Interactive graphical analysis with ParaView
prepare the preconfigured Paraview session for UseCase1
ssh hydra.rzg.mpg.de mkdir -p $HOME/Desktop cp /u/mjr/public/NOMAD-VIZ/UseCase1_Paraview.desktop $HOME/Desktop
connect to pRVS
launch the preconfigured Paraview session for UseCase1
double click on the Desktop launcher named NOMAD-VIZ_UseCase1_Paraview
or start Paraview manually on the commandline:
module load paraview vglrun paraview --state=/u/mjr/public/NOMAD-VIZ/UseCase1_Paraview.pvsm
(the --state=... option manually loads the preconfigured session for UseCase1 on the commandline)
![paraview_screenshot1](paraview_usecase_hydra_screenshot.png "Screenshot of a pRVS ParaView visualization of the same use-case data as shown with VisIT and VMD. ParaView "Ruler" tool is active and shows the distance between two atoms. View window is in query mode and displays the property list of the chosen object.")
The 3D view window of the preconfigured ParaView state file shows the following:
- an outline of the spatial dimensions of the data, with scale on X, Y, Z axis
- atoms as balls, positioned, colored, and sized according to the given data
- electron density field as a volume, with color legend
- solid slice of the electron density field, colored according to the legend
- isovolume contours of the electron density on the solid slice
Instructions for working with the GUI
to rotate the 3D view, left-click and drag. Zoom with the right button or by scrolling the mouse wheel, and pan with the middle button.
to play an animation, or to move one step in time, use the video controls on the toolbar. The animation is loaded one file at a time, causing a lag between the steps. The length of this lag depends on the data size and the complexity of the scene. Note that currently ParaView does not read cube files sequentially as animation, so a file conversion would be needed to get this feature to work.
distance between two atoms: in the "Pipeline Browser" panel on the left, click "Ruler1" text to show its "Properties" in the panel below it. Now, hover mouse pointer on one atom in the view window, and press "P" on the keyboard. Then do the same for another atom, to get their relative distance displayed on the screen.
query about the parameters of an individual atom: click the button with a question mark on it, on the top of the view window, second button from the right. The query mode is active when the button is in its pressed-down state. Now hover the mouse pointer on any object in the view window, to show a list of its parameter values. (Note that a ball consists of many polygons which differ from their polygon-related values, but share the atom related parameters.) Click the button again to get out of the query mode.
re-position the volume slice: click the "Slice1" text in the "Pipeline Browser" to make the slice tool interactive. Move the slice by grabbing its red outline rectangle, and click Apply in the "Properties" panel.
adjust the electron density field color and opacity mapping: click "Gridded data" text in "Pipeline Browser", scroll the "Properties" panel until you find "Coloring", and click "Edit" to open the graphical editor. The key points defining color and opacity can be interactively moved around, or their values edited.