Visualization Plugin for ParaView

Transcription

1 Alexey I. Baranov Visualization Plugin for ParaView version 2.0 Springer

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3 Contents 1 Visualization with ParaView ParaView plugin installation Installation of precompiled plugins Compilation of ParaView plugins Visualization Visualizing the Structures Basics of Grid Data Visualization Clipping in ParaView Saving state in ParaView Tips and Tricks

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5 Chapter 1 Visualization with ParaView The visualization of DGrid generated data can be performed with the freeware program ParaView R which is available for many platforms including Microsoft Windows R, Linux R and macos R. An additional ParaView plugin is necessary for that. It provides routines which read DGrid file formats, adds handy ParaView filters and GUI controls. Plugin for the version consists of the single shared (dynamically linked) library (earlier versions of plugin contain more files). The ParaView plugin installation is described in Sec Brief introduction into ParaView controls and basic visualization steps is given in Sec Detailed information about the ParaView can be found in the Internet at ParaView plugin installation ParaView plugins are made available as a separate part of the DGrid package. There are two ways to deploy them: Precompiled plugins are available for x86 32-bit and 64-bit versions of official builds of ParaView for Microsoft Windows and 64-bit version of ParaView for macos X. At the time of writing this User s Guide the version of ParaView is supported. The x86 64-bit plugins have been tested on Microsoft Windows 7 Professional, Microsoft Windows 10 Home and macos X They can be downloaded from DGrid website as separate packages. The next subsection describes how to install the binary plugin. The plugins can be build from the source code. To do this, one has to build the ParaView from the source code in advance on the same machine. 5

6 6 1 Visualization with ParaView This is the way to obtain the plugins when pre-build binary plugins are not available for target ParaView version or when customized build of ParaView is used (compiler or libraries differ from those for official built). See the Sec for instructions how to build the plugins from source code Installation of precompiled plugins When installing a precompiled plugin, download the package from the DGrid website and unpack it. Copy the plugin files 1 : SMMDGridPlugin (or libsmmdgridplugin) elf mk.xml into folder e.g. PVDGrid ParaView should be informed about new plugins capable to work with DGrid files. One way to do it is to set up system variable called PV PLUGIN PATH to the path of that plugin folder. Another way is to load plugin via Plugin Manager (menu Tools Manage Plugins ). ParaView Wiki ( HowTo#Using Plugins) contains additional information on loading plugins in ParaView Compilation of ParaView plugins First of all, download ParaView source code and build ParaView. Detailed instructions can be obtained at ParaView website at And Install. To compile ParaView, some other software packages like Qt or CMake must be available. Then download the plugin source code from DGrid website, create a folder dgrid-4.6/pvdgrid and unpack the plugin source code into it. As for ParaView, plugin build process is controlled by CMake build control system ( in which one should set up appropriate variables and 1 Plugin versions for ParaView < include more files.

7 1.2 Visualization 7 then generate the build configuration files like Makefile under Linux or Microsoft Visual Studio solution file (*.sln) under Microsoft Windows. Usually, the only important variable which has to be set up when configuring ParaView plugin build in CMake is the ParaView DIR which should point to ParaView build directory (and NOT to the ParaView source directory). Finally the plugin is build using the generated configuration file, e.g., invoking make command under Linux or opening the solution in Microsoft Visual Studio and building it. When everything runs successfully, plugin library file called SMMDGridPlugin or libsmmdgridplugin should appear in the plugin build folder. Consult the Sec on how to configure the ParaView to use the plugins. 1.2 Visualization Start ParaView by typing paraview or clicking its icon. Load the DGrid plugin via Plugin Manager if it is not loaded automatically yet (cf ). ParaView plugin can visualize two types of files prepared by DGrid: DGrid Property files containing the calculated properties on the grid. DGrid Structure files (STR) containing molecular/crystal structures or topological graphs. To test plugins prepare some property grid (for instance the electron density grid for oxazole as described in DGrid User s Guide). 1. Select the file to open (e.g. via menu File Open ). 2. Select the grid file. It will be scanned and boxes representing data sets found in this file appear in the Pipeline Browser window. Normally each grid file contains Structure data set with the structure and Property data set with the scalar field on the grid (Fig. 1.1). A window may appears with the suggestion to select the particular format. Select then the appropriate DGrid format. 3. Press Apply button at the Properties tab to load the data. Some controls of the data set become then available at Properties tab. General information about data set can be found at Information tab. Remark 1.1. If the file is not listed in the selector box and cannot be chosen, select All files (*) in the Files of Type menu of the selector box and try to open that file. This can happen if the file has the extention which was not recognized by ParaView.

