Create SpaceGroup class and factory

[Michael Wedel]

As part of the changes in #10262, a new class SpaceGroup should be introduced. It will be constructed from a list of SymmetryOperation-objects (see also #10280), a space group number and the Hermann-Mauguin symbol. There will be two subclasses which implement different initialization methods. TabulatedSpaceGroup takes a complete list of symmetry operations for a space group, while GeneratedSpaceGroup takes a list of generators (also SymmetryOperation-objects) and generates all operations from that list. That way we don't need one class per space group.

SpaceGroup-instances will be constructed by SpaceGroupFactory, which also takes care of initialization of the objects. Because the initialization can be costly (either reading symmetry operations from a string, file or elsewhere or generating them), this will be done only once. Subsequent object creation will approximately follow the Prototype-pattern.

Currently the interface will be limited to generating all equivalent positions for a given coordinate vector V3D.

[Michael Wedel]

Refs #10281. Added Group and CyclicGroup

Changeset: 3b2e6faedaac9821e16d214009ca321b12b61a80

[Michael Wedel]

Refs #10281. Removed counting variable from Group.

It was only used for testing purposes (counting number of required operations).

Changeset: d281ab24182a7b4a05dcc5bec24752b606ceb8c1

[Michael Wedel]

Refs #10281. Added simple factory function for Group-objects.

Since groups can be constructed from strings only and are probably not used directly in code so much, this solution seems simpler than a complete factory.

Changeset: c2cbd2b5a9cbb780fde0ed0cf3f14186e0db3dcd

[Michael Wedel]

Refs #10281. Creating vectors of symmetry operations.

Changeset: ce95b6742782920fa944b581aa5368b0badb0bae

[Michael Wedel]

Refs #10280. Added class to deal with lattice centering

Changeset: 93c1bedec25ace8ef1c59547ea18bbaae041af62

(Accidentally put ticket #10280, sorry)

[Michael Wedel]

Refs #10281. Moved helper class out of CenteringGroup

Changeset: d6d8875daf194b89e0c40c31d33e32e532af9c34

[Michael Wedel]

Re #10281. Removing static members from SymmetryOperationSymbolParser

Changeset: 417b63577b95c504fd4b33f0733b5b9e4279645b

[Michael Wedel]

Refs #10281. Added string constructor to Group.

Changeset: 87910525cd8746053db901100a058c3999397ca9

[Michael Wedel]

Refs #10281. Added ProductGroup class

Changeset: e293a31cfb1beaf65250736d85f112c4f323127c

[Michael Wedel]

Refs #10281. Added SpaceGroup class.

Changeset: 4d1072a27942917c17c70128c0b71a416de36e33

[Michael Wedel]

Notes

• After starting implementation of groups and their relations I realized there is no need for having "GeneratedSpaceGroup" and "TabulatedSpaceGroup", this can be handled by implementing ProductGroup (will be useful for PointGroup as well) and offering two different registration modes in the factory.

• The factory needs to be a bit flexible concerning space group numbers, because often there are different settings for one group and they all occur under the same number. The Herrmann-Mauguin symbol is unique (appending "S" and "Z" if there are two origin choices) and is a better identifier for the groups in the factory.

• Currently I'm leaning towards solving this "problem" like that: The factory will return one space group when creation is performed via the symbol and a vector of space groups when the number is used.

[Michael Wedel]

Refs #10281. Checkpointing SpaceGroupFactory.

Changeset: b67b10b230783fca273683d33fb4a0d730625e6f

[Michael Wedel]

Refs #10281. Changed SpaceGroupFactory

Changeset: 42151b78810ac058a4e3947c1406d59b37ddf747

[Michael Wedel]

Refs #10281. Updating documentation.

Changeset: 992f7fc8bdd9a264879f2d1964960ba62806c4c1

[Michael Wedel]

Refs #10281. More work on SpaceGroupFactory.

Changeset: eed522ec4f2eca7d009d38b34ca23d8e02ca777d

[Michael Wedel]

Refs #10281. Removing unused include.

Changeset: 7ee2b583df11f883f9a767b14c3c2e01532509cf

[Michael Wedel]

Refs #10281. Removed static variable from CenteringGroupCreationHelper

Changeset: 95d3167b4f210e9784afb81f39feb6e587a373c0

[Michael Wedel]

Refs #10281. Changed CenteringGroupCreationHelper again.

Changeset: 711e675fa753fd411ebfc0e2d395cf7b4c288cf0

[Michael Wedel]

Refs #10281. Decided to change CenteringGroup helper once more

Having a singleton is better than having a static member variable which depends on initialization order. And it's better than to fill the symbol/type map every time a centering group is constructed.

Changeset: 589a3a86189d38e73582f6e243d03716500f26a4

[Michael Wedel]

Refs #10281. Removing output generating unit tests

Changeset: 14ce7da805cef84f2955ccea74f870acc9d780ed

[Michael Wedel]

Refs #10281. Added system test for space group factory.

The test generates all registered space groups and checks that their symmetry operations are correct.

