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processing:synthetic_dataset
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processing:synthetic_dataset [2019/02/18 10:11] 127.0.0.1 external edit |
processing:synthetic_dataset [2019/02/23 19:43] (current) estelle [Input file example 3: olivine from a CIF file] |
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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 of olivine from //Pbnm// to //Pnma// an other space group used for olivine which does have a space group number. | + | 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 : | The transformation from //Pbnm// to//Pnma// is not complicated, it is only an interchange of axis : | ||
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| 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//. | 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 can be found [[fileformat:olivinecif|at this location]]. | + | [[fileformat:cif|Here]] is the obtained CIF file. |
| 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 : | ||
processing/synthetic_dataset.1550484719.txt.gz · Last modified: 2019/02/18 10:11 by 127.0.0.1
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