Preparation of data

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Preparation of data for the DATA routine

       This routine reads the basic crystallographic information like cell parameters, space group symbol (it may be also found by the program, using "findspace" directive), wavelength, unit cell content and the counts (or reflections). It includes a modified version of the subroutine SYMM Burzlaff & Hountas (1982). Symmetry operators are directly derived from the space group symbol.
An external file (containing counts or reflections) is supplied by the user. If an external reflection file is supplied (avoiding the extraction step),diffraction data are checked in order to find out equivalent reflections or systematically absent reflections (which are then excluded from the data set).


ALPHA

It is used to start the alpha2 stripping.

CELL a b c α β γ

cell dimensions a, b, and c are in angstroms, α, β and γ in degrees.

CONTENTS El1 n1 El2 n2 El3 n3 .........

Unit cell contents. Eli is the chemical symbol of atomic species i, ni is the corresponding number of atoms in the unit cell (to a maximum of 8 atomic species). For each chemical element up to Cf (Z=98) X-ray scattering factor constants are stored, together with information on the atomic number and weight, covalent and Van-der-Waals radii, etc. in a file (see notes on implementation). Neutron scattering factors are coded in the program for elements up to Pu (Z=94).

EQUIPORTION

If this directive is given the overall intensity of a group of overlapping reflections is equiportioned among the reflections in the group (equal E-values are obtained).

EXTEFILE string

This directive is used to supply an external file containing 'd' or '2θ' values of peak positions. In the latter case the additional '2-THETA' directive has to be used.
If this directive is used the program will skip the automatic "peaksearch " procedure.

FILETYPE string

This directive is used to specify the format of input file containing the diffraction data. string defines the type of file and can be 'counts', 'xy', 'double', 'gsas'.

If the directive FILETYPE string is absent or  string is 'counts' the first three number at the beginning of the counts file must be the 2theta minimum, 2theta step and 2theta maximum. The following lines must be counts. The number of counts for row or the format of counts can vary.

#Example 1: use, in the input file, the directive 'FILETYPE counts' or nothing
 7.00   0.020 100.00
    3017    2925    3056    2983    3008    2953    2875    2976    2886    2928
    2973    2831    2960    2821    2854    2900    2857    2798    2876    2798
    2819    2865    2830    2735    2771    2813    2806    2704    2823    2878
    2793    2795    2756    2722    2705    2736    2802    2657    2811    2736
    2753    2722    2780    2734    2795    2741    2812    2808    2713    2746
    2696    2747    2799    2876    2741    2921    2776    2966    3017    3082
    3058    3193    3147    3309    3319    3404    3490    3554    3684    3845
    4015    4069    4293    4450    4657    4905    5201    5587    5796    6172
    6646    7225    7834    8918    9767   10641   11891   13411   15091   17902
  ....................................................................................................................
#Example 2: use, in the input file, directive 'FILETYPE counts' or nothing
6   0.01  55.98
    412.98
    404.51
    412.40
    405.57
    403.30
    405.94
    404.89
    389.39
    396.55
    408.00
    403.24
    385.44
    396.46
    393.20
    390.52
    401.58

 .............................................................................................................

If string is 'xy' the counts file contains 2theta in the first column and the intensities in the second one. The format of counts can vary.

#The use of directive 'FILETYPE xy'
 4.700    4769.000     69.05795
 4.714    4860.000     69.71370
 4.729    4794.000     69.23872
 4.743    4857.000     69.69218
 4.758    4837.000     69.54855
 4.772    4891.000     69.93568
 4.787    4788.000     69.19537
 4.801    4886.000     69.89993
 4.816    4720.000     68.70226
 4.830    4688.000     68.46897
 4.845    4690.000     68.48357
 4.859    4867.000     69.76389
 4.874    4800.000     69.28204
 4.888    4863.000     69.73521
 ...........................................................................................................................

If string is 'double'  the first line in the counts file contains 2theta minimum, 2theta step, 2theta maximum. The rest of file contains intensities and standard deviations on separated lines.

