def attach_randomly_and_broadcast(atoms1,
atoms2,
distance,
rng=np.random,
comm=world):
"""Randomly attach two structures with a given minimal distance
and ensure that these are distributed.
Parameters
----------
atoms1: Atoms object
atoms2: Atoms object
distance: float
Required distance
rng: random number generator object
defaults to np.random.RandomState()
comm: communicator to distribute
Communicator to distribute the structure, default: world
Returns
-------
Joined structure as an atoms object.
"""
if comm.rank == 0:
joined = attach_randomly(atoms1, atoms2, distance, rng)
broadcast(joined, 0, comm=comm)
else:
joined = broadcast(None, 0, comm)
return joined
def new_generator(*args, **kwargs):
if world.rank == 0:
for result in generator(*args, **kwargs):
result = broadcast(result)
yield result
broadcast(None)
else:
result = broadcast(None)
while result is not None:
yield result
def new_generator(*args, **kwargs):
if world.rank == 0:
for result in generator(*args, **kwargs):
result = broadcast(result)
yield result
broadcast(None)
else:
result = broadcast(None)
while result is not None:
yield result
def new_method(*args, **kwargs):
if world.rank == 0:
result = method(*args, **kwargs)
else:
result = None
result = broadcast(result)
return result
def new_method(*args, **kwargs):
if world.rank == 0:
result = method(*args, **kwargs)
else:
result = None
result = broadcast(result)
return result
def new_method(*args, **kwargs):
ex = None
result = None
if world.rank == 0:
try:
result = method(*args, **kwargs)
except Exception as ex:
pass
ex, result = broadcast((ex, result))
if ex is not None:
raise ex
return result
def new_method(*args, **kwargs):
ex = None
result = None
if world.rank == 0:
try:
result = method(*args, **kwargs)
except Exception as ex:
pass
ex, result = broadcast((ex, result))
if ex is not None:
raise ex
return result
def calculate(self,
atoms=None,
properties=['energy'],
system_changes=all_changes):
# We don't call FileIOCalculator.calculate here, because that method
# calls subprocess.call(..., shell=True), which we don't want to do.
# So, we reproduce some content from that method here.
Calculator.calculate(self, atoms, properties, system_changes)
# If a parameter file exists in the working directory, delete it
# first. If we need that file, we'll recreate it later.
localparfile = os.path.join(self.directory, '.dftd3par.local')
if os.path.isfile(localparfile):
os.remove(localparfile)
# Write XYZ or POSCAR file and .dftd3par.local file if we are using
# custom damping parameters.
self.write_input(self.atoms, properties, system_changes)
command = self._generate_command()
# Finally, call dftd3 and parse results.
with paropen(self.label + '.out', 'w') as f:
if world.rank == 0:
# DFTD3 does not run in parallel
# so we only need it to run on 1 core
errorcode = subprocess.call(command,
cwd=self.directory,
stdout=f)
else:
errorcode = None
world.barrier() # Wait for the call() to complete on the master node
errorcode = broadcast(errorcode, root=0)
if errorcode:
raise RuntimeError('%s returned an error: %d' %
(self.name, errorcode))
self.read_results()
def read_results(self):
# parse the energy
outname = os.path.join(self.directory, self.label + '.out')
self.results['energy'] = None
self.results['free_energy'] = None
if world.rank == 0:
with open(outname, 'r') as f:
for line in f:
if line.startswith(' program stopped'):
if 'functional name unknown' in line:
message = 'Unknown DFTD3 functional name "{}". ' \
'Please check the dftd3.f source file ' \
'for the list of known functionals ' \
'and their spelling.' \
''.format(self.parameters['xc'])
else:
message = 'dftd3 failed! Please check the {} ' \
'output file and report any errors ' \
'to the ASE developers.' \
''.format(outname)
raise RuntimeError(message)
if line.startswith(' Edisp'):
e_dftd3 = float(line.split()[3]) * Hartree
self.results['energy'] = e_dftd3
self.results['free_energy'] = e_dftd3
break
else:
raise RuntimeError('Could not parse energy from dftd3 '
'output, see file {}'.format(outname))
self.results['energy'] = broadcast(self.results['energy'], root=0)
self.results['free_energy'] = broadcast(self.results['free_energy'],
root=0)
