... | ... | @@ -25,9 +25,94 @@ establish a TurboVNC connection to the MPCDF remote visualization service [[as d |
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click on the Desktop launcher named NOMAD-VIZ_UseCase1
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![screenshot1](usecase1_screenshot1.png "usecase1_screenshot1.png")
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![visit_screenshot1](usecase1_screenshot1.png "usecase1_screenshot1.png")
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### common analysis workflows
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## Interactive graphical analysis with ParaView |
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\ No newline at end of file |
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## Interactive graphical analysis with ParaView
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### connect to pRVS
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establish a TurboVNC connection to the MPCDF remote visualization service [[as described here|MPCDF-RVS]]
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### Start ParaView.
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```
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~>module load paraview
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~>vglrun paraview
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```
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### Instructions for working with the GUI
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From the file menu, choose File/Load State. Locate the
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pre-built ParaView state file for the preferred NoMaD data type. For the
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demo data cube files, choose UseCase1_ParaView.pvsm and click OK. "Fix
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Paths in State File" window opens. This window takes the location of the
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NoMaD data file as input. Click the three dots on the right hand side of
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the file name slot, to browse files. The browser displays numbered files
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in a sub-folder, under their common name. For animation, choose this
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common name from the upper level, and click OK. ParaView loads the first
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file and treats the rest of the files as animation steps. In a few
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seconds, ParaView state file opens, and the interface is ready for an
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interactive inspection of the data.
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The 3D view window (Layout1) of this particular ParaView state file
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shows the following:
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* an outline of the spatial dimensions of the data, with scale on X, Y, Z axis
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* atoms as balls, positioned, colored, and sized according to the given data
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* electron density field as a volume, with color legend
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* solid slice of the electron density field, also colored according to the legend
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### ways to interactively inspect the data:
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* To rotate the view, left-click and drag. Zoom with right button or mouse
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wheel, and pan with middle button.
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* To play an animation, or to move one step in time, use the video player
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type of controls on the toolbar, just below the file menu. Note that the
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animation is loaded one step at a time, causing a lag between the steps.
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The length of this lag depends on the data size and the complexity of
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the scene.
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* Distance between two atoms:
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in the "Pipeline Browser" panel on the left, click "Ruler1" text to show
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its "Properties" in the panel below it. Now, hover mouse pointer above a
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ball in the Layout1 window, and press "P" on the keyboard. Then do the
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same for another ball, to get their relative distance displayed on the
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screen.
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* Query about parameters of an individual atom:
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click the "hover points on" button on the top of Layout1 window, second
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from the right. The query mode is active when the button is in its
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pressed-down state. Now hover the mouse pointer over any element in the
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Layout1 window, to show a list of its parameter values. (Note that a
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ball consists of many polygons which differ from their polygon-related
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values, but share the atom related parameters.) Click the button again
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to get out of the query mode.
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* Re-position the volume slice:
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clicking the Slice text in the "Pipeline Browser" makes the slice
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visible and interactive. Move the slice by grabbing its red outline
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rectangle, mouse left button pressed, and click Apply in the Properties
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panel.
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* Adjust the electron density field color and opacity mapping:
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click "Gridded data" text in "Pipeline Browser", scroll the "Properties"
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panel until you find "Coloring", and click "Edit" to open the graphical
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editor. The points on color and opacity lines can be directly moved
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around, or their numerical values edited. The changes are reflected in
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the 3D view window.
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![paraview_screenshot1](screenshot_paraview_ruler.png "screenshot_paraview_ruler.png")
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Screenshot of a ParaView visualization of the same use-case data as
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shown with VisIT in Figure 1. ParaView "Ruler" tool is displayed showing
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the distance between two atoms. (Notes: (1) Although the screenshot
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shows a local rendering result, ParaView was tested to work equally well
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in NOMAD remote rendering setup. (2) ParaView's out-of-the-box cube file
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reader, when applied to the numbered NoMaD demo data cube files, reads
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the files individually but not as animation. Rewriting the cube reader
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would fix this but was postponed until final NoMaD data types have been
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decided.) |