WINPOW Rietveld refinement framework Written and collected by Kenny Ståhl Department of Chemistry Technical University of Denmark 2800 Lyngby, Denmark kenny@kemi.dtu.dk To install WINPOW in a Windows environment, simply copy the WINPOW.EXE file to your favourite Rietveld refinement program directory. Double-click the icon or drag-and-drop a rec-file to start. The Windows graphics user interface is essentially a file handler supplied with dialog boxes to edit the various input parameters and some plot routines for display of diffraction patterns, profile functions, Fourier maps and, optionally, crystal structures. The essence of the file handler is the following: The input parameters and controls are given in an input records file, the project file (name.rec). On opening a project, this project file is copied to a parameter file (%name.par). The parameter file is used internally when editing, calculating distances, plotting, etc. The only part of WINPOW that uses the project file directly is the Rietveld refinement program. In order for new parameters to have any effect on further refinements, the parameter file has to be copied back to the project file, i.e. the project has to be updated. You can “update” using the menu item “Update” in the “Edit project menu”, do “Update and Run” in the “Run” menu or by pressing “Refine”, “Compare” or “Calculate” from a dialog box. The Rietveld program will as its main result produce a new parameter file (%name.par). The new parameter file may then be examined and modified before a new update of the project file and a new refinement. It is possible and advisable to occasionally backup the parameter file. The refinements can then be restored from this point. Default file names for output files are created from the project file name stripped of extension, with a leading % and an extension according to its use. WINPOW also make use of a general text editor. Normally Notepad from Windows is sufficient. The full path to this or any other preferred editor should be given in the winpow.ini file or in “Settings/Preferences”. Another option is to include a crystal structure viewer. Presently Mercury 3.8 can be recommended. It can be downloaded free of charge from http://www.ccdc.cam.ac.uk/. The full path should be given in the winpow.ini file or “Settings/Preferences”. Just a few more unsorted hints: · When starting a new project, make sure all your files related to that project (powder data files, CIF-, edt-, exp-, mlt-files etc) are in the same directory. There may be problems to handle a project from more than one directory, i.e. WINPOW will start by setting a default directory for the project. However, when saving a project with “Save project as” it is possible, and sometimes advisable, to change directory. Only remember that all files associated with the new project must be in this new directory. · Dragging with the mouse you can zoom the pattern plot. The full pattern is restored with F1. Using the arrow keys you can move an expanded window left or right, zoom out (up) or zoom in (down) it. · WINPOW uses “site occupancy factors” (SOF), i.e. occupancy factors should normally be given as 1.0. It is the user’s responsibility not to refine special coordinates and keep track of restrictions in coordinates and anisotropic thermal parameters, although some help is given in the Edit atom menu. · Space group symbols are assumed to be entered according to the old International Tables Vol. 1. However, new symbols like Fm-3m will be automatically transformed to Fm3m. When there is a choice of origin, the program will always assume the one with inversion at the origin. For those 20 spacegroups with an origin ambiguity, there is an optional “Change Origin” button in the Edit Phase menu, which will allow you to switch between the different origin choices. · Rhombohedral structures must be given in their hexagonal settings and monoclinic with a unique b-axis. · Do not start refining occupancy factors from zero, or splitting of special positions from exactly the special position. The derivatives usually become zero, and the program stops. · The atomic types are entered as the atomic numbers. The form factor curve (X-rays) and scattering lengths (neutrons) are stored in the program. Also anomalous scattering factors are stored for a set of fixed wavelengths (Ta, Ag, Mo, Cu, Co). When the wavelength does not match those wavelengths it will use interpolated values. This may be a serious problem if you have atom types which are close to their absorption edges. In order to have correct anomalous scattering factors it will be necessary to calculate them separately and enter them manually. · It is possible to refine up to 10 different phases simultaneously. Whether or not this is advisable depends on the quality of your data and the relative amounts of the phases. Be critical! When refining more than one phase Table will calculate the weight and volume % of the phases. It is essential that temperature factors and profile parameters are comparable for the different phases otherwise this calculation becomes unreliable. Large differences in absorption coefficients between the different phases may also give unreliable results. Starting the program Double-klick the WINPOW icon or drag-and-drop a project (rec-) file on the icon. The main top window is also the graphics window; the bottom window is a text window for log messages about program actions, problems, errors and progress during refinement cycles. When the program is opened it will read a winpow.ini-file to find preferences for text editor, visualizer and starting directory as well as the four latest opened project files. If no winpow.ini-file exists, a new will be created from defaults and placed in the same directory as the program file. This file is a text file and can be edited