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processing:synthetic_dataset

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processing:synthetic_dataset [2019/01/17 15:22] – estelleprocessing:synthetic_dataset [2019/02/23 20:43] (current) – [Input file example 3: olivine from a CIF file] estelle
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 ====== Creation of the synthetic dataset ====== ====== Creation of the synthetic dataset ======
  
-Synthetic data sets are useful to learn how to process data. You can input the experimental parameters you will use in your actual experiment and your actual sample. The software to do so is [[software:polyxsim|PolyXSim]]+Synthetic data sets are useful to learn how to process data. You can input the experimental parameters you will use in your actual experiment and your actual sample. The software to do so is [[software:polyxsim|PolyXSim]]. 
 + 
 +For high pressure experiments, the purpose of this step is to simulate the outcome of a DAC experiment (grains with random orientations, random strains etc.). You can check the possible outcome of an actual experiment. You can also check if your workflow for data processing is actually working as the input parameters are known.  
 + 
 +The simulation will provide 2D diffraction images but also G-vectors, inverse UB matrices (UBi) for all grains, and some more files. You will get at least 7 different files from the simulation as well as the diffraction images. The amount of diffraction images depends on the ω range and the step size defined in the input file. For example, a ω range Δω = [-28°;+28°] with a step size δω = 0.5° produces 112 images (with numbers from 0 to 111). 
  
 ===== Basic usage ===== ===== Basic usage =====
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 This third example is a test of calculation from a [[fileformat:cif|CIF file]] for the crystal structure. In order to run this simulation, you need to install the [[software:PyCifRW|PyCifRW]] python package otherwise it will not work. This third example is a test of calculation from a [[fileformat:cif|CIF file]] for the crystal structure. In order to run this simulation, you need to install the [[software:PyCifRW|PyCifRW]] python package otherwise it will not work.
  
-Our problem was that the widely used space group for olivine, Pbnm, do not have a space groupe number and we need a space group number for the index.ini input file for GrainSpotter. So we use a CIF file to translate the cristallographic properties from Pbnm to Pnma, an other space group used for olivine, which have a space group number. The transformation is not complicated, it is only an interchange of axis : +Our problem was that the widely used space group for olivine, //Pbnm//, do not have a space groupe number and we need a space group number for the index.ini input file for GrainSpotter. So we use a CIF file to translate the crystallographic properties of olivine from //Pbnm// to //Pnma// an other space group used for olivine which does have a space group number.  
 + 
 +The transformation from //Pbnm// to//Pnma// is not complicated, it is only an interchange of axis : 
   * a (Pbnm) -> c (Pnma)   * a (Pbnm) -> c (Pnma)
   * b (Pbnm) -> a (Pnma)   * b (Pbnm) -> a (Pnma)
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 But we need to specify it to PolyXSim in order to have the good symetry of the olivine, and hence, the good corresponding diffraction peaks. But we need to specify it to PolyXSim in order to have the good symetry of the olivine, and hence, the good corresponding diffraction peaks.
  
-We get a Pbnm CIF file from the American Mineralogist crystal structure database and we transform it to have a CIF file for Pnma space group. To transform it, we only change the cell length on each axes (a,b,c) like shown before, and the x, y, z axes in the symetry operations (x to z,y to x, z ot y). Do not forget to change the space group name from 'Pbnm' to Pnma'.+First get a //Pbnm// CIF file from the American Mineralogist crystal structure database and transform it to have a CIF file for //Pnma// space group. In order to do so, only change the cell length on each axes (//a//,//b//,//c//) like shown before, and the //x//, //y//, //z// axes in the symetry operations (//x// to //z//, //y// to //x//, //z// to //y//). Do not forget to change the space group name from //Pbnm// to //Pnma//.
  
 [[fileformat:cif|Here]] is the obtained CIF file. [[fileformat:cif|Here]] is the obtained CIF file.
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 Then, before the simulation of your data, in the .inp file for PolyXSim you should put a # before the space group line and make the structure_phase_0 line active. You should have : Then, before the simulation of your data, in the .inp file for PolyXSim you should put a # before the space group line and make the structure_phase_0 line active. You should have :
  
