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 %continue
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 |