def test_dist_traj():
natoms = 10
nstep = 100
cell = rand(nstep, 3, 3)
stress = rand(nstep, 3, 3)
forces = rand(nstep, natoms, 3)
etot = rand(nstep)
cryst_const = crys.cell2cc3d(cell, axis=0)
coords_frac = np.random.rand(nstep, natoms, 3)
coords = crys.coord_trans3d(coords=coords_frac,
old=cell,
new=num.extend_array(np.identity(3),
nstep,
axis=0),
axis=1,
timeaxis=0)
assert cryst_const.shape == (nstep, 6)
assert coords.shape == (nstep, natoms, 3)
symbols = ['H'] * natoms
traj = Trajectory(
coords_frac=coords_frac,
cell=cell,
symbols=symbols,
forces=forces,
stress=stress,
etot=etot,
timestep=1,
)
for pbc in [True, False]:
# (nstep, natoms, natoms, 3)
distvecs_frac = traj.coords_frac[:,:,None,:] - \
traj.coords_frac[:,None,:,:]
assert distvecs_frac.shape == (nstep, natoms, natoms, 3)
if pbc:
distvecs_frac = crys.min_image_convention(distvecs_frac)
distvecs = np.empty((nstep, natoms, natoms, 3))
for ii in range(traj.nstep):
distvecs[ii, ...] = np.dot(distvecs_frac[ii, ...], traj.cell[ii,
...])
# (nstep, natoms, natoms)
dists = np.sqrt((distvecs**2.0).sum(axis=-1))
assert np.allclose(dists, crys.distances_traj(traj, pbc=pbc))
def test_dist_traj():
natoms = 10
nstep = 100
cell = rand(nstep,3,3)
stress = rand(nstep,3,3)
forces = rand(nstep,natoms,3)
etot=rand(nstep)
cryst_const = crys.cell2cc3d(cell, axis=0)
coords_frac = np.random.rand(nstep,natoms,3)
coords = crys.coord_trans3d(coords=coords_frac,
old=cell,
new=num.extend_array(np.identity(3),
nstep,axis=0),
axis=1,
timeaxis=0)
assert cryst_const.shape == (nstep, 6)
assert coords.shape == (nstep,natoms,3)
symbols = ['H']*natoms
traj = Trajectory(coords_frac=coords_frac,
cell=cell,
symbols=symbols,
forces=forces,
stress=stress,
etot=etot,
timestep=1,
)
for pbc in [True, False]:
# (nstep, natoms, natoms, 3)
distvecs_frac = traj.coords_frac[:,:,None,:] - \
traj.coords_frac[:,None,:,:]
assert distvecs_frac.shape == (nstep, natoms, natoms, 3)
if pbc:
distvecs_frac = crys.min_image_convention(distvecs_frac)
distvecs = np.empty((nstep, natoms, natoms, 3))
for ii in range(traj.nstep):
distvecs[ii,...] = np.dot(distvecs_frac[ii,...], traj.cell[ii,...])
# (nstep, natoms, natoms)
dists = np.sqrt((distvecs**2.0).sum(axis=-1))
assert np.allclose(dists, crys.distances_traj(traj, pbc=pbc))
def fdist(traj):
return crys.distances_traj(traj, pbc=True)
def fdist(traj):
return crys.distances_traj(traj, pbc=True)
