AVolte #1
Member since Jun 2018 · 5 posts
Group memberships: Members
Subject: Writing z-matrices for rigid body in Rietveld refinement
Hello,
I am doing Rietveld refinement on molecular crystals, and I would want to fix certain parts of the molecule. For this, I use Z-matrices (which I write by myself, since I didn't find the software to do it automatically).
Some of the matrices I wrote are correct, but TOPAS is complaining about the others, e.g. :

rigid
F1
P1 F1 1.586
F2 P1 1.573 F1 174.4
F3 P1 1.618 F1 89.3
F4 P1 1.612 F1 89.6
F5 P1 1.540 F1 92.1
F6 P1 1.620 F1 86.5
}

and here, TOPAS writes:

at LINE 415
See log file C:\Topas6\topas.log

• Error at: P1
Maybe an equations starting with an equal sign and
ending in a semicolon is what is meant.
Note that fractions such as 1/3 should be entered as =1/3;

It's the same for the other part:

rigid
N2
C10 N2 1.5
H10A C10 0.97 N2 108.7
H10B C10 0.97 N2 108.8
C11 C10 1.53 N2 113.8
H11A C11 0.96 C10 109.4 N2 -179
H11B C11 0.96 C10 109.4 N2 61
H11C C11 0.96 C10 109.5 N2 -59
H2 N2 0.91 C10 108.5 C11 -59
C9 N2 1.5 C10 112.6 C11 62
H9A C9 0.97 N2 110 C10 -67
H9B C9 0.97 N2 110 C10 51
C8 C9 1.49 N2 109 H2 -68
H8A C8 0.97 C9 109 N2 -172
H8B C8 0.97 C9 109 N2 71
}

where TOPAS says:

at LINE 330
See log file C:\Topas6\topas.log

• Error at: C11
Maybe an equations starting with an equal sign and
ending in a semicolon is what is meant.
Note that fractions such as 1/3 should be entered as =1/3;

I really don't know where the errors are. I also tried to define Z-matrices with the method:

rigid
F1
P1 1 1.586
F2 2 1.573 1 174.4
F3 2 1.618 1 89.3
F4 2 1.612 1 89.6
F5 2 1.540 1 92.1
F6 2 1.620 1 86.5
}

But it doesn't work either. Does anybody has any idea about that ?

AVolte
AlanCoelho #2
Member since Aug 2011 · 259 posts
Group memberships: Members
Hi AVolte

The third line of the z-matrix needs to contain 4 atoms. Please see the Technical Reference; for example here's a Benzene ring:

str...
site X1... occ C 0
site X2... occ C 0
rigid
X1
X2   X1  1.0
C1   X2  1.3   X1  90
C2   X2  1.3   X1  90  C1  60.0
C3   X2  1.3   X1  90  C2  60.0
C4   X2  1.3   X1  90  C3  60.0
C5   X2  1.3   X1  90  C4  60.0
C6   X2  1.3   X1  90  C5  60.0
}

cheers
alan
AVolte #3
Member since Jun 2018 · 5 posts
Group memberships: Members
Hi AlanCoelho,

I spotted this error, but with the configuration of molecule I work on, I couldn't figure a way to arrange the z-matrix like that. I will try to think harder.

AVolte
Member since May 2018 · 7 posts
Group memberships: Members
Hi,

The fourth atom that needs to be included from the third line on in a z-matrix is needed to define torsion angles.
In your case I guess that you are trying to build an hexafluorophosphate anion, where there are no torsion angles to be defined.
In order to be able to do this, you should use one or more dummy atoms that will allow you to define those torsion angles. The dummy atom will not contribute to the overall scattering of your structure, it is there only for geometrical reasons.

Marco
AVolte #5
Member since Jun 2018 · 5 posts
Group memberships: Members
I will try with the dummy atom !

avolte
Member since May 2018 · 7 posts
Group memberships: Members
No problem, happy to help.

Marco
AVolte #7
Member since Jun 2018 · 5 posts
Group memberships: Members
Hi again,
I tried to use dummy atoms to describe rigid bodies, but couldn't find anywhere how to add a dummy atom in the phase structure. I tried by setting all its coordinates to zero, along with occupancy:
site X1_        x 0.0           y 0.0           z 0.0           occ C    0
but TOPAS tells me that it can't load point_for_site for this atom.
Could somebody give me a hint on how to do this properly ?
Thanks a lot,

AVolte
AlanCoelho #8
Member since Aug 2011 · 259 posts
Group memberships: Members
To include a dummy atom the set its occupancy to zero; ie.

site X1 occ C 0
rigid
point_for_site X1

Also, see the "Z-C5 H5.rgd" file in the Rigid directory. Load the file into the Rigid body editor for viewing.
alan
This post was edited on 2018-07-10, 02:08 by AlanCoelho.
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