1199

WinCSD
Version 4-2016
Program Package for
Crystallographic Calculations

Examples

1

Example 1 - Na24Si136
Simple cubic structure.
First steps to learn to work with WinCSD on single-crystal diffraction data

* = mKB_013bm
Open file *.original using any editor:
experimental data are written in shelx format (cf. reflections 044, 333).
Close file *.original.

Call EdhCSD:

- Open file *.original using File/Open REF command with the parameter FileType=Shelx.
- Write *.ref file using command Edit/FilterForRefFile with the parameters V=0.0,
OrderSorting=none, nDIM=3:
N(r) = 5307 R(s) = 2.80%
Exit EdhCSD:
file *.ref appears on the working directory.

Call EdhCSD:

- Open file *.ref using File/Open REF command with the parameter FileType=WinCSD-
Ref.
- Start parity analysis with Pari button:
nalysis of extinction condition gives extinction in accordance with the face-centred lattice.

Exit EdhCSD.
Open file *.ref with a text editor. Analyze the extinctions:

the conditions
hkl: k + l = 2n; h + l = 2n; h + k = 2n;
0kl: l = 2n, k = 2n, k + l = 4n;
h00: h = 4n;
hhl: h + l = 2n
2

are in agreement with the space group Fd3m.
Close file *.ref.

Call ParinCSD:

- Input primary information taken from the CIF file obtained after the data collection using
sequentially button Cubic and commands Cell, Data, Elements.
- Save file *.par using command File/Save *.PAR.
- Look on the output using button List and save its content to the file *.out applying the button
WriteOut.
Exit ParinCSD.

Call EdhCSD:

- Open file *.par using File/Open PAR command.
- Perform data input and reduction using command Execute/Refin with
SelectSourceOfRawReflectionData=FormattedDataFileRef,
TheInputFileContains=SquaredStructureFactors, NormalizeDataAfter=Rogers:
5306 reflections were read.
- Look on the output using button List and save its content to the file *.out applying the
button WriteOut.
- Perform data averaging using command Execute/Avex with parameters
SourceDataFile=Working *.hkl, DestinationFile=Working *.hkl, SelectWhatToDo=Merge
equivalents:
310 symmetry independent reflections (R(eqv) = 0.0203) were written.
- Look on the output using button View/Output and save its content to the file *.out applying
the button WriteOut.
Exit EdhCSD:
file *.hkl appears in the working folder.

Call MainCSD:
3

- Solve the structure using Execute/DirectPhaseDetermination command with default
parameters:
solutions may be different in details in different attempts.
- Open peak list with the button PeakList.
- Copy 5 first atomic positions from the peak list to the main list assigning them type Si with
button IP.
- Close the peak list with the button FullScreen.
- Calculate the distances with the button DS:
two positions have too large distances for silicon.
- Change atom type for these two positions from SI to Na using button CT.
- Sort main list using button SO.
- Change atom’s identifiers with the button ID.
- Save the file *.par with the button Save*.par.
- Perform refinement in isotropic approximation using command Execute/LeastSquares:
R(F) = 0.0192 for 314 reflections.
- Change rank of displacement approximation to 2 using button RN.
- Perform refinement in anisotropic approximation using command Execute/LeastSquares:
- Add extinction coefficient to the refinement using Reality/Extinction command (sheldrick-2
with the parameter=0.01).
- Transform atomic coordinates in accordance with the structure type Clathrate-I using the
buttons CX and/or IV. Use PARIN for listing of Wyckoff positions.
- Calculate residual density using command Execute/FTT with parameter DiffFourierMap.
- View peak list with the button PeakList.
- Calculate the distances of the first peaks to the atoms: all distances are non-physical.
- Save *.par file using command File/Save.
- Look on the output using button List and save its content to the file *.out applying the button
WriteOut.
4

Exit MainCSD.

Call GeomCSD:

- Define type of listing using command Tools/Options/List and type of the calculations using
command Tools/Options/Distances/Angles.
- Mark all atoms (button SelectAll).
- Perform calculations of interatomic distances and angles using button DS.
- Look on the *.cif file and save it using command View/CIF and View/CIF/File/SaveCIF.
- Look on the output using button View/OUT and save its content to the file *.out applying
command View/OUT/File/SaveOUT.
- Draw the structure using command Draw:
save the image in the png format.
Exit GeomCSD:
files *.cif and *.png appear in the working directory.
5

Example 2 – ZrPtSi
Orthorhombic crystal structure.
Learn to work with the data of lower symmetry

* = sa0007

Open file f2plus.dat using any editor:
experimental data are written in F2plus format.
Close file f2plus.dat.

Call EdhCSD:

- Open file F2plus.dat using File/Open REF command with the options

FileType=FreeFormatFile and PropertiesOfFile=F2PlusRigakuFile.

- Write *.ref file using command Edit/FilterForRefFile with the parameters
V=0.0, OrderSorting=none, nDIM=3:
N(r) = 10411 R(s) = 3.44 % .

Exit EdhCSD:

file f2plus.ref appears in the working directory, rename it to sa0007.ref (hereafter *.ref).

Call EdhCSD:

- Open file *.ref using File/Open REF command.


analysis of extinction condition gives extinction in accordance with the space group Pmnb.

Exit EdhCSD.

Call ParinCSD:

- Input primary information taken from the texray.inf file obtained after the data collection
using sequentially button Orth and commands Cell, Data, Elements.

button WriteOut.
6

- Exit ParinCSD:

file *.par appears on the working directory.
Call EdhCSD:

- Perform data input and reduction using command Execute/Refin with the options
SelectSourceOfRawReflectionData=F2plusRigakuFile,
- Look on the output using button View/Output and save its content to the file *.out
applying the button WriteOut.
SourceDataFile=Working *.hkl, DestinationFile=Working *.hkl,
SelectWhatToDo=Merge equivalents:
- Look on the output using button View/Output and save its content to the file *.out
applying the button WriteOut.
Exit EdhCSD:

Call MainCSD:


- Solve the structure using Execute/DirectPhaseDetermination command with
default parameters:

- Copy 3 first atomic positions from the peak list to the main list assigning them type Pt, Zr
and Si, respectively with button IP.

fhe distances have chemically reasonable values.


