Workshop on Jana2006
Michal Dušek and Václav Petříček
Institute of Physics of the ASCR, v.v.i., Na Slovance 2, 18221 Praha, Czech Republic
Jana2006 is the last generation of the computing system Jana. Its development has started in early eighties when Václav Petříček developed several programs for analysis of three-dimensional structures from single-crystal X-ray diffraction data known as the SDS system. Later on, during the stay in Buffalo, USA, he wrote program Jana specialized to refinement and Fourier calculations for modulated structures. Both systems were developing separately until 1998 when they have been merged into a universal system Jana98. Another important milestone was adding a support for powder refinement in 2001 and possibility of an arbitrary combination of data sources in 2006. The latest development aims to magnetic structures, electron diffraction and, at the same time, to user friendliness. Jana system has currently about 1300 registered users around the world and it is almost exclusive tool for solution of modulated and composite structures.
The scope of Jana2006 is broad, from semi-automated service crystallography to difficult modulated structures. The user tools are universal; using Jana2006 for standard structures is therefore an advantage for anybody going to switch to modulated or difficult structures. In the field of basic crystallography the program offers usual tasks like automatic determination of space group, searching for higher symmetry, calling of SIR or Superflip for structure solution, evaluation of Fourier maps, adding of hydrogen atoms etc. Advanced tools can be used for transformations, calculation of generally oriented Fourier sections, definition of twinning or rigid bodies, multiphase refinement, multipole refinement, introduction of local symmetry etc. We should point our elaborated transformation tools enabling seamless group-subgroup transformations necessary for investigation of merohedric twinning. The rigid body approach is very important for description of disorder of organic molecules and for lowering number of refinement parameters when the structure model gets complicated. Another powerful concept are user equations, restraints and constraints which can define arbitrary linear relationship between the parameters of the structure model.
Incommensurate structures can be investigated up to the dimension 3+3. The superspace symmetry can be found from the diffraction pattern using the same semi-automatic tools like for standard structures. Jana2006 offers traditional harmonic modulation functions for occupancy, position and ADP as well as discontinous functions (crenel and sawtooth). In the crenel-like description the positions and ADP parameters can also be described with Legendre polynomials. Rigid bodies can also be modulated. The modulated structures can be visualized by calling an external plotting program for a structure transformed to P1 symmetry, by plotting modulated parameters as function of t coordinate or by investigating two-dimensional sections by 3+d-dimensional Fourier map. For solution of modulated structures Jana2006 can directly call program Superflip based on charge flipping which can also be used for verification of superspace symmetry. Commensurate structures represent very useful concept for description of structure families. Jana2006 can determine a supercell symmetry corresponding to the t value used for the calculation and it can transform commensurate structure for a given t to the equivalent three-dimensional supercell. Composite (or intergrown) structures are also supported.
Jana2006 can combine powder and single crystal diffraction data from X-ray, synchrotron and neutron diffraction. The most practical issue is combination of powder neutron data with single crystal synchrotron or X-ray data measured at similar conditions, which is useful for differentiation of chemical elements in mixed sites or reliable determination of hydrogen positions. Another possibility concerns the latest option just being developed in Jana2006: it is possible to combine refinement of magnetic structure from powder data with nuclear structure from synchrotron data. The latest version of Jana2006 contains a convertor between representation analysis and magnetic (super)space groups which enables crystallographic approach to magnetic structures.
A workshop on all topics covered by Jana2006 would last many days. Because in the Czech Republic Jana software is rather rarely used the main focus of the present workshop will be on standard three-dimensional structures. Using single crystal and powder diffraction data of a simple structure we shall present the basic “philosophy” of the program. The rest of the workshop will deal with moderately difficult problems like twinning, mixed-sites refinement and disorder. Finally, solution of a simple modulated structure will be presented.