Mcsqs symmetry analysis

Alloy Theoretic Automated Toolkit (ATAT)
1

Hi,

I am trying to do an mcsqs calculation on the gamma-Forsterite phase (space group 227). This crystal has 3 sublattices and 48 symmetry operators (see attached .cif file). However, when I run corrdump and mcsqs, the code only finds 6 symmetry operators (in the sym.out) and a total of 19 sublattices (in the rndstrgrp.out). This makes it difficult to run calculations, because a some of the sublattices found have only 1 site. So a very large supercell would be required in order to achieve low concentrations.

I also attach here the inputs. For the purposes of this discussion, I ran the codes using the following commands:

corrdump -l=rndstr.in -ro -noe -nop -clus -2=4

mcsqs -rc

Best regards and thanks for your time,

Jacques

2

Sorry, I don’t see an attachment.
Could you paste in your rndstr.in file?

3

I ran your example. A few comments:

  1. this is not the smallest unit cell you can use. You can find the smallest one with cellcvrt -s < rndstr.in (it has 14 sites)
  2. I get 48 symmetry operations…
  3. The 3 sublattices have 4,2 and 8 atoms.

I tried version 3.18 and 3.35 and both gave the same answer…

I can’t reproduce your problem. Note that low concentrations always tend to require large cells…

4

Hi,

Sorry, I guess I am having trouble attaching files. I believe that this was the rndstr.in:

8.066 8.066 8.066 90. 90. 90.
1 0 0
0 1 0
0 0 1
0.12500 0.62500 0.62500 Mg=0.5,Si=0.5
0.12500 0.12500 0.12500 Mg=0.5,Si=0.5
0.87500 0.87500 0.12500 Mg=0.5,Si=0.5
0.37500 0.87500 0.62500 Mg=0.5,Si=0.5
0.37500 0.12500 0.37500 Mg=0.5,Si=0.5
0.87500 0.62500 0.37500 Mg=0.5,Si=0.5
0.62500 0.37500 0.87500 Mg=0.5,Si=0.5
0.62500 0.12500 0.62500 Mg=0.5,Si=0.5
0.12500 0.87500 0.87500 Mg=0.5,Si=0.5
0.37500 0.37500 0.12500 Mg=0.5,Si=0.5
0.62500 0.62500 0.12500 Mg=0.5,Si=0.5
0.87500 0.12500 0.87500 Mg=0.5,Si=0.5
0.12500 0.37500 0.37500 Mg=0.5,Si=0.5
0.62500 0.87500 0.37500 Mg=0.5,Si=0.5
0.37500 0.62500 0.87500 Mg=0.5,Si=0.5
0.87500 0.37500 0.62500 Mg=0.5,Si=0.5
0.50000 0.00000 0.00000 Mg=0.5,Si=0.5
0.00000 0.00000 0.50000 Mg=0.5,Si=0.5
0.50000 0.50000 0.50000 Mg=0.5,Si=0.5
0.00000 0.50000 0.00000 Mg=0.5,Si=0.5
0.75000 0.75000 0.75000 Mg=0.5,Si=0.5
0.25000 0.75000 0.25000 Mg=0.5,Si=0.5
0.25000 0.25000 0.75000 Mg=0.5,Si=0.5
0.75000 0.25000 0.25000 Mg=0.5,Si=0.5
0.86850 0.36850 0.36850 O
0.86850 0.86850 0.86850 O
0.13150 0.13150 0.86850 O
0.63150 0.13150 0.36850 O
0.63150 0.86850 0.63150 O
0.63150 0.36850 0.13150 O
0.13150 0.36850 0.63150 O
0.36850 0.63150 0.13150 O
0.36850 0.86850 0.36850 O
0.86850 0.13150 0.13150 O
0.63150 0.63150 0.86850 O
0.13150 0.63150 0.36850 O
0.36850 0.36850 0.86850 O
0.13150 0.86850 0.13150 O
0.86850 0.63150 0.63150 O
0.36850 0.13150 0.63150 O
0.11850 0.11850 0.38150 O
0.88150 0.38150 0.88150 O
0.61850 0.88150 0.11850 O
0.61850 0.38150 0.61850 O
0.11850 0.38150 0.11850 O
0.38150 0.61850 0.61850 O
0.61850 0.61850 0.38150 O
0.88150 0.11850 0.61850 O
0.38150 0.11850 0.11850 O
0.38150 0.88150 0.88150 O
0.38150 0.38150 0.38150 O
0.11850 0.61850 0.88150 O
0.88150 0.88150 0.38150 O
0.88150 0.61850 0.11850 O
0.11850 0.88150 0.61850 O
0.61850 0.11850 0.88150 O

And here is the sqscell.out:

1

1 0 0
0 1 0
0 0 1

5

What does your sym.out file look like? I assume that this is where you find the symmetry operators. Mine only has 6 operators and looks like this:

6
1.00000 -0.00000 0.00000
0.00000 0.00000 1.00000
0.00000 1.00000 -0.00000

-0.00000 -0.00000 0.00000

1.00000 0.00000 0.00000
0.00000 1.00000 0.00000
0.00000 0.00000 1.00000

0.00000 0.00000 0.00000

-0.00000 -0.00000 1.00000
0.00000 1.00000 -0.00000
1.00000 0.00000 0.00000

-0.50000 0.00000 -0.50000

-0.00000 1.00000 -0.00000
0.00000 0.00000 1.00000
1.00000 0.00000 0.00000

-0.50000 -0.00000 -0.50000

-0.00000 -0.00000 1.00000
1.00000 0.00000 0.00000
0.00000 1.00000 -0.00000

-0.50000 -0.50000 0.00000

-0.00000 1.00000 -0.00000
1.00000 0.00000 0.00000
0.00000 0.00000 1.00000

-0.50000 -0.50000 0.00000

This is using version 3.34

6

My sym.out starts with:

192
0.00000 0.00000 1.00000
1.00000 -0.00000 -0.00000
0.00000 1.00000 -0.00000

0.50000 -0.50000 -0.00000
…

If I use the smallest unit cell, then I get:
48
1.00000 0.00000 0.00000
0.00000 0.00000 1.00000
0.00000 1.00000 0.00000

0.00000 -0.00000 0.00000
…

Maybe your input file contains invisible control characters. Do
cat -v rndstr.in
to see them.

7

Yes, that appears to have been the problem. Thanks it works now. :smiley:

Jacques