def test_cart2frac_traj():
nstep = 100
coords = rand(nstep,20,3)
coords_copy = coords.copy()
cell = rand(nstep,3,3)
c1 = np.array([np.dot(coords[ii,...], np.linalg.inv(cell[ii,...])) for ii in \
range(nstep)])
c2 = _flib.cart2frac_traj(coords, cell)
c3 = crys.coord_trans3d(coords, new=cell,
old=num.extend_array(np.identity(3),
nstep=nstep, axis=0))
assert (coords == coords_copy).all()
assert np.allclose(c1, c2)
assert np.allclose(c1, c3)
assert c2.flags.f_contiguous
def test_frac2cart_traj():
nstep = 100
coords_frac = rand(nstep,20,3)
coords_frac_copy = coords_frac.copy()
cell = rand(nstep,3,3)
c1 = np.array([np.dot(coords_frac[ii,...], cell[ii,...]) for ii in \
range(nstep)])
c2 = _flib.frac2cart_traj(coords_frac, cell)
c3 = crys.coord_trans3d(coords_frac, old=cell,
new=num.extend_array(np.identity(3),
nstep=nstep, axis=0))
assert (coords_frac == coords_frac_copy).all()
assert np.allclose(c1, c2)
assert np.allclose(c1, c3)
assert c2.flags.f_contiguous
def test_cart2frac_traj():
nstep = 100
coords = rand(nstep, 20, 3)
coords_copy = coords.copy()
cell = rand(nstep, 3, 3)
c1 = np.array([np.dot(coords[ii,...], np.linalg.inv(cell[ii,...])) for ii in \
range(nstep)])
c2 = _flib.cart2frac_traj(coords, cell)
c3 = crys.coord_trans3d(coords,
new=cell,
old=num.extend_array(np.identity(3),
nstep=nstep,
axis=0))
assert (coords == coords_copy).all()
assert np.allclose(c1, c2)
assert np.allclose(c1, c3)
assert c2.flags.f_contiguous
def test_frac2cart_traj():
nstep = 100
coords_frac = rand(nstep, 20, 3)
coords_frac_copy = coords_frac.copy()
cell = rand(nstep, 3, 3)
c1 = np.array([np.dot(coords_frac[ii,...], cell[ii,...]) for ii in \
range(nstep)])
c2 = _flib.frac2cart_traj(coords_frac, cell)
c3 = crys.coord_trans3d(coords_frac,
old=cell,
new=num.extend_array(np.identity(3),
nstep=nstep,
axis=0))
assert (coords_frac == coords_frac_copy).all()
assert np.allclose(c1, c2)
assert np.allclose(c1, c3)
assert c2.flags.f_contiguous
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_coords_trans():
natoms = 10
nstep = 100
cell = rand(nstep, 3, 3)
cryst_const = crys.cell2cc3d(cell, axis=0)
coords_frac = 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)
traj = Trajectory(coords_frac=coords_frac, cell=cell)
assert np.allclose(cryst_const, traj.cryst_const)
assert np.allclose(coords, traj.coords)
traj = Trajectory(coords=coords, cell=cell)
assert np.allclose(coords_frac, traj.coords_frac)
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_coords_trans():
natoms = 10
nstep = 100
cell = rand(nstep,3,3)
cryst_const = crys.cell2cc3d(cell, axis=0)
coords_frac = 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)
traj = Trajectory(coords_frac=coords_frac,
cell=cell)
assert np.allclose(cryst_const, traj.cryst_const)
assert np.allclose(coords, traj.coords)
traj = Trajectory(coords=coords,
cell=cell)
assert np.allclose(coords_frac, traj.coords_frac)
def test_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 = 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
# automatically calculated:
# coords
# cell
# pressure
# velocity (from coords)
# temperature (from ekin)
# ekin (from velocity)
traj = Trajectory(coords_frac=coords_frac,
cell=cell,
symbols=symbols,
forces=forces,
stress=stress,
etot=etot,
timestep=1,
)
# Test if all getters work.
for name in traj.attr_lst:
print "test if getters work:", name
traj.try_set_attr(name)
assert getattr(traj, name) is not None, "attr None: %s" %name
assert eval('traj.get_%s()'%name) is not None, "getter returns None: %s" %name
print "test if getters work:", name, "... ok"
aaae(coords_frac, traj.coords_frac)
aaae(coords, traj.coords)
aaae(cryst_const, traj.cryst_const)
aaae(np.trace(stress, axis1=1, axis2=2)/3.0, traj.pressure)
assert traj.coords.shape == (nstep,natoms,3)
assert traj.cell.shape == (nstep,3,3)
assert traj.velocity.shape == (nstep, natoms, 3)
assert traj.temperature.shape == (nstep,)
assert traj.ekin.shape == (nstep,)
assert traj.nstep == nstep
assert traj.natoms == natoms
traj = Trajectory(coords_frac=coords_frac,
symbols=symbols,
cell=cell)
aaae(coords, traj.coords)
