RE: fundamental parameters approach

[Whitfield, Pamela]

>In addition, the raytracing fundamental
>approach describes at now (planar) transmission geometry and
>capillar geometry.

Don't know about the planar transmission (never done it), but I can happily
fit capillary data off my system.  I have no quibbles about the
effectiveness of ray-tracing, but what I'm using currently with our machine
(including tube-tails) does a pretty good job.  It eventually gets to the
stage that sample prep issues (particle statistics, etc) will have greater
effects than very slight inadequacies of the profile fit.


Pam

Dr Pamela Whitfield CChem MRSC
Energy Materials Group
Institute for Chemical Process and Environmental Technology
Building M12
National Research Council Canada
1200 Montreal Road
Ottawa  ON   K1A 0R6
CANADA
Tel: (613) 998 8462 Fax: (613) 991 2384
Email: 
ICPET WWW: http://icpet-itpce.nrc-cnrc.gc.ca

Re: fundamental parameters approach

[Jörg Bergmann]

Dear all,

just a remainder for a less popular (and, sorry, less academic
published) fundamental parameters aproach: raytracing the 
geometric part of fundamental parameters as done in BGMN
www.bgmn.de
(download a free trial version at www.bgmn.de/download.html).
At my opinion, folding the geometric part from partial
divergence functions (as done in the cited papers) has
some minor faults. In addition, the raytracing fundamental
approach describes at now (planar) transmission geometry and
capillar geometry.
If you want a deeper insight into raytracing fundamental
parameters approach, please read
www.bgmn.de/download/srm660a.pdf
And, you may download hundreds of checked str files in BGMN
format for free at
www.bgmn.de/download-structures.html
In addition, PowderCell (a freely available program) may
convert CIF files into BGMN str files.

Just some remark.

J"org Bergmann, (independent) author of BGMN

*** This EComStation system uptime is 16 days 23 hours ***

fundamental parameters approach

[Whitfield, Pamela]

Jilin

As far as I'm aware there is no repository for Topas str files.  Bruker does
sell a (fairly) comprehensive set for those without the time or inclination
to make their own.  Topas will import CIF files, but the ICSD doesn't always
export CIF files in the same format as Topas is expecting.  Consequently you
sometimes have to edit the CIF file by hand.  Sounds tedious but it's better
than typing in a 100+ atom cell by hand!  I suppose someone could create
such a repository, but some mineral structures do vary somewhat
(occasionally alarmingly so) in the literature and I would be wary of saying
that the one I use is the 'correct' one.

Pam

Dr Pamela Whitfield CChem MRSC
Energy Materials Group
Institute for Chemical Process and Environmental Technology
Building M12
National Research Council Canada
1200 Montreal Road
Ottawa  ON   K1A 0R6
CANADA
Tel: (613) 998 8462 Fax: (613) 991 2384
Email: 
ICPET WWW: http://icpet-itpce.nrc-cnrc.gc.ca


-Original Message-
From: Jilin Zhang [mailto:[EMAIL PROTECTED]
Sent: June 4, 2004 9:28 AM
To: [EMAIL PROTECTED]


Dear Dr. Whitfield:

It appears to me you are using koalariet or topas by Dr. Coehlo et al. Do
you know a web site where we can down load  a bunch of .str files for
minerals, as BGMN.de has the .str files for BGMN.

Thanks.

jilin zhang
omni labs
8845 fallbrook
houston tx 77064
phone 832-237-4000

-Original Message-
From: Whitfield, Pamela [mailto:[EMAIL PROTECTED]
Sent: Friday, June 04, 2004 8:15 AM
To: '[EMAIL PROTECTED]'


Nandini

The best people to reply on behalf of fundamental parameters would be Alan
Coehlo or Arnt Kern.   
But until they do here goes

The more general form is convolution-based profile fitting.  This can be
used for all peak profile types, whereas 'pure' fundamental parameters has
only been inmplemented for the simple Bragg-Brentano case (no
monochromators).  Other geometries have to be empirically modelled using a
standard and some sort of user-defined convolution on top of the source
profile.  Better fits can often be obtained using this type of fitting than
the normal pseudo-Voigt or Pearson VII functions (in my experience at
least).  Where convolution-based fitting really comes into its own in in
complex quantitative Rietveld analysis where the number of refined variables
would become untenable for normal peak fitting.  Using convolution-based
fitting it is possible to cope with upwards of 10 phases with severe peak
overlap and still get good results with good stability. For example,
quantitative Rietveld analysis of cements is becoming routine.

