def test_hydrogen_remove_gaff():
p3ht = Compound("c1cscc1CCCCCC")
p3ht_Hs = [h for h in p3ht.particles_by_element("H")]
packer = Pack(
p3ht,
ff=FORCEFIELD["gaff"],
n_compounds=2,
density=0.01 * u.g / u.cm**3,
remove_hydrogen_atoms=True,
)
system = packer.pack()
assert "H" not in [a.name for a in system.atoms]
assert p3ht.n_particles * 2 - len(system.atoms) == len(p3ht_Hs) * 2
def test_smiles_opvgaff_raises(self):
p3ht = Compound("c1cscc1CCCCCC")
with pytest.raises(NotImplementedError):
packer = Pack(
p3ht,
ff=FORCEFIELD["gaff-custom"],
n_compounds=2,
density=0.01 * u.g / u.cm**3,
)
def test_typed_gaff_raises(self):
p3ht = Compound(COMPOUND["P3HT-16-gaff"])
with pytest.raises(NotImplementedError):
packer = Pack(
p3ht,
ff=FORCEFIELD["gaff"],
n_compounds=2,
density=0.01 * u.g / u.cm**3,
)
def test_gaff_noH_raises(self):
p3ht = Compound("c1cscc1CCCCCC")
with pytest.raises(NotImplementedError):
packer = Pack(
p3ht,
ff=FORCEFIELD["gaff"],
n_compounds=2,
density=0.01 * u.g / u.cm**3,
remove_hydrogen_atoms=True,
)
def test_hydrogen_removal(compound_name):
comp = Compound(COMPOUND[compound_name])
packer = Pack(
comp,
ff=FORCEFIELD["gaff-custom"],
n_compounds=2,
density=0.1 * u.g / u.cm**3,
remove_hydrogen_atoms=True,
)
system = packer.pack()
assert 1 not in [a.atomic_number for a in system.atoms]
assert len(system.atoms) != comp.n_particles * 2
def test_mixture():
pcbm = Compound(COMPOUND["PCBM-gaff"])
p3ht = Compound(COMPOUND["P3HT-gaff"])
packer = Pack(
[pcbm, p3ht],
ff=FORCEFIELD["gaff-custom"],
n_compounds=[2, 3],
density=0.01 * u.g / u.cm**3,
)
system = packer.pack()
my_sim = Simulation(
system,
kT=[3.0],
tau=[1.0],
n_steps=[1e3],
gsd_write=1e2,
log_write=1e2,
mode="cpu",
shrink_steps=1e3,
)
my_sim.run()
def test_simple_sim(self, compound_name):
compound = Compound(COMPOUND[compound_name])
packer = Pack(compound, n_compounds=2, density=0.01 * u.g / u.cm**3)
system = packer.pack()
my_sim = Simulation(
system,
kT=3.0,
gsd_write=1e2,
log_write=1e2,
e_factor=1,
n_steps=3e3,
mode="cpu",
shrink_steps=1e3,
target_length=packer.L,
)
my_sim.run()
def test_bad_temps_raises(self):
p3ht = Compound("c1cscc1CCCCCC")
packer = Pack(
p3ht,
ff=FORCEFIELD["gaff"],
n_compounds=2,
density=0.01 * u.g / u.cm ** 3,
)
system = packer.pack()
with pytest.raises(AssertionError):
my_sim = Simulation(
system,
kT=[3.0, 4.0],
tau=[1.0],
n_steps=[1e3],
mode="cpu",
)
def test_temps_ramp(self):
p3ht = Compound("c1cscc1CCCCCC")
packer = Pack(
p3ht,
ff=FORCEFIELD["gaff"],
n_compounds=2,
density=0.01 * u.g / u.cm ** 3,
)
system = packer.pack()
my_sim = Simulation(
system,
kT=[3.0, 4.0],
tau=[1.0, 1.0],
n_steps=[1e3, 1e3],
shrink_steps=1e3,
target_length=packer.L,
mode="cpu",
)
def test_hydrogen_removal():
pcbm = Compound(COMPOUND["PCBM-gaff"])
packer = Pack(
pcbm,
ff=FORCEFIELD["gaff-custom"],
n_compounds=2,
density=0.1 * u.g / u.cm**3,
remove_hydrogen_atoms=True,
)
packer._remove_hydrogen()
for atom in packer.compound[0].particles():
assert atom.name not in [
"_hc",
"_ha",
"_h1",
"_h4",
], "Hydrogen found in system!"
