Diamond Version 5 User Manual: Structure files

Database with inorganic structure types

- Diamond comes with a small database with the most common inorganic structure types. You can use the command "From Structure Type Database..." in the "Structure" menu to browse through a list of structure types and insert a dataset from this database into the current document. (The datasets have been taken from latest COD ("Crystallography Open Database") version.) A structure picture for that dataset can be created automatically or by an assistant. You can also load one or more ready-to-use structure pictures for that dataset.
- The "New Document" dialog (via "File/New..." command) has an option (radio button) "Load a structure from structure type database", which forwards you to the command "Insert From Structure Type Database..." ("Structure" menu).

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Starting a new document with a structure from the structure type database

Up to version 4.3 of Diamond you had the three options when creating a new document:
- to start with a completely blank document,
- to start with a blank document, too, but immediately followed by entering structural parameters for a new data set, and
- to start with a blank document and then insert one or more structure data sets into that document.

Now you have a fourth choice: Instead of entering structural parameters from scratch, you can begin with a ready-to-use data set from a small database of inorganic crystal structure types and adjust its parameters, i.e. cell, space group, add or modify atom positions etc., with the corresponding commands in the "Structure" menu, e.g. "Atomic Parameters...". (Note: There is also a way to use the "New Structure" assistant where you start from a structure type dataset as template, see below.)

This option leads you to the "Insert Structure From Type" dialog. The dropdown list of the input box shows the latest used structure types. (If you run this dialog for the first time, both input box and dropdown list are empty and you have to run "Browse..." to call the "Structure Type" dialog.) We will come to the further options concerning the structure pictures later down ...

Pushing the "Browse..." button will open the actual "Structure Type" dialog where you have a table of the most common inorganic structure types with the following informations:
- Description: Chemical formula of a (or the most) prominent representative, and optionally modification and mineral name
- More: Chemical formulas, modifications, and/or mineral names of more representatives of the same structure type
- The code that is used by "Strukturbericht" as well as Hermann-Mauguin space group symbol, Int. Tables space group number, and the Pearson symbol.
- ICSD cnt.: Number of entries in the Inorganic Crystal Structure Database associated with that structure type.
- PCD cnt.: Number of entries in the Pearson's Crystal Database associated with that structure type via the "entry prototype" definition.

In our example, we will take "analcime 1C" [10].

Note:
The structure type informations displayed in this dialog have been compiled from a list of structure types in a Wikipedia article about "Strukturbericht" [2], which used the Inorganic Crystal Structure Database (ICSD) [3] as source, and a series of structure type definitions from "Strukturbericht" [9] as well as the "entry prototype" informations in Pearson's Crystal Data (PCD) [6] (cf. the chapter "Prototype Assignment" (p. 75) in the PCD manual (http://www.crystalimpact.de/pcd/download.htm)).
The counts of database entries "ICSD cnt." assigned to a structure type each for the Inorganic Crystal Structure Database (ICSD) [5] have been taken from/updated in April 2016 (184,748 entries total) [2].
The entry counts "PCD cnt." for Pearson's Crystal Data (PCD) refer to the release 2016/17 (288,846 entries total) [6].
Due to legal reasons, the actual structure parameter data sets, which are associated with a structure type in the table each, are taken from the Crystallography Open Database (COD; November 2016; about 369,000 entries total) [7,8].

Returning back to the "Insert Structure From Type" dialog with the "analcime 1C" dataset, we now choose to take the ready-defined pictures for this dataset ("Load structure pictures"). Alternatively we could let Diamond start a new picture object, intialized with Diamond's structure picture proposal ("Create automatically") or by a user-defined building scheme, or assisted by the Structure Picture Assistant, or left blank, and we build it up step-by-step using the commands from the "Build" menu.

Closing the dialog with OK inserts the structure data along with all - in this example three - pictures, so Diamond will switch to the thumbnail preview. If there is just one picture associated with a dataset of the structure type database, Diamond will directly come up with the picture edit view.

(Note: Screenshot made with version 4 of Diamond.)