- Perform refinement in isotropic approximation using command
7

Execute/LeastSquares:
R(F) = 0.0556.

- Perform refinement in anisotropic approximation using command
R(F) = 0.0539.
- Add extinction to the refinement using Reality/Extinction command.
R(F) = 0.0292.


- Calculate the distances of the first peaks to the
atoms: all distances are non-physical.

- Look on the output using button List and save its content to the file *.out applying
Exit MainCSD.

Call GeomCSD:


- Define type of listing using command Tools/Options/List and type of the calculations
using command Tools/Options/Distances/Angles.


- Look on the output using button View/OUT and save its content to the file *.out
applying command View/OUT/File/SaveOUT.
- Exit GeomCSD.
8

Example 3 – CsGaP3O10H
Monoclinic crystal structure.
Learn to work with the data on non-centrosymmeric structure

* = JXM_0136am

Open file *.ref using any editor:

experimental data are written in WinCSD format.

Close file *.ref.

Call EdhCSD:



analysis of extinction condition gives extinction in accordance with the space groups C2,
Cm, C2/m. Use C2 below.
Exit EdhCSD.

Call ParinCSD:

sequentially button Mono and commands Cell, Data, Elements. Use first the space group
C2/m with the highest symmetry.

button WriteOut.
Exit ParinCSD:


Call EdhCSD:


SelectSourceOfRawReflectionData=FormattedDataFile,
9


button WriteOut:
the statistics of the data clearly shows the non-centrosymmetricity of the crystal structure.

Exit EdhCSD:
Call ParinCSD:

sequentially button Mono and commands Cell, Data, Elements. (Try with the space group
Cm and discover that the structure solution and refinement below do not yield satisfactory
result). Use first the non- centrosymmetric space group C2.

button WriteOut.
Exit ParinCSD:

Call EdhCSD:



button WriteOut:
the statistics of the data clearly shows the non-centrosymmetricity of the crystal structure.

SelectWhatToDo=Merge Equivalents, MergeFriedelPairs=false:

10

Exit EdhCSD:
Call MainCSD:


- Solve the structure using Execute/DirectPhaseDetermination command with
default parameters:

- Copy 9 first atomic positions from the peak list to the main list assigning them type Cs
(one), Ga (one), P(two) and O (five), respectively with button IP.

the distances for one of the oxygen atoms have chemically non-reasonable values.

- Remove the wrong oxygen and take the next peak from the list.


- Transform atomic coordinates to achieve y(Cs) = 0.0 using the buttons IV and CX.

- Fix the y coordinate of the Cs position using the FP button.

- Perform refinement in isotropic approximation using command
R(F) = 0.0847.

R(F) = 0.0725.
One of the oxygen positions has unphysical displacement parameters.

- Remove the wrong oxygen position.
- Calculate difference Fourier map using the command
Execute/FFT/DifferenceFourierMap.
- Find missed oxygen position in the map (usually the first unassigned peak) and add it to
the main list using the button IV.

11

R(F) = 0.0210.

R(F) = 0.0173.
- Calculate difference Fourier map using the command Execute/FFT with the option
Diff. Fourier map.
- Identify the H position in the peak list and move it to the main list using button IV.

- Perform refinement in anisotropic approximation for all atoms but H using command
R(F) = 0.0172.



- Set options for listing using command Tools/Options.

Exit MainCSD.

Call GeomCSD:




Exit GeomCSD.
12

Example 4 – (NH3CH2CH2NH3)2ZnCl6
Orthorhombic crystal structure with organic cation
* = Zn

Open file *.original using any editor:

experimental data are not written in WinCSD format.

Close file *.original.

Call EdhCSD:

- Open file *.original using File/Open REF command with the option FileType/Shelx.

- Write *.ref file using command Edit/FilterForRefFile with the parameters
V=0.0, OrderSorting=none, nDIM=3:
N(r) = 22277, R(s) = 7.28%.

Exit EdhCSD:

file *.ref appears in the working directory.

Call EdhCSD:



analysis of extinction condition gives extinction in accordance with the space groups
Pbnm, Pbn21. Use Pbnm for further work.
Exit EdhCSD.

Call ParinCSD:

- Input primary information taken from the CIF file obtained after the data collection
using sequentially button Ortho and commands Cell, Data, Elements.
- Look on the output using button List and copy its content to the file *.out applying a
text editor.

13

Exit ParinCSD:

Call EdhCSD:

- Look on the output using button List and copy its content to the file *.out applying a
text editor. Statistics of the reflections confirms the centrosymmetric group.
SelectWhatToDo=Merge Equivalents, MergeFriedelPairs=true:

Exit EdhCSD:


Call MainCSD:


- Solve the structure using Execute/DirectPhaseDetermination command with parameter
PhaseRefinementOnly=true:
- Copy 9 first atomic positions from the peak list to the main list assigning them type Zn
(one), Cl (four), N(two) and C (two), respectively with button IP.
the distances for all atoms have chemically reasonable values.
R(F) = 0.0630.
R(F) = 0.0451
14

R(F) = 0.042.
- Calculate difference Fourier map using the command Execute/FFT with the option
Diff. Fourier map.
- Identify the H positions in the peak list and move it to the main list using button IV.
Execute/LeastSquares (dampfing factor).
- Repeat three operations until all H position will be localized.
Execute/LeastSquares (dampfing factor):
R(F) = 0.029.
Exit MainCSD.

Call GeomCSD:


Exit GeomCSD.
15

Example 21 – AuZn3

Simple cubic crystal structure
First steps to use WinCSD for the powder diffraction data
* = auzn

Look at the experimental data by a text editor:
the data in the file *.pro are in WinCSD format.

Call CellCSD:

- Open *.pro using command File/OpenPRO.

- Set wavelength to CuKa1 using command Radiation.

- Perform profile analysis with command Window/Profan:
- Use command Execute/FindPeaks for peak search with default value of the search
parameter.
- Process profile analysis using commands starting with the right mouse button. File *.pks
appears in the working directory.
- After finishing profile analysis check the *.pks file and – if necessary - remove the doubled
data (by a text editor).
- Switch to the main window by command Window/Full.

