def test_traj_from_txt():
shape = (10, 20, 30)
arr3d_orig = np.random.rand(*shape)
axis = 0
# general stuff for axis != 0, here for axis=0 we have written_shape==shape
shape_2d_chunk = shape[:axis] + shape[(axis + 1):]
written_shape = (shape[axis], ) + shape_2d_chunk
print("axis, written_shape:", axis, written_shape)
fn = pj(testdir, 'arr_test_traj_from_txt_axis%i.txt' % axis)
arrayio.writetxt(fn, arr3d_orig, axis=axis, header=False)
with open(fn) as fd:
arr3d = parse.traj_from_txt(fd.read(), axis=axis, shape=written_shape)
fd.seek(0)
# test if the "old" way of reading also works
arr3d_readtxt = arrayio.readtxt(fd, shape=written_shape, axis=axis)
assert (arr3d_readtxt == arr3d_orig).all()
# now test traj_from_txt result
assert arr3d.shape == arr3d_orig.shape, \
("axis={}, shapes: read={} written={} orig={}".format(axis,
arr3d.shape, written_shape, arr3d_orig.shape))
assert (arr3d == arr3d_orig).all()
def test_traj_from_txt():
shape = (10,20,30)
arr3d_orig = np.random.rand(*shape)
axis = 0
# general stuff for axis != 0, here for axis=0 we have written_shape==shape
shape_2d_chunk = shape[:axis] + shape[(axis+1):]
written_shape = (shape[axis],) + shape_2d_chunk
print "axis, written_shape:", axis, written_shape
fn = pj(testdir, 'arr_test_traj_from_txt_axis%i.txt' %axis)
arrayio.writetxt(fn, arr3d_orig, axis=axis, header=False)
with open(fn) as fd:
arr3d = parse.traj_from_txt(fd.read(), axis=axis,
shape=written_shape)
fd.seek(0)
# test if the "old" way of reading also works
arr3d_readtxt = arrayio.readtxt(fd, shape=written_shape, axis=axis)
assert (arr3d_readtxt == arr3d_orig).all()
# now test traj_from_txt result
assert arr3d.shape == arr3d_orig.shape, \
("axis={0}, shapes: read={1} written={2} orig={3}".format(axis,
arr3d.shape, written_shape, arr3d_orig.shape))
assert (arr3d == arr3d_orig).all()
'time',
]
assert_attrs_not_none(traj, none_attrs=none_attrs)
# for test_return_3d_if_no_cell_unit
_cell = parse.traj_from_txt("""
1.004152675 0.000000000 0.000000000
-0.502076337 0.869621726 0.000000000
0.000000000 0.000000000 1.609289155
1.004147458 0.000000000 0.000000000
-0.502073729 0.869617208 0.000000000
0.000000000 0.000000000 1.609759673
1.004050225 0.000000000 0.000000000
-0.502025112 0.869533001 0.000000000
0.000000000 0.000000000 1.610320650
1.003992235 0.000000000 0.000000000
-0.501996117 0.869482780 0.000000000
0.000000000 0.000000000 1.610416170
1.003981055 0.000000000 0.000000000
-0.501990527 0.869473099 0.000000000
0.000000000 0.000000000 1.610369398
1.003981055 0.000000000 0.000000000
-0.501990527 0.869473099 0.000000000
0.000000000 0.000000000 1.610369398
""", shape=(6,3,3))
def test_return_3d_if_no_cell_unit():
filename = tools.unpack_compressed('files/pw.vc_relax_no_cell_unit.out.gz',
prefix=__file__)
pp = PwMDOutputFile(filename=filename)
pp.parse()
