def test_lmp_predict(gp_model, mgp_model, ase_calculator, lmp_calculator):
"""
test the lammps implementation
"""
currdir = os.getcwd()
label = 'tmp_lmp'
for f in os.listdir("./"):
if label in f:
os.remove(f)
if f in ['log.lammps']:
os.remove(f)
clean()
lammps_location = mgp_model.lmp_file_name
# lmp file is automatically written now every time MGP is constructed
mgp_model.write_lmp_file(lammps_location)
# create test structure
np.random.seed(1)
cell = np.diag(np.array([1, 1, 1])) * 4
nenv = 10
unique_species = gp_model.training_statistics['species']
cutoffs = gp_model.cutoffs
struc_test, f = get_random_structure(cell, unique_species, nenv)
# build ase atom from struc
ase_atoms_flare = struc_test.to_ase_atoms()
ase_atoms_flare = FLARE_Atoms.from_ase_atoms(ase_atoms_flare)
ase_atoms_flare.set_calculator(ase_calculator)
ase_atoms_lmp = struc_test.to_ase_atoms()
ase_atoms_lmp.set_calculator(lmp_calculator)
try:
lmp_en = ase_atoms_lmp.get_potential_energy()
flare_en = ase_atoms_flare.get_potential_energy()
lmp_stress = ase_atoms_lmp.get_stress()
flare_stress = ase_atoms_flare.get_stress()
lmp_forces = ase_atoms_lmp.get_forces()
flare_forces = ase_atoms_flare.get_forces()
except Exception as e:
os.chdir(currdir)
print(e)
raise e
os.chdir(currdir)
# check that lammps agrees with mgp to within 1 meV/A
print("energy", lmp_en, flare_en)
assert np.isclose(lmp_en, flare_en, atol=1e-3).all()
print("force", lmp_forces, flare_forces)
assert np.isclose(lmp_forces, flare_forces, atol=1e-3).all()
print("stress", lmp_stress, flare_stress)
assert np.isclose(lmp_stress, flare_stress, atol=1e-3).all()
def __init__(
self,
atoms,
timestep,
number_of_steps,
dft_calc,
md_engine,
md_kwargs,
calculator=None,
trajectory=None,
**otf_kwargs
):
self.atoms = FLARE_Atoms.from_ase_atoms(atoms)
if calculator is not None:
self.atoms.set_calculator(calculator)
self.timestep = timestep
self.md_engine = md_engine
self.md_kwargs = md_kwargs
if md_engine == "VelocityVerlet":
MD = VelocityVerlet
elif md_engine == "NVTBerendsen":
MD = NVTBerendsen
elif md_engine == "NPTBerendsen":
MD = NPTBerendsen
elif md_engine == "NPT":
MD = NPT_mod
elif md_engine == "Langevin":
MD = Langevin
elif md_engine == "NoseHoover":
MD = NoseHoover
else:
raise NotImplementedError(md_engine + " is not implemented in ASE")
self.md = MD(
atoms=self.atoms, timestep=timestep, trajectory=trajectory, **md_kwargs
)
force_source = dft_source
self.flare_calc = self.atoms.calc
# Convert ASE timestep to ps for the output file.
flare_dt = timestep / (units.fs * 1e3)
super().__init__(
dt=flare_dt,
number_of_steps=number_of_steps,
gp=self.flare_calc.gp_model,
force_source=force_source,
dft_loc=dft_calc,
dft_input=self.atoms,
**otf_kwargs
)
self.flare_name = self.output_name + "_flare.json"
self.dft_name = self.output_name + "_dft.pickle"
self.atoms_name = self.output_name + "_atoms.json"
def test_lmp_predict(all_lmp, all_gp, all_mgp, bodies, multihyps):
"""
test the lammps implementation
"""
# pytest.skip()
prefix = f"{bodies}{multihyps}"
mgp_model = all_mgp[prefix]
gp_model = all_gp[prefix]
lmp_calculator = all_lmp[prefix]
ase_calculator = FLARE_Calculator(gp_model,
mgp_model,
par=False,
use_mapping=True)
# create test structure
np.random.seed(1)
cell = np.diag(np.array([1, 1, 1])) * 4
nenv = 10
unique_species = gp_model.training_statistics["species"]
cutoffs = gp_model.cutoffs
struc_test, f = get_random_structure(cell, unique_species, nenv)
# build ase atom from struc
ase_atoms_flare = struc_test.to_ase_atoms()
ase_atoms_flare = FLARE_Atoms.from_ase_atoms(ase_atoms_flare)
ase_atoms_flare.calc = ase_calculator
ase_atoms_lmp = deepcopy(struc_test).to_ase_atoms()
ase_atoms_lmp.calc = lmp_calculator
try:
lmp_en = ase_atoms_lmp.get_potential_energy()
flare_en = ase_atoms_flare.get_potential_energy()
lmp_stress = ase_atoms_lmp.get_stress()
flare_stress = ase_atoms_flare.get_stress()
lmp_forces = ase_atoms_lmp.get_forces()
flare_forces = ase_atoms_flare.get_forces()
except Exception as e:
os.chdir(curr_path)
print(e)
raise e
os.chdir(curr_path)
# check that lammps agrees with mgp to within 1 meV/A
print("energy", lmp_en - flare_en, flare_en)
assert np.isclose(lmp_en, flare_en, atol=1e-3)
print("force", lmp_forces - flare_forces, flare_forces)
assert np.isclose(lmp_forces, flare_forces, atol=1e-3).all()
print("stress", lmp_stress - flare_stress, flare_stress)
assert np.isclose(lmp_stress, flare_stress, atol=1e-3).all()
# check the lmp var
# mgp_std = np.sqrt(mgp_pred[1])
# print("isclose? diff:", lammps_stds[atom_num]-mgp_std, "mgp value", mgp_std)
# assert np.isclose(lammps_stds[atom_num], mgp_std, rtol=1e-2)
clean(prefix=prefix)