckoff posit.
cite symmetry
coordinates

U. Mueller, Gargnano 2008

jueves 6 de diciembre de 12

Family tree of hettotypes of ReO3

Baernighausen Trees

U. Mueller, Gargnano 2008

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Structure Relationships
PROBLEM:

Highsymmetry
structure

Consider two structures (specified by their unit-cell

parameters and atomic coordinates) with group-subgroup
related symmetry groups G>H
Search for a mapping of the two structures such that the
global distortion accompanying the mapping is tolerably small.
symmetry
controlled
mapping

most similar
configuration

affine
transformation

(High-symmetry
phase)Low

G> H
relationship
atomic species
correspondence
scheme

(G)H

global
distortion of
the mapping
Lattice deformation
Atomic displacement
field

STRUCTURE RELATIONS
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Lowsymmetry
structure

Problem 3.8

Symmetry
relations
Problem:
between crystal structures

Hettotype of CsCl structure

Show that the crystal structure of CoU maybe interpreted
as a slightly distorted CsCl (or brass, CuZn)-type
structure. Using the structural data in the Exercise Data
file, characterize the structural relationship between the
CoU structure and CsCl structure.

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Problem 3.8
SOLUTION

STRUCTURE RELATIONS
formula units
per unit cell

highsymmetry
structure

lowsymmetry
structure

tolerances
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atomic species
correspondence
scheme
Co Cu
U
Zn

Problem 3.9

Symmetry
relations
Problem:
between crystal structures

HT-quartz and LT-quartz

(i) Upon heating above 573 C the LT-quartz transforms to its
HT form. Set up the corresponding Baernighausen tree that
describes the symmetry relations between the two quartz
forms. Which additional degree of freedom are present in the
lower symmetry form? (The crystal structures of HT-quartz
and LT-quartz can be found in the ExerciseData file.)
(ii) Consider the structure data of AlPO4 listed in the
ExerciseData file. Describe its structural relationship to quartz
and construct the corresponding Baernighausen tree.
Hint: In order to find the structural relationship between quartz
and AlPO4 consider the splitting of Si positions into two: one for Al
and one for P.
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Problem 3.9

SOLUTION

HT-quartz and LT-quartz

Structural
relationships and
Baernighausen tree
between
quartz and AlPO4
U. Mueller, Gargnano 2008
jueves 6 de diciembre de 12

Problem 3.10

Symmetry
relations
Problem:
between crystal structures

The structure of -XOF (X=La, Y, and Pu) can be derived from that of
cubic CaF2 (fluorite structure) by splitting the fluorine positions into two:
one for oxygen and one for fluorine, and by shifting the metal positions
along c. By these changes the space-group symmetry is reduced.

a=1/2(a-b), b=1/2(a+b); p=(1/4, 0, 1/4)

G=Fm-3m(225)

(P,p)
H=P4/nmm(129)
Hahn, Wondratschek. Symmetry of Crystals, Sofia, 1994
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Problem 3.10

Questions

(i) Display the relation between the old (a,b,c) and the new (a,b,c)
unit cell by means of a drawing.
(ii) Which is the crystal system of the new unit cell? Which is its
centring type? (The lattice of CaF2 is F-centred cubic(fcc),a=b=c,==.)
(iii) Construct the transformation matrix P describing the change
of the basis.
(iv) What is the volume of the new unit cell compared to that of
the old one?
(v) What are the coordinates of the atoms of the CaF2 structure
referred to the new coordinate system?
(vi) Can the structure of -LaOF be considered as a hettotype
(derivative structure) of the aristo- type (basic) structure of CaF2 ?
(structure data of -LaOF in Exercise Data file)
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Problem 3.10

SOLUTION
STEP-BY-STEP

(i) Relations between

the old (a,b,c) and
the new basis
(a,b,c)
(ii) The new unit cell is tetragonal I
(iv) Volume new cell to Volume old cell:

Vnew/Vold = 1/2

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Problem 3.10
Comparison:

CaF2
structure

lattice
parameters

c/a=1.414

ICSD data LaFO

origin choice 1
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SOLUTION
STEP-BY-STEP

-XOF
structures

Problem 3.10

Origin 2 description of LaFO

SOLUTION
STEP-BY-STEP

SETSTRU
CaF2 in subgroup basis

TRANSFORM

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Problem 3.10
SOLUTION

STRUCTURE RELATIONS
formula units
per unit cell

highsymmetry
structure

lowsymmetry
structure

tolerances
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atomic species
correspondence
scheme
La Ca
F
F1
O
F2

Problem 3.10

SOLUTION

STRUCTURE RELATIONS

Hettotypes of CaF2 structure

Fm-3m High-symmetry structure

lattice
deformation
S=

alternative
transformation matrices

sX
1

structural
descriptor

2
i

Global
distortion

(P,p)1=
(P,p)2=

P4/nmm Low-symmetry structure

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maximal distance

average
distancesX
dav =

1
n

mi u2i