ABST - Analytical Absorption Correction


ABSORPTION CORRECTION TOOLS PLATON HOMEPAGE

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:

  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)...
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


20-Apr-2001 A.L.Spek