User-manual.md

@@ -3,6 +3,25 @@ Launch vEXP with Nomad
 
 vEXP is capable of gathering data from nomad in order to display them in the reciprocal view. To do this, before launching vEXP, launch Nomad and wait until it is fully loaded. Then, launch vEXP using the provided launcher. 
 
+Customize experiment parameters
+---
+
+#### Sample parameters
+
+Sample parameters can be changed using the sample panel (Panels > Show sample). Then edit wanted inputs.
+
+#### Scattering plane
+
+Scattering plane can be moved using the scattering plane panel (Panels > Show Scattering plane). Then edit wanted inputs, it will update the plane representation on the reciprocal view.
+
+#### Atoms & unitcell
+
+Atoms can be added to define the crystal structure in the atoms panel (Panels > Show atoms). Atoms can be added, removed or moved in this panel. Each atom has also a graphic representation on the unitcell view (Panels > Show unit cell).
+
+#### Scattering parameters
+
+There is different way to set scattering parameters. The first one, is by moving scattering vectors in the reciprocal view. Just grab the green spheres and drop them to change scattering parameters. The second one, is by setting scattering parameters value in the scattering parameters panel (Panels > Show scattering parameters).
+
 vEXP Modes
 ---
 
@@ -35,13 +54,9 @@ In the same way, you can define multiple trajectories by following the same step
 #### Export to nomad
 To exports all trajectories into a XBU file readable by Nomad, click on "Export to nomad" button on the trajectory panel (Panels > Show Trajectory). It will create a XBU file named vEXP.xbu under the user's XBU path.
 
-Customize experiment parameters
+Configurations
 ---
 
-#### Sample parameters
+vEXP is capable of saving all experiment parameters into one file that can be opened later on. To save the current experiment configuration, open the configuration panel (Panels > Show configuration). Then click on "Save configuration" button. The current configuration is now saved and can be restored by clicking on the "Restore" button in corresponding entry in the configuration list.
 
-Sample parameters can be changed using the sample panel (Panels > Show sample). Then edit wanted inputs.
-
+By default, the configuration list is not saved when vEXP is closed. To make that list persistent, click on "Export configuration" button to export it in a file. The file can be loaded when reopening vEXP by clicking on the file input.
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-#### Scattering plane
-
-Scattering plane can be moved using the scattering plane panel (Panels > Show Scattering plane). Then edit wanted inputs, it will update the plane representation on the reciprocal view. 
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