- Open *.pks file using command File/OpenPKS: the peak’s data appear in the left window.
- Perform indexing using command Tools/Autoindexing:

- Make a choice of the solution (here - cubic) by the mouse double click:

the list of possible indexes and calculated diffraction angles appears in the middle window.
- Assign indexes to the experimental peak positions with the button Indexing.
- Check the assignment and add (if necessary) missed indexes or change the indexing using left
mouse button first in the middle and then in the left large window at the appropriate line.
- Refine lattice parameter using button LS:

a = 7.8935(1) A.
16

- Prove the quality of the refinement by analyzing the difference values between the
experimental and calculated peak positions in the left window or graphically, using the button
ListResults or using command Window/Work. If necessary (e.g. hkl = 0 5 7), exclude the
reflection from the refinement by clicking its cn (changes to 0).
- Repeat lattice parameter refinement using button LS:

a = 7.89365(7) A.

- Refine the lattice parameter using button LD.

- Check for systematic errors using button ListResults:

if LD is larger as 3-4 e.s.d. use results of the LD refinement.

- Save the results in the output file using command File/SaveOUT/Lattice.

- Copy the lattice parameter(s) using command Edit/Cell/Edit/Copy.

Exit CellCSD:

file *.out appears in the working directory.

Open *.out file with any text editor and analyze systematic extinctions in the reflection list:
Extinction condition 2h + l = 2n for reflections hhl is in agreement with the space group
Pm3n.

Call ParinCSD:

- Set symmetry to cubic with button Cubic.

- Select space group Pm3n in the right window:

in the left window appear symmetrical operations of the chosen space group in matrix form;

in the middle window appear the general information and Wyckoff positions of the chosen
space group like in the International Tales for X-ray Crystallography.
- Input the lattice parameter using command Cell. In case the lattice parameters were copied
to the clipboard in the program CellCSD or copied to the clipboard from the *.out file, use
the command Cell/Edit/Paste.
- Input data type using the command Data with the parameters DataCollectionGeometry =
Bragg-Brentano, makeHKL = false, Rad = Cu and alfa-1 = true.
- Input atom sorts using command Elements (n(Au) = 8, n(Zn) = 24).

- Save the *.par file using command File/SavePAR.

- Look on the output using button ListResults and save its content to the file *.out applying
17

Exit ParinCSD:

files*.par and *.out appear in the working directory.
Call CellCSD:

- Open *.par using command File/OpenPAR.
- Create list of reflections using command Tools/Karta:
Do not change the maximal value of 2theta for calculation of the hkl list and use button
Control to proceed.
- Perform the complete profile deconvolution using command
Windows/PowderPatternDecomposition:
final R(P) should be < 0.045.
- Save the evaluated intensities in the file *.ref using the button
ExportVar/ExportRefFile/Full
- Write overall profile parameters U, V, W into the *.par file using button
ExportVar/WriteUVWInFile*Par.
Exit CellCSD:

Call EdhCSD:

- Open the *.par file using command File/OpenPAR.

- Perform data reduction using command Execute/Refin with DataCollectionGeometry

=Bragg-Brentano:
number of reflections processed 76.
Exit EdhCSD:
file *.hkl appears on the working directory.

Call MainCSD:

18


- Solve the crystal structure using Execute/DirectPhaseDetermination command with
default parameters:
white background of the main window indicates the successful finish of the structure
solution;
solutions may be different in details in different attempts because of the random generation
of the starting electron density.
- Close the window Structure determination

- See list of the obtained peaks using button PeakList.

- Copy 3 first atomic positions from the peak list to the main list assigning them type Au (first
two) and Zn (the third one), respectively with button IP.
- Close the list of peaks using the button FullScreen.
- Mark the obtained atom positions and calculate the distances with the button DS:
- Save the obtained model in the file *.par using the button Save*.Par.

R(I) = 0.04, R(P) = 0.14; all displacement parameters are negative.
- Add linear absorption coefficient to the refinement using Tools/Absorption command with
the options Bregg-Brentano = yes and mr = 0.07, Fix = yes.
R(I) = 0.047, R(P) = 0.071.

R(I) = 0.047, R(P) = 0.070.
‐ Calculate the distances of the first peaks to the atoms:
all distances are non-physical.


- Look on the output using button View/List and save its content to the file *.out applying the
button WriteOut.
19

Exit MainCSD:
file *_DirectPhase.max appears in the working directory.

Call GeomCSD:


- Perform calculations of interatomic distances and angles using buttons SelectAll and DS.

- Close the window List.

- Draw the structure using command Draw.
- Save the image in the png format.
Exit GeomCSD:
20

Example 22 – BaGe5
Complex crystal structure, two-phase sample

* = UA08162
- Look at the experimental data by a text editor:
the data in *.pro are in WinCSD format.

Call CellCSD:


- Set data type using the command Data/SynchrotronHighResolutionData.
- Set synchrotron radiation using command Radiation with parameter X(n) = yes and
wavelength of 0.35415 Ǻ.
-Use command Execute/FindPeaks for peak search.
Process profile analysis until 2theta = 12° using commands starting with the right mouse
button:
file *.pks appears in the working directory.
- After finishing profile analysis check the *.pks file and remove the doubled data (by text
editor).
- Open *.pks file using command File/OpenPKS: the peak data appear in the left window.
- Perform indexing using command Tools/Autoindexing.
- Make a choice of the solution by the mouse double click (here – orthorhombic with the
smallest volume of the unit cell):
mouse button first in the left and then in the right large window at the appropriate lines.
- Refine lattice parameters using button LS:

a = 10.723(1) Å, b = 14.795(2) Å, c = 9.2842(9) Å.
- Prove the quality of the refinement by analyzing the difference values between the
experimental and calculated peak positions in the left window or graphically, using the button
21

ListResults or command Windows/Work. If necessary (e.g. 2theta = 6.217, 10.159, etc),
exclude reflection(s) from the refinement by clicking its cn:
cn changes to 0.
a = 10.7241(5) Å, b = 14.7929(7) Å, c = 9.2843(4) Å.
- Check for systematic errors refining the lattice parameter with LD.
- Control the LD value using the button ListResults:
- Save the project using command File/SaveProject.

Exit CellCSD:

Extinction conditions h = 2n for reflections h0l and h + k = 2n for hk0 are in agreement with
the space group Pman (standard setting Pmna).

