Jana2006

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Jana2006 Program for structure analysis of
crystals periodic in three or more dimensions
from diffraction data Václav Petrícek Michal
Duek Luká PalatinusInstitute of Physics
Prague Czech Republic
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History 1980 SDSProgram for solution and
refinement of 3d structures 1984 JanaRefinement
program for modulated structures 1994 SDS94 and
Jana94Set of programs for 3d (SDS) and modulated
(Jana) structures running in text mode. 1996
Jana96Modulated and 3d structures in one
program. Graphical interface for DOS and UNIX
X11. 1998 Jana98Improved Jana96. First widely
used version. Graphical interface for DOS DOS
emulation and UNIX X11 2001 Jana2000Support for
powder data and multiphase refinement. Graphical
interface for Win32 and UNIX X11. 2008
Jana2006Combination of data sources magnetic
structures TOF data. Dynamical allocation of
memory. Only for Windows.
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Data repository
X-rays OR synchrotron OR neutrons
Domains of raw single crystal data
Domains of reduced single crystal data
Powder data of multiphases
OR
OR
Import Wizard
Format conversion cell transformation sorting
reflections to twin domains
Data Repository
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Program Scheme
M95 M50
Determining symmetry merging symmetry equivalent
reflections absorption correction
M90
Solution
M40 M41
Refinement TransformationIntroduction of
twinningChange of symmetry
M95 data repositoryM90 refinement reflection
fileM50 basic crystal information form
factors program optionsM40 structure model
Plotting geometry parameters Fourier maps .
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Topics Basic crystallographyAdvanced
tools Incommensurate structuresCommensurate
structures Composite structuresMagnetic
structures Jana2006 is single piece of code.
This allows for development of universal tools
working by the same way for various dimensions
(3d (31)d ) and for different data types
(single crystals powders). both 3d and modulated
structures. Jana2006 also works as an interface
for some external programs SIR9720002004
EXPO EXPO2004 Superflip MC (marching cube) and
software for plotting of crystal structures.
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Basic crystallography Wizards for symmetry
determinationExternal calls to Charge flipping
and Direct methods Tools for editing structure
parameters Tools for adding hydrogen
atoms Constrains Restrains Fourier
calculation Plotting (by an external program) CIF
output Under development graphical tools for
atomic parameters CIF editor
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Advanced tools Fourier sections Transformation
tools group-subgroup relations Twinning
(merohedric or general) treating of overlapped
reflections User equations Disorder Rigid body
approach Multiphase refinement for powder
data Multiphase refinement for single
crystals Multipole refinement Powder
data Anisotropic strain broadening (generalized
to satellites) Fundamental approach TOF
data Local symmetry
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Fourier maps
General section
Predefined sections
M81
Contour can plot predefined section or it can
calculate and plot general sections. For
arbitrary general sections the predefined section
must cover at least asymmetric unit of the
elementary cell.
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Group-subgroup transformation
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Twinning (non-merohedric three-fold twin)
Twinning matrices for data indexed in hexagonal
cell
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Disorder and rigid bodies
Disorder of tert-butyl groups in
N-(3-nitrobenzoyl)-N N-bis (tert-butyl)
phosphoric triamide. The groups were described
like split rigid bodies. One of rigid body
rotation axis was selected along C-N bond in
order to estimate importance of rotation along
C-N for description of disorder.
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Restraints Constraints User Equations
restric C39a 2 C39b restric C9a 2 C9b . . .
. equation xc8xxc8 equation
yc8xyc8 equation zc8xzc8 equation
xn3xxn3 equation yn3xyn3
equation zn3xzn3 . . . . equation
aimolmol121-aimolmol11 equation
aimolmol221-aimolmol21 equation
aimolmol421-aimolmol41 equation
aimolmol521-aimolmol51 equation
aimolmol621-aimolmol61 . . . . keep
hydro triang C3 2 1 C2 C4 0.96 H1c3 keep ADP
riding C3 1.2 H1c3 keep hydro tetrahed C13 1 3
C8x 0.96 H1c13 H2c13 H3c13 keep ADP riding C13
1.2 H1c13 H2c13 H3c13
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Fundamental approach for powder profile parameters
The fundamental approach allows for separation of
instrumental parameters and sample-dependent
parameters (size and strain). It is based on a
general model for the axial divergence aberration
function as described by R.W.Cheary and
A.A.Coelho in J.Appl.Cryst. (1998) 31 851-861.
It has been developed for a conventional X-ray
diffractometer with Soller slits in incident
and/or diffracted beam and it has been already
incorporated in program TOPAS. Example of
instrumental parameters Primary radius of
goniometer 217.5 mm Secondary radius of
goniometer 217.5 mm Receiving slits 0.2mm Fixed
divergence slits 0.5 deg Source length
12mm Sample length 15mm Receiving slit length
12mm Primary soller 5 deg Secondary soller 5 deg
With fundamental approach profile parameters
(particle size and strain) have clear physical
meaning because they are separated of
instrumental parameters .
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Anharmonic description of ADP (ionic conductor
Ag8TiSe6)
Plot Jana calculates electron density map and
calls Marching Cube.
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Local symmetry
Local icosahedral symmetry for atom C of C60
Powder data (J.Appl.Cryst. (2001). 34 398-404)
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Single crystal multiphase systems
View along a Lindströmite
View along a Krupkaite
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Incommensurate structures Modulation of
occupation position and ADP Traditional way of
solving from arbitrary displacements Solving by
charge flipping Modulation of anharmonic
ADP Modulation of Rigid bodies including TLS
parameters Special functions Fourier
sections Plotting of modulated parameters as
functions of t Plotting of modulated
structures Calculation of geometric parameters
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Symmetry Wizard for (31)d modulated strucure
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Harmonic modulation from arbitrary displacements
The atom is displaced from its basic position by
a periodic modulation function that can be
expressed as a Fourier expansion. In the first
approximation intensities of satellites
reflections up to order m are determined by
modulation waves of the same order.
