RE: troublesome unit cell

[alan coelho]

Title: Message

Pam,

 

I looked at your INP file and there was a problem in regards to how atomic coordinates were defined. As you know TOPAS uses computer algebra with a tollerance of 1.0e-15 for checking the equivalence of equivalent positions. If I use

 

x = 1/9; y = 5/9;  etc,,,

 

then the structures are similar.

 

It is not often obvious these equations but it is easy to check using the number of equivalent positions or by inspecting the bond lengths.

 

My guess is that the other programs may have conventions that are also not obvious.

 

it is always good to do some checking

cheers

alan

 

 

-----Original Message-----
From: Whitfield, Pamela [mailto:[EMAIL PROTECTED]
Sent: Monday, October 18, 2004 10:32 PM
To: '[EMAIL PROTECTED]'
Subject: RE: troublesome unit cell

Alan

I'm afraid that the cif files weren't overly good ones - I don't normally use them.  For the R-3m the Li 1/2 fractional coordinate is for the z, not y.  The structures are related by a Ö3a x Ö3a relationship with Z = 3 for the R-3m and Z = 9 for the P3112.
Here are the STR files.  You can refine the 3a and 3b positions for the P3112, but there is a strict relationship that has to be maintained between the x and y coordinates - I have to do it in launch mode to make it work.  It's a very picky space group to work with.

Pam



Dr Pamela Whitfield CChem MRSC
Energy Materials Group
Institute for Chemical Process and Environmental Technology
Building M12
National Research Council Canada
1200 Montreal Road
Ottawa  ON   K1A 0R6
CANADA
Tel: (613) 998 8462         Fax: (613) 991 2384
Email: <mailto:[EMAIL PROTECTED]>
ICPET WWW: http://icpet-itpce.nrc-cnrc.gc.ca


-----Original Message-----
From: alan coelho [mailto:[EMAIL PROTECTED]]
Sent: October 18, 2004 4:16 PM
To: [EMAIL PROTECTED]
Subject: RE: troublesome unit cell


Pam,

As a developer and someone who uses other software to test against, I
have been following the discussion with interest. This is a complex area
and it goes to show the importance of having a few programs if only for
testing purposes.

I am puzzled by your cif data however as I cant get past verifying the
equivalence of the number of equivalent positions for the Li site.

In R-3m you have as fractional atomic coordinates for Li1:

  x = 0    y = 0.5  and  z = 0

For P3112 you have three Li sites with x, y, z's as

0.77780 0.22220 0.83330
0.11110 0.88890 0.83330
0.44440 0.55560 0.83330

which translates to:

0.77780 0.22220 5/6
0.11110 0.88890 5/6
0.44440 0.55560 5/6

Listed below are equivalent positions for a general site.

What I dont understand is that for R-3m I get 9 non-overlapping fully
occupied equivalent positions within the unit cell with a volume of
101.2975.

For P3112 I get 18 non-overlapping equivalent positions with a volume
three times as large of 303.8968. I was expecting to get 27 if the two
structure were to be equivalent.

Thus, from your cif data I am left to conclude that I am generating the
wrong number of equivalent positions, or, if I am generating the correct
number of equivalent positions then the two cif data sets should indeed
give different powder patterns.

Have you checked what the number of non-overlapping fully occupied
equivalent positions for Li should be for the two structures.

alan





P3112
xyzs
{
        -x+y, -x, z-1/3
        -x+y, y, -z+1/3
        -y, -x, -z-1/3
        -y, x-y, z+1/3
        x, y, z
        x, x-y, -z
} 6


R-3m
xyzs
{
        -x, -x+y, -z
        -x, -y, -z
        -x+y, -x, z
        -x+y, y, z
        -y, -x, z
        -y, x-y, z
        y, -x+y, -z
        y, x, -z
        x-y, -y, -z
        x-y, x, -z
        x, y, z
        x, x-y, z
        ' +(-1/3, 1/3, 1/3) -------------------------
        -x-1/3, -x+y+1/3, -z+1/3
        -x-1/3, -y+1/3, -z+1/3
        -x+y-1/3, -x+1/3, z+1/3
        -x+y-1/3, y+1/3, z+1/3
        -y-1/3, -x+1/3, z+1/3
        -y-1/3, x-y+1/3, z+1/3
        y-1/3, -x+y+1/3, -z+1/3
        y-1/3, x+1/3, -z+1/3
        x-y-1/3, -y+1/3, -z+1/3
        x-y-1/3, x+1/3, -z+1/3
        x-1/3, y+1/3, z+1/3
        x-1/3, x-y+1/3, z+1/3
        ' +(1/3, -1/3, -1/3) -------------------------
        -x+1/3, -x+y-1/3, -z-1/3
        -x+1/3, -y-1/3, -z-1/3
        -x+y+1/3, -x-1/3, z-1/3
        -x+y+1/3, y-1/3, z-1/3
        -y+1/3, -x-1/3, z-1/3
        -y+1/3, x-y-1/3, z-1/3
        y+1/3, -x+y-1/3, -z-1/3
        y+1/3, x-1/3, -z-1/3
        x-y+1/3, -y-1/3, -z-1/3
        x-y+1/3, x-1/3, -z-1/3
        x+1/3, y-1/3, z-1/3
        x+1/3, x-y-1/3, z-1/3
} 36



/* Fractional atomic coordinates for for R-3m
Li1
         0.00000  0.50000  0.00000
         0.50000  0.00000  0.00000
         0.50000  0.50000  0.00000
         0.66667  0.83333  0.33333
         0.16667  0.33333  0.33333
         0.16667  0.83333  0.33333
         0.33333  0.16667  0.66667
         0.83333  0.66667  0.66667
         0.83333  0.16667  0.66667
*/


/* Fractional atomic coordinates for P3112
Li
         0.44440  0.22220  0.50000
         0.77780  0.22220  0.83333
         0.77780  0.55560  0.16667
Li
         0.77780  0.88890  0.50000
         0.11110  0.88890  0.83333
         0.11110  0.22220  0.16667
Li
         0.11120  0.55560  0.50000
         0.44440  0.55560  0.83333
         0.44440  0.88880  0.16667
*/