manually. File menu Open project for an existing project, or start a new project either from defaults (manually) or from a CIF. Projects can be updated or saved as a new project. In the latter case all parameter from the existing project is transferred to the new project. It is possible to save to a new directory. The graphics area can be printed and/or saved in jpg, bmp or eps formats. The text in the log window can be printed and/or saved. The four last project files will show up at the bottom of the File menu for easy restart of previous projects. Browse for your CIF. Name a new project file and make sure it is placed in the same directory as your CIF and diffraction data. The new project file name must be new, otherwise the program will use an old project. Settings menu The debug setting will generate a number of pop-ups to help finding out where the program fails. (May be tiresome). The colour of the graphics frame can be selected. Preferences for text editor, visualizer and starting directory can be set (see below). These will be stored in the winpow.ini-file. Edit project menu Give access to Files, Control parameters, Global parameters and Phase specific parameters. With ‘Add phases’ a new phase can be entered either from defaults (manually), a CIF or from a previous project file. For multi-phase refinements, phases can be deleted. ‘Edit all’ opens the parameter file in the text editor. ‘Update’ copies the parameter file into the project file. With ‘Backup project’ a copy of the parameter file is saved as %name.bck. With ‘Restore project’ a %name.bck file is copied into the parameter file. With ‘View rawdata’ the contents of the raw data file are displayed with the text editor. Edit files · It is advisable to enter a proper project title as the title will appear on various outputs from the program. · It is essential to specify the raw data input format so as the program can correctly read your powder diffraction data. If your file extensions are given accordingly you can easily browse for the raw data file. · Unless you want to use special background and weighting files, the rest of the input can be left unchanged. · When a background file is entered, this will be subtracted with the background factor given. It is possible to refine this factor by checking the box. · When refining a set of data, the environmental info can be used to include temperature, pressure, time, sequence number etc. It can later be extracted for output in tables. Edit controls · Some default settings are: X-rays, pseudo-Voigt profile, 5-peak asymmetry, Chebyshev background and weighting by 1/Yobs. · Corrections: With synchrotron radiation use a polarization of 0.02. With a Guinier camera the standard angle is 45°. For autodivergence slit the standard value is 12 mm. The cylinder μR is for capillary samples and the value has to be calculated manually. The μ-value can be found in the Table output. · The wavelength is by default set to CuKα1 and CuKα2 with an α2/α1 ratio of 0.5. With only one wavelength it should be entered in both places and with a ratio of 1. · Least-squares control: No. of halfwidths in peak is by default 10, but can be increased to 25 for simple structures. With more complicated structures a too high value will result in a program halt due to “excessive peak overlap”. Try reducing this value. · Diagonal damping will reduce the least-squares shifts and may dampen wild behaviour of the refinements. Convergence will normally be slower. Suitable values are in the range 1.01-1.10, 1.00 corresponds to no damping. · Refining every second step will speed up initial refinements. · The 2θ-step given will only affect pattern calculations. For refinements and comparisons, the 2θ-step is found from the diffraction data. When non-standard wavelengths are used it may be necessary to enter anomalous scattering corrections manually. The atom type is entered with one or two letters. Note that the atom type on the coordinate records now must refer to the numbers to the left. Up to 20 excluded regions may be entered. Edit globals · Use only the constant 2θ-zero correction. Never use more than one type. · Do not change the wavelength part. It is an option for wavelength refinements in connection with synchrotron or neutron data only. When used, remember to fix the unit cell parameters. Press “Update” to update the value in the Controls menu. · The number of background parameters should be determined from their standard deviations. If the actual background parameter is less than 2-3 times the standard deviation it can be omitted. Check the output in Table. Edit phase · When starting a new project, make sure all parameters, spacegroup etc is correctly interpreted by the program. · Preferred orientation: It is possible to use two different directions, but unless special reasons use only one. · In order to refine a parameter write 1 in the small refinement code word box to the right of the actual parameter, or below in case of atomic parameters. Parameters can be coupled by adding a number multiplied by 10. For example, to couple the x- and y- coordinates of an atom, use the code word 11 in the x- and y-code word boxes. If you want to couple some other parameters you have to add 20 and so on. The atomic occupancy factor, g, is assumed to be a site occupancy factor, i.e. it will normally be 1. If you have mixed occupancies and are entering two or more atoms in the same position, the occupancy factors have to be adjusted accordingly. Remember that when refining the coordinates, occupancies, g:s, and temperature factors, B:s, of such a set of atoms, the coordinates, occupancies and B-factors should be coupled. · The program does not necessarily treat atoms in special positions in any special way. It is the user’s responsibility to ensure that only refinable coordinates are refined and