# Cell calculated from cryst_const has defined orientation in space which may be
# different from the original `cell`, but the volume and underlying cryst_const
# must be the same.
traj = Trajectory(coords_frac=coords_frac,
symbols=symbols,
cryst_const=cryst_const)
np.testing.assert_almost_equal(crys.volume_cell3d(cell),
crys.volume_cell3d(traj.cell))
aaae(cryst_const, crys.cell2cc3d(traj.cell))
# extend arrays
cell2d = rand(3,3)
cc2d = crys.cell2cc(cell2d)
traj = Trajectory(coords_frac=coords_frac,
cell=cell2d,
symbols=symbols)
assert traj.cell.shape == (nstep,3,3)
assert traj.cryst_const.shape == (nstep,6)
for ii in range(traj.nstep):
assert (traj.cell[ii,...] == cell2d).all()
assert (traj.cryst_const[ii,:] == cc2d).all()
traj = Trajectory(coords_frac=coords_frac,
cryst_const=cc2d,
symbols=symbols)
assert traj.cell.shape == (nstep,3,3)
assert traj.cryst_const.shape == (nstep,6)
for ii in range(traj.nstep):
assert (traj.cryst_const[ii,:] == cc2d).all()
# units
traj = Trajectory(coords_frac=coords_frac,
cell=cell,
symbols=symbols,
stress=stress,
forces=forces,
units={'length': 2, 'forces': 3, 'stress': 4})
aaae(2*coords, traj.coords)
aaae(3*forces, traj.forces)
aaae(4*stress, traj.stress)
# iterate, check if Structures are complete
traj = Trajectory(coords=coords,
symbols=symbols,
cell=cell,
forces=forces,
stress=stress,
etot=etot,
timestep=1.0)
for struct in traj:
assert struct.is_struct, "st is not Structure"
assert not struct.is_traj, "st is Trajectory"
assert_attrs_not_none(struct)
struct = traj[0]
for attr_name in traj.attr_lst:
if attr_name in struct.attrs_only_traj:
msg = "tr[0] %s is not None" %attr_name
assert getattr(struct,attr_name) is None, msg
else:
msg = "tr[0] %s is None" %attr_name
assert getattr(struct,attr_name) is not None, msg
# slices, return traj
keys = traj.attr_lst[:]
tsl = traj[10:80:2]
assert tsl.nstep == traj.nstep / 2 - 15
assert_attrs_not_none(tsl, attr_lst=keys)
tsl = traj[slice(10,80,2)]
assert tsl.nstep == traj.nstep / 2 - 15
assert_attrs_not_none(tsl, attr_lst=keys)
tsl = traj[np.s_[10:80:2]]
assert tsl.nstep == traj.nstep / 2 - 15
assert_attrs_not_none(tsl, attr_lst=keys)
assert tsl.is_traj
# iteration over sliced traj
tsl = traj[10:80:2]
for x in tsl:
pass
for x in tsl.copy():
pass
# repeat iter
for i in range(2):
cnt = 0
for st in traj:
cnt += 1
assert cnt == nstep, "%i, %i" %(cnt, nstep)
# copy
traj2 = traj.copy()
for name in traj.attr_lst:
val = getattr(traj,name)
if val is not None and not (isinstance(val, types.IntType) or \
isinstance(val, types.FloatType)):
val2 = getattr(traj2,name)
print "test copy:", name, type(val), type(val2)
assert id(val2) != id(val)
assert_all_types_equal(val2, val)
assert_dict_with_all_types_equal(traj.__dict__, traj2.__dict__,
keys=traj.attr_lst)
def test_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 = 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
# automatically calculated:
# coords
# cell
# pressure
# velocity (from coords)
# temperature (from ekin)
# ekin (from velocity)
traj = Trajectory(
coords_frac=coords_frac,
cell=cell,
symbols=symbols,
forces=forces,
stress=stress,
etot=etot,
timestep=1,
)
