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

load z_matrix {

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:

See log file C:\Topas6\topas.log

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

load z_matrix {

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:

See log file C:\Topas6\topas.log

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

load z_matrix {

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 ?

Thanks in advance,

AVolte

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

load z_matrix {

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:

- Error loading sstring_in

See log file C:\Topas6\topas.log

- Error at: P1

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

load z_matrix {

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:

- Error loading sstring_in

See log file C:\Topas6\topas.log

- Error at: C11

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

load z_matrix {

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 ?

Thanks in advance,

AVolte