Pam 

Dr Pamela Whitfield CChem MRSC
Energy Materials Group
Institute for Chemical Process and Environmental Technology
Building M12
National Research Council Canada
1200 Montreal Road
Ottawa  ON   K1A 0R6
CANADA
Tel: (613) 998 8462 Fax: (613) 991 2384
Email: 
ICPET WWW: http://icpet-itpce.nrc-cnrc.gc.ca


-Original Message-
From: Nandini Devi Radhamonyamma [mailto:[EMAIL PROTECTED]
Sent: June 4, 2004 6:42 AM
To: [EMAIL PROTECTED]


Dear All,


Is the fundamental parameter approach better than
mathematical approach used in most of the Rietveld
refinement programs? Does that mean programs which use
that approach are better? Any suggestions?

Nandini




__
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Re: fundamental parameters approach

[Whitfield, Pamela]

Our system has double mirrors and I could never get FCJ to give as good a
fit, but then that may be a peculiarity of these optics.  My memory is a bit
hazy so I can't remember what function the simple axial model uses, but I
don't think it's a function of diffractometer characteristics.  Topas is
flexible enough that you can convolute just about any equation you care to
come up with with any kind of angular dependence (or not), but they do make
your size/strain results somewhat useless if they are added as an
afterthought (e.g. to fit turbostratic disorder).

Pam

Dr Pamela Whitfield CChem MRSC
Energy Materials Group
Institute for Chemical Process and Environmental Technology
Building M12
National Research Council Canada
1200 Montreal Road
Ottawa  ON   K1A 0R6
CANADA
Tel: (613) 998 8462 Fax: (613) 991 2384
Email: 
ICPET WWW: http://icpet-itpce.nrc-cnrc.gc.ca


-Original Message-
From: Maxim V. Lobanov [mailto:[EMAIL PROTECTED]
Sent: June 4, 2004 10:27 AM
To: [EMAIL PROTECTED]


In Topas there are two options for treating low-angle asymmetry using
diffractometer characteristics (i.e., "fundamental parameters") called
"simple axial model" and "full axial model". But (this is my impression
only) it seems that FCJ (Finger et al) approach works equally well.
Starting from Topas2.1 it is implemented too, and you can easily compare.
On the other hand, a very useful feature of Topas is the possibility to
treat irregular peak asymmetry originating from "sample effects"... 
Sincerely,  Maxim.

>Again, does this approach take care of low angle peak
>asymmetry better?

__
Maxim V. Lobanov
Department of Chemistry
Rutgers University
610 Taylor Rd
Piscataway, NJ 08854
Phone: (732) 445-3811

Re: fundamental parameters approach

[Patrick Mercier]

Hi all,

Here are the references to these papers:

Cheary RW, Coelho AA (1998a) Axial divergence in a conventional X-ray powder
diffractometer. I. theoretical foundations. J. Appl. Cryst. 31:851-861

Cheary RW, Coelho AA (1998b) Axial divergence in a conventional X-ray powder
diffractometer. II. Realization and evaluation in a fundamental-parameter
profile fitting procedure. J. Appl. Cryst. 31:862-868

Cheary RW, Coelho AA (1992) A fundamental parameters approach to X-ray
line-profile fitting. J. Appl. Cryst. 25:109-121

Patrick Mercier

"Whitfield, Pamela" wrote:

