Examples
On this page, you can find a series of working examples to get acquainted with the functionality of Bramble.
Note
Note that all code snippets assume that Bramble has been
built in a separate build folder as per the
installation instructions.
Rh FCC111
The following code is used to run this example:
./build/bramble -p patterns/patterns.json -i src/test/data/POSCAR_Rh111 -o pa_fcc111.txt
In pa_fcc111.txt, the results as shown below can be found. We can readily see
that there Bramble has identified two types of atoms corresponding
to surface atoms with a 3(4,2,1)6(3,1,1) CNA fingerprint and bulk atoms with
a 12(4,2,1) CNA fingerpint:
----------------------------------------------------------------------------------------------------
# atom x y z color pattern fingerprint
----------------------------------------------------------------------------------------------------
0001 Rh 0.000000 0.000000 10.000000 49ade1 FCC(111) 3(4,2,1)6(3,1,1)
0002 Rh 1.343503 0.775672 12.193931 0b3d05 FCC bulk 12(4,2,1)
0003 Rh 0.000000 1.551344 14.387862 0b3d05 FCC bulk 12(4,2,1)
0004 Rh 0.000000 0.000000 16.581793 0b3d05 FCC bulk 12(4,2,1)
0005 Rh 1.343503 0.775672 18.775724 0b3d05 FCC bulk 12(4,2,1)
0006 Rh 0.000000 1.551344 20.969656 0b3d05 FCC bulk 12(4,2,1)
0007 Rh 0.000000 0.000000 23.163586 49ade1 FCC(111) 3(4,2,1)6(3,1,1)
----------------------------------------------------------------------------------------------------
The statistics block reflects this from which it can be seen that there are in total 5 bulk atoms and 2 surface atoms in this structure to be recognized:
Statistics
----------------------------------------------------------------------------------------------------
#atom perc pattern fingerprint
----------------------------------------------------------------------------------------------------
5 71.43% FCC bulk 12(4,2,1)
2 28.57% FCC(111) 3(4,2,1)6(3,1,1)
----------------------------------------------------------------------------------------------------
We can continue the analysis by performing a similarity analysis on the slab model by running:
./build/bramble -s -i src/test/data/POSCAR_Rh111 -o sa_fcc111.txt
The result of this similarity analysis is shown in the image below. From this image we can readily see that both surface atoms are completely indentical with respect to each other \(\mu_{ij} = 0.0\). The same can be said about all the bulk atoms. In contrast, the minimized Hilbert-Schmidt norm between the surface and bulk atoms amounts to \(\mu_{ij} = 30.8\).
Execution times
To get an impression of typical execution times and the benefit of GPU acceleration, we refer to the Table as seen below.
System |
Execution time (averaged) |
|---|---|
Intel(R) Core(TM) i9-10900K (20 threads) |
172.58s |
Intel(R) Core(TM) i9-10900K (20 threads) + RTX 4090 |
90.18s |
Intel(R) Core(TM) i5-8400 (6 threads) |
311.84s |
Intel(R) Core(TM) i5-8400 (6 threads) + RTX 2070 |
125.08s |
Intel(R) Xeon(R) Platinum 8360Y (18 threads) + A100-SXM4-40GB |
147.06s |
Intel(R) Xeon(R) Platinum 8360Y (36 threads) + 2x A100-SXM4-40GB |
72.59s |
Co HCP 11-21
The following code is used to run this example:
./build/bramble -p patterns/patterns.json -i src/test/data/POSCAR_Co1121 -o pa_co1121.txt
The Co11-21 slab model contains 48 atoms which are all recognized by the CNA algorithm. A detailed listing is given below:
----------------------------------------------------------------------------------------------------
