Tutorials#
Here we will learn some bvlain routines on the example of NaVPO\(_4\)F compound (see fig. 1 below)
Figure 1. Crystal structure of KTP-structured NaVPO\(_4\)F. Black spheres are Na\(^{+}\) ions
How it is supposed to work#
The sequence of steps for calculation is following:
Import class from the package
from bvlain import LainDefine the calculator
calc = Lain()Read structure
calc.read_file('file.cif')Define parameters for BVSE distribution calculation
params = {'some_param': some_value, ...}Calculate BVSE distribution
calc.bvse_distribution(**params)After the last step we have the distribution
Apply method on the top of this distribution:
calc.percolation_analysis(encut = 5.0), etc.
Note: methods depending on BVSE distribution won’t work before calc.bvse_distribution(**params) is invoked
Import#
[1]:
from bvlain import Lain
Calculation of BVSE distribution#
[2]:
file = '/Users/artemdembitskiy/Downloads/NaVPO4F.cif' # your .cif file, only ordered structures allowed
calc = Lain(verbose = True) # define calculator
calc.read_file(file) # read structure
# define params
params = {
'mobile_ion': 'Na1+',
'r_cut': 10.0,
'resolution': 0.2,
'k': 100
}
_ = calc.bvse_distribution(**params) # calculate bvse distribution
getting BVSE distribution...
collecting force field parameters... Na | charge: 1.0
collecting neighbors...
distribution is ready
Percolation analysis#
[8]:
calc.percolation_barriers(encut = 5.0)
[8]:
{'E_1D': 0.166, 'E_2D': 0.4395, 'E_3D': 0.4492}
That’s it. As you could see, there is a quite low activation threshold for 1D percolation (see fig.2). At 0.45 eV the percolation network becomes 3-dimensional (not shown). Note that the percolation thresholds are found with 0.01 eV precision.
Write .grd file for VESTA 3.0#
[9]:
calc.write_grd(file)
Figure 2. Na\(^+\) 1D percolation trajectory in VPO\(_4\)F framework. Black spheres are Na\(^{+}\) ions
BVS mismatch#
Also we can check if assigned oxidation states are in agreement with crystal structure. It can be done with Lain.mismatch method that calculates Bond Valence sum mismatch.
[10]:
table = calc.mismatch(r_cut = 4.0)
print(table.to_string())
atom x/a y/b z/c formal_charge bvs mismatch
0 Na 0.7735 0.2784 0.3557 1 0.727085 -0.272915
1 Na 0.2265 0.7784 0.6443 1 0.727085 -0.272915
2 Na 0.7265 0.2784 0.8557 1 0.727085 -0.272915
3 Na 0.2735 0.7784 0.1443 1 0.727085 -0.272915
4 Na 0.7942 0.0479 0.1034 1 0.793218 -0.206782
5 Na 0.2058 0.5479 0.8966 1 0.793218 -0.206782
6 Na 0.7058 0.0479 0.6034 1 0.793218 -0.206782
7 Na 0.2942 0.5479 0.3966 1 0.793218 -0.206782
8 V 0.4992 0.0064 0.3828 3 2.736372 -0.263628
9 V 0.5008 0.5064 0.6172 3 2.736372 -0.263628
10 V 0.0008 0.0064 0.8828 3 2.736372 -0.263628
11 V 0.9992 0.5064 0.1172 3 2.736372 -0.263628
12 V 0.2506 0.2509 0.2415 3 2.690837 -0.309163
13 V 0.7494 0.7509 0.7585 3 2.690837 -0.309163
14 V 0.2494 0.2509 0.7415 3 2.690837 -0.309163
15 V 0.7506 0.7509 0.2585 3 2.690837 -0.309163
16 P 0.3393 0.2642 0.4917 5 4.762002 -0.237998
17 P 0.6607 0.7642 0.5083 5 4.762002 -0.237998
18 P 0.1607 0.2642 0.9917 5 4.762002 -0.237998
19 P 0.8393 0.7642 0.0083 5 4.762002 -0.237998
20 P 0.5017 0.5053 0.1829 5 4.819918 -0.180082
21 P 0.4983 0.0053 0.8171 5 4.819918 -0.180082
22 P 0.9983 0.5053 0.6829 5 4.819918 -0.180082
23 P 0.0017 0.0053 0.3171 5 4.819918 -0.180082
24 O 0.5046 0.1593 0.4772 -2 1.882046 -0.117954
25 O 0.4954 0.6593 0.5228 -2 1.882046 -0.117954
26 O 0.9954 0.1593 0.9772 -2 1.882046 -0.117954
27 O 0.0046 0.6593 0.0228 -2 1.882046 -0.117954
28 O 0.4674 0.3876 0.4985 -2 1.842362 -0.157638
29 O 0.5326 0.8876 0.5015 -2 1.842362 -0.157638
30 O 0.0326 0.3876 0.9985 -2 1.842362 -0.157638
31 O 0.9674 0.8876 0.0015 -2 1.842362 -0.157638
32 O 0.1923 0.2743 0.3959 -2 1.789972 -0.210028
33 O 0.8077 0.7743 0.6041 -2 1.789972 -0.210028
34 O 0.3077 0.2743 0.8959 -2 1.789972 -0.210028
35 O 0.6923 0.7743 0.1041 -2 1.789972 -0.210028
36 O 0.2051 0.2406 0.5891 -2 1.749525 -0.250475
37 O 0.7949 0.7406 0.4109 -2 1.749525 -0.250475
38 O 0.2949 0.2406 0.0891 -2 1.749525 -0.250475
39 O 0.7051 0.7406 0.9109 -2 1.749525 -0.250475
40 O 0.3104 0.5339 0.1131 -2 1.865734 -0.134266
41 O 0.6896 0.0339 0.8869 -2 1.865734 -0.134266
42 O 0.1896 0.5339 0.6131 -2 1.865734 -0.134266
43 O 0.8104 0.0339 0.3869 -2 1.865734 -0.134266
44 O 0.6928 0.4885 0.1125 -2 1.794946 -0.205054
45 O 0.3072 0.9885 0.8875 -2 1.794946 -0.205054
46 O 0.8072 0.4885 0.6125 -2 1.794946 -0.205054
47 O 0.1928 0.9885 0.3875 -2 1.794946 -0.205054
48 O 0.5288 0.6173 0.2592 -2 1.844736 -0.155264
49 O 0.4712 0.1173 0.7408 -2 1.844736 -0.155264
50 O 0.9712 0.6173 0.7592 -2 1.844736 -0.155264
51 O 0.0288 0.1173 0.2408 -2 1.844736 -0.155264
52 O 0.4633 0.3898 0.2529 -2 1.816623 -0.183377
53 O 0.5367 0.8898 0.7471 -2 1.816623 -0.183377
54 O 0.0367 0.3898 0.7529 -2 1.816623 -0.183377
55 O 0.9633 0.8898 0.2471 -2 1.816623 -0.183377
56 F 0.5094 0.8728 0.2730 -1 0.998247 -0.001753
57 F 0.4906 0.3728 0.7270 -1 0.998247 -0.001753
58 F 0.9906 0.8728 0.7730 -1 0.998247 -0.001753
59 F 0.0094 0.3728 0.2270 -1 0.998247 -0.001753
60 F 0.4915 0.1279 0.2614 -1 0.945241 -0.054759
61 F 0.5085 0.6279 0.7386 -1 0.945241 -0.054759
62 F 0.0085 0.1279 0.7614 -1 0.945241 -0.054759
63 F 0.9915 0.6279 0.2386 -1 0.945241 -0.054759