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:
- no title longer than 60 characters; the title may contain blanks
and ends whith a linefeed;
- identifiers should not be longer than 6 characters;
- the mixing of uppercase and lowercase characters in file names
should comply to the operating system conventions;
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.
c | character
|
c[n] | n characters max without blank
|
d | decimal
|
f | float
|
s | string
|
% | kind of block
|
@ | variable in block
|
Title and output info
Title | s | | title of the refinement | up to the end of the line
|
---|
ListName | s | | name of the listing file (eg xnd.lst) | up to the end of the line
|
---|
basic and refinement info
nCycle | d | | number of cycle to perform
(if negative, the program performs internal tests)
|
---|
nSym | d | | number of symmetry tables to be read in xnd.k
(excluding tables defined in xnd_sym.d.)
|
---|
nAno | d | | number of tables of anomalous scattering factors to be read
|
---|
nDif | d | | number of the scattering tables to be read in xnd.k
(excluding tables defined in xnd_dif.d.)
|
---|
EpsStop | f | | the refinement stops if the variation of the refined parameters
is lesser than the product of EpsStop and their e.s.d.
|
---|
EpsProf | f | | the reflection is calculated in the region where
(Y_cal(i)-Y_bkg(i)) > EpsProf sigma(Y_obs(min))
|
---|
Stabilise | f | | damping factor
|
---|
method info
Method | d | 0 | full-matrix least square refinement
|
---|
| | +1 | linear
|
| | +2 | weight 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).
|
BkGround | d | 0 | linear interpolation
|
---|
| | 1 | spline
|
Profil | d | 0 | pseudo-Voigt (ref)
|
---|
| | 1 | Voigt
|
MaxOrder | d | | maximum number of terms in the polynome (Temp) expansion
|
---|
ValidRef | d | 0 | no interpretation of refinement codes
|
---|
| | 2-9 | alternate refinement
|
printing codes
PrtSym | d | 0 | symmetry operations not printed in the listing file
|
---|
| | +1 | symmetry operations explicitely read in xnd.k
file are printed in the listing file
|
| | +2 | symmetry operations read in xnd_sym.d file are printed in
the listing file
|
PrtDif | d | 0 | diffusion factors tables not printed in the listing file
|
---|
| | +1 | scattering factors tables explicitely read in xnd.k file are printed in
the listing file
|
| | +2 | scattering factors tables read in xnd_dif.d file are printed in
the listing file
|
PrtCor | d | 0 | correlation matrix not printed in the listing file
|
---|
| | 1 | the whole correlation matrix is printed at the last cycle
|
| | 2-9 | correlation matrix elements greater than 20-90% are printed
|
files definition
PrtNew | d | 0 | no actualized copy of the xnd.k file and no NewName to read
|
---|
| | n>0 | creates the n+1 actualized copy of xnd.k
|
| | n<0 | no copy of xnd.k but NewName has to be read
|
NewName | s | | name of the actualized file (eg xnd.new)
|
---|
PrtKhl | d | 0 | no print of the hkl summary and no HklName to read
|
---|
| | 1 | prints the hkl summary at the last cycle
|
| | 2 | additional print of all the neglected reflections in the listing file
|
| | 3 | additional print of all the null or neglected reflections in the listing file
|
| | 103 | additional print of all the reflections in the listing file
|
| | n<0 | no file but HklName has to be read
|
HklName | s | | name of the file containing the hkl summary (eg xnd.hkl)
|
---|
PrtProf | d | 0 | no print of the file displaying the calculated profile
|
---|
| | 1 | prints the file displaying the calculated profile at the last cycle
|
| | -1 | no file but ProfName has to be read
|
ProfName | s | | name of the profile file (eg xnd.plg)
|
---|
other files information
Disk$\delta y\delta p$ | d | 0 | automatic dimension of the points and of the derivatives matrix\\
|
---|
| | n | dimension charged into memory
|
DiskData | d | 0 | data file is saved in a binary temporary file
|
---|
| | 1 | data file is saved in a binary permanent file
|
| | 2 | data file is read from a binary file; then the binary file is destroyed
|
| | 3 | data file is read from a binary permanent file
|
DataName | d | | name of the binary file containing data information
|
---|
DiskPath | d | 0 | standard path to xnd_dif.d, xnd_sym.d and temporary files\\
|
---|
| | +1 | explicit definition of the path to xnd_dif.d, xnd_sym.d
|
| | +2 | explicit definition of the path to temporary files
|
PathName | d | | path to xnd_dif.d, xnd_sym.d
|
---|
TempName | d | | path to temporary files
|
---|
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.
If nAno defined in the header is non zero, the nAno
diffusion tables are read here.
ADifName | c[6] | name of the element identifier
|
---|
>nLambda | d | number of wavelenghts for
which the correction is defined
|
---|
the following three values repeated nLambda times.
|
Lambda | f | wavelenght at which the correction is defined
|
---|
f_prime | f | correction on the real part of the diffusion table
|
---|
f_second | f | imaginary 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.
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.