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Creating a rigid body

TOPAS includes a 'rigid-body editor' which can be used to create and test rigid bodies. There are some examples of rigid bodies in the 'C:\TOPAS7\rigid' folder; if at any point you get stuck while editing the z_matrix for this section, it may help to look at some of the examples in this folder.

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1. Start a fresh PDF refinement using "para_300K_pdf.xy" as the filename (TOPASforPDF > 1. PDF data > Select PDF Data File) and save the input file as 'para_300K_optimise.inp'. We will use this file to optimise the geometry of the rigid body.

2. Enter a dQ damping with a value of 0.08 (TOPASforPDF > 2. Instrumental parameters > dQ damping).

3. Load structure from para.cif (TOPASforPDF > 3. Phase information > 3b. add new phase from CIF > i. Read a .CIF File).

4. Add the rigid body information to the file, which will be used to calculate the fractional coordinates of the sites (TOPASforPDF > 3. Phase information > rigid bodies > read an .RGD File).. The text area you have been editing in TOPAS can be directly copied into the inp file in jEdit.

   1. Also allow the translation and rotation of the rigid body to be refined (TOPASforPDF > 3. Phase information > constraints and restraints > rigid bodies > translate rigid body and rotation rigid body).

5. If you run a TOPAS refinement now, you will get an error of 'Cannot find site: X1'. That is because the dummy atoms X1, X2 and X3 are in the rigid body description, but aren't declared as sites. Add one site line for each dummy atom, but with zero site occupancy. (hint below)

6. Create a copy of all of the real atom sites (not X1, X2 and X3), but re-name these sites dummyC1, dummyC2 , dummyC3 etc. and set their occupancy to zero. These will be dummy sites which we will use to move the rigid body sites onto the original atomic positions from the cif file.

7. Add a distance restraint (TOPASforPDF > 3. Phase information > constraints and restraints > distance restraint). Edit the line to apply the restraint between sites dummyC1 and C1 for a distance of 0 and tolerance of 0.

   Distance_Restrain Restraint creates a penalty for when two sites are beyond a given distance. Here we are using to minimise the distance between two sites, but normally it would be used to force a bond length towards a known value.

8. Use Rectangular Selection in jEdit to copy and edit the file to give you one Distance_Restrain line per dummy site.

9. Add view_structure so you can watch how the refinement progresses.

10. Add the keyword only_penalties to your input file. The tells TOPAS not to fit to the data, and instead only minimise the distance penalties.

11. Run the refinement, and watch the rigid body move onto the atomic coordinates from the .cif file using the structure viewer. When the refinement finishes, click Yes to update the .inp file with the values from the refinement.

    1. How well does the rigid body fit to the published crystal structure from the .cif file?

    2. Are there other angles within the rigid body that you could refine to improve the fit?

12. The C7-N1-C4 bond angle is the source of the largest error between the published crystal structure and the idealised rigid body where it is fixed to 120°. Add a new refined bond angle, e.g. aCNC, and set the angle between C7, N1 and C4 to be equal to this parameter.

    Note that you can refine rigid body parameters by putting an @ sign before the value, but when you may re-use the parameter elsewhere it is best to provide your own name for it.

13. Run the refinement again, and click Yes to update the .inp file and complete this refinement.

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