# atom x y z color pattern fingerprint
----------------------------------------------------------------------------------------------------
0001 Co 3.810546 -0.660171 7.610554 a72424 HCP(11-21) 1(4,2,2)1(3,2,2)1(3,1,1)1(2,1,1)2(2,0,0)
0002 Co 3.740586 4.073047 7.709530 a72424 HCP(11-21) 1(4,2,2)1(3,2,2)1(3,1,1)1(2,1,1)2(2,0,0)
0003 Co 1.976955 0.571096 8.648905 a72424 HCP(11-21) 3(4,2,2)2(4,2,1)1(3,2,2)3(3,1,1)1(2,0,0)
0004 Co 1.897765 5.352941 8.661025 a72424 HCP(11-21) 3(4,2,2)2(4,2,1)1(3,2,2)3(3,1,1)1(2,0,0)
0005 Co 0.189433 1.908735 9.902833 cd1212 HCP bulk 6(4,2,2)6(4,2,1)
0006 Co 0.168029 6.645793 9.926156 cd1212 HCP bulk 6(4,2,2)6(4,2,1)
0007 Co 7.684312 -2.686362 7.688474 a72424 HCP(11-21) 1(4,2,2)1(3,2,2)1(3,1,1)1(2,1,1)2(2,0,0)
0008 Co 7.518976 2.095552 7.644121 a72424 HCP(11-21) 1(4,2,2)1(3,2,2)1(3,1,1)1(2,1,1)2(2,0,0)
0009 Co 5.797700 -1.353450 8.664054 a72424 HCP(11-21) 3(4,2,2)2(4,2,1)1(3,2,2)3(3,1,1)1(2,0,0)
0010 Co 5.751478 3.382846 8.712483 a72424 HCP(11-21) 3(4,2,2)2(4,2,1)1(3,2,2)3(3,1,1)1(2,0,0)
0011 Co 4.012030 -0.065299 9.896270 cd1212 HCP bulk 6(4,2,2)6(4,2,1)
0012 Co 4.004269 4.684700 9.936931 cd1212 HCP bulk 6(4,2,2)6(4,2,1)
0013 Co 2.271563 1.265690 11.088835 cd1212 HCP bulk 6(4,2,2)6(4,2,1)
0014 Co 2.239254 5.989902 11.086904 cd1212 HCP bulk 6(4,2,2)6(4,2,1)
0015 Co 0.529500 2.573367 12.372792 a72424 HCP(11-21) 3(4,2,2)4(4,2,1)1(3,2,2)2(3,1,1)1(3,0,0)
0016 Co 0.516629 7.332281 12.359231 a72424 HCP(11-21) 3(4,2,2)4(4,2,1)1(3,2,2)2(3,1,1)1(3,0,0)
0017 Co 6.122317 -0.728325 11.085389 cd1212 HCP bulk 6(4,2,2)6(4,2,1)
0018 Co 6.102395 4.034584 11.067144 cd1212 HCP bulk 6(4,2,2)6(4,2,1)
0019 Co 4.395721 0.588033 12.250446 a72424 HCP(11-21) 3(4,2,2)4(4,2,1)1(3,2,2)2(3,1,1)1(3,0,0)
0020 Co 4.352049 5.332994 12.380740 a72424 HCP(11-21) 3(4,2,2)4(4,2,1)1(3,2,2)2(3,1,1)1(3,0,0)
0021 Co 2.608498 1.904113 13.446673 a72424 HCP(11-21) 1(4,2,2)1(4,2,1)1(3,2,2)2(3,1,1)1(3,0,0)1(2,1,1)1(2,0,0)
0022 Co 2.617157 6.656903 13.369873 a72424 HCP(11-21) 1(4,2,2)1(4,2,1)1(3,2,2)2(3,1,1)1(3,0,0)1(2,1,1)1(2,0,0)
0023 Co 6.386291 -0.061239 13.452359 a72424 HCP(11-21) 1(4,2,2)1(4,2,1)1(3,2,2)2(3,1,1)1(3,0,0)1(2,1,1)1(2,0,0)
0024 Co 6.468642 4.640786 13.375854 a72424 HCP(11-21) 1(4,2,2)1(4,2,1)1(3,2,2)2(3,1,1)1(3,0,0)1(2,1,1)1(2,0,0)
0025 Co 0.226813 3.631587 8.103227 a72424 HCP(11-21) 1(4,2,2)1(4,2,1)1(3,2,2)2(3,1,1)1(3,0,0)1(2,1,1)1(2,0,0)
0026 Co 0.218154 8.351897 8.180027 a72424 HCP(11-21) 1(4,2,2)1(4,2,1)1(3,2,2)2(3,1,1)1(3,0,0)1(2,1,1)1(2,0,0)
0027 Co 4.136333 1.659554 8.097541 a72424 HCP(11-21) 1(4,2,2)1(4,2,1)1(3,2,2)2(3,1,1)1(3,0,0)1(2,1,1)1(2,0,0)
0028 Co 4.053981 6.430630 8.174046 a72424 HCP(11-21) 1(4,2,2)1(4,2,1)1(3,2,2)2(3,1,1)1(3,0,0)1(2,1,1)1(2,0,0)
0029 Co 2.305811 2.962334 9.177108 a72424 HCP(11-21) 3(4,2,2)4(4,2,1)1(3,2,2)2(3,1,1)1(3,0,0)
0030 Co 2.318682 7.676520 9.190669 a72424 HCP(11-21) 3(4,2,2)4(4,2,1)1(3,2,2)2(3,1,1)1(3,0,0)
0031 Co 0.563748 4.270010 10.461065 cd1212 HCP bulk 6(4,2,2)6(4,2,1)
0032 Co 0.596058 9.018898 10.462996 cd1212 HCP bulk 6(4,2,2)6(4,2,1)
0033 Co 6.126902 1.010282 9.299454 a72424 HCP(11-21) 3(4,2,2)4(4,2,1)1(3,2,2)2(3,1,1)1(3,0,0)
0034 Co 6.170574 5.738421 9.169159 a72424 HCP(11-21) 3(4,2,2)4(4,2,1)1(3,2,2)2(3,1,1)1(3,0,0)
0035 Co 4.400305 2.326640 10.464510 cd1212 HCP bulk 6(4,2,2)6(4,2,1)
0036 Co 2.667282 -1.110093 11.623743 cd1212 HCP bulk 6(4,2,2)6(4,2,1)
0037 Co 4.420228 7.036831 10.482756 cd1212 HCP bulk 6(4,2,2)6(4,2,1)
0038 Co 2.645878 3.626966 11.647067 cd1212 HCP bulk 6(4,2,2)6(4,2,1)
0039 Co 0.937546 0.182760 12.888876 a72424 HCP(11-21) 3(4,2,2)2(4,2,1)1(3,2,2)3(3,1,1)1(2,0,0)
