Related Instruction: ABST mu (NOCHECK)
Where mu linear absorption coefficient (mm or cm depending on FACE)
NOCHECK Optional: for accepting direction cosines without checking. This option should be used with care.
See also Absorption Correction Menu
Analytical Absorption Correction following the de Meulenaer & Tompa algorithm (see. N.W. Alcock (1970). Crystallographic Computing, p 271)
The de Meulenaer,Tompa & Alcock code for numerical absorption correction has been implemented in PLATON and adapted to fit into the direction cosine regime introduced with SHELX-76 (compatible with SHELXL97).
Two files are needed for the calculations:
PLATON/ABST instruction file format:
TITL text
CELL lambda a b c alpha beta gamma
FACE h k l d
...(etc)...
ABST mu
Notes:
PLATON/ABST may be run for name.ins through:
platon name.ins
The corrected data are written to (SHELX HKLF 4 style): name.hkp
The standard published testdata (Alcock, N.W. (1974). Acta Cryst, A40, 332-335.) set 'abstest' is included below and may be run with:
platon abstest.ins
Three additional tests (test1, test2 & stand) are provided on the ftp-server illustrating the alternative use of 'absolute-psi'-values (Flack et al.) instead of direction cosines on 'shelxl.hkl' (Adapted from the Alcock distribution):
Contents of abstest.ins:
TITL ABSTEST CELL 1.5418 10.0006 11.0002 12.0012 95.81 101.31 106.8 FACE 1 0 0 1 FACE 0 1 1 1.5 FACE 0 -2 1 0.5 FACE -3 0 1 0.3 FACE 1 1 -4 1.3 ABST 1.0
Contents of abstest.hkl
0 1 1 734 2 1-0.76194 0.84042-0.24264 0.41352 0.44558-0.28769 0 1 1 734 2 1-0.87952 0.95800-0.01798 0.18886 0.19452-0.03663 0 0 1 454 2 1-0.83199 0.86344-0.69424 0.71659 0.06645 0.06645 0 0 -1 454 2 1 0.83199-0.86344 0.69424-0.71659-0.06645-0.06645 1 2 3 2255 2 1-0.53890 0.89307 0.01820 0.39840 0.68323-0.19531 1 2 -3 888 2 1 0.28445-0.11900 0.92766-0.64519 0.51498-0.82452 1 -2 3 1355 2 1-0.53152 0.69757-0.97176 0.79426-0.20838 0.59637 1 -2 3 1355 2 1-0.74569 0.91174-0.82812 0.65061-0.01234 0.40032 1 -2 -3 1851 2 1 0.82116-0.84382 0.44390-0.75554-0.30546-0.10401 -1 2 3 1851 2 1-0.82116 0.84382-0.44390 0.75554 0.30546 0.10401 -1 2 -3 1405 2 1 0.53152-0.69757 0.97176-0.79426 0.20838-0.59637 -1 -2 3 937 2 1-0.28445 0.11900-0.92766 0.64519-0.51498 0.82452 -1 -2 -3 2237 2 1 0.53890-0.89307-0.01820-0.39840-0.68323 0.19531
Summary of the calculations:
Crystal Face Defining Data ========================== Nr h k l Distance(mm) -------------------------------------------------------------------------------- 1 1.00 0.00 0.00 1.000 2 0.00 1.00 1.00 1.500 3 0.00 -2.00 1.00 0.500 4 -3.00 0.00 1.00 0.300 5 1.00 1.00 -4.00 1.300 Points of Intersection of Planes ================================ Crystal System Inters. of Planes -------------------------------------------------------------------------------- Vertex x y z Face No. -------------------------------------------------------------------------------- 1 = 1 0.10751 0.03693 0.17256 1 2 3 2 = 2 0.10751 0.23524 -0.02575 1 2 5 3 = 3 0.10751 -0.10472 -0.11074 1 3 5 4 = 4 0.02617 0.03693 0.17256 2 3 4 5 = 5 -0.05047 0.26684 -0.05735 2 4 5 6 = 6 -0.08677 -0.13247 -0.16625 3 4 5 NR EDGE LENGTH (mm) ============================== 1 1 2 3.387 2 1 3 3.594 3 1 4 0.813 4 2 3 3.775 5 2 5 1.694 6 3 6 1.849 7 4 5 4.037 8 4 6 4.090 9 5 6 4.343 Analytical Absorption Correction Program ------------------------------------------------------------------- (see. N.W. Alcock (1970). Cryst. Computing, p271) :: Mu = 1.000 mm(-1) Crystal Volume = 8.51033344209 mm3 H K L F**2 Sig(F**2) Transmission Volume (mm3) - - - ---- --------- ------------ ------------ 0 1 1 2191.85 5.97 0.33488 8.51033344209 0 1 1 2367.26 6.45 0.31006 8.51033344209 0 0 1 1336.56 5.89 0.33968 8.51033344209 0 0 -1 1336.56 5.89 0.33968 8.51033344209 1 2 3 7047.89 6.25 0.31995 8.51033344209 1 2 -3 5286.08 11.91 0.16799 8.51033344209 1 -2 3 5287.38 7.80 0.25627 8.51033344209 1 -2 3 4360.63 6.44 0.31073 8.51033344209 1 -2 -3 5513.00 5.96 0.33575 8.51033344209 -1 2 3 5513.00 5.96 0.33575 8.51033344209 -1 2 -3 5285.33 7.52 0.26583 8.51033344209 -1 -2 3 5283.90 11.28 0.17733 8.51033344209 -1 -2 -3 7045.97 6.30 0.31749 8.51033344209 :: Array Size Needed = 340 :: 13 Reflections Processed :: MIN Transmission = 0.16799 for the 1, 2, -3 :: MAX Transmission = 0.33968 for the 0, 0, 1 :: MEAN Transmission = 0.29318 :: Average Time per Reflection = 0.0013 Seconds