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All posts by AlanCoelho (302)

topic: Negative FWHM encountered  in the forum: Forums topas
AlanCoelho #1
Member since Aug 2011 · 302 posts
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You could output the total gauss_fwhm and total lor_fwhm by getting the lor_conv and gauss_conv objects and using phase_out; ie.

      phase_out file append load out_record out_fmt out_eqn
      {
          "%4.0f " = H;
          "%4.0f " = K;
          "%4.0f " = L;
          " %9g   " = Get(lor_conv);
          " %9g\n" = Get(gauss_conv);
      }

If using pv peak types the you can simply output the pv_fwhm parameter using phase_out.

Cell parameters should have limits especially for small weight_percents.
topic: Negative FWHM encountered  in the forum: Forums topas
AlanCoelho #2
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In reply to post ID 2152
In V6 the keyword force_positive_fwhm can be used. Be careful as it modifies the meaning of your equations. IMO the cause of the negative FWHM should be identified rather than use force_positive_fwhm.
topic: x_calculation_step vs convolution_step  in the forum: Forums topas
AlanCoelho #3
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In reply to post ID 2148
There is a difference.

The x_calculation_step applies to all equations involving Ycalc.

convolution_step changes the peak_calculation_step which affects convolutions only.

convolution_step also divides the peak_calculation_step such that the original data points coincide with the new data points.

The above means that using convolution_step is a lot quicker than using changing x_calculation_step; additionally it is more accurate if x_calculation_step does not have the new data points coinciding with the original data points.
topic: Uninitialized_Variable  in the forum: Forums indexing
AlanCoelho #4
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In reply to post ID 2146
I get all peaks refining.

Can you contact me off the TOPAS wiki please.
topic: Uninitialized_Variable  in the forum: Forums indexing
AlanCoelho #5
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In reply to post ID 2144
Using V5, I just ran your INP file on a local PbSO4.RAW file and all seemed to have worked; the output I get is:

Non-linear least squares (c) 1992-2014 Alan A. Coelho
Loading C:\c2\t5-ta5\ta-web2\topas.inc
Number of independent parameters : 65
  0  Time   0.19  Rwp   99.906    0.000 MC   0.00 0
Loading C:\c2\t5-ta5\ta-web2\topas.inc
Loading C:\c2\t5-ta5\ta-web2\interface.inc
Sparse matrix methods invoked - 66.7% of the A matrix elements are zero
  1  Time   0.26  Rwp   95.440   -4.466 MC   0.96 3
  2  Time   0.26  Rwp   77.978  -17.462 MC   0.17 1
  3  Time   0.26  Rwp   69.862   -8.116 MC   0.04 1
  4  Time   0.26  Rwp   69.736   -0.125 MC   2.42 1
  5  Time   0.27  Rwp   66.280   -3.457 MC   0.31 1
  6  Time   0.27  Rwp   63.230   -3.050 MC   0.07 1
  7  Time   0.27  Rwp   59.558   -3.671 MC   0.02 1
  8  Time   0.28  Rwp   55.714   -3.845 MC   0.14 1
  9  Time   0.29  Rwp   46.998   -8.716 MC   0.04 1
 10  Time   0.29  Rwp   43.574   -3.423 MC   0.01 1
 11  Time   0.30  Rwp   37.699   -5.875 MC   0.00 1
 12  Time   0.31  Rwp   33.413   -4.286 MC   0.00 1
 13  Time   0.32  Rwp   29.495   -3.918 MC   0.16 2
 14  Time   0.32  Rwp   27.000   -2.495 MC   0.04 1
 15  Time   0.34  Rwp   26.919   -0.081 MC   0.01 1
 16  Time   0.35  Rwp   26.918   -0.000 MC   2.13 2
--- 0.355 seconds ---

*** Parameter(s) close to limit(s).
    Check for LIMIT_MIN and LIMIT_MAX in Grid/Text
File C:\c\t5\test_examples\aac.out updated
    with parameters from last iteration

Process Times (secs)
    0.02 = Ycalc calculation and Penalties
    0.00 = Summing peaks to Ycalc
    0.02 = A and Y matrix dot products and derivatives
    0.01 = Peak buffer derivatives
    0.00 = A and Y matrix dot products
    0.00 = Solution to the normal equations

The error seems like a licensing problem. Can you run any of the test examples.
topic: Exception Caught  in the forum: Forums indexing
AlanCoelho #6
Member since Aug 2011 · 302 posts
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In reply to post ID 2141
The error doesn't help much. Does the program work in a test_example, does the following run:

tc indexing\ex2
topic: Exception Caught  in the forum: Forums indexing
AlanCoelho #7
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In reply to post ID 2134
I ran indexing twice on your INP file using V5 and the GUI and all seems ok.