# FIXME: Calculator.get_potential_energy() simply inspects
# self.results for the free energy rather than calling
# Calculator.get_property('free_energy'). For example, GPAW does
# not actually present free_energy as an implemented property, even
# though it does calculate it. So, we are going to add in the DFT
# free energy to our own results if it is present in the attached
# calculator. TODO: Fix the Calculator interface!!!
if self.dft is not None:
try:
efree = self.dft.get_potential_energy(force_consistent=True)
self.results['free_energy'] += efree
except PropertyNotImplementedError:
pass
if self.parameters['grad']:
# parse the forces
forces = np.zeros((len(self.atoms), 3))
forcename = os.path.join(self.directory, 'dftd3_gradient')
self.results['forces'] = None
if world.rank == 0:
with open(forcename, 'r') as f:
for i, line in enumerate(f):
forces[i] = np.array([float(x) for x in line.split()])
self.results['forces'] = -forces * Hartree / Bohr
self.results['forces'] = broadcast(self.results['forces'], root=0)
if any(self.atoms.pbc):
# parse the stress tensor
stress = np.zeros((3, 3))
stressname = os.path.join(self.directory, 'dftd3_cellgradient')
self.results['stress'] = None
if world.rank == 0:
with open(stressname, 'r') as f:
for i, line in enumerate(f):
for j, x in enumerate(line.split()):
stress[i, j] = float(x)
stress *= Hartree / Bohr / self.atoms.get_volume()
stress = np.dot(stress, self.atoms.cell.T)
self.results['stress'] = stress.flat[[0, 4, 8, 5, 2, 1]]
self.results['stress'] = broadcast(self.results['stress'],
root=0)
def main():
atoms = build.bulk("Al")
atoms = atoms * (2, 2, 2)
print(len(atoms))
nRuns = 10
optimizerFname = "optimizer.pck"
for i in range(nRuns):
nMgAtoms = np.random.randint(0, len(atoms) / 2)
# Insert Mg atoms
system = cp.copy(atoms)
if (parallel.rank == 0):
for j in range(nMgAtoms):
system[i].symbol = "Mg"
# Shuffle the list
for j in range(10 * len(system)):
first = np.random.randint(0, len(system))
second = np.random.randint(0, len(system))
symb1 = system[first].symbol
system[first].symbol = system[second].symbol
system[second].symbol = symb1
system = parallel.broadcast(system)
# Initialize the calculator
calc = gp.GPAW(mode=gp.PW(400), xc="PBE", kpts=(4, 4, 4), nbands=-10)
system.set_calculator(calc)
traj = Trajectory("trajectoryResuse.traj", 'w', atoms)
if (i == 0):
relaxer = PreconLBFGS(UnitCellFilter(system), logfile="resuse.log")
else:
relaxer = None
relaxParams = None
if (parallel.rank == 0):
with open(optimizerFname, 'rb') as infile:
relaxParams = pck.load(infile)
relaxParams = parallel.broadcast(relaxParams)
precon = Exp(r_cut=relaxParams["r_cut"],
r_NN=relaxParams["r_NN"],
mu=relaxParams["mu"],
mu_c=relaxParams["mu_c"])
relaxer = PreconLBFGS(UnitCellFilter(system),
logfile="resuse.log",
precon=precon)
relaxer.attach(traj)
relaxer.run(fmax=0.05)
print(relaxer.iteration)
if (parallel.rank == 0):
with open(optimizerFname, 'wb') as outfile:
relaxParams = {
"r_cut": relaxer.precon.r_cut,
"r_NN": relaxer.precon.r_NN,
"mu": relaxer.precon.mu,
"mu_c": relaxer.precon.mu_c
}
pck.dump(relaxParams, outfile, pck.HIGHEST_PROTOCOL)
parallel.barrier()
