def main():
tomlfile = sys.argv[1] if len(sys.argv) > 1 else "input.toml"
rxparams = RXParams.from_toml(tomlfile)
nreplicas = rxparams.nreplicas
nprocs_per_replica = rxparams.nprocs_per_replica
kB = 8.6173e-5
comm = RX_MPI_init(rxparams)
# RXMC parameters
# specify temperatures for each replica, number of steps, etc.
kTstart = rxparams.kTstart
kTend = rxparams.kTend
kTs = kB * np.linspace(kTstart, kTend, nreplicas)
# Set Lreload to True when restarting
Lreload = rxparams.reload
nsteps = rxparams.nsteps
RXtrial_frequency = rxparams.RXtrial_frequency
sample_frequency = rxparams.sample_frequency
print_frequency = rxparams.print_frequency
dftparams = DFTParams.from_toml(tomlfile)
if dftparams.solver == 'vasp':
solver = VASPSolver(dftparams.path)
elif dftparams.solver == 'qe':
solver = QESolver(dftparams.path)
else:
print('unknown solver: {}'.format(dftparams.solver))
sys.exit(1)
# model setup
# we first choose a "model" defining how to perform energy calculations and trial steps
# on the "configuration" defined below
energy_calculator = runner(base_input_dir=dftparams.base_input_dir,
Solver=solver,
nprocs_per_solver=nprocs_per_replica,
comm=MPI.COMM_SELF,
perturb=dftparams.perturb,
solver_run_scheme=dftparams.solver_run_scheme)
model = dft_latgas(energy_calculator, save_history=False)
# defect sublattice setup
configparams = DFTConfigParams.from_toml(tomlfile)
spinel_config = defect_config(configparams)
configs = []
for i in range(nreplicas):
configs.append(copy.deepcopy(spinel_config))
obsparams = ObserverParams.from_toml(tomlfile)
# RXMC calculation
RXcalc = TemperatureRX_MPI(comm, CanonicalMonteCarlo, model, configs, kTs)
if Lreload:
RXcalc.reload()
obs = RXcalc.run(
nsteps,
RXtrial_frequency,
sample_frequency,
print_frequency,
observer=default_observer(comm, Lreload),
subdirs=True,
)
if comm.Get_rank() == 0:
print(obs)
def test_input(self):
tomlfile = os.path.join(self.datadir, "input.toml")
DFTParams.from_toml(tomlfile)
rxparams = RXParams.from_toml(tomlfile)
self.assertEqual(rxparams.nreplicas, 2)
self.assertEqual(rxparams.nprocs_per_replica, 1)
self.assertEqual(rxparams.kTstart, 1000.0)
self.assertEqual(rxparams.kTend, 1200.0)
self.assertEqual(rxparams.nsteps, 2)
self.assertEqual(rxparams.RXtrial_frequency, 3)
self.assertEqual(rxparams.sample_frequency, 4)
self.assertEqual(rxparams.print_frequency, 5)
self.assertEqual(rxparams.seed, 12345)
configparams = DFTConfigParams.from_toml(tomlfile)
spinel_config = defect_config(configparams)
cellsize = np.array([2, 1, 1])
self.assertTrue((spinel_config.cellsize == cellsize).all())
A = np.zeros((3, 3))
A[0, 0] = 2.0
A[1, 1] = 1.0
A[2, 2] = 0.5
B = cellsize * A
invB = inv(B)
self.assertTrue(np.allclose(B, spinel_config.supercell))
r = np.zeros((5, 3))
r[1, :] = [0.5, 0.5, 0.5]
r[2, :] = [0.0, 0.5, 0.5]
r[3, :] = [0.5, 0.0, 0.5]
r[4, :] = [0.5, 0.5, 0.0]
st = Structure(A, ["O", "O", "Se", "Se", "Se"], r)
seldyns = np.array([
[True, True, False],
[True, True, False],
[True, False, True],
[True, False, True],
[True, False, True],
[True, False, True],
[False, False, False],
[False, False, False],
[True, True, True],
[True, True, True],
])
self.assertTrue(spinel_config.base_structure.matches(st))
self.assertTrue(
(spinel_config.base_structure.site_properties["seldyn"] == seldyns
).all())
gs = [
group("Al", ["Al"], coords=[[[0.0, 0.0, 0.0]]]),
group("OH", ["O", "H"],
coords=[[[0.0, 0.0, 0.0], [0.1, 0.1, 0.1]]]),
]
for i in range(2):
g = spinel_config.defect_sublattices[0].groups[i]
self.assertEqual(gs[i].name, g.name)
self.assertEqual(gs[i].species, g.species)
self.assertEqual(gs[i].natoms, g.natoms)
self.assertTrue(np.allclose(np.dot(gs[i].coords, invB), g.coords))