http://nanometrologie.cz/xraytrace/wiki/ 2026-05-25T18:25:30+02:00 http://nanometrologie.cz/xraytrace/wiki/ http://nanometrologie.cz/xraytrace/wiki/lib/tpl/dokuwiki/images/favicon.ico text/html 2019-02-17T10:36:16+02:00 http://nanometrologie.cz/xraytrace/wiki/doku.php?id=ag_semispheres&rev=1550396176&do=diff Ag semispheres Ag half-spheres on silicon, unknown height, 3450 eV, 0.35937 nm wavelength text/html 2018-01-27T22:47:10+02:00 http://nanometrologie.cz/xraytrace/wiki/doku.php?id=au_particles&rev=1517089630&do=diff Au particles An example of measurements on Au particles of different heights on silicon is in work of by Tiwari et. al [1]. The measurement is performed for 15 keV incident beam energy, i.e. 0.0826 nm wavelength. Two graphs taken from Ref [1] are show here for reference, top one is for 90 nm particles and bottom one for 250 nm particles. text/html 2018-01-24T16:47:27+02:00 http://nanometrologie.cz/xraytrace/wiki/doku.php?id=computational_domain&rev=1516808847&do=diff Computational domain The calculation is performed on a rectangular domain that is divided into rectangular voxels. Through these voxels the rays are passing, leaving some intensity information there to be accumulated, summed with the other rays or being somehow interpreted. text/html 2019-02-23T22:39:59+02:00 http://nanometrologie.cz/xraytrace/wiki/doku.php?id=cr_ordered&rev=1550957999&do=diff Cr pads, ordered Ordered circular Cr pads 50 nm pads 50 um distance [1], 2.7 um diameter, 8040 eV, i.e. 0.15423 nm. Square patterns, PTB poster data, 7 keV, 0.1772 nm: Reference [1] S. H. Nowak, F. Reinhardt, B. Beckhoff,J.-C. Dousse and J. Szlachetko, Journal of Analytical Atomic Spectrometry, 28 (5) 689-696, 2013. text/html 2019-02-19T23:03:30+02:00 http://nanometrologie.cz/xraytrace/wiki/doku.php?id=cr_pads_ptb&rev=1550613810&do=diff Cr pads, disordered Non-continuous layers on which the TER happens on the substrate below them, including particles, semi-spheres, not aligned pads, etc. Here the TER effect on the top surface is very small, so simple semi-analytical model can still be used. text/html 2018-01-27T17:45:02+02:00 http://nanometrologie.cz/xraytrace/wiki/doku.php?id=cr_structures&rev=1517071502&do=diff Cr pads, film and bulk 50 nm chromium pads and film on silicon presented by Nowak et al [1], 5.5 keV (guessed, not provided), 0.22543 nm wavelength By using the simple model we get the following curves: Reference [1] S.H. Nowak, D. Banaśb, W. Błchucki, W. Cao, J.-Cl. Dousse, P. Hönicke, J. Hoszowska, Ł. Jabłoński, Y. Kayser, A. Kubala-Kukuś, M. Pajek, F. Reinhardt, A.V. Savu, J. Szlachetko, Spectrochimica acta part B: Atomic Spectroscopy 98, 2014, 65-75 text/html 2018-01-25T12:33:34+02:00 http://nanometrologie.cz/xraytrace/wiki/doku.php?id=getting_started&rev=1516880014&do=diff Getting started Xraytrace is run from console, using a parameter file as argument. Parameter file is a plain text file with some commands (described in the other sections of this documentation) and with links to other files. A very minimum set needed for a reasonable calculation is shown here. It consist of three files: parameter file, sample geometry definition file and table of material parameters. You can paste the content below to newly created files or you can text/html 2018-01-26T19:05:07+02:00 http://nanometrologie.cz/xraytrace/wiki/doku.php?id=gpu_use&rev=1516989907&do=diff GPU use Warning: graphics card use is still in the evaluation phase, so it is reasonable to check every calculation first on CPU (e.g. for a single angle) and then to run the graphics card calculation. Use of graphics card (GPU - graphics processing unit) is the cheapest way how to speedup some calculations based on repeating some simple algorithm many times. It can be very efficient in cases when the algorithm runs can be made independent, so individual calculations do not depend on the other… text/html 2020-05-15T11:04:56+02:00 http://nanometrologie.cz/xraytrace/wiki/doku.php?id=input_reference&rev=1589533496&do=diff Input syntax reference Parameter file format and options Here follows a list of all the parameters and their options that can be used within parameter file. Some of them have meaning only if used with other parameters, please refer to other parts of documentation or examples in case of doubts. text/html 2018-01-24T13:47:53+02:00 http://nanometrologie.cz/xraytrace/wiki/doku.php?id=installation&rev=1516798073&do=diff Installation Xraytrace is now installed only from source code, no stable executables are available. This might change in future. To get the actual version, checkout it from the repository (you must have access to it first): cvs -d prutok.cmi.cz:/cvs co xraytrace text/html 2019-02-21T23:44:37+02:00 http://nanometrologie.cz/xraytrace/wiki/doku.php?id=material_parameters&rev=1550789077&do=diff Material parameters The materials used within the calculation are represented by materials table, which is supplied as a an input file, defined at the same moment as the data are loaded (see the computational domain section). This file has a simple structure - a set of entries for individual material indices, defining how the system should get the material data. Each row starts by material