Visualization of densities, orbitals potentials, …¶
The AMSview module has many features. The basic use of AMSview is explained in the first tutorial.
In this tutorial some additional features of the AMSview module are demonstrated. As a toy molecule the anthracene molecule is used:
Step 1: Get Single-Point calculation results with ADF on Anthracene¶
Step 2: Details: Divergent and Rainbow Colormap, scalar range of field on isosurface¶
Now lets generate an isosurface of the density colored by the electrostatic potential:
- Add → Isosurface: ColoredLeft field selector at bottom: Density → SCFRight field selector at bottom: Potential → Coulomb Potential SCF
The image is not as smooth as it could be, as a result of the coarse grid used to calculate the density and potential. So improve it by using a better grid:
- Fields → Grid → MediumClick Yes to recalculate the 2 fieldsPlay around with the isovalue, and note how the two numbers on the right change
When you change the iso value, the default range for the coloring scheme will be adjusted automatically (provided you have not changed them yourself). This range corresponds to the minimum and maximum value of the coloring field (in this case the SCF Potential) across the isosurface (in this case of the SCF Density), at the isovalue you specify.
Many more details can be set. First, begin by showing the color legend:
- Check the Bar check box at the bottom right(note: on some systems the text Bar might be partially invisible due to a resize box)Click once in the color bar
The color bar shows the mapping of the colors used to the scalar values of the potential. By clicking on the color bar you open the detail settings, three extra lines with extra controls. Another way to open the details line is using the pull-down menu located on the left, currently with title “Isosurface: Colored”. In that menu you will find a “Show Details” and a “Hide Details” command. If you have the color bar visible, you can also just click on it to toggle the detailed controls.
The first line of the detailed controls allows you to set what the surface looks like: opacity, diffuse, specular and power. Roughly speaking these control how shining or dull the surface looks like, they are called the material properties controls. Additionally, there is the option to change the method to interpret the given isovalue. The default “Normal” method uses the isovalue without modification. The “Contained” and “Squared” method finds the isosurface that contains the given percentage of the integrated field, and integrated squared field, respectively. The “Volume” method finds the isosurface that matches the given percentage of the total grid volume.
The second line controls the color mapping. The Hue, Saturation and Value fields give you the option to specify two colors. The colormap option gives you an option to change how the transition from one color to the other goes. The default colormap is the Diverging colormap: it goes from one pure color to white to the other pure color. Another colormap implemented is the Rainbow colormap: it goes from one color to the other color via other pure colors.
The third line allows you to control a clipping plane, cutting through the isosurface so you can look inside.
- Select the Rainbow Colormap
In general the Divergent colormap makes it easier to see small variations in some property, although the Rainbow colormap is obviously much more colorful. If you have a symmetric scalar range, the divergent colormap will put the zero value at the white color. For the electrostatic potential this is not useful, but for example for a difference density it makes sense:
- Delete the Colored Isosurface (use the left pull-down menu on that line)Fields → CalculatedIn the Calculated Field C-1 controls: select left field Density → SCFIn the Calculated Field C-1 controls: select right field Density → Density Sum FragAdd → Isosurface: ColoredIn the Colored Isosurface line: Left field selector at bottom: Density → SCFIn the Colored Isosurface line: Right field selector at bottom: Other → C-1In the Colored Isosurface line: change isovalue to 0.1In the Colored Isosurface line: show the color legendIn the Colored Isosurface line: Specify a symmetric scalar range like -0.025 to 0.025
Step 3: Multi Isosurface¶
An even better way to see what happens to the density when forming a molecule out of the atomic fragments can be made using the multi-iso option. The idea is that a whole set of isosurfaces is generated, for a range of iso values. The surfaces will be colored by there isovalue.
- In the Colored Isosurface line: Use the Delete command from the left pull-down menuAdd → Isosurface: MultiIn the Multi Isosurface line:in the field select menu select the density difference: Other → 1 → C-1set N (the number of isosurfaces) to 7change the min-max range to -0.01 … 0.01Click on the -XY button to use a Clip plane in the XY plane(the sign determines from which side you can see)Use cmd/ctrl - Minus repeatedly to make the atomic spheres very smallFields → Grid → FineClick OK to confirm recalculating the fieldsRotate and zoom to get a good view
Now you can very clearly see that the electron density in the bonds is increased (blue), and where that electron density comes from (everywhere else, including close to the atoms)
The clip plane allows you to cut away part of an isosurface, such that you can look inside. The buttons on the last detail line allow you to position the clip plane as needed.
Instead of using a clipping plane you can make the isosurfaces transparent:
- Remove the clipping plane (uncheck the Use Clip Plane check box)Change the Opacity to 20 %View → View Direction → Along Z-axesZoom a little closer
Step 4: Combining visualization techniques¶
You can also combine several visualization methods in one image.
- In the Isosurface: Multi lineset Opacity to 100click the -XY button to use a clipping planerotate to look from the sideCheck the “Interactive Plane” check boxDrag the red line to move the clipping plane slightly above the atom plane(you might need to use the -XY button to realign it first)UnCheck the “Interactive Plane” check boxAdd → Cut Plane: ColoredIn the Cut Plane: colored lineSelect the C-1 fieldSelect three atoms, and click the Position plane with atoms button(note you can select atoms by shift-dragging a rectangle around an atom,repeating this trick 3 times)Use the same scalar range as for the Multi Isosurface (without log option!)Zoom to get a close view
Now you get a picture using the multi-iso and colored plane options at the same time.
Step 5: Play with lights¶
AMSview has also some options to control lights. This allows you to change an image the way you like it by adding a directed light source that casts shadows. You can also control the amount of ambient light and directed light. It is hard in general to say what is the best setting, so just try and play around:
- View → Show Scene LightIn the extra scene light line (the topmost of the control lines at the bottom):Check the box to turn the light onCheck the box to position the lightPosition the light as you like it(you may have to rotate to be able to control the light properly)Change the intensity of the extra light and the ambient light(the Scene/Camera light controls)Uncheck the box to position the lightRotate and zoom as you prefer
One possible image you can make this way looks like this:
Step 6: Special fields¶
AMSview has access to a few fields that need extra clarification. One of these is the Steric Interaction, which uses the Van der Waals radius to visualize steric bulk. The field is the minimum distance to the Van der Waals surface of the selected atoms.
- Delete the other surfaces presentAdd an isosurfaceSelect an hydrogen atomSelect → Select Atoms Of Same TypeAt the bottom click Select Field… and choose Properties → Steric Interaction 1.
It is possible to make different selections and generate their own Steric Interaction field.