Preparation of data

Preparation of data (%data command) 

In this step the program reads the basic crystallographic information like unit cell parameters (if available, otherwise they can be determined by the command %ntreor, see Indexing), space group symbol (if available, otherwise it can be determined by the directive findspace, see Space group determination), the experimental wavelength, the unit cell content and the counts (or reflections). Symmetry operators are directly derived from the space group symbol. EXPO2014 uses a modified version of the subroutine SYMM Burzlaff & Hountas (1982). 
An external file (containing counts or reflections) is provided by the user. If a reflection file is supplied, the extraction step is skipped and diffraction data are checked in order to find out equivalent reflections or systematically absent reflections (which are then excluded from the data set).

Directives in %data command

The following directives must be added after the command %data in the input file to supply basic crystallographic information and/or to activate specific non-default procedures:

alpha2
To carry out the Kα2 stripping. It can be used only if the directive pattern is supplied.

cell a b c α β γ
To supply the unit cell parameters. Cell dimensions a, b, and c are in angstroms, α, β and γ in degrees. 

content string
string is the unit cell content and has to satisfy the following criteria:
– Chemical elements are represented by valid atomic symbols (IUPAC-nomenclature), each, optionally, followed by a number (omitted if it is one);
– both upper- and lower-case letters are allowed. To avoid ambiguity, in case of a two-letter symbol the second letter should be a lower-case letter; e.g., string “Sb” is interpreted as one antimony atom, while “SB” as one antimony atom and one boron atom. string can contain blanks (e.g., ‘S B‘, is interpreted as one antimony atom and one boron atom) and/or brackets ( ), [ ], { }.
Some examples of valid unit cell contents are the following one:
(C10H16N6S)4
(C10 H16 N6 S)4
s 4 c 40 n 24 h 64

[(C7H8N4O2)(C7H7NO)]8
The first three strings indicate the same unit cell content.
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, in the file expo.xen. Neutron scattering factors are coded in the program for elements up to Pu (Z=94).

equiportion
To equiportion the overall intensity of a group of overlapping reflections among the reflections in the group (equal E-values are obtained).
If an external reflection file is supplied, this directive has to be used if the file contains the information on the FWHM of reflections (i.e., only if the directive ref2 is introduced).

extefile string
To supply an external file containing “d” or “2θ” values of peak positions to be used by the indexing program. In the latter case the additional directive 2-theta has to be introduced in the input file.
If this directive is used the program will skip the automatic peak search procedure.

filetype double
To be used in case of a counts file containing, in the first line,  the minimum 2θ, 2θ step and maximum 2θ values and, in the rest of file, intensities and standard deviations on separated lines (see the corresponding example of counts file described in case of the directive pattern).

findspace
To find a possible space group when the unit cell parameters are known.

fobserved
This directive has to be used in combination with the directive reflections or ref2, if the external reflection file contains |Fobs| instead of |Fobs|**2.

fwhm x
To supply the value of
x for the overlapping calculation. Two reflections are assumed to be overlapping if 2θ1 -2θ2 < x * FWHM, where 2θj is the theoretical angular position of j-th reflection (j=1,2) and FWHM is the full width at half-maximum of the reflection nr. 2. Default is x = 0.1. 

histogram n
n is the number of bars in the histogram for the Kα2 stripping procedure (only if the  directive alpha2 is used). The allowed values for n are 3, 5, 7 (default is n = 3).

isotope El sf
To modify the value of the neutron scattering factor for the chemical element El using the value sf. It must be introduced if the directive neutron is given.

neutron
To specify that neutron radiation has been used to collect the powder pattern.

norefine
To skip the cluster refinement step in the peak search procedure.

pattern filename
Filename is the name of the profile counts file.
The following powder diffraction data ASCII files can be imported:

  • Free format X,Y data file (*.xy). File contains 2θ in the first column and intensities in the second one. # could be used in any position for comment line or to exclude data ranges. Additional column(s) after the second one will be ignored. Optionally, the wavelength can be supplied in the first line of the file.
  • Free format DAT file (*.dat). File contains minimum 2θ, 2θ step, maximum 2θ values in the first row and one or more counts in free format in the subsequent lines. Caption lines can be introduced at the beginning of data file provided the first character is ‘#’ or ‘!’ or ‘>’.
  • CCDC Mercury xye file (*.xye).
  • Data file from GSAS software, format STD and ESD (*.gda).
  • CIF powder file (*.rtv, *.cif).
  • Siemens data file (*.uxd).
  • Sietronics Sieray data file (*.cpi).
  • XDD data file (*.xdd).
  • DBWS data file (*.dbw).
  • XDA data file (*.xda).
  • Philips UDF data file (*.udf).
  • PANalytical XRDML data file (*.xrdml).

