Diamond Features: Manual building and designing of a picture

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Building a picture manually step by step

Commonly, the first step when working with Diamond is to either import structure data (in most cases crystal structure data from a file or manually enter the abstract crystal structure data. Unless you did not apply one of the "automatic picture creation" functions described in one of the previous feature articles, the graphics pane is still empty after entering/importing the crystal structure data, i.e. there is no structure picture yet. 

At this point, Diamond "knows" about the infinite three-dimensional arrangement of atoms described by the crystal structure data, however, it does not know what you would like to visualize. Hence, the next step is to create a picture based on the data which have been entered/imported, or, in other words, to build up a structural model.

This is straight forward: All you have to do is to tell Diamond which atoms or parts of the crystal structure described by your data shall be displayed. Once the model has been built (all atoms, molecules, polyhedra etc. are visible on the screen), you can modify the design of the picture (e.g. the colors of the atoms or bonds) in order to best express your understanding of the structure.

One way is to define the steps in a multiple-page dialog, called "assistant". The other way - the hard way but offering all functionalities of Diamond - is to start from scratch, meaning from a blank picture.

Creating a picture using the Structure Picture Creation Assistant

While in one of the previous feature articles several ways to create a structure picture automatically, there is another way to achieve this "semi-manually" using the Structure Picture Creation Assistant. This special dialog guides you step by step through the process of building up a structure picture and provides the most common options for creating crystal structure pictures. It can be used both to create a structure picture from scratch or to modify an existing picture.

To keep it simple, we use the quartz sample from the Diamond tutorial and fill a "super cell" and create polyhedra around the Si atoms:

Adapting the design of the picture

Now, we will see how the design of the model can be changed to emphasize certain aspects you would like to present to your audience. We will continue working on the structure picture right at the point where we stopped in the previous chapter.

The "Display" menu offers a bunch of functions to define or adjust the design of atoms, bonds, and polyhedra, alongside with the "Objects" menu that helps you to define additional objects like labels, vectors, planes or lines, etc. Most likely you will use e.g. the "Atom Group and Site Design" dialog to define the colors and styles of atoms based on atom type or site level, or select the atoms you want to re-design simply from the picture and adjust their appearance on an individual basis.

In the quartz sample from the tutorial (p. 13 ff.) the aim concerning this structure picture is to present different aspects of the crystal structure of quartz to your audience. In this context, it would be nice to have parts of the structure being displayed in different models, each focusing on different aspects (like packing of atoms, 3d-network, local atomic environments).

Starting from the picture created by the Structure Picture Creation Assistant (top left picture), we change a selection of Si and O atoms in the "bottom right corner" to space-filling model and remove some polyhedra in the "upper left part" (top right picture), then change the model to two-colored tubes (bottom left picture) and finally change the color of all Si atoms from cyan to grey (bottom right picture):

Building a structure picture from scratch

If your data describe a new or even unknown crystal structure, it is quite difficult to create pictures revealing the underlying principles right away. Instead, you should first use Diamond's various options to explore the structure. For example, you might want to start exploring the individual atomic environments, and study the three-dimensional arrangement of these building blocks afterwards.

Connectivity
Typically, the first step when exploring a new crystal structure is to have a look at the distances between the various atoms. By comparing interatomic distances with typical distances, the intervals for chemical bonding and coordination spheres can be defined with the so-called "connectivity". Once these distance intervals have been fixed, you can e.g. start from some individual atom, add its coordinating atoms, use the created atoms as new starting points, etc. By doing so, you can build a complete crystal structure or molecule starting with one single atom. Step-by-step you learn about the atomic environments as well as about their connection, helping you to fully understand the fundamental building principles of the structure.

The "Connectivity" dialog allows the discussion of connectivity assisted by histograms showing the distribution of distances between selected atom types and from the bond parameters, together with automatic calculation and checking of distance ranges. On the "Bonds" page of this dialog, you can define interatomic distance interval(s) based on which Diamond decides if some atom belongs to the coordination sphere of some other atom, or, in other words, which atoms are chemically bonded. These distance intervals can be adjusted individually for each pair of atom groups (the so-called "bond groups"). Once you have defined appropriate distance intervals for each bond group, you can easily use building operations like the creation of polyhedra, the automatic search for molecules in the atomic parameter list, or the filling of coordination spheres. After the building operation(s) has/have been carried out, you can change the "Connectivity" settings for the next building operation without affecting the current structural model.

Atomic environments
Besides the definition of connectivity on atom type level, you can also define/adjust/discuss the environments of atoms on atom site level - optionally from Dirichlet domains of the atom sites - using the "Atomic Environments" dialog.

The atomic environment of "Sb1 after checking the Dirichlet domains: The last distance of 3.13 Å before the gap is excluded from the bonding neighbours ...