8 8 1 Visualization with ParaView If there is a problem to load the file, check in the ParaView Plugin Manager (accessible via menu items Tools Manage Plugins ) if the DGrid plugins were found and loaded. When plugins are not found, check how to add them to ParaView in the Sec When plugins are found but can not be loaded, consult Sec how to recompile them or reinstall the proper version of ParaView. The detailed instructions on the visualization of the grid data and the usage of all the tools is described in details in ParaView guide. A lot of valuable information can also be found at (Wiki, Tutorials, FAQ). A brief guide how to create isosurfaces, slices and basins is given in Sec Following section describes the visualization of Structure data set with current ParaView plugin. Fig. 1.1 Visualization pipeline for structure plot and Atoms tab of ParaView plugin Visualizing the Structures Property files in DGrid format include also the structure data of the molecule or crystal structure. To visualize the structure, select the Structure data set in the Pipeline Browser and then apply Plot Structure filter to it (select from

9 1.2 Visualization 9 the menu Filters Alphabetical Plot Structure and press Apply on the Properties tab. Two additional data sets Ball-n-Stick and Labels appear in the Pipeline Browser. First contains the geometrical representation of molecular structure and second contains labels of the structure elements (Fig. 1.1). Structure plot appearance is controlled via Properties tab of PlotStructure data set. The option Map Scalars, which maps the colors assigned to visual objects using a colormap is activated by default. This means, that the color for an atom, bond, path etc. set at the corresponding tab of Plot Structure filter will be mapped and the object appears on the screen with different color. To switch this option off, select Structure pipeline object, go to its Property tab, find there the section Scalar Coloring (if it is not shown press the button with the gear symbol at the top of the tab to show all the properties of the tab) and uncheck the box Map Scalars Atoms tab The controls for the Atoms tab are shown in Fig Desired atom can be selected using pop-up selector. Each atom type has default radius and color. They can be changed via Set Radius field and Set Color button. When several atoms of the same element type are present, a general name like All C appears in the atom list. This item allow to set same parameters for all atoms of that element type. Please note, that this item will discard the actual parameters of specific atoms! Bonds tab The controls for the Bonds tab are shown in Fig Atoms forming bond can be selected using popup selectors Bond between. General names are also available just like for atoms. Each bond type can have unique radius and color. They can be changed via Set Radius field and Set Color button. The minimal and maximal bond lengths can be modified via Set Min./Max. Distance fields.

10 10 1 Visualization with ParaView Fig. 1.2 ParaView plugin Bonds tab Paths tab To visualize the interconnection paths first the file with the data for the critical points and the path points, written in the DGrid Structure format, must be read in. When file is read the Plot Structure filter can be started in the same way as in case of the structure data, cf. page 8. In contrast to the atomic data, now the Atoms tab does not contain atomic symbols but the symbols for the critical points (and cores), i.e., Attr, Saddle, Ring, Min and Core respectively. General names for both critical points and path types are also available. The controls for the Paths tab are shown in Fig Fig. 1.3 ParaView plugin Paths tab

11 1.2 Visualization 11 Desired path can be chosen using pop-up selector. Each path type has default radius and color given in the DGrid Structure file, cf. DGrid User s Guide. They can be changed via Set Radius field and Set Color button. Path can be made hidden using Visible checkbox Cell tab The buttons for the Cell tab are shown in Fig Fig. 1.4 ParaView plugin Cell tab The unit cell can be visualized using Cell tab controls. The unit cell data are taken from the Lattice vectors part of the Property file, cf, DGrid User s Guide. The color and radius of the cell cylinders can be set via Set Radius field and Set Color button. The unit cell plot is activated when Show Unit Cell box is checked General scale The field Scale below the tab control sets up the general scale factor for all the spheres and cylinders used in the structure plot.

