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 ===== Your first simulation =====
-XSvit example No.1
+<html>
+<h2>Basic FDTD algorithm operation example</h2>
+<h3>Summary</h3>
+<p>We will use cubic volume with centered point source, similar to a dipole located in center of computation space.
+Outputs will be different cross-section planes to Gwyddion file and a text file (from single point).
+Calculation will be performed on CPU or on GPU and material mode selection for speedup will be tested.
+</p>
+<p>
+What can be tested using this example:
+<ul>
+<li>basic performance of the software (first test to see whether it works after installation)
+<li>performance of Yee algorithm with none material properties (compare with material mode calling
+full algorithm, resulting in different speed and memory allocation.)
+<li>GPU performance
+<li>GPU performance with none/full material properties (combine GPU and material mode checking)
+<li>scaling of basic calculation speed and memory requirements (varying computational volume size)
+<li>point source properties (varying the orientation or using file input for source).
+</ul>
+<p>
+</p>
+<h3>Setup all this with XSvit</h3>
+<p><i>Note that some of the screenshots might be from an older version of XSvit.</i></p>
+<p>First, start the XSvit application. If haven't done this before, setup the location of GSvit and Gwyddion under
+File->Preferences menu, so you can run the calculation from the GUI and see the results afterwards. Otherwise
+you will be able to use GUI only for parameter file setup.</p>
+<p>When you start XSvit, there is already a default parameter file loaded, using computational space of size 100x100x100 voxels.
+We will use this computational space and we will add point souce and point output. In the next figure you can
+see how the default settings look after XSvit start (you can rotate the 3D projection by mouse, so this was done to get a better view).
+Note the values of discretisation step (1e-6 m) in the list of all the entries on the left side of the window; if we work in vacuum
+(which is the case in this example) we should not
+use source with wavelength that is smaller than this step multiplied by ten. You can alter the discretisation
+settings and computational volume size by double clicking on its values in the list. </p>
+<a href="http://gsvit.net/images_v18/ex1_init.png"><img src="http://gsvit.net/images_v18/ex1_init.png" width="800"></a>
+<p>It is reasonable to save your parameter file at this stage using <i>File->Save</i> command. We can do it also later,
+just before running computation, however doing it right now will set the current directory and other input/output files
+set later can be referred to it (instead of using absolute path). Moreover, by saving parameter file we also set default directory
+for temporary files (e.g. generated sources), which is also important.</p>
+<p>First we will add <b>point source</b>. This can be done using menu entry <i>Edit parameters->Add point source</i>.
+The dialogue shown below appears. We set the point source properties, i.e. its position in voxel coordinates,
+its type (load from file or construct a temporary file for it with sine wave or sine impulse)
+and orientation given for temporary file sources by two angles (see the angles for TSF in GSvit documentation).
+Here we have chosen sine source given by Ez component only.</p>
+<img src="http://gsvit.net/images_v18/ex1_psource.png">
+<p>After adding the source we can see it in the 3D window as shown below and also on the list of entries. If we are not satisfied with its position
+we can double-click on the entry and correct it. </p><p><i>Hint: if we switch to "par. file" tab we can edit the source in native GSvit format
+file much faster and see the position changes immediately.</i></p>
+<a href="http://gsvit.net/images_v18/ex1_source.png"><img src="http://gsvit.net/images_v18/ex1_source.png" width="800"></a>
+<p>Next we will add <b>point and image outputs</b>. This is done by menu entry <i>Edit parameters->Add point output</i>
+and <i>Edit parameters->Add image output</i> that again open dialogues for specifying how often (parameter "skip")
+and which component should be output. Point output is collected from a single point within computational volume
+and is stored into a text file. Image output comes to general output file that can be opened by <a href=gwyddion.net>Gwyddion</a>
+open source software. A cross section in certain normal direction is output, selected as shown below. We will add
+a cross section in every direction, so we will call the dialog three times.</p>
+<img src="http://gsvit.net/images_v18/ex1_imout.png">
+<p>Similarily we will add point output as shown below.</p>
+<img src="http://gsvit.net/images_v18/ex1_pout.png">
+<p>Note that all the outputs can be also seen in 3D view window. We can adjust some more computational parameters,
+here namely we will increase <b>number of steps</b> to be calculated to 300 (clicking to any of the entries in "Basic parameters" group).
+Physical length of the time step is calculated automatically on the basis of space discretisation.</p>
+<img src="http://gsvit.net/images_v18/ex1_steps.png">
+<p>Finally we need to save the parameter file if we haven't done it at beginning, as since now we worked only with a temporary file or at least modified file
+(it is important to save it always before running computation which is not done automatically). This is done by <i>File->Save</i> command as usual. Then we can
+<b>start the computation</b> clicking on the arrow in the toolbar or using <i>Execute->Run</i> menu command.</p> <p><i>Hint: if we don't want to use
+the GUI for starting the computation we can always run GSvit manually on our parameter file.</i></p>
+<a href="http://gsvit.net/images_v18/ex1_nonebcout.png"><img src="http://gsvit.net/images_v18/ex1_nonebcout.png" width="800"></a>
+<p>While computation is running we can see the GSvit output (if the verbose level is not 0) and we can choose any text file output
+to be visualised in the graph window. You can also watch preview of last saved images - slices through the computational volume - directly in 3D view.
+The GSvit output is directly what you would see if you run it at console, with no GUI.
+Note that graph is updated at maximum as often as the data are saved, so if we skip every 100 points
+while setting the output we will see the graph updated only e.g. every few seconds (depending on computational volume size, etc.).
+Similarily, the images in the 3D view are updated when these are saved by the computational core (so you can affect the update frequency
+by image output skipping parameter).</p>
+<p>When computation is finished or killed by the Stop command (again via toolbar or menu), we can <b>open the output</b> file. As most of the
+data are output in Gwyddion file we can directly open it using Gwyddion called from the menu or toolbar. Gwyddion is a powerfull 2D/3D data
+processing software, however we will only use it to see the images in this example. As image outputs are saved succesively as the GSvit
+is running, we will be probably having more channels to see in Gwyddion, so we pick what is interesting for us in the Gwyddion Data Browser.</p>
+<a href="http://gsvit.net/images_v18/ex1_shortwrong.png"><img src="http://gsvit.net/images_v18/ex1_shortwrong.png" width="800"></a>
+<p>Note that in this example we have clicked on <i>Data Process->Presentation->Logscale</i> for every displayed output to see the data in
+better scale. We can see that in different cross-sections of the computational space there is a wave similar to a dipole output.</p>
+<p>If we check the data in further time steps, we can see that they look much worse.</p>
+<a href="http://gsvit.net/images_v18/ex1_longwrong.png"><img src="http://gsvit.net/images_v18/ex1_longwrong.png" width="800"></a>
+<p>This behavior is caused by unset <b>boundary conditions</b> that behave like mirrors here.
+In order to let the wave go out of the computational
+space we need to apply an absorbing boundary condition, so we click on any entry in "Boundary conditions" set to change the boundary conditions
+on all the faces to a simple absorbing condition (Liao).</p>
+<img src="http://gsvit.net/images_v18/ex1_bcs.png">
+<p>After that (and saving the file, running computation and redisplaying data again) we can see that the output is already propagating
+freely outside of the computation volume.</p>
+<a href="http://gsvit.net/images_v18/ex1_longok.png"><img src="http://gsvit.net/images_v18/ex1_longok.png" width="800"></a>
+</html>

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