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Institute of Physics
Department of Structure Analysis
Cukrovarnicka 10
16253 Praha 6
Czech Republic

Academy of Sciences Institute of Physics
Dept of Structure Analysis Laboratory of Crystallography
ECA-SIG#3 Contact Us

Crystallographic Computing System for Standard and Modulated Structures

Vaclav Petricek, Michal Dusek & Lukas Palatinus

Jana2006 is a crystallographic program focused to solution, refinement and interpretation of difficult, especially modulated structures. It calculates structures having up to three modulation vectors from powder as well as single crystal data measured with X-ray or neutron diffraction. The input diffraction data can be unlimitedly combined, the combination of powder neutron data with single crystal X-ray data being a typical example. The structure solution can be done using the built-in charge flipping algorithm or by calling an external direct methods program. Jana can handle multiphase structures (for both powder and single crystal data), merohedric twins as well as twins with partial overlap of diffraction spots, commensurate and composite structures. It contains powerful transformation tools for symmetry (group-subgroup relations), cell parameters and commensurate-supercell relations. Wide scale of constrains and restrains is available including a powerful rigid body approach and possibility to define a local symmetry affecting only part of the structure. The latest development of Jana concerns magnetic structures.

More about Jana2006 (PowerPoint presentation, 10MB)

NewsAugust 22 - 30, 2020 The 25th IUCr Congress: Prague, Czech Republic

IUCr 25 Highlights related to aperiodic crystallography:
Magnetic structures
Aperiodic structures
Satellite workshop on aperiodic and magnetic structures

August 20 - 21, 2020 Workshop on Aperiodic and Magnetic Structures: satelllite of IUCr, Prague, Czech Republic

May 31 - June 9, 2019 Magnetic Crystallography: Erice, Italy

March 11 - 13, 2019 Jana basic Workshop in Jena, Germany

December 10 - 13, 2018 Jana Modulation Workshop: La Jolla CA, USA

October 26-27, 2017 Workshop on magnetic option in Jana2006, Garching, Germany

August 11, 2016 Deadline for the late abstract submission to ECM30 in Basel, Switzerland

July 4-8, 2015 3rd International School on Aperiodic Crystals: application deadline 1 April 2016

October 28, 2015 Maintenance release of Jana2006 for Windows can be obtained in Download area. It cumulates many improvements, supports better magnetic structures and electron diffraction.

January 24, 2015 APERIODIC2015: abstract submission, deadline 30 April

May 01, 2014 New reference for Jana2006: Petricek, V., Dusek, M. & Palatinus, L. (2014). Z. Kristallogr. 229(5), 345-352. DOI 10.1515/zkri-2014-1737

March 12, 2014 Zeitschrift fuer Kristallographie offers free online access to the journal's present and previous issues until June 30,2014.

February 14, 2014 Postal stamp with crenel function has been issued in Slovakia at the occassion of the IYCr2014. The stamp and e-shop

August 14-16, 2014 Magnetic Workshop in Hamilton, Canada. Satellite workshop of the IUCr congress on the Role of Magnetic Symmetry in the Description & Determination of Magnetic Structures.

March 15, 2013 Maintenance release of Jana2006 for Windows can be obtained in Download area. It cumulates many improvements, supports better magnetic structures and electron diffraction.

November 25 - December 3, 2012 Workshop in Uberlandia, Brazil. Workshop on Jana2006 at the International School on Fundamental Crystallography.

June 11-14, 2012 Workshop in Klatovy, Czech Republic. Workshop on Jana2006 at the Colloquium of the Czech Crystallographic Association.

June 7-9, 2012 Workshop in Izmir, Turkey. Workshop on Jana2006 at the 3rd Turkish Crystallographic Meeting.

May 7-12, 2012 3rd Shanghai Workshop of X-Ray Crystallography, China.

February 23 - March 08, 2012 Workshops in Kosice, Slovakia. Four half-day workshops about solution of 3d structures in Jana2006, in Czech language. Dates: 23.2., 1.3., 6.3., 8.3. Contact: dusek@fzu.cz.

July 01, 2011 Maintenance release of Jana2006 for Windows can be obtained in Download area. It cumulates small improvements before larger changes planned for the summer 2011.

May 03, 2011 Maintenance release of Jana2006 for Windows can be obtained in Download area. It cumulates various improvements and bug fixes. More ....

