phb issues while generating phase diagram

Alloy Theoretic Automated Toolkit (ATAT)
1

Hi Axel and everyone,

I am trying to generate a phase-diagram of binary BCC Cu-Pd system. I am getting some errors that I have not encountered before in ATAT.

When I use the following command, after printing two lines the ATAT seems to get stuck (I have attached the input and output files) and does not do anything.
phb -gs1=0 -gs2=1 -dx=.0100 -dT=10 -ltep=1e-3 -er=16 -o=phb.txt -k=8.617e-5 > output-phb.txt

Next, when I try to increase the cell size by ‘phb -gs1=0 -gs2=1 -dx=.0100 -dT=10 -ltep=1e-3 -er=20 -o=phb.txt -k=8.617e-5 > output-phb.txt’ I get the following error:
‘Missing sites in user-specified initial configuration (-is option)’

My suspicion is probably my input files are not correct but I am not fully sure where I am doing the mistake. If anyone can help that would be much appreciated!

Tanmoy

2

Sorry, can you paste in your input files. The attachment feature does not seem to work right now.

3

Ahh, sorry! I didn’t notice that earlier either. Here are my files, Thanks!

lat.in:
3.01989871153 3.01989871153 3.01989871153 90 90 90
-0.5 0.5 0.5
0.5 -0.5 0.5
0.5 0.5 -0.5
0 0 0 Pd,Cu

gs_str.out:
3.019800 0.000000 0.000000
0.000000 3.019800 0.000000
0.000000 0.000000 3.019800
-0.5 0.5 0.5
0.5 -0.5 0.5
0.5 0.5 -0.5
0.000000 0.000000 0.000000 Pd
end

3.019800 0.000000 0.000000
0.000000 3.019800 0.000000
0.000000 0.000000 3.019800

  1. 0 0
    0 1. 0
    0 0 1.
    0.000000 0.000000 0.000000 Cu
    0.500000 0.500000 0.500000 Pd
    end

3.019800 0.000000 0.000000
0.000000 3.019800 0.000000
0.000000 0.000000 3.019800
-0.5 0.5 0.5
0.5 -0.5 0.5
0.5 0.5 -0.5
0.000000 0.000000 0.000000 Cu
end

eci.out:
-0.05709
-9.81E-04
0.01386
-0.00136
0.00354
-7.52E-05
1.35E-04
5.08E-04
-8.76E-04
-0.00376
-0.00179
-0.00172
-2.28E-04

clusters.out:
1
0.000000
0

1
0.000000
1
0.000000 0.000000 0.000000

6
2.687006
2
0.000000 0.000000 0.000000
-0.000000 0.500000 -0.500000

3
3.800000
2
0.000000 0.000000 0.000000
-1.000000 0.000000 0.000000

12
4.654031
2
0.000000 0.000000 0.000000
-1.000000 -0.500000 0.500000

6
5.374012
2
0.000000 0.000000 0.000000
0.000000 -1.000000 1.000000

12
6.008328
2
0.000000 0.000000 0.000000
-0.500000 -1.500000 0.000000

4
6.581793
2
0.000000 0.000000 0.000000
-1.000000 -1.000000 1.000000

24
7.109144572
2
0.000000 0.000000 0.000000
-1.500000 -1.000000 -0.500000

3
7.600003468
2
0.000000 0.000000 0.000000
-2.00000 0.000000 0.000000

6
8.061021126
2
0.000000 0.000000 0.000000
-1.50000 -1.500000 0.000000

12
8.061021126
2
0.000000 0.000000 0.000000
-2.000000 -0.500000 -0.500000

12
8.497056566
2
0.000000 0.000000 0.000000
-2.000000 -1.00000 -0.000000

output-phb.txt:
Phase 1 size: 19 19 19
Phase 2 size: 20 20 20
0 -0.110223 -1.000000 0.000000 -0.143807 -0.143807

phb.txt:
0 -0.110223 -1.000000 0.000000 -0.143807 -0.143807

4

Your cluster.out seems to have been generated from another structure.
For instance, the pair cluster
6
2.687006
2
0.000000 0.000000 0.000000
-0.000000 0.500000 -0.500000

has the site "-0.000000 0.500000 -0.500000" which is not a bcc site.

BTW, I checked this by running the command:

corrdump.exe -s=gs_str.out  -c

and seeing that the code crashes while outputting the 3rd cluster.
-Axel

5

Ok, thanks Axel for pointing out the error. Here are my new ‘clusters.out’ file below. Could you please check my ‘gs_str.out’ file once? I am not fully sure if I wrote the CuPd structure (the middle one in the gs_str.out) correctly. Does it represent a bcc 50% (B2) structure for that lat.in or need to modify? My ‘lat.in’ is the correct one but I made ‘by-hand’ the ‘gs_str.out’ file, that’s why my confusion arises.

Secondly, after using this ‘cluster.out’ file together with previously mentioned files it seems working (at least giving some data - we need to check whether it makes sense later) when I use ‘phb -gs1=0 -gs2=1 -dx=.0005 -dT=1 -ltep=1e-3 -er=20 -o=phb.out -k=8.617e-5 > output-phb.txt’ but if I try to increase the cell size say, -er=20, ATAT tells me Missing sites in user-specified initial configuration (-is option). If I go to even higher cell size say, -er=30 it tells me ‘Bus error: 10’.

1
0.00000
0

1
0.00000
1
0.50000 0.50000 0.50000 0 0

4
2.61531
2
0.50000 0.50000 0.50000 0 0
-0.00000 -0.00000 1.00000 0 0

3
3.01990
2
0.50000 0.50000 0.50000 0 0
0.50000 0.50000 1.50000 0 0

6
4.27078
2
0.50000 0.50000 0.50000 0 0
-0.50000 0.50000 1.50000 0 0

12
5.00794
2
0.50000 0.50000 0.50000 0 0
-1.00000 -0.00000 0.00000 0 0

4
5.23062
2
0.50000 0.50000 0.50000 0 0
1.50000 1.50000 1.50000 0 0

3
6.03980
2
0.50000 0.50000 0.50000 0 0
-1.50000 0.50000 0.50000 0 0

12
6.58172
2
0.50000 0.50000 0.50000 0 0
-1.00000 1.00000 -1.00000 0 0

12
6.75270
2
0.50000 0.50000 0.50000 0 0
-1.50000 -0.50000 0.50000 0 0

12
7.39721
2
0.50000 0.50000 0.50000 0 0
1.50000 2.50000 1.50000 0 0

12
7.84593
2
0.50000 0.50000 0.50000 0 0
-0.00000 3.00000 0.00000 0 0

4
7.84593
2
0.50000 0.50000 0.50000 0 0
-1.00000 -1.00000 -1.00000 0 0

6
8.54156
2
0.50000 0.50000 0.50000 0 0
0.50000 2.50000 2.50000 0 0

24
8.93298
2
0.50000 0.50000 0.50000 0 0
-1.00000 -0.00000 3.00000 0 0

6

Your ‘gs_str.out’ file seems ok.

If it says "missing sites" I suspect your cluster.out is still not quite right.
Did you try corrdump.exe -s=gs_str.out -c ?

Maybe recompile the code after changing the following lines in atat/src/makefile
CXXFLAGS=(PATCHCXXFLAGS) -DDEBUG -g #-DDEGE_GS #CXXFLAGS=(PATCHCXXFLAGS) -O3
(only one of the CXX… lines should be uncommented).
This will give an error message if bound checks are violated at run time.