Call ParinCSD:

- Set symmetry to orthorhombic with button Orth.

- Select space group Pmna in the right window:
- Input the lattice parameters (saved in the *.out file) using command Cell:
a = 10.7241(5) Å, b = 9.2843(4) Å, c = 14.7929(7) Å because of the standard setting of the
space group!
Bragg-Brentano, makeHKL = false, X(n) = true and wavelength of 0.35415 Å.
- Input atom sorts using command Elements (n(Ba) = 10, n(Ge) = 50).
button WriteOut
22

Exit ParinCSD:
file *.par appears in the working directory.

Call CellCSD:


- Set data type using the command Data/SynchrotronHighResolutionData.
change the maximal value of 2theta to 12 degree for calculation of the hkl list.
- Perform the profile deconvolution using command
it is enough to achieve the R(P) = 0.16.
- Save file *.ref using the button ExportVar/ExportRefFile/Full.
Exit CellCSD:

Call EdhCSD:


=BreggBrentano.
Exit EdhCSD:

Call MainCSD:


- Solve the structure using command Execute/DirectPhaseDetermination with default
23

parameters:
solution;

- Copy 3 first atomic positions from the peak list to the main list assigning them type Ba and
next 9 assigning the type Ge with button IP.
- Save the obtained model in the file *.par using the button Save*Par.
Exit MainCSD.

Call CellCSD:


do not change the maximal value of 2theta (22 degree) for calculation of the hkl list.
- Save the file *.ref using the command File/SaveREF/Karta:
overwrite the preexisting file.

Exit CellCSD.

Call EdhCSD:


= Bragg-Brentano.
Exit EdhCSD.

24

Call MainCSD:


- Check the 2theta range for the calculation with Profile/Ranges:
2thetamax = 140 degree; the starting values of U, V and W (if they are not present) should be
used as obtained above from CellCSD; HighResolutionSynchrotronData=true.
- Give the parameters of the Pseudo-Voigt function free for refinement with
Profile/PseudoVoigt.
- Save parameters in the file *.par using the button Save*.PAR.
- Perform refinement of the profile parameters, atomic coordinates and occupation parameters
for two last Ge positions - Ge8 (0.16; 0.0; 0.0) and Ge9 (0.0; 0.03; 0.91) with fixed
displacement parameters in isotropic approximation (B = 1.0 for all atoms) using command
R(I) = 0.15, R(P) = 0.19.
- Add linear absorption coefficient to the refinement using command Tools/Absorption and
continue refinement with command Execute/LeastSquares:
R(I) = 0.12, R(P) = 0.16.
- Watch presence of the additional peaks of free germanium in the powder diffraction pattern
with Execute/GraphicServer.
- Save parameters in the file *.par using the button Save*.PAR.
Exit MainCSD.

Call ParinCSD:

- Set symmetry to cubic with button Cubic.

- Select space group Fd3m in the right window:

space group like in the International Tales for X-ray Crystallograaphy.
- Input the lattice parameter of Ge (taken from a data base) using command Cell:
a = 5.6575 Å.
- Input data type, radiation type and wavelength using the command Data with the parameter
25

makeHKL=false.
- Input atom sorts using command Elements (n(Ge) = 8).
- Save the Ge.par file using command File/SavePAR.
- Look on the output using button List and save its content to the file Ge.out applying the
button WriteOut
Exit ParinCSD:
file Ge.par appears in the working directory.

Call CellCSD:

- Open Ge.par using command File/OpenPAR.

set the maximal value of 2theta to 22 degree for calculation of the hkl list.
- Save the file Ge.ref using the command File/SaveREF/Karta.

Exit CellCSD.

Call EdhCSD:

- Open the Ge.par file using command File/OpenPAR.

= Bragg-Brentano.
Exit EdhCSD.

Call MainCSD:


- Add second phase to the calculation using the command Tools/Phase:
the buttons Phase1 and Phase 2 appear.
- Switch to phase 2 using the button Phase2.
- Input the atomic parameters using the button IN:
x = 0.125; y = 0.125; z = 0.125; B = 1.0.
- Check the 2theta range for the calculation with Profile/Ranges:
26

2thetamax = 140 deg; the starting values of U, V and W should be used as obtained above for
phase 1; HighResolutionSynchrotronData = true.
- Perform refinement profile parameters and atomic coordinates using command
R(I)phase1 = 0.09, R(I)phase2 = 0.18, R(P) = 0.13.
- Fix the profile parameters with the commands Profile.
- Perform refinement in anisotropic approximation for all Ba and Ge8 and Ge9 using
command Execute/LeastSquares:
R(I)phase1 = 0.076, R(I)phase2 = 0.16, R(P) = 0.12;
for Ge8 B33>>B33≈B22, thus Ge9 is not located on the 2-fold rotation axis.
- Change the z coordinate of the position Ge9 to 0.05 and set the occupation parameter to 0.5
using the commands CX and CG, respectively.
- Perform the final structure refinement in the isotropic approximation for Ge and anisotropic
approximation for Ba atoms using command Execute/LeastSquares:
- Calculate residual density using command Execute/FTT with parameter DiffFourierMap:
- Calculate the distances of the first peaks to the atoms:

button WriteOut.
Exit MainCSD:

file *DirectPhase.max appears in the working directory.

Call GeomCSD:


- Define type of listing using command Tools/Options/List and type of the calculations using
27

command Tools/Options/Distances/Angles.
- Perform calculations of interatomic distances and angles using button DS:
all distances beside d(Ge8-Ge9) and d(Ge8-Ge8) have physically correct values.
- Look on the *.cif file and save it using commands View/CIF and View/CIF/File/SaveCIF.
- Save the image in the tif format.
Exit GeomCSD:
files *.cif and *. tif appear in the working directory.
28

Example 23 – OsSe2Br12
Monoclinic crystal structure with very strong scattering atoms
* = OsSe2Br12
- Look at the experimental data by any text editor:
Call CellCSD:

