MAUD指导手册.doc

Processing radial diffraction data with Maud(/RDX/index.php?n=Maud.RadialDiffraction)Ok, Ill assume that you have done your radial diffraction experiment, in angular dispersive geometry. You also have your calibration and data files ready for processing. Outline of the tutorial 一、 Preprocessing of data with Fit2d 1. Why? 2. Calibration with Fit2d a) First steps b) Calibration c) Calibration check. 3. Conversion of data with Fit2d a) Maud input files b) Binning of diffraction data with Fit2d: manual c) Binning of diffraction data with Fit2d: automatic d) Converting chi file series for use in Maud 二、 Maud Calibration 1. Starting Maud a) Loading the data b) Setting up instruments parameters c) Restriction of the data interval d) Phases e) Save the file 2. First Step: Manual Adjustment a) Incident intensity and first background parameter 3. Global refinement a) Incident intensity, detector distance, and main backgrounds b) Incident intensity and peak profiles c) Individual backgrounds d) Detector re-calibration e) Material properties f) Putting it all together g) The perfect Calibration 4. Check Orientations a) Importance of orientations in the refinement b) Setting orientations in MAUD 5. Intensity calibration a) Polynomial angle intensity b) Refining parameters for the Polynomial angle intensity model三、 Data processing 1. Setting up Maud a) Setting up Maud b) Loading the data c) Setting up a material 2. Unit cell and backgrounds a) Manual adjustment b) Refinement cycles. c) Do you have stress? d) Do you have texture? 3. Stress a) Residual stress (lattice strain) analysis b) Applying residual stress c) Refinement 4. Lattice preferred orientations a) Displaying LPO b) Preferred orientation models c) E-WIMW: no symmetry d) E-WIMW: symmetry 四、 Advanced topics 1. Define the compression direction a) Data coverage in axial and radial diffraction experiment b) Finding out orientation coverage in Maud c) Locating the compression direction d) Fixing things out 2. Pole figures and data coverage a) Using pole figures to represent directions in space b) Data Coverage In Axial Diffraction Experiments c) Data Coverage In Radial Diffraction Experiments一、Preprocessing of data with Fit2d Why should you use fit2d?Maud does include some utility to convert Tiff images directly. However, in the context of high pressure experiments, I prefer to perform a first processing with fit2d before starting a refinement in Maud. Why? Here is the list I use Fit2d anyway o on the beamline, o to have a first look at the data, o to calibrate the wavelength, detector distance, detector tilt. o and I know it well. Not all diffraction images are in Tiff format If you really want to use Maud to convert the images o you still need to define a beam center, one way or another. o you might not be consistent from one image to the next. High pressure data tend to be dirty, with a lot of background, huge stresses, and very few peaks. Therefore, I find it easier to start a Rietveld refinement if I corrected some of it already. Now, I should point out that beam center, detector tilt, and detector distance from fit2d will only be used as a starting point. detector tilt and detector distance will be recalibrated in Maud, with the standard, beam center will be adjusted in Maud for each diffraction image. Calibration With Fit2dOn the use of a standardFirst stepsIf you did your experiment properly, you should know the wavelength at which you performed your experiment, have the diffraction image from a standard. CalibrationThe diffraction image from the standard is used to calibrate many things such as detector tilt or beam to detector distance. In Fit2d, go into the Powder Diffraction (2-D) submenu select the Input button, and choose the diffraction image from your standard. Dark field, flat field, and spatial distortion correction depend on the experimental setup. In general, data from Rigaku or Mar345 image plates do not require any correction, but you should talk with your beamline scientist for more information. Once the data is loaded into fit2d, you can calibrate your experiment as follow select Calibrant, select the material you used or, if not on the list, User Defined, if you selected User Defined. you will need to create an input file with the d-spacings of your material, one after the other, and one per line. For instance, this is an input file corresponding to silver In the following panel, enter an approximate sample to detector distance, the correct wavelength and pixel sizes. You will refine the beam center, detector distance, and detector tilt. You will not refine the wavelength. You will be asked to select a few points along the inner ring. Do so (about 6 of them, and all around the ring if possible). And let it go. At this point, fit2d should be able to work alone and calculate a calibration. To obtain the numerical results, click on Integrate and you should see a panel like this one. Calibration check.You still need to make sure that your calibration is Ok. Sometimes, things can go wrong and you HAVE to catch it now otherwise your whole analysis will be wrong! Calibration check is done visually with the Cake function: In the main Image Processing Menu. Choose the Cake function. When asked what to do with the beam center, select No Change Start azimuth should be zero if you have full diffraction rings. End azimuth should be start+360 if you have full diffraction rings. Inner Limit can be beam center, or any point before the rings youre interested in. Outer Limit should be after the rings youre interested in. In the cake function main menu, choose Integrate. First set of numbers should be OK. Second set of numbers should be OK as well. You