Examples

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Examples of input for EXPO2014

Example 1

The following example shows the default use of EXPO2014 in case of indexed pattern. Most of the structures can be solved in this way. Diffraction data are in the file crox.pow. The content of the file crox.exp is

%structure crox

%job CROX- data from home diffractometer

%initialize

%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



Default "profile counts file" name: crox.pow
crox.pow content:

  6.0000 0.02  100.0
   1166.   1179.   1224.   1172.   1221.   1159.   1204.   1347.   1295.   1146.
   1353.   1188.   1214.   1250.   1253.   1240.   1285.   1344.   1314.   1324.
   1438.   1444.   1463.   1522.   1664.   1548.   1836.   1865.   1913.   2160.
   2367.   2412.   2856.   3186.   3681.   4280.   4941.   5883.   7298.   8978.
  11248.  14375.  20187.  25377.  23771.  15690.   8496.   6385.   5553.   5022.
   4643.   4371.   4202.   3840.   3684.   3296.   3199.   3047.   2833.   2710.
   2567.   2334.   2412.   2156.   2163.   2134.   1981.   1981.   2033.   1901.
   1849.   1768.   1761.   1709.   1654.   1616.   1580.   1629.   1561.   1609.
   1658.   1609.   1493.   1334.   1298.   1331.   1305.   1289.   1292.   1214.
   1149.   1182.   1081.   1146.   1094.   1065.   1030.   1055.    981.   1020.
   1046.    981.    971.   1049.    975.    965.    900.    929.    861.    858.
    874.    929.    835.    793.    839.    787.    907.    858.    822.    826.


Example 2

The Kα2 stripping with a 3 bars histogram is requested.

%structure dada

%job DADA- data from home diffractometer

%initialize

%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.pow 

       alpha2 

       histogram 3

%continue 


dada.pow content is:


10.00 0.02   95.00
      457.0
      437.0
      421.0
      475.0
      469.0
      425.0
      465.0
      405.0
      447.0
      461.0
      433.0
      433.0
      433.0
      415.0
      453.0
      451.0
      429.0
      453.0
      427.0

 

Example 3

Data are from neutron source.

%structure cfcl

%job CFCL - data from neutron source

%initialize

%data 

       pattern cfcl.pow 

       cell 10.168 14.964 5.100 90.000 90.000 90.000 

       content C 8 F 16 Cl 16 

       spacegroup f d d 2 

       wavelength 1.595 

       neutron 

%continue


Example 4

A Pseudo-Voigt function will be used and the background in each interval will be described by a constant. The counts file format is not the default one and the graphic window is suppressed.

%structure mes

%job MES - data from home diffractometer

%initialize

%data 

       pattern mes.pow 

       cell 8.588 9.931 11.105 90.0 93.754 90.0 

       content C 24 N 4 O 20 S 4 H 52 

       spacegroup p 21/c 

       wavelength 1.5406 

%extraction 

       pvoigt 

       polynomial 0

%end

 

Example 5

The starting values of the integrated intensities in the extraction step are supplied by the user in the file "yono.ext" and the number of least-square cycles is set to 40.

%structure yono

%job YONO - Synchrotron data

%initialize

%data 

       pattern yono.pow 

       cell 9.385 16.394 3.627 90.000 101.067 90.000 

       content Y 8 O 26 N 2 H 18 

       spacegroup p 21 

       wavelength 1.2323 

       synchrotron

%extraction 

       frecycle yono.ext 

       ncycle 40

%end



Example 6

The preliminary fitting of the standard peak is skipped and the starting 2q shift value is supplied by the user (the program refines it).

%structure agpz

%job AGPZ - data from home diffractometer

%init

%data 

       pattern agpz.pow 

       cell 6.526 20.059 6.464 90.000 90.000 90.000 

       spacegroup p b c a 

       content Ag 8 N 16 C 24 H 24 

       wavelength 1.54056

%extraction 

       nosing 

       zeroprof 0.02

%continue


 

Example 7

Neutron data and a deuterium atom in the cell content are used. Fast graphic interaction for the integrated intensities extraction process is activated.