> Nandini
>
> If you're using standard Bragg-Brentano the true fundamental parameters
> fitting from first principles will happily fit low angle asymmetry, as the
> mathematical basis for it is well known (look for some papers that Alan
> Coehlo and Bob Cheary did a while back, in J.Appl.Cryst I think).  Axial
> divergence is dealt with through modelling the effect of Soller slits,
> source length, sample width and receiving slit length if my memory serves.
> Monochromators, etc, also have effects, but these have to be determined
> empirically.
>
> Pam
>
> Dr Pamela Whitfield CChem MRSC
> Energy Materials Group
> Institute for Chemical Process and Environmental Technology
> Building M12
> National Research Council Canada
> 1200 Montreal Road
> Ottawa  ON   K1A 0R6
> CANADA
> Tel: (613) 998 8462 Fax: (613) 991 2384
> Email: 
> ICPET WWW: http://icpet-itpce.nrc-cnrc.gc.ca
>
> -Original Message-
> From: Nandini Devi Radhamonyamma [mailto:[EMAIL PROTECTED]
> Sent: June 4, 2004 9:46 AM
> To: [EMAIL PROTECTED]
>
> Thanks, Pam and Jon for the clarifications.
> Again, does this approach take care of low angle peak
> asymmetry better?
> thanks,
>
> nandini
>
> --- "Whitfield, Pamela"
> <[EMAIL PROTECTED]> wrote:
> > Nandini
> >
> > The best people to reply on behalf of fundamental
> > parameters would be Alan
> > Coehlo or Arnt Kern.
> > But until they do here goes
> >
> > The more general form is convolution-based profile
> > fitting.  This can be
> > used for all peak profile types, whereas 'pure'
> > fundamental parameters has
> > only been inmplemented for the simple Bragg-Brentano
> > case (no
> > monochromators).  Other geometries have to be
> > empirically modelled using a
> > standard and some sort of user-defined convolution
> > on top of the source
> > profile.  Better fits can often be obtained using
> > this type of fitting than
> > the normal pseudo-Voigt or Pearson VII functions (in
> > my experience at
> > least).  Where convolution-based fitting really
> > comes into its own in in
> > complex quantitative Rietveld analysis where the
> > number of refined variables
> > would become untenable for normal peak fitting.
> > Using convolution-based
> > fitting it is possible to cope with upwards of 10
> > phases with severe peak
> > overlap and still get good results with good
> > stability. For example,
> > quantitative Rietveld analysis of cements is
> > becoming routine.
> >
> > Pam
> >
> > Dr Pamela Whitfield CChem MRSC
> > Energy Materials Group
> > Institute for Chemical Process and Environmental
> > Technology
> > Building M12
> > National Research Council Canada
> > 1200 Montreal Road
> > Ottawa  ON   K1A 0R6
> > CANADA
> > Tel: (613) 998 8462 Fax: (613) 991 2384
> > Email: 
> > ICPET WWW: http://icpet-itpce.nrc-cnrc.gc.ca
> >
> >
> > -Original Message-
> > From: Nandini Devi Radhamonyamma
> > [mailto:[EMAIL PROTECTED]
> > Sent: June 4, 2004 6:42 AM
> > To: [EMAIL PROTECTED]
> >
> >
> > Dear All,
> >
> >
> > Is the fundamental parameter approach better than
> > mathematical approach used in most of the Rietveld
> > refinement programs? Does that mean programs which
> > use
> > that approach are better? Any suggestions?
> >
> > Nandini
> >
> >
> >
> >
> > __
> > Do you Yahoo!?
> > Friends.  Fun.  Try the all-new Yahoo! Messenger.
> > http://messenger.yahoo.com/
>
>
>
> __
> Do you Yahoo!?
> Friends.  Fun.  Try the all-new Yahoo! Messenger.
> http://messenger.yahoo.com/

--
Dr. Patrick H.J. Mercier, P.Phys., ing. jr
Research Associate
Department of Physics
University of Ottawa
150 Louis Pasteur
Ottawa, Ontario, Canada K1N 6N5
Telephone: (613)562-5800 extension 6743
Fax: (613)562-5190
E-mail: [EMAIL PROTECTED]

Re: fundamental parameters approach

[Maxim V. Lobanov]

In Topas there are two options for treating low-angle asymmetry using
diffractometer characteristics (i.e., "fundamental parameters") called
"simple axial model" and "full axial model". But (this is my impression
only) it seems that FCJ (Finger et al) approach works equally well.
Starting from Topas2.1 it is implemented too, and you can easily compare.
On the other hand, a very useful feature of Topas is the possibility to
treat irregular peak asymmetry originating from "sample effects"... 
Sincerely,  Maxim.

>Again, does this approach take care of low angle peak
>asymmetry better?

__
Maxim V. Lobanov
Department of Chemistry
Rutgers University
610 Taylor Rd
Piscataway, NJ 08854
Phone: (732) 445-3811

Re: fundamental parameters approach

[Whitfield, Pamela]

Nandini

If you're using standard Bragg-Brentano the true fundamental parameters
fitting from first principles will happily fit low angle asymmetry, as the
mathematical basis for it is well known (look for some papers that Alan
Coehlo and Bob Cheary did a while back, in J.Appl.Cryst I think).  Axial
divergence is dealt with through modelling the effect of Soller slits,
source length, sample width and receiving slit length if my memory serves.
Monochromators, etc, also have effects, but these have to be determined
empirically.