# Test if all getters work.
for name in traj.attr_lst:
print("test if getters work:", name)
traj.try_set_attr(name)
assert getattr(traj, name) is not None, "attr None: %s" % name
assert eval('traj.get_%s()' %
name) is not None, "getter returns None: %s" % name
print("test if getters work:", name, "... ok")
aaae(coords_frac, traj.coords_frac)
aaae(coords, traj.coords)
aaae(cryst_const, traj.cryst_const)
aaae(np.trace(stress, axis1=1, axis2=2) / 3.0, traj.pressure)
assert traj.coords.shape == (nstep, natoms, 3)
assert traj.cell.shape == (nstep, 3, 3)
assert traj.velocity.shape == (nstep, natoms, 3)
assert traj.temperature.shape == (nstep, )
assert traj.ekin.shape == (nstep, )
assert traj.nstep == nstep
assert traj.natoms == natoms
traj = Trajectory(coords_frac=coords_frac, symbols=symbols, cell=cell)
aaae(coords, traj.coords)
# Cell calculated from cryst_const has defined orientation in space which may be
# different from the original `cell`, but the volume and underlying cryst_const
# must be the same.
traj = Trajectory(coords_frac=coords_frac,
symbols=symbols,
cryst_const=cryst_const)
np.testing.assert_almost_equal(crys.volume_cell3d(cell),
crys.volume_cell3d(traj.cell))
aaae(cryst_const, crys.cell2cc3d(traj.cell))
# extend arrays
cell2d = rand(3, 3)
cc2d = crys.cell2cc(cell2d)
traj = Trajectory(coords_frac=coords_frac, cell=cell2d, symbols=symbols)
assert traj.cell.shape == (nstep, 3, 3)
assert traj.cryst_const.shape == (nstep, 6)
for ii in range(traj.nstep):
assert (traj.cell[ii, ...] == cell2d).all()
assert (traj.cryst_const[ii, :] == cc2d).all()
traj = Trajectory(coords_frac=coords_frac,
cryst_const=cc2d,
symbols=symbols)
assert traj.cell.shape == (nstep, 3, 3)
assert traj.cryst_const.shape == (nstep, 6)
for ii in range(traj.nstep):
assert (traj.cryst_const[ii, :] == cc2d).all()
# units
traj = Trajectory(coords_frac=coords_frac,
cell=cell,
symbols=symbols,
stress=stress,
forces=forces,
units={
'length': 2,
'forces': 3,
'stress': 4
})
aaae(2 * coords, traj.coords)
aaae(3 * forces, traj.forces)
aaae(4 * stress, traj.stress)
# iterate, check if Structures are complete
traj = Trajectory(coords=coords,
symbols=symbols,
cell=cell,
forces=forces,
stress=stress,
etot=etot,
timestep=1.0)
for struct in traj:
assert struct.is_struct, "st is not Structure"
assert not struct.is_traj, "st is Trajectory"
assert_attrs_not_none(struct)
struct = traj[0]
for attr_name in traj.attr_lst:
if attr_name in struct.attrs_only_traj:
msg = "tr[0] %s is not None" % attr_name
assert getattr(struct, attr_name) is None, msg
else:
msg = "tr[0] %s is None" % attr_name
assert getattr(struct, attr_name) is not None, msg
# slices, return traj
keys = traj.attr_lst[:]
tsl = traj[10:80:2]
assert tsl.nstep == traj.nstep / 2 - 15
assert_attrs_not_none(tsl, attr_lst=keys)
tsl = traj[slice(10, 80, 2)]
assert tsl.nstep == traj.nstep / 2 - 15
assert_attrs_not_none(tsl, attr_lst=keys)
tsl = traj[np.s_[10:80:2]]
assert tsl.nstep == traj.nstep / 2 - 15
assert_attrs_not_none(tsl, attr_lst=keys)
assert tsl.is_traj
# iteration over sliced traj
tsl = traj[10:80:2]
for x in tsl:
pass
for x in tsl.copy():
pass
# repeat iter
for i in range(2):
cnt = 0
for st in traj:
cnt += 1
assert cnt == nstep, "%i, %i" % (cnt, nstep)
# copy
traj2 = traj.copy()
for name in traj.attr_lst:
val = getattr(traj, name)
if val is not None and not (isinstance(val, int) or \
isinstance(val, float)):
val2 = getattr(traj2, name)
print("test copy:", name, type(val), type(val2))
assert id(val2) != id(val)
