ISODISTORT

Version History

Harold T. Stokes. Branton J. Campbell, and Dorian M. Hatch
Department of Physics and Astronomy, Brigham Young University, Provo, Utah

Version 6.4.0: Nov 2017. (1) Minor bug fixes, (2) Rotational order-parameters now supported throughout most of the code, except that rotational decompositions are not yet possible. (3) Rigid-bodies and their rotations are generated in TOPAS output automatically when rotational order parameters are turned on, so that rigid-body refinements can be performed. (4) On the distortion page, we added detailed information (basis, origin, ssgtype, index, volume) for each incommensurate primary or secondary irrep. (5) Method 2 now allows the user to specify an OPD manually or to consider only OPDs involving a single arm-pair of the k-star, which is useful when generating the full list of OPDs is computationally expensive (e.g. some non-special commensurate k vectors of a magnetic cubic parent).

Version 6.3.5: August 2017. (1) Minor bug fixes. (2) In the subgroup-tree feature of ISODISTORT, monoclinic and triclinic structures are now transformed by default to a setting with nicer cell parameters (short edge lengths, angles close to but greater than 90 degrees where possible). (3) Inquiries from external software packages enabled (only for Method 2). (4) One can now control the initial and final values of the x,y,z ranges sent to the interactive applet, rather than merely specifying integer multiples of the unit cell along each direction. (5) Preparations for upcoming features.

Version 6.3.4: April 2017. (1) Minor bug fixes. (2) Symmetry-mode parameter sets are now available in non-standard space-group settings for commensurate non-magnetic and magnetic structures; must check the "Use alternate (possibly non-standard) setting" checkbox on the distortion page. (3) After the firefox browser permanently disabled java-applets (and other NPAPI plugins) in March 2017, we moved from HTML to JNLP to deliver the applet and structure-visualization data; most users won't notice much difference. JNLP has a 1MB file limit; for larger JNLP files, you can copy the data string from the JNLP file into a pre-March2017 HTML file (generated using the legacy 5.6.1 version of ISODISTRT) and open it with a java-applet-enabled PaleMoon browser; we're currently researching ways to overcome this limitation.

Version 6.3.3: January 2017. (1) Minor bug fixes. (2) Preparations for future development.

Version 6.3.2: November 2016. (1) Throughout ISODISTORT and also ISOTROPY, we now use "|" rather than ";" to separate OPD contributions from different irreps, and instead use ";" to separate OPD contributions of different k-vectors (or +/-k pairs) of the same irrep. (2) Because the magCIF format has now been approved by the IUCr, all magnetic CIF routines have been updated to the new standard. (3) Now accepts uppercase X,Y,Z symbols in space-group operators from CIF input. (5) Minor bug fixes.

Version 6.3.1: September 2016. (1) The "distortion" page now presents only those user decisions that are relevant to the order-parameter types selected on the "search" page. Saved distortion files now include more complete information about user decisions. (2) Minor bug fixes.

Version 6.3.0: August 2016. (1) (a) New code for finding isotropy subgroups at incommensurate k-vectors. The number of incommensurate modulations entered in Method 2 is now interpreted as the number of independent modulations (i.e. internal superspace dimensions) rather than the total number of modulations. The previous approach led to many isotropy subgroups that are better obtained (and understood) by superposing two instances of the same irrep at slightly-different k-vectors. (b) Furthermore, the new code does not allow one to superpose two instances of the same irrep at the same k vector, but instead allows the more general order-parameter directions of an incommensurate order parameter associated with modulation-phase shifts. With this approach, global phase shifts, which were previously prevented, are now possible when the order parameter includes a phase shift and only one symmetry-unique atom of the basic unit cell experiences a modulation. (2) Preparations for new features (3) Minor bug fixes.

Version 6.2.0: June 2016. (1) New subgroup tree feature released. Automates the calculation of all intermediate isotropy subgroups between the parent and child symmetries. Automatically generates TOPAS.str output for each intermediate distorted structure if user requests it (via checkbox). (2) Added occupational and magnetic modes to Fullprof.pcr output. (3) Minor bug fixes.

Version 6.1.11: January 2016. (1) Added CIF-movie output option to the distortion page. (2) Minor bug fixes.