index (to match the indices in the VTK file or vector file defining the text/html 2018-01-27T14:30:00+02:00 http://nanometrologie.cz/xraytrace/wiki/doku.php?id=nickel_film&rev=1517059800&do=diff Nickel film Continuous layers on which the TER happens on the top surface. Only evanescent wave is probing the material volume below the critical angle. This is easy for the simple semi-analytical model (set the SIMPLE directive to 1) and very challenging for the raytracing model. text/html 2018-01-24T21:02:22+02:00 http://nanometrologie.cz/xraytrace/wiki/doku.php?id=outputs&rev=1516824142&do=diff Outputs There are various options what to output from the computation. First of all, by verbosity level we can control what the software prints on the console. The calculation result, either single value or whole angular scan is placed to a text file that is controlled by this directive: text/html 2018-01-28T13:32:56+02:00 http://nanometrologie.cz/xraytrace/wiki/doku.php?id=running&rev=1517142776&do=diff Running the computation When we have everything ready, like sample geometry, materials and source, we can run the calculation. There are may controls that can be used here. First of all, as we are raytracing, we should set the number of rays that will be casted, e.g. text/html 2018-01-24T18:19:05+02:00 http://nanometrologie.cz/xraytrace/wiki/doku.php?id=sample_geometry&rev=1516814345&do=diff Sample geometry As mentioned in the computational domain section, everything is computed on rectangular domain consisting of rectangular voxels. Ways of loading medium data from different input file types are described there as well. As we are working with voxel data, first aspect to note that there is a staircasing effect in the data, present nearly for any more complicated geometries. This means that e.g. a half-spehere looks like this: text/html 2018-01-28T15:42:31+02:00 http://nanometrologie.cz/xraytrace/wiki/doku.php?id=sc2o3_film&rev=1517150551&do=diff Sc₂O₃ film Information from Philipp: It is from this paper: 10.3390/ma7043147X The sample structure is slightly different however: Its Al2O3 on Sc2O3 on Si The thicknesses of 0.14nm for Sc2O3 and 0.15nm for Al2O3 are only estimates. Here we would also need to have either a modeling using the thicknesses and densities or you try different densities and keeping the quantified mass depositions constant (product of density and thickness). text/html 2018-01-27T15:17:27+02:00 http://nanometrologie.cz/xraytrace/wiki/doku.php?id=sidebar&rev=1517062647&do=diff Basics * Xray standing wave basics * Installation * Getting started Documentation * Computational domain * Sample geometry * Material parameters * Source regimes * Running the solver * Outputs * GPU use * Visualisation * Input formats reference Examples * Nickel film * Cr pads, disordered * Cr pads, ordered * Cr pads, film and bulk * Au particles * Ag semispheres Back to homepage text/html 2019-03-13T21:21:19+02:00 http://nanometrologie.cz/xraytrace/wiki/doku.php?id=source_regimes&rev=1552508479&do=diff Source regimes To create the X-ray standing wave field we need to let the incoming rays to be totally reflected and get interfered with other incoming rays. We have different ways how the rays can be sourced: Rays can be simply casted from a plane outside of the computational volume, hitting some interface in the computational volume where the total reflection condition is met and create the standing wave field. For small angles this however means to have really large computational volume. Thi… text/html 2018-01-24T16:45:24+02:00 http://nanometrologie.cz/xraytrace/wiki/doku.php?id=start&rev=1516808724&do=diff Xraytrace is a solver for X-ray standing wave (XSW) related tasks computation using raytracing in a voxel based sample geometry. This command-line software can be used to calculate field distribution inside a nanostructure or set of nanostructures placed in a standing wave field and to get simulated distributions of intensity vs. incident angle. Majority of algorithms is however implemented for more general case of a ray interacting with an object, so it can be most probably used also for other … text/html 2018-01-24T13:32:03+02:00 http://nanometrologie.cz/xraytrace/wiki/doku.php?id=tagline&rev=1516797123&do=diff tagline, whaever it means text/html 2018-01-26T16:57:01+02:00 http://nanometrologie.cz/xraytrace/wiki/doku.php?id=visualisation&rev=1516982221&do=diff Visualisation To visualize the results (intensity sums, angular scans) we can use any graph plotting software, on Linux it is e.g. gnuplot. To visualize the VTK files we recommend Paraview. An example of Paraview use for VTK files visualisation was shown already in text/html 2018-01-27T16:02:44+02:00 http://nanometrologie.cz/xraytrace/wiki/doku.php?id=xsw&rev=1517065364&do=diff Xray standing wave technique Xraytrace was built to be able to handle various second-order effects in X-ray standing wave (XSW) based measurement. XSW technique is based on total external reflection of x-rays on a sample surface, which leads to formation of a standing wave above surface. By changing the incident angle we can change the period of the standing wave which can be used for profiling the objects on the surface.