XCrySDen --
(X-Window) CRYstalline Structures and DENsities

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Isosurfaces: controlling display parameters

Table of Contents

Description of isosurface display parameters
    Isosurface controlling window
    Description of widgets functions
        Checkbutton: Display Isosurface
        Scale: tri-cubic spline interpolation
        Labels: Minimum/Maximum Grid Value
        Entry: Isovalue
        Checkbutton: Render +/- isovalue
        Frame: Expand Isosurface:
        Radiobuttons: Render isosurface as
        Radiobuttons: Isosurface's Shade Model
        Radiobuttons: Two-sided lighting
        Radiobuttons: Transparency of isosurface
        Illumination of the isosurface
            Button: Revert (+) Sides
            Button: Revert (-) Sides
            Buttons: Revert (+) Normals
            Buttons: Revert (-) Normals
            Button: Set COLOR parameters
            Button: Set TRANSPARENCY parameters
        Buttons on the bottom: [Hide]/[Close]/[Save Grid]/[Submit]

Description of isosurface display parameters

XCrySDen tessellate the isosurface from a 3D grid of values. This 3D grid of values span some box, and beside the isosurface display it is also possible to render the contours and colorplanes on the slices of three basal planes of the grid-box (what is really meant by this will be explained below), namely, on AB, AC, and BC planes.

Isosurface controlling window

The isosurface display requires a lot of parameters to be specified. Of course XCrySDen sets those parameters to some default values, but nevertheless these defaults are rarely sufficient for a good quality display of isosurface. Therefore when rendering the isosurface the Isosurface/Property-plane Controls window appear shown below.

Important: as there are many items on the below window, the figure was made interactive in order to facilitate easier explanation of items functions. Simply mouse-click appropriate item (widget) to get its explanation.

Isosurface/Property-plane Controls - window
Isosurface rendering parameters Plane #1 rendering parameters Plane #2 rendering parameters Plane #3 rendering parameters toggles the display of isosurface sets the degree of tri-cubic spline interpolation minimum and maximum grid values isovalue of rendered isosurface renders also the isosurface with negative isovalue (i.e.: -1 x isovalue) sets the display of the periodic replicas sets the display-mode of the isosurface sets the shading model of isosurface toggles two sided lighting toggles the transparency of the isosurface reverts the front and back sides of isosurface reverts the isosurface normals direction sets the color parameters of isosurface sets transparency parameters of isosurface hides this window closes this window saves the datagrid in XSF format submits/updates the new setting of isosurface

Description of widgets functions

Checkbutton: Display Isosurface

This radiobutton toggles the display of isosurface.

Scale: tri-cubic spline interpolation

Allows to interpolated the 3D grid values by tri-cubic spline interpolation. The term degree determines how many additional points will be interpolated. The value of 1 means no-interpolation, while the value of 2 means calculate a middle points between two sequential points. Here this is shown graphically for 2D example:
Interpolation degree - figure

Labels: Minimum/Maximum Grid Value

These two labels displays the minimum and maximum grid values. The specified isolevel should be in this range.

Entry: Isovalue

In this entry one specifies the isovalue (isolevel) for the isosurface. When this value is changes the [Submit] button should be pressed to load the newly specified value and to update the display of the isosurface.

Checkbutton: Render +/- isovalue

Toggles the display of isosurface with -isovalue value. An example: when displaying the isosurface of a molecular orbital, then it is a good idea to display both positive and negative valued isosurface (for example the -0.02/0.02 sqrt(BOHR^3/electrons)). By default the positive isosurface is rendered in red, while negative in blue. If one does not see these colors, then she/he should play with the [Revert (+) Sides], [Revert (-) Sides], [Revert (+) Normals], [Revert (-) Normals] buttons. The functions of these buttons is explained bellow.

Frame: Expand Isosurface:

The radiobuttons and scales on this frame only appears for periodic structures. The widgets allows to control the display of the periodic replicas of the isosurface. I hope these widgets are self-explanatory and we can try them out by testing.

Warning:

  1. press the [Submit] button to update new expand setting.
  2. The isosurface can be expanded just to the size of the currently displayed structure. Hence use the Modify-->Number of units drawn menu to change the number of displayed unit cells.

Radiobuttons: Render isosurface as

Controls the display-style of the isosurface. Currently the solid, wire and dot display styles are implemented.

Radiobuttons: Isosurface's Shade Model

Controls the shading of the isosurface, which is either smooth or flat.