assert_all_types_equal(val2, val)
assert_dict_with_all_types_equal(traj.__dict__,
traj2.__dict__,
keys=traj.attr_lst)
def test_coord_trans():
#-----------------------------------------------------------
# 2D
#-----------------------------------------------------------
c_X = rand(20,3)
# basis vecs are assumed to be rows
X = rand(3,3)*5
Y = rand(3,3)*3
# transform and back-transform
c_Y = coord_trans(c_X, old=X, new=Y)
c_X2 = coord_trans(c_Y, old=Y, new=X)
aaae(c_X, c_X2)
# simple dot product must produce same cartesian results:
# X . v_X = I . v_I = v_I
X = np.identity(3)
Y = rand(3,3)*3
c_X = rand(20,3)
c_Y = coord_trans(c_X, old=X, new=Y)
# normal back-transform
c_X2 = coord_trans(c_Y, old=Y, new=X)
# 2 forms w/ dot(), assume: basis vecs = rows of X and Y
c_X3 = np.dot(c_Y, Y)
c_X4 = np.dot(Y.T, c_Y.T).T
aaae(c_X, c_X2)
aaae(c_X, c_X3)
aaae(c_X, c_X4)
# some textbook example
#
v_I = np.array([1.0,1.5])
I = np.identity(2)
# basis vecs as rows
X = sqrt(2)/2.0*np.array([[1,-1],[1,1]]).T
Y = np.array([[1,1],[0,1]]).T
# "identity" transform
aaae(coord_trans(v_I,I,I), v_I)
# v in basis X and Y
v_X = coord_trans(v_I,I,X)
v_Y = coord_trans(v_I,I,Y)
aaae(v_X, np.array([1.76776695, 0.35355339]))
aaae(v_Y, np.array([-0.5, 1.5]))
# back-transform
aaae(coord_trans(v_X,X,I), v_I)
aaae(coord_trans(v_Y,Y,I), v_I)
# higher "x,y,z"-dims: 4-vectors
c_X = rand(20,4)
X = rand(4,4)*5
Y = rand(4,4)*3
c_Y = coord_trans(c_X, old=X, new=Y)
c_X2 = coord_trans(c_Y, old=Y, new=X)
aaae(c_X, c_X2)
#-----------------------------------------------------------
# 3D
#-----------------------------------------------------------
# x,y,z case
c_X = rand(20,3,10)
X = rand(3,3)*5
Y = rand(3,3)*3
c_Y = coord_trans(c_X, old=X, new=Y, axis=1)
c_X2 = coord_trans(c_Y, old=Y, new=X, axis=1)
aaae(c_X, c_X2)
c_X = rand(20,10,3)
c_Y = coord_trans(c_X, old=X, new=Y, axis=-1)
c_X2 = coord_trans(c_Y, old=Y, new=X, axis=-1)
aaae(c_X, c_X2)
c_X = rand(3,20,10)
c_Y = coord_trans(c_X, old=X, new=Y, axis=0)
c_X2 = coord_trans(c_Y, old=Y, new=X, axis=0)
aaae(c_X, c_X2)
# 3d, higher "x,y,z"-dims, i.e. 4-vectors: trajectory of 5 atoms, 10 steps,
# "4d-coordinates"
c_X = rand(20,4,10)
X = rand(4,4)*5
Y = rand(4,4)*3
c_Y = coord_trans(c_X, old=X, new=Y, axis=1)
c_X2 = coord_trans(c_Y, old=Y, new=X, axis=1)
aaae(c_X, c_X2)
#-----------------------------------------------------------
# ND
#-----------------------------------------------------------
# arbitrary collection of 4-vectors
c_X = rand(20,4,10,8)
X = rand(4,4)*5
Y = rand(4,4)*3
c_Y = coord_trans(c_X, old=X, new=Y, axis=1)
c_X2 = coord_trans(c_Y, old=Y, new=X, axis=1)
aaae(c_X, c_X2)
#-----------------------------------------------------------
# special case 3d
#-----------------------------------------------------------
# Note that axis=1 is always the xyz-axis (length 3) if the timeaxis
# (length 10) would be removed from all arrays (2d case then).
c_X = rand(20,3,10)
X = rand(3,3,10)*5
Y = rand(3,3,10)*3
c_Y = coord_trans3d(c_X, old=X, new=Y, axis=1, timeaxis=2)
c_X2 = coord_trans3d(c_Y, old=Y, new=X, axis=1, timeaxis=2)
aaae(c_X, c_X2)
c_X = rand(20,10,3)
X = rand(3,10,3)*5
Y = rand(3,10,3)*3
c_Y = coord_trans3d(c_X, old=X, new=Y, axis=1, timeaxis=1)
c_X2 = coord_trans3d(c_Y, old=Y, new=X, axis=1, timeaxis=1)
aaae(c_X, c_X2)
c_X = rand(10,20,3)
X = rand(10,3,3)*5
Y = rand(10,3,3)*3
c_Y = coord_trans3d(c_X, old=X, new=Y, axis=1, timeaxis=0)
c_X2 = coord_trans3d(c_Y, old=Y, new=X, axis=1, timeaxis=0)
aaae(c_X, c_X2)
