def test_bad_dtype(TNG_EXAMPLE, dtype):
with pytng.TNGFileIterator(TNG_EXAMPLE, 'r') as tng:
positions = np.empty(shape=(tng.n_atoms, 3), dtype=dtype)
with pytest.raises(TypeError) as excinfo:
positions = tng[0].get_positions(positions)
message = "PYTNG ERROR: datatype of numpy array not supported"
assert message in str(excinfo.value)
def test_supported_dtype_wrong_block(TNG_EXAMPLE, dtype):
with pytng.TNGFileIterator(TNG_EXAMPLE, 'r') as tng:
positions = np.empty(shape=(tng.n_atoms, 3), dtype=dtype)
with pytest.raises(TypeError) as excinfo:
positions = tng[0].get_positions(positions)
message = "does not match TNG dtype float"
assert message in str(excinfo.value)
def test_DOCS_example(TNG_EXAMPLE):
with pytng.TNGFileIterator(TNG_EXAMPLE, 'r') as tng:
positions = tng.make_ndarray_for_block_from_name("TNG_TRAJ_POSITIONS")
for ts in tng[0:len(tng):tng.block_strides["TNG_TRAJ_POSITIONS"]]:
positions = ts.get_positions(positions)
if not ts.read_success:
raise IOError
def test_tng_example_getitem_single_invalid(idx, TNG_EXAMPLE):
with pytng.TNGFileIterator(TNG_EXAMPLE) as tng:
with pytest.raises(TypeError) as excinfo:
tng[idx]
message = ("Trajectories must be an indexed using an integer,"
" slice or list of indices")
assert message in str(excinfo.value)
def test_tng_example_getitem_bool(arr, cls, TNG_EXAMPLE, TNG_EXAMPLE_DATA):
slx = cls(arr)
ref = np.arange(TNG_EXAMPLE_DATA.length)[slx]
with pytng.TNGFileIterator(TNG_EXAMPLE) as tng:
for ref_ts, ts in zip(ref, tng[slx]):
assert ref_ts == ts.step
def test_argon_npt_compressed_last_positions(ARGON_NPT_COMPRESSED,
ARGON_NPT_COMPRESSED_DATA):
with pytng.TNGFileIterator(ARGON_NPT_COMPRESSED) as tng:
pos = np.empty(shape=(1000, 3), dtype=np.float32)
pos = tng[len(tng) - 1].get_positions(pos)
assert_array_almost_equal(
ARGON_NPT_COMPRESSED_DATA.last_frame_last_10_pos, pos[990:1000, :])
def test_argon_npt_compressed_last_box(ARGON_NPT_COMPRESSED,
ARGON_NPT_COMPRESSED_DATA):
with pytng.TNGFileIterator(ARGON_NPT_COMPRESSED) as tng:
box = np.empty(shape=(1, 9), dtype=np.float32)
box = tng[len(tng) - 1].get_box(box)
assert_array_almost_equal(ARGON_NPT_COMPRESSED_DATA.last_box,
box.reshape(3, 3))
def test_tng_example_tng_example_pos_through_read_step(TNG_EXAMPLE_DATA,
TNG_EXAMPLE):
with pytng.TNGFileIterator(TNG_EXAMPLE) as tng:
pos = np.empty(shape=(15, 3), dtype=np.float32)
tngstep = tng.read_step(0)
pos = tngstep.get_positions(pos)
assert np.array_equal(TNG_EXAMPLE_DATA.first_frame, pos)
def test_tng_example_sliced_iteration(slice_idx, TNG_EXAMPLE):
start, stop, step = slice_idx
ref_steps = np.arange(0, 10)[start:stop:step]
with pytng.TNGFileIterator(TNG_EXAMPLE) as tng:
for ref_ts, ts in zip(ref_steps, tng[start:stop:step]):
assert ref_ts == ts.step
def test_tng_example_getitem_multipl_ints(slx, cls, TNG_EXAMPLE,
TNG_EXAMPLE_DATA):
slx = cls(slx)
indices = np.arange(TNG_EXAMPLE_DATA.length)
with pytng.TNGFileIterator(TNG_EXAMPLE) as tng:
for ref_step, ts in zip(indices[slx], tng[slx]):
assert ref_step == ts.step
def test_tng_example_first_and_last_seq_positions(TNG_EXAMPLE_DATA,
TNG_EXAMPLE):
with pytng.TNGFileIterator(TNG_EXAMPLE) as tng:
pos = np.empty(shape=(15, 3), dtype=np.float32)
pos = tng[0].get_positions(pos)
assert np.array_equal(TNG_EXAMPLE_DATA.first_frame, pos)
pos = tng[9].get_positions(pos)
assert np.array_equal(TNG_EXAMPLE_DATA.last_frame, pos)
def test_README_example(TNG_EXAMPLE):
with pytng.TNGFileIterator(TNG_EXAMPLE, 'r') as tng:
positions = np.empty((tng.n_atoms, 3), dtype=np.float32)
for ts in tng:
time = ts.get_time()
ts.get_positions(positions)
if not ts.read_success:
raise IOError
def test_argon_npt_compressed_off_stride_is_nan(ARGON_NPT_COMPRESSED):
with pytng.TNGFileIterator(ARGON_NPT_COMPRESSED) as tng:
positions = tng.make_ndarray_for_block_from_name("TNG_TRAJ_POSITIONS")
step = 42
assert (tng.block_strides["TNG_TRAJ_POSITIONS"] % step != 0)