Pam

Dr Pamela Whitfield CChem MRSC
Energy Materials Group
Institute for Chemical Process and Environmental Technology
Building M12
National Research Council Canada
1200 Montreal Road
Ottawa  ON   K1A 0R6
CANADA
Tel: (613) 998 8462 Fax: (613) 991 2384
Email: 
ICPET WWW: http://icpet-itpce.nrc-cnrc.gc.ca


-Original Message-
From: Nandini Devi Radhamonyamma [mailto:[EMAIL PROTECTED]
Sent: June 4, 2004 9:46 AM
To: [EMAIL PROTECTED]


Thanks, Pam and Jon for the clarifications. 
Again, does this approach take care of low angle peak
asymmetry better?
thanks,

nandini

--- "Whitfield, Pamela"
<[EMAIL PROTECTED]> wrote:
> Nandini
> 
> The best people to reply on behalf of fundamental
> parameters would be Alan
> Coehlo or Arnt Kern.   
> But until they do here goes
> 
> The more general form is convolution-based profile
> fitting.  This can be
> used for all peak profile types, whereas 'pure'
> fundamental parameters has
> only been inmplemented for the simple Bragg-Brentano
> case (no
> monochromators).  Other geometries have to be
> empirically modelled using a
> standard and some sort of user-defined convolution
> on top of the source
> profile.  Better fits can often be obtained using
> this type of fitting than
> the normal pseudo-Voigt or Pearson VII functions (in
> my experience at
> least).  Where convolution-based fitting really
> comes into its own in in
> complex quantitative Rietveld analysis where the
> number of refined variables
> would become untenable for normal peak fitting. 
> Using convolution-based
> fitting it is possible to cope with upwards of 10
> phases with severe peak
> overlap and still get good results with good
> stability. For example,
> quantitative Rietveld analysis of cements is
> becoming routine.
> 
> Pam 
> 
> Dr Pamela Whitfield CChem MRSC
> Energy Materials Group
> Institute for Chemical Process and Environmental
> Technology
> Building M12
> National Research Council Canada
> 1200 Montreal Road
> Ottawa  ON   K1A 0R6
> CANADA
> Tel: (613) 998 8462 Fax: (613) 991 2384
> Email: 
> ICPET WWW: http://icpet-itpce.nrc-cnrc.gc.ca
> 
> 
> -Original Message-
> From: Nandini Devi Radhamonyamma
> [mailto:[EMAIL PROTECTED]
> Sent: June 4, 2004 6:42 AM
> To: [EMAIL PROTECTED]
> 
> 
> Dear All,
> 
> 
> Is the fundamental parameter approach better than
> mathematical approach used in most of the Rietveld
> refinement programs? Does that mean programs which
> use
> that approach are better? Any suggestions?
> 
> Nandini
> 
> 
>   
>   
> __
> Do you Yahoo!?
> Friends.  Fun.  Try the all-new Yahoo! Messenger.
> http://messenger.yahoo.com/ 





__
Do you Yahoo!?
Friends.  Fun.  Try the all-new Yahoo! Messenger.
http://messenger.yahoo.com/ 

Re: fundamental parameters approach

[Nandini Devi Radhamonyamma]

Thanks, Pam and Jon for the clarifications. 
Again, does this approach take care of low angle peak
asymmetry better?
thanks,

nandini

--- "Whitfield, Pamela"
<[EMAIL PROTECTED]> wrote:
> Nandini
> 
> The best people to reply on behalf of fundamental
> parameters would be Alan
> Coehlo or Arnt Kern.   
> But until they do here goes
> 
> The more general form is convolution-based profile
> fitting.  This can be
> used for all peak profile types, whereas 'pure'
> fundamental parameters has
> only been inmplemented for the simple Bragg-Brentano
> case (no
> monochromators).  Other geometries have to be
> empirically modelled using a
> standard and some sort of user-defined convolution
> on top of the source
> profile.  Better fits can often be obtained using
> this type of fitting than
> the normal pseudo-Voigt or Pearson VII functions (in
> my experience at
> least).  Where convolution-based fitting really
> comes into its own in in
> complex quantitative Rietveld analysis where the
> number of refined variables
> would become untenable for normal peak fitting. 
> Using convolution-based
> fitting it is possible to cope with upwards of 10
> phases with severe peak
> overlap and still get good results with good
> stability. For example,
> quantitative Rietveld analysis of cements is
> becoming routine.
> 
> Pam 
> 
> Dr Pamela Whitfield CChem MRSC
> Energy Materials Group
> Institute for Chemical Process and Environmental
> Technology
> Building M12
> National Research Council Canada
> 1200 Montreal Road
> Ottawa  ON   K1A 0R6
> CANADA
> Tel: (613) 998 8462 Fax: (613) 991 2384
> Email: 
> ICPET WWW: http://icpet-itpce.nrc-cnrc.gc.ca
> 
> 
> -Original Message-
> From: Nandini Devi Radhamonyamma
> [mailto:[EMAIL PROTECTED]
> Sent: June 4, 2004 6:42 AM
> To: [EMAIL PROTECTED]
> 
> 
> Dear All,
> 
> 
> Is the fundamental parameter approach better than
> mathematical approach used in most of the Rietveld
> refinement programs? Does that mean programs which
> use
> that approach are better? Any suggestions?
> 
> Nandini
> 
> 
>   
>   
> __
> Do you Yahoo!?
> Friends.  Fun.  Try the all-new Yahoo! Messenger.
> http://messenger.yahoo.com/ 





