Visualization of densities, orbital potentials, etc.
****************************************************

ADF AMSview Isosurface Contour lines Coulomb (electrostatic) potential

The AMSview module has many features. The basic use of AMSview is
explained in the first tutorial.

In this tutorial, some additional features of AMSview are demonstrated
using anthracene as a toy molecule:


Step 1: Get Single-Point calculation results with ADF on Anthracene
===================================================================

   Start AMSinput
   Set up an anthracene molecule (e.g. search for 'anthracene' in the search box [image: Search][image] and select the 'Anthracene (ADF)' molecule)
   Run (**File → Run**) the calculation with all default settings
   When the calculation has completed, open AMSview (**SCM → View**)
 [image]


Step 2: Details: Diverging and Rainbow Colormap, scalar range of field on isosurface
====================================================================================

Now let's generate an isosurface of the density colored by the
electrostatic potential:

   **Add → Isosurface: Colored**
   In the *Select Field...* box in the new controls: **Density → SCF**
   In the *Select Color Field...* box in the controls: **Potential → Coulomb Potential SCF**
   Tick the "Log" box at the right
 [image]

The image is not as smooth as it could be, because of the coarse grid
used to calculate the density and potential. Improve it by using a
better grid:

   **Fields → Grid → Medium**
   Click Yes to recalculate the 2 fields
   Play 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 is adjusted automatically (provided you have not changed it
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 the SCF Density), at the isovalue you
specify.

There is also an option to change the method used to interpret the
given isovalue. The default "Normal" method uses the isovalue without
modification. The "Contained" and "Squared" methods find 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.

Many more details can be set. First, begin by showing the color
legend:

   Check the Bar checkbox at the right
   Click once in the color bar
 [image]

The color bar shows the mapping from colors to scalar values of the
potential.

Clicking the color bar opens the detail controls.

Another way to open the details pane is to click the arrow on the left
of the controls, in front of the visualization type (currently
"Isosurface: Colored").

The first part of the detailed controls allows you to adjust the
appearance of the surface using settings like opacity, diffuse,
specular, and power. Roughly speaking, these control how shiny or dull
the surface looks and are referred to as the material properties
controls.

The second part controls the color mapping. The Hue, Saturation, and
Value fields allow you to specify two colors. The colormap option
allows you to change how the transition from one color to the other
works. The default colormap is Diverging: it goes from one pure color
to white to the other pure color. Another colormap is Rainbow: it goes
from one color to the other via other pure colors.

The third part allows you to control a clipping plane, cutting through
the isosurface so you can look inside.

   Select the Rainbow Colormap
 [image]

In general, the Diverging colormap makes it easier to see small
variations in a property, although the Rainbow colormap is much more
colorful. If you have a symmetric scalar range, the Diverging colormap
puts the zero value at white. For the electrostatic potential this is
not useful, but for a difference density it makes sense:

   Delete the Colored Isosurface (use the left pull-down menu on that line)
   **Fields → Calculated**
   In the Calculated Field C-1 controls: select left field **Density → SCF**
   In the Calculated Field C-1 controls: select right field **Density → Density Sum Frag**
   **Add → Isosurface: Colored**
   In the Colored Isosurface controls on the right-hand side: Left field selector: **Density → SCF**
   In the Colored Isosurface controls on the right-hand side: Right field selector: **Other → C-1**
   In the Colored Isosurface controls: change isovalue to 0.1
   In the Colored Isosurface controls: show the color legend
   In the Colored Isosurface controls: Specify a symmetric scalar range like -0.025 to 0.025
 [image]


Step 3: Multiple Isosurfaces
============================

An even better way to see what happens to the density when forming a
molecule from atomic fragments is the multiple-iso option. The idea is
that a whole set of isosurfaces is generated for a range of iso
values. The surfaces are colored by their isovalue.

   In the Colored Isosurface line: Use the Delete command from the left pull-down menu

   **Add → Isosurface: Multiple**

   In the Multiple Isosurface line:
   In the "Select Field" menu select the density difference: **Other → 1 → C-1**
   set N (the number of isosurfaces) to 7
   change the min-max range to -0.01 ... 0.01

   Use Cmd/Ctrl + Minus repeatedly to make the atomic spheres very small

   **Fields → Grid → Fine**
   Click OK to confirm recalculating the fields

   Rotate and zoom to get a good view
 [image]

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, so 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-axes**
   Zoom a little closer
 [image]


Step 4: Combining visualization techniques
==========================================

You can also combine several visualization methods in one image.

   In the Isosurface: Multiple controls, open the details and:
   set Opacity to 100
   rotate to look from the side
   Check the "Interactive Plane" check box
   Drag 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 box

   **Add → Plane: Colored**
   In the Plane: Colored controls:
   Select the C-1 field
   Select 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 Multiple Isosurface (without log option!)
   Zoom to get a close view

Now you get a picture using the multiple-iso and colored-plane options
at the same time.

[image]


Step 5: Play with lights
========================

AMSview also has options to control lighting. This allows you to tune
an image by adding a directed light source that casts shadows. You can
also control the amount of ambient and directed light. It is hard in
general to say what the best setting is, so try and play around:

   **View → Show Light Controls**

   In the extra light controls at the right side of the window:
   Check the box to turn the light on
   Check the box to position the light
   Position 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 light
   Rotate and zoom as you prefer

One possible image you can make this way looks like this:

[image][image]


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 present
   Add an isosurface
   Select a hydrogen atom
   **Select → Select Atoms Of Same Type**
   In the controls on the right-hand side, click Select Field... and choose Properties → Steric Interaction 1.

It is possible to make different selections and generate their own
Steric Interaction field.

[image]
