Modify CrystalStructure to use space group and scatterers

[Michael Wedel]

The last step of #10262 will be to change the existing CrystalStructure-class so that it uses the features implemented in #10281 and #10282.

At that point it will be possible to construct a crystal structure with the scatterers in the asymmetric unit and use the information about the space group to generate all scatterers in the unit cell and obtain structure factors for reflections (given by HKL).

[Michael Wedel]

Generation of symmetrically equivalent scatterers is performed directly by the scatterers, so CrystalStructure will not need to do this.

An important question I can see is generation of crystal structures. It must be possible to construct a crystal structure from a file.

For our purposes at POLDI it will be enough (for now) to be able to read a file with a structure like this:

# Crystal structure of Silicon
# Unit cell
5.43 5.43 5.43 90 90 90
# Space group
F d -3 m
# Element x y z occupancy Uiso
Si 0.0 0.0 0.0 1.0 0.05

What would be a good way to do this?

[Michael Wedel]

I have moved the loading issue to another ticket (#10426), because it's really a separate issue. But in this context I realized that I need to change the interface of IScatterer a bit, to make string based creation easier later on, so I will probably have to rebase this branch or pull in master after #10282 has been closed.

[Michael Wedel]

Rebased this branch to use the changes from #10282. I assume no one had checked out this branch previously.

[Michael Wedel]

Since there had to be some changes to #10282 in the end, I have to delete the old branch for this ticket and push a new one. Sorry for the confusion, but this ticket was very close to #10282, so I wanted to see "how things work out" with the different approaches.

[Michael Wedel]

Refs #10283. Modified PointGroupFactory to accept space group symbols

Changeset: 4b91b23818a270b8383d2f0b0e118cc4b9916ab3

[Michael Wedel]

Refs #10283. Adding a symbol to ReflectionCondition

Changeset: ebe9d89687a06ef66219b6cb901f9364229644b3

[Michael Wedel]

Refs #10283. Adapted CrystalStructure.

Changeset: a010cb2a7adc4770550acd6ab38ee978dc3b3cb8

[Michael Wedel]

Refs #10283. Added more documentation.

Changeset: 649a81fa8a2dda4f96cc5206bdd7431b7a146eeb

[Michael Wedel]

Refs #10283. Added unit test for comparison

Using ReflectionCondition and structure factor calculation should give the same result for the same input.

Changeset: 166c4c52be3f30c90fffd7f254691c210ef08eb2

[Michael Wedel]

Refs #10283. Moving calculation of F and d

Putting those calculations in their own methods makes it easier to add other calculations later.

Changeset: 09c0ed966e267f0c90bd023cc63450ee5fb6e0c3

[Michael Wedel]

Refs #10283. Re-adding F^{2 method to BraggScatterer}

Changeset: 833b402d769cbff916c1eb1a3abe1ac1fdd88872

[Michael Wedel]

Refs #10283. Adapting CrystalStructure to final design of scatterer

Changeset: e8d3117e658a19382540a35769509f36a64ec43f

[Michael Wedel]

Refs #10283. Suppressing some gmock warnings.

Changeset: 88b46d5eda9e3b3658e29ae2f247c90bc5bd1ce8

[Michael Wedel]

Refs #10283. Adding possibility to clear CompositeBraggScatterer.

Changeset: 69c0a8f5ce057af561de7d71b8326dfb786d6837

[Michael Wedel]

Refs #10283. Some cleaning up in CrystalStructure

Changeset: 71a226f089eb88967950857f8de063b251cb1ab3

[Michael Wedel]

Refs #10283. Replacing front and back with substr

Changeset: ffa54aa778d1c92c4c9617d451281ff401daffc5

[Michael Wedel]

Refs #10283. Changing back constructor of CrystalStructure

Apparently VS does not like boost::make_shared as default argument in a constructor.

Changeset: ad1be5459e570a0a0a418f8eaff6fd4f55e7efaf

[Michael Wedel]

Notes

The "old" interface and behaviour of CrystalStructure is mostly preserved. The only caveat is that point group and centering cannot be set if a space group has been set before. I think this is reasonable behaviour, since the space group determines both.

Testing information

Code review. The general design was covered in #10282, which contains also the UML diagram. I did not change PointGroup/PointGroupFactory, so for now PointGroupFactory "transforms" a given space group symbol to the corresponding point group symbol and creates a point group from that. Has the limitation that currently only centrosymmetric space groups can be used that way (because only the Laue classes are present in the point group department).

[Anders Markvardsen]

Merge remote-tracking branch 'origin/feature/10283_adapt_crystal_structure'

Full changeset: ​3562e896522d6d25022f031292261d1a02bd781e

[Stuart Campbell]

This ticket has been transferred to github issue ​11125