Diamond Version 5 User Manual: Working with Diamond

About documents, structures and pictures

A Diamond document may contain multiple structural parameter sets and multiple pictures for every structure

- About crystal and molecular structures
- One or more pictures for a structure parameter set each
- Multiple structure parameter sets
- Multiple documents
- Exchanging data between documents

Next article: The Diamond user interface

Before we present the user interface of the Diamond software and the several views where you can edit a structure picture or manage a multitude of structure pictures or retrieve different informations from tables of atoms etc., distances, powder pattern etc., we will have a look at the structure of a Diamond document.

Diamond uses a native binary file format with the extension "diamdoc" for its "Diamond documents". A Diamond document (as file - or in memory when Diamond is running) may contain multiple structural parameter sets and multiple pictures for every structure parameter set.

Diamond uses the "diamdoc" format since version 3, with version 3, 4, and 5 document files being backward compatible. The "DSF" format used by version 2, which contains only one structure picture (or in special cases multiple structure data sets without pictures, e.g. from a database recherche), can be read by all versions of Diamond.

Crystal and molecular structures
The typical case is you have one structure parameter set, in most cases imported from a crystal structure data file (CIF, ShelX or other formats). This structure parameter set can be a crystal structure or a "molecular structure". The more frequent case of a crystal structure uses translational symmetry, which means there are the cell parameters and a space group that define, how and where the atoms of the most important part of the structure data, the atomic parameters are located. The second case, the "molecular structure" in contrast does not have translational symmetry, meaning a set of atoms is defined having coordinates directly in Angstroem ("orthogonal coordinates") rather than fractional coordinates x/a, y/b, z/c (and cell parameters and space group are not defined).

One or more pictures for a structure parameter set each
For this structure parameter set, you can create a single structure picture containing atoms, bonds, and several other objects that depend on the basic structure parameter set or you can create a multitude of structure pictures, all of them dependent from the single structure parameter set. (That means the cell parameters, space group, and atomic parameters are not stored redundantly for every structure picture in the document. If you want to change structure data for one or more of the pictures - independent from the other pictures - you have a function to "separate" the structure, meaning creating a second (or third etc.) set of structure data and assign the "separated" pictures to these new structure data.)

These multiple structure pictures can be e.g. a first picture showing a single molecule and a second one with a packing diagram, more pictures showing them in several views, with different atom designs, in ball-and-stick or as ellipsoids, etc.

Multiple structure parameter sets
You can import multiple structure parameter sets directly into a single Diamond document, either "open" the complete input file or insert one or more of these structure parameter sets into a new blank document (or add to already existing structure parameter sets in an already open document). Such multiple structure parameter sets have typically been downloaded from a crystal structure database. Each of the structure parameter sets can have one or multiple pictures.

Multiple documents
Well, not enough that there are multiple structures and multiple pictures, Diamond also has the Multiple document interface (MDI), an interface used by several Windows applications. That means, if you already have a document open in your Diamond session, you can open a second (or third etc.) document without being forced to first save and close the previous document (single document interface, SDI). The open documents are listed in the Window menu, there are standard command to arrange the document windows, e.g. in cascades or side by side. A document window contains several parts, often called "panes", showing different aspects of the active or "current" structure or structure picture in graphical or textual form. These parts are described in detail in the next article: "The Diamond user interface".

Exchanging data between documents
If two or more documents are open in a Diamond session, you can copy or move structures or pictures between these documents.

In the following you will see different scenarios of documents opened in Diamond. More screenshots showing views of multiple structures and pictures are coming in the next article: "The Diamond user interface", where the different parts (panes) of the user interface are introduced in more detail.

Example 1: One structure, one picture

This is the simplest case: There is just one structure data set in the imported file (a CIF file from the Crystallography Open Database, COD:7106313), and there is just one structure picture: a packing diagram that has been created automatically. The picture is in the "Picture Edit view" (the main view where you have all editing commands available). The "data sheet" (a summary of the structure data) and the "properties view" (here: the contents of the structure picture) are in the right half of the document window.

Example 2: One structure, multiple pictures

The same input file with a single structure data set as in example 1 - but here with multiple pictures: Again the main graphics view (Picture Edit view) with data sheet and properties view to the right. But here additionally the "More Pictures" docking window showing thumbnails of all pictures already made for COD:7106313, The "Caption bar" on top of the document window shows the current picture's title as well as structure and document title in bold and the titles of the residual pictures at the right end of the bar.

Example 3: Multiple structures with a picture each

This is a typical case of importing files containing multiple structures coming from crystal structure database recherches, in this example from the Inorganic Crystal Structure Database (ICSD). 

The structure table (top pane in the following screen shot) gives a compact overview of the structure data sets in the Diamond document. In this example one structure picture has been created automatically for a structure data set each, the thumbnails of the pictures shown in the "thumbnails preview" (bottom left pane). The data pane (right beneath the thumbnails preview) here shows the data sheet of the current structure data set in upper half and the properties of the current picture in the lower part of the data pane.

Example 4: Multiple documents open

The following screen shot shows a typical situation with two documents open ("COD-7103386.diamdoc" and "Na3PS4-10-pictures.diamdoc"). While structure data set "7103386" has only one picture assigned ("Packing diagram"), "Na3PS4" has ten, with the picture "Super cell 2x2x2 ..." being edited. The pictures of the active document "Na3PS4-10-pictures.diamdoc" are represented as thumbnails in the "More Pictures" control window, here docked at the right side of the Diamond application window. The "Navigation" window (docked left) shows a tree of all open documents and their containing structure data sets and pictures. Navigation and thumbnail window may be hidden or moved to different position. Additionally, the links at the top of a document window, looking like tabs, can be used to switch to another view, too.

Next article: The Diamond user interface