Version 6.1.10: October 2015. (1) Limit the size of temporary files used for large calculations (to prevent filling up the hard drive). (2) We now log input data for the purpose of debugging problems (e.g. large calculations) that excessively tax the server resources. Daily logs are delete weekly.

Version 6.1.10: October 2015. (1) Limit the size of temporary files used for large calculations (to prevent filling up the hard drive). (2) We now log input data for the purpose of debugging problems (e.g. large calculations) that excessively tax the server resources. Daily logs are delete weekly.

Version 6.1.09: October 2015. (1) a considerable variety of bug fixes based on internal and external bug reports. (2) under-the-hood changes in preparation for upcoming features.

Version 6.1.1-8: June-November 2014. (1) bug fixes related to new features.

Version 6.1: June 2014. (1) It is now possible to create arbitrary superpositions of displacive, magnetic and occupational order parameters at commensurate and incommensurate k-points, leading to structures with (3+d)D superspace-group and magnetic superspace-group symmetry for d = 1,2,3. For distortions with non-magnetic superspace-group symmetry, the correct symmetry group from the ISO(3+d)D table is identified and the superspace transformation to the canonical setting of the group is provided. Such an identification is not yet availailable for magnetic superspace groups. The full-group IR matrices presented for incommensurate distortions come from the ISO-IR tables.
(2) Both CIF and Modes-Details output now accomodate (3+d)D modulated structures (magnetic and non-magnetic).
(3) This release uses the provisional magCIF format for describing commensurate and incommensurate magnetic structures. We hope that the IUCr COMCIFs will soon formalize this format. Commensurate parent and child structures can be imported using either the provisional magCIF format or our older magnetic-CIF format, though the older format will eventually be abandoned.
(4) Improved capabilities for dealing with parent and child structures with large numbers of atoms.
(5) A more robust and efficient atom-matching algorithm for structural decompositions.
(6) Improved capabilities for dealing with distortions involving large atomic displacements.
(7) The orthogonality of modes arising from different copies of the same irrep (same parent atom, same space-group irrep, same local point-group irrep, same OPD parameter) of monoclinic and triclinic parent symmetry groups is now strictly enforced. In prior versions, this requirement was sometimes relaxed to allow order parameters to align with simple lattice directions, which caused problems with the rigorous accounting of mode amplitudes.
(8) Pre-2011 irrep matrices are no longer supported. New group-theoretical algorithms require the novel features of the 2011 ISO-IR tables. Eliminating this backwards compatibility greatly simplifies the maintenance of the code.
(9) The new ISO(3+d)D symmetry-group tables have replaced the old ISO(3+1)D tables for calculations involving d=1 incommensurate structures.
(10) Old distortion files from previous versions cannot be used with the new version. This is neccessary due to the loss of some backwards compatibilities, as described above. To ensure the long-term ability to explore and compare against older results, a permanent legacy copy of ISODISTORT version 5.6.1 (August 2013) is available at http://iso.byu.edu/isodistort_version5.6.1/isodistort.php.
(11) Three-index integer multiples of the distorted superstructure can now be visualized in the ISODISTORT applet.
(12) CIF input must now be uploaded -- the cut/paste options has been eliminated. The separate pre-processed CIF page for reviewng/accepting uploaded CIF content has also been eliminated, and space-group preferences have been moved to the bottom of the Search page.
(13) Isotropy subgroups are always calculated automatically for method 2 -- the manual "Generate Isotropy Subgroups" button has been eliminated.
(14) Order-parameter-type selections are now grouped by chemical composition at the top of the Search page. We feel that most users prefer economy over flexibility in this feature.
(15) Many incremental developments and bug fixes accumulated during the past year.

Version 5.6.1: August 2013. (1) Fixed the symbols for type-4 magnetic superspace groups.

Version 5.6: July 2013. (1) Revised how strain is applied to a lattice. Compatible with old distortion files.

Version 5.5: June 2013. (1) Made major changes in the appearance and layout of the web pages. (2) Set the 2011 version of IR matrices the default. (3) We redefined how strain modes are normalized. This changes the meaning of strain mode amplitudes from previous versions of isodistort. When you import a distortion file that was created by an earlier version of ISODISTORT, the old normalized modes are automatically used. We also redefined strains in monoclinic and triclinic structures so that the strain modes are orthogonal to each other. (4) Removed esds (estimated standard deviations) from output. As we have added new features to ISODISTORT, these were becoming increasingly cumbersome to calculate. (5) Introduced new nonstandard tags in CIF files to give information about space-group settings. (6) Fixed various bugs that caused ISODISTORT to crash.