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Re: indexing problem

[Armel Le Bail]

Topas software is very good at solving such short axis problems.  The 
advantage is that it will look at all of the peaks you feed it, instead of 
using just the first twenty or so to generate candidate solutions (the way 
that ITO and TREOR work).
There is a way with McMaille to fix the cell parameters deduced
from a series of h0l, to enter up to 100 peak positions, and to
explore exclusively the lacking parameters. This can be done
either by Monte Carlo or by grid-search. But if only 3 or 4
peaks for a total of 31 are not h0l and involve k, then the
ambiguity is too large IMHO.
Armel

fundamental parameters approach

[Jilin Zhang]

Dear Dr. Whitfield:

It appears to me you are using koalariet or topas by Dr. Coehlo et al. Do you know a 
web site where we can down load  a bunch of .str files for minerals, as BGMN.de has 
the .str files for BGMN.

Thanks.

jilin zhang
omni labs
8845 fallbrook
houston tx 77064
phone 832-237-4000

-Original Message-
From: Whitfield, Pamela [mailto:[EMAIL PROTECTED]
Sent: Friday, June 04, 2004 8:15 AM
To: '[EMAIL PROTECTED]'


Nandini

The best people to reply on behalf of fundamental parameters would be Alan
Coehlo or Arnt Kern.   
But until they do here goes

The more general form is convolution-based profile fitting.  This can be
used for all peak profile types, whereas 'pure' fundamental parameters has
only been inmplemented for the simple Bragg-Brentano case (no
monochromators).  Other geometries have to be empirically modelled using a
standard and some sort of user-defined convolution on top of the source
profile.  Better fits can often be obtained using this type of fitting than
the normal pseudo-Voigt or Pearson VII functions (in my experience at
least).  Where convolution-based fitting really comes into its own in in
complex quantitative Rietveld analysis where the number of refined variables
would become untenable for normal peak fitting.  Using convolution-based
fitting it is possible to cope with upwards of 10 phases with severe peak
overlap and still get good results with good stability. For example,
quantitative Rietveld analysis of cements is becoming routine.

Pam 

Dr Pamela Whitfield CChem MRSC
Energy Materials Group
Institute for Chemical Process and Environmental Technology
Building M12
National Research Council Canada
1200 Montreal Road
Ottawa  ON   K1A 0R6
CANADA
Tel: (613) 998 8462 Fax: (613) 991 2384
Email: 
ICPET WWW: http://icpet-itpce.nrc-cnrc.gc.ca


-Original Message-
From: Nandini Devi Radhamonyamma [mailto:[EMAIL PROTECTED]
Sent: June 4, 2004 6:42 AM
To: [EMAIL PROTECTED]


Dear All,


Is the fundamental parameter approach better than
mathematical approach used in most of the Rietveld
refinement programs? Does that mean programs which use
that approach are better? Any suggestions?

Nandini




__
Do you Yahoo!?
Friends.  Fun.  Try the all-new Yahoo! Messenger.
http://messenger.yahoo.com/ 

fundamental parameters approach

[Whitfield, Pamela]

Nandini

The best people to reply on behalf of fundamental parameters would be Alan
Coehlo or Arnt Kern.   
But until they do here goes

The more general form is convolution-based profile fitting.  This can be
used for all peak profile types, whereas 'pure' fundamental parameters has
only been inmplemented for the simple Bragg-Brentano case (no
monochromators).  Other geometries have to be empirically modelled using a
standard and some sort of user-defined convolution on top of the source
profile.  Better fits can often be obtained using this type of fitting than
the normal pseudo-Voigt or Pearson VII functions (in my experience at
least).  Where convolution-based fitting really comes into its own in in
complex quantitative Rietveld analysis where the number of refined variables
would become untenable for normal peak fitting.  Using convolution-based
fitting it is possible to cope with upwards of 10 phases with severe peak
overlap and still get good results with good stability. For example,
quantitative Rietveld analysis of cements is becoming routine.

