Creation CIF-file

hot-summertime

Hallo,

is there any possibility to get the "largest ratio of the final least-squares parameter
shift to the final standard uncertainty" (CIF-Label _refine_ls_shift/su_max) from Topas for an Rietveld refinement of powder data?

Does an macro exist for such an CIF-file to get for example the molecular geometry automatically like it is needed for a CIF-file?

Thanks

johnsoevans

You can get some cif output with the macro:

Out_CIF_STR("Untitled-2.cif")

and you can modify that macro to include more items as you want. You might want to include blocks like the one below. More work's needed on .cif output.....it would be great if somebody took this on and contributed it to the wiki!

I don't know a direct way to get the shift/su max.

John

macro Out_PowderDataBlock(file)
{
out file
Out_String("loop_")
Out_String("\n_pd_meas_2theta_scan")
Out_String("\n_pd_proc_intensity_total")
Out_String("\n_pd_calc_intensity_total")
Out_String("\n_pd_proc_ls_weight")
Out_String("\n")
xdd_out file append load out_record out_fmt out_eqn
{
" %11.5f " = X;
" %11.5f " = Yobs;
" %11.5f " = Ycalc;
" %11.5f\n" = 1./(SigmaYobs*SigmaYobs);
}
}

armandb

Hi everyone,

In addition to this subject Alan some time ago wrote me that:

_refine_ls_number_parameters - Number of parameters refined.

This is only obtained by viewing the refinement output; ie:
Number of independent parameters : 18

_refine_ls_shift/su_max - Maximum shift/s.u. ratio after final refinement cycle.

This is not determined and probably has little meaning in the context of TOPAS.

_refine_diff_density_max - Maximum value of final difference map (e A-3).
_refine_diff_density_min - Minimum value of final difference map (e A-3).
These are also not determined. They will be in a future version when Fourier maps are displayed.

However I heard that people just write here something like:
_refine_ls_shift/su_max 0.001,

because:
"_refine_ls_shift/su_mean ? " causes Alert C (as I good remember).

I think, that in this case, the requirements (for CIF form TOPAS refinement) of IUCr to Acta Cryst C and E should be changed.

nprietveld

Hello,
I tried to use the above macro Out_PowderDataBlock, but the refinement ends in error, with the message "Exception caught!" Any suggestion will be welcome!

alancoelho

Hi nprietveld

Could you e-mail me the INP and data file and I will see whats happening
alan

annakater

Hi everyone and happy new year.

I also got an "Exception caught" message with Out_PowderDataBlock, so I tried listing the SigmaYobs values and it seems that they are all zero. Apparently the exception is that we are trying to divide by zero.

I can't find any information about SigmaYobs in the technical reference, but if I remember my XRD theory correct, its supposed to be square-root(yobs), is this right?

The creating and editing of .cif has taken me the best part of a day. There must be a better way to do this, like gsas2cif - is there not any equivalent for TOPAS?

cc0u50fd

Hi,

So I had ago at making a cif macro with a little bit of success. Basically it ends up out putting everything except backgound, dispersion coefficients and molecular geometries.
But the real problem is trying to get this macro to work over multiple types of data in a combined refinement. I can't figure out a way of getting the macro to discriminate between the different types of data, ie X-ray and TOF, and then output a separate xdd_out list for each data set.
When the .cif file is generated you end up with either x-ray names for each column of data or TOF specific names.

Is there a way of getting a macro to check the data type before it generates the out put file?

Thanks
Alec.

alancoelho

Hi annakater

The creating and editing of .cif has taken me the best part of a day. There must be a better way to do this, like gsas2cif - is there not any equivalent for TOPAS?

I'm afraid I wont be wasting my time writing anything like gsas2cif; . CIF will be supported but in a manner that is sufficient to get the job done. Much of CIF is useful but there's also a lot of garbage

Get(refine_ls_shift_on_su_max) has been implemented in Version 5; this one really is a complete waste of time but it was done because many has asked for it.

Get(number_of_parameters) has also been implemented.

Version 5 also outputs bond angles and lengths in CIF format.

In version 4 the work around for _refine_ls_shift/su_max is to use out_prm_vals_per_iteration

Also, in the Technical reference of TA there's at least 5 matches for SigmaYobs. In XYE files it corresponds to the error found in the file. Files that do not have esds have SigmaYobs set to zero.

cc0u50fd wrote:

But the real problem is trying to get this macro to work over multiple types of data in a combined refinement.

