GSAS Tutorial - Steps in Refinement

Leslie Struble (University of Illinois) and Paul Stutzman (National Institute of Standards and Technology)

Version 1 (March 2015)

Steps in Refinement

This section is taken largely from Cranswick and Swainson [7]. Additional information is given there, with many figures showing the interface window and many specific examples. The program offers many options, but the instructions here are limited to those you are expected to use in these tasks.

1. Run EXPGUI. This opens a text window and an interface window. Use the interface window to set refinement parameters. Some results will be returned to you in the text window, which can also be used to monitor the .lst file. The interface window has drop-down menus at the top that lead to usa-buttons that call for specific action and tabs that take you from one window to another. From here on, instructions are given only for this window (in terms of menu, usa-button, or tab).

2. Open a new or existing .exp file. When you first run EXPGUI, the program instructs you to open an existing file. If EXPGUI is already running, you may open a file using the file drop-down menu. If you wish to create a new file, type in the desired name and click the read usa-button.

3. Enter crystal structure data for phases in the .exp file. Note that qualitative analysis must be done (JADE is one of a number of graphical display programs for XRD data) before undertaking the refinement. (Note that the GSAS program refines rhombohedral structures in the hexagonal setting.) To enter structure data, select the phase tab and then the add phase usa-button. This will bring up an add new phase dialog where you input the phase title, the Space Group (R –3 c) (make sure to include the spaces), and the unit cell values. Then select the add usa-button. GSAS will then give a symmetry analysis output for you to check to make sure you have entered the space group correctly (use the International Tables or similar database to validate the output). Select continue once you are satisfied with the structure data. This will give the main EXPGUI screen with the cell information but no atoms.

   Now select the add new atoms usa-button and add in the atom information using the keyboard.

   Select the add atoms usa-button to go back to the main EXPGUI screen where all the crystallographic information is now visible. The GSAS default values for vibrational parameters, UISO (0.025), are usually too large for inorganic structures, so it is better to reset the starting UISO values to 0.01 (by selecting the UISO values one at a time with the mouse and changing to 0.01). The structure database contains vibrational parameters, which are generally best retained and not refined.

   An alternate way to add phase data is to import it directly from the database. This approach can be used after you gain experience entering the structure data manually. When you select the add phase usa-button and a new box appears, use the option in the lower right to import the phase data. Four options for import file format are provided--select the GSAS .exp format (the .cif format is also provided in the database), which will open a third box to search subdirectories for the appropriate .exp file for the phase you wish to load. After selecting a specific .exp file, the add new phase box will be automatically filled out with the data for that phase. If the .exp file contains multiple phases, a list will be shown for selection of the specific phase. Select Continue and a list of symmetry operators appears; upon acceptance of the defaults, a list of atoms, coordinates, occupancies and vibrational parameters is displayed. Select add atoms to complete the import of the remaining structure data as a new phase. You may wish to replace the default phase title in EXPGUI to the actual phase name, otherwise it reflects the path and filename of the .exp file.

4. Create or open an instrument parameter file. For the tasks in these instructions, open the file provided, which contains the parameters from Stutzman for the powder data used here. But if you wish to create a new file, select from the top menu Powder, Instedit.

   The instrument parameter file format is discussed in the GSAS manual (page 228).

5. Open a histogram (powder diffraction data). Select the powder tab followed by the add histogram usa-button. Find and add the data file and the instrument parameter file. If you wish to edit this file, select from the top menu Powder, Instedit.
6. Fit the background. This is a preliminary fit, which you will refine below. First run powpref followed by genles using the usa-buttons. Then fit a GSAS background function to the data. Now select the save in EXP file & exit icon at the bottom right of the screen to save the fitted background profile. When EXPGUI prompts that the EXP file has been modified, select load new.
7. Fit the profile. In the profile tab, set the profile type to 3 (Pseudo-Voight with Finger-Cox-Jephcoat peak asymmetry function).

8. Perform refinements. For each refinement, run genles using the usa-buttons, preceeded by powpref when you have changed specific variables such as peak profile cutoff, or peak profile, sample displacement, or an instrument parameter. GSAS generally will warn you if you are attempting to run genles after changing a key parameter. Run liveplot (and keep this window open) to see the state of the refinement in terms of how well the calculated pattern is fitting the data. The black crosses are the raw data; the red line is the calculated pattern and the blue line below is the difference. The aim is to get the calculated pattern to match the observed pattern so the difference is as close to a flat line as possible. Set the number of cycles to 8 and in the profile tab set the profile cutoff to 0.001. (Since you have changed the peak profile cutoff, you will need to run powpref before you run genles.)

   There is no fixed order in which to release parameters when performing a Rietveld refinement. Ideally, all parameters should be refined simultaneously. But when refining complicated mixtures like clinker or cement, some phases and parameters inevitably correlate, and a sequential refinement reduces the likelihood of problems related to the correlations. The instructions here provide suggestions and should not be blindly followed in all cases.

   Monitor the difference profile plot to assess your refinement. A valid refinement shows only minor differences between computed and measured patterns.

   Monitor the Χ² in the text window. If this increases progressively, the refinement is diverging and you should stop, determine which highly-correlated variables may be creating the divergence and deselect refinement of one, or revert to an earlier .exp file (see the section titled Helpful Hints) and then continue. A correlation matrix is included in the .lst file if Print Option #2 of the LS Controls tab of EXPGUI is selected..

   Multiple parameters may be refined at the same time, but you must be careful if the parameters are cross-correlated, as refinement results may be misleading. The correlation matrix indicates parameters that are cross-correlated. For some parameters a constraint makes sense and reduces potential correlations. For example, specimen displacement affects all phases similarly so a constraint in the peak profile parameters for this variable will hold each to the same value (set through the Peak Profile Constraints window).

   Refine scale and background.

   Refine the shift, unit cell parameters, and peak (GV) width.

   Set peak profile cutoff to 0.001 and run powpref and then genles.