%structure baco

%job BACO - Neutron data

%initialize

%data 

       neutron 

       isotope H 0.67 

       pattern baco.pow 

       cell 10.0632 7.9330 6.8487 90.0 122.3423 90.0 

       spacegroup C 2/m 

       content Ba 4 C 8 O 20 H 8 

       wavelength 1.909

%extraction 

       fast

%continue 


Example 8

The program restarts from the PHASE procedure.

A random approach is used and the best 100 sets of phases, over 250 trials, are retained in the direct access file. No Fourier is required.

%structure nizr

%phase 

       random 

       maxtrials 250 

       minfom 1.0 100

%end


 

Example 9

The program restarts from the FOURIER procedure.

Only the E-map corresponding to the set number 7 and the complete FOURIER/LEAST-SQUARES procedure for set number 10 are requested by the user.

%structure nbpo

%fourier 

       set 7 

       recyc 0

%fourier 

       set 10

%continue 


Example 10

To view only the structure previously produced by FOURIER routine.

%window

%structure crox

%menu

%end



Example 11

Use of the pseudotranslational symmetry (if it is present) as prior information for a new extraction process is inhibited. Use of nopse directive after command %normal.

%structure agpz

%job AGPZ - data from home diffractometer

%initialize

%data 

       pattern agpz.pow 

       cell 6.526 20.059 6.464 90.000 90.000 90.000 

       spacegroup p b c a 

       content Ag 8 N 16 C 24 H 24 

       wavelength 1.54056

%extraction

%normal 

       nopseudo

%continue


Example 12

Use of the triplets estimation as prior information for a new extraction process.

%structure mes

%job MES - data from home diffractometer

%initialize

%data 

       pattern mes.pow 

       cell 8.588 9.931 11.105 90.0 93.754 90.0 

       content C 24 N 4 O 20 S 4 H 52 

       spacegroup p 21/c 

       wavelength 1.5406 

%extraction

%normal 

       nopseudo

%invariants 

       estimation

%continue


 

Example 13

Use of the Patterson map inversion as prior information for a new extraction process.

%structure lasi

%job lasi - Neutron data

%initialize

%data 

       pattern lasi.pow 

       cell 5.4059 8.7934 14.2754 90.000 112.731 90.00 

       content La 8 Si 8 O 8 

       spacegroup p 21/c 

       wavelength 2.3400 

       neutron

%extraction

%normal 

       nopse

%patterson 

       inverse

%continue



Example 14

A known fragment is used to complete the structure by applying the FOURIER/LEAST-SQUARES procedure. The binary file "sapo.bin" must exist.

%structure sapo

%fourier 

       fragment SAPO.FRA

%continue


Coordinates are in the file "SAPO.FRA" which contains

Si .00000 .00000 .00000

 

Example 15

The indexing process is performed.

%structure gapo

%job GAPO - Synchrotron data

%initialize

%data 

       wave 1.24012 

       pattern gapo.pow 

       synchrotron 

%ntreor

%end



Example 16

If a set of d (or 2 θ) values is already available, the automatic peak search procedure is skipped:

%structure mes

%job MES - data from home diffractometer

%initialize

%data 

       pattern mes.pow 

       wavelength 1.5406 

       2-theta 

       extefile mes.pea

%ntreor 

       VOL = 6000, CEM = 40,

%end


'mes.pea' is an ASCII file containing the 2θ peak positions.

The N-TREOR09 directives 'VOL = 6000' and 'CEM = 40' activate a search for a cell having a maximum volume of 6000 Å3 and maximum axis value of 40 Å.

Example 17

Use of the change label procedure to relabel the peaks of an electron density map obtained by applying the FOURIER procedure. The binary file "vfi.bin" must exist.

