<* $Id: xnd_file.html,v 1.1.1.1 1999/07/31 10:41:00 berar Exp $ *>
Files used in xnd program.
Files used in xnd program.
The following files specified, with their current extension, are described below :
These other file are described apart:
This output file is used in the reading part to give user a detailled
copy of all data in the ".k" file. This allow the correction of the ".k"
file when some mistakes occur.
Then during the refinement procedure, it produces a summary of what
append. At the beginning of each cycle, the scale factor of each phase is
given after its correction by the phase transition coefficent. The number
of used (significant) Bragg lines is given and compared with the number
of generated and non zero lines.
The displacement of the parameters are presented in a table containing
the new position, the shift and the standard deviation. If the shift
can be seen as small according to EpsStop and to the
standard deviation a star "*" is added at the end of the line.
Then some statistical ratio are given.
Rwp standard reliability factor sqrt (Sum(WdI^2) / Sum(WIo^2));
Rp unweigthed reliability factor Sum(Abs(dI)) / Sum(Io)
Rwp_c modified reliability factor to take into account local correlation
Berar,Lelann, J.Appl.Cryst. 24 (1991) p15
GoF Goodness of Fit Rwp/Rexp
Rwp_b background modified Rwp sqrt (Sum(WdI^2) / Sum(W(IoIback)^2));
Rp_b background modified Rp Sum(Abs(dI)) / Sum(IoIback);
N_b number of points where there is an intensity over the background
these points are used in calculating Rwp_b et Rp_p,
R_exp statistical limit expected for Rwp
d2 DurbinWatson distance 2, without correlation the limit is 0
Ne efficient number of points (N decreased of the parameters number)
N number of data points
Minimised_Sum Raw value of the minimised sum
Penalities weigth (percent) of penalities like bond length in the minimised sum
At the last cycle, result on integrated intensities are also given for
each phase before values over all phases.
R_Bragg reliability factor on hkl intensities Sum(Ihkl) / Sum(Ihkl_o)
S_I sum of the calculated hkl intensities Sum(Ihkl)
hkl number of lines used in the calculation
Rw_B weighted factor sqrt(Sum(W Ihkl^2) / Sum(W Ihkl_o^2))
S_wI weighted sum of the calculated hkl intensities
R_f reliability factor on structure factors Sum(Fhkl) / Sum(F_o)
S_f sum of the calculated Fc Sum(Ihkl)
Rwf weighted factor sqrt(Sum(W Fhkl^2) / Sum(W F_o^2))
S_wf weighted sum of the calculated hkl intensities
hkl number of lines used in the calculation
This is a faithfull copy of the .k file containing the
actualized values of the refined parameters. This file also contains
all the comments present in the ".k" file.
When the number of data points in the ".k" file does not agree with
the data file, the real number is printed in the ".new" file.
The value of prtNew is increased and a comment line
with prtNew and the final value of the minimized sum
is added at the end of the file.
Without specifications, the ".new" is writen according
to the current release input.
It is a 6 columns file suitable to be graphically displayed.
A common way to display pattern on unix station is to use the
xmgr software originaly writen by P.Turner.
To display all data use "xmgr nxy file.plg
" or read the sets
with the XY1Y2... options.
xmgr is now refered as
grace ( http://plasmagate.weizmann.ac.il/Grace ).
After the header lines (#) the 6 columns are:
1  2theta

2  Yobs  observed counts


3  Ycalc  sum of calculated counts


4  Ybkg  calculated background


4  dY  error or discrepency between observed and calculated counts


4  dy/sY  relative error


This file contains the list of the calculated hkl,
their positions, their integrated intensities and some information on the
profile characteristics. For classical samples the columns are described in
the following table.
1   line number

2  p  phase number according to xnd or pseudophase number


3  h  Miller indices


4  k


5  l


6   lambda number


7  2theta  line position including zero shift...


8   symbol according to the confidence in i_obs estimation


9  i_obs 


10  i_calc 


11  f_a  real part of structure factor


12  f_b  imaginary component of structure factor


13  w_l  FWHM of the Lorenzian component in the Voigt function


14  w_g  FWHM of the Gaussian component in the Voigt function


15  as_1  asymetry linear coefficient


16  as_3  asymetry cubic coefficient


17  mu  line multiplicity


18  orien  prefered orientation value


19  cor  Lorentzpolarisation factor


20  d_hkl  interplanar distance


21  s_i  ESD on i_obs


22   first angle used in the profile function

22   last angle used in the profile function

The observed intensities are calculated according to method : the first
uses the classical Rietveld formula, it gives a value for the whole intensity
seen in the calculation range; the second method uses a weighting scheme
and is more sensitive to the intensity near the line center. The difference between
both estimations is used to obtain the confidence indicator :
a < 2%; b < 4%; c< 8%; d < 16%; e < 32%; else f.
No particular extension is necessary. The known formats are
described below. They are ascii files and in all cases the only
real rule is that all data points have strictly increasing angles.
If overlapp are needed, more than one experimental file are needed.
If the weight are not specified, they are assumed to be Poissonian
(W=1/Io). If standard deviation are read, the weight are (W=1/s^2)
Simple files with angles and counts
The simpliest files contain the angle and the count on each line, they
are recognized according to:
code  columns