October 23, 2010 Maintenance release of Jana2006 for Windows can be obtained in Download area. It cumulates various improvements and bug fixes. More ....

April 1, 2010 Maintenance release of Jana2006 for Windows can be obtained in Download area. It cumulates various improvements and bug fixes. More ....

January 26, 2010 The Third Ad Hoc Workshop on Jana2006, 8-9 March 2010. More ....

January 06, 2010 The Second Ad Hoc Workshop on Jana2006, 18-19 Jan 2010. More ....

January 05, 2010 International school on aperiodic crystals.More ....

October 21, 2009 Maintenance release of Jana2006 for Windows can be obtained in Download area. It cumulates various improvements and bug fixes. More ....

September 16, 2009 Ad hoc workshops on Jana. We offer informal two days workshops on topics selected by paticipants. More ... .

October 23, 2008 Maintenance release of Jana2006 for Windows can be obtained in Download area. It cumulates various improvements and bug fixes. More ....

October 14, 2008 Eset NOD32 antivirus slows down Jana2006. More ...

July 25, 2008 The first stable version of Jana2006 for Windows. This program is the successor of Jana2000. Currently only Windows version is available, Unix version as well as manual are under development. The Stable version will be changed occassionally, the everyday work will be immediately available in the Latest version. Registered users will be informed about new Stable versions. Jana2006 can be obtained in Download area.

July 22, 2008 New web page for Jana contains all information about Jana2006 and the previous version Jana2000. We have partially changed also download locations, please do not use old links.

December 28, 2007 Final version of Jana2000 - see the Download area. No further development is expected in Jana2000.

Download

Shortcuts:Jana2006 for Windows Installation notes Free Registration

Jana system is a freeware but we are interested who is using it. We would like our users to register. Registered users get e-mails about major updates.

Jana2000: development of this program has been finished. Jana2000 input files can be used in Jana2006, the necessary conversions are done automatically.

Jana2006 for UNIX: porting of Jana2006 to UNIX is in progress but it is not yet finished.
User manuals: not yet available. The old manuals for Jana98 and Jana2000 are still partially useful.

Program	Version string	Download from jana.fzu.cz
Jana2020 for Windows	jana2020Inst.msi
Jana2006 for Windows, STABLE	janainst.msi
Jana2006 for Unix, STABLE	- - - -	not available
Jana2006 for Windows, LATEST	janainst.msi
Jana2006 for Unix, LATEST	- - - -	not available
Jana2000 for Windows, FINAL	janainst.exe janainst.exe.zip
Jana2000 for Unix, FINAL (jana2000Pack.exe contains installation procedure)	jana2000Pack.exe.gz jana2000.tar.gz Debroglie's repository (third party) Jana2000 on MAC OSX 10.12
Manuals (partially useful also for Jana2006)	- - - -	manual98.pdf manual2000_part1.pdf powder_parameters.pdf manual2000_part1_examples.zip superflip_user_manual.pdf
Cookbook Jana Cookbook cumulates examples from Jana workhops. The last version is always copied here together with input data. Raw data for electron diffraction examples are provided separately due to their size.	- - - -	cookbook.zip (~100MB, PDF+data) Jana2006 Cookbook.PDF raw_data_eld.zip (~600MB) raw data for Example 5.3.1 (Cr2P2O7) (~1500MB) raw data for Example 5.5.1 (Melilite) (~1000MB)

STABLE versions are not frequently changed, registered users get information about their releases. LATEST versions are changed frequently and contain the latest development. FINAL versions are not further developed. BETA versions are pre-releases of new major upgrades.

Installation

Jana2006 for Windows. Execute janainst.msi and follow the instructions. Execute jana2006.exe and check the version string in Tools->About Jana2006.

Jana2006 for Windows, old way of installation from janainst.exe. Follow the instructions for Jana2000. For the system environment variable use the name JANA2006DIR instead of JANADIR.

Jana2006 for UNIX. Unix version is not yet available.

Jana2000 for Windows. Execute the self-extracting archive janainst.exe. Before the extraction choose installation directory. After the extraction go to Control panel - System - Advanced - Environment variables and set the system-wide environment variable JANADIR to the name of the installation directory. Go to Display Properties - Effects and make sure Clear type fonts are not used for smoothing edges of screen fonts. Execute jana2000.exe.
For upgrade execute the self-extracting archive janainst.exe and choose the same installation directory where the original version of Jana2000 has been installed.

