def test_snapshot_from_initial(self):
import hoomd
from mbuild.formats.hoomd_snapshot import to_hoomdsnapshot
part = mb.Compound(name="Ar")
box = mb.Box(lengths=[5, 5, 5], angles=[90, 90, 90])
system = mb.fill_box(part, n_compounds=10, box=box)
if hoomd_version.major == 2:
hoomd.context.initialize("")
init_snap = hoomd.data.make_snapshot(N=10,
box=hoomd.data.boxdim(L=10))
else:
init_snap = hoomd.Snapshot()
init_snap.particles.N = 10
init_snap.configuration.box = hoomd.Box.cube(L=10)
snap, _ = to_hoomdsnapshot(system, hoomd_snapshot=init_snap)
assert snap.particles.N == 20
assert snap.bonds.N == 0
assert snap.angles.N == 0
if hoomd_version.major == 2:
assert (snap.box.Lx, snap.box.Ly, snap.box.Lz) == (50, 50, 50)
assert (snap.box.xy, snap.box.xz, snap.box.yz) == (0, 0, 0)
else:
np.testing.assert_allclose(snap.configuration.box,
[50, 50, 50, 0, 0, 0])
def test_compound_to_snapshot(self, ethane):
from mbuild.formats.hoomd_snapshot import to_hoomdsnapshot
snap, _ = to_hoomdsnapshot(ethane)
assert snap.particles.N == 8
assert snap.bonds.N == 7
assert snap.angles.N == 0
def test_non_param_struc_to_snapshot(self, ethane):
from mbuild.formats.hoomd_snapshot import to_hoomdsnapshot
structure = ethane.to_parmed()
snap, _ = to_hoomdsnapshot(structure)
assert snap.particles.N == 8
assert snap.bonds.N == 7
assert snap.angles.N == 0
def test_particles_to_snapshot(self):
from mbuild.formats.hoomd_snapshot import to_hoomdsnapshot
part = mb.Compound(name="Ar")
box = mb.Box(lengths=[5, 5, 5], angles=[90, 90, 90])
system = mb.fill_box(part, n_compounds=10, box=box)
snap, _ = to_hoomdsnapshot(system)
assert snap.particles.N == 10
assert snap.bonds.N == 0
assert snap.angles.N == 0
def test_empty_initial_snapshot(self):
import hoomd
from mbuild.formats.hoomd_snapshot import to_hoomdsnapshot
part = mb.Compound(name="Ar")
box = mb.Box(lengths=[5, 5, 5], angles=[90, 90, 90])
system = mb.fill_box(part, n_compounds=10, box=box)
init_snap = hoomd.data.make_snapshot(N=0, box=hoomd.data.boxdim(L=10))
with pytest.raises(RuntimeError):
snap, _ = to_hoomdsnapshot(system, hoomd_snapshot=init_snap)
def test_param_structure_to_snapshot(self, ethane):
from foyer.forcefield import Forcefield
from mbuild.formats.hoomd_snapshot import to_hoomdsnapshot
ff = Forcefield(name="oplsaa")
structure = ff.apply(ethane)
snap, _ = to_hoomdsnapshot(structure)
assert snap.particles.N == 8
assert snap.bonds.N == 7
assert snap.angles.N == 12
assert snap.dihedrals.N == 9
assert snap.pairs.N == 9
def test_snapshot_from_initial(self):
import hoomd
from mbuild.formats.hoomd_snapshot import to_hoomdsnapshot
part = mb.Compound(name="Ar")
box = mb.Box(lengths=[5, 5, 5], angles=[90, 90, 90])
system = mb.fill_box(part, n_compounds=10, box=box)
init_snap = hoomd.data.make_snapshot(N=10, box=hoomd.data.boxdim(L=10))
snap, _ = to_hoomdsnapshot(system, hoomd_snapshot=init_snap)
assert snap.particles.N == 20
assert snap.bonds.N == 0
assert snap.angles.N == 0
assert (snap.box.Lx, snap.box.Ly, snap.box.Lz) == (50, 50, 50)
assert (snap.box.xy, snap.box.xz, snap.box.yz) == (0, 0, 0)
def test_compound_from_gsdsnapshot(self, ethane):
import gsd.hoomd
from mbuild.formats.hoomd_snapshot import (
from_snapshot,
to_hoomdsnapshot,
)
lengths = [5, 5, 5]
filled = mb.fill_box(ethane, n_compounds=5, box=mb.Box(lengths))
snap, _ = to_hoomdsnapshot(filled)
# copy attributes from the snapshot to a gsd snapshot
gsd_snap = gsd.hoomd.Snapshot()
gsd_snap.particles.N = snap.particles.N
gsd_snap.particles.types = snap.particles.types
gsd_snap.particles.typeid = snap.particles.typeid
gsd_snap.particles.position = snap.particles.position
if hoomd_version.major == 2:
gsd_snap.configuration.box = np.array([
snap.box.Lx,
snap.box.Ly,
snap.box.Lz,
snap.box.xy,
snap.box.xy,
snap.box.yz,
])
else:
gsd_snap.configuration.box = snap.configuration.box
gsd_snap.bonds.N = snap.bonds.N
gsd_snap.bonds.group = snap.bonds.group
gsd_snap.particles.charge = snap.particles.charge
gsd_snap.validate()
new_filled = from_snapshot(gsd_snap, scale=0.1)
assert filled.n_bonds == new_filled.n_bonds
assert filled.n_particles == new_filled.n_particles
assert np.array_equal(filled.box.angles, new_filled.box.angles)
assert np.array_equal(filled.box.lengths, new_filled.box.lengths)
for i in range(filled.n_particles):
assert np.allclose(filled[i].pos, new_filled[i].pos)
def test_compound_from_snapshot(self, ethane):
from mbuild.formats.hoomd_snapshot import (
from_snapshot,
to_hoomdsnapshot,
)
lengths = [5, 5, 5]
filled = mb.fill_box(ethane, n_compounds=5, box=mb.Box(lengths))
snap, _ = to_hoomdsnapshot(filled)
new_filled = from_snapshot(snap, scale=0.1)
assert filled.n_bonds == new_filled.n_bonds
assert filled.n_particles == new_filled.n_particles
assert np.array_equal(filled.box.angles, new_filled.box.angles)
assert np.array_equal(filled.box.lengths, new_filled.box.lengths)
for i in range(filled.n_particles):
assert np.allclose(filled[i].pos, new_filled[i].pos)
def test_empty_initial_snapshot(self):
import hoomd
from mbuild.formats.hoomd_snapshot import to_hoomdsnapshot
part = mb.Compound(name="Ar")
box = mb.Box(lengths=[5, 5, 5], angles=[90, 90, 90])
system = mb.fill_box(part, n_compounds=10, box=box)
if hoomd_version.major == 2:
hoomd.context.initialize("")
init_snap = hoomd.data.make_snapshot(N=0,
box=hoomd.data.boxdim(L=10))
else:
init_snap = hoomd.Snapshot()
init_snap.configuration.box = hoomd.Box.cube(L=10)
with pytest.raises(RuntimeError):
snap, _ = to_hoomdsnapshot(system, hoomd_snapshot=init_snap)
def test_bad_input_to_snapshot(self):
from mbuild.formats.hoomd_snapshot import to_hoomdsnapshot
with pytest.raises(ValueError):
to_hoomdsnapshot("fake_object")
