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All posts by johnsoevans (221)

topic: Incommensurable magnetic structure  in the forum: Forums topas
johnsoevans (Administrator) #1
User title: John Evans
Member since Aug 2009 · 221 posts
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Incommensurate isn't possible.  The only thing you can try is an approximate commensurate superstructure appropriately constrained.  JANA or FULLPROF are probably better options for this.
topic: Inquiry scale_pks = D_spacing^4  in the forum: Forums topas
johnsoevans (Administrator) #2
User title: John Evans
Member since Aug 2009 · 221 posts
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In reply to post ID 2099
This is the Lorentz factor for a time of flight data set.  It should be d^4 unless data have been transformed in some way.
topic: plot slice through fourier_map?  in the forum: Forums structure solution
johnsoevans (Administrator) #3
User title: John Evans
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In reply to post ID 2092
Vesta lists its formats in the manual.  .grd is on P136.  Nothing particular to recommend that specific format, just that it's familiar from e.g. rmcprofie.  You'd need access to map values to write a .grd file......

https://jp-minerals.org/vesta/archives/VESTA_Manual.pdf

I haven't looked at the fcf for>15 years but list 3 rings vague bells.  I've pasted something below which was on my hard drive called "topas_works.fcf" and dated 2003.  Please check carefully though....I haven't got proper notes to hand to be sure it was correct.

John

data_
_shelx_refln_list_code          3
_cell_length_a 2.8599
_cell_length_b 14.64044
_cell_length_c 5.25965
_cell_angle_alpha 90
_cell_angle_beta  90
_cell_angle_gamma 90
_shelx_F_squared_multiplier 1
loop_
_symmetry_equiv_pos_as_xyz
    '-x, -y, z+1/2'
    '-x, y, z'
    'x, -y, z+1/2'
    'x, y, z'
    '-x+1/2, -y+1/2, z+1/2'
    '-x+1/2, y+1/2, z'
    'x+1/2, -y+1/2, z+1/2'
    'x+1/2, y+1/2, z'
loop_
_refln_index_h
_refln_index_k
_refln_index_l
_refln_F_meas
_refln_F_sigma
_refln_A_calc
_refln_B_calc
   0   2   0        4.74        0.00        5.43        0.00
   0   2   1        1.82        0.00        0.63       -1.34
   0   4   0        4.25        0.00        4.60        0.00
   0   4   1        1.71        0.00        0.72        1.13
   1   1   0        5.04        0.00        3.93       -0.00
...etc
topic: Topas crash on combined Neutron and X-Ray refinement with magnetic structure  in the forum: Forums topas
johnsoevans (Administrator) #4
User title: John Evans
Member since Aug 2009 · 221 posts
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In reply to post ID 2089
I think this is only possible with a "mag_only_for_mag_sites" str.  You should be able to do mag_only_for_mag_sites with either Shubnikov or distortion mode approaches.
topic: Topas crash on combined Neutron and X-Ray refinement with magnetic structure  in the forum: Forums topas
johnsoevans (Administrator) #5
User title: John Evans
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In reply to post ID 2087
Just for the record.....I didn't realise how easy the solution was until I talked to Alan :-) !
topic: plot slice through fourier_map?  in the forum: Forums structure solution
johnsoevans (Administrator) #6
User title: John Evans
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In reply to post ID 2085
Matthew,

I don't know a way off hand.  Before Topas had its built in viewer we used to export .fcf files to external single crystal software packages to calculate and replot Fourier maps.  These allowed slices.  I think we used wingx, but there are other packages.

If I was doing it now I'd probably be trying to get the map into .grd format for vesta. 

John
topic: Topas crash on combined Neutron and X-Ray refinement with magnetic structure  in the forum: Forums topas
johnsoevans (Administrator) #7
User title: John Evans
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In reply to post ID 2083
Dear Mathias,

You probably have this sorted by now. Just in case, I put an example of doing a magnetic neutron plus X-ray at the end of the magnetism tutorial:

http://community.dur.ac.uk/john.evans/topas_workshop/tutor…

The INP file with "if Obj_There(neutron)" is at:

http://community.dur.ac.uk/john.evans/topas_workshop/data/…

John
topic: pipe tc results (handle computed profile without writing to disk)  in the forum: Forums topas
johnsoevans (Administrator) #8
User title: John Evans
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In reply to post ID 2078
A file write is the only way I know.
topic: Distortion mode refinement, strain, lattice parameters  in the forum: Forums topas
johnsoevans (Administrator) #9
User title: John Evans
Member since Aug 2009 · 221 posts
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In reply to post ID 2072
Chloe,

Do you really need to refine the strain directly?