... leading to this distance histogram of Sb+3 --- F in the Connectivity dialog:

Filter
Another example is the "Filter": This command enables you to exclude selected atoms of the parameter list or selected symmetry operators temporarily from manual building operations. This is especially useful, if you want to exclude unwanted disorder parts from your structure picture. Once you have defined filter settings, the excluded atoms and symmetry operations won't be taken into account during the next building operations (e.g. filling the unit cell). However, when the building operation(s) have been carried out, you can perfectly change or even disable the filter settings without any harm to the current structure picture.

Filter dialog with only atom site "Si1"/"Al1" selected for building up a Si-Al sub-lattice as in the "Zeolite framework" chapter of the tutorial.

In summary, you should use the following steps when creating pictures for unknown crystal structures:
1. Import or enter crystal structure data.
2. Check the connectivity based on interatomic distances, supported by distance statistics.
3. Build fragments for the structure by creating individual atoms and filling their coordination spheres stepwise until you understand the structural principles.
4. Create one or more new picture(s) clearly showing these principles for publication and/or your students.

Functions for manual building of structure pictures

This is a short summary of the functions that can be used to explore and build up a structure picture manually:

• Filling of unit cell, multiple cells, any cell range, or boxes or spheres around selected central atoms.
• Filling of user-defined rectangular areas within the screen.
• Filling of slabs along a plane (hkl or least-squares) or between a plane and the walls of the coordinate system.
• Support for disorder parts when searching for neighbouring atoms and bonds as well as in "Filter" function.
• Creation of bonds automatically, basing on connecitivity, or manually by inserting bonds between two atoms each.
• Adding all atoms (and optionally bonds, H-bonds, contacts) of atomic parameter lists as well as from connection parameter lists.
• Generation of atoms from parameter list serving as initial atoms for building up complex frameworks.
• Completion of coordination spheres around selected atoms.
• "Pump up": Generation of multiple spheres around selected atoms and its reversal ("shrink").
• Automatic generation of molecules or completion of fragments which have e.g. been clipped at cell edges.
• Definition of molecular units (from atomic parameter list).
• Generation of molecules from molecular units at symmetry-equivalent positions.
• Search for molecules in the neighbourhood of selected atoms or molecules.
• Creation of molecular packings (parallelepiped, sphere, slab, or layer).
• "Grow" and "cut: Expansion and reduction of polymers or molecular fragments.
• Creation of "broken-off" bonds to signal infinitesimal chains, layers, or 3D-frameworks. Conversion between "broken-off" and normal bonds.
• Definition of H-bond and non-bonding contact connectivity. Creation of H-bonds and contacts.
• Expansion to neighbouring atoms or molecules via H-bonds and/or contacts to build up molecule clusters and reversal ("reduce").
• Discussion of contact spheres and expansion or reduction of molecule clusters with the mouse wheel.
• User-controlled dismantling of built-up frameworks.

General functions for working with structure pictures manually

• Conversion between "crystal" and "molecular" structures, i.e. adding or removal of cell and symmetry information.
• Cut, copy and paste of structural parts between structure pictures:
  • A fragment of a structure picture (or the whole picture) can be copied.
  • The copied fragment can be pasted into a blank or another picture of the same data set.
• Multiple-step Undo and Redo function (with picture thumbnails) to enable safe experimentation with even high-complicated and unknown structural frameworks.

Exploring an Unknown Structure

The tutorial chapter "Exploring an Unknown Structure" demonstrates how to start from a blank screen by adding a single P atom and checking the environment by calling subsequently the Coordination Spheres command to generate a first building block (left picture) The P-atoms in the structure are tetrahedrally coordinated by O-atoms, which themselves are connected to three W-atoms each. Due to the fact that this is a typical inorganic oxide building block, a polyhedra representation (metal/non-metal atoms coordinated by oxygen) should be better. The building of coordination polyhedra around the P and the W atoms with the Add Polyhedra command leads to the right picture.

Using the command to fill the unit cell and another call to "Add Polyhedra" lead to the second Keggin ion in the structure that we are exploring (left picture). The command Destroy non-bonded atoms removes vagabonding atoms (here: O atoms) but keeps the O--H bonded water atoms (right picture).

Zeolite Framework

The last chapter in the tutorial dealing with the manually building up of an inorganic framework demonstrates how to present even complex structures in a few steps and how to apply filter, dummy atoms and selections effectively.

Faujasite is a famous representative of the zeolites. One of the components in the linking pattern of this aluminosilicate is the so-called "β-cage". Each corner of this polyhedron contains one silicon or aluminium atom; each edge contains an oxygen atom which links two atoms in the corners. The β-cages are connected with each other via hexagonal prisms.

Here we show a sequence of structure pictures where the β-cages in the Faujasite structure as well as their connection among each other by hexagonal prisms will be clearly visible.

View of the Si-Al-substructure in Faujasite using the filter function (left picture). Polyhedron view of the β-cage in Faujasite using a dummy atom in the center of the polyhedron (right picture).

For the prisms we also use dummy atoms to create polyhedra (left picture). Adding coordination spheres of Si/Al atoms repeatedly and finally adding polyhedra leads to the right picture.

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