Tutorial isoriet wo3 simple
Symmetry-Mode (ISODISTORT) Rietveld refinement – WO3
Files needed: wo3_pm3m.cif, wo3_p21n_80056.cif, d8_03901_030c_traditional.inp, d8_03901_030c.xy
Learning Outcomes: This example is based on lab x-ray diffraction data from the distorted structure of room-temperature WO3, which has space group P21/n (#14) and a 2 x 2 x 2 supercell relative to the cubic ReO3 parent structure. Because each of the atoms sit on general Wyckoff sites, there are a total of 24 displacive degrees of freedom. We will begin by decomposing the structure reported by Woodward et al., J. Phys. Chem. Solids 56, 1305-1315 (1995) into symmetry-motivated distortion modes relative to the cubic parent. We will then modify a working TOPAS input file to use symmetry-mode amplitudes as the refinable structural parameters. On this basis, the redetermination of the structure is fairly straightforward.
Authors: Branton and John.
Note: the tutorial was written for jEdit, but you can use VS Code topas-editor instead. The only difference is that you follow the standard menus for “Rietveld or Pawley INP file” then select “Structure from str or ISODISTORT” at the relevant point.
Note: June 2025. To view distortion modes in step 4 you may need to save an isoviz file and run isoviz as a stand alone application (see the isodistort page for how to do this). Alternatively you could try the development visualiser on the isodistort site.
1 Download the files listed above to the working directory on your local computer. The TOPAS input file provided will allow you to start with working refinement of the P21/n structure of WO3 using traditional xyz atomic coordinates — the profile shape, cell parameters and other experimental details have already been worked out.
2. Go to the ISODISTORT website and follow the “Import parent structure from a CIF structure file” instruction. Browse to find the “wo3_pm3m.cif” file in your working directory, click the “Upload” button, and then click “OK” to proceed to the “search” page.
3. Under the heading “Method 4: Mode decomposition of a distorted structure”, upload the distorted WO3 structure file from “wo3_p21n_80056.cif” and click “OK” to proceed to the “distorted structure (basis)” page. Here, select 2,0,0,0,2,0,0,0,2 from the drop-down menu of candidate basis and keep all other default settings. Click “OK” to perform the mode decomposition.
4. Having arrived at the “distortion” page, use either the interactive viewer or isoviz to view the distortions. For isoviz, first save the interactive distortion file to a local disk. Back on the “distortion page”, click on the “TOPAS.STR” bullet then OK to save this child structure to a file called “wo3_p21n_isodisplace.str” in the working directory.
5. Copy the traditional input file (“d8_03901_030c_traditional.inp”) to a new filename (“d8_03901_030c_symmodes.inp”) and open the new file in topas-editor or jEdit. Run a single-convergence refinement in TOPAS to verify the quality of the fit. Rwp should be approximately 8.8% with 26 refined parameters.
6. Convert the input file (“d8_03901_030c_symmodes.inp”) to use symmetry modes as follows.
(a) Use “/* …. */” to comment out the entire str section, including the five lines at the bottom from “scale” to “Phase Density_g_on_cm3”.
(b) Create a few blank lines above the old str section and position the cursor in this space in preparation for creating a new str.
(c) Within topas-editor TOPAS_Durham/Rietveld/4. Rietveld or Pawley” select “Strcutre from str or ISODISTORT”. This will read in the structure. There may be a typo in the line that says “site origin…” a space is needed between the word “origin” and “num_posns”; alternatively you can delete the line altogether as it’s not needed. If you use jEdit then copy/paste from the str file and add any other lines needed.
(d) Copy the cell parameters from the old str section and use them to replace the cell parameters in the new str section. Also copy the TCHZ() peak shape line. Change the space group to “P21/n”.
(e) In topas-editor try hitting ctrl-k0. This will fold away the ISODISTORT equations and make the INP file easier to navigate.
7. Turn on an overall isotropic thermal parameter for each atom by adding “bval 0.5” immediately after each “beq” keyword. Observe that the excellent fit to the data means that mode amplitudes are already pretty good based on the decomposition of the published structure.
8. Set all mode amplitudes to zero and fix them with !. Do a single-convergence refinement of the scale factor by itself. The result should be pretty ugly. Then enable only the five most important modes (a1, a3, a7, a8, a19) that we identified from the decomposition, and switch to simulated-annealing mode by uncommenting the “continue_after_convergence” and “randomize_on_errors” lines. Run several convergence cycles, which should bring Rwp down below 10%. Much of the work is done now. Note that in old versions of the tutorial it used to be (a2, a3, a7, a8 and a19) that were needed. This is probably just relabelling in ISODISTORT.
9. Turn off “continue_after_convergence” and refine all the mode amplitudes from this point. The model should converge rapidly to an Rwp near 8.8%. Note that turning on all 24 symmetry modes at once would not have helped much, even in simulated annealing mode. Knowing which modes are important is more than half the battle. How might one figure out which modes are important without prior knowledge of the distorted structure?
10. To bypass the workshop exercise and go straight to the result, download this input file: d8_03901_030c_symmodes.inp.