Bugs when detecting the sites of step Ru105 surface

[zzkmirok]

Discription

When simply reading the xyz fil of Ru105 surface and running site detection with autoadsorbate, I failed to get all sites, especially B5 sites with the default parameters of touch_sphere_size and precision in the Surface creation.

Tests:

I ran the tests on the main branch of the code.:

from autoadsorbate.autoadsorbate import Surface

from ase import Atoms
from ase.io import read

import numpy as np
import copy

slab_Ru105 = read('Ru_105_surface.xyz')

Surface_Ru105 = Surface(slab_Ru105)
Surface_Ru105_df = Surface_Ru105.site_df

Changing touch_sphere_size

I did some tests by changing the touch_sphere_size and fixing the precision=0.25:

Here are the results by checking the number of elements in each site_formula:

touch_sphere_size from 2.6 to 3.3

When touch sphere size is 2.600:
    we detected set of Ru: {1, 2, 3}
        len(Ru: 1) = 18
        len(Ru: 2) = 46
        len(Ru: 3) = 9
When touch sphere size is 2.650:
    we detected set of Ru: {1, 2, 3}
        len(Ru: 1) = 18
        len(Ru: 2) = 41
        len(Ru: 3) = 11
When touch sphere size is 2.700:
    we detected set of Ru: {1, 2, 3}
        len(Ru: 1) = 18
        len(Ru: 2) = 49
        len(Ru: 3) = 11
When touch sphere size is 2.750:
    we detected set of Ru: {1, 2, 3}
        len(Ru: 1) = 18
        len(Ru: 2) = 48
        len(Ru: 3) = 13
When touch sphere size is 2.800:
    we detected set of Ru: {1, 2, 3, 4}
        len(Ru: 1) = 18
        len(Ru: 2) = 39
        len(Ru: 3) = 12
        len(Ru: 4) = 2
When touch sphere size is 2.850:
    we detected set of Ru: {1, 2, 3, 4}
        len(Ru: 1) = 18
        len(Ru: 2) = 42
        len(Ru: 3) = 8
        len(Ru: 4) = 6
When touch sphere size is 2.900:
    we detected set of Ru: {1, 2, 3, 4}
        len(Ru: 1) = 17
        len(Ru: 2) = 37
        len(Ru: 3) = 5
        len(Ru: 4) = 7
When touch sphere size is 2.950:
    we detected set of Ru: {1, 2, 3, 4, 5}
        len(Ru: 1) = 15
        len(Ru: 2) = 41
        len(Ru: 3) = 19
        len(Ru: 4) = 2
        len(Ru: 5) = 5
When touch sphere size is 3.000:
    we detected set of Ru: {1, 2, 3, 4, 5}
        len(Ru: 1) = 15
        len(Ru: 2) = 36
        len(Ru: 3) = 22
        len(Ru: 4) = 2
        len(Ru: 5) = 2
When touch sphere size is 3.050:
    we detected set of Ru: {1, 2, 3, 4, 5}
        len(Ru: 1) = 15
        len(Ru: 2) = 36
        len(Ru: 3) = 18
        len(Ru: 4) = 1
        len(Ru: 5) = 2
When touch sphere size is 3.100:
    we detected set of Ru: {1, 2, 3}
        len(Ru: 1) = 15
        len(Ru: 2) = 31
        len(Ru: 3) = 2
When touch sphere size is 3.150:
    we detected set of Ru: {1, 2}
        len(Ru: 1) = 12
        len(Ru: 2) = 7
When touch sphere size is 3.200:
    we detected set of Ru: set()
When touch sphere size is 3.250:
    we detected set of Ru: set()
When touch sphere size is 3.300:
    we detected set of Ru: set()

Changing precision

Now changing the precision and fixing the touch_sphere_size=3.0:

Here are the results by checking the number of elements in each site_formula:

