ABST - Analytical Absorption Correction

ABSORPTION CORRECTION TOOLS PLATON HOMEPAGE

Related Instruction: ABST mu (NOCHECK)(LIST)

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.

LIST Optional listing of reflections with corrections.

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:

  1. name.ins : instruction file:

  2. name.hkl : reflection file: (hkl F^2 sig(F^2) + direction cosines)
    with SHELXL HKLF 4 format (3I4, 2F8.2,I4,6F8.5).

PLATON/ABST instruction file format:

TITL text
CELL lambda a b c alpha beta gamma
FACE h k l d
...(etc)...
HKLF 4
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):

Absorption Correction Test Data and Results

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

ABSORPTION CORRECTION TOOLS PLATON HOMEPAGE

03-Feb-2014 A.L.Spek