Output distance between atoms

rowlesmr

Hi all

Is it possible to ask Topas to give me the distance between two atoms, without having to use append_bond_lengths or Out_CIF_Bonds_Angles?

Ideally, I'd like to say something like:

prm bond_length = Get_the_atom_distance(Na1:0, F2:6)

where Na1 and F2 are the site names, and :0 and :6 denote the particular atom derived from symmetry.

This is for some insitu data, so I have quite a bit of output...

Matthew

johnsoevans

Matthew,

The answer used to be yes (though there were some minor glitches at one point) and I think it still is (but haven't checked). We used to use macros like those in distance_restrain. See:

http://topas.dur.ac.uk/topaswiki/doku.php?id=get_distance&s[]=get&s[]=distance

John

rowlesmr

Thanks for that.

I must have gone through the listing several times, missing yours each time.

It appears to work for me.

Matthew

hanna

This is probably a rather stupid question, but I don't understand how to implement the instructions in the above page.

I added the line

macro Get_Distance(Mn O, mo1mo2, 4)

just below the structural information and the line

Out(mo1mo2, "%11.5f\t")

to my output file. TOPAS ran fine but it did not produce an output file at all, but commenting out the macro line did. I tried adding the numbers after Mn and O, but it didn't help.

Thanks in advance,
Hanna

johnsoevans

You need the macro defined either in your INP file or in local.inc:

macro Get_Distance(sites, c, d_calc)
{
#m_ifarg c ""
#m_unique_not_refine c
#m_endif
sites_distance c
load site_to_restrain { sites }
prm = c; : d_calc
}

In the INP file you then just put:

Get_Distance(Mn O, moo, 2)

This would report the distance between the site "Mn 0 0 0 0" and "O 0 0 0 0". You should see the "2" updated to its actual value after refinement. You can compare it to the value given by append_bond_lengths.

John

hanna

And it works! Thanks John.