When precision is 0.050:
    we detected set of Ru: {1, 2, 3, 4, 5}
        len(Ru: 1) = 15
        len(Ru: 2) = 36
        len(Ru: 3) = 34
        len(Ru: 4) = 23
        len(Ru: 5) = 6
When precision is 0.100:
    we detected set of Ru: {1, 2, 3, 4, 5}
        len(Ru: 1) = 15
        len(Ru: 2) = 36
        len(Ru: 3) = 29
        len(Ru: 4) = 6
        len(Ru: 5) = 6
When precision is 0.150:
    we detected set of Ru: {1, 2, 3, 4, 5}
        len(Ru: 1) = 12
        len(Ru: 2) = 36
        len(Ru: 3) = 29
        len(Ru: 4) = 3
        len(Ru: 5) = 5
When precision is 0.200:
    we detected set of Ru: {1, 2, 3, 4, 5}
        len(Ru: 1) = 15
        len(Ru: 2) = 36
        len(Ru: 3) = 25
        len(Ru: 4) = 1
        len(Ru: 5) = 4
When precision is 0.250:
    we detected set of Ru: {1, 2, 3, 4, 5}
        len(Ru: 1) = 15
        len(Ru: 2) = 36
        len(Ru: 3) = 22
        len(Ru: 4) = 2
        len(Ru: 5) = 2
When precision is 0.300:
    we detected set of Ru: {1, 2, 3}
        len(Ru: 1) = 12
        len(Ru: 2) = 35
        len(Ru: 3) = 25
When precision is 0.350:
    we detected set of Ru: {1, 2, 3}
        len(Ru: 1) = 12
        len(Ru: 2) = 36
        len(Ru: 3) = 17
When precision is 0.400:
    we detected set of Ru: {1, 2, 3, 5}
        len(Ru: 1) = 14
        len(Ru: 2) = 32
        len(Ru: 3) = 13
        len(Ru: 5) = 2
When precision is 0.450:
    we detected set of Ru: {1, 2, 3, 4, 5}
        len(Ru: 1) = 12
        len(Ru: 2) = 33
        len(Ru: 3) = 11
        len(Ru: 4) = 1
        len(Ru: 5) = 2

Conclusion:

From observation, the number of Top site ({Ru:1}) must be 18, and the number of B5 site (Ru: 5) must be 6 in this case, which we can not get the correct results with the default parameters. With touch_sphere_size=2.95 and precision=0.08, we can get the correct number of both top sites and b5 sites:

    we detected set of Ru: {1, 2, 3, 4, 5}
        len(Ru: 1) = 18
        len(Ru: 2) = 42
        len(Ru: 3) = 48
        len(Ru: 4) = 21
        len(Ru: 5) = 6

---

The XYZ file (can be not updated):