#The use of directive 'FILETYPE double'
   3.000   0.005  41.600
  3567.2  3405.3  3370.1  3432.4  3476.2  3526.9  3354.7  3596.6  3476.8  3676.7
   67.27   65.44   65.16   65.78   66.12   66.55   64.64   67.14   66.08   67.88
  3623.0  3703.6  3555.1  3500.3  3558.6  3584.8  3606.2  3556.8  3710.3  3704.8
   67.46   68.33   66.89   66.12   66.77   67.00   67.75   66.77   68.73   68.03
  3721.0  3670.7  3775.1  3796.4  3820.9  3880.8  3809.1  3922.7  3963.5  3919.6
   68.76   67.82   68.60   69.04   69.28   70.05   69.39   69.91   70.44   70.11
  4062.6  4104.5  4148.8  4219.5  4221.6  4376.3  4294.3  4439.1  4349.1  4500.5
   71.69   71.85   71.87   72.61   72.61   73.94   73.66   74.44   74.18   75.39
  4449.2  4704.1  4833.7  4851.3  4892.2  5105.9  5143.3  5161.8  5272.0  5418.5
   74.34   77.34   78.13   78.37   78.02   79.82   80.53   80.55   81.09   81.93
  5543.3  5635.8  5918.0  6007.9  6406.6  6395.2  6515.0  6753.3  7255.9  7464.6
   83.36   84.18   86.37   86.95   89.58   89.58   90.60   91.99   95.62   96.94
  7811.5  8415.6  8597.6  9251.3  9995.7 10714.5 11097.2 11067.4 10678.3  9864.0
   98.89  102.81  103.75  107.71  111.43  115.71  117.76  117.40  115.54  110.72
 .............................................................................................................................

In the previous cases comment records can appear at the beginning of data file if the first character is '#' or '!' or '>'. Examples in directory examples.

'FILETYPE gsas' can be used to read counts files in GSAS standard format with keyword TYPE='STD' and TYPE='ESD'.

FINDSPACE

This directive is used in order to find a possible space group when the cell parameters are known.

FWHM x

This directive supplies the value of x for the overlapping calculation. Two reflections are assumed to be in overlapping if 2θ1 -2θ2 < x * FWHM. Default is x = 0.1.

HISTOGRAM n

n is the number of bars in the histogram for the alpha2 stripping procedure (only if ALPHA directive is used).

ISOTOPE El sf

To modify the value of the neutron scattering factor for element El using the value sf. (It must be used if NEUTRON directive is given).

MOREPEAKS

This directive is used together with the peaksearch directive in order to add more low intensity peaks to the set of peaks already detected via the peaksearch directive.

NEUTRON

This directive is used to specify that neutron radiation has been used.

NOREFINE

This directive is used to skip the cluster refinement step in the peak search procedure.

PATTERN filename

Filename is the name of the profile counts file (up to 40 characters). It is used to change the default. [Default is name.pow where name is defined using the command %STRUCTURE].

RANGE thmin thmax

Only intensities included in the range thmin-thmax will be considered; thmin and thmax are the minimum and maximum 2θ value of the powder pattern respectively.

REF2 string

This directive is used to supply an external reflection file. EXPO reads directly the output provided by any profile fitting program. HKL, FWHM and F**2 must be supplied [default format is (3i4,2f15.4)]. If a comment line is at the beginning of the reflection file, the first character must be '>'. If this directive is used, the directives 'pattern' and 'range' must not be introduced.

SHIFT sx sy sz

Origin shift components if desired by the user. They must be integral multiples of 1/24.

SPACEGROUP string

String is the symbol of the space group, according to International Tables (1974). Blanks are necessary among the terms constituting the space group symbol (see examples at the end of this manual).

SYNCHROTRON

This directive is used to specify that synchrotron radiation has been used.

STEP step_value

You can use this directive to specify that your data were collected at fixed step. This directive is activated when the data file contains two columns (2theta values and intensities) and you are using the directive 'FILETYPE xy'. If you use the directive STEP, the first column is ignored and the program automatically recreates the 2theta values by using step_value for the step and the first 2theta value in the data file.

THCORR x

x is the Δθ0 value that is used to correct by zeropoint shift the set of 2θ peak positions.
The shift value will be egual to 2(n-1)Δθ0, where n is the sequential number of the N-TREOR trial.
If this directive is not introduced the Δθ0 default value is the experimental 2θ step.

2-THETA

This directive is used combined with the EXTEFILE directive to supply to the indexing program N-TREOR09 an external file containing 2θ values of peak positions.

WAVELENGTH w

w is the wavelength (in Angstrom) used to collect the powder pattern.


References

Burzlaff H. & Hountas A. (1982). J. Appl. Cryst. 15, 464-467.

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