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Pvdgrid PDF
Pvdgrid PDF
Baranov
Springer
Contents
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
v
List of Tables
vii
List of Figures
ix
Chapter 1
Visualization with ParaView
The visualization of DGrid generated data can also be performed with the freeware
program ParaView which is available for many platforms including Microsoft Win-
dows, Linux and MacOS. An additional ParaView plugin is necessary for that. It
provides routines which read DGrid file formats, adds handy ParaView filters and
GUI controls. Plugin consists of two shared (dynamically linked) libraries.
The ParaView plugin installation is described in Sec. 1.1. Brief introduction into
ParaView controls and basic visualization steps is given in Sec. 1.2.
ParaView plugins are made available as separate part of the DGrid package. There
are two ways to deploy them:
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.
This is the way to obtain the plugins when pre-build binary plugins are not avail-
able for target ParaView version or when customized build of ParaView is used
(compiler or libraries differ from those for official built).
See the Sec. 1.1.2 for instructions how to build the plugins from source code.
1
2 1 Visualization with ParaView
When installing a precompiled plugin, download the package from the DGrid web-
site and unpack it. Copy the plugin files 1 :
libGUIDGridPlugin
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 (http://www.paraview.org/Wiki/Plugin HowTo#Using Plugins) con-
tains additional information on loading plugins in ParaView.
dgrid-4.6/PVDGrid
First of all, download ParaView source code and build ParaView. Detailed in-
structions can be obtained at ParaView website
http://paraview.org/Wiki/ParaView:Build And Install. To compile ParaView, some
other tools like Qt or CMake must be available.
The configuration and build process for plugin is similar to that for ParaView
itself. 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).
1 The versions of plugin for ParaView < 4.2.0 includes also additional .xml files.
1.2 Visualization 3
1.2 Visualization
Start ParaView by typing paraview or clicking the appropriate icon. Load the DGrid
plugins via Plugin Manager if they are not loaded automatically (cf. 1.1.1).
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, se-
lect 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.
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. 1.1.1. When plugins are found but can not be loaded, consult Sec. 1.1.2
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 (available as hardcopy book
4 1 Visualization with ParaView
Fig. 1.1 Visualization pipeline for structure plot and Atom tab of ParaView plugin.
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
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.
1.2 Visualization 5
The controls for the Atoms tab are shown in Fig. 1.1.
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!
The controls for the Bonds tab are shown in Fig. 1.2.
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.
6 1 Visualization with ParaView
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 4. 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. 1.3.
Each path type has default radius and color given in the DGrid Structure file,
cf. DGrid Users Guide. They can be changed via Set Radius field and
Set Color button.
The buttons for the Cell tab are shown in Fig. 1.4.
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 Users 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.
1.2 Visualization 7
The field Scale below the tab control sets up the general scale factor for all the
spheres and cylinders used in the structure plot.
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:
1. Go over ALL BUT Label data set boxes in Pipeline Browser , select Properties
tab and deactivate Pickable checkbox. 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 win-
dow (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.
6. If numbers appears instead of text labels, press Edit Selection Label Properties
button (with gear label) below Point Labels button and modify Point Label Format
field to %s. Press Apply or OK button.
7. Label appearance (size, font, color etc.) can be tuned by pressing Edit Selection Label Properties
button (with gear label).
1.2.2.1 Isosurface
Select the desired data set in the Pipeline Browser and apply Contour filter
(from menu Filters ). The filter control panel appears on the Properies tab. Spec-
ify the isosurface level at the Value Range window there and press Apply to
show the isosurface. The color of the isosurface can be modified at Properties
tab.
1.2.2.2 Slice
Select the desired data set in the Pipeline Browser and apply Slice filter (from
menu Filters ). The filter control panel appears on the Properies tab. For flat
slice plot select Plane as slice type. Its position and orientation can be modified
1.2 Visualization 9
by the visual controls shown on the 3D plot or via Origin and Normal fields on
the Properties tab.
The colormap settings can be modified on the Properties tab. For instance, to
load a classic ELF colormap click on Edit Color Map button, press in the window
appeared a Choose Preset button and import elf mk.xml file, shipped as a part of
ParaView plugin. Then close the Preset Color Scale window.
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.
1.2.2.3 Basin
The basin file contains a field of integer values which can be read in with the inter-
face as described for the property grids on page 3. Special route must be followed
for the visualization of the basins as separate solid objects:
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. The basin to be visualized can be
selected on the Property tab.
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.
10 1 Visualization with ParaView
Fig. 1.6 ParaView plugin Density basin surface colored according to laplacian values
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.
The visualization scene produced with ParaView can be very complex. When Par-
aView is closed the whole arrangement, called state, is lost unless saved. The sav-
ing of a state is performed with File Save State . The state can then be later
loaded with File Load State .
checkbox. Modify it when necessary and click on the button with floppy label right
to View(Render View) button to save the settings.
In ParaView 4.2.0 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 .
In ParaView 4.2.0 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, uncheck box Map Scalars under section Scalar Coloring on
the Property tab of Plot Structure filter and press a button with the floppy logo
right to the Display (GeometryRepresentation) control.
Index
colormap, 9
13