Pam 

Dr Pamela Whitfield CChem MRSC
Energy Materials Group
Institute for Chemical Process and Environmental Technology
Building M12
National Research Council Canada
1200 Montreal Road
Ottawa  ON   K1A 0R6
CANADA
Tel: (613) 998 8462 Fax: (613) 991 2384
Email: 
ICPET WWW: http://icpet-itpce.nrc-cnrc.gc.ca


-Original Message-
From: Nandini Devi Radhamonyamma [mailto:[EMAIL PROTECTED]
Sent: June 4, 2004 6:42 AM
To: [EMAIL PROTECTED]


Dear All,


Is the fundamental parameter approach better than
mathematical approach used in most of the Rietveld
refinement programs? Does that mean programs which use
that approach are better? Any suggestions?

Nandini




__
Do you Yahoo!?
Friends.  Fun.  Try the all-new Yahoo! Messenger.
http://messenger.yahoo.com/ 

Re: indexing problem

[A. van der Lee]

> >The sample was in-situ crystallised by putting a drop of the mother
> >liquid on a silicon substrate and letting evaporate the solvent. This
> >should favour a random orientation of the crystallites, not?
> 
> Unfortunately NOT.
> I have seen preferential crystallization occurring exactly by doing
> the same kind of experiments.
> 
> Just put your sample under a microscope..
> 
You are absolutely right. I wonder now why I did not do that 
before... like I always do before starting a single-crystal 
diffraction experiment.

> Norberto (fully agreeing with Armel's opinion, and possessing some
> unindexed "2D" patterns as well)
> 
Well, it is my number one.
Arie


***
A. van der Lee
Institut Européen des Membranes (UMR 5635)
Université de Montpellier II - cc 047
Place E. Bataillon
34095 Montpellier Cedex 5
FRANCE

visiting address: 300 Av. Prof. E. Jeanbrau

tél.: 00-33-(0)4.67.14.91.35
FAX.: 00-33-(0)4.67.14.91.19
***

Re: fundamental parameters approach

[Jon Wright]

Is the fundamental parameter approach better than
mathematical approach used in most of the Rietveld
refinement programs? 

Perhaps someone is about to explain the difference is between 
"fundamental parameters" and anything else? I used to think it might 
mean convoluting something which was actually measured into the 
peakshape description, but this doesn't always seem to be the case? I'm 
guessing it has to be more than choosing suitable equations for peak 
width parameters and peak positions as a function of scattering 
variable, otherwise all programs are using fundamental parameters 
already, just some are better approximations for certain diffractometers 
than others.

In any case, if the calculated peakshape matches the observed peakshape 
then it makes no difference for refinement of a crystal structure. For 
deriving microstructural parameters, like "size" and "strain", then a 
better description of the instrument can help, and can be a good 
indicator of diffractometer misalignment. In that sense, zero shift is a 
fundamental parameter, but does not seem to be unique to "fundamental 
parameters" programs. Perhaps the difference is that programs which 
don't do "fundamental parameters" make you compute "size" and "strain" 
from the peakshape parameters yourself.

Jon

Re: indexing problem

[Dr. J. Bergmann]

Am Fr, 2004-06-04 um 14.38 schrieb [EMAIL PROTECTED]:
> Topas software is very good at solving such short axis problems.  The
> advantage is that it will look at all of the peaks you feed it,
> instead of using just the first twenty or so to generate candidate
> solutions (the way that ITO and TREOR work).
> 
The BGMN related programs use all refelctions as
available, too. They are distributed for free at
www.bgmn.de/related.html
Sorry, but there is no GUI available at this time,
unlike BGMNwin for the BGMN programs. You must 
bother with command line programs.

J"org Bergmann, Dresden

Re: indexing problem

[Yaroslav Filinchuk]

Try Chekcell and Truecell (they work as one program) to test your
solutions. You can import a list of solutions from a CRYSFIRE file.
The latter is generated by both Treor and/or Dicvol, if you run them
from Fullprof Suite. Or you can run any indexing program from
CRYSFIRE.

