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authorThomas White <taw@physics.org>2011-06-16 17:53:28 +0200
committerThomas White <taw@physics.org>2012-02-22 15:27:28 +0100
commit34b21127ea75e6a714a6c04a09f226180b2eb541 (patch)
treedb5d75b4365cbbda4728f0d512d24abcdd3ece88 /doc/symmetry.txt
parentaa4d05d94275baa8c87acc6343a23d16f1877b24 (diff)
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-How CrystFEL handles symmetry
------------------------------
-
-Most programs in CrystFEL understand point group symmetry. The exception is
-"get_hkl", which you can read about below. You give the point group following
-the "-y" option to the programs.
-
-Please read doc/process_hkl for important information on how symmetry is used
-during the indexing and merging procedures. It's important to understand how
-this works before, for example, trying to merge a dataset.
-
-Symmetry definitions are included in src/symmetry.c. Point group definitions
-are required for merging and the display of merged results, but space groups are
-not taken into account since merging does not care about systematic absences -
-as far as CrystFEL is concerned, systematic absences are just measurements
-which happen to have values of zero. Each space group belongs to exactly one
-point group, which you can look up in the International Tables for X-Ray
-Crystallography. Alternatively, "twin-calculator.pdf" in the same directory as
-this file lists all the space groups according to point group, Laue class and
-holohedry.
-
-
-Adding a new point group
-------------------------
-
-Point groups are being added here as they are required, so it's likely that the
-exact one you want hasn't been added yet. Here's how to add a new one by
-editing src/symmetry.c.
-
-First, expand the check_cond() function to include a description of the
-asymmetric reciprocal unit cell for the point group. Every reflection in the
-whole of reciprocal space must map onto exactly one reflection in the asymmetric
-unit cell so defined. The asymmetric cell is usually defined with positive h, k
-and l, but it doesn't really matter. Working out the required condition means
-visualising the cell and taking care to properly handle situations such as the
-(000) reflection. Get this right, otherwise you'll go crazy when it breaks in
-weird ways.
-
-Next, expand the num_general_equivs() function. Given a point group, this
-function must return the number of equivalent reflections for a general
-reflection, including the input reflection. High-symmetry reflections (usually
-ones with zeroes in their indices) have fewer equivalents, but the num_equivs()
-function will work this out for you.
-
-Finally, add the new point group to the get_general_equiv() function. This
-function takes a set of Miller indices, a point group and an index "n", and
-returns (by reference) the indices of the "n"th equivalent reflection. You just
-have to worry about the general position, because get_equiv() will work out the
-special positions for you. get_general_equiv() must return the original indices
-when idx=0.
-
-If you want the new point group to be used for simulation on the GPU, you will
-also need to modify src/diffraction-gpu.c and data/diffraction.cl. Choose a
-simple capitalised name for the point group and add it to the list of OpenCL
-preprocessor definitions in setup_gpu(). Then add a corresponding list of
-equivalents following the established pattern in molecule_factor(). That's it.