12 12 1 Visualization with ParaView Plotting labels Labels can be shown for atoms, critical points and path fragments to make them recognizable on the plot. Labels are created by Plot Structure filter and are shown as additional data set called Labels. To plot the labels on the screen (see Fig. 1.5) do the following: Fig. 1.5 ParaView plugin Plotting labels 1. Go over ALL BUT Label data set boxes in Pipeline Browser, select Properties tab and deactivate Pickable checkbox (if it is not shown press the button with the gear symbol to show all the properties of the tab). Alternatively one may switch off the visibility of the data set by clicking on the eye icon left to the box in the Pipeline Browser and turn it on back when the labels are plot. 2. Click on Select Points Through button at the top of the visualization window (small buttons below Layout #1 text label on Fig. 1.5) and select with the mouse the part of scene for which the labels should be shown. 3. Go to menu View and activate Selection Display Inspector checkbox if not activated yet. You may like to attach its window to the Properties and Information tabs like shown on the Fig. 1.5 to save more space for the visualization window. 4. Go to the Selection Display Inspector and click on Point Labels. 5. Activate labels checkbox.

13 1.2 Visualization Label appearance (size, font, color etc.) can be tuned by pressing Edit Selection Label Properties button (with gear symbol) Basics of Grid Data Visualization Isosurface Select the desired data set in the Pipeline Browser and apply Contour filter (from menu Filters ). The filter control panel appears on the Properties tab. Specify the isosurface level at the Value Range window there and press Apply to show the isosurface. Check whether the Representation popup is set to Surface and set it to this value. The color of the isosurface can be modified at Properties tab Slice Select the desired data set in the Pipeline Browser and apply Slice filter (from menu Filters ). The filter control panel appears on the Properties tab. Check that Map Scalars checkbox is activated and that the Representation popup is set to Surface. The position and orientation of the slice can be modified by the visual controls shown on the 3D plot or via the fields on the Properties tab. The colormap used for the slice can be changed by pressing the Choose Preset button (with a heart symbol), selecting a colormap in the Choose Preset window that appears and pressing Apply. Classical ELF colormap can be loaded by pressing Import button on the Choose Preset window and loading elf mk.xml file, shipped as a part of ParaView plugin. To set custom range of values, corresponding to the full colorscale, press Rescale to custom range button and modify the range min and max values in the window appeared Basin The basin file contains a field of integer values which can be read in with the interface as described for the property grids on page 7. Special route must be followed for the visualization of the basins as separate solid objects:

14 14 1 Visualization with ParaView 1. After the basin file is read, apply Generate Basin Surfaces filter (from menu Filters ) on its Property data set. This will create new data set called GenerateBasinSurfaces. 2. Apply Plot Basin filter on this new data set. Set Representation popup to Surface. The basin number to be visualized can be selected on the Property tab. 3. Additionally, basin shape can be smoothed to produce more nice-looking plots. This is done by extracting the basin surface with ParaView Extract Surface filter and smoothing it with ParaView Smooth filter. The degree of smoothing can be controlled by Number of iterations parameter. Very fine smoothing (> 500) are not recommended since it may spoil out important shape features and is time-consuming. Basin color and other visualization settings can be modified on the Properties tab. The color of the isosurface or basin can not only be constant for all the points of the object but be controlled by the value of other property at that point (Fig. 1.6). To make such plots, data sets containing property for generating object (e.g. basin or isosurface) and property used to color it should be merged into new combined data set using Append Attribute filter from menu Filters. More than 2 properties can be merged as well. The property used to color the object can be selected, using popup control in the Coloring section of the Properties tab. Fig. 1.6 ParaView plugin Density basin surface colored according to laplacian values

15 1.2 Visualization Clipping in ParaView The visualization elements in ParaView can be clipped with the Clip filter (from menu Filters ). Several types of clipping surfaces are available (e.g. Box, Sphere) and one can clip either internal or external of that (activate Inside Out for the latter). One can also clip the Ball-n-Stick structure plots Saving state in ParaView The visualization scene produced with ParaView can be very complex. When ParaView is closed, the whole arrangement, called state, is lost unless saved. The saving of a state is performed with File Save State. The state can then be later loaded with File Load State Tips and Tricks The colormap is shown automatically by default for any kind of data, i.e. also for the structures. To switch it off permanently, go to menu Edit Settings, select tab General and modify under Color/Opacity Map Range Options middle popup control from Automatically Show and/or Hide Color Bars to Automatically Hide Unused Color Bars. To avoid pressing each time Apply button one can activate Apply changes to parameters automatically button from the Paraview toolbar.