- Set radiation to CuKa1 using command Radiation.
- Use command Execute/FindPeaks for peak search.
- Process profile analysis until 2theta = 65 ° using commands starting with the right mouse
button:
- After finishing profile analysis check the *.pks file and remove – if necessary - the doubled
data (by text editor).
- Open *.pks file using command File/OpenPKS:
the peak data appear in the left window.
make a choice of the solution by the mouse double click:
monoclinic body-centred (I) lattice with the parameters a = 13.0535 Å, b = 11.0392 Å, c =
6.4908 Å and  = 95.23 deg
- Change the non-standard setting of the lattice from I to C using the command
Edit/Matrix/Cell and the matrix (1 0 1; 0 1 0; 0 0 -1):
the new cell is: a = 14.0386 Å, b = 11.0392 Å, c = 6.4908 Å and  = 112.19 deg.
- Set crystal system to monoclinic using command System.
- Set space group to C2/m in the right window and press button OK:
the space group information appears in the middle window.
- Create the list of reflections possible in the chosen space group with the command
Tools/Karta.
- Show the list of reflections in the middle window with the button ListHKL:
29

the list of indexes and calculated diffraction angles appears in the middle window.
- Check the assignment and add (if necessary) missed indexes using left mouse button first in
the middle and then in the left window at the appropriate lines.
a = 14.0309(6) Å, b = 11.0410(9) Å, c = 6.4944(3) Å,  = 112.252(5) deg.
- Prove the quality of the refinement by analysing the difference values between the
experimental and calculated peak positions in the left window or graphically, using the
button List Results or the command Window/Work (right window). If necessary, exclude
reflection(s) from the refinement by clicking its cn (changes to 0).
- Repeat lattice parameter refinement using button LS.
- Check for systematic errors refining the lattice parameter with button LD:
- Calculate the profile function parameters using the command Tools/HWParms.
- Save the U, V, W values using the button Edit/WriteOUT in the window UVW-Function.
- Save the refinement project using the command File/SaveProject.
Exit CellCSD:
files *.out and *.sav appear in the working directory.
extinction condition h+l = 2n for all reflections is in agreement with the space group C2/m.

Call ParinCSD:

- Set symmetry to monoclinic with button Mono.

- Select space group C2/m in the right window:
- Input the lattice parameters using command Cell. In case the lattice parameters were copied
to the clipboard in the program CellCSD use the command Cell/Edit/Paste or copied to the
30

clipboard from the *.out file use the MSWindows command Paste.
Bragg-Brentano, makeHKL = false, Rad = Cu and alfa-1=true.
- Input atom sorts using command Elements (n(Os) = 2, n(Se) = 4, n(Br) = 24).


Exit ParinCSD:
Call CellCSD:

do not change the maximal value of 2theta for calculation of the hkl list and use button
Control to proceed.
the final R(P) should be < 0.040.
Exit CellCSD:

Call EdhCSD:

- Perform data reduction using command Execute/Refin with DataCollectionGeometry=
Bragg-Brentano:
31

456 reflections processed
Exit EdhCSD:

Call MainCSD:


parameters:
solution.
Solutions may be different in details in different attempts.
- Copy 6 first atomic positions from the peak list to the main list with button IP assigning them
type Os (first), Se (second) and Br (3rd to 6th), respectively.
the distances for all atoms have chemically reasonable values; Se is in contact with Br only.
- Save the obtained model in the file *.par using the button Save*Par.
R(I) = 0.046, R(P) = 0.065.
- Fix profile parameters.
- Perform refinement in anisotropic approximation using command Execute/LeastSquares
with DampLeastSquaresShifts = 42:
R(I) = 0.039, R(P) = 0.061.
- Calculate the distances of the first peaks to the atoms: all distances are non-physical.
- Look on the output using button View/List and save its content to the file *.out with the
32

button WriteOut.
Exit MainCSD:
Call GeomCSD:


- Define type of listing using command Tools/Options/List with ListFull = true and ListUij
= true.
- Define type of the calculations using command Tools/Options/Distances/Angles.
- Save the image in the tif format.
Exit GeomCSD:
files *.cif and *.tif appear in the working directory.
33

Example 24 – Sr2[BN2]Br
Rhombohedral crystal structure with atoms of very different scattering ability
* = Sr2[BN2]Br
Call CellCSD:

- Set radiation to CuKa1 using command Radiation.
- Process profile analysis in the range with 2 < 65 deg using commands starting with the
right mouse button:
the peaks’ data appear in the left window.
- Make a choice of the solution by the mouse double click: rhombohedral (R) lattice with
the parameters a = 4.117 Å and c = 52.923 Å:
- Check the assignment and add (if necessary) missed indexes or change the indexing using
left mouse button first in the middle and then in the left large window at the appropriate
lines.
- Refine lattice parameters using button LS:
The new cell is: a = 4.1170(2) Å and c = 52.923(3) Å.
- Analyse the hkl indexes for the reflections in the left window:
there are only the reflections with l = 2n present, therefore the lattice parameter c is
artificially doubled.
34

- Change the setting of the lattice from using the command Edit/Matrix/Indices and the
matrix (1 0 1; 0 1 0; 0 0 0.5).
The new cell is: a = 4.1170(2) Å and c = 26.462(2) Å.
the reflection from the refinement by clicking its cn (changes to 0):
all reflections have -h + k + l = 3n or h - k + l = 3n suggesting the rhombohedral lattice.
- Set crystal system to trigonal using command System.
- Set space group to R-3m in the right window and press button OK:
the space group information appears in the middle window.
- Create the list of reflections possible in the chosen space group with the command
Tools/Karta.
- Show the list of reflections in the middle window with the button ListHKL:
the list of indexes and calculated diffraction angles appears in the middle window.
- Check the assignment and add (if necessary) missed indexes using left mouse button first in
the middle and then in the left large window at the appropriate lines.
a = 4.1170(2) Å and c = 26.462(2) Å.
- Check for systematic errors refining the lattice parameter with LD:
Exit CellCSD:
extinction condition -h + k + l = 3n for all reflections is in agreement with the space group
R-3m.

35

Call ParinCSD:

- Set symmetry to trigonal with button Trig.