should get an image like this one: Cake Image in Fit2dMake sure that all rings became straight lines (zoom-in, test. really carefully). If theyre not: something is wrong with your calibration. Sometimes (on Linux for instance) zooming functions seem to be crashing: simply remove the double-click option and youll be fine. To go back to the main diffraction menu with fit2d, click on Exchange and Exit. Youre ready for the next step! Conversion Of Data With Fit2dCreating Maud Input files with Fit2dMaud input filesTo process your data with Maud, you will need to have slices of data (e.g. data integrated between azimuth -2.5 and azimuth 2.5, data integrated between azimuth 2.5 and azimuth 7.5.). For each slice, you have a 2 theta / intensity diffraction pattern for use in the Rietveld refinement. Binning of diffraction data with Fit2d: manual First, we will use fit2d to obtain one slice of data. This step is necessarey for two reasons: we will calibrate the few paramaters needed by fit2d it is part of the learning process. Heres the trick Load up your data (or calibration file) into fit2d. Select the cake function, if you just performed your calibration or used the cake function already, you wont get any question. Otherwise, youll be asked for o A beam center, select the best option. o Start azimuth, could be zero if you have full diffraction rings. o End azimuth, could be start+360 if you have full diffraction rings. o Inner Limit, can be beam center, or any point before the rings youre interested in. o Outer Limit, should be after the rings youre interested in. In the cake menu, choose integrate First set of questions should be OK In the second set of questions, we want to a slice of data between azimuth -2.5 and azimuth 2.5, integrated onto a 1-D spectrum, therefore o select -2.5 as start azimuth o select +2.5 as end azimuth o select 1 as number of azimuthal bins o Intensity corrections (be careful with this, new 01/20/2006). There are options in fit2d to apply corrections to the integrated intensity. For the results of fit2d to be compatible with MAUD, you want to set Intensity conservation to NO and Geometrical corrections to intensity to NO as well. Maud will do the intensity corrections by itself. Click OK and fit2d will integrate your slice of data: A slice of data in fit2d On Linux platforms, there may be a bug: the Y-Axis will be labelled with strange symbols or nothing at all: THIS HAS TO BE CORRECTED! otherwise the rest of the analysis will crash. o select Exit, Options, Z-Axix Label and enter whatever you wish (I like Intensity). o go back to the Cake function. The data can be saved into a text file, with a chi extension. Proceed as follow o Select Exit, Output, and Chiplot o Choose your file name. o Clik OK. o Have a look at the file you just created. You can use it for plotting, or post-processing with many kinds of software. Binning of diffraction data with Fit2d: automaticFor the analysis of radial diffraction patterns, one has to bin the data over a large number of orientations. One could repeat the process above by hand, but 5 degrees slices over 360 degrees represent 72 chi files, so creating them by hand could take a while. Luckily, one can script fit2d and things become easier. In any case, the process above has to be performed at least once: to calibrate parameters such as inner and outer radius, but also to correct the nasty bug on Z-Axis label on unix platforms. To create macro files for Fit2d, one can use the sofware Fit2d2maud. Simply download the archive a run it: on a mac or windows: double click on the file on unix: type java -jar fit2d2maud.jar The Fit2d2maud main windowYou will be asked to define the wavelength and sample to detector distance the directory with the diffraction data the directory that will contain the chi files the directory that will be used to store the Maud data files I strongly recommend that you use separate directories for all of those. Once everything is set up, click on Create Macro for Fit2d youll be asked to define basename, start azimuth, end azimuth and interval. For instance, if you choose agCalib for basename, 0 for start azimuth, 360 for end azimuth and 5 for interval, the macro will create the following chi files agCalib_0.chi for a slice integrated between -2.5 and 2.5agCalib_5.chi for a slice integrated between 2.5 and 7.5agCalib_10.chi for a slice integrated between 7.5 and 12.5 .agCalib_360.chi for a slice integrated between 357.5 and 2.5 Macro will be saved in a file basename.mac in your data directory. Running the macro in fit2d, make sure that you have the image of the 2-D diffraction pattern (play with the exchange button) leave the diffraction mode: Exit enter the macro mode: Macros / Log file select Run Macro, choose the file you just created (agCalib.mac in my case), and fit2d should go ahead and create the chi files (72 of them if you chose and interval of 5 degrees between 0 and 360 degrees). Converting chi file series for use in MaudIn Maud, data are stored in a file with an esg extension. They contain all data for all azimuth angles within a single text file. The fit2d2maud software can convert series of chi files into esg: click on Convert Chi to Esg enter your basename, start azimuth, end azimuth and interval. click OK. Fit2d2maud will read all chi files and create a big esg file for use in Maud. In my case, I have 72 chi files, each of them is 50 kbytes, and the esg file is 2.3 Mbytes, so it takes a few seconds. but it works. Maud Calibration Starting MaudMaud StartupLoading the dataStart Maud, youll probably have an empty window asking to load a datafile. Select the dataset in the tab on the right, and click the eye icon to