The program recognizes automatically the file format by the filename extension. The more general extension .pow can be associated to a file .xy and .dat. Two example are reported here for the .xy and .dat format files.

#An example of XY file
  4.700    4769.000     
  4.714    4860.000     
  4.729    4794.000     
  4.743    4857.000     
  4.758    4837.000     
  4.772    4891.000     
  4.787    4788.000     
  4.801    4886.000     
  4.816    4720.000     
  4.830    4688.000     
  4.845    4690.000     
  4.859    4867.000     
  4.874    4800.000     
  4.888    4863.000     
  .....................................................................................................
# An example of DAT file
  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
   .....................................................................................................

If your data file format doesn’t appear in the list of files supported by expo, you might use external programs for file format conversion, e.g., PowDLL, POWF, xyconv.

range thmin thmax
Only experimental counts included in the range thminthmax are considered
.

reflections string
To supply an external (and single-crystal like) reflection file. Each record should contain: Miller indices h,k,l, |Fobs|**2 and σ(|Fobs|**2) values. The default format is (3i4,2f8.2); free format (with fields separate by blanks) is also allowed and automatically read by the program.
If the reflection file contains |Fobs| instead of |Fobs|**2, the additional directive fobserved has to be introduced in the input file (default values are |Fobs|**2 ).
If the directive reflections is used, the directive pattern and all the directives introduced in combination with this last one (e.g., range, alpha2, …) must to be absent in the input file.
The next command to be used is %normal or %continue.

ref2 string
To supply an external reflection file containing, for each record, Miller indices h,k,l, FWHM and |Fobs|**2. FWHM is the full width at half-maximum of  reflection. Reflection file in free format (with fields separate by blanks) can be read by the program.
If the reflection file contains |Fobs| instead of |Fobs|**2, the additional directive fobserved has to be introduced in the input file (default values are |Fobs|**2).
If the directive ref2 is used, the directive pattern and all the directives used in combination with this last one (e.g., range, alpha2, …) must to be absent in the input file.
The next command to be used is %normal or %continue.

search  thmin  thmax  npeaks  thre
To change the search conditions applied to locate the peaks supplied to the indexing process.
thmin and thmax set, respectively, the minimum and maximum 2θ value of the range to be considered for the peak search (the default values of thmin and thmax are the minimum and maximum experimental 2θ, respectively).
 npeaks is the number of the most intense peaks for which the intensity percentage is larger than the intensity percentage threshold thre (the default value of thre  is 1.5).
If negative or zero values are assigned to thmin, thmax and thre they are ignored and replaced by their default values.
It is not necessary to specify all values (e.g., it is possible to set thmin and thmax only or thmin, thmax and npeaks only).
Some examples of use of the search directive follow:
• to locate the 25 most intense peaks in the 2θ range 5-80:
  search 5 80 25
• to search the 20 most intense peaks belonging to the full experimental pattern:
 search 0 0 20
• to search all the peaks for which the intensity percentage threshold is larger than 2.5%:
  search 0 0 0 2.5

shift sx sy sz
To supply origin shift components. They must be integral multiples of 1/24.

spacegroup string
String is the symbol of the space group, according to International Tables for Crystallography 

synchrotron
To specify that synchrotron radiation has been used to collect the powder pattern.

thcorr x
x is the
Δ2θ value that is used to correct by zeropoint shift the set of 2θ peak positions (to be supplied to the indexing process), according to the procedure described in the paper by Altomare et al. (2000). If this directive is not introduced the Δθ0 default value is the experimental 2θ step.