%structure vfi

%job VFI - Synchrotron data

%changelab 

       label 3 al 3 p 

       coord 4 4 

       dwei 3.1 0.5 

       dlig 1.9 0.5

%continue


Example 18

The POLPO1 procedure is applied to locate the light atoms around each specified heavy atoms. The crox.fra file contains the cations coordinates.
The binary file 'crox.bin' must exist.

%structure crox

%job CROX - home diffractometer data

%polyhedra

               fragment crox.fra 

       octahedron 1 1.92 0.2 0.2 

       tetrahedron 2 1.75 0.2 0.2

       tetrahedron 3 1.75 0.2 0.2 

       tetrahedron 4 1.75 0.2 0.2

%continue



Example 19

The POLPO2 procedure is applied to locate one or more missing cations and surronding anions. The sapo.fra file contains the located cations coordinates.
The binary file 'sapo.bin' must exist.

%structure sapo

%job SAPO - data from home diffractometer

%polyhedra 

       fragment sapo.fra 

       tetrahedron Si 1 1.6 0.2 0.2 

       tetrahedron Si 2 1.6 0.2 0.2 

       missing 1 2 Si tetrahedron 1.6 0.2 0.2 

       missing 1 2 Si tetrahedron 1.6 0.2 0.2

%continue



Example 20

To find the space group.

%structure cf3br

%job CF3BR - Neutron data

%init

%data 

       pattern cf3br.pow 

       cell 8.146 5.85 7.962 90. 111.722 90. 

       cont c 4 br 4 f 12 

       wave 1.911 

       neutro 

       findspace

%continue 


Table 1

Classes of reflections corresponding to the low index pseudo-translational symmetry.

1)

h+k+l= 1n

2)

h= 2n

3)

k= 2n

4)

l= 2n

5)

h+k+l= 2n

6)

h+k= 2n

7)

h+l= 2n

8)

k+l= 2n

9)

h= 3n

10)

k= 3n

11)

l= 3n

12)

h+k= 3n

13)

h+l= 3n

14)

k+l= 3n

15)

h+k+l= 3n

16)

h+k+2l= 3n

17)

h+2k+l= 3n

18)

2h+k+l= 3n

19)

h+2k= 3n

20)

h+2l= 3n

21)

k+2l= 3n

22)

l= 4n

23)

k= 4n

24)

h= 4n

25)

h+k= 4n

26)

h+l= 4n

27)

k+l= 4n

28)

h+k+l= 4n

29)

2h+2k+l= 4n

30)

2h+k+2l= 4n

31)

h+2k+2l= 4n

32)

2h+k+l= 4n

33)

h+2k+l= 4n

34)

h+k+2l= 4n

35)

h+2k= 4n

36)

h+2l= 4n

37)

k+2l= 4n

38)

2h +k= 4n

39)

2h+l= 4n

40)

2k+l= 4n

41)

3h+3k+l= 4n

42)

3h+k+3l= 4n

43)

h+3k+3l= 4n

44)

h+2k+3l= 4n

45)

h+3k+2l= 4n

46)

3h+k+2l= 4n

47)

h+3k= 4n

48)

h+3l= 4n

49)

k+3l= 4n

50)

3k+2l= 6n

51)

2k+3l= 6n

52)

2h+3k= 6n

53)

3h+2k= 6n

54)

3h+2l= 6n

55)

2h+3l= 6n

56)

2h+2k+3l= 6n

57)

3h+2k+3l= 6n

58)

3h+3k+2l= 6n

59)

4k+3l=12n

60)

4h+3l=12n

61)

4h+3k=12n

62)

3k+4l=12n

63)

3h+4k=12n

64)

3h+4l=12n

65)

h = 2n & k = 2n

66)

h = 2n & l = 2n

67)

k = 2n & l = 2n

68)

h = 2n & k+l = 2n

69)

k = 2n & h+l = 2n

70)

l = 2n & h+k = 2n

71)

h+k = 2n & h+l = 2n

72)

h = 2n & k= 2n & l= 2n

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