72
Lattice="8.156758991 0.0 0.0 1.359459832 12.53368649 0.0 0.0 0.0 49.019105761" Properties=species:S:1:pos:R:3:move_mask:L:1:magmoms:R:1:forces:R:3 magmom=-8.75e-05 stress="0.017827628757769477 8.170135445781184e-06 -9.362263688824888e-06 8.170135445781184e-06 0.016799983004720177 -0.0004477221741269838 -9.362263688824888e-06 -0.0004477221741269838 0.008248591215493538" free_energy=-658.65399883 energy=-658.64957114 pbc="T T F"
Ru 1.35946000 5.89787000 20.00000000 F -0.00000000 0.00020000 -0.62707000 1.56846400
Ru 2.71892000 11.79608000 20.13461000 F -0.00000000 0.00155900 -0.45809400 1.48211000
Ru 2.71892000 3.68607000 20.80768000 F -0.00000000 -0.00328000 0.66199300 0.81621100
Ru 1.35946000 9.58428000 20.94229000 F -0.00000000 0.00054700 0.65337100 0.66091700
Ru 1.35946000 1.47427000 21.61536000 F -0.00000000 0.00042800 0.01397500 0.00020700
Ru 2.71892000 7.37248000 21.74998000 F -0.00000000 -0.00154000 0.07587200 -0.45497700
Ru 1.35946000 11.79616000 22.42304000 F -0.00000000 -0.00024500 -0.21299300 -1.07090300
Ru 1.35946000 5.16069000 22.55766000 F -0.00000000 0.00083500 -0.21512800 -1.09165500
Ru 2.71892000 9.58437000 23.23072000 F -0.00000000 0.00059800 0.06981400 -0.52579200
Ru 2.71892000 2.94889000 23.36534000 F -0.00000000 -0.00235800 -0.06126600 -0.73648700
Ru 1.35946000 7.37257000 24.03841000 F 0.00000000 0.00241600 -0.07059200 -0.29851500
Ru 1.35946000 0.73709000 24.17302000 F -0.00000000 0.00032200 0.13684100 -0.35564900
Ru 2.71888000 5.13681000 24.81555000 T -0.00000000 -0.00005500 0.00459300 0.00267400
Ru 1.35953000 11.04318000 24.96181000 T 0.00000000 -0.00002500 0.00249500 -0.00643800
Ru 1.35957000 2.94573000 25.63404000 T -0.00000000 0.00004600 0.00046100 0.00185700
Ru 2.71919000 8.83544000 25.74101000 T -0.00000000 -0.00033700 0.00068300 0.00466900
Ru 2.71883000 0.73379000 26.42804000 T -0.00000000 -0.00010700 0.00624600 0.00276500
Ru 1.35937000 6.61268000 26.56828000 T -0.00000000 0.00014600 0.00551700 0.00283900
Ru 2.71936000 11.04024000 27.25505000 T -0.00000000 0.00003600 -0.00214500 0.00196800
Ru 2.71863000 4.41387000 27.35538000 T -0.00000000 0.00060600 0.00127900 0.00256000
Ru 1.35983000 8.80413000 27.95279000 T -0.00000000 0.00042900 0.00345600 -0.00403700
Ru 1.35963000 2.16164000 28.08439000 T -0.00000000 -0.00011800 -0.00006700 -0.00078900
Ru 2.71873000 6.71308000 28.70973000 T -0.00000000 0.00014700 0.00427800 -0.00084300
Ru 0.00025000 0.07156000 28.84806000 T -0.00000000 -0.00025100 0.00648200 -0.00115800
Ru 4.07838000 5.89787000 20.00000000 F -0.00000000 0.00020000 -0.62707000 1.56846400
Ru 5.43784000 11.79608000 20.13461000 F -0.00000000 0.00155900 -0.45809400 1.48211000
Ru 5.43784000 3.68607000 20.80768000 F -0.00000000 -0.00328000 0.66199300 0.81621100
Ru 4.07838000 9.58428000 20.94229000 F -0.00000000 0.00054700 0.65337100 0.66091700
Ru 4.07838000 1.47427000 21.61536000 F -0.00000000 0.00042800 0.01397500 0.00020700
Ru 5.43784000 7.37248000 21.74998000 F -0.00000000 -0.00154000 0.07587200 -0.45497700
Ru 4.07838000 11.79616000 22.42304000 F -0.00000000 -0.00024500 -0.21299300 -1.07090300
Ru 4.07838000 5.16069000 22.55766000 F -0.00000000 0.00083500 -0.21512800 -1.09165500
Ru 5.43784000 9.58437000 23.23072000 F -0.00000000 0.00059800 0.06981400 -0.52579200