-  * ### Structural +<code> 
-  * unit_cell  10.1902 5.9787 4.7534 90.0 90.0 90.0 #unit_cell a [Ã…] b [Ã…] c [Ã…] alpha [°] beta [°] gamma [°] , Y being the phase number id +### Structural 
-  * #sgno 62              #space group number +unit_cell  10.1902 5.9787 4.7534 90.0 90.0 90.0 #unit_cell a [Ã…] b [Ã…] c [Ã…] alpha [°] beta [°] gamma [°] , Y being the phase number id 
-  * #oR +#sgno 62              #space group number 
-  * #sgname_phase_0 'Pbnm'          #remember to put quotation marks around the string if more phases  then have the keywords unit_cell_phase_1, sgno_phase_1 etc. +#oR 
-  * #or +#sgname_phase_0 'Pbnm'          #remember to put quotation marks around the string if more phases  then have the keywords unit_cell_phase_1, sgno_phase_1 etc. 
-  * structure_phase_0 'Fosterite_Pnma.cif' +#or 
- +structure_phase_0 'Fosterite_Pnma.cif' 
-Don't forget to change the order of the axes in the unit_cell line of PolyXSim too! +</code>
- +
-From here, PolyXSim simulate grains in the Pnma system so the peaks you obtain (and then the G-vectors) are in Pnma. Be carefull when comparing with real data study where the Pbnm system is more widespread! Use the space group number 62 in the .ini file of GrainsPotter to find the grains from these Pnma G-vectors.+
  
 +Do not forget to change the order of the axes in the unit_cell line of PolyXSim as well!
  
 +From here, PolyXSim simulate grains in the //Pnma// system so the peaks you obtain (and then the G-vectors) are in //Pnma//. Be carefull when comparing with other studies for which the //Pbnm// system is more common! Use the space group number 62 in the .ini file of GrainsPotter to find the grains from these Pnma G-vectors.
  
 ==== Remarks ==== ==== Remarks ====
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 ===== Output files ===== ===== Output files =====
  
-There are a number of possible output files from this procedure. Possible output files include:+There are a number of possible output files from this procedure. Most are usually created quite fast.  
 + 
 +The time consuming process is the creation of synthetic diffraction images. This time highly depends on the parameters in the input file, e.g. the amount of grains, the peak shape, strain tensors, or additional noise. For a simple test, it is wise to use an input file with very simple parameters (only a few grains, no strain tensors, no noise, small ω range etc.).  
 + 
 +Possible output files include:
   * [[fileformat:edf|edf]]: diffraction images, with a header including the omega angle. Be careful, you might be generating gigabytes of data!   * [[fileformat:edf|edf]]: diffraction images, with a header including the omega angle. Be careful, you might be generating gigabytes of data!
   * [[fileformat:tif|tif]]: diffraction images in TIFF format. Be careful, you might be generating gigabytes of data!   * [[fileformat:tif|tif]]: diffraction images in TIFF format. Be careful, you might be generating gigabytes of data!
-  * [[fileformat:flt|flt]] - peaks, as you would get them from a peak searching routine and that can be loaded in ImageD11. +  * [[fileformat:flt|flt]] - peaks, as you would get them from a [[processing:search_for_peaks|peak searching routine]] and that can be loaded in [[software:imaged11|ImageD11]]. 
-  * [[fileformat:gff|gff]] - a file containing grain information, 1 grain on each line +  * [[fileformat:gff|gff]] - a file containing grain information, 1 grain on each line. 
-  * [[fileformat:gve|gve]] - a list of g-vectors, as you should see them in an experiment. The peaks are transformed into scattering vectors (g-vectors). This file can be used for indexing in either GrainSpotter or ImageD11- index. +  * [[fileformat:gve|gve]] - a list of g-vectors, as you should see them in an experiment. The peaks are transformed into scattering vectors (g-vectors). This file can be used for indexing in either [[software:grainspotter|GrainSpotter]] or [[software:imaged11|ImageD11]] indexing. 
-  * [[fileformat:ini|ini]] - an sample input file for indexing with [[software:grainspotter|GrainSpotter.]] Using the .gve file is written. It will then be possible to try the GrainSpotter indexing program immediately.+  * [[fileformat:ini|ini]] - an sample input file for indexing with [[software:grainspotter|GrainSpotter]] using the .gve file. It will then be possible to try the GrainSpotter indexing program immediately.
   * [[fileformat:ubi|ubi]] - a list of the UBi matrices of the simulated grains. Grain orientations as inv(U*B).   * [[fileformat:ubi|ubi]] - a list of the UBi matrices of the simulated grains. Grain orientations as inv(U*B).
   * [[fileformat:ref|ref]] - reflection files (one per grain) having all the information about the reflections.   * [[fileformat:ref|ref]] - reflection files (one per grain) having all the information about the reflections.
-  * [[fileformat:par|par]] - the input parameters for PolyXSim written in the par format of for [[software:ImageD11|ImageD11]].+  * [[fileformat:par|par]] - the input parameters for PolyXSim written in the par format for [[software:ImageD11|ImageD11]] processing.
  
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