Create PoldiPeakCollection from unit cell, point group

[Michael Wedel]

For indexing POLDI peaks, it would be useful to generate a list of symmetry independent miller indices from a unit cell metric, centering and point group.

This information may come for example from a file.

I looked at the way pointgroups are represented in Mantid::Geometry and it's very easy to check whether two reflections are symmetry equivalents. I would like to extend the interface of PointGroup a bit with these functions:

std::vector<V3D> getEquivalentReflections(V3D hkl);
V3D getReflectionFamily(V3D hkl);

The latter function would return the same V3D for all reflections that are equivalent. For example in a cubic point group it would return (1 0 0) for all of these: (1 0 0), (0 1 0), (0 0 1), (-1 0 0), (0 -1 0), (0 0 -1).

Under the hood all transformations are done using matrix operations as defined in the international tables for crystallography.

[Michael Wedel]

Refs #9993. Added SymmetryOperation interface.

Two operations implemented as example: Identity and Inversion.

Changeset: 424b6b66999feb9370e9d3716adea9c3faf0428d

[Michael Wedel]

Refs #9993. Added more symmetry operations

Changed PointGroup interface. Changed unit test for 6/mmm, since (1 2 3) is a special hkl in that group. The test now uses (7 2 3).

Changeset: b3b488c2c643e7c29bedaab47ae65759f061d7d7

[Michael Wedel]

Refs #9993. Removed superfluous symmetry operations.

They were not used anywhere in the PointGroup code, but maybe they will come back later.

Changeset: ac100250757325864304ef3d9d27542e789449ef

[Michael Wedel]

Refs #9993. Added unit tests for all symmetry operations.

Re-structered tests a bit, so that each operation can be tests with a single call to testSymmetryOperation with the expected parameters.

Changeset: 7b029811f1f968c6b2cbc1a0fdb3455476c36684

[Michael Wedel]

Refs #9993. Symmetry operations have identifier now

Changeset: 2b09c2d96661c37fec13f78bb333248c38c1dabe

[Michael Wedel]

Refs #9993. Added documentation for SymmetryOperation

Changeset: c3c6b4d12d11d588ca253bcbf6106bb4d40f7bc0

[Michael Wedel]

Refs #9993. Improved unit tests for SymmetryOperation

Identifiers are checked agains regex, added more meaningful output on error through the use of TSM_...

Changeset: 60a88e04fb605de8020c39b86a0ec7fccd69768b

[Michael Wedel]

Refs #9993. Hiding symmetry operation storage of PointGroup

Changeset: cc98321525f2a4303ada2cfa147dac91bb8dfac6

[Michael Wedel]

Refs #9993. Checkpointing work

Changeset: 734b8e82bedbf49d905d9b08c5d89d877d4912ed

[Michael Wedel]

Refs #9993. Completing work on PointGroup

Added documentation and some more tests.

Changeset: 044e49906f4a8b87b2d950f2692cc4b3cfc59887

[Michael Wedel]

Refs #9993. Integrating point group extension into PoldiPeakCollection

Changeset: 9cc715387daebcb046f915e71524491f78de3337

[Michael Wedel]

Refs #9993. Extended MillerIndices for interoperability with V3D

Changeset: 2285058997be5af3bb9f4eefbca5fd82ae9acc9f

[Michael Wedel]

Refs #9993. Added unit tests for PoldiPeakCollection

Changeset: f7af4be8be78c732dc3e8e3233bc65ad8ef77070

[Michael Wedel]

Refs #9993. Added another unit test.

Changeset: 0f5d9434e782c788a1d4ffa376608e35edd80e5a

[Michael Wedel]

Refs #9993. Pointgroups now belong to a crystal system

Changeset: a85e80012c61456a6fb77c3622cb3e1f613acc9f

[Michael Wedel]

Refs #9993. Added CrystalStructure-class

Things like unit cell, point group, lattice centering often occur together and this class reflects their connection.

Changeset: 0507acb278666ccd95ac70f05d04aaef3bc99cb8

[Michael Wedel]

Refs #9993. Adapted PoldiPeakCollection to use CrystalStructure

Changeset: efd761f9d6ab3e1fd9827483c0105b712cb31656

[Michael Wedel]

Refs #9993. Making comparison operator const

Changeset: d9223bfb71e5e249ba6b4b9c6c0d3fa226388b57

[Michael Wedel]

Refs #9993. Including <stdexcept> in CrystalStructure.cpp

Changeset: 3964f5c952a9f7c9addcec9e94c86be9d7819ea5

[Michael Wedel]

Refs #9993. Changing CrystalStructure-constructor for VC

Changeset: c5bba0de2508cf520ca3ed30efb6cbc1599203d4

[Michael Wedel]

Refs #9993. Replacing std::to_string with boost::lexical_cast

Changeset: 3718bab8df5a78b52be458aeab5f38519a735f9a

[Michael Wedel]

Refs #9993. Replacing wrong code in unit test

Out-of-bounds vector access made the test fail in VC.

Changeset: 14196c11d454d483a7a21c9dbb0b10b7b1fe81da

[Michael Wedel]

Errornous merge - sorry for the confusion.

[Michael Wedel]

Refs #9993. Merge master into branch to solve merge conflicts

Conflicts:

Code/Mantid/Framework/SINQ/inc/MantidSINQ/PoldiUtilities/MillerIndices.h Code/Mantid/Framework/SINQ/inc/MantidSINQ/PoldiUtilities/PoldiPeakCollection.h Code/Mantid/Framework/SINQ/src/PoldiUtilities/MillerIndices.cpp Code/Mantid/Framework/SINQ/src/PoldiUtilities/PoldiPeakCollection.cpp Code/Mantid/Framework/SINQ/test/MillerIndicesTest.h Code/Mantid/Framework/SINQ/test/PoldiPeakCollectionTest.h

Changeset: 617f53bd930f49e626e8556d5117f745ae1a6bd6

[Michael Wedel]

Testing information

There is no algorithm to try out in this ticket, so it's mainly code review. SymmetryOperation and CrystalStructure are new classes, but PointGroup is used by other components. Even though I did not touch the existing interface, it's probably a good idea to take a detailed look there.

[Andrei Savici]

Merge remote-tracking branch 'origin/feature/9993_poldi_symmetry_independent_hkl'

Full changeset: ​5226f7e8cd4bff6d6a018c9cee4b379d2ca2999e

[Andrei Savici]

Ticket #10135 deals with exposing some of the classes to python, and with writing a documentation. Ticket #10134 deals with merging POLDI related algorithms and concepts with single crystal peaks and peaks workspaces

[Stuart Campbell]

This ticket has been transferred to github issue ​10835