Diamond Version 5 User Manual: Display of structure picture

Representation of Mixed and Defect Sites

This article in brief:
- Overview
- Choosing how to display the components of a mixed site
- Definition of colors for mixed site representation
- Setting the opacity to site occupation factor (S.O.F.)
- Using random distribution of mixed site components.

Previous article: Drawing ellipsoids
Next article: Color differentiation

Overview

Diamond offers a method to display the distribution of atoms on a mixed site by:

1. displaying only the representative,

2. mixing the colors of all atoms on the mixed site using the ratio of the site occupation factors,

3. displaying the ratio of site occupation as sectors (or as pie diagram in flat representation).

The colors for multiple (trace) elements are defined with their corresponding atom groups and/or atom sites.

In both Atom Group and Site Designs and Atom Designs dialog you can assign atoms on defect or mixed sites an opacity that equals the site occupation, i.e. opacity = site occupation factor (S.O.F.) or transparency = 1 - SOF. The opacities of bonds between transparent atoms can be automatically adjusted to the atoms' opacities.

Mixed site representations - such as sectors showing the components occupation factors - have a special option "Random distribution of mixed site components". Here only one of the components is shown at a certain (symmetry-equivalent) position of the structure picture - with the possibility to choose a different component rather than the one Diamond has chosen at this position.

Choosing how to display the components of a mixed site

The Atom Group and Site Designs dialog offers two styles on its Style and Colors page to either show
- the components of a mixed site as sectors of a sphere where the size of a sector each reflects the relative site occupation factor of its component
- or simply to mix the colors of the components basing on the site occupation factors.
(The other styles are described in the article "Designing atoms".)

Screenshot of "Atom Group and Site Designs" dialog for sample compound "COD-9013698-mixed-sites.diamdoc" with style "Mixed/Defect site sectors" selected for atom site Na/K/Ca.

The two styles that support mixed site representation are:

Mixed site color mix
This option mixes the colors of the components in a ratio depending on the atom site's site occupation factors and uses this mixed color as fill color rather than the color that is defined on the Style and Colors page under Fill color.

Mixed/Defect site sectors
This option draws sphere sectors for a component each with the size depending on the site occupation factor and the color for the component each. The Fill color on the Style and Colors page is ignored. This also works for defect sites. If the sum of the site occupation factors of the components is less than one, an open sector will remain.

The option if and how to represent the components of a mixed site is reflected on the Mixed Site page of the Atom Group and Site Designs dialog. The components of the atom group or site (selected in the Atom groups and sites tree list) are listed at Component, the color can be changed with the color select box Color.

Note: There are special options "random distribution of mixed sites' components" as well as "setting the opacity to site occupation factor" described below in this article.

Definition of colors for mixed site representation

Up to eight colors can be defined for each atom group (or atom site) having two or more components in the Atom Groups and Sites dialog. To open the Atom Groups and Sites dialog, choose the Atom Design command from the Display menu. If an atom group represents a mixed site and one of the mixed site representation styles is selected under Define if and how to represent the components of a mixed site, the items Component and Color available. Otherwise these items are disabled (grayed). The components (elements with oxidation numbers) of the mixed site are given in the list Component, the corresponding colors in the color select box Color:

Example: One atom in the structure picture representing a mixed site with the chemical composition 0.543Al + 0.41Fe + 0.037Ti + 0.01Mg + 0.003Zn.

The default settings for the colors are those used for the atom type components. That means, if you have defined brown for the atom type "Fe+3" in the Diamond atom type resource (stored in the Windows Registry), all Fe+3 components on mixed sites will become brown by default.

Opacity = site occupation factor

The "Atom Group and Sites Designs" dialog now shows site occupation factors (for defect sites) as well as the disorder part (if defined) for the atom sites in the "Atom groups and sites" tree on the left side, where you select the atom group(s) and/or site(s) from.

The former "Reset" button in the lower left has turned to a "Set or Reset" dropdown button, while the "Reset" command has moved to a "Reset Atom Group and Site Designs" command (and shows the corresponding dialog as before) in the dropdown menu.

An additional command "Adjust Designs to Site Occupations..." shows a new dialog with several options to set or reset transparency values of all or selected atom sites. The main purpose of this dialog is to equate all or a large number of atom sites the opacity to the site occupation (SOF) factor each. Since the opacity is one minus transparency, this results in transparency = 1 - SOF.

