def test_default(self):
with TemporaryDirectory() as tmp_dir:
gsdfile = os.path.join(tmp_dir, 'testfile.gsd')
posfile = os.path.join(tmp_dir, 'testfile.pos')
with open(gsdfile, "wb") as f:
f.write(base64.b64decode(garnett.samples.GSD_BASE64))
with garnett.read(gsdfile) as traj:
with self.assertRaises(AttributeError):
traj[-1].shapedef
garnett.write(traj, posfile)
with garnett.read(posfile) as traj:
for frame in traj:
for name in frame.shapedef.keys():
self.assertEqual(frame.shapedef[name],
DEFAULT_SHAPE_DEFINITION)
def make_gsd(job):
try:
with garnett.read(job.fn('dump.pos')) as traj:
garnett.write(traj, job.fn('dump.gsd'))
except garnett.errors.ParserError as e:
print(e)
job.doc.failed = True
def test_write_pos(self):
with self.create_tmp_and_traj() as (tmp_dir, traj):
tmp_name = os.path.join(tmp_dir, 'test.pos')
garnett.write(traj, tmp_name)
# Read back the file and check if it is the same as the original
with garnett.read(tmp_name) as traj2:
self.assertEqual(len(traj), len(traj2))
def test_read_gsd_template(self):
with garnett.read(
get_filename('template-missing-shape.gsd'),
template=get_filename('template-missing-shape.pos')) as traj:
self.assertGreater(len(traj), 0)
# Make sure a shape definition was parsed from the POS file
self.assertGreater(len(traj[0].shapedef), 0)
def test_write_format(self):
with self.create_tmp_and_traj() as (tmp_dir, traj):
# No suffix is given to the temp file, so no format is detected
tmp_name = os.path.join(tmp_dir, 'test')
garnett.write(traj, tmp_name, fmt='pos')
# Read back the file and check if it is the same as the original
with garnett.read(tmp_name, fmt='pos') as traj2:
self.assertEqual(len(traj), len(traj2))
def test_write_io(self):
with self.create_tmp_and_traj() as (tmp_dir, traj):
tmp_name = os.path.join(tmp_dir, 'test_io.gsd')
with open(tmp_name, 'wb') as gsdfile:
garnett.write(traj, gsdfile)
# Read back the file and check if it is the same as the original
with garnett.read(tmp_name) as traj2:
self.assertEqual(len(traj), len(traj2))
def test_write_sphere_shapedef(self):
# Write to / read from a temp file
tmpfile = tempfile.NamedTemporaryFile(mode='wb')
with tmpfile:
with garnett.read(get_filename('FeSiUC.pos')) as traj:
self.writer.write(traj, tmpfile)
written_traj = self.reader.read(tmpfile)
assertEqualShapedefs(written_traj[0].shapedef,
traj[0].shapedef)
def get_structure(description):
filename = description['href'].replace('./', '').replace('.html', '.cif')
rcif = requests.get(
'http://aflowlib.org/CrystalDatabase/CIF/{}'.format(filename))
handle = io.StringIO(rcif.content.decode())
handle.name = 'test.cif'
short_name = get_short_name(description)
type_map = collections.defaultdict(lambda: len(type_map))
with garnett.read(handle, fmt='cif') as traj:
frame = traj[-1]
types = [type_map[t] for t in frame.types]
return dict(name=short_name,
positions=frame.positions.tolist(),
types=types,
space_group=description['Space Group Number'],
box=frame.box.get_box_array())
def test_write_defaults(self):
tmpfile = tempfile.NamedTemporaryFile(mode='wb')
with tmpfile:
with garnett.read(get_filename('shapes/ellipsoid_3d.pos')) as traj:
self.writer.write(traj, tmpfile)
written_traj = self.reader.read(tmpfile)
assert np.array_equal(written_traj[0].mass,
np.ones(27).astype(float))
assert np.array_equal(written_traj[0].velocity,
np.zeros([27, 3]).astype(float))
assert np.array_equal(written_traj[0].diameter,
np.ones(27).astype(float))
assert np.array_equal(written_traj[0].moment_inertia,
np.zeros([27, 3]).astype(float))
assert np.array_equal(written_traj[0].angmom,
np.zeros([27, 4]).astype(float))
assert np.array_equal(written_traj[0].charge,
np.zeros([27]).astype(float))
assert np.array_equal(written_traj[0].image,
np.zeros([27, 3]).astype(np.int32))
def test_read(file, template=None):
with garnett.read(file, template=template) as traj:
for frame in traj:
frame.load()
print(frame)
def read(*args, **kwargs):
with garnett.read(*args, **kwargs) as traj:
yield Trajectory(traj)
snapshot.particles.position[:] = [
[2, 0, 0],
[4, 0, 0],
[0, 4, 0],
[0, 0, 4],
]
system = hoomd.init.read_snapshot(snapshot)
mc = hoomd.hpmc.integrate.convex_polyhedron(seed=452784, d=0.2, a=0.4)
mc.shape_param.set('A', vertices=cube_verts)
gsd_dump = hoomd.dump.gsd('cube.gsd', period=10, group=hoomd.group.all())
gsd_dump.dump_state(mc)
gsd_dump.dump_shape(mc)
hoomd.run(1000)
# Restore a snapshot from saved data
with garnett.read('cube.gsd') as traj:
snapshot2 = system.take_snapshot()
traj[-1].to_hoomd_snapshot(snapshot2)
with hoomd.context.SimulationContext():
# Create a HOOMD snapshot from a garnett Trajectory frame
with garnett.read('cube.gsd') as traj:
snapshot = traj[-1].to_hoomd_snapshot()
system = hoomd.init.read_snapshot(snapshot)
mc = hoomd.hpmc.integrate.convex_polyhedron(seed=452784, d=0.2, a=0.4)
mc.shape_param.set('A', vertices=cube_verts)
gsd_dump = hoomd.dump.gsd('cube.gsd', period=10, group=hoomd.group.all())
gsd_dump.dump_state(mc)
gsd_dump.dump_shape(mc)
hoomd.run(1000)
def main(args):
with garnett.read(args.infile) as traj:
traj_centered = garnett.trajectory.Trajectory(
(center(frame) for frame in traj))
garnett.write(traj_centered, args.outfile)
