Inorganic Structure Prediction

3       DLS menu card

This chapter discusses the DLS menu card found in the Cerius2 Structure Solve deck of cards.

Introduction

This chapter explains...

A note about the scope of this documentation 34

Overview 35

Design of the Cerius2 DLS user interface 35

DLS controls: initializing and running 36

DLS constraints 37

Unit cell parameters 39

Refinement options 39

Advanced features 39

DLS control panels

For information about		See
More on DLS		DLS-76 documentation available over the web or via conventional mail request (see below)
Discover		Cerius2 Discover manual

40

Accessing the tools

To access the card in the C²·DLS module, click the deck selector in the main control panel and choose STRUCTURE SOLVE from the list that appears. Then click the title of the DLS card to bring it to the fore. The deck of cards menu area should now look like this:

A note about the scope of this documentation

To get the most from the DLS interface, therefore, you are strongly advised to read the full DLS-76 documentation. You can do this by pointing your browser to:

http://kristall.erdw.ethz.ch/software/dls76manual.html

S.L. Lawton
Research Department
Mobil Research and Development Corporation
Paulsboro
NJ 08066
USA

Dr. E.W. Radoslovich
CSIRO
Division of Soils
Glen OSmond
South Australia 5064

Cerius² DLS is complemented by the Cerius² Diffraction-Crystal module for simulation of powder diffraction patterns and Cerius² Rietveld for further refinement of structures using powder diffraction data.

Design of the Cerius2 DLS user interface

Once the user has sketched an initial crystal, using the model building tools available in the Cerius² Visualizer and Cerius² Crystal Builder, a set of default distance and angle constraints can be automatically applied, and then edited manually if required. Running DLS-76 is then as simple as pressing a button -- the results are fed directly back to the screen in the form of the refined structure.

DLS controls: initializing and running

On first entering DLS, it is necessary to initialize it for the current crystal model. This performs two functions:

• Examination of the crystal bonding, to compile a list of bonds and their default lengths.

• Initialization of the constraints on which cell parameters may vary. This takes into account the space group of the crystal.

In generating a list of bonds, the following rules are applied:

• Each atom in the asymmetric unit is examined, and a list compiled of all atoms bonded to the atom. The list is then culled to remove symmetrically equivalent bonds.

• Checks are also made for indirectly bonded atom pairs such as the oxygen atoms separated by a tetrahedral atom (O-T-O), or in fact any pair of atoms connected to a third. Again, only symmetrically inequivalent bonds are recorded. Distance constraints in these cases are only applied if a default bond angle of 1-3 distance has been supplied.

DLS is run from the DLS Controls control panel, accessible by clicking Controls on the DLS menu card. It may be run either INTERACTIVELY, or in the BACKGROUND (set in the Mode of running DLS popup). For most work, it is envisaged that interactive operation will be fast enough. The user should specify a seed filename in the Current filename seed entry box, which will be used for all files generated by the run. The default seed is "dls".

The Write DLS command file option is provided for your convenience. In order to run DLS, you need only click Run DLS using current parameters.

The results of an interactive run are automatically recovered and displayed on the screen. If running in the background, it is necessary to use the Recover results of DLS run button to recover the results manually.

Further control may be exercised over the run by using the Refinement Options control panel (see "Refinement options" on page 39).

DLS constraints

Atom pair constraints

The distance constraints and weightings that Cerius² assigns to each bond are taken from the constraint list in the DLS Set-up Atom Pair Constraints control panel (accessible by selecting Constraints Set-up Atom Pairs). There is a default set in the list when Cerius² is run -- others may be loaded from file or put in by hand and the existing list may be edited.

There are three different constraint types (see the List of constraints in the DLS Set-up Atom Pair control panel).

BOND: constraints between directly bonded atoms.

ANGLE: constraints for indirectly bonded atoms.

13DIST: constraints for indirectly bonded atoms.

If Cerius² finds a 1-3 distance in the model which is not included in the constraint list, then the distance will not be constrained.

If Cerius² finds a 1-2 distance in the model but not in the constraint list, then Cerius² will give a warning and, if Use Slater radii is set to YES, will substitute a distance equal to the sum of the elemental Slater radii.

The distance constraint list can be easily edited to add or remove bonds, change distances and angles and change the bond weight.

The controls on the dialog box require the following input (all input to text boxes is in "free format"):

Add bond constraint: 	atom1	atom2	distance	weight


Add 1-3 constraint: 	atom1	atom2	atom3	distance 		weight


Add angle constraint: 	atom1	atom2	atom3	angle		weight


Change value of con-	List number	new
straint:		value 


Change weight of	List number	new
constraint:		weight


Remove constraint 	List number 
from list:

Cerius² has a default constraint file containing constraints for some common atom pairs which are initially loaded into Cerius². Once you have a customized constraint file you can load that instead.

Fixed atom constraints

Cerius² lets you fix the x, y and z coordinates of any atom in the model by entering it into the fixed atom list in the DLS Fixed Atom Constraints control panel, accessible from Constraints Fixed Atoms. Cerius² automatically fixes any non-bonded atoms in the model.

Atoms are added to the fixed atom list by selecting the atom(s) from the model and clicking the Add selected atoms to list button. It may be necessary to fix one atom to get DLS to converge. Be careful constraining special position atoms -- DLS does not like this!

Unit cell parameters

Refinement options

Advanced features

The Edit Atom Pair Table control panel lets you edit individual atom pair constraints. The whole atom pair table can be listed and also sorted by NUMBER or ELEMENT for clarity. Selecting two atoms on the screen and clicking the Show constraint for selected atoms button displays the current constraint, if any, for the atom pair. The current constraint can then be modified or a fresh constraint added.

DLS control panels

For more information on the controls within the panels and subpanels, please refer to the online help text. To access the help text, place your mouse cursor over a control or panel and press the right mouse button.

DLS Controls control panel

This panel allows you to set up a control file for a DLS run from the current model structure, to run the control file, and to recover results from a run.

To open this panel, click Controls on the DLS menu card.

DLS Set-up Atom Pair
Constraints control panel

This panel allows you to list and modify the table of atom pair constraints for the DLS run.

To open this panel, select Constraints Set-up Atom Pairs from the DLS menu card.

DLS Load/Save Atom Pair Constraints control panel

This control pane allows you to load from a file, or save to a file, the DLS atom pair constraints.

To open this panel, select Constraints Load/Save Atom Pairs from the DLS menu card.

DLS Fixed Atom
Constraints control panel

This control panel allows you to set up and edit the list of fixed atoms for the DLS run.

To open this panel, select Constraints Fixed Atoms from the DLS menu card.

DLS Unit Cell Constraints control panel

This control panel allows you to specify constraints on the unit cell parameters for a DLS run.

To open this panel, select Constraints Unit Cell Parameters from the DLS menu card.

DLS Refinement Options control panel

This control panel allows the user to modify the refinement options for the DLS run.

To open this panel, click Refinement Options on the DLS menu card.

DLS Edit Atom Pair Table control panel

This control panel allows the user to list and edit the table of current atom pair distance constraints for a DLS run.

To open this panel, select Advanced Features Edit Atom Pair Table from the DLS menu card.