root / ase / test / center.py @ 13
Historique | Voir | Annoter | Télécharger (2,21 ko)
| 1 |
"Test that atoms.center() works when adding vacuum ()"
|
|---|---|
| 2 |
|
| 3 |
import numpy as np |
| 4 |
from math import pi, sqrt, cos |
| 5 |
from ase import data |
| 6 |
from ase.lattice.cubic import FaceCenteredCubic |
| 7 |
|
| 8 |
def checkang(a, b, phi): |
| 9 |
"Check the angle between two vectors."
|
| 10 |
cosphi = np.dot(a,b) / sqrt(np.dot(a,a) * np.dot(b,b)) |
| 11 |
assert np.abs(cosphi - cos(phi)) < 1e-10 |
| 12 |
|
| 13 |
symb = "Cu"
|
| 14 |
Z = data.atomic_numbers[symb] |
| 15 |
a0 = data.reference_states[Z]['a']
|
| 16 |
|
| 17 |
# (100) oriented block
|
| 18 |
atoms = FaceCenteredCubic(size=(5,5,5), symbol="Cu", pbc=(1,1,0)) |
| 19 |
assert len(atoms) == 5*5*5*4 |
| 20 |
c = atoms.get_cell() |
| 21 |
checkang(c[0], c[1], pi/2) |
| 22 |
checkang(c[0], c[2], pi/2) |
| 23 |
checkang(c[1], c[2], pi/2) |
| 24 |
assert np.abs(5 * a0 - c[2,2]) < 1e-10 |
| 25 |
|
| 26 |
# Add vacuum in one direction
|
| 27 |
vac = 10.0
|
| 28 |
atoms.center(axis=2, vacuum=vac)
|
| 29 |
c = atoms.get_cell() |
| 30 |
checkang(c[0], c[1], pi/2) |
| 31 |
checkang(c[0], c[2], pi/2) |
| 32 |
checkang(c[1], c[2], pi/2) |
| 33 |
assert np.abs(4.5 * a0 + 2* vac - c[2,2]) < 1e-10 |
| 34 |
|
| 35 |
# Add vacuum in all directions
|
| 36 |
vac = 4.0
|
| 37 |
atoms.center(vacuum=vac) |
| 38 |
c = atoms.get_cell() |
| 39 |
checkang(c[0], c[1], pi/2) |
| 40 |
checkang(c[0], c[2], pi/2) |
| 41 |
checkang(c[1], c[2], pi/2) |
| 42 |
assert np.abs(4.5 * a0 + 2* vac - c[0,0]) < 1e-10 |
| 43 |
assert np.abs(4.5 * a0 + 2* vac - c[1,1]) < 1e-10 |
| 44 |
assert np.abs(4.5 * a0 + 2* vac - c[2,2]) < 1e-10 |
| 45 |
|
| 46 |
# Now a general unit cell
|
| 47 |
atoms = FaceCenteredCubic(size=(5,5,5), directions=[[1,0,0], [0,1,0], [1,0,1]], |
| 48 |
symbol="Cu", pbc=(1,1,0)) |
| 49 |
assert len(atoms) == 5*5*5*2 |
| 50 |
c = atoms.get_cell() |
| 51 |
checkang(c[0], c[1], pi/2) |
| 52 |
checkang(c[0], c[2], pi/4) |
| 53 |
checkang(c[1], c[2], pi/2) |
| 54 |
assert np.abs(2.5 * a0 - c[2,2]) < 1e-10 |
| 55 |
|
| 56 |
# Add vacuum in one direction
|
| 57 |
vac = 10.0
|
| 58 |
atoms.center(axis=2, vacuum=vac)
|
| 59 |
c = atoms.get_cell() |
| 60 |
checkang(c[0], c[1], pi/2) |
| 61 |
checkang(c[0], c[2], pi/4) |
| 62 |
checkang(c[1], c[2], pi/2) |
| 63 |
assert np.abs(2 * a0 + 2* vac - c[2,2]) < 1e-10 |
| 64 |
|
| 65 |
# Recenter without specifying vacuum
|
| 66 |
atoms.center() |
| 67 |
c = atoms.get_cell() |
| 68 |
checkang(c[0], c[1], pi/2) |
| 69 |
checkang(c[0], c[2], pi/4) |
| 70 |
checkang(c[1], c[2], pi/2) |
| 71 |
assert np.abs(2 * a0 + 2* vac - c[2,2]) < 1e-10 |
| 72 |
|
| 73 |
# Add vacuum in all directions
|
| 74 |
vac = 4.0
|
| 75 |
atoms.center(vacuum=vac) |
| 76 |
c = atoms.get_cell() |
| 77 |
checkang(c[0], c[1], pi/2) |
| 78 |
checkang(c[0], c[2], pi/4) |
| 79 |
checkang(c[1], c[2], pi/2) |
| 80 |
assert np.abs(4.5 * a0 + 2* vac - c[1,1]) < 1e-10 |
| 81 |
assert np.abs(2 * a0 + 2* vac - c[2,2]) < 1e-10 |
| 82 |
|