I dont understand what you are trying to do; if you send me the INP/data file then I will have a look.

cheers
alan

cc0u50fd

Hi,

So far I've got this macro to output everything except composition, which I'm working on.
Many thanks to Alan for helping me get it that far.

What I could do with is someone to help me with checking I've put the correct values in the correct places and that I've not gotten confused with the IUCr definitions of what constitutes a particular term.

Also if any one has a CIF that was generated using a scanning type data (as opposed to a fixed 2TH step size) can you send it to me so I can check how it fits in?

Thanks
Alec.

pamwhitfield

The code below doesn't care whether it's fixed or variable step/count xye data (I use the latter routinely) and seems to get the weighting even in xy datasets where there is no SigmaYobs. It's very similar to John's with a couple of small tweaks... Can't pretend it's all my own work - Alan suggested the Get(weighting) which simplifies things

As Alan says version 5 outputs the geometry with bond lengths/angles but it can be a case of beware getting what you ask for! It gives you every conceivable bond length/angle in the cell so you may end up deleting some to reduce the G alerts down to something manageable, especially with Z' >1.

macro Out_PowderCIFDataBlock(file)
{
out file
Out_String("loop_")
Out_String("\n_pd_proc_point_id")
Out_String("\n_pd_meas_2theta_scan")
Out_String("\n_pd_proc_intensity_total")
Out_String("\n_pd_calc_intensity_total")
Out_String("\n_pd_proc_ls_weight")
Out_String("\n")
xdd_out file append load out_record out_fmt out_eqn
{
" %9.0f" = Xi+1;
" %11.5f" = X;
" %11.5f" = Ycalc;
" %11.5f" = Yobs;
" %11.5f\n" = Get(weighting);
}
}

winwalk

I also got an "Exception caught" message with Out_PowderDataBlock

iainoswald

I have been trying to extend the output of the Out_CIF_STR macro to include the density of the crystal but anytime I put any of the following:

Out(Phase_Density_g_on_cm3, "\n_Density %V ")
Out(Phase_Density_Eqn_g_on_cm3, "\n_Density %V ")
Out(Get(Phase_Density_g_on_cm3), "\n_Density %V ")
Out(Get(Phase_Density_Eqn_g_on_cm3), "\n_Density %V ")

they all fail. Not really sure whay these are not working. Excuse the simpleness of question.

Best wishes,

Iain

mfisch

This won't work this way as you are mixing up macro names with parameter names. Try to define a new parameter which contains the cell density:

prm cell_density = Get(cell_mass) / Get(cell_volume) ;

And then the following should work:

Out(cell_density, "\n_Density %V")

iainoswald

Hi everyone,

It's been a long two days.

Out(Phase_Density_Eqn_g_on_cm3, "\n_exptl_crystal_density_diffrn %V")

This actually works if you put in into the Out_CIF_STR macro.

Sorry for bothering you all.

Iain

originlab1

Dear Alan,

Could you please give me some tips on how to incorporate the bong angle information in *.cif format while using TOPAS V4.1.

Using

append_bond_lengths consider_lattice_parameters

I can output the bond length and angle information to the *.out file but that is not useful for publications if i want to submit the *.cif file. I agree with you that lot of *.cif is not relevant but almost all publications with *.cif file requires that it passes the test in IUCr website. Sadly, the TOPAS generated *.cif as output of

Out_CIF_STR

is not at all close.

I am a bit disappointed with TOPAS as I was not expecting this could be an issue for a professional software. I will really appreciate if you could respond to this problem and/or provide a work around for TOPAS 4.1/2. I feel that atleast the things that are required by the IuCr CheckCIF should be easily incorporated when the *.CIF is generated.
--
Thanks,
AB

alancoelho

I'm afraid that V4.1 only has append_bond_lengths.

>I am a bit disappointed with TOPAS as I was not expecting this
>could be an issue for a professional software.

Not sure what you mean by 'professional'. The work around is to massage the bond lengths data which should not be too difficult with a good editor.
cheers
alan

[deleted]

Dear all,
I have some problem with bond and angle distances reported in the cif file.
I am using the macro

macro Out_CIF_Bonds_Angles(file)
{
out file append
Out(Get(cif_bonds_angles), "%s")
}
but the distances are too long for organic molecules. The list contains all the distances between two atoms less than 3.2 A, which means a lot of non bonding distances.
Is there a way to introduce a parameter to look only at the covalent bonds?
Thanks a lot
Lucia