coordinates are coupled appropriately. Consult International Tables Volume I or Volume A for your spacegroup. Atomic parameters can be edited directly in the Phase menu or by pressing the Edit button. When using the Edit menu, symmetry restricted coordinates will be greyed. Restraints can be set up with the restraints menu. Select a central atom and press OK. Ligands within the min. and max distances will be listed. Check your choice and press OK. The coding will appear below. Remember to set the overall weighting factor in the Controls menu. Run menu “Run” or “Update and run” will start previous “Calculate”, “Compare” or “Refine” command. “View output” will show the output from the Rietveld refinement section. It is sometimes a good way to find out where and why the program had stopped inadvertently. Plot menu “Full pattern” or F1 will reset any zooming. “Plot halfwidths” or F2 will show the FWHM and gamma factor as functions of 2θ. “Plot structure” or F3 will draw the structure if a structure drawing program has been given (see Preferences). The appearance and colours of the powder plot can be adjusted. Fourier menu Fourier calculations can be performed according to the settings in “Fourier options”. The found peak positions can be (temporarily) added to the atoms list and distances calculated. Peak positions can be picked from a list and added (permanently) to the atoms list. The Fourier maps can be plotted. Select type of Fourier synthesis. Set scan level for peak search. Set data limits and cut-offs. Set the summation limits. It is advisable to set the limits slightly beyond the actual limits for the asymmetric unit. Otherwise peaks on the border may be missed. Mark the peak you want to add to the atom list and press Add. The added peak will be deleted from the peak list. Output menu “Table” will generate a table containing information on all parameters and settings for the Rietveld refinement. “Table+” will in addition give a list of reflections (may be long). “Distances and angles” will give a list of distances and angles. “CIF” will generate a CIF. Please note that this file have to be substantially edited before it can be sent to a journal or for deposition. To get a complete list of relevant distances and angles it may be necessary to increase the default calculation limits. The crystallinity can be calculated in a given 2θ-interval. Please note that the result is only valid if the refined background is exclusively a result of amorphous scattering. SHORTCUTS F1 Full pattern F2 FWHM and peak shape vs. 2θ F3 Structure plot (if a suitable visualizer is given, see Settings/Preferences) F5 Edit Files dialog F6 Edit Controls dialog F7 Edit Globals dialog F8 Edit Phase 1 dialog F9 Edit Phase 2 dialog F10 Edit Phase 3 dialog Alt+F4 Edit phase 4 Alt+F5 Edit phase 5 Alt+F6 Edit phase 6 Alt+F7 Edit phase 7 Alt+F8 Edit phase 8 Alt+F9 Edit phase 9 Alt+F10 Edit phase 10 Ctrl-I Soft interrupt Ctrl-U Update and run Ctrl-B Backup project file Ctrl-R Restore project file Ctrl-D Distance and angle calculation Ctrl-T Table REFERENCES The Rietveld program is based on the LHPM1 program by R.J. Hill and C.J. Howard (ANSTO Report M122, Lucas Heights Research Laboratories, Australia, 1986). It has been extensively modified to allow for variable step data, Chebyshev polynomial background, restraints, split pseudo-Voigt profile function, asymmetry according to Finger, Cox and Jephcoat, transparency corrections etc. The distances and angle calculations program and the Fourier calculations and Fourier plot programs are based on DISTAN, FORDUP and FOPLOT by J.-O. Lundgren (Uppsala University Report No. UUIC-B13-4-05, Uppsala, Sweden, 1983). Also these programs have been modernised and extensively modified to fit into the WINPOW framework. MULTIPLE REFINEMENTS MLT - run a set of rec-files through WINPOW Create a text file containing a list of the names of the individual rec-files. Save the file using “mlt” as file extension. Open this mlt-file in WINPOW and start refinements. The mlt-file can be edited using “edit all”. N.B. update will be necessary for the changes to take effect. After refinements the program will ask if you want to update the files. You can update individual files, all files or none. (Make sure the “Notes” window is active before responding.) Rerunning the mlt-file will now be from the updated rec-files. N.B. If you run Table or Distan you will obtain the results from all the rec-files in one output file. EXP - expansion of for example a temperature run With a large number of data sets with small structural changes in between, it is practical to be able to start the next refinement with parameters from the previous. Again, create a text file, now with the extension “exp”. It should contain for each refinement the rec-file name (even if it does not yet exist), the lines in the rec-file that need to be changed from the previous rec-file, plus one blank line: pz35b_450.rec TITL PbNb2O6 pz35b 450 PWDT pz35b_450_bgs.xy PWWG pz35b_450.xy Starting WINPOW with such an exp-file will always start from the first rec-file and then apply the same set of parameters to the following rec-files. If your data contain abrupt changes, phase transitions etc, it is likely that this procedure will screw up. In this case the exp-file should be split up into several files, each for data sets containing reasonable changes. EDT - multiple refinements with changes of parameters If you want to introduce changes like locking parameters for all data sets, these can be introduced in an edt-file. Like before, create a text file with the extension “edt”. It should contain the rec-file name, the lines that you want to change and a blank line for each data set. BaCuSi_095.rec PKSH 0.35 CPKS 0.00 Now refinements will start from existing rec-files and work very much like with mlt-files.