Besides this, you can use this dialog to select all atom sites having a site occupation factor less than one, in order to change other properties than the transparency to differentiate defect sites from full occupied sites, e.g. use dotted lines in a flat mode picture.

A push button "Set opacity to S.O.F." is also available on the "Style and Colors" page of the "Atom Design" dialog (and in the "Atom Group and Site Designs" dialog as well). This will set the transparency to 1 - SOF of the selected atom (and works also for multiple atoms).

Note that, if the atom (site) is a mixed atom site, the used site occupation factor (SOF) is the sum of the site occupation factors of all components of the mixed site.

To simplify the assignment of transparencies to bonds between transparent atoms, a corresponding option has been added to the "Bond Group Designs" dialog as well as to the "Bond Design" dialog. On the "Style and Colors" page, the checkbox "Adjust bond transparency to atoms' transparencies" has been added below the "Transparency" input field. If the checkmark is set, Diamond uses a higher transparency value (than the one defined at "Transparency"), if at least one of the connected atoms is transparent. The effective transparency is then the maximum transparency of the two atoms.

The picture shows the unit cell of synthetic mordenite [1] with transparent atoms and transparent bonds between (sample file "amcsd_0003443_0003444_mordenite.diamdoc"):

Random distribution of mixed site components

For this part we use the sample file "COD-9013698-mixed-site-random-distribution.diamdoc" [2].

There are two options already available to show the components of a mixed site, one uses sphere sectors with an arc and color representing the component's site occupation factor (S.O.F.) and element, rsp., each, another one mixes the element colors weighted by S.O.F. each.

Now we have another option, called "Random distribution of mixed site components", which shows only one of the two or more components of a mixed site at a symmetry-equivalent position.

These options as well as the colors for the components are defined like before in the "Atom Group and Site Designs" dialog, but the page - previously named "Mixed colors" - has been renamed to "Mixed sites". (That is because you define more than just the components' colors here.) The options are available under "Define if and how to represent the components of a mixed site". For the random distribution, there is also the option "Set opacity to S.O.F." to set the opacities of the (symmetry-equivalent) positions to the site occupation factor of the component that is shown at the (symmetry-equivalent) position each.

(Please note that for backward compatibility, the options "Mixed/Defect site sectors" and "Mixed site color mix" are also and still available as "Style" on the "Style and colors" page.)

Random assignment and manual change of component
If you choose the random distribution option and close the dialog with "OK", Diamond will assign randomly one component to a position in the structure picture. To change the component at a certain position, select the atom and run "Picture/Atom Designs..." (and choose the option to edit the design of the selected atom rather than to open the "Atom Group and Site Designs" dialog), or call the command "Edit/Atom Designs..." from the structure picture context menu. This works also for multiple selected atoms at a time.

The "Atom Design" dialog shows a new page "Components" as first page. (This page appears for mixed sites only but not for normal sites) where you can select a different component to be shown at the selected symmetry-equivalent position (than the one the "random distribution" has made for you). Provided you use the random distribution option, you can choose a different component from the "Component to be displayed at selected position" dropdown list.

Atom labels for mixed sites
The option "Content = Composition" has been added to the "Add (or Edit) Atom Label" dialog ("Objects" menu) to show the site occupation factor, element and oxidation state (if given) of either the representative of the mixed site or the component on this site or to list all components of a mixed site. If to list all components or one only, is defined under the new dropdown list "Mixed site".

Previous article: Drawing ellipsoids
Next article: Color differentiation

[1] AMCSD: 0003444. Simoncic P, Armbruster T; "Peculiarity and defect structure of the natural and synthetic zeolite mordenite: A single-crystal X-ray study Sample: synthetic"; American Mineralogist, 89, 421-431 (2004)

[2] COD: 9013698. Ertl, A.; Marschall, H.; Geister, G.; Henry, D.; Schertl, H. P.; Ntaflos, T.; Luvizotto, G.; Nasdala, L.; Tillmanns, E.; "Metamorphic ultrahigh-pressure tourmaline: structure, chemistry, and correlations to P-T conditions Locality: Saxonian Erzgebirge, Germany "; American Mineralogist, 95, 1-10 (2010)