- Select space group R-3m in the right window:
- Input the lattice parameters using command Cell. In case the lattice parameters were copied
to the clipboard in the program CellCSD or copied to the clipboard from the *.out file, use the
command Cell/Edit/Paste.
Guinieer, G u n i e r / T r a n s m i s s i o n = y e s , G u n i e r / F i l m = y e s , makeHKL =
false, RadCu = true and alfa-1=true.
- Input atom sorts using command Elements (n(Sr) = 6, n(B) = 3, n(N) = 6, n(Br) = 3).
Exit ParinCSD:
Call CellCSD:


do not change the maximal value of 2theta for calculation of the hkl list and use button
Control to proceed.


- Save file *.ref using the button ExportVar/ExportRefFile/Full
ExportVar/WtiteUVWInFile*Par.
36

Exit CellCSD:

Call EdhCSD:

- Perform data reduction using command Execute/Refin with DataCollectionGeometry=
Guinier, G u n i e r / T r a n s m i s s i o n = y e s , G u n i e r / F i l m = y e s :
70 reflections processed.
Exit EdhCSD:

Call MainCSD:


parameters:
solution;
- Copy 4 first atomic positions from the peak list to the main list with button IP assigning them
type Sr (first two), Br (second one), B and N (3rd and 4th).
The distances for all atoms have chemically reasonable values; Se is in contact with Br only.
- Perform refinement in isotropic approximation using command Execute/LeastSquares using
DampLeastSquaresShift = 21:
R(I) = 0.039, R(P) = 0.113.
37

R(I) = 0.039, R(P) = 0.113.
- Calculate the distances of the first peaks to the atoms: All distances are non-physical.
button WriteOut.
Exit MainCSD:

Call GeomCSD:


- Define type of listing using command Tools/Options/List with ListFull = true.
Exit GeomCSD:
38

39

Example 25 – YbNiGa
Orthorhomic crystal structure, diffraction data of average quality.
* = YbNiGa_300K
Call CellCSD:

- Input N-ray = true and wavelength = 1.5480 using command Radiation.
- Process profile analysis in the range with 2 < 83 deg using commands starting with the
right mouse button:
the peaks’ data appear in the left window.
make a choice of the solution by the mouse double click: orthorhombic lattice with the
parameters a = 6.714 Å, b = 7.309 Å and c = 4.220 Å:
- Check the assignment and (if necessary) add missed indexes or change indexing using left
mouse button first in the middle and then in the left large window at the appropriate lines.
the new cell is: a = 6.712(1) Å, b = 7.301(2) Å and c = 4.2253(8) Å.
the reflection from the refinement by clicking its cn (changes to 0).
40

- Check for systematic errors refining the lattice parameter with LD:
Exit CellCSD:

extinction condition h = 2n for h0l reflections and k + l = 2n for 0kl reflections is in
agreement with the space group Pnam (in the standard setting Pnma);
there is pseudo extinction h + k = 2n for reflections hk0.

Call ParinCSD:

- Set symmetry to orthorhombic with button Orth.

- Select space group Pnma in the right window:
- Input the lattice parameter using command Cell taking into account the standard space
group setting:
a = 7.301(2) Å, b = 6.712(1) Å and c = 4.2253(8) Å.
Bregg-Brentano, N e u t r o n D a t / c y l i n d r i c a l = y e s , W a v e l e n g t h = 1 . 5 4 8 0 ,
makeHKL = false, Rad N-ray = true.
- Input atom sorts using command Elements (n(Yb) = 4, n(Ni) = 4, n(Ga) = 4).


41

Exit ParinCSD:
Call CellCSD:


Control to proceed.
ExportVar/WtiteUVWInFile*Par.
Exit CellCSD:

Call EdhCSD:

- Perform data reduction using command Execute/Refin with DataCollectionGeometry =
Bregg-Brentano:
246 reflections processed.
Close EdhCSD:

Call MainCSD:


42

parameters:
solution;
- Close the window Structure determination.
- Copy 3 first atomic positions from the peak list to the main list with button IP assigning
them type Yb, Ga and Ni, respectively.

R(I) = 0.070, R(P) = 0.130 and negative displacement for the Ga and large positive for the Ni
position, respectively.
- Exchange Ga and Ni using the button CT.
R(I) = 0.057, R(P) = 0.107.
R(I) = 0.057, R(P) = 0.107;
anisotropy in displacement does not change the residuals.
button WriteOut.
Exit MainCSD:
43


Call GeomCSD:


- Define type of listing using command Tools/Options/List with ListFull = true.
Exit GeomCSD:
44

Example 28 – La0.67TiO3
Simple crystal structure, deformation derivative from a cubic one, peak overlapping
problem
* = LaXTiO3
Look at the experimental data by a text editor:

the data in the file *.pro are in WinCSD format.
Call CellCSD:

- Set wavelength to CuKa1 using command Radiation.

- Look on different half-widths of the reflections
- Process profile analysis using commands starting with the right mouse button. Because of
the complex profiles, it is recommended to process each peak separately. File *.pks appears
in the working directory.

the peak’s data appear in the left window.
- Use Unknown symmetry and NumberNonidexedRefl=3-8 and evtl. ZeroShift=0.01
(position of the first peak!).
- Make a choice of the best solution (here – tetragonal with a ≈ 5.50 Å and c ≈ 7.78 Å) by the
mouse double click:
45

a = 5.5003(9) A, c = 7.7766(7) A.
- Refine the lattice parameter using button LD:
a = 5.5012(8) A, c = 7.7741(8), LD = -0.08(3). If |LD| > 3 e.s.d. use the LD values of the
lattice parameters.
Extinction condition h + k = 2n for reflections hk0 is in agreement with the space group
P4/nmm.
- Set window splitting using the command Window/Full

- Set symmetry to tetragonal with button Tetr.
- Select space group P4/nmm in the right window.
- Press button OK.
Сhange the maximal value of 2theta=100° for calculation of the hkl list and use button
Control to proceed.
- Show full list of possible reflections in the middle window using the button List
- Save the file *.ref using command File/SaveRef/Ind.
- Exclude the reflections with large half-widths from the list by double-click of the
according H value.
- Calculate the coefficients for the half-width parameters for the ‘narrow’ reflections
using command Tools/HWParms.
- Save the calculated parameters to the file *.out using Edit/WriteOut in the window
Tools/HWParms.
- Include the reflections with large half-widths to the list and exclude the reflections with
46

small half-widths from the list by double-click of the according H value.
- Calculate the coefficients for the half-width parameters for the ‘wide’ reflections using
command Tools/HWParms.
- Save the calculated parameters to the file *.out using Edit/WriteOut in the window
Tools/HWParms.
Exit CellCSD:
Files *.out and *.pks appear on the working directory.
Call ParinCSD:

- Select space group P4/nmm in the right window:
Guinier, Rad = Cu, alfa-1 = true.
- Input atom sorts using command Elements (n(La) = 4, n(Ti) = 4, n(O) = 12).
Exit ParinCSD:
file*.par appears in the working directory; file *.out contains already basic information about
the structure.
Call EdhCSD:

47

= Guinier:
93 reflections are processed.
Exit EdhCSD:
Call MainCSD:

default parameters:
solution;
- Copy 6 first atomic positions from the peak list to the main list assigning them type La (first
two) and Ti (the third one), and 3 positions of O, respectively with button IP.
- Write overall profile parameters U, V, W for the majority (‘narrow’) reflections with
command Profile/Ranges using CombinedProfile = yes.
Save the file *.par using the button Save*.Par.
- Set displacement parameters of the atoms to B(La) = 0.5, B(Ti) = 0.7 and B(O)=1.0.
- Fix all displacement parameters.
- Refine linear absorption coefficient using Tools/Absorption command with the options
48

Transmission = yes, mr = 2.0, fix = no with subsequent some cycles of least squares applying
the command Execute/LeastSquares.
- Fix the linear absorption coefficient and perform refinement in isotropic approximation
using command Execute/LeastSquares:
- Write overall profile parameters U, V, W for the ‘wide’ reflections in the second line in the
window using the command Profile/Ranges.
Save the file *.par using the button Save*.Par.
Exit CSDMain:
Using any text editor change the first column in the file *.ref for the ‘wide’ reflections from
1 to 2 using the file *.out for identification of the ‘wide‘ reflections. Save the so-corrected
file *.ref.
Call EdhCSD:

= Guinier.
Exit EdhCSD:
Call MainCSD:

49

Exit MainCSD.
Call GeomCSD:

Exit GeomCSD:
50

Example 29 – Tb1+xRe4B4
Composite structure
* = TbRe4B4
- Look at the experimental data by a text editor:

The data in the file *.pro are in WinCSD format.
STEP I – evaluation of the first substructure
Call CellCSD:

- Set wavelength to X(n) = 0.43046 Å using command Radiation and set data type using
command Data/Synchrotron.HighResolutionData.
- Use command Execute/FindPeaks for peak search with search factor 3.5.
- Process profile analysis (bis 2θ ≈ 19о) using commands called with the right mouse button:
File *.pks appears in the working directory.
- Set Assignment precision (1/d^2) = 0.00030
- Set Number of non-indexed refl. = 6
- Set symmetry to tetragonal with the button Tetr.
- Make a choice of the best solution by the mouse double click:
51

a = 10.531(1) A, c = 4.2300(6) A.
- Refine the lattice parameter using button LD.
a = 10.532(1) A, c = 4.2296(5) A.
- Check for systematic errors using button ListResults:
Extinction condition h + k + l = 2n for reflections hkl and h + k = 2n with h = 2n for
reflections hk0 and 2h + l = 4n for reflections hhl is in agreement with the space group
I41/amd.
- Select space group I41/amd in the right window.
- Press button OK.
Сhange the maximal value of 2theta=19° for calculation of the hkl list and use button
Control to proceed and close the widow Karta.
- Show the full list of reflections in the middle window using the button List.
- Save the file *.ref using command File/Save Ref/Ind.
- Set Data/SynchrotronHighResolutionData.
- Calculate overall profile parameters End2theta=180°, U=-0.34, V=0.11, W=0.004 using
command Tools/HWParms.
- Save parameters U, V, W using Save*.par = yes and Save*.out= yes in the window
Tools/HWParms.
Exit CellCSD:
52

Call ParinCSD:

- Select space group I41/amd in the right window:
SynchrotronCoxGeom, Rad = X(n)=0.43046.
- Input atom sorts using command Elements (n(Tb)= 4, n(Re) = 16, n(B) = 16).
Exit ParinCSD:
files*.par and *.out appear in the working directory.
Call EdhCSD:

= SynchrotronCoxGeom.
Exit EdhCSD
Call MainCSD:

default parameters:
53

solution;
- Copy first atomic positions from the peak list to the main list assigning them type Tb,
respectively with button IP.
the distances are too small for Tb-Tb.
- Change the type of the atom to Re using the button CT.
- Change the atom identifier using the button ID (no marked atoms in the main window)
- Write overall profile parameters U, V, W into the *.par file using the command
Profile/Ranges and the data from the file *.out. Set High Res. Synchr. Data=yes.
- Save the file *.par using the button Save*.Par.
R ≈ 25÷30%.
- Calculate difference Fourier map using the command Execute/FFT with the option Diff.
Fourier map.
- Open the peak list with the button PeakList.
- Identify the B position in the peak list by calculation of the interatomic distances and copy it
to the main list using button IP.
- Look on the output using command View/List and save its content to the file *.out applying
Exit MainCSD:
Call GeomCSD:
54

- Draw the structure using command Draw with Scene=[0.0,2.0,0.0,2.0,0.04.0].
- Save the image in the png format:
The obtained structure reveals channels with the axes at ¼ 0 z (¾ 0 z, ¼ 0 z, ¾ ½ z) suitable

for the location of Tb atoms.
Exit GeomCSD:
STEP II – evaluation of the lattice parameters of the second substructure
Call CellCSD:
- Set wavelength to X(n)=0.43046 using command Radiation and set Data/Synchrotron.
HighResolutionData.
- Exclude the reflections of the first substructure from the further processinh by double-click
of the according H value.
- Perform indexing using command Tools/Autoindexing with default parameters
- Set tetragonal symmetry using button Tetragonal in the window Autoindexing.
55