Changeset: d58f7e6454ee9cdb525a2714bc82243a23d4c577

[Michael Wedel]

Refs #10281. Exporting SpaceGroup and Factory to python

Changeset: fd637c9e7a815f287836fbe3bf609d02666f81c2

[Michael Wedel]

Refs #10281. Changed system test.

Changeset: 11e842b747abad1e2c4d868e92998091918640e0

[Michael Wedel]

Refs #10281. Added some space groups to the factory

Unfortunately I don't have time right now to add all of them, so I will make a new ticket for that.

Changeset: f3069b8dd7a4336106a94ece8054c26d1b64ef2d

[Michael Wedel]

Refs #10281. Forgot const pointer export problem.

Changeset: 0dfe66e71d65b7996021ee4860bf94489bb781cb

[Michael Wedel]

Notes

The goal of these ticket was to implement a SpaceGroup class that can be used to generate equivalent positions in the unit cell from the asymmetric unit. Example: A compound crystallizes in the space group Fm-3m and an atom is located at the position (0.21, 0.47, 0.86). Because of the high symmetry, this position is mapped to 192 equivalent positions in the unit cell - having to specify all these positions is very inconvenient.

A space group is a group of symmetry operations and applying all symmetry operations to the coordinates of the position results in all equivalent positions. Instead of reading this from a file, I chose to pursue the "group theoretical approach", creating the symmetry operations from a small set of generators. This way, it's very easy to refactor PointGroup later to fit into this scheme, take into account non-standard space group settings, perform transformations and so on.

The basis is provided by the class "Group", which most notably defines a multiplication operator with other groups. Then there is "CyclicGroup", which defines a group which can be expressed as powers of one generating symmetry operation. Another class "ProductGroup" automatically generates a cyclic group for each generator supplied to its constructor and multiplies these groups. Each space group can be generated by such a ProductGroup (using the generators from ITA) and the centering related symmetry operations (which are encapsulated in "CenteringGroup").

Space groups are registered in a factory, which uses the prototype pattern to minimize those generation efforts (in case of Fm-3m, which has 192 operations, it takes under 300 symmetry operation multiplications, this should be the worst case) to doing it only once - when the space group is subscribed into the factory. Creation is then performed like this:

SpaceGroup_const_sptr spaceGroup = SpaceGroupFactory::Instance().createSpaceGroup("F m -3 m");

SpaceGroup and SpaceGroupFactory are exported to python, but I only exported it to the degree so that it can be used in a system test(which checks the generated symmetry operations against reference data. All 230 space group types are in the reference data (but not all possible settings etc.), so this should cover the "first steps".

For my purposes, this is enough right, but I am willing to expand the code, as I started diving a bit deeper into this aspect of crystallographic computation and find it quite interesting.

Testing

• Code review

[Anders Markvardsen]

Hi Michael,

Initially a bit surprised by the number of new classes, but looking in more details looks good.

I just have one class name I am not so happy with, if I understand you code correction, and that is ProductGroup. I would prefer you rename it to ProductCyclicGroup (Or ProductOfCyclicGroups or equivalent) since it is a group specific to hold a product of CyclicGroups. Is this OK? At the moment the name may lead a user to think that ProductGroup can be used to multiply any groups.

[Michael Wedel]

Hi Anders,

thanks for testing - it turned out to be a bit bigger than I thought. After going through the literature a bit it seemed much easier building up the group things from the beginning. I think the math behind it comes out a bit more clear this way.

Looking at the class name again you are right. In the texts about point group generation this was called "product group", so I just went with that, but since the product is already implemented via operator* it makes sense to distinguish a bit.

Do you see anything else that needs to be changed?

[Anders Markvardsen]

No, looks clear and well tested otherwise to me. Note you don't need to reopen the ticket in order to make further commits to it

[Michael Wedel]

Refs #10281. Renamed ProductGroup to ProductOfCyclicGroups.

Following Anders' suggestion to name the class after what it actually does.

Changeset: 394251df3b0f6d395b63b8a89d38d6a217b4a38a

[Michael Wedel]

Merge branch 'feature/10281_space_group_and_factory' into develop

Conflicts:

Code/Mantid/Framework/Geometry/CMakeLists.txt

Refs #10281

Changeset: 868e1679977484905b12856b8282b88b7d7f4e06

[Michael Wedel]

Regarding the chat message from Martyn today: I added a system test to systemtests as well.

[Anders Markvardsen]

Resolve merge conflict related to removed of tabs. re #10281

Merge remote-tracking branch 'origin/feature/10281_space_group_and_factory'

Conflicts:

Code/Mantid/Framework/Geometry/CMakeLists.txt

Changeset: 3c582585997265202bbacbb3cfa70b8bf17388cd

[Anders Markvardsen]

Hi,

Fixed trivial merged conflict and merged in systemtest also

[Anders Markvardsen]

Fix bad merge conflict. re #10281

Changeset: 3ae9c14395f4bb21ecbed924df07c4209254a84d

[Stuart Campbell]

This ticket has been transferred to github issue ​11123