def test_hoomdsimulation_restart(self):
import gsd.hoomd
import hoomd
from foyer.forcefield import Forcefield
from mbuild.formats.hoomd_simulation import create_hoomd_simulation
box = mb.Compound()
box.add(mb.Compound(name="Ar", pos=[1, 1, 1]))
box.add(mb.Compound(name="Ar", pos=[1, 1, 1]))
ff = Forcefield(forcefield_files=get_fn("lj.xml"))
structure = ff.apply(box)
structure.box = [10, 10, 10, 90, 90, 90]
sim = hoomd.context.SimulationContext()
with sim:
hoomd_obj, ref_vals = create_hoomd_simulation(
structure, 2.5, restart=get_fn("restart.gsd"))
sim_forces = hoomd.context.current.forces
pair_force = import_("hoomd.md.pair")
assert isinstance(sim_forces[0], pair_force.lj)
snap = hoomd_obj[0]
with gsd.hoomd.open(get_fn("restart.gsd")) as f:
rsnap = f[0]
assert np.array_equal(snap.particles.position,
rsnap.particles.position)
def test_structure_to_hoomdsimulation(self, ethane):
import hoomd
from foyer.forcefield import Forcefield
from mbuild.formats.hoomd_simulation import create_hoomd_simulation
ff = Forcefield(name="oplsaa")
structure = ff.apply(ethane)
sim = hoomd.context.SimulationContext()
with sim:
create_hoomd_simulation(structure, 2.5)
sim_forces = hoomd.context.current.forces
pair_force = import_("hoomd.md.pair")
charge_force = import_("hoomd.md.charge")
special_pair_force = import_("hoomd.md.special_pair")
bond_force = import_("hoomd.md.bond")
angle_force = import_("hoomd.md.angle")
dihedral_force = import_("hoomd.md.dihedral")
assert isinstance(sim_forces[0], pair_force.lj)
assert isinstance(sim_forces[1], charge_force.pppm)
assert isinstance(sim_forces[2], pair_force.ewald)
assert isinstance(sim_forces[3], special_pair_force.lj)
assert isinstance(sim_forces[4], special_pair_force.coulomb)
assert isinstance(sim_forces[5], bond_force.harmonic)
assert isinstance(sim_forces[6], angle_force.harmonic)
assert isinstance(sim_forces[7], dihedral_force.opls)
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_lj_to_hoomd_forcefield(self):
import hoomd
from foyer.forcefield import Forcefield
from mbuild.formats.hoomd_forcefield import create_hoomd_forcefield
box = mb.Compound()
box.add(mb.Compound(name="Ar", pos=[1, 1, 1]))
box.add(mb.Compound(name="Ar", pos=[1, 1, 1]))
ff = Forcefield(forcefield_files=get_fn("lj.xml"))
structure = ff.apply(box)
structure.box = [10, 10, 10, 90, 90, 90]
snapshot, forces, ref_values = create_hoomd_forcefield(structure, 2.5)
assert isinstance(forces[0], hoomd.md.pair.LJ)
def test_hexa_coordinated():
ff = Forcefield(forcefield_files=get_fn('pf6.xml'))
mol2 = pmd.load_file(get_fn('pf6.mol2'), structure=True)
pf6 = ff.apply(mol2)
types = [a.type for a in pf6.atoms]
assert types.count('P') == 1
assert types.count('F1') == 2
assert types.count('F2') == 2
assert types.count('F3') == 2
assert len(pf6.bonds) == 6
assert all(bond.type for bond in pf6.bonds)
assert len(pf6.angles) == 15
assert all(angle.type for angle in pf6.angles)
def test_hexa_coordinated(self):
ff = Forcefield(forcefield_files=get_fn("pf6.xml"))
mol2 = pmd.load_file(get_fn("pf6.mol2"), structure=True)
pf6 = ff.apply(mol2)
types = [a.type for a in pf6.atoms]
assert types.count("P") == 1
assert types.count("F1") == 2
assert types.count("F2") == 2
assert types.count("F3") == 2
assert len(pf6.bonds) == 6
assert all(bond.type for bond in pf6.bonds)
assert len(pf6.angles) == 15
assert all(angle.type for angle in pf6.angles)
def test_hexa_coordinated():
ff = Forcefield(forcefield_files=get_fn('pf6.xml'))
mol2 = pmd.load_file(get_fn('pf6.mol2'), structure=True)
pf6 = ff.apply(mol2)
types = [a.type for a in pf6.atoms]
assert types.count('P') == 1
assert types.count('F1') == 2
assert types.count('F2') == 2
assert types.count('F3') == 2
assert len(pf6.bonds) == 6
assert all(bond.type for bond in pf6.bonds)
assert len(pf6.angles) == 15
assert all(angle.type for angle in pf6.angles)
def test_structure_to_hoomd_forcefield(self, ethane):
import hoomd
from foyer.forcefield import Forcefield
from mbuild.formats.hoomd_forcefield import create_hoomd_forcefield
ff = Forcefield(name="oplsaa")
structure = ff.apply(ethane)
snapshot, forces, ref_values = create_hoomd_forcefield(structure, 2.5)
assert isinstance(forces[0], hoomd.md.pair.LJ)
assert isinstance(forces[1], hoomd.md.pair.Ewald)
assert isinstance(forces[2], hoomd.md.long_range.pppm.Coulomb)
assert isinstance(forces[3], hoomd.md.special_pair.LJ)
assert isinstance(forces[4], hoomd.md.special_pair.Coulomb)
assert isinstance(forces[5], hoomd.md.bond.Harmonic)
assert isinstance(forces[6], hoomd.md.angle.Harmonic)
assert isinstance(forces[7], hoomd.md.dihedral.OPLS)
def test_lj_to_hoomdsimulation(self):
import hoomd
from foyer.forcefield import Forcefield
from mbuild.formats.hoomd_simulation import create_hoomd_simulation
box = mb.Compound()
box.add(mb.Compound(name="Ar", pos=[1, 1, 1]))
box.add(mb.Compound(name="Ar", pos=[1, 1, 1]))
ff = Forcefield(forcefield_files=get_fn("lj.xml"))
structure = ff.apply(box)
structure.box = [10, 10, 10, 90, 90, 90]
sim = hoomd.context.SimulationContext()
with sim:
create_hoomd_simulation(structure, 2.5)
sim_forces = hoomd.context.current.forces
pair_force = import_("hoomd.md.pair")
assert isinstance(sim_forces[0], pair_force.lj)