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Checking results in Fourier Ai-A4 Fourier
sections
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Charge Flipping (Superflip of Lukas Palatinus)
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Special modulation functions Cr2P2O7
incommensurately modulated phase at room
temperaturePalatinus L. Dusek M. Glaum R.
El Bali B. (2006). Acta Cryst. (2006). B62
556566
O2
O2
Average structure
Modulated structure
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Special modulation functions Fourier map after
using many harmonic modulation functions
P (cyan) O1 (green) O2 (red) O3 (blue)
Phosphorus and O2 are in the plane of the
Fourier section
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Special modulation functions Indication of crenel
(O2) and sawtooth (O3) function
O3
O2
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Parameters of crenel function
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Parameters of sawtooth function
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Combination of crenel and sawtooth function with
additional position modulation
O2
O3
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The additional modulation is expressed by
Legendre polynomials
o and e indicate odd and even member. The
first polynom i.e. P1o defines a line. The
three coefficients of P1xo P1yo and P1zo are
refined either to crenel or sawtooth shape.
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Modulation parameters as function of t
t0
t1
Reason for t coordinate modulation diplacement
from the basic position is calculated in the real
space i.e. along a3 not A3. Due to translation
periodicity all possible modulation displacements
occur between t0 and 1.
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Plotting of modulated structures in an external
program
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Twinning of modulated structures
The twinning matrix is 3x3 matrix regardless to
dimension.Twinning may decrease dimension of the
problem. Example La2Co1.7 Acta Cryst. (2000).
B56 959-971.Average structure 4.89 4.89 4.34
90 90 120 P63/mmcModulated structure
modulated composite structure C2/m(a0ß)6-fold
twinning around the hexagonal c
Reconstruction of (hk1.835) from CCD
measurement.
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Disorder in modulated structures Cr2P2O7
incommensurately modulated phase at room
temperature
Cr1 (0.500000 -0.187875 0.000000)Cr1 1 New
atomCr1a (0.47 -0.187875 0.03)t40Cr1a
t40Cr0.5 Cr1 Cr1 Cr1 - xCr1a
x New parameters for refinementx and position
of Cr1a Temperature parameters of Cr1a can be put
equal to Cr1. No modulation can be refined for
Cr1a. Analogically one can split positions of
P1 O2 and O3. Refinement is very difficult the
changes should be done simultaneously.
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Commensurate structures
incommensurate structure
commensurate structure
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R3
The set of superspace symmetry operators realized
in the supercell depends on t coordinate of the
R3 section. For given t Jana2006 can transform
commensurate structure from superspace to a
supercell.
Superspace description superspace symmetry
operators
basic cell
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Choosing commensurate model In our case we shall
use symmetry operators and definition points
corresponding to 3x1x2 supercell. Change of tzero
should be followed by new averaging of data.
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Commensurate families In this example known
M2P2O7 diphosphates are derived from the same
superspace symmetry.
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Typical Fourier section
Composite structures
Hexagonal perovskitesTwo hexagonal subsystems
with common ab but incommensurate c.
q is closely related with composition
c1
c2
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Modulated structure of Sr14/11CoO3q
0.63646(11) 7/11Acta Cryst. (1999). B55
841-848
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Levyclaudite Two triclinic composite subsystems
with satellites up to the 4th order related by
5x5 W matrix. Acta Cryst. (2006). B62 775-789.
View of the peak table along c. A B C
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Magnetic structures
Neutrons posses a magnetic moment that enables
their interaction with magnetic moments of
electrons. Therefore below the temperature of
the magnetic phase transition - we can observe
both magnetic and nuclear reflections.
Symmetry contains time inversion which is
combined with any symmetry operation. It yields
magnetic point groups and magnetic space groups.
Extinction rules and symmetry restrictions can be
diferent for nuclear and magnetic symmetry.
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Tool for testing magnetic symmetry
Crystallographic approach we are looking for
magnetic symmetry that corresponds with the
observed powder profile.
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Diffraction pattern described without magnetic
moments
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Diffraction pattern of magnetic structure
described with
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Diffraction pattern of magnetic structure
described with
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Tool for representative analysis
In special cases the equivalence between magnetic
group and a given representation needs an
additional condition for instance that sum of
magnetic moments related by a former 3-fold axis
is zero (P321 - P1)
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Superspace approach
The elementary cell of magnetic structure can be
the same or different of the cell of the nuclear
structure. For the same cell the magnetic
reflections contribute to nuclear reflections.
For a different cell part of magnetic reflections
or all of them form a separate peaks. The
distribution of the magnetic moments over the
nuclear structure can be described by a
modulation wave
The structure factor of modulated magnetic
structures is similar to that for non-modulated
magnetic structure. Each n-th term in the above
equation will create magnetic satellites of the
order n. The magnetic cell is often a simple
supercell with q vector (wave vector) having a
simple rational component and the structure can
be treated like a commensurate one.
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R3
For magnetic wave the property is not position
but the spin moment. This approach allows for
very complicated magnetic structures and for
combination of magnetic and nuclear modulation
(using the same or more q vectors). Warning this
is a new tool tested with only a few magnetic
structures.
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Future of Jana system Development magnetic
structures electron diffraction . Polishing
wizards graphical tools Better support for
simple structures Jana2006 is available in
www-xray.fzu.cz/jana