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