Best regards,
 Yaroslav Filinchuk


AvdL> Dear all,
AvdL> It is generally assumed that a high value of the M20 index gives a 
AvdL> high probability that the solution is correct. I have a particular 
AvdL> problem for which I have a couple of different solutions with M20 
AvdL> between 40 and 100. The problem resides in the fact that the a and c 
AvdL> axes of the monoclinic cell are much larger (both around 20 A) than 
AvdL> the b-axis (3-6A?) The solution depends therefore on the angular 
AvdL> range which is taken for the indexation process. Taking the first 20 
AvdL> reflections with significant intensity gives a 6A b-axis with the 010 
AvdL> reflection as the last one in the list. Taking 5 reflections more, 
AvdL> the length of the b-axis decreases and the 010 remains the last in 
AvdL> the list. And so on. The compound is organic and there is not much 
AvdL> scattering left beyond 2Theta=30degr, giving a total of 31 
AvdL> reflections to be used for the indexation.
AvdL> How to pick up the right solution between these high M20 solutions? 

AvdL> Thanks in advance, Arie
AvdL> ***
AvdL> A. van der Lee
AvdL> Institut Européen des Membranes (UMR 5635)
AvdL> Université de Montpellier II - cc 047
AvdL> Place E. Bataillon
AvdL> 34095 Montpellier Cedex 5
AvdL> FRANCE

AvdL> visiting address: 300 Av. Prof. E. Jeanbrau

AvdL> tél.: 00-33-(0)4.67.14.91.35
AvdL> FAX.: 00-33-(0)4.67.14.91.19
AvdL> ***

Re: indexing problem

[pstephens]

Topas software is very good at solving
such short axis problems.  The advantage is that it will look at all
of the peaks you feed it, instead of using just the first twenty or so
to generate candidate solutions (the way that ITO and TREOR work).

If you don't have access to Topas, I
suggest the following, which has been quite successful for me in the past.
 Use the two axes you have to completely index the zone that contains
the first reflections, and run a profile (Le Bail) fit using, e.g., fullprof.
 Put in a dummy b axis of 1 angstrom, so it doesn't generate any reflection
markers in the range of your data.  Refine the lattice parameters,
so you get a clear indication of which peaks belong to your first zone
and which do not.  The next step is to pray that your sample is monoclinic,
so you can leave alpha and gamma = 90, and you only have to determine the
lattice parameter b.  The first peak not indexed by your zone is probably
the (010), (110), (011), (111), or (-111), and you can quickly calculate
what the b parameter would have to be to fit each of those cases.  Type
it in, run another profile, and see which one works best.  If that
doesn't work, and you think your material is triclinic, it is still possible,
but you have to identify three (h 1 ell) peaks and suggest indexations
for them.  That needs at least half a dozen good peaks outside of
the first zone, and a little computer program to search the candidates.
 I don't know of any public domain software for that, but it's a good
project to give a student to help them learn about reciprocal space geometry.

Good luck,
Peter

~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~
Peter W. Stephens, Professor
Department of Physics & Astronomy
State University of New York
Stony Brook, NY 11794-3800

Re: indexing problem

[Norberto Masciocchi]

Following up the '2D' indexing..

The sample was in-situ crystallised by putting a drop of the mother
liquid on a silicon substrate and letting evaporate the solvent. This
should favour a random orientation of the crystallites, not?
Unfortunately NOT.
I have seen preferential crystallization occurring exactly by doing
the same kind of experiments.
Just put your sample under a microscope..
Norberto (fully agreeing with Armel's opinion, and possessing some
unindexed "2D" patterns as well)

Re: indexing problem

[A. van der Lee]

Dear Norberto,
Thanks for your rapid answer.
> The obvious way out from this second problem can be a different
> preparation of the sample, changing "texture coefficients", just
> aiming to detect the 'missing informative peaks'.
> 
The sample was in-situ crystallised by putting a drop of the mother 
liquid on a silicon substrate and letting evaporate the solvent. This 
should favour a random orientation of the crystallites, not?

> If, instead, the lattice metrics are such that one (short) axis can
> barely be identified (for short d's), (as it happens in many fully
> aromatic planar organics), you may want to 'constrain' this value
> by geometric, database, energetic, etc. considerations.
> 
> Even if unobservable at all, the short axis can indeed confidently
> estimated by density/volume calculations, etc.
> 
Good idea. Thanks.
Arie
***
A. van der Lee
Institut Européen des Membranes (UMR 5635)
Université de Montpellier II - cc 047
Place E. Bataillon
34095 Montpellier Cedex 5
FRANCE

visiting address: 300 Av. Prof. E. Jeanbrau

tél.: 00-33-(0)4.67.14.91.35
FAX.: 00-33-(0)4.67.14.91.19
***

Re: indexing problem

[Armel Le Bail]