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

2-theta
This directive is used in combination with the directive extefile, to supply to the indexing program an external file containing the 2
θ values of peak positions.

Examples

Example 1
To skip the peak search procedure and supply to the Indexing step a set of 2θ peak positions (see the ASCII file mes.pea).

%structure mes
%job MES - data from home diffractometer
%data 
       pattern mes.pow       
       wavelength 1.5406 
       2-theta 
       extefile mes.pea
%ntreor 
%continue

mes.pea content:

12.0014
13.6797
15.5003
16.0599
16.2003
17.8815
18.5194
19.6196
20.5805
20.7582
21.6204
...............

Example 2
To activate the space group determination procedure in case of neutron data.

%structure cfcl
%job CFCL - data from neutron source
%data 
       pattern cfcl.pow       
       cell 10.168 14.964 5.100 90.000 90.000 90.000 
       content C 8 F 16 Cl 16 
       findspace
       wavelength 1.595 
       neutron 
%continue

Example 3
Minimal crystallographic information to be provided to EXPO2014 if unit cell parameters and space group are known.

%structure crox
%job CROX- data from home diffractometer
%data 
        pattern crox.pow        
        cell 5.447 6.5576 12.1147 106.382 95.715 77.970 
        content Cr 8 O 21 
        wavelength 1.3922 
        spacegroup p -1
 %continue

Example 4
The Kα2 stripping with a 5 bars histogram is requested.

%structure dada
%job DADA- data from home diffractometer
%data 
       spacegroup p 21 21 21 
       cell 7.13115 9.9077 12.9256 90.0 90.0 90.0 
       content Si 12 Ti 4 K 8 O 40 
       wavelength 1.540562 
       pattern dada.dat 
       alpha2 
       histogram 5
%continue

Example 5
To supply a reflection file containing Miller indices h,k,l, |Fobs|**2 and σ(|Fobs|**2) values (see the ASCII file mes.hkl; the extraction step is skipped).

%structure mes
%job MES - data from home diffractometer
%data 
       reflections mes.hkl
       wavelength 1.5406 
       content c 24 n 4 o 20 s 4 h 52
       cell 8.5884 9.9309 11.1046 90.000 93.754 90.000
       spacegroup p 21/c
%normal
%continue

mes.hkl content:

>   H   K   L   Fobs**2  sigma(Fobs**2)
    1   0   0    0.01    0.01
    0   1   1    0.17    0.01
    1   1   0    0.29    0.01
    1   1  -1    0.41    0.01
    0   0   2    0.36    0.01
    1   1   1    0.41    0.01
    0   2   0    1.34    0.01
    0   1   2    0.00    0.01
    1   0  -2    0.59    0.01
    0   2   1    0.63    0.01
    1   0   2    0.04    0.01
    1   1  -2    1.81    0.01
..............................

Example 6
To supply a reflection file containing Miller indices h,k,l, FWHM and |Fobs|**2  values (see the ASCII file mes_ref2.hkl; the extraction step is skipped).

%structure mes
%job MES - data from home diffractometer
%data 
       ref2 mes_ref2.hkl
       wavelength 1.5406 
       content c 24 n 4 o 20 s 4 h 52
       cell 8.5884 9.9309 11.1046 90.000 93.754 90.000
       spacegroup p 21/c
%normal
%continue

mes_ref2.hkl content:

>   H   K   L     FWHM      Fobs**2
    1   0   0    0.1064    0.0108
    0   1   1    0.1065    0.1671
    1   1   0    0.1066    0.2948
    1   1  -1    0.1066    0.4085
    0   0   2    0.1066    0.3635
    1   1   1    0.1067    0.4123
    0   2   0    0.1067    1.3356
    0   1   2    0.1068    0.0014
    1   0  -2    0.1068    0.5944
    0   2   1    0.1068    0.6280
    1   0   2    0.1068    0.0363
    1   1  -2    0.1069    1.8067
..............................

 

References

Altomare, A., Giacovazzo, C., Guagliardi, A., Moliterni, A. G. G., Rizzi, R. & Werner, P.-E. (2000). J. Appl. Cryst. 33, 1180-1186.
Burzlaff H. & Hountas A. (1982).
J. Appl. Cryst. 15, 464-467.