Radiobuttons: Two-sided lighting

Toggles the display of two-sided lighting. By default two-sided lighting is disabled. This feature needs some more explanation. Any surface has two sides, which we will call the front and back sides. Now if we render the isosurface of molecular charge density, then this isosurface will be closed and only one side will be visible (let's say front side). Hence we can disable the lighting of the back side in order to gain the rendering performance (i.e. speed). However it is very common to get an open surface for the crystalline structures, since we are only rendering a part of it, namely, some number of unit cells. To correctly render such a case, the two-sided lighting should be enabled, otherwise the illumination of the back-side will be incorrect. Furthermore, the choice of the front and back sides can be quite arbitrary. Why? Let us take a look of the charge density of the TiC crystal at two different isovalues, that differs for the factor of 10.
TiC - exmaple 1 TiC - example 2
The isosurface on the right figure is rendered at 10 times lower isovalue with respect to the left one. We can realize that what we would normally define as front-side is different for left an right figure. Normally I would define the blue-surface on the left figure as a front-side and a red-surface on the right as the front-side. Therefore, due to this arbitrariness of the choice of the front side, XCrySDen provide [Revert (+) Sides] and [Revert (-) Sides] buttons, which swaps the front and back sides. The (+) button is meant for isovalue isosurfaces, while (-) button for -isovalue isosurfaces. Furthermore, there are also [Revert (+) Normals] and [Revert (-) Normals] buttons. Their function is the following: sometimes the illumination of the isosurface looks as from-the-back. In these case revert the normals to get the correct from-the-front illumination.

Radiobuttons: Transparency of isosurface

Toggles the transparency of isosurface.

Illumination of the isosurface

Sometimes the isosurface is not illuminated correctly. Hence several command buttons exist to improve upon that.

Button: Revert (+) Sides

Swaps the front and back sides of the isovalue (i.e. (+)) isosurface. See also the discussion on two-sided lighting.

Button: Revert (-) Sides

Swaps the front and back sides of the -isovalue (i.e. (-)) isosurface. See also the discussion on two-sided lighting.

Buttons: Revert (+) Normals

Reverts the isosurface normals (i.e. nnew = -nold) of the isovalue (i.e. (+)) isosurface. See also the discussion on two-sided lighting.

Buttons: Revert (-) Normals

Reverts the isosurface normals (i.e. nnew = -nold) of the -isovalue (i.e. (-)) isosurface. See also the discussion on two-sided lighting.

Button: Set COLOR parameters

Here we can set the color parameters for the isosurface. When this button is pressed, the following window appears:
Isosurface color parameters
In this window we see a whole bunch of parameters, but this is how it is. To get an extensive description of all of these refer to some OpenGL guide. There should be plenty sides on the WEB, where the lighting is explained. Here we just shortly summaries.

At the top of the window the [Front Side Color] and [Back Side Color] tabs are located. Pressing one of them displays the values of corresponding parameters.

At the bottom we see the [Close] and [Update] buttons. The first one closes the window, while the latter update the current color setting. It is mandatory to press this button to load the new setting.

In the middle we the the Ambient, Diffuse, Specular and Shininess parameters.

Ambient color
this is the color that the object inherits from the environment. For example an object will appear in different color under day light or in some room with some artificial color of light.
Diffuse color
These are the most important parameters, since the color of the isosurface is mostly determined by them. The red/green/blue determines the color, while alpha is used for transparency.
Specular color & Shininess
Determine the appearance (i.e. shinnines) of the isosurface. For example specifying the specular color as white (1.0,1.0,1.0) and putting the specular exponent to large value (app. 100) will make the isosurface to appear like a metal surface, while specifying low specular color (0.1,0.1,0.1) will make the isosurface to appear like a paper.

Please note that there are two sets of color parameters, one for non-transparent isosurface and one for transparent isosurface. If we press the [Set COLOR parameters] button then we will edit the color parameters for non-transparent mode. To edit the color parameters for transparent mode press the [Set TRANSPARENCY parameters] button.

Button: Set TRANSPARENCY parameters

Here we can set the transparency and color parameters for the transparent mode of the isosurface. When this button is pressed, the following window appears:
Isosurface color parameters
At the top of the window the [Transparency], [Front Side Color], and [Back Side Color] tabs are located. The meaning of the last two is the same as the ones appearing for Set Color parameters task. Pressing the first button displays the transparency parameters. Refer to the any OpenGL guide for the meaning of these parameters.

At the bottom we see the [Close] and [Update] buttons. The first one closes the window, while the latter update the current color setting. It is mandatory to press this button to load the new setting.

Buttons on the bottom: [Hide]/[Close]/[Save Grid]/[Submit]

At the bottom of Isosurface/Property-plane Controls the [Hide]/[Close]/[Save Grid]/[Submit] buttons are located. The function of these buttons is as follows:
[Hide]
Hides the Isosurface/Property-plane Controls window. Hiding means that window is iconified, i.e. the window disappears and its icon appears on XCrySDen main render window. Pressing the icon pop-ups the window
[Close]
Closes the window. The 3D grid data will be flushed (cleared).
[Save Grid]
Saves the 3D grid data in XSF format.
[Submit]
Loads new isosurface parameters and renders an updated isosurface.

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This document was last modified on Wed Oct 7 16:08:44 CEST 2015