Ru 5.43784000 2.94889000 23.36534000 F -0.00000000 -0.00235800 -0.06126600 -0.73648700
Ru 4.07838000 7.37257000 24.03841000 F 0.00000000 0.00241600 -0.07059200 -0.29851500
Ru 4.07838000 0.73709000 24.17302000 F -0.00000000 0.00032200 0.13684100 -0.35564900
Ru 5.43780000 5.13681000 24.81555000 T -0.00000000 -0.00005500 0.00459300 0.00267400
Ru 4.07845000 11.04318000 24.96181000 T 0.00000000 -0.00002500 0.00249500 -0.00643800
Ru 4.07849000 2.94573000 25.63404000 T -0.00000000 0.00004600 0.00046100 0.00185700
Ru 5.43811000 8.83544000 25.74101000 T -0.00000000 -0.00033700 0.00068300 0.00466900
Ru 5.43775000 0.73379000 26.42804000 T -0.00000000 -0.00010700 0.00624600 0.00276500
Ru 4.07829000 6.61268000 26.56828000 T -0.00000000 0.00014600 0.00551700 0.00283900
Ru 5.43828000 11.04024000 27.25505000 T -0.00000000 0.00003600 -0.00214500 0.00196800
Ru 5.43755000 4.41387000 27.35538000 T -0.00000000 0.00060600 0.00127900 0.00256000
Ru 4.07875000 8.80413000 27.95279000 T -0.00000000 0.00042900 0.00345600 -0.00403700
Ru 4.07855000 2.16164000 28.08439000 T -0.00000000 -0.00011800 -0.00006700 -0.00078900
Ru 5.43765000 6.71308000 28.70973000 T -0.00000000 0.00014700 0.00427800 -0.00084300
Ru 2.71917000 0.07156000 28.84806000 T -0.00000000 -0.00025100 0.00648200 -0.00115800
Ru 6.79730000 5.89787000 20.00000000 F -0.00000000 0.00020000 -0.62707000 1.56846400
Ru 8.15676000 11.79608000 20.13461000 F -0.00000000 0.00155900 -0.45809400 1.48211000
Ru 8.15676000 3.68607000 20.80768000 F -0.00000000 -0.00328000 0.66199300 0.81621100
Ru 6.79730000 9.58428000 20.94229000 F -0.00000000 0.00054700 0.65337100 0.66091700
Ru 6.79730000 1.47427000 21.61536000 F -0.00000000 0.00042800 0.01397500 0.00020700
Ru 8.15676000 7.37248000 21.74998000 F -0.00000000 -0.00154000 0.07587200 -0.45497700
Ru 6.79730000 11.79616000 22.42304000 F -0.00000000 -0.00024500 -0.21299300 -1.07090300
Ru 6.79730000 5.16069000 22.55766000 F -0.00000000 0.00083500 -0.21512800 -1.09165500
Ru 8.15676000 9.58437000 23.23072000 F -0.00000000 0.00059800 0.06981400 -0.52579200
Ru 8.15676000 2.94889000 23.36534000 F -0.00000000 -0.00235800 -0.06126600 -0.73648700
Ru 6.79730000 7.37257000 24.03841000 F 0.00000000 0.00241600 -0.07059200 -0.29851500
Ru 6.79730000 0.73709000 24.17302000 F -0.00000000 0.00032200 0.13684100 -0.35564900
Ru 8.15672000 5.13681000 24.81555000 T 0.00000000 -0.00005500 0.00459300 0.00267400
Ru 6.79737000 11.04318000 24.96181000 T 0.00000000 -0.00002500 0.00249500 -0.00643800
Ru 6.79741000 2.94573000 25.63404000 T -0.00000000 0.00004600 0.00046100 0.00185700
Ru 8.15703000 8.83544000 25.74101000 T -0.00000000 -0.00033700 0.00068300 0.00466900
Ru 8.15666000 0.73379000 26.42804000 T -0.00000000 -0.00010700 0.00624600 0.00276500
Ru 6.79720000 6.61268000 26.56828000 T -0.00000000 0.00014600 0.00551700 0.00283900
Ru 8.15720000 11.04024000 27.25505000 T -0.00000000 0.00003600 -0.00214500 0.00196800
Ru 8.15647000 4.41387000 27.35538000 T -0.00000000 0.00060600 0.00127900 0.00256000
Ru 6.79767000 8.80413000 27.95279000 T -0.00000000 0.00042900 0.00345600 -0.00403700
Ru 6.79747000 2.16164000 28.08439000 T -0.00000000 -0.00011800 -0.00006700 -0.00078900
Ru 8.15657000 6.71308000 28.70973000 T -0.00000000 0.00014700 0.00427800 -0.00084300
Ru 5.43809000 0.07156000 28.84806000 T -0.00000000 -0.00025100 0.00648200 -0.00115800