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processing:compute_gvectors
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processing:compute_gvectors [2019/02/20 19:47] smerkel |
processing:compute_gvectors [2023/03/14 14:29] (current) smerkel |
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| ===== O-Matrix ===== | ===== O-Matrix ===== | ||
| - | At this point, you should know the O-Matrix of your experiment. If not, go back to the section on understanding the [[processing:o_matrix|concept of the O-Matrix]]. | + | At this point, you should know the O-Matrix of your experiment. If not, go back to the section on understanding the [[dac_experiments:geometry|concept of the O-Matrix]]. |
| ===== Loading peaks ===== | ===== Loading peaks ===== | ||
| - | ImageD11 can be started by typing the following command in a terminal | + | For calculating the G vectors, we use [[software:imaged11|ImageD11]]. The software can be started by typing the following command in a terminal: |
| ImageD11_gui.py | ImageD11_gui.py | ||
| - | Peaks found during [[processing:search_for_peaks|peak search]] can be loaded by clicking on ''Transformation –> Load filtered peaks'' and choose the corresponding ''.flt'' file. You can display the peaks by calling the corresponding menu item in ''Transformation''. You can either plot peaks in the 2D diffraction geometry (y/z plot), or after transforming detector peak positions into diffraction 2θ and the azimuth η angles (2θ/η plot). | + | Peaks found during [[processing:search_for_peaks|peak search]] can be loaded by clicking on ''Transformation –> Load filtered peaks'' and choosing the corresponding ''.flt'' file. You can display the peaks by calling the corresponding menu item in ''Transformation''. You can either plot peaks in the 2D diffraction geometry (y/z plot), or after transforming detector peak positions into diffraction 2θ and the azimuth η angles (2θ/η plot). |
| If things look weird after you switch from (y/z) to 2θ/η plots of vice-versa, trying calling the ''Clear plot'' button at the bottom of the interface. ''Clear'' does only erase the plot, the data is still there. | If things look weird after you switch from (y/z) to 2θ/η plots of vice-versa, trying calling the ''Clear plot'' button at the bottom of the interface. ''Clear'' does only erase the plot, the data is still there. | ||
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| ===== ImageD11 Calibration ===== | ===== ImageD11 Calibration ===== | ||
| - | Preferably, this step should be performed with data collected on calibrant, for which you are sure of the unit cell parameters. | + | Preferably, this step should be performed with data collected on calibrant, for which you are sure of the unit cell parameters, which is free of strain, and with a controlled microstructures. |
| + | |||
| + | In diamond anvil cell beamlines, this step is often performed with a CeO<sub>2</sub> or a LaB<sub>6</sub> standard. | ||
| Go in to ''Transformation –> Edit parameters'' and enter all parameters you know. These include | Go in to ''Transformation –> Edit parameters'' and enter all parameters you know. These include | ||
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| * the O-Matrix, | * the O-Matrix, | ||
| * the x-ray wavelength, | * the x-ray wavelength, | ||
| - | * the sample to dectector, | + | * the sample to detector distance, |
| * information on beam center. | * information on beam center. | ||
| Line 42: | Line 44: | ||
| * need to refine the detector tilts. | * need to refine the detector tilts. | ||
| - | {{ :imaged11_plotttheta_straight.png?400 | ImageD11 plotting peaks in the 2θ/η plot. After calibration, and if your sample is not strained, these should appear as straight lines.}} | + | [{{ :imaged11_plotttheta_straight.png?400 | ImageD11 plotting peaks in the 2θ/η plot. After calibration, and if your sample is not strained, these should appear as straight lines. Predicted unit cell peaks positions are in red. ImageD11 crystallography is not complete. There are more predicted peaks that in the actual sample.}}] |
| At this point, you should click on ''Transformation –> Add unit cell peaks''. Red tick marks will appear which indicate the expected positions of the vertical lines. With this you can check whether your input parameters (cell parameters, detector distance, …) are correct. | At this point, you should click on ''Transformation –> Add unit cell peaks''. Red tick marks will appear which indicate the expected positions of the vertical lines. With this you can check whether your input parameters (cell parameters, detector distance, …) are correct. | ||
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| At the end of the calibration, the imaginary lines should now be completely straight (if you don't have strain). If they are not, you have more work to do. | At the end of the calibration, the imaginary lines should now be completely straight (if you don't have strain). If they are not, you have more work to do. | ||