return 0
# Copyright (c) 2020 The Regents of the University of Michigan
# All rights reserved.
# This software is licensed under the BSD 3-Clause License.
import garnett
import signac
project = signac.get_project()
for job in project:
print(job)
with job:
with garnett.read('dump.gsd') as traj:
print(traj)
with garnett.read('dump.dcd') as traj:
print(traj)
with garnett.read("dump.gsd", template='dump.pos') as traj:
print(traj)
with garnett.read("dump.gsd", template='init.xml') as traj:
print(traj)
def test_read_xml(self):
with garnett.read(get_filename('hoomd.xml')) as traj:
self.assertGreater(len(traj), 0)
def main(args):
with garnett.read(args.infile) as traj:
garnett.write(traj, args.outfile)
return 0
def test_read_gsd(self):
with garnett.read(get_filename('dump.gsd')) as traj:
self.assertGreater(len(traj), 0)
def test_read_gtar(self):
with garnett.read(get_filename('libgetar_sample.tar')) as traj:
self.assertGreater(len(traj), 0)
def test_garnett_dcd(self):
import garnett
with garnett.read(LJ_DCD) as traj:
self.run_analyses(traj)
def test_read_nonexistent(self):
with self.assertRaises(FileNotFoundError):
with garnett.read(get_filename('does_not_exist.pos')):
pass
def test_read_unsupported_template(self):
with self.assertRaises(ValueError):
with garnett.read(
get_filename('FeSiUC.pos'),
template=get_filename('template-missing-shape.pos')):
pass
def test_read_cif(self):
with garnett.read(get_filename('cI16.cif')) as traj:
self.assertGreater(len(traj), 0)
def test_read_io(self):
with open(get_filename('dump.gsd'), 'rb') as gsdfile:
with garnett.read(gsdfile) as traj:
self.assertGreater(len(traj), 0)
def test_read_unsupported(self):
with self.assertRaises(NotImplementedError):
with garnett.read(get_filename('unsupported.ext')):
pass
def test_read_pos(self):
with garnett.read(get_filename('FeSiUC.pos')) as traj:
self.assertGreater(len(traj), 0)
def test_minkowski_structure_metrics(self):
for structure in ["fcc", "bcc", "hcp", "sc"]:
expected_ql = _get_structure_data(structure, "q")
expected_avql = _get_structure_data(structure, "avq")
expected_wl = _get_structure_data(structure, "w")
expected_avwl = _get_structure_data(structure, "avw")
with garnett.read(
os.path.join(
os.path.dirname(__file__),
"files",
"minkowski_structure_metrics",
f"{structure}.gsd",
)) as traj:
frame = traj[0]
box = frame.box
positions = frame.position.copy()
voro = freud.locality.Voronoi()
voro.compute((box, positions))
for sph_l in range(expected_ql.shape[1]):
# These tests fail for unknown (probably numerical) reasons.
if structure == "hcp" and sph_l in [3, 5]:
continue
# Test ql
comp = freud.order.Steinhardt(sph_l, weighted=True)
comp.compute((box, positions), neighbors=voro.nlist)
npt.assert_allclose(comp.order,
expected_ql[:, sph_l],
rtol=5e-5,
atol=1e-3)
# Test Average ql
comp = freud.order.Steinhardt(sph_l,
average=True,
weighted=True)
comp.compute((box, positions), neighbors=voro.nlist)
npt.assert_allclose(comp.order,
expected_avql[:, sph_l],
rtol=5e-5,
atol=1e-3)
# These tests fail for unknown (probably numerical) reasons.
if sph_l != 2:
# Test wl
comp = freud.order.Steinhardt(sph_l,
wl=True,
weighted=True,
wl_normalize=True)
comp.compute((box, positions), neighbors=voro.nlist)
npt.assert_allclose(comp.order,
expected_wl[:, sph_l],
rtol=5e-5,
atol=1e-3)
# Test Average wl
comp = freud.order.Steinhardt(sph_l,
wl=True,
average=True,
weighted=True,
wl_normalize=True)
comp.compute((box, positions), neighbors=voro.nlist)
npt.assert_allclose(comp.order,
expected_avwl[:, sph_l],
rtol=5e-5,
atol=1e-3)
def create_tmp_and_traj(self):
with TemporaryDirectory() as tmp_dir:
with garnett.read(get_filename('dump.gsd')) as traj:
yield (tmp_dir, traj)
