xnd: input file

Generalities

In this section, the input data file to the program is described in detail. The coordinate file is often used with a .k extension this is not mandatory but allows the use of cycling procedures. In this document the input file will be refered as xnd.k.

The xnd.k file is not automatically checked for physical consistency of input data and these short guides to the preparation of this file can not replace the necessary knowledges in crystallography. All the others file names are specified in it.

When the xnd.k file seems to be filled, you can try to run the program by typing xnd, you will be asked for the input file or if you prefer you can type directly xnd xnd.k. In the xnd.k coordinate file, the cristallographic parameters are grouped into blocks. Each block has a specific function and several blocks are necessary to have a complete coordinate files. The blocks may be grouped as follows

In the coordinate file, there are also some alphanumeric fields as file names, symmetry identifiers, atoms identifiers. The following restrictions apply: The whole structure on the input file is described in the following tables. Each parameter is detailled, it is fisrt following by a code which is used to indentify its nature. Then typical value are precised and the input is commented. Two special codes are used to identify the nature of the variables block '%' and the variable parameters '@'. Their use is described in the part encoding the variables in standard block after the header part in which there is no variable parameters.

It is possible to insert a block of comments between each block of the program; each line of comment must began with a character '#'. If not explicitly stated, comments are forbidden inside the programs blocks. The comments are faithfully reproduced in the xnd.new file.

Here the block structure of the coordinate file is detailed, giving the meaning of each parameter. In the first column, an identifier defines the nature of the variable.
ccharacter
c[n]n characters max without blank
ddecimal
ffloat
sstring
%kind of block
@variable in block

Coordinates file header

Title and output info

Titlestitle of the refinementup to the end of the line
ListNamesname of the listing file (eg xnd.lst)up to the end of the line

basic and refinement info

nCyclednumber of cycle to perform (if negative, the program performs internal tests)
nSymdnumber of symmetry tables to be read in xnd.k (excluding tables defined in xnd_sym.d.)
nAnodnumber of tables of anomalous scattering factors to be read
nDifdnumber of the scattering tables to be read in xnd.k (excluding tables defined in xnd_dif.d.)
EpsStopfthe refinement stops if the variation of the refined parameters is lesser than the product of EpsStop and their e.s.d.
EpsProffthe reflection is calculated in the region where (Y_cal(i)-Y_bkg(i)) > EpsProf sigma(Y_obs(min))
Stabilisefdamping factor

method info

Methodd0full-matrix least square refinement
+1linear
+2weight taken on calculated rather than from observed profile
+4(reserved to take care of local correlations)
+8(reserved for ponderation ascheme calculating weights on the intensity exceeding bakground level).
BkGroundd0linear interpolation
1spline
Profild0pseudo-Voigt (ref)
1Voigt
MaxOrderdmaximum number of terms in the polynome (Temp) expansion
ValidRefd0 no interpretation of refinement codes
2-9alternate refinement

printing codes

PrtSymd0symmetry operations not printed in the listing file
+1symmetry operations explicitely read in xnd.k file are printed in the listing file
+2symmetry operations read in xnd_sym.d file are printed in the listing file
PrtDifd0diffusion factors tables not printed in the listing file
+1scattering factors tables explicitely read in xnd.k file are printed in the listing file
+2scattering factors tables read in xnd_dif.d file are printed in the listing file
PrtCord0correlation matrix not printed in the listing file
1the whole correlation matrix is printed at the last cycle
2-9correlation matrix elements greater than 20-90% are printed

files definition

PrtNewd0 no actualized copy of the xnd.k file and no NewName to read
n>0creates the n+1 actualized copy of xnd.k
n<0no copy of xnd.k but NewName has to be read
NewNamesname of the actualized file (eg xnd.new)
PrtKhld0no print of the hkl summary and no HklName to read
1prints the hkl summary at the last cycle
2additional print of all the neglected reflections in the listing file
3additional print of all the null or neglected reflections in the listing file
103additional print of all the reflections in the listing file
n<0no file but HklName has to be read
HklNamesname of the file containing the hkl summary (eg xnd.hkl)
PrtProfd0no print of the file displaying the calculated profile
1prints the file displaying the calculated profile at the last cycle
-1no file but ProfName has to be read
ProfNamesname of the profile file (eg xnd.plg)

other files information

Disk$\delta y\delta p$d0automatic dimension of the points and of the derivatives matrix\\
ndimension charged into memory
DiskDatad0data file is saved in a binary temporary file
1data file is saved in a binary permanent file
2data file is read from a binary file; then the binary file is destroyed
3data file is read from a binary permanent file
DataNamedname of the binary file containing data information
DiskPathd0standard path to xnd_dif.d, xnd_sym.d and temporary files\\
+1explicit definition of the path to xnd_dif.d, xnd_sym.d
+2explicit definition of the path to temporary files
PathNamed path to xnd_dif.d, xnd_sym.d
TempNamedpath to temporary files

Symmetry tables

If nSym defined in the header is non zero, the nSym symmetry tables are read here. They use the same entries than in the xnd_sym.d file.

Anomalous diffusion tables

If nAno defined in the header is non zero, the nAno diffusion tables are read here.
ADifNamec[6]name of the element identifier
>nLambdadnumber of wavelenghts for which the correction is defined
the following three values repeated nLambda times.
Lambdafwavelenght at which the correction is defined
f_primefcorrection on the real part of the diffusion table
f_secondfimaginary part of the correction
This module has to be repeated for each table needed in the refinement. The correction (ITC vol C, p 219--222) is applied to the wavelengths differing less than 2e-4 A from the wavelenght defined in the table.

Diffusion tables

If nDif defined in the header is non zero, the nDif diffusion tables are read here. They use the same entries than in the xnd_rdif.d file.

Encoding the variables in xnd

In the experiments and in the phases descriptions there are a lot of variables parameters which can be refined. They all used the same encoding and are group into blocks of parameters having the same behaviour. follows in the xnd.k file.

Experiments and Phases

Description of the experiments and of the phases follows in the xnd.k file.