Re: [Ifeffit] EXAFS analysis with FEFF

2007-02-27 Thread Bruce Ravel

Hi Gemma,

I am not sure that I have the whole answer for you.  I too have had
trouble at times getting feff8 to run with hydrogen atoms in the
cluster.  I am CCing my response to the mailing lists for Feff and
Ifeffit in hopes that someone else might have some more wisdom for
you.   The feff.inp file you sent me is appended to the end of this
email, in case any of the brains on the mailing lists need to see it. 

On Tuesday 27 February 2007 11:27, Gemma GUILERA wrote:
 I am currently running FEFF8.2 for one of my systems which include some H
 atoms (as hydrides). These are actually very important in the structure and
 I want to consider them in the run.
 For this I used the FOLP function in POT  with an overlapping value of 0.8
 for H as suggested in the manual. Also, since I think that the AFOLP card
 gets deactivated, I also added these cards for the rest of the potentials
 keeping them at 1.15.
 I obviously do something completely wrong because the program stops and
 appears an error message of the type:

 FOLP for POTENTIAL type   0 is too big.
   Reduce overlap using FOLP and rerun.

 I do not understand what I need to do, because the potential 0 is not the
 one I am modifying with respect to the default values.
 I would really appreciate if you could have a look at the feff.inp file and
 tell me what did I do wrongly...and sorry for wasting your time.

Well, my understanding is that Feff's various overlapping methods do
have effects that are not restricted to the ipots that you are
explicitly modifying.  That is, if you restrain the size of one muffin
tin, other muffin tins can get a bit bigger or smaller to compensate.
It depends on the geometry and how the atom you are modifying is
represented in the cluster.

My first thought is that you need to play around with the FOLP value
for the absorber.  Try smaller values to see if you can get Feff to
run to completion.

My second thought is to abandon the FOLP keywords and try using
AFOLP. 

Another thought is that you may need to use a larger cluster.  Some
atom types -- B for example -- have few representatives in your
cluster and so their muffin tin radii might be improperly constrained.

Does anyone else have any good suggestions for Gemma?

B



 
 TITLE   FeBH6Fe complex
  
 EDGE  K
 S02   1.0

 * potxsph  fms   paths genfmt ff2chi
 CONTROL   1  1 1 1 1  1
 PRINT 1  0 0 0 0  3
  
 * r_scf   [ l_scf  n_scf  ca ]
 SCF   2.90160   0  15 0.1

 * ixc  [ Vr  Vi ]
 EXCHANGE  0  0   0

 FOLP  0  1.15
 FOLP  1  0.8   !Use 0.8 muffin-tin radii overlapping factor for H
 FOLP  2  1.15
 FOLP  3  1.15
 FOLP  4  1.15
 FOLP  5  1.15

 EXAFS
 RPATH 6

 * kmax  [ delta_k  delta_e ]
 *XANES 4.0 0.07 0.5
 * r_fms [ l_fms ]
 *FMS   2.90160 0
 *
 *RPATH 0.1
 * emin  emax  resolution
 *LDOS  -2020   0.1

 POTENTIALS
 *   ipot   z [ label   l_scmt  l_fms  stoichiometry ]
   0   26Fe -1  -1   0
   11H  -1  -1   6
   25B  -1  -1   1
   3   15P  -1  -1   6
   46C  -1  -1  46
   5   26Fe -1  -1   2
  
 ATOMS
   0.0 0.0 0.00   Fe1  0.0
  -0.71680-1.08741-0.207971   H42  1.31891
  -1.33000 0.40717 0.041901   H41  1.39156
  -0.20933-0.03121-1.569771   H40  1.58398
  -1.50973-0.47766-1.071962   B1   1.91221
   0.07929-0.26849 2.163493   P3   2.18152
   0.78129 2.03650 0.109393   P2   2.18397
   2.03623-0.76920-0.204403   P1   2.18625
  -2.30265 0.13209-1.935941   H42  3.01123
  -2.81012-0.92412-0.574141   H40  3.01338
  -1.68946-1.36249-2.185811   H41  3.08033
   3.15055-0.21476 1.167744   C22  3.36686
   0.19242-2.02477 2.690824   C25  3.37301
   2.87884-0.31857-1.754624   C13  3.38643
   1.52559 0.58481 2.968484   C24  3.38840
   2.32803 2.20201 1.140034   C49  3.40121
  -0.35734 3.30346 0.817734   C37  3.42188
   1.28771 2.89227-1.433624   C43  3.47544
   2.68114 0.97735 2.028274   C23  3.50109
  -1.29194 0.30124 3.242464   C31  3.50334
   2.42741-2.57443-0.173954   C1   3.54263
   1.08472 2.33572-2.686974   C48  3.72183
  -2.31005 1.13130 2.753524   C36  3.76803
  -3.01946-0.95533-2.143915   Fe1  3.82441
  -0.91239-2.83347 2.421084   C26  3.83701
   1.44841-3.56032

Re: [Ifeffit] Fwd: Re: why ss_2 is negative?

2007-02-27 Thread Carlo Segre

Hello Hao:

I took a look at your fits _very_ briefly.  Just a couple of things to 
note.

The range of chi(k) which you use in the fit is probably a bit large. 
You are starting at 2.1 and the data at that point is really not usable. 
I would start at 3 or so.  On the high end, it seems OK.

The estimated standard deviations on lots of your parameters are very 
large, on the order of the parameter values themselves.  This is a red 
flag and it generally indicates that the fit has too many variables.  This 
is the biggest concern that I have.  Look at the values:

   dr  = 0.0010050   +/-  0.0111490
   ss  = 0.0031940   +/-  0.0021850
   dr_1= 0.0464110   +/-  0.1100960
   ss_1= 0.0130090   +/-  0.0188820
   dr_2= 0.0896690   +/-  0.0765040
   ss_2= 0.0043400   +/-  0.0106960
   n1  = 3.3690270   +/-  3.5237430

most of these values are indistinguishable from zero.  (As an aside, are 
you getting an error box when you try to fit?  The parameter dr is not 
allowed in newer versions of Artemis.)  Here is my suggestion:

Change the chi(k) range to 3-13.2.  Change the fitting range to 1-2.65 or 
so.  Link the ss_1 and ss_2 parameters together and set dr to 0.0 as it is 
basically there already and has a large uncertainty.

By doing this you will have reduced significantly the number of parameters 
and the uncertainties will be more manageable.  More importantly, when you 
work on a model, start with a more highly constrained one (fewer paths, 
for example) and try to work your way up while always making sure that the 
results make sense.  You will be able to reduce the parameter space that 
you have to cover this way.  Keep a close eye on the Reduced Chi-square 
as you add more guess parameters.  If it goes up, you may be 
overreaching on your model even though the R-factor goes down!

HTH

Carlo


-- 
Carlo U. Segre -- Professor of Physics
Associate Dean for Special Projects, Graduate College
Illinois Institute of Technology
Voice: 312.567.3498Fax: 312.567.3494
[EMAIL PROTECTED]   http://www.iit.edu/~segre   [EMAIL PROTECTED]
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