- Make a choice of the best solution by the mouse double click:
a = 10.531(1) A, c = 3.5435(2) Å.
Exit CellCSD:
The information about the refined lattice parameters of the second substructure appears in
the file *.out.
STEP III – refinement of the 4D lattice parameters.
Call CellCSD
- Set wavelength to X(n) -> 0.43046 using command Radiation.
- Set data type with Data/SynchrotronHighResolutionData.
- Set the space dimensionality using the command Space/3D+1 with Composite
structure=true and OneDImensionalModulationAlong=z.
- Select space group I41/amd in the right window.
- Press button OK.
- Set superspace group I41/amd(00p)0000
- Input the lattice parameter using command use the command Cell/Edit
using the information from the file *.out: a = 10.532 Å, c = 4.229 Å, d = 3.543 Å.
- Open *.pks file using command File/OpenPKS: the peak’s data appear in the left
window.
Сhange the maximal value of 2theta=19 for calculation of the hkl list and use button
Control to proceed.
- Assign indexes to the experimental peak positions with the button Indexing or
manually.
56

- Refine lattice parameter using button LS and LD.
a = 10.5300(2); c = 4.2296(2); d = 3.5435(2), LD =0.004(1).
- Write the results to the file *.out using command File/SaveOUT/Lattice.
- Exit CellCSD.
Open file *.out with a text editor. The extinction conditions define the space superspace
group I41/amd(00p)00ss (cf. data from the publication of A. Yamamoto).
STEP IV - Structure refinement.
Call ParinCSD:
-Select Space/3D+1/Composite Structure.

- Select space group I41/amd in the right window
- Select superspace group I41/amd(00p)00ss
- Input the lattice parameters a,c,d using command Cell. In case the lattice parameters were
copied to the clipboard in the program CellCSD or copied to the clipboard from the *.out file,
use the command Cell/Edit/Paste.
- Input data type using the command Data with the parameters DataCollectionGeometry=
SynchrotronCoxGeom, Rad = X(n) = 0.43046.
- Input atom sorts using command Elements (n(Tb) = 4, n(Re) = 16, n(B) = 16).
- Save the *.par file using command File/SavePAR owerwriting the existing file.
- Exit ParinCSD.
Call CellCSD:

57

Control to proceed.
- Save the file *.ref using command File/Save Ref/Karta.
Exit CellCSD
Call EdhCSD:

= SynchrotronCoxGeom.
Exit EdhCSD:
Call MainCSD:

- Input the coordinates of Re and B using the button IN and the data from the file *.out.
- Input the coordinates of the Tb atom as ¼ 0 z with z = ¼ (other values yield non-physical
distances)
- Input profile parameters U, V, W from the file *.out using command Profile/Ranges F with
HighResSynchrData = true.
- Refine the atomic parameters using command Execute/LeastSquares with the damping
factor Dump > 10.00, WightingScheme=1/sqrt(I) and Varying= true
- Refine linear absorption coefficient
- Refine isotropic/anisotropic displacement parameters
- Write the results to the file *.out using the command View/List/WriteOUT.
Close MainCSD
Call GeomCSD:
- Open file *.par using command File/Open PAR and

58

Composite or Host-Guest structure.Do you want to rebuild it ? = Yes:
In the window Composite Case chose the smallest value giving the smallest difference
between the approximant and composite structure.
- Save the approximant model to the file *.cif using command View/CIF/File/SafeCIF.
- Draw the crystal structure using the command Draw: Save the picture in png format.
Close GeomCSD.
59

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Open file *.ref with a text editor. Analyze the extinctions:

- Open file *.par using File/Open PAR command.

- Open file *.par using File/Open PAR command.

- Open file *.ref using File/Open REF command.

- Open file *.par using File/Open PAR command.

- Open file *.par using File/Open PAR command.

- Perform refinement in anisotropic approximation using command

- Open file *.par using File/Open PAR command.

Orthorhombic crystal structure with organic cation

- Open file *.par using File/Open PAR command.

- Open file *.par using File/Open PAR command.

- Open *.pro using command File/OpenPRO.

files *.cif and *.png appear in the working directory.

Complex crystal structure, two-phase sample

- Open *.pro using command File/OpenPRO.

- Refine lattice parameters using button LS:

- Set symmetry to orthorhombic with button Orth.

- Open *.par using command File/OpenPAR.

- Open the *.par file using command File/OpenPAR.

- Open the *.par file using command File/OpenPAR.

solutions may be different in details in different attempts.

- Open *.par using command File/OpenPAR.

- Open the *.par file using command File/OpenPAR.

- Open the *.par file using command File/OpenPAR.

- Set symmetry to cubic with button Cubic.

- Open Ge.par using command File/OpenPAR.

- Open the Ge.par file using command File/OpenPAR.

- Open the *.par file using command File/OpenPAR.

all distances are non-physical.

file *DirectPhase.max appears in the working directory.

- Open file *.par using File/Open PAR command.

- Open *.pro using command File/OpenPRO.

- Set symmetry to monoclinic with button Mono.

- Save the *.par file using command File/SavePAR.

- Open *.par using command File/OpenPAR.

- Open the *.par file using command File/OpenPAR.

- Open the *.par file using command File/OpenPAR.

- Open file *.par using File/Open PAR command.

- Open *.pro using command File/OpenPRO.

- Set symmetry to trigonal with button Trig.

- Open *.par using command File/OpenPAR.

- Perform the complete profile deconvolution using command

- Open the *.par file using command File/OpenPAR.

- Open the *.par file using command File/OpenPAR.

- Open file *.par using File/Open PAR command.

- Open *.pro using command File/OpenPRO.

- Set symmetry to orthorhombic with button Orth.

- Save the *.par file using command File/SavePAR.

- Open *.par using command File/OpenPAR.

- Open the *.par file using command File/OpenPAR.

- Open the *.par file using command File/OpenPAR.

the distances for all atoms have chemically reasonable values.

- Open file *.par using File/Open PAR command.

Look at the experimental data by a text editor:

- Open *.pro using command File/OpenPRO.

- Perform profile analysis with command Window/Profan:

- Open *.pks file using command File/OpenPKS:

- Set window splitting using the command Window/Full

- Set symmetry to tetragonal with button Tetr.

- Open the *.par file using command File/OpenPAR.

- Open the *.par file using command File/OpenPAR.

- See list of the obtained peaks using button PeakList.

- Open the *.par file using command File/OpenPAR.

- Perform refinement in isotropic approximation using command Execute/LeastSquares:

files .cif and .png appear in the working directory.

files .cif and .png appear in the working directory.