Version 5.4.1: (1) Fixed "karms" feature on the distortion page. Sometimes, wrong number of k vectors was listed. Now the feature is called "k-active" and is only displayed if the 2011 version of IR matrices are used. (2) Added list of active arms of the star of k for lists of order parameters (on order parameter direction page) generated by methods 1 and 2. This feature is only displayed if the 2011 version of IR matrices are used.

Version 5.4:
(1) Resolved some problems related to the decomposition of magnetic structures and the output of magnetic symmetry modes, changed the way that magnetic symmetry modes are handled, and changed the way that symmetry mode information is presented in CIFs. If you have old distortion files containing magnetic symmetry modes in supercells with non-orthogonal axes, we recommend that you import and resave them. If you have previously decomposed a magnetic structure where lattice strains were also present, your magnetic mode amplitudes will be slightly off -- redo the decomposition to correct them. If you use CIF-formatted symmetry-mode information (a format in progress), and want to better understand what has changed, feel free to contact us for more information.
(2) Replaced CGI with PHP; may have browser-dependent effects.
(3) Added the capability to create CIF files using nonstandard settings. See the fields at the bottom of the Distortion page.
(4) Added more complete Fullprof output.

Version 5.3:
(1) Superposed IRs with incommensurate k points implemented.
(2) New matrices for many IRs. These new matrices keep the contributions from different k vectors separated in the order parameter.
(3) By popular demand, improved human-readable format for saved distortion files. This fixes the problem with distortion files becoming invalid after short periods of time. Unfortunately, this means that all distortion files generated with earlier versions of ISODISTORT will be invalid. However, we expect that the new distortion files will be backwards compatible with all future versions of ISODISTORT.

Version 5.2:
(1) Amplimode-format output for FullProf

Version 5.1:
(1) Modes details for incommensurate structures. Additional information about individual atoms is given in a new option, "Complete modes details."
(2) Incommensurate magnetic structures for a single IR in search method 2. Implementation of this feature is based on private communication from J. M. Perez-Mato.
(3) Basic space-group setting option for incommensurate structures.

Version 5.0:
(1) Changed name from ISODISPLACE to ISODISTORT, since atomic displacement is only one of four different types of distortions treated.
(2) Magnetic moments and magnetic space groups.
(3) Improved decomposition algorithm in method 4 on the search page, including an optional specification of space-group origin.

Version 4.8:
(1) On the Search page, the user can select what kinds of distortions to consider. Ordering distortions are no longer shown by default, but must be selected here.
(2) User can now save interactive applet images to file. Note that allowing an internet-based applet to save files to your computer requires first accepting a security certificate that is presented when you start the applet. Everything but the new "Save Image" feature should still work if you reject the certificate.

Version 4.7:
(1) The format of the data sent by ISODISPLACE to the interactive java applets (isoDisplaceApplet.jar and isoDiffractApplet.jar) has been changed in order to make it easier for other software packages to utilize the applets.

Version 4.6:
(1) Powder diffraction capabilities added to interactive applet.
(2) Mode decomposition utility now automatically searches for probable superlattice-basis candidates.

Version 4.5:
(1) Fixed the applet so that is runs with the new version of Apple JVM.
(2) Added TOPAS.STR button to export a file for structure refinement using distortion-mode amplitudes.

Version 4.4:
(1) New method for normalization of mode amplitudes
(2) Modes details page
(3) Additional option for search method 3

Version 4.3:
(1) Includes atomic occupancy.

Version 4.2:
(1) ISOCIF utility for creating and modifying CIF files.
(2) Improved choices for monoclinic and triclinic unit cells of distorted structures.

Version 4.0:
(1) Order parameters and slide bars for atomic ordering.
(2) Incommensurate distortions leading to (3+1)-dimensional superspace groups.
(3) Width of applet controlled by user input so that it can fit on low-resolution screens.
(4) Mode decomposition of large structures.
(5) CIF output containing linear transformation between atomic coordinates and mode amplitudes.

Version 3.3:
Interactive visualization of single-crystal x-ray and neutron diffraction patterns