| - | Save the experimental parameters with ''Transformation –> Save Parameters'', with a [[fileformat:imageD11_pars|.par]] or [[fileformat:imageD11_pars|.prm]] extension preferably. You will be able to use those for the rest of the processing of the current experiment. | + | Save the experimental parameters with ''Transformation –> Save Parameters'', with a [[fileformat:prm|.prm]] extension preferably. You will be able to use those for the rest of the processing of the current experiment. |
| You are ready for G-vectors calculations. | You are ready for G-vectors calculations. | ||
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| - load your peaks (e.g. the [[fileformat:flt|.flt]] file from the [[processing:search_for_peaks|peak search]], | - load your peaks (e.g. the [[fileformat:flt|.flt]] file from the [[processing:search_for_peaks|peak search]], | ||
| - make sure the ImageD11 parameters are ok or load them using ''Transformation –> Load Parameters'' , | - make sure the ImageD11 parameters are ok or load them using ''Transformation –> Load Parameters'' , | ||
| - | - Click ''Transformation// --> //Assign peaks to powder rings'' (nothing will happen) | ||
| - Click ''Transformation --> Compute g-vectors''(nothing will happen) | - Click ''Transformation --> Compute g-vectors''(nothing will happen) | ||
| - Click ''Transformation --> Save g-vectors'' and save your list of g-vectors with a [[fileformat:gve|.gve]] extension. | - Click ''Transformation --> Save g-vectors'' and save your list of g-vectors with a [[fileformat:gve|.gve]] extension. | ||
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| [[software:imaged11|ImageD11]] will use the experimental wavelength, the rotation angle ω, and the positions of the peaks on the detector in order to compute the coordinates of each g-vector in the laboratory reference frame. | [[software:imaged11|ImageD11]] will use the experimental wavelength, the rotation angle ω, and the positions of the peaks on the detector in order to compute the coordinates of each g-vector in the laboratory reference frame. | ||
| - | Note that, at this point, [[software:imaged11|ImageD11]] does not use any crystallography information. The calculations of g-vectors is a geometric operation. It is ok if the sample properties (e.g. cell lattice and parameters) in the parameter file does not match you sample. | + | Note that, at this point, [[software:imaged11|ImageD11]] does not use any crystallography information. The calculations of g-vectors is a geometric operation. It is ok if the sample properties (e.g. cell lattice and parameters) in the parameter file does not match you sample. G-vectors will be correct. |
| + | |||
| + | While [[processing:indexing_with_grainspotter|indexing grains]], however, the header with crystallographic information (i.e. cell parameters and information about fitting reflections) will be used. | ||
| + | |||
| + | ===== Optional step: evaluating g-vectors ===== | ||
| + | |||
| + | In [[software:imaged11|ImageD11]], you click on ''Indexing'' > ''load g-vectors'' and load your gve file. You can then select ''Indexing'' > ''Assign peaks to powder rings''. ImageD11 will use the crystallographic information defined in its parameters to attempt an quick indexing of the g-vectors. | ||
| + | |||
| + | The results are visible in the command window, for each potential Debye ring, the output shows h, k, l, the multiplicity of the reflection, and the number of g-vectors that can be potentially assigned to this ring. Intense powder diffraction rings should have many g-vectors assigned, low-intensity rings should have few g-vectors assigned, and extinct rings should have none. | ||
| + | |||
| + | Note that this information is not saved in the //.gve// file. G-vectors do not know which crystal they belong to. | ||
| + | |||
| + | |||
| + | ===== Optionnal step: better list of g-vectors based on cif file ===== | ||
| + | |||
| + | In some cases (complex silicates with many peaks, multi-phase indexing, etc) it can be useful to have a better list of peaks in the g-vector file. This list should be calculated from a CIF file for the phase you will try to index. | ||
| + | |||
| + | The procedure is a bit tedious, as follow: | ||
| + | * Create a CIF file for the phase you are trying to index, with the proper unit cell parameters and atomic positions, | ||
| + | * Use the [[processing:list-peaks-from-cif|timelessPeaksFromCIF]] to generate a list of peaks, with h, k, l, intensity, ds, and 2theta | ||
| + | * Peaks | ||
processing/compute_gvectors.1550692055.txt.gz · Last modified: 2019/02/20 19:47 by smerkel
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