0040 Co 0.858356 4.964604 12.900995 a72424 HCP(11-21) 3(4,2,2)2(4,2,1)1(3,2,2)3(3,1,1)1(2,0,0)
0041 Co 6.518353 -3.086385 11.612969 cd1212 HCP bulk 6(4,2,2)6(4,2,1)
0042 Co 6.510593 1.663614 11.653630 cd1212 HCP bulk 6(4,2,2)6(4,2,1)
0043 Co 4.771145 -1.784530 12.837416 a72424 HCP(11-21) 3(4,2,2)2(4,2,1)1(3,2,2)3(3,1,1)1(2,0,0)
0044 Co 4.724922 2.951765 12.885846 a72424 HCP(11-21) 3(4,2,2)2(4,2,1)1(3,2,2)3(3,1,1)1(2,0,0)
0045 Co 3.003647 -0.497237 13.905779 a72424 HCP(11-21) 1(4,2,2)1(3,2,2)1(3,1,1)1(2,1,1)2(2,0,0)
0046 Co 2.838310 4.284677 13.861425 a72424 HCP(11-21) 1(4,2,2)1(3,2,2)1(3,1,1)1(2,1,1)2(2,0,0)
0047 Co 6.782037 -2.474732 13.840369 a72424 HCP(11-21) 1(4,2,2)1(3,2,2)1(3,1,1)1(2,1,1)2(2,0,0)
0048 Co 6.712077 2.258486 13.939345 a72424 HCP(11-21) 1(4,2,2)1(3,2,2)1(3,1,1)1(2,1,1)2(2,0,0)
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The statitics block contains a summary of the above data from which it can be seen that this slab model contains 16 bulk atoms and 32 surface atoms of four different types:
Statistics
----------------------------------------------------------------------------------------------------
#atom perc pattern fingerprint
----------------------------------------------------------------------------------------------------
16 33.33% HCP bulk 6(4,2,2)6(4,2,1)
8 16.67% HCP(11-21) 1(4,2,2)1(4,2,1)1(3,2,2)2(3,1,1)1(3,0,0)1(2,1,1)1(2,0,0)
8 16.67% HCP(11-21) 3(4,2,2)4(4,2,1)1(3,2,2)2(3,1,1)1(3,0,0)
8 16.67% HCP(11-21) 3(4,2,2)2(4,2,1)1(3,2,2)3(3,1,1)1(2,0,0)
8 16.67% HCP(11-21) 1(4,2,2)1(3,2,2)1(3,1,1)1(2,1,1)2(2,0,0)
----------------------------------------------------------------------------------------------------
Clearly, we can see that all atoms are correctly identified. The majority of the periodic unit cell is made up of bulk HCP atoms. The different types or surface atoms are automatically recognized.
Continuing the study by performing a similarity analysis by running:
./build/bramble -s -i src/test/data/POSCAR_Co1121 -o sa_fcc111.txt
yields the result as shown in the image below. Comparing the image with the
CNA pattern per atom above, we can readily interpret this result. The light
squares inside the figure correspond to pairs of atoms which have the same
CNA fingerprint and are thus expected to have a very low \(\mu_{ij}\) value.
Furthermore, we can readily see that surface atoms are much more similar to
each other as compared to bulk atoms. For example, surface atoms with the
1(4,2,2)1(3,2,2)1(3,1,1)1(2,1,1)2(2,0,0) fingerprint have a
\(\mu_{ij} \approx 28\) with surface atoms with a
3(4,2,2)2(4,2,1)1(3,2,2)3(3,1,1)1(2,0,0) motif and \(\mu_{ij} \approx 17\)
with surface atoms with a
1(4,2,2)1(4,2,1)1(3,2,2)2(3,1,1)1(3,0,0)1(2,1,1)1(2,0,0) motif. In contrast, with respect
to bulk atoms, \(\mu_{ij} \approx 36\) is found.
Execution times
To get an impression of typical execution times and the benefit of GPU acceleration, we refer to the Table as seen below.
System |
Execution time (averaged) |
|---|---|
Intel(R) Core(TM) i9-10900K (20 threads) |
5207s |
Intel(R) Core(TM) i9-10900K (20 threads) + RTX 4090 |
2368s |
Intel(R) Xeon(R) Platinum 8360Y (18 threads) + A100-SXM4-40GB |
2543s |
Intel(R) Xeon(R) Platinum 8360Y (36 threads) + 2x A100-SXM4-40GB |
1366s |
Intel(R) Core(TM) i5-8400 (6 threads) + RTX 2070 |
2986s |
Intel(R) Xeon(R) Gold 6234 (16 threads) + A5000 |
3912s |
Intel(R) Core(TM) i5-12400F (12 threads) + 1x GTX 1080 Ti |
2759s |
Intel(R) Core(TM) i5-12400F (12 threads) + 2x GTX 1080 Ti |
2067s |