Out_CIF_mag

lnaglecocco

Hi all,

I have a problem with the version of Out_CIF_mag on the Topas wiki here: https://topas.awh.durham.ac.uk/doku.php?id=out_cif_mag

The CIF it outputs crashes Vesta and won't load. I've tried the modification the Wiki suggests and that doesn't work either. Does anyone have a version of this macro that works with Vesta?

My structures contains the magnetic ions Mn4+, Pr3+, and Nd3+ if that is relevant

Liam

lnaglecocco

I tried modifying the macro as described in this previous post but it didn't work for me
https://topas.awh.durham.ac.uk/flarum/public/d/685-outputting-mcif-file

rowlesmr

Can you post the CIF? Do you get any message from Vesta re crash? I mean, it is kind of impressive...

lnaglecocco

Hi Matthew,

Thanks for getting back to me. I don't get any message. Vesta tries to open, I see the window but no crystal structure and my cursor symbol indicates something is loading, then Vesta closes.

There was a typo in my previous message, the Ln ions are 4+ not 3+.

Here is an example CIF:

mf1-c1.txt

1kB

rowlesmr

I don't recognise any of the _magnetic_* data names, so Vesta might not either. THere is an IUCr version of the magnetic structure dictionary: https://www.iucr.org/resources/cif/dictionaries/cif_mag, as well as the development version: https://github.com/COMCIFS/magnetic_dic

Might be worth seeing what Vesta supports in terms of magnetic structures.

Do you specifically want to see magnetic information, or is structural sufficient? Could try outputting a "regular" cif and see if that works.

lnaglecocco

Yeah, when I modify the filename to remove the magnetic prefixes I am able to make it load in Vesta, but it won't show the spins and it doesn't understand that it's supposed to be a magnetic structure. But Vesta definitely does support mCIFs, for instance I got this structure on MAGNDATA and it loads fine (just with a very different structure than the Macro on the Topas wiki produces):

010-dyfeo3.txt

3kB

I'm trying to visualise the different magnetic structures I get from refinement to neutron diffraction data in Vesta. Obviously this could be done with the view_structure flag but I much prefer using Vesta. A regular CIF is produced just fine.

I think a new macro needs to be written and put on the Topas wiki here: https://topas.awh.durham.ac.uk/doku.php?id=out_cif_mag

I will play around with it and see if I can get something that works

johnsoevans

The mag_cif macro was written before the modern magnetic cif standards. It was only meant to give a quick view of the moments in vesta. Glen Hebberd has suggested a couple of modifications that might make it work. I've put them on the wiki page (https://topas.awh.durham.ac.uk/doku.php?id=out_cif_mag). They can probably be automated in the macro if somebody has time to do it. If somebody wants to do this properly it would be great!

lnaglecocco

Hi John,

This still didn't quite work for me at first. However I then modified the macro like this:

	macro Out_CIF_mag(file) {
		out file
 		Out_String("data_topas_output")
		Out(Get(sp_grp_char), "\n\n_space_group_magn.number_BNS %s")
		Out(Get(a), "\n_cell_length_a  %V")
		Out(Get(b), "\n_cell_length_b  %V")
		Out(Get(c), "\n_cell_length_c  %V")
		Out(Get(al), "\n_cell_angle_alpha %V")
		Out(Get(be), "\n_cell_angle_beta  %V")
		Out(Get(ga), "\n_cell_angle_gamma %V")	
 
		Out_String("\n\nloop_")
		Out_String("\n_magnetic_space_group_symop_id")
		Out_String("\n_magnetic_space_group_symop_operation_xyz")
		Out(Get(mag_sp_xyzs_txt_with_id),  "%s")
 
		Out_String("\n\nloop_")
                 Out_String("\n_atom_site_label")
                 Out_String("\n_atom_site_type_symbol")
                 Out_String("\n_atom_site_fract_x")
                 Out_String("\n_atom_site_fract_y")
                 Out_String("\n_atom_site_fract_z")
                 Out_String("\n_atom_site_occupancy")
                 Out_String("\n_atom_site_B_iso_or_equiv")
		atom_out file append
		load out_record out_fmt out_eqn
                 {
		"\n%s" = Get_From_String(Get(current_atom), site);
		" %s" = Get_From_String(Get(current_atom), atom);
		" %V" = Get_From_String(Get(current_atom), x);
		" %V" = Get_From_String(Get(current_atom), y);
	        " %V" = Get_From_String(Get(current_atom), z);
	        " %V" = Get_From_String(Get(current_atom), occ);
	        " %V" = Get_From_String(Get(current_atom), beq);
                 }
 
                  out file append      
		Out_String("\n\nloop_")
		Out_String("\n_atom_site_moment.label")
		Out_String("\n_atom_site_moment.crystalaxis_x")
                 Out_String("\n_atom_site_moment.crystalaxis_y")
                 Out_String("\n_atom_site_moment.crystalaxis_z")
		atom_out file append
		load out_record out_fmt out_eqn
                 {
		"\n%s" = Get_From_String(Get(current_atom), site);
		"%11.5f" = Get(a) Get_From_String(Get(current_atom), mlx);        
		"%11.5f" = Get(b) Get_From_String(Get(current_atom), mly);        
	         "%11.5f" = Get(c) Get_From_String(Get(current_atom), mlz);        
                  }	
                  }

At that point, the fix suggested by Glen works.

The problem line is this one: Get(mag_sp_xyzs_txt_with_id)

If I could do some string manipulation I could fix this. I.e. in Python i would do string.replace("mx,my,mz,",",") and that would work. Do you know how to do string manipulation in Topas? Alternatively maybe there's another term like mag_sp_xyzs_txt_with_id which does not include the mx,my,mz but I have no idea how I would find it.

rowlesmr

mag_sp_xyzs_txt_with_id would be an Alan question.

I don't know the current state of the magCIF dictionary, but they are writing up another edition of Volume G, so maybe there is some more certainty in how things should be repreesented...?