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All posts by AlanCoelho (288)

topic: Topas crash on combined Neutron and X-Ray refinement with magnetic structure  in the forum: Forums topas
AlanCoelho #1
Member since Aug 2011 · 288 posts
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Hi Mathias

Please send me a simplified version of your INP/data file and I will have a look.

Also, to work on only the x-ray part then remove the magnetic moment part; ie. something like the following will work:

 
  macro X_RAY_only { 1 }
   macro Mag_Stuff(text)
      {
         #if (X_RAY_only)
         #else
            text
         #endif
      }
   str
      site ...
         Mag_Stuff(mlx...)

cheer
alan
topic: pipe tc results (handle computed profile without writing to disk)  in the forum: Forums topas
AlanCoelho #2
Member since Aug 2011 · 288 posts
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In reply to post ID 2080
John is correct.
topic: "Exception Caught" error for sequential refinement ("Run_Number" limited by 10 bits?)  in the forum: Forums topas
AlanCoelho #3
Member since Aug 2011 · 288 posts
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In reply to post ID 2066
An update on the crash.

Jonas sent me 100 data files and all worked on my computer using TA.EXE and TC.EXE.

I then asked Jonas to use TC.EXE on the more than 1000 files and that worked on his computer.

I then changed the INP file to work with 1200 data files (loading the same 100 twelve times) and all worked with TA.EXE and TC.EXE.

I can only speculated that the text display of the Fit Windows is running out of Windows memory on his computer.

Thus in cases of 1000s of data files and a similar crash - its best to run the INP file using TC.EXE.

cheers
alan
topic: partial PDFs  in the forum: Forums topas
AlanCoelho #4
Member since Aug 2011 · 288 posts
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In reply to post ID 2067
The only way at present is to comment out the sites not wanted. The scaling can be simplified using pdf_scale_simple which outputs:

   S(r)/(Np r)

where Np is the number of atoms in the unit cell as determined by occ parameters and num_posns.
topic: Program crash  in the forum: Forums topas
AlanCoelho #5
Member since Aug 2011 · 288 posts
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In reply to post ID 2069
Hi Kipil


Is the crash happening all the time on a particular INP file; if yes then send me the INP and data file.

If the crash is happening randomly on the same INP file then again still send me the INP and data file.

If the crash is happening randomly then this is odd and you need to describe more like whats the operating system etc...

cheers
alan
topic: ai_no_self_interation not helping atoms to go to special positions during SA  in the forum: Forums structure solution
AlanCoelho #6
Member since Aug 2011 · 288 posts
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In reply to post ID 2054
Hi Magnus

For two atoms O1 and O2 say, then to remove a distance penalty using sites_distance then you would use the following:

      sites_distance d_o1_o2 load site_to_restrain { O1 O2 }
            local = d_o1_o2; : 0 ' report the distance
            penalty = If (d_o1_o2 < 0.5, 0, (d_o1_o2 - 0.5)^2);

You can further scale the penalty relative to other penalty depending on what you are doing.

If using atomic_interaction then you would write a similar equation; ie.

      atomic_interaction d_o1_o2 = If(R < 0.5, 0, (R - 0.5)^2);
            ...

cheers
alan
topic: "Exception Caught" error for sequential refinement ("Run_Number" limited by 10 bits?)  in the forum: Forums topas
AlanCoelho #7
Member since Aug 2011 · 288 posts
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In reply to post ID 2064
Its not possible to determine why the INP file crashes at run number 1024 by simply looking at the INP file. Can you e-mail me the INP file with 100 data files in the list and include the file that is run number 1024.

Apart from that the above the parameter with out hard limits are the parameters in the following macros:

   TCHZ_Peak_Type
   Specimen_Displacement

and the a_bgg lattice parameter.  The parameters have "moving window limits" ie.

      If_Prm_Eqn_Rpt(u, uv, min = Max(-1, Val-.1); max = Min(2, Val+.1); del 1.0e-4)
      etc...