edit. Starting upMauds Dataset WindowIn the dataset window, select the Datafiles tab to load the data. Click on Browse and select the esg file you created earlier. All the 2-D diffraction patterns you created with fit2d should show up. If you select one of the datasets and click on view, you should be able to plot it. You can zoom in, and do many other things. Play around and explore! If the data does not show, try to set the instruments paramaters (see below). Maud will not plot the data if the data in the ESG file is incompatible with the instrument. Setting up instruments parametersMaud instrument windowIn this same dataset window, select the general tab, edit the diffraction instrument, and youll end up with the Instrument Window. For radial diffraction experiments, select Intensity Calibration: none cal, no option Angular Calibration: Flat Image Transmission, options: entre the correct Detector Distance, in millimeters Geometry: Image 2D, options: select Monochromator Measurement: 2 theta, no option Source: Synchrotron, option: entre the correct Wavelength in angtroms Detector: Scintillation, no option. There are many other options for the Angular Calibration (tilt, beam center.), they will be refined later on. New 01/20/2006! Also, in the Aberations tab, make sure that the assymetry coefficients are set to 0. In general synchrotron data should not use those parameters. Restriction of the data intervalIn this same dataset window, in the general tab, you have the option to restrict the 2 theta interval to work on. Enter the minimum and maximum values of 2 theta you want to work with, and press Apply Now. The 2 theta interval has to be selected in a way that you have relevant data for all orientations. You should also inspect ALL patterns for orientations and make sure that nothing is wrong (large spot, weak intensity because of a beam stop.). If anything is wrong, simply remove the spectra for this orientation (hit Remove). I you have an interval over which the data should be ignored, you can set it up in the Excluded Region tab. Click Add Term and enter the 2 theta range you want to exclude. PhasesPhase definition in MaudIn the main Maud window, on the right side, select the Phases tab. It should be empty. You can create a new one (box icon, right next to the eye) or load a sample from the database (following icon). Things are much easier if your material is in the database: click on the icon select the file structures.mdb in the Maud directory if youre lucky, your phase is in the list. If your material is not in the database, youll have to create a new phase: click on the icon: itll add a phase called phase_x in the phase list select the phase_x and click on the eye icon (edit): youll end up with the phase window, in the General and Structure tab, enter the information on your material. Save the fileAt this point you are done with the initial setup. You should save everything before starting to your refinement: in the File menu, select the option Save As choose a file name with the .par extension. First Step：Manual AdjustmentIncident intensity and first background parameterAt this point, a few parameters can be adjusted by hand: incident beam intensity and background. Maud with a calculated spectrumManual adjustment of parameterFirst, you should calculate a spectrum: in the main Maud window, click the the Calculator icon, and the Maud window should look like this: in black: the calculate pattern, in blue: the experimental data, both for the first azimuth. Unless youre really lucky, its probably very far off. Now, Maud has a very good function that allows you to manually adjust paramaters and see the effects immediately: in the main window, select the Dataset panel, and edit your dataset (click on the eye icon) in the dataset window, select the Datafiles panel, and select on of the spectra, click on View, in the View window, select the Tools menu and Change Parameter option, and you should end up with something like the screen shot that allows you to manually adjust parameters. In the panel, adjust both Intensity (scale factor) Background Polynomial Coef 0 of the Dataset in order to get something reasonable. You will notice that your peaks do not exactly match the experimental data in terms of peak positions, peak profiles, ratios of intensities, high order background parameters. We will now adjust all of this with a real refinement. Maud plot window after a first manual refinementGlobal RefinementRietveld RefinementRefinement of parameters with MaudIn the main Maud window, the parameters to refine are located in the main window, below the plots. You can force the refinement of a parameter by clicking on Fixed, it should bring up a menu to set it to Refined. Incident intensity, detector distance, and main backgroundsForcing Maud to refine intensitiesAs a first step, we will refine: the incident intensity the sample to detector distance the main background paramaters, under dataFileSet_x, background polynomial coeff 0, background polynomial coeff 1 and background polynomial coeff 2. Once you have made those parameters as Refinable, hit the hammer icon (on top of the window), and youll see the refinement results. Once the refinement is finished, in the bottom panel, you can see the new value of the parameters, and an error. If this error is equal to -1, there was an error: Maud is not able to refine this parameter. You can plot the result in many way: by going back into the dataset, selecting a datafile, and hitting View. in the main window, by using the Plot 2D function: it will show you the original dataset (below) and the recalculated one (above). At each step, you should always check that you fit is Ok and that