You can delete unwanted pictures (from your new document) by simply selecting them in the thumbnail view and running "Delete" from the "Edit" menu.

Using a structure type dataset as template

In the above example we directly inserted a structure data set along with its associated pictures from the structure type database into a new blank document. Now we want to edit a new structure data set but do not want to start from scratch (a = b = c = 1, alpha = beta = gamma = 90, no atoms) but by modifiying the parameters of a dataset from the structure type database. So we run the "File/New..." command again:

Unlike the "Load structure from structure type database" (what we have used in the above example), choosing the "Create a document and type in or modify structure parameters" option leads us to the "New Structure" assistant. On the first page after the Welcome page you have the choice to enter all parameters from scratch ("Type in new structure parameters") - as you know from this assistant before, but also to use the parameters of a data set from the structure type database as a template (and adjust its parameters and add or modify atom positions in the subsequent steps of the assistant). A template can also be saved for later use. You can access such already-defined templates with the third option "Load a structure template".

In our example we use zircon (ZrSiO₄) [11] as template, press "Next" and come to ...

... the page where we accept or modify cell parameters and space group and after that ... 

... to the page where we can modify the atomic parameter list, especially modify atom types and/or modify free parameters of special sites or the coordinates of the general site - or add or remove atoms:

Finally the New Structure assistant ends with the choice how to start a picture object for the new dataset, i.e. automatic picture creation, or running a building scheme, or build up step-by-step from a blank picture.

Inserting a dataset from the structure type database into an existing document

You can use the command From Structure Type Database in the Structure menu to insert a dataset - with or without the associated ready-to-use pictures - into an existing document, i.e. add another structure parameter set to the existing one(s). The procedure is the same as described at the top of this article:
- Insert Structure From Type dialog,
- browsing the Structure Type dialog, if necessary,
- then choosing if and how to make or insert pictures.

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Next article: Saving and exporting structure data

[1] https://commons.wikimedia.org/wiki/Strukturbericht
[2] https://de.wikipedia.org/wiki/Strukturtyp (in German)
[3] Bergerhoff, G. and Brown, I.D. (1987). Inorganic crystal structure database. Crystallographic Databases, Chap. 2.2, pp. 77-95. Bonn/Cambridge/Chester: International Union of Crystallography.
[4] Inorganic Crystal Structure Database (ICSD): Copyright 1998-2016 by Fachinformationszentrum Karlsruhe, Germany.
[5] Rudolf Allmann, Roland Hinek: The introduction of structure types into the Inorganic Crystal Structure Database ICSD, Acta Cryst. A63, 2007, 412-417.
[6] Pierre Villars, Karin Cenzual: Pearson's Crystal Data - Crystal Structure Database for Inorganic Compounds, Release 2016/17, ASM International, Materials Park, Ohio, USA.
[7] Grazulis, S., Chateigner, D., Downs, R. T., Yokochi, A. T., Quiros, M., Lutterotti, L., Manakova, E., Butkus, J., Moeck, P. & Le Bail, A. (2009) "Crystallography Open Database - an open-access collection of crystal structures". J. Appl. Cryst. 42, 726-729.
[8] http://www.crystallography.net/cod/
[9] Strukturbericht 1913-1928 : Zeitschrift für Kristallographie, Kristallgeometrie, Kristallphysik, Kristallchemie; Ergänzungsband. Edited by C. Hermann, Paul Peter Ewald, Akademische Verlagsgesellschaft, Leipzig (1931).
[10] COD: 9008207. Ferraris, G.; Jones, D. W.; Yerkess, J.; "A neutron-diffraction study of the crystal structure of analcime, NaAlSi2O6*H2O Locality: Cyclopean Islands, Catania Province, Sicily, Italy Note: z(O1) corrected to match reported bond lengths"; Zeitschrift fur Kristallographie, 135, 240-252 (1972).
[11] COD: 9000684. Hazen, R. M.; Finger, L. W.; "Crystal structure and compressibility of zircon at high pressure crystal No. 1, 1 atm - before P"; American Mineralogist, 64, 196-201 (1979).