1  2theta  int


2  theta  2theta  int


3  2theta  int  s


4  theta  2theta  int  s


A general coding rule (100199) allow to read other files belong this kind
'1nm' means skip n columns, read 2theta, skip m values and read intensity.
Then '1' appears as a short way for '100' and '2' for '110'.
Similarly the coding rule (10001999) allows to read file with standard
deviations. Then '3' is a short for '1000' and '4' for '1100'.
Fixed step files
This files nead an header which allow to read more than one block. The
known files are.
code  content

10  1 column


11  8 columns


12  10 columns whitout number of counters


13  10 columns whit the number of counters ignored


14  10 columns whit the number of counters used


15  8 columns whit the number of counters ignored


16  8 columns whit the number of counters used


With their header, these files look like
BLOCK SCALE WSCALE
2THETA0 PAS 2THETAF MONO 2T0 2TF
i0 i1 i2 i3 i4 i5 i6 i7 xxx
i8 i9 ....
2THETA1 ...
where
BLOCK  number of blocks to be read


SCALE  values are multiplied by SCALE when read


WSCALE  standard deviation are multiplied by WSCALE


2THETA0  first used value in the block which begin at 2TO


2THETAF  last used value in the block which end at 2TF


MONO  monitor count or zero


2T0  first writen value in the block, not mandatory if equal to 2THETA0


2TF  last writen value in the block, not mandatory if equal to 2THETAF


This allow the use of data recorded with various counting time or monitoring.
The effective values are
INT = Ix * SCALE
SIGMA = WSCALE * sqrt (INT) + sqrt(MONO)
If the number of counters is specified, this is modified in
INT = Ix * SCALE
SIGMA = WSCALE * sqrt (INT/n) + sqrt(MONO)
Multiple files
Few files containing more than one experiment are recognized.
code  kind of files

20  ILL D1B, D20 (1990 format)


21  XDMI files from LURE...


 D1B files : these files have an header in which a control variable
can be extracted according to ots position ( 1 to 22). If the time has to
be used (case 0), it is counted in seconds starting at the first data set.
 XDMI files : this is for files obtained from the Direct Memory
Incrementation card of IPN (Orsay) which have been tranformed diffraction
data using xdmi at LURE. The number of parameters to be read is specified in
the header. This header is followed by the table made off the measured angles
and if required (nEFF non zero) by the efficiency table. For each set, the number is read
(case 0) then the parameters and the intensisies table.
nSETS nPTS nPAR nEFF
2theta00 2theta01 ....
2theta10 2theta11 ....
eff00 eff01 ....
eff10 eff11 ....
0 par1(0) ....
int00 int01 ....
int10 int11 ....
....
1 par1(1) ....
int0 int1 ....
....
Currently this file is presented with 10 values on each line. The reference number
of the control value have to be lower than nPAR, which is the number of
parameters in the file. The efficiency table is used to correct the data
if nEff is equal to 1; if nEff is equal to 1, the correction has soon be done
on data but the weight have to be corrected.
To allow a faster access to data files. These files can be created by
xnd, when they are used a very short check is done to ensure that
the number of points in the file agrees with the number declared in
the ".k" file.
Le programme utilise deux fichiers temporaires binaires. Le premier
contient les donnees experimentales des divers diagrammes, il peut etre
conserve pour eviter la relecture de ces donnees, son nom doit alors etre
fournit par l'utilisateur. Le second contient la table des derivees des
parametres sur le diagramme en cours d'affinement, et les valeurs des
intensites. Il sert d'extension a la memoire si cela est necessaire
(parametre disk_dydp et fonctions ...dydp). Sur microordinateur de type PC
ou MAC, le compilateur place les fichiers temporaires dans le directory
courant, on peut utiliser un disque virtuel (ram_disk, memoire etendue...)
pour loger ces fichiers en utilisant ce disque comme directory de travail.
En indiquant un nom complet avec path les fichiers coordonnees, listing...
peuvent resider sur un autre disque, le gain de temps peut etre important
et atteindre 30% (cf essai sur MacSE30). La taille necessaire pour loger ce
fichier est indiquer dans le listing a la fin de la phase de lecture.
JFB Aug 25th, 1999