How to use the gsd.hoomd.open function in gsd

snap0 = gsd.hoomd.Snapshot()

    snap0.state['hpmc/sphere/radius'] = [2.0]
    snap0.state['hpmc/sphere/orientable'] = [1]

    snap1 = gsd.hoomd.Snapshot()

    snap1.state['hpmc/convex_polyhedron/N'] = [3]
    snap1.state['hpmc/convex_polyhedron/vertices'] = [[-1, -1, -1], [0, 1, 1],
                                                      [1, 0, 0]]

    with gsd.hoomd.open(name=tmp_path / "test_state.gsd",
                        mode=open_mode.write) as hf:
        hf.extend([snap0, snap1])

    with gsd.hoomd.open(name=tmp_path / "test_state.gsd",
                        mode=open_mode.read) as hf:
        assert len(hf) == 2
        s = hf.read_frame(0)

        numpy.testing.assert_array_equal(s.state['hpmc/sphere/radius'],
                                         snap0.state['hpmc/sphere/radius'])
        numpy.testing.assert_array_equal(s.state['hpmc/sphere/orientable'],
                                         snap0.state['hpmc/sphere/orientable'])

        s = hf.read_frame(1)

        numpy.testing.assert_array_equal(
            s.state['hpmc/convex_polyhedron/N'],
            snap1.state['hpmc/convex_polyhedron/N'])
        numpy.testing.assert_array_equal(
            s.state['hpmc/convex_polyhedron/vertices'],

def test_view_slicing_and_iteration(tmp_path, open_mode):
    """Test that trajectories can be sliced."""
    with gsd.hoomd.open(name=tmp_path / "test_slicing.gsd",
                        mode=open_mode.write) as hf:
        hf.extend((create_frame(i) for i in range(40)))

    with gsd.hoomd.open(name=tmp_path / "test_slicing.gsd",
                        mode=open_mode.read) as hf:
        view = hf[::2]

        # Test len()-function on trajectory and sliced view.
        assert len(view) == 20
        assert len(view[:10]) == 10
        assert len(view[::2]) == 10

        # Test len()-function with explicit iterator.
        assert len(iter(view)) == len(view)
        assert len(iter(view[:10])) == len(view[:10])

        # Test iteration with implicit iterator.
        # All iterations are run twice to check for issues
        # with iterator exhaustion.
        assert len(list(view)) == len(view)

def test_defaults(tmp_path, open_mode):
    """Test that the property defaults are properly set."""
    snap = gsd.hoomd.Snapshot()
    snap.particles.N = 2
    snap.bonds.N = 3
    snap.angles.N = 4
    snap.dihedrals.N = 5
    snap.impropers.N = 6
    snap.constraints.N = 4
    snap.pairs.N = 7

    with gsd.hoomd.open(name=tmp_path / "test_defaults.gsd",
                        mode=open_mode.write) as hf:
        hf.append(snap)

    with gsd.hoomd.open(name=tmp_path / "test_defaults.gsd",
                        mode=open_mode.read) as hf:
        s = hf.read_frame(0)

        assert s.configuration.step == 0
        assert s.configuration.dimensions == 3
        numpy.testing.assert_array_equal(
            s.configuration.box,
            numpy.array([1, 1, 1, 0, 0, 0], dtype=numpy.float32))
        assert s.particles.N == 2
        assert s.particles.types == ['A']
        assert s.particles.type_shapes == [{}]
        numpy.testing.assert_array_equal(

def test_pickle(tmp_path, open_mode):
    """Test that hoomd trajectory objects can be pickled."""
    with gsd.hoomd.open(name=tmp_path / "test_pickling.gsd",
                        mode=open_mode.write) as traj:
        traj.extend((create_frame(i) for i in range(20)))
        with pytest.raises(pickle.PickleError):
            pkl = pickle.dumps(traj)
    with gsd.hoomd.open(name=tmp_path / "test_pickling.gsd",
                        mode=open_mode.read) as traj:
        pkl = pickle.dumps(traj)
        with pickle.loads(pkl) as hf:
            assert len(hf) == 20

def test_append(tmp_path, open_mode):
    """Test that gsd files can be appended to."""
    snap = gsd.hoomd.Snapshot()
    snap.particles.N = 10

