def test_build_3():
"""Verify VerletList.build_grid against VerletList.build_simple."""
cutoff = 5.0
max_neighbours = 100
n_squares = 3
box = et_ppmd.Box(0., 0., n_squares * 5. * et_ppmd.hcp.uc_centered_a,
n_squares * 3. * et_ppmd.hcp.uc_centered_b)
x, y = box.generateAtoms(r=et_ppmd.hcp.radius)
# compute grid
the_grid = grid.Grid(cell_size=cutoff,
wx=box.xur - box.xll,
wy=box.yur - box.yll,
max_atoms_per_cell=100)
the_grid.build(x, y)
# build grid-based verlet list
vl = verlet.VerletList(cutoff=cutoff, max_neighbours=max_neighbours)
vl.build_grid(x, y, the_grid)
print(vl)
pairs = vl2set(vl)
vlsimple = verlet.VerletList(cutoff=cutoff, max_neighbours=max_neighbours)
vlsimple.build_simple(x, y)
print(vlsimple)
expected = vl2set(vlsimple)
assert pairs == 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)
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_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_build_2():
"""Verify VerletList.build against VerletList.build_simple."""
cutoff = 5.0
max_neighbours = 50
n_squares = 3
box = et_ppmd.Box(0., 0., n_squares * 5. * et_ppmd.hcp.uc_centered_a,
n_squares * 3. * et_ppmd.hcp.uc_centered_b)
x, y = box.generateAtoms(r=et_ppmd.hcp.radius)
vl = verlet.VerletList(cutoff=cutoff, max_neighbours=max_neighbours)
vl.build(x, y)
print(vl)
pairs = vl2set(vl)
vlsimple = verlet.VerletList(cutoff=cutoff, max_neighbours=max_neighbours)
vlsimple.build_simple(x, y)
print(vlsimple)
expected = vl2set(vlsimple)
assert pairs == 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))
from et_stopwatch import Stopwatch
import matplotlib.pyplot as plt
if __name__ == '__main__':
cutoff = 5.0
max_neighbours = 60
# some lists to store our results
n_at = [] # number of atoms
t_bs = [] # timings for VerletList.build_simple
t_b = [] # timings for VerletList.build
t_bg = [] # timings for VerletList.build_grid
for n_squares in range(1, 16):
# a single square contains on average 30 atoms ( 6 rows of each 5 atoms)
box = et_ppmd.Box(0., 0., n_squares * 5. * et_ppmd.hcp.uc_centered_a,
n_squares * 3. * et_ppmd.hcp.uc_centered_b)
x, y = box.generateAtoms(r=et_ppmd.hcp.radius)
n_atoms = len(x)
# store n_atoms in the result array
n_at.append(n_atoms)
vl = verlet.VerletList(cutoff=cutoff, max_neighbours=max_neighbours)
# time building the Verlet list
with Stopwatch(message=f"VerletList.build_simple for {n_atoms} atoms"
) as sw_build_simple:
vl.build_simple(x, y)
# store the timing in the result array
t_bs.append(sw_build_simple.time)
# time building the Verlet list
with Stopwatch(