JANA2006 is a freely available program for structure determination of standard, modulated and magnetic samples based on X-ray or neutron single crystal/ powder diffraction or on electron diffraction. The system has been developed for 30 years from specialized tool for refinement of modulated structures to a universal program covering standard as well as advanced crystallography. The aim of this article is to describe the basic features of JANA2006 and explain its scope and philosophy. It will also serve as a basis for future publications detailing tools and methods of JANA.

The recently published method for the structure refinement from threedimensional precession electron diffraction data using dynamical diffraction theory [Palatinus et al. (2015). Acta Cryst. A71, 235-244] has been applied to a set of experimental data sets from five different samples -Ni 2 Si, PrVO 3 , kaolinite, orthopyroxene and mayenite. The data were measured on different instruments and with variable precession angles. For each sample a reliable reference structure was available. A large series of tests revealed that the method provides structure models with an average error in atomic positions typically between 0.01 and 0.02 Å . The obtained structure models are significantly more accurate than models obtained by refinement using kinematical approximation for the calculation of model intensities. The method also allows a reliable determination of site occupancies and determination of absolute structure. Based on the extensive tests, an optimal set of the parameters for the method is proposed.

Accurate structure refinement from electron-diffraction data is not possible without taking the dynamical-diffraction effects into account. A complete three-dimensional model of the structure can be obtained only from a sufficiently complete three-dimensional data set. In this work a method is presented for crystal structure refinement from the data obtained by electron diffraction tomography, possibly combined with precession electron diffraction. The principle of the method is identical to that used in X-ray crystallography: data are collected in a series of small tilt steps around a rotation axis, then intensities are integrated and the structure is optimized by least-squares refinement against the integrated intensities. In the dynamical theory of diffraction, the reflection intensities exhibit a complicated relationship to the orientation and thickness of the crystal as well as to structure factors of other reflections. This complication requires the introduction of several special parameters in the procedure. The method was implemented in the freely available crystallographic computing system Jana2006.

We report a new structure determination of the Sr1.2872NiO3 incommensurate composite hexagonal perovskite compound. Three different refinement strategies are presented:  (i) a 3D supercell approximation with a nonharmonic development of the atomic displacement factor, (ii) an original (3+1)D incommensurate composite description with the use of crenel functions, and (iii) a (3+1)D commensurate composite model. The three strategies are discussed and compared to previous refinements carried out for the hexagonal perovskites in a classical way or with the superspace group formalism. Out of the three methods, the incommensurate composite approach gives slightly better results with a final global R value of 2.89% for 635 independent reflections (at a I/σ(I) > 2 level) and only 60 parameters (R3̄m(00γ)0s superspace group; a = 9.5177(7) Å, c = 2.5739(2) Å, q = 0.64359(4)c*, V = 201.93(4) Å3, and Z = 3). The use of crenel functions notably improves previously reported results. New structural features are evidenced for Sr1.2872NiO3:  (i) an incommensurate character, (ii) a splitting of the trigonal prismatic nickel atoms over 5 positions, (iii) a definite stoichiometry which induces a perfect charge balance, and (iv) a nonharmonic behavior of some Sr atoms. Those characteristics seem general to most hexagonal perovskite compounds and essential for correctly interpreting their interesting magnetic properties. Finally, a new generic formulation is proposed, which explains the various stoichiometries observed and suggests a new compound possibility.

Synthetic tetrahedrite, Cul2Sb4SI3, obtained by reaction of the elements, has been investigated at various temperatures in the 295-573 K range. It crystallizes in the cubic system with a = 10.3293 (6) A, V = 1102.1 (2) ]k 3, space group 143m and Z = 2 at room temperature. The structure refinement converged to a residue of R = 0.0165 (at room temperature, wR = 0.0200) for 389 independent reflections and 34 refined parameters. A Gram-Charlier non-harmonic development of the atomic displacement factor for both independent Cu atoms was used. The results show a disorder for the three-coordinated Cu atom, within and perpendicular to the plane of the three surrounding S atoms. However, although the non-harmonic probability density deformation increases with raising the temperature within this plane, it barely changes in the perpendicular direction. This suggests two different types of disorder: static in-plane and dynamic out-of-plane, therefore underlining a possible diffusion pathway for copper ions. To check the significance of the observed effects, the errors for the one-particle potentials and the probability density function maps were calculated by means of a Monte-Carlo method.

Superspace symmetry has been for many years the standard approach for the analysis of non-magnetic modulated crystals because of its robust and efficient treatment of the structural constraints present in incommensurate phases. For incommensurate magnetic phases, this generalized symmetry formalism can play a similar role. In this context we review from a practical viewpoint the superspace formalism particularized to magnetic incommensurate phases. We analyse in detail the relation between the description using superspace symmetry and the representation method. Important general rules on the symmetry of magnetic incommensurate modulations with a single propagation vector are derived. The power and efficiency of the method is illustrated with various examples, including some multiferroic materials. We show that the concept of superspace symmetry provides a simple, efficient and systematic way to characterize the symmetry and rationalize the structural and physical properties of incommensurate magnetic materials. This is especially relevant when the properties of incommensurate multiferroics are investigated.

We present the structure of anhydrous sodium carbonate at room temperature (phase ) and 110 K (phase ) based on single-crystal X-ray diffraction data. The incommensurate phase was determined almost 30 years ago in the harmonic approximation using one modulation wave and ®rst-order satellites. In our work we use satellites up to ®fth order and additional harmonic waves to model the anharmonic features of the structure. The commensurate phase is presented for the ®rst time. Using the superspace approach, both phases are compared in order to ®nd common trends in the whole range of the sodium carbonate phases. We present arguments supporting the hypothesis that the driving force of the phase transitions may originate in the unsaturated bonding potential of one of the Na ions.

Single-crystal x-ray diffraction data on the 2:2:1:2Bi-Sr-Ca-Cu-0 superconducting phase have been used in a four-dimensional refinement of the modulations of both the metal and oxygen atoms.An expression for an analytical temperature-factor modulation function has been derived and applied to the bismuth atoms. The large value of the temperature factor of Bi in some of the unit cells indicates a contribution from static disorder. The modulation of the oxygen atoms in the bismuth layer is best described by a function that allows the displacement to vary linearly with unit-cell position and incorporates the possibility of excess oxygen near the end of a modulation period. The results on oxygen occupancy and the behavior of the Bi temperature factor are compatible with models that attribute the origin of the modulation to the existence of extra oxygen atoms in the Bi-0 layers. Refinement in the noncentrosymmetric super space group M:A2aa:111 leads to significantly better results than the centrosymmetric treatment.