Jana2000 for UNIX, fresh installation. Requisities: FORTRAN compiler, C compiler, SDK for X11. Download jana2000Pack.exe and put it one level above the future installation directory (for jana2000Pack.exe in directory xxx, the installation directory will be xxx/jana2000). Start csh or tcsh, execute `source jana2000Pack.exe' and follow instructions of the installation procedure. No JANADIR is necessary if the installation stays in the default directory.

Common troubleshooting for Windows.

Premature end of instalation from janainst.msi: often caused by Adobe Acrobat updater, which must be killed from task manager
Installation from janainst.exe: Make sure that JANADIR or JANA2006DIR contains correct name of installation directory.
Installation from CD: Make sure that files copied from CD are not read-only.
Jana2000 cannot be used with Clear type fonts.
Installation directory should not be Desktop (too complicated pathname) or flashdisk (too slow)
Installation from janainst.msi over older version installed from janainst.exe: in most cases it runs normally. The installation procedure sets automatically system environment variable JANA2006DIR but does not define the user environment variable. In case of version mismatch please ensure that the user variable JANA2006DIR is undefined.
In rare cases the installation from janainst.msi leaves the original files unchanged. This can be recognized in Tools->About where the version string is not updated after installation. In such case the installation directory of Jana2006 should be deleted (keep copy of ini and hst file) as well as the user or system environment variable JANA2006. Then repeat installation from janainst.msi.

Common troubleshooting for UNIX. Make sure SDK for X11 is installed, in most Linux distributions only run-time libraries are present by default. The installed Jana executable cannot be moved from the default installation directory jana2000 without special arrangements.

LINKS:Installation of Jana for Windows Installation of Jana for Mac OS X(both slightly outdated)

External Programs

Main parts of Jana are our own computer code. For some special functionalities Jana can call external programs. Some of them are distributed with Jana, the others must be downloaded from their web pages. The configuration of external programs is done through Tools -> Programs.

Program	Description	www
Superflip	Program for solving structures by charge flipping. Distributed with Jana and immediately available.	superflip.fzu.cz
MCE	Program for electron densities visualization. Distributed with Jana, available after defining the path in Tools->Programs->3d map visualization.	www.vscht.cz
VESTA	Program for electron densities visualization. Available after download, installation and defining the path in Tools->Programs->3d map visualization.	www.geocities.jp
SIR97, SIR2002, SIR2004	Program for solving structures by direct methods from single crystal diffraction data. Available after download, installation and defining the path in Tools->Programs.	www.ic.cnr.it
EXPO, EXPO2004	Program for solving structures by direct methods from powder diffraction data. Available after download, installation and defining the path in Tools->Programs.	www.ic.cnr.it
SHELXT	Program for solving structures by charge flipping. Available after download, installation and defining the path in Tools->Programs.	shelx.uni-goettingen.de
graphic viewer	Programs for plotting crystal structures. It can be any program accepting CIF as an input in command line, for instance Diamond, Atoms, Platon. Available after download, installation and defining the path in Tools->Programs->Graphic viewer.	many possibilities

Ad hoc workshops on Jana

Ad hoc workshops are small two days workshops organized in Praha by authors of Jana software. A new workshop is usually organized when we find an overlap in topics in the list of preliminary registrations for at least five people. In such case the program details and the dates are discussed with participants and fixed. Another participants can register for a workshop with fixed program and date up to 12-15 people. Participants pay themselves all their expenses and they are expected to bring their own laptops with Windows. However, we can lend one or two laptops to those who cannot bring their own ones. The registration fee is zero (in Czech Crowns). Workshop certificates are issued by our skilled artists on demand.

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Topics

(INT1) Introduction to Jana software, solution of simple 3d structures
(INT2) Introduction to modulated structures, solution of simple 4d structures
(PWD) Refinement of powder data
(PROF) Powder profile functions
(TW) Twins and multiphases of 3d and modulated structures
(CHF) Application of charge flipping to 3d and modulated structures
(DIS) Disorder, mixed sites, application of rigid body refinement for disordered structures
(RIG) Rigid body refinement and application of local symmetry
(GEOM) How to keep geometry
(LOC) Application of local symmetry
(CRENEL) Discontinuous modulation functions (crenel and sawtooth)
(COMM) Commensurate structures
(COMP) Composite structures (i.e. samples with two coexisting lattices)
(FIVE) Five dimensional structures
(MAG) Magnetic structures
(ELD) Electron diffraction
any other topic (please specify)

