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/hydra/u/mjr/public/NOMAD-VIZ/cubes-smaller
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```
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## Interactive graphical analysis with VisIT
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## Interactive graphical analysis
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* [VisIT] (UseCase1_visit)
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* [ParaView] (UseCase1_paraview)
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* [VMD] (UseCase1_vmd)
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### prepare the preconfigured VisIt session for UseCase1
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```
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ssh hydra.rzg.mpg.de
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mkdir -p $HOME/Desktop
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cp /u/mjr/public/NOMAD-VIZ/NOMAD-VIZ-UseCase1.desktop $HOME/Desktop
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```
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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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### launch the preconfigured VisIt session for UseCase1
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click on the Desktop launcher named NOMAD-VIZ_UseCase1
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![visit_screenshot1](usecase1_screenshot1.png "usecase1_screenshot1.png")
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The preconfigured session (saved as an XML file) presents the user with a number of predefined "views" of the data. Specifically, the following "plots" and "operators" (these are the fundamental concepts of the VisIT tool) have been prepared:
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* a pseudo-realistic volume-rendering plot of the electron density
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* a molecular plot showing a balls-and-sticks model of the atoms
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* a pseudocolor plot with selected contours of two planes (selected by the slice operator)
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* a pseudocolor plot of iso-surfaces of the electron density
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### Instructions for working with the GUI
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The leftmost panel provides the main interaction facilities for (from top to bottom)
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* opening and closing files
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* a time-slider for navigating between time steps
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* buttons for adding plots and operators
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* a number of preconfigured visualizations (a "plot" with a pipeline of "operators").
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* by selecting a plot and toggling the "Hide/Show" button visualizations that are hidden in the default view after starting the session are displayed
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* by double-clicking on an operator or plot (highlighted in blue) a context menu pops up which allows to change the default parameters, e.g., the replication factors of the unit cell (rightmost panel)
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The plots are rendered in the main, central display, which also allows basic mouse interactions such as
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* rotations (left mouse button)
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* translations (shift + left mouse button)
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* zooming (mouse wheel)
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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 pre-built ParaView
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state file UseCase1_ParaView.pvsm and click OK. "Fix Paths in State File"
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window opens. This window takes the location of the NoMaD data file as
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input. Click the three dots on the right hand side of the file name slot,
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to browse files. "Use case 1" data is in /hydra/u/mjr/public/NOMAD-VIZ/cubes-smaller
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folder. The browser displays numbered files in a sub-folder. To load the
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files as animation, choose this sub-folder and click OK. In a few seconds,
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ParaView state file opens, and the interface is ready for an interactive
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inspection of the data.
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The 3D view window of this particular ParaView state file 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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* isovolume contours of the electron density on the solid slice
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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 by
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scrolling mouse wheel, and pan with middle button.
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* to play an animation, or to move one step in time, use the video controls
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on the toolbar. The animation is loaded one file at a time, causing a lag
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between the steps. The length of this lag depends on the data size and the
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complexity of the scene. Note that currently ParaView does not read cube
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files sequentially as animation, so a file conversion would be needed to
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get this feature to work.
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* distance between two atoms: in the "Pipeline Browser" panel on the left,
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click "Ruler1" text to show its "Properties" in the panel below it. Now,
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hover mouse pointer on one atom in the view window, and press "P" on the
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keyboard. Then do the same for another atom, to get their relative distance
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displayed on the screen.
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* query about the parameters of an individual atom: click the button with
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a question mark on it, on the top of the view window, second button from
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the right. The query mode is active when the button is in its pressed-down
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state. Now hover the mouse pointer on any object in the view window, to
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show a list of its parameter values. (Note that a ball consists of many
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polygons which differ from their polygon-related values, but share the atom
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related parameters.) Click the button again to get out of the query mode.
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* re-position the volume slice: click the "Slice1" text in the "Pipeline
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Browser" to make the slice tool interactive. Move the slice by grabbing
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its red outline rectangle, and click Apply in the "Properties" panel.
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* adjust the electron density field color and opacity mapping: click
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"Gridded data" text in "Pipeline Browser", scroll the "Properties" panel
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until you find "Coloring", and click "Edit" to open the graphical editor.
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The key points defining color and opacity can be interactively moved
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around, or their values edited.
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![paraview_screenshot1](paraview_usecase_hydra_screenshot.png "paraview_usecase_hydra_screenshot.png")
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Screenshot of a pRVS ParaView visualization of the same use-case data as
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shown with VisIT in Figure 1. ParaView "Ruler" tool is active and shows
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the distance between two atoms. View window is in query mode and displays
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the property list of the chosen object. |