How to pick up the right solution between these high M20 solutions?
No exact solution to that problem related to the "needle to
be found in a hay bundle."
The ultimate proof that a solution is the right one is to solve
the structure. Having only 31 hkls, this is not completely impossible
with an organic compound if you already know the molecular
formula. You "just have to" place that molecule inside of the
cell by a direct space approach. If really you believe that the
correct cell is in your list of possibilities, first eliminate of the list
those cells leading to a strange Z value. Then guess a space
group for every remaining cell, and apply either PSSP or
FOX or ESPOIR or DASH or etc.
Now, if you think that the chance is to 100% waste a lot
of time, I have a drawer almost full of such ambiguous cases.
There remains a small place for your problem ;-).
Armel

Re: indexing problem

[Norberto Masciocchi]

Dear Arie,
what you mention is a rather common occurrence, which may depend on
(at least) to factors:
a) the presence of a short axis or a dominant zone (making the whole
powder pattern indexable by a 2D reciprocal lattice)
b) sample morphology (say, needles) leading to a partial sampling
of the reciprocal lattice.
The obvious way out from this second problem can be a different
preparation of the sample, changing "texture coefficients", just
aiming to detect the 'missing informative peaks'.
If, instead, the lattice metrics are such that one (short) axis can
barely be identified (for short d's), (as it happens in many fully
aromatic planar organics), you may want to 'constrain' this value
by geometric, database, energetic, etc. considerations.
Even if unobservable at all, the short axis can indeed confidently
estimated by density/volume calculations, etc.
Otherwise, check consistency of the indexing by a Le Bail fit
and step-by-step increase of the short axis (the other two being
fixed at their nominal 'best' values).
Best Regards
Norberto
At 13.07 04/06/04 +0200, you wrote:
Dear all,
It is generally assumed that a high value of the M20 index gives a
high probability that the solution is correct. I have a particular
problem for which I have a couple of different solutions with M20
between 40 and 100. The problem resides in the fact that the a and c
axes of the monoclinic cell are much larger (both around 20 A) than
the b-axis (3-6A?) The solution depends therefore on the angular
range which is taken for the indexation process. Taking the first 20
reflections with significant intensity gives a 6A b-axis with the 010
reflection as the last one in the list. Taking 5 reflections more,
the length of the b-axis decreases and the 010 remains the last in
the list. And so on. The compound is organic and there is not much
scattering left beyond 2Theta=30degr, giving a total of 31
reflections to be used for the indexation.
How to pick up the right solution between these high M20 solutions?
Thanks in advance, Arie
***
A. van der Lee
Institut Européen des Membranes (UMR 5635)
Université de Montpellier II - cc 047
Place E. Bataillon
34095 Montpellier Cedex 5
FRANCE
visiting address: 300 Av. Prof. E. Jeanbrau
tél.: 00-33-(0)4.67.14.91.35
FAX.: 00-33-(0)4.67.14.91.19
***
--
Norberto Masciocchi, Prof.
Dipartimento di Scienze Chimiche ed Ambientali,
Università dell'Insubria, via Valleggio 11, 22100 Como (Italy)
Phone: +39-031-326227; FAX: +39-031-2386119
[EMAIL PROTECTED]
http://scienze-como.uninsubria.it/masciocchi/
--

indexing problem

[A. van der Lee]

Dear all,
It is generally assumed that a high value of the M20 index gives a 
high probability that the solution is correct. I have a particular 
problem for which I have a couple of different solutions with M20 
between 40 and 100. The problem resides in the fact that the a and c 
axes of the monoclinic cell are much larger (both around 20 A) than 
the b-axis (3-6A?) The solution depends therefore on the angular 
range which is taken for the indexation process. Taking the first 20 
reflections with significant intensity gives a 6A b-axis with the 010 
reflection as the last one in the list. Taking 5 reflections more, 
the length of the b-axis decreases and the 010 remains the last in 
the list. And so on. The compound is organic and there is not much 
scattering left beyond 2Theta=30degr, giving a total of 31 
reflections to be used for the indexation.
How to pick up the right solution between these high M20 solutions? 

Thanks in advance, Arie
***
A. van der Lee
Institut Européen des Membranes (UMR 5635)
Université de Montpellier II - cc 047
Place E. Bataillon
34095 Montpellier Cedex 5
FRANCE

visiting address: 300 Av. Prof. E. Jeanbrau

tél.: 00-33-(0)4.67.14.91.35
FAX.: 00-33-(0)4.67.14.91.19
***

fundamental parameters approach

[Nandini Devi Radhamonyamma]

Dear All,


Is the fundamental parameter approach better than
mathematical approach used in most of the Rietveld
refinement programs? Does that mean programs which use
that approach are better? Any suggestions?

Nandini




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