def written_xtc(tmpdir, xtc):
fname = str(tmpdir.join("foo.xtc"))
with XTCFile(fname, 'w') as f:
for frame in xtc:
f.write(*frame)
with XTCFile(fname) as f:
yield f
def test_write_different_x_xtc():
with XTCFile(XTC_multi_frame) as f_in, XTCFile('foo.xtc', 'w') as f_out:
assert_equal(f_out.n_atoms, 0)
frame = f_in.read()
f_out.write(frame.x, frame.box, frame.step, frame.time, frame.prec)
x = np.ones((f_in.n_atoms - 1, 3))
f_out.write(x, frame.box, frame.step, frame.time, frame.prec)
def test_write_different_prec():
mf_xtc = XTCFile(XTC_multi_frame)
with XTCFile('foo.xtc', 'w') as f_out:
assert_equal(f_out.n_atoms, 0)
frame = mf_xtc.read()
f_out.write(frame.x, frame.box, frame.step, frame.time, frame.prec)
f_out.write(frame.x, frame.box, frame.step, frame.time, 10000.0)
def test_write_different_prec():
mf_xtc = XTCFile(XTC_multi_frame)
with XTCFile('foo.xtc', 'w') as f_out:
assert_equal(f_out.n_atoms, 0)
frame = mf_xtc.read()
f_out.write(frame.x, frame.box, frame.step,
frame.time, frame.prec)
f_out.write(frame.x, frame.box, frame.step,
frame.time, 10000.0)
def test_write_prec(tmpdir, xtc):
outname = str(tmpdir.join('foo.xtc'))
with XTCFile(outname, 'w') as f_out:
assert f_out.n_atoms == 0
frame = xtc.read()
f_out.write(frame.x, frame.box, frame.step, frame.time, 100.0)
xtc = XTCFile(outname)
assert len(xtc) == 1
frame = xtc.read()
assert frame.prec == 100.0
def test_xtc():
f = XTCFile(XTC_single_frame)
assert_equal(f.n_atoms, 10)
xyz, box, step, time, prec = f.read()
# xtc only saves with 3 decimal places precision
assert_array_almost_equal(xyz.flat, np.arange(30), decimal=3)
assert_array_almost_equal(box, np.eye(3) * 20, decimal=3)
assert_equal(step, 0)
assert_equal(time, 10.0)
assert_equal(prec, 1000.0)
def test_xtc():
f = XTCFile(XTC_single_frame)
assert_equal(f.n_atoms, 10)
xyz, box, step, time, prec = f.read()
# xtc only saves with 3 decimal places precision
assert_array_almost_equal(xyz.flat, np.arange(30), decimal=3)
assert_array_almost_equal(box, np.eye(3) * 20, decimal=3)
assert_equal(step, 0)
assert_equal(time, 10.0)
assert_equal(prec, 1000.0)
def test_write_prec(tmpdir, xtc):
outname = str(tmpdir.join('foo.xtc'))
with XTCFile(outname, 'w') as f_out:
assert f_out.n_atoms == 0
frame = xtc.read()
f_out.write(frame.x, frame.box, frame.step, frame.time, 100.0)
xtc = XTCFile(outname)
assert len(xtc) == 1
frame = xtc.read()
assert frame.prec == 100.0
def test_write_different_prec(tmpdir, xtc):
outname = str(tmpdir.join('foo.xtc'))
with XTCFile(outname, 'w') as f_out:
assert f_out.n_atoms == 0
frame = xtc.read()
f_out.write(frame.x, frame.box, frame.step, frame.time, frame.prec)
with pytest.raises(IOError):
f_out.write(frame.x, frame.box, frame.step, frame.time, 10000.0)
def test_write_xtc():
with XTCFile(XTC_multi_frame) as f_in, XTCFile('foo.xtc', 'w') as f_out:
assert_equal(f_out.n_atoms, 0)
for frame in f_in:
f_out.write(*frame)
with XTCFile('foo.xtc') as f:
assert_equal(len(f), 10)
ones = np.ones(30).reshape(10, 3)
box_compare = np.eye(3) * 20
for i, frame in enumerate(f):
xyz, box, step, time, prec = frame
assert_array_almost_equal(xyz, ones * i, decimal=3)
assert_array_almost_equal(box, box_compare, decimal=3)
assert_equal(step, i)
assert_equal(time, i * 0.5)
assert_equal(prec, 1000.0)
def test_different_box_xtc(tmpdir, xtc):
"""test if we can write different box-sizes for different frames.
"""
orig_box = None
fname = str(tmpdir.join('foo.xtc'))
with XTCFile(fname, 'w') as f_out:
assert f_out.n_atoms == 0
frame = xtc.read()
f_out.write(frame.x, frame.box, frame.step, frame.time, frame.prec)
orig_box = frame.box.copy()
box = frame.box.copy() + 1
f_out.write(frame.x, box, frame.step, frame.time, frame.prec)
with XTCFile(fname) as xtc:
assert len(xtc) == 2
frame_1 = xtc.read()
frame_2 = xtc.read()
assert_array_almost_equal(frame_1.box, orig_box)
assert_array_almost_equal(frame_1.box + 1, frame_2.box)
def test_write_xtc_array_like(tmpdir, array_like, xtc):
fname = str(tmpdir.join("foo.xtc"))
with XTCFile(fname, 'w') as f:
for frame in xtc:
x = array_like(frame.x)
box = array_like(frame.box)
f.write(xyz=x,
box=box,
step=frame.step,
time=frame.time,
precision=frame.prec)
def test_write_xtc_dtype(tmpdir, dtype, xtc):
fname = str(tmpdir.join("foo.xtc"))
with XTCFile(fname, 'w') as f:
for frame in xtc:
x = frame.x.astype(dtype)
box = frame.box.astype(dtype)
f.write(xyz=x,
box=box,
step=frame.step,
time=frame.time,
precision=frame.prec)
def test_different_box_xtc():
"""test if we can write different box-sizes for different frames.
"""
fname = 'foo.xtc'
orig_box = None
with XTCFile(XTC_multi_frame) as f_in, XTCFile(fname, 'w') as f_out:
assert_equal(f_out.n_atoms, 0)
frame = f_in.read()
f_out.write(frame.x, frame.box, frame.step, frame.time, frame.prec)
orig_box = frame.box.copy()
box = frame.box.copy() + 1
f_out.write(frame.x, box, frame.step, frame.time, frame.prec)
with XTCFile(fname) as xtc:
assert_equal(len(xtc), 2)
frame_1 = xtc.read()
frame_2 = xtc.read()
assert_array_almost_equal(frame_1.box, orig_box)
assert_array_almost_equal(frame_1.box + 1, frame_2.box)
def test_read_multi_frame_xtc():
with XTCFile(XTC_multi_frame) as f:
f.seek(5)
assert_equal(f.tell(), 5)
assert_equal(len(f), 10)
assert_equal(f.tell(), 5)
f.seek(0)
assert_equal(f.tell(), 0)
ones = np.ones(30).reshape(10, 3)
box_compare = np.eye(3) * 20
for i, frame in enumerate(f):
xyz, box, step, time, prec = frame
assert_array_almost_equal(xyz, ones * i, decimal=3)
assert_array_almost_equal(box, box_compare, decimal=3)
assert_equal(step, i)
assert_equal(time, i * 0.5)
assert_equal(prec, 1000.0)
def xtc():
with XTCFile(XTC_multi_frame) as f:
yield f