# poscar.write_file("POSCAR.vasp")
################### model setup ###############################
# baseinput = VaspInput.from_directory("baseinput")
# energy_calculator = vasp_runner(base_input_dir="./baseinput",
# path_to_vasp="/home/i0009/i000900/src/vasp.5.3/vasp.spawnready.gamma",
# nprocs_per_vasp=nprocs_per_replica,
# comm=MPI.COMM_SELF, perturb=0.1)
energy_calculator = SolverBase()
model = dft_latgas(energy_calculator, save_history=True)
##############################################################
################### RXMC calculation #########################
kTs = kB * np.array([kTstart * kTstep**i for i in range(nreplicas)])
grid = grid_1D(dr, dr, maxr)
RXcalc = TemperatureRX_MPI(comm, CanonicalMonteCarlo, model, configs, kTs)
obs = RXcalc.run(eqsteps,
RXtrial_frequency,
sample_frequency,
observfunc=observables,
subdirs=True)
# RXcalc.reload()
obs = RXcalc.run(nsteps,
RXtrial_frequency,
sample_frequency,
observfunc=observables,
subdirs=True)
if comm.Get_rank() == 0:
for i in range(len(kTs)):
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)
drone = SimpleVaspToComputedEntryDrone(inc_structure=True)
queen = BorgQueen(drone)
model = dft_HAp(calcode="VASP",
vasp_run=vasprun,
base_vaspinput=baseinput,
queen=queen)
# matcher=matcher, matcher_site=matcher_site, queen=queen, selective_dynamics=["Pt"])
if worldrank == 0:
print(config.structure)
# print(model.xparam(config))
kTs = kB * np.array([500.0 * 1.1**i for i in range(nreplicas)])
# configs = pickle.load(open("config.pickle","rb"))
# configs = [copy.deepcopy(config) for i in range(nreplicas)]
RXcalc = TemperatureRX_MPI(comm, CanonicalMonteCarlo, model, configs, kTs)
# RXcalc.reload()
obs = RXcalc.run(
nsteps=10,
RXtrial_frequency=2,
sample_frequency=1,
observfunc=observables,
subdirs=True,
)
if worldrank == 0:
for i in range(len(kTs)):
with open("T" + str(i) + ".dat", "w") as f:
f.write("\n".join(
[str(obs[i, j]) for j in range(len(obs[i, :]))]))
for i in range(9):
for i in asites:
if calc_state.config.structure.species[i] == Element(self.Bspecie):
x += 1
x /= float(len(asites))
return x
def logfunc(self, calc_state):
return calc_state.energy, self.DOI(calc_state)
Asite_struct = cation_str.copy()
Asite_struct.remove_species(["Al"])
myobserver = observer_spinel(Asite_struct, "Al")
################### RXMC calculation #########################
RXcalc = TemperatureRX_MPI(comm, CanonicalMonteCarlo, model, configs, kTs)
# obs = RXcalc.run(eqsteps, RXtrial_frequency, sample_frequency, observer=myobserver, subdirs=True)
if Lreload:
RXcalc.reload()
obs = RXcalc.run(
nsteps,
RXtrial_frequency,
sample_frequency,
print_frequency,
observer=myobserver,
subdirs=True,
)
if comm.Get_rank() == 0:
print(obs)