output of particular bond distances/angles

ahhill

Hi, I am aware of the append_bond_lengths macro to see all the bond distances and angles in the topas inp file.

Is there a way to output a specific bond distance/angle?

This output file could hopefully then be appended to so that a txt file is created with the bond angles/distances listed by columns changing with temperature?

Thanks again, and apologies if it is explained somewhere in the manual, I couldn't really see anything obvious.

Adrian

johnsoevans

Adrian,

One way is to adapt the language that's used in the macros for distance and angle restraints. It's relatively straightforward to give each distance and individual parameter name that can be output.

John

ahhill

thanks for the tips.

I am trying to output the following parameters, Np-O bond length and Np-O-Np angles. These appear as the following in

		append_bond_lengths{
...
O:0       Np:1      -1  -1   0   2.32389(69) 
          Np:0       0   0   0   2.32389(69)  108.159(24)
          Np:1      -1   0   0   2.32389(69)  108.159(24) 112.129(48)
...
*/}

I can isolate the distance value using either

Get_Distance(Np O, c, 2.32389`_0.00069)

- defined on the macros page of this wiki.

or

Distance_Restrain(Np O 1 0 0 0, 2.32, 2.32389_0.00069, 0, 0)

However, I am having no luck isolating the angles.

I have tried various permutations of

Angle_Restrain(Np O Np 1,110, 56.65081_0.03378,0, 0)

but get an angle of 56°. Not what I wanted. Any further tips?

In the macro definition, how would I assign a name to the output value to later pull out to a txt file?

Thanks again, and sorry for not being able to work this one out myself.

Adrian

johnsoevans

Adrian,

I think you need:

Distance_Restrain(C2 0 H1 0 0 0 0,c2h1,1.092, 1.08893`, 0, 1)
Angle_Restrain(C2 C3 C4, c2c3c4, 118.270, 119.33428`, 0, 0.001)
....
Out(c2h1, " %11.5f"," %11.5f")
Out(c2c3c4, " %11.5f"," %11.5f")

To get the correct angle you just need the right combination of "Np O 1 0 0 0" for the two atoms to pull out the correct sites in unit cell (or adjacent).

John

alancoelho

The sites_geometry keyword is also useful especially as it follows the format of z-matrices.

Have a look at the test_examples:

test_examples\sites_geometry_1.inp
test_examples\sites_geometry_2.inp

For example, you will see a line in test_examples\sites_geometry_1.inp that looks like:

prm = Sites_Geometry_Angle(c4); : 0

c4 is a name corresponding to a sites_geometry entry of:

sites_geometry c4
load site_to_restrain { C4 C3 C2 C1 }

If the Sites_Geometry_Distance(c4) function is used then it will return the z-matrix distance. If Sites_Geometry_Angle(c4) is used then it will return the z-matrix angle. If Sites_Geometry_Dihedral_Angle(c4) is used then it will return the z-matrix dihedral angle.

sites_geometry does not care if a z-matrix is defined but knowing z-matrix format means that the the meaning of the three functions

Sites_Geometry_Distance
Sites_Geometry_Angle
Sites_Geometry_Dihedral_Angle

are easily undertsood.

alancoelho

>sorry for not being able to work this one out myself.

Actually Adrian, what you are trying to do is a little more involved than one would think.

You will see in the append_bond_lengths output numbers such as :0 or :1 after the site names. This corresponds to the equivalent position as listed in the space group file. Appearing after that are three numbers such as -1 -1 0. These three numbers corresponds to lattice vector translations of –a, -b, 0. Thus the first bond length of 2.32389(69) corresponds to:

- the distance between the O atom of equivalent position 0
- and the Np atom of equivalent position 1 translated by minus the “a” lattice vector and then minus the “b” lattice vector.

This distance can be obtained as follows:

sites_geometry onp
site_to_restrain O
site_to_restrain Np 1 -1 -1 0

Use of Sites_Geometry_Distance(onp) should then return 2.32389.

Obtaining the Np-O-Np angle may be a little more difficult as you would need to increase the sphere being reported on in append_bond_lengths; this can be done using max_r; ie.

site Np .... max_r 5

Once you get the right append_bond_lengths it should be then possible to formulate the appropriate sites_geometry.

This does seem a painful way of getting to a bond angle and I wonder why you can’t simply use the append_bond_lengths output.

ahhill

Alan, John.

Thanks very much for the responses. I realise I could look at the numbers given out from the append_bond_lengths macro, I was just being lazy, to see if there was a simple way to output just one or two parameters for plotting changes with temperature. I'll keep playing with your suggestions.

I can't actually find the test_examples. Do they only ship with the academic version? I am using the full version from bruker.

Cheers

Adrian

alancoelho

test_examples comes with TOPAS-Academic, its a subdirectory of the main TA directory. The Bruker TOPAS should also have these examples but maybe a different directory structure. Try a serach from the dos promt from your TOPAS directory, ie.

dir sites_geometry* /s

If you dont have luck then download the self extracting file TA1.EXE found at the bottom of the web page www.Topas-Academic.net to a directory; ie. call it tmp-ta or something. Then run the self extracting file TA1.EXE. Within tmp-ta you will see a directory called test_examples.

ahhill

Cheers Alan, no luck with the directory (using both search methods), so downloaded from your site.

adrian

alancoelho

Most (if not all) of the test_examples are listed under the Examples tab of XInsert in jEdit. They can therefore be easily viewed and run.

Dmitry

Dear all,

Apologies for bringing the old conversation back to life, but where exactly could I find the aforementioned macro append_bond_lengths? I ctrl+F'd through the inc files and the test_examples folder - so far no luck.
(I'm using Topas 7, if matters)

Thank you,
Dmitry

johnsoevans

It's not a macro so not in the inc file. It's just an instruction in the INP that will include distances and angles in {} after running topas. Sorry if I've missed the point of your question.

Dmitry

johnsoevans thank you, it explains why I couldn't find it.
I was hoping to somehow include longer bond distances on the list generated by this instruction, i.e. to change the setting that stores (?) the interatomic distances that count as "bond lengths". Is there a way to change this setting either in the software or in the current inp file?

johnsoevans

Yes. You can just put e.g. “max_r 4” a the end of a site line. You can have a different value for each site.

Dmitry

johnsoevans this is brilliant. Exactly what I was looking for. Thank you kindly