jkd
March 26, 2025, 9:05pm
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
avdw
March 26, 2025, 9:07pm
2
Sorry, I don’t see an attachment.
Could you paste in your rndstr.in file?
avdw
March 26, 2025, 9:08pm
3
I ran your example. A few comments:
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)
I get 48 symmetry operations…
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…
jkd
March 26, 2025, 9:11pm
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
jkd
March 26, 2025, 11:49pm
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
avdw
March 26, 2025, 11:52pm
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.
jkd
March 26, 2025, 11:53pm
7
Yes, that appears to have been the problem. Thanks it works now.
Jacques