Can you run using TC.EXE to check if its the GUI.
topic: Output a single quote into a file  in the forum: Forums topas
AlanCoelho #8
Member since Aug 2011 · 302 posts
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In reply to post ID 2135
There's no way to do what you want from the INP file. You can however work around it as follows:

Output a special character (ie. £) instead of ' to the file you are writing to (lets call this out_file.txt)

From the command line, replace the special character using the following batch file (copy the following text to a file called rep.bat):


@echo off
REM -- Prepare the Command Processor --
SETLOCAL ENABLEEXTENSIONS
SETLOCAL DISABLEDELAYEDEXPANSION
::BatchSubstitude - parses a File line by line and replaces a substring"
::syntax: BatchSubstitude.bat OldStr NewStr File
::          OldStr [in] - string to be replaced
::          NewStr [in] - string to replace with
::          File   [in] - file to be parsed
:$changed 20100115
:$source https://www.dostips.com
if "%~1"=="" findstr "^::" "%~f0"&GOTO:EOF
for /f "tokens=1,* delims=]" %%A in ('"type %3|find /n /v """') do (
    set "line=%%B"
    if defined line (
        call set "line=echo.%%line:%~1=%~2%%"
        for /f "delims=" %%X in ('"echo."%%line%%""') do %%~X
    ) ELSE echo.
)


rep.bat is from DOStips.com. Here's how to use it:

   rep £ ' out_file.txt > out_file_new.txt

cheers
alan
topic: Generating rigid bodies from CIF  in the forum: Forums topas
AlanCoelho #9
Member since Aug 2011 · 302 posts
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In reply to post ID 2131
Another way is to describe the  CIF coordinates using point_for_site within a rigid body. Place the atoms in the Rigid Body Editor  and then use the "First guess z-matrix". I'm not sure how good the "First guess z-matrix" would be but it may be as good as any other guess.
topic: R Bragg over 99% (Simultaneous Rietveld & PDF refinement in sequential mode of synchrotron data)  in the forum: Forums topas
AlanCoelho #10
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In reply to post ID 2128
Thanks for looking into that Matthew.

Negative intensities would play havoc in the Io formula:

   Io(hkl) = Sum[ Peak(i) Yobs(i)/Yc(i), i]

I think it would be best to set the intensities to zero.
topic: R Bragg over 99% (Simultaneous Rietveld & PDF refinement in sequential mode of synchrotron data)  in the forum: Forums topas
AlanCoelho #11
Member since Aug 2011 · 302 posts
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In reply to post ID 2125
Hi Xavier

I got the XY files but I don't see the INP file attached. Can you e-mail me the INP file please
cheers
alan
topic: R Bragg over 99% (Simultaneous Rietveld & PDF refinement in sequential mode of synchrotron data)  in the forum: Forums topas
AlanCoelho #12
Member since Aug 2011 · 302 posts
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In reply to post ID 2117
R-Bragg in terms of the observed intensity Io and calculated intensity Ic is defined as:

R-Bragg = Sum[ Abs(Io(hkl) - Ic(hkl)), hkl ] / Sum[Io(hkl), hkl ]

where

    Io(hkl) = Sum[ Peak(i) Yobs(i)/Yc(i), i]
   
    Peak(i) = a scaled hkl peak

        and the summations are over all hkls

To get high R-Bragg values then Sum[Io(hkl), hkl ] is probably close to zero. Which means that all of Peak(i) intensities are close to zero.

In other words the phase is non-existent. You may instead want to plot the scale parameter for that phase and see how that changes.

cheers
alan
topic: Anisotropic refiement with ADPs_Keep_PD  in the forum: Forums structure solution
AlanCoelho #13
Member since Aug 2011 · 302 posts
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In reply to post ID 2098
I just looked and the macro seems to be in error; ie.

    move_to u11 min 0
    move_to u22 min 0
    move_to u33 min 0
    move_to u12 min = -Sqrt(Get(u11) Get(u22)); max = Sqrt(Get(u11) Get(u22));
    move_to u13 min = -Sqrt(Get(u11) Get(u33)); max = Sqrt(Get(u11) Get(u33));
    move_to u23 min = -Sqrt(Get(u22) Get(u33)); max = Sqrt(Get(u22) Get(u33));

It should be:

    move_to u11 min 0
    move_to u22 min 0
    move_to u33 min 0
    move_to u12 min 0 max = Sqrt(Get(u11) Get(u22));
    move_to u13 min 0 max = Sqrt(Get(u11) Get(u33));
    move_to u23 min 0 max = Sqrt(Get(u22) Get(u33));

Please make the change and see what happens.

cheers
alan
topic: Crystallite size wrong values (What is the reason for my Crystallite size always reach the maximum value in the TOPAS macro?)  in the forum: Forums topas
AlanCoelho #14
Member since Aug 2011 · 302 posts
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In reply to post ID 2094
The larger the values the smaller the effects. In other words large crystals result in small peak broadening and large errors in the crystallite size.
topic: Topas crash on combined Neutron and X-Ray refinement with magnetic structure  in the forum: Forums topas
AlanCoelho #15
Member since Aug 2011 · 302 posts
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In reply to post ID 2081
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
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