ts = tng[step]
ts.get_positions(positions)
assert (ts.read_success == False)
assert (np.all(np.isnan(positions)))
def test_water_npt_uncompressed_vels_forces_last_vels(
WATER_NPT_UNCOMPRESSED_VELS_FORCES,
WATER_NPT_UNCOMPRESSED_VELS_FORCES_DATA):
with pytng.TNGFileIterator(WATER_NPT_UNCOMPRESSED_VELS_FORCES) as tng:
vel = np.empty(shape=(2700, 3), dtype=np.float32)
vel = tng[len(tng) - 1].get_velocities(vel)
assert_array_almost_equal(
WATER_NPT_UNCOMPRESSED_VELS_FORCES_DATA.last_frame_last_10_vels,
vel[2690:2700, :],
decimal=2) # decimal = 2 really slack
def test_water_npt_uncompressed_vels_forces_first_frc(
WATER_NPT_UNCOMPRESSED_VELS_FORCES,
WATER_NPT_UNCOMPRESSED_VELS_FORCES_DATA):
with pytng.TNGFileIterator(WATER_NPT_UNCOMPRESSED_VELS_FORCES) as tng:
frc = np.empty(shape=(2700, 3), dtype=np.float32)
frc = tng[0].get_forces(frc) # todo forces
assert_array_almost_equal(
WATER_NPT_UNCOMPRESSED_VELS_FORCES_DATA.first_frame_first_10_frc,
frc[:10, :],
decimal=2,
) # decimal = 2 really slack
def test_tng_example_reached_eof(TNG_EXAMPLE):
with pytng.TNGFileIterator(TNG_EXAMPLE) as tng:
# test with iter protocol
for ts in tng:
pass
with pytest.raises(StopIteration):
next(tng)
# test __getitem__
tng.read_step(0)
for ts in tng[:]:
pass
with pytest.raises(StopIteration):
next(tng)
def test_tng_example_iter(TNG_EXAMPLE):
with pytng.TNGFileIterator(TNG_EXAMPLE) as tng:
for i, dummy in enumerate(tng):
tng.read_step(i)
def test_tng_example_len(TNG_EXAMPLE):
with pytng.TNGFileIterator(TNG_EXAMPLE) as tng:
assert_equal(len(tng), 10)
def test_water_npt_uncompressed_vels_forces_open(
WATER_NPT_UNCOMPRESSED_VELS_FORCES, ):
with pytng.TNGFileIterator(WATER_NPT_UNCOMPRESSED_VELS_FORCES) as tng:
pass
def test_tng_example_time(TNG_EXAMPLE_DATA, TNG_EXAMPLE):
with pytng.TNGFileIterator(TNG_EXAMPLE) as tng:
for ref_time, ts in zip(TNG_EXAMPLE_DATA.time, tng):
assert ref_time == tng.current_integrator_step.get_time()
def test_tng_example_open_mode_w(MISSING_FILEPATH):
with pytest.raises(NotImplementedError):
pytng.TNGFileIterator(MISSING_FILEPATH, mode="w")
def test_tng_example_open_invalide_mode(TNG_EXAMPLE):
with pytest.raises(ValueError) as excinfo:
pytng.TNGFileIterator(TNG_EXAMPLE, mode="invalid")
assert 'mode must be one of' in str(excinfo.value)
def test_tng_example_read_not_open(TNG_EXAMPLE):
with pytng.TNGFileIterator(TNG_EXAMPLE) as tng:
pass
with pytest.raises(IOError) as excinfo:
tng.read_step(0)
assert "File is not yet open" in str(excinfo.value)
def test_tng_example_getitem_int(idx, TNG_EXAMPLE, TNG_EXAMPLE_DATA):
indices = np.arange(TNG_EXAMPLE_DATA.length)
with pytng.TNGFileIterator(TNG_EXAMPLE) as tng:
ts = tng[idx]
assert ts.step == indices[idx]
def test_argon_npt_compressed_open(ARGON_NPT_COMPRESSED):
with pytng.TNGFileIterator(ARGON_NPT_COMPRESSED) as tng:
pass
def test_tng_example_read_step_write(MISSING_FILEPATH):
with pytng.TNGFileIterator(MISSING_FILEPATH, mode="w") as tng:
with pytest.raises(IOError) as excinfo:
tng.read_step(0)
assert "read_step not allowed in write mode" in str(excinfo.value)
def test_tng_example_property_not_open(prop, TNG_EXAMPLE):
with pytng.TNGFileIterator(TNG_EXAMPLE) as tng:
pass
with pytest.raises(IOError) as excinfo:
getattr(tng, prop)
assert "File is not yet open" in str(excinfo.value)
def test_tng_example_read_not_mode_r(MISSING_FILEPATH):
with pytest.raises(IOError) as excinfo:
with pytng.TNGFileIterator(MISSING_FILEPATH, mode="w") as tng:
tng.read_step(0)
assert 'Reading only allow in mode "r"' in str(excinfo.value)
def test_argon_npt_compressed_len(ARGON_NPT_COMPRESSED):
with pytng.TNGFileIterator(ARGON_NPT_COMPRESSED) as tng:
assert tng.n_steps == 500001
assert len(tng) == 500001
def test_argon_npt_compressed_n_particles(ARGON_NPT_COMPRESSED,
ARGON_NPT_COMPRESSED_DATA):
with pytng.TNGFileIterator(ARGON_NPT_COMPRESSED) as tng:
assert ARGON_NPT_COMPRESSED_DATA.natoms == tng.n_atoms