Registration By e-mail to Michal Dusek (dusek@fzu.cz). For workshops without fixed program or for future not yet announced workshops please give a list of selected topics, rated by importance. Although a workshop can usually have only four topics (one topic takes 1/2 of day) the number of selected topics can be higher, it helps finding overlaps. Please indicate if you have already experience with Jana software. New users should select the topic 'INT1'. Those who would like to participate in an advanced workshop (without INT1) but don't have an experience with Jana should make Example 1.1 and 2.1 of the cookbook as a homework.

Passed workshops:
1st Jana2006 ad hoc workshop
2nd Jana2006 ad hoc workshop
3rd Jana2006 ad hoc workshop
4th Jana2006 ad hoc workshop
5th Jana2006 ad hoc workshop (ADV)
6th Jana2006 ad hoc workshop
7th Jana2006 ad hoc workshop (MAG)
8th Jana2006 ad hoc workshop
9th Jana2006 ad hoc workshop
10th Jana2006 ad hoc workshop
11th Jana2006 ad hoc workshop
12th Jana2006 ad hoc workshop
13th Jana2006 ad hoc workshop (PWD)
14th Jana2006 ad hoc workshop (MAG)
15th Jana2006 ad hoc workshop (ELD)
16th Jana2006 ad hoc workshop
17th Jana2006 ad hoc workshop (BAS)
18th Jana2006 ad hoc workshop (Adv)
19th Jana2006 ad hoc workshop (ELD)
20th Jana2006 ad hoc workshop (MAG)
21st Jana2006 ad hoc workshop (BAS)
22nd Jana2006 ad hoc workshop (ADV)
23rd Jana2006 ad hoc workshop (BAS)
24th Jana2006 ad hoc workshop (ADV)
25th Jana2006 ad hoc workshop (MAG)
26th Jana2006 ad hoc workshop (PWD)
27th Jana2006 ad hoc workshop (ELD)
28th Jana2006 ad hoc workshop (BAS)
29th Jana2006 ad hoc workshop (BAS)
30th Jana2006 ad hoc workshop (BAS, ADV)
31st Jana2006 ad hoc workshop (BAS, ADV)
32nd Jana2006 ad hoc workshop (BAS, ADV)
33rd Jana2006 ad hoc workshop (MOD)
34th Jana2006 ad hoc workshop (BAS, ADV)
35th Jana2006 ad hoc workshop (BAS, ADV)
36th Jana2006 ad hoc workshop (BAS-ELD-MAG)
37th Jana2006 ad hoc workshop (MAG)
38th Jana2006 ad hoc workshop (ELD)
39th Jana2006 ad hoc workshop (BAS-ELD-MAG)
40th Jana2006 ad hoc workshop (BAS)
41st Jana2006 ad hoc workshop (ELD)

Forthcoming workshops: See here

Citation & support

The main reference:
Petricek, V., Dusek, M. & Palatinus, L. (2014). Z. Kristallogr. 229(5), 345-352. DOI 10.1515/zkri-2014-1737
'Crystallographic Computing System JANA2006: General features'

Petricek, V., Eigner, V., Dusek, M. & Cejchan, A. (2016). Z. Kristallogr. 231(5), 301-312. DOI 10.1515/zkri-2015-1913
'Discontinuous modulation functions and their application for analysis of modulated structures with the computing system JANA2006'

Petricek, V., Dusek, M. & Plasil, J. (2016). Z. Kristallogr. 231(10), 583-599. DOI 10.1515/zkri-2016-1956
'Crystallographic computing system Jana2006: solution and refinement of twinned structures'

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Development of Jana is continuously supported by the Czech Science Foundation and Academy of Sciences of the Czech Republic. Thanks to this support we can make the program freely available to everybody.

Program development is not possible without user feedback and interaction. Please contact us with bug reports, feature suggestions and structure determination difficulties. We also provide measurement of interesting samples in our laboratory.

Vaclav Petricek	Michal Dusek	Lukas Palatinus
petricek@fzu.cz	dusek@fzu.cz	palat@fzu.cz
Main developer	Unix, manuals, web, features design	Charge flipping, MacOSX

Address: Institute of Physics, Cukrovarnicka 10, 16253 Praha, Czech Republic

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