def test_smiles_gaff(self):
p3ht = Compound("c1cscc1CCCCCC")
packer = Pack(
p3ht,
ff=FORCEFIELD["gaff"],
n_compounds=2,
density=0.01 * u.g / u.cm**3,
)
system = packer.pack()
my_sim = Simulation(
system,
kT=3.0,
gsd_write=1e2,
log_write=1e2,
e_factor=1,
n_steps=3e3,
mode="cpu",
shrink_steps=1e3,
target_length=packer.L,
)
def test_hydrogen_removal_and_sim():
pcbm = Compound(COMPOUND["PCBM-gaff"])
packer = Pack(
pcbm,
ff=FORCEFIELD["gaff-custom"],
n_compounds=2,
density=0.1 * u.g / u.cm**3,
remove_hydrogen_atoms=True,
)
system = packer.pack()
my_sim = Simulation(
system,
kT=[3.0],
tau=[1.0],
n_steps=[1e3],
gsd_write=1e2,
log_write=1e2,
mode="cpu",
shrink_steps=1e3,
)
my_sim.run()
def test_nlist(self):
p3ht = Compound("c1cscc1CCCCCC")
packer = Pack(
p3ht,
ff=FORCEFIELD["gaff"],
n_compounds=2,
density=0.01 * u.g / u.cm ** 3,
)
system = packer.pack()
my_sim = Simulation(
system,
kT=[3.0],
tau=[1.0],
n_steps=[1e3],
gsd_write=1e2,
log_write=1e2,
mode="cpu",
shrink_steps=1e3,
target_length=packer.L,
nlist="tree",
)
def sample(job):
import glob
import warnings
import unyt as u
from planckton.sim import Simulation
from planckton.init import Compound, Pack
from planckton.utils import units
from planckton.forcefields import FORCEFIELD
with job:
inputs = [get_paths(i, job) for i in job.sp.input]
with warnings.catch_warnings():
warnings.simplefilter("ignore")
compound = [Compound(i) for i in inputs]
packer = Pack(
compound,
ff=FORCEFIELD[job.sp.forcefield],
n_compounds=list(job.sp.n_compounds),
density=units.string_to_quantity(job.sp.density),
remove_hydrogen_atoms=job.sp.remove_hydrogens,
)
system = packer.pack()
print(f"Target length should be {packer.L:0.3f}")
if job.isfile("restart.gsd"):
restart = job.fn("restart.gsd")
target_length = None
else:
restart = None
target_length = packer.L
total_steps = sum(job.sp.n_steps, job.sp.shrink_steps)
my_sim = Simulation(system,
kT=job.sp.kT,
tau=job.sp.tau,
n_steps=job.sp.n_steps,
dt=job.sp.dt,
e_factor=job.sp.e_factor,
r_cut=job.sp.r_cut,
gsd_write=max([int(total_steps / 100), 1]),
log_write=max([int(total_steps / 10000), 1]),
shrink_steps=job.sp.shrink_steps,
shrink_kT=job.sp.shrink_kT,
shrink_tau=job.sp.shrink_tau,
mode=job.sp.mode,
target_length=target_length,
restart=restart)
job.doc["done"] = my_sim.run()
ref_distance = my_sim.ref_values.distance * u.Angstrom
ref_energy = my_sim.ref_values.energy * u.kcal / u.mol
ref_mass = my_sim.ref_values.mass * 0.9999938574 * u.amu
job.doc["T_SI"] = [
units.quantity_to_string(units.kelvin_from_reduced(kT, ref_energy))
for kT in job.sp.kT
]
job.doc["real_timestep"] = units.quantity_to_string(
units.convert_to_real_time(job.sp.dt, ref_mass, ref_distance,
ref_energy).to("femtosecond"))
job.doc["ref_mass"] = units.quantity_to_string(ref_mass)
job.doc["ref_distance"] = units.quantity_to_string(ref_distance)
job.doc["ref_energy"] = units.quantity_to_string(ref_energy)
outfiles = glob.glob(f"{job.ws}/job*.o")
if outfiles:
tps, time = get_tps_time(outfiles)
job.doc["average_TPS"] = tps
job.doc["total_time"] = time
def test_bad_units():
pcbm = Compound(COMPOUND["PCBM-gaff"])
with pytest.raises(UnitConversionError):
packer = Pack(pcbm, n_compounds=2, density=2 * u.m)
def test_no_units():
pcbm = Compound(COMPOUND["PCBM-gaff"])
with pytest.raises(TypeError):
packer = Pack(pcbm, n_compounds=2, density=2)
def test_load_smiles():
p3ht = Compound("c1cscc1CCCCCC")