def test_computeForces():
""""""
box = md.Box(0., 0., 5. * md.hcp.uc_centered_a, 0.5 * md.hcp.uc_centered_b)
atoms = md.MD(box, cutoff=2.5)
if __plot:
cmn.figure()
cmn.plotBox(box)
cmn.plotAtoms(atoms.x, atoms.y, radius=atoms.radius)
cmn.plt.show()
atoms.buildVerletLists()
print(atoms.vl)
cpp.computeForces(
atoms.x,
atoms.y # atom positions
,
atoms.vl.vl_size,
atoms.vl.vl_list # linearized verlet list data structure
,
atoms.ax,
atoms.ay # atom forces
)
print(f'ax={atoms.ax}')
print(f'ay={atoms.ay}')
r = md.hcp.uc_centered_a
r01sq = r**2
r02sq = (2 * r)**2
fx01 = lj.force_factor(r01sq) * r
fx02 = lj.force_factor(r02sq) * 2 * r
expected = np.array([fx01, fx01, fx01, fx01, 0.00]) \
+ np.array([fx02, fx02, fx02, 0.00, 0.00]) \
- np.array([0.00, fx01, fx01, fx01, fx01]) \
- np.array([0.00, 0.00, fx02, fx02, fx02])
assert np.all(atoms.ax == expected)
assert np.all(atoms.ay == np.zeros((atoms.n_atoms, ), dtype=float))
def test_MDCtor():
box = md.Box(0., 0., 5. * md.hcp.uc_centered_a, 3. * md.hcp.uc_centered_b)
atoms = md.MD(box)
cmn.figure()
cmn.plotBox(box)
cmn.plotAtoms(atoms.x, atoms.y, radius=atoms.radius)
if __plot:
cmn.plt.show()
def test_plotAtomsInBox():
r0 = 1
xll, yll = 0.0, 0.0
w = r0
h = sqrt3
box = md.Box(xll, yll, xll + 3 * w, yll + 3 * h)
x, y = box.generateAtoms(r=r0, noise=.1)
md.figure()
md.plotAtoms(x, y) # dots
md.plotAtoms(x, y, radius=r0 / 2) # circles with atom radius
md.plotBox(box) # containing box
md.plt.show()
def test_computeEnergy():
""""""
box = md.Box(0., 0., 5. * md.hcp.uc_centered_a, 0.5 * md.hcp.uc_centered_b)
atoms = md.MD(box, cutoff=2.5)
if __plot:
cmn.figure()
cmn.plotBox(box)
cmn.plotAtoms(atoms.x, atoms.y, radius=atoms.radius)
cmn.plt.show()
atoms.buildVerletLists()
print(atoms.vl)
energy = atoms.computeEnergy()
r01sq = md.hcp.uc_centered_a**2
r02sq = (2 * md.hcp.uc_centered_a)**2
expected = 4 * lj.potential(r01sq) + 3 * lj.potential(r02sq)
print(energy)
print(expected)
assert energy == expected
def test_computeForces():
""""""
box = md.Box(0., 0., 5. * md.hcp.uc_centered_a, 0.5 * md.hcp.uc_centered_b)
atoms = md.MD(box, cutoff=2.5)
if __plot:
cmn.figure()
cmn.plotBox(box)
cmn.plotAtoms(atoms.x, atoms.y, radius=atoms.radius)
cmn.plt.show()
atoms.buildVerletLists()
print(atoms.vl)
energy = atoms.computeForces()
r = md.hcp.uc_centered_a
r01sq = r**2
r02sq = (2 * r)**2
fx01 = lj.force_factor(r01sq) * r
fx02 = lj.force_factor(r02sq) * 2 * r
expected = np.array([fx01, fx01, fx01, fx01, 0.00]) \
+ np.array([fx02, fx02, fx02, 0.00, 0.00]) \
- np.array([0.00, fx01, fx01, fx01, fx01]) \
- np.array([0.00, 0.00, fx02, fx02, fx02])
assert np.all(atoms.ax == expected)
print(atoms.ay)
assert np.all(atoms.ay == np.zeros((atoms.n_atoms, ), dtype=float))