def test_fdist():
natoms = 5
coords_frac = np.random.rand(natoms,3)
cell = np.random.rand(3,3)*3
struct = crys.Structure(coords_frac=coords_frac,
cell=cell)
for pbc in [0,1]:
print("pbc:", pbc)
pyret = pydist(coords_frac, cell, pbc)
# uses _flib.distsq_frac()
pyret2 = crys.distances(struct, pbc=pbc, squared=True, fullout=True)
for ii in [0,1,2]:
print(ii)
assert np.allclose(pyret[ii], pyret2[ii])
def test_fdist():
natoms = 5
coords_frac = np.random.rand(natoms,3)
cell = np.random.rand(3,3)*3
struct = crys.Structure(coords_frac=coords_frac,
cell=cell)
for pbc in [0,1]:
print "pbc:", pbc
pyret = pydist(coords_frac, cell, pbc)
# uses _flib.distsq_frac()
pyret2 = crys.distances(struct, pbc=pbc, squared=True, fullout=True)
for ii in [0,1,2]:
print ii
assert np.allclose(pyret[ii], pyret2[ii])
def pydist_loop(traj, pbc=True):
dists = np.empty((nstep, natoms, natoms))
for ii,struct in enumerate(traj):
dists[ii,...] = crys.distances(struct, pbc=pbc)
return dists
def pydist_loop(traj, pbc=True):
dists = np.empty((nstep, natoms, natoms))
for ii, struct in enumerate(traj):
dists[ii, ...] = crys.distances(struct, pbc=pbc)
return dists