You should just be able to refine a/b/c/al/be/ga in the same way as you would for a conventional refinement.  i.e. fix al/ga to 90.  Just check that the low symmetry description is in a standard b-unique monoclinic setting.

John
topic: How to Use remove_phase Keyword in TOPAS 6  in the forum: Forums topas
johnsoevans (Administrator) #10
User title: John Evans
Member since Aug 2009 · 221 posts
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In reply to post ID 2057
I've never personally used the remove phase option.  I've always preferred to set the file up in such a way that if a phase disappears its scale factor refines to zero (within uncertainty).  This can be done parametrically or often more simply by equating peak shapes etc between phases (to stop peaks becoming extremely broad and correlating with scale factors).  There's a bit on this in chapter 12 of the Rietveld/Topas book.

You can also set up phases for different ranges manually.  e.g. the book has this example code in it:

' Phase boundaries
#prm t = 100 + (Run_Number 4);   ‘Temperature = 100 + Run_Number * 4
#if Or(t < 158, t > 226);
   #define Phase1
#elseif And(t > 158, t < 198);
   #define Phase1
   #define Phase2
#elseif And(t > 198, t < 226);  
   #define Phase2
#endif
...
#ifdef Phase1
          str
         ...
#endif
topic: Rietveld Refinement Negative Peak Value  in the forum: Forums topas
johnsoevans (Administrator) #11
User title: John Evans
Member since Aug 2009 · 221 posts
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In reply to post ID 2059
Do you really mean the calculated intensity of the peak is negative, or do you men the intensity is lower then observed?  The only way that calculated peaks can be negative is if you're applying a preferred orientation correction that has refined to extreme values.
topic: Topas 6, running tc via Python subprocess  in the forum: Forums topas
johnsoevans (Administrator) #12
User title: John Evans
Member since Aug 2009 · 221 posts
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In reply to post ID 2055
We've used python to control topas v6 in the past without issues, so I'm not aware of any fundamental issues.  The tutorial at http://community.dur.ac.uk/john.evans/topas_workshop/tutor… used this approach.
topic: Rwp lower than Rexp  in the forum: Forums topas
johnsoevans (Administrator) #13
User title: John Evans
Member since Aug 2009 · 221 posts
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In reply to post ID 2039
Some of the Rietveld texts discuss why you can sometimes get unusual Chi^2 values (either much greater than one or less than one).  Missing experimental uncertainties from the DAC data could be one cause.  Was your file initially an .xye file?
You might look at Lynn McCusker et al's Rietveld guidelines paper: J. Appl. Cryst. 1999, 32, 36-50.  It discusses some of the common issues with Rwp.
topic: Saving results using parametric refinement  in the forum: Forums topas
johnsoevans (Administrator) #14
User title: John Evans
Member since Aug 2009 · 221 posts
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In reply to post ID 2043
Dear Florian,

It shouldn't take that long.  Do you have do_errors turned on?  You might try without errors.

John
topic: Distortion analysis  in the forum: Forums structure solution
johnsoevans (Administrator) #15
User title: John Evans
Member since Aug 2009 · 221 posts
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In reply to post ID 2030
Hi Matthew,

Three possibilities if it's not easy to spot by eye:

1. For most of the "classic" structure types the aristotype is normally well known.  If it's less obvious you could look in the icsd and find the highest symmetry report for your structure type.  e.g. try the ANX/AB type formula or structure type search.
2. You could try a routine like "findsym" (part of the ISODISTORT suite) or one of the Bilbao routines with a high tolerance.  You could try this after making some coordinates closer to special values.  e.g. if you had an O at 0.23 you might move it to 0.25.
3. Parents don't always have to be real or even realistic structures.  Sometimes it can be convenient to increase symmetry to something that no longer makes chemical sense.  I don't think there's a recipe for that other than intuition.
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