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All posts by johnsoevans (231)

topic: Symmetry mode analysis - min max  in the forum: Forums structure solution
johnsoevans (Administrator) #1
User title: John Evans
Member since Aug 2009 · 231 posts
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Dear Ross,

As you say, you can't put penalties on dependent parameters to my knowledge. 

When we did similar things in the past (e.g. some of the Ln2O2ZnSe2 type materials) we used penalties of the type you suggest.  I think we did a combination of conditional penalties on individual sites (e.g. if occ<0.25 set to zero) and/or penalties on the overall composition.  There will obviously be some instabilities associated with conditional penalties.  One we had the right answer we could remove the penalties.

John
topic: Define strings in TOPAS  in the forum: Forums topas
johnsoevans (Administrator) #2
User title: John Evans
Member since Aug 2009 · 231 posts
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In reply to post ID 2212
Dear Hanna,

have you looked at:

http://topas.dur.ac.uk/topaswiki/doku.…?id=string_equati…
http://topas.dur.ac.uk/topaswiki/doku.…?id=concatenate_s…

John
topic: Error int Topas V4.2 with rigid and prm  in the forum: Forums structure solution
johnsoevans (Administrator) #3
User title: John Evans
Member since Aug 2009 · 231 posts
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In reply to post ID 2190
You need to include more of your INP file so people cans see where the error might be.
topic: Reading filenames in sequential refinements  in the forum: Forums topas
johnsoevans (Administrator) #4
User title: John Evans
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In reply to post ID 2185
Does it run with the data files in the same  directory?  If not, the error  may be somewhere else in the INP
file.
topic: Reading filenames in sequential refinements  in the forum: Forums topas
johnsoevans (Administrator) #5
User title: John Evans
Member since Aug 2009 · 231 posts
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In reply to post ID 2183
Hanna,

What you have ought to work from a quick glance.

This doesn't directly answer your question, but the lines below work in one INP file I have handy.  I often set things up with the data_directory in a separate macro as it can speed things up when moving between different computers. 

John

[#list section like yours then....]

macro data_directory { C:\data\iid22_experiment\ma0001_exp001_002\ }
macro filename { File_Name(Run_Number) }
macro filename_use {data_directory##filename}

xdd filename_use
topic: refinement of partially crystallized sample  in the forum: Forums topas
johnsoevans (Administrator) #6
User title: John Evans
Member since Aug 2009 · 231 posts
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In reply to post ID 2172
Yes.

If you do a google search of "amorphous content topas" it will lead you to a couple of papers by Jim Cline and Pam Whitfield.  If you search the topas tech ref or the wiki for "amorphous" you'll get the topas keywords.  There's also discussion in (e.g.) the chapter by Nikki Scarlett and Ian Madsen in the Dinnebier/Billinge book.
topic: Issues with conditional modification of a variable using IF  in the forum: Forums topas
johnsoevans (Administrator) #7
User title: John Evans
Member since Aug 2009 · 231 posts
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In reply to post ID 2161
I haven't looked at your specific example in detail.  I find the best way to learn/remember topas syntax is to look in "topas.inc" which contains 2500 lines of topas macros.  There's normally a similar example, and it's often easier to find things than in "tech ref".  It's in the main topas directory or via Topas_Durham_Menus/Help/Alans macros if you use jEdit.  Just be careful not to change the file when you read it (perhaps make yourself a backup copy).

There are 21 "If(" statements in there.

jEdit tip: highlight the text you're interested in the hit alt-fullstop.
topic: R Bragg over 99% (Simultaneous Rietveld & PDF refinement in sequential mode of synchrotron data)  in the forum: Forums topas
johnsoevans (Administrator) #8
User title: John Evans
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In reply to post ID 2123
If changing 2theta or d range had an effect it might be worth plotting esd vs X. Are there any rogue data points or esds in the xye file?
topic: R Bragg over 99% (Simultaneous Rietveld & PDF refinement in sequential mode of synchrotron data)  in the forum: Forums topas
johnsoevans (Administrator) #9
User title: John Evans
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In reply to post ID 2116
Nothing obvious springs to mind.
Do you get the same behaviour if you run one of the misbehaving refinements again?
What happens if you change the finish_X slightly?
topic: Generating rigid bodies from CIF  in the forum: Forums topas
johnsoevans (Administrator) #10
User title: John Evans
Member since Aug 2009 · 231 posts
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In reply to post ID 2113
Chris,

It's not clear whether your issue is how to create a z-matrix description or how to map a z-matrix description onto your cif format solution.

Have you looked at: https://github.com/mspillman/zmatrix-to-inp?

My recollection is that it uses dash to create the rigid bodies from a dash-output cif, but you could do the same with your cif.

There's a z-matrix thread on using topas' rigid body editor to create the z-matrix at: http://topas.dur.ac.uk/unb/forum.php?req=thread&id=362

The book has some hints on how to map the z-matrix rigid body onto your cif coordinates, or there's an outline on the wiki at: http://topas.dur.ac.uk/topaswiki/doku.…?id=matching_a_ri…

Hope that's some help.

John
topic: Incommensurable magnetic structure  in the forum: Forums topas
johnsoevans (Administrator) #11
User title: John Evans
Member since Aug 2009 · 231 posts
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In reply to post ID 2101
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) #12
User title: John Evans
Member since Aug 2009 · 231 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) #13
User title: John Evans
Member since Aug 2009 · 231 posts
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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) #14
User title: John Evans
Member since Aug 2009 · 231 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) #15
User title: John Evans
Member since Aug 2009 · 231 posts
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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 :-) !
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