A comes in, but ..

I was a little over excited to hear that A finally came in.  My expectation was very high.

But the database seems stuck as I don't have the right on the computer.  Fortunately, the it still runs under DOS although the built version seems several years old.

back to square 1. in reality 

Coming back to set eflech=. and set path=%path%;.  it still works fine. 

Just dug out so many lines of old code that can be savaged. for example, from dif to val and cpi.  this is for the case when you have more than 1000 files.  do this on a single file is a waste of time.


1.bat{
ls *.dif | sed -f 2val-dif
call 3.bat}

2val-dif{
s/\(.*\)\(...\)/cat & | sed -f 2valx_dif >5 \
mv 5 \1val\
cat \1val | sed -f 2val_dif_cpix >5 \
mv 5 \1cpi\
/w 3.bat}
2valx_dif {
1 {
s/\(.*\)\ *\(.*\)/FilePar\
\2\
\
1\
0\
N\
CU\
0\
1\
0\
1\
BerPar01\
99/g
}
2 {
s/^ //
s/\(.*\)\ \ \(.*\)\ \ .*\ Cu\ .*\ \ \(.*\)\ \ \(.*\)/\1\
\3\
\2\
T\
99\
1\
\4\
N\
N\
0\
Intens01/
}
s/^ //
s/  /\
/g
}

2val_dif_cpix {
1 s/.*/SIETRONICS XRD SCAN/
2 h
2,13 d
17,21 d
22 s/.*/CU\
1.54056\
11\/13\/01\
1/
23 x
24 s/.*/SCANDATA/}

Profex is quite convenient

Profex is quite a convenient tool to put things together.

It can read Bruker's latest format of diffraction files; whereas other commercial products cannot.
It also put the sticks in cache. so it is not necessary to regenerate the sticks each single time. Moreover, double clicking will find you a match.

But when you read from CIF, it doesn't recognize the HM symbols and leaves the Wyckoff letters blank.  The Wyckoff letters have to be put there manually.

Occasionally it hiccups.  This morning I found there are so many entries in the registry table.  hard to guess how these were generated.  but after deleting all the related items, it worked fine. The entries in the registry table became neat and necessary again.

Odd rietveld analysis

 

In the oil and gas industry, so many people pretend to do Rietveld analysis.  The smart ones don't put a diffractogram on the side; there would be simply some text: Rietveld analysis shows 3% of graphite.

 

 

The following graph is from http://www.searchanddiscovery.com/documents/2011/110150laughrey/ndx_laughrey.pdf

 

intensity with probabilities

so tough to draw on a pad

Fmult

The lengthy calculation now comes from vector stacking; suppose we know the scattering capacity F along certain direction vector, u, for each layer a,b,c,d.  The origins of neighbouring layers form vectors R,


Fa(u)+Fb(u)_corrected_by_Rab+Fc(u)_corrected_by_(Rab+Rbc)+Fd(u)_corrected_by_(Rab+Rbc+Rcd)

so vector manipulation is a lengthy one if you have one thousand layers.

but it is not that bad if they can be clustered.


_____________________
BGMN provided two phase functions, reFmult and Fmult; the 1st one, I tend to call it a physical phase, and the 2nd one, I tend to call it a metaphysical phase; for the Fmult, the F_i and phi_i are automatically calculated, i being from 1 and N as defined in the statement Fmult=N. 

intensity 3

A bunch of other things would lower the intensity, assuming the Xray is a perfect parallel beam, such as
absorption
Lorentz factor
polarization
The amount of material irradiated
thermal vibration of the dots

Talking about the thermal vibration thing.  Various software call it different names, such as U, beq, TDS, etc.  note the conversion and unit.  What is interesting is that a guy wrote a good thesis on this in Ruperto-Carola University of Heidelberg. 


Jacopo Negroni, 2012. Validation of Crystallographic B Factors and Analysis of Ribosomal Crystal Structures.

Permission to use this graph is NOT granted.  will take it off in a short while.

intensity 2

The following graph shows the process of adding all of them together.  I don't know the credit goes to whom.  But when I did the dielectric log interpretation, we always did the similar graph.  The real part in that case was the permittivity and the imaginary part was conductivity.  After plotting the square root of the vector for each mineral, you add them up (with the length shortened in a way proportional to the volumetric fraction), and the total should be what you measured.  if they are not matching, you can start pulling your hair like I did.

certainly in this case, the length is represented by the scattering capacity of the atom/dot in the lattice (sounds like a vegetable).  Note that each dot has different capacity, and the capacity changes with 2theta. 

 

Finally we have one Ftotal and Phi_total; in my junior years, I was thinking whether we could measure the amplitude and phase angle at each spot.  The my dream broke, at each point, you could see only a bright spot in old days or a count number of Xrays as of today.  The intensity or power or brightness is the only thing we can measure, which is normally related to the squares of the amplitudes.