Does the parameter output file show any parameters going astray.
topic: "Exception Caught" error for sequential refinement ("Run_Number" limited by 10 bits?)  in the forum: Forums topas
AlanCoelho #8
Member since Aug 2011 · 288 posts
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In reply to post ID 2058
Run_Number is a double precision number, not 10 bits.

The exception caught could be anything such as no min/max limits on lattice parameters for example.

If the exception-caught always happen at Run_Number 1024 then that INP file is causing the crash. Post a stripped down version of that INP file and I will have a closer look. Or, e-mail to me the simplified INP file with the data file in question.

cheers
alan
topic: ai_no_self_interation not helping atoms to go to special positions during SA  in the forum: Forums structure solution
AlanCoelho #9
Member since Aug 2011 · 288 posts
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In reply to post ID 2050
Hi Magnus

ai_no_self_interation is not working. The bug has been foxed for Version 7 to be released in the future but fir teh present
and I can only reommend a work-aroud. The work-aroud involves writing neagtive penalties for self interactions.

For example, consder three sites:

    site Cl1
    site Cl2
    site Na1

    atomic_interaction ai1 ... 
        ai_sites_1 Cl*
        ai_sites_2 Cl*
        ...
        penalty = ai1;
       
If you wanted to have ai_no_self_interation ON then include penalties to cancel out the self intercatiions; ie.

    atomic_interaction ai1_1 ... 
        ai_sites_1 Cl1
        ai_sites_2 Cl1
        ...
        penalty = -ai1_1;
       
    atomic_interaction ai1_2 ... 
        ai_sites_1 Cl2
        ai_sites_2 Cl2
        ...
        penalty = -ai1_2;

cheers
alan
topic: ai_no_self_interation not helping atoms to go to special positions during SA  in the forum: Forums structure solution
AlanCoelho #10
Member since Aug 2011 · 288 posts
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In reply to post ID 2049
Hi Magnus

You have found a bug; I will do some more investigations and then get back to you. Apologies for the inconvenience and strange this has not been brought to my attention.

cheers
alan
topic: Saving results using parametric refinement  in the forum: Forums topas
AlanCoelho #11
Member since Aug 2011 · 288 posts
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In reply to post ID 2044
John is probably correct; how many independent parameters are there and is do_errors ON.

If there are more than about 5000 parameters then the singular value decomposition matrix inversion used (when calculating errors) may well be taking the time.

In such cases use the boot strap method of error determination.
topic: applying instrumental corrections directly to data  in the forum: Forums topas
AlanCoelho #12
Member since Aug 2011 · 288 posts
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In reply to post ID 2040
TOPAS cant apply convolutions to observed data. It would be a simple thing to implement using the 'user_y' keyword and then allowing convolutions on fit_objs. However, the only work around is to fit many peaks to teh observed data and then convolution what you want into the newly calculated pattern.

To describe the observed data exactly then insert a peak at each data point; fix the peak shapes and then refine the intensities. From there convolution into the calculated pattern can proceed.
topic: Rwp lower than Rexp  in the forum: Forums topas
AlanCoelho #13
Member since Aug 2011 · 288 posts
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In reply to post ID 2039
Hi Hanna

The formula for Rwp is given in Technical_Reference.PDF in the section headed "Criteria of fit".

>How does TOPAS determine weights in the absence of errors

The default weighting is as follows:

   weighting = 1 / Max(Yobs, 1);

cheers
alan
topic: Custom Scattering Factors  in the forum: Forums topas
AlanCoelho #14
Member since Aug 2011 · 288 posts
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In reply to post ID 2037
Search the Technical_Reference.PDF for f0_f1_f11_atom. This keyword allows for user defined atomic scattering factors which can then be refined.
topic: append str peak multiplicites, 2Th, and F^2 to input file?  in the forum: Forums topas
AlanCoelho #15
Member since Aug 2011 · 288 posts
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In reply to post ID 2008
Related to your question is th keyword I_parameter_names_have_hkl int which can assign names to intensities of a hkl_Is phase.
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