1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
|
import numpy as np
from scipy.optimize import check_grad
from ase import Atoms
from ase.vibrations import Vibrations
from ase.calculators.morse import MorsePotential, fcut, fcut_d
from ase.build import bulk
De = 5.
Re = 3.
rho0 = 2.
def test_gs_minimum_energy():
atoms = Atoms('H2', positions=[[0, 0, 0], [0, 0, Re]])
atoms.calc = MorsePotential(epsilon=De, r0=Re)
assert atoms.get_potential_energy() == -De
def test_gs_vibrations(testdir):
# check ground state vibrations
atoms = Atoms('H2', positions=[[0, 0, 0], [0, 0, Re]])
atoms.calc = MorsePotential(epsilon=De, r0=Re, rho0=rho0)
vib = Vibrations(atoms)
vib.run()
def test_cutoff():
# check that fcut_d is the derivative of fcut
r1 = 2.0
r2 = 3.0
r = np.linspace(r1 - 0.5, r2 + 0.5, 100)
for R in r:
assert check_grad(fcut, fcut_d, np.array([R]), r1, r2) < 1e-5
def test_forces():
atoms = bulk('Cu', cubic=True)
atoms.calc = MorsePotential(A=4.0, epsilon=1.0, r0=2.55)
atoms.rattle(0.1)
forces = atoms.get_forces()
numerical_forces = atoms.calc.calculate_numerical_forces(atoms, d=1e-5)
assert np.abs(forces - numerical_forces).max() < 1e-5
|