    with gsd.hoomd.open(name=tmp_path / "test_append.gsd",
                        mode=open_mode.write) as hf:
        for i in range(5):
            snap.configuration.step = i + 1
            hf.append(snap)

    with gsd.hoomd.open(name=tmp_path / "test_append.gsd",
                        mode=open_mode.read) as hf:
        assert len(hf) == 5

def test_extend(tmp_path, open_mode):
    """Test that the extend method works."""
    snap = gsd.hoomd.Snapshot()
    snap.particles.N = 10

    with gsd.hoomd.open(name=tmp_path / "test_extend.gsd",
                        mode=open_mode.write) as hf:
        hf.extend((create_frame(i) for i in range(5)))

    with gsd.hoomd.open(name=tmp_path / "test_extend.gsd",
                        mode=open_mode.read) as hf:
        assert len(hf) == 5

snap0.log['particles/net_force'] = [[1, 2, 3], [4, 5, 6]]
    snap0.log['particles/pair_lj_energy'] = [0, -5, -8, -3]
    snap0.log['value/potential_energy'] = [10]
    snap0.log['value/pressure'] = [-3]

    snap1 = gsd.hoomd.Snapshot()

    snap1.log['particles/pair_lj_energy'] = [1, 2, -4, -10]
    snap1.log['value/pressure'] = [5]

    with gsd.hoomd.open(name=tmp_path / "test_log.gsd",
                        mode=open_mode.write) as hf:
        hf.extend([snap0, snap1])

    with gsd.hoomd.open(name=tmp_path / "test_log.gsd",
                        mode=open_mode.read) as hf:
        assert len(hf) == 2
        s = hf.read_frame(0)

        numpy.testing.assert_array_equal(s.log['particles/net_force'],
                                         snap0.log['particles/net_force'])
        numpy.testing.assert_array_equal(s.log['particles/pair_lj_energy'],
                                         snap0.log['particles/pair_lj_energy'])
        numpy.testing.assert_array_equal(s.log['value/potential_energy'],
                                         snap0.log['value/potential_energy'])
        numpy.testing.assert_array_equal(s.log['value/pressure'],
                                         snap0.log['value/pressure'])

        s = hf.read_frame(1)

        # unspecified entries pull from frame 0

def main_read(args):
    """Main function to launch a Python interpreter with an open GSD file."""
    # Default to a new line for well-formatted printing.
    local_ns = {
        'gsd': sys.modules['gsd'],
        'gsd.hoomd': sys.modules['gsd.hoomd'],
        'gsd.fl': sys.modules['gsd.fl'],
    }
    attributes = {}

    if args.schema == 'hoomd':
        traj = hoomd_open(args.file, mode=args.mode)
        handle = traj.file
        local_ns.update({
            'handle': handle,
            'traj': traj,
        })
        attributes.update({"Number of frames": len(traj)})
    else:
        if args.mode not in ['rb', 'rb+', 'ab']:
            raise ValueError("Unsupported schema for creating a file.")
        handle = fl.open(args.file, args.mode)
        local_ns.update({
            'handle': handle,
        })

    extras = "\n".join(
        "{}: {}".format(key, val) for key, val in attributes.items())

with gsd.hoomd.open(name='test.gsd', mode='wb') as hf:
        start = time.time()
        write_file(hf, nframes, N, position, orientation)

    # ensure that all writes to disk are completed and drop file system cache
    call(['sudo', '/bin/sync'])
    call(['sudo', '/sbin/sysctl', 'vm.drop_caches=3'], stdout=PIPE)

    end = time.time()

    timings['write'] = actual_size / 1024**2 / (end - start)

    # time how long it takes to open the file
    print("Opening file... ", file=sys.stderr, flush=True, end='')
    start = time.time()
    with gsd.hoomd.open(name='test.gsd', mode='rb') as hf:
        end = time.time()

        print(end - start, "s", file=sys.stderr, flush=True)

        timings['open_time'] = (end - start)

        # Read the file sequentially and measure the time taken
        print("Sequential read file:", file=sys.stderr, flush=True)
        start = time.time()
        read_sequential_file(hf, nframes, nframes_read, N, position,
                             orientation)
        end = time.time()

        timings['seq_read'] = bmark_read_size / 1024**2 / (end - start)

        # drop the file system cache