def update(self):
zmax = self.atoms.get_cell()[2,2]
z = self.atoms.get_positions()[:,2]
group = np.round(z/zmax * self.blocks).astype(int)
group = np.clip(group, 0, self.blocks-1)
p = self.atoms.get_momenta()
ekin = (p*p).sum(axis=1) / (2 * self.atoms.get_masses())
ekinsum = np.zeros(self.blocks)
blocksum = np.zeros(self.blocks, int)
for i in range(self.blocks):
thisblock = np.equal(group, i)
ekinsum[i] = ekin[thisblock].sum()
blocksum[i] = thisblock.sum()
world.sum(ekinsum)
world.sum(blocksum)
if master:
np.clip(blocksum, 1, blocksum.max(), out=blocksum)
T = ekinsum / ( 1.5 * units.kB * blocksum)
for i in range(self.blocks):
self.output.write("%i %.1f\n" % (i, T[i],))
self.output.write("&\n")
self.output.flush()
atoms = FaceCenteredCubic(size=size*layout, symbol='Cu')
atoms.set_calculator(EMT())
natoms = atoms.get_number_of_atoms()
print "Number of atoms:", natoms
assert natoms == ncpu * 500000
print "Potential energy:", atoms.get_potential_energy()
start = time.time()
d = 0.1
for i in range(nsteps):
atoms.arrays['positions'][50][0] += d
d = -d
f = atoms.get_forces()
wall = time.time() - start
if cmd in "SM":
master = world.rank == 0
wall = world.sum(wall)
wall /= world.size
else:
master = True
if master:
report_timing()
print "Wall time elapsed:", wall
f = open(sys.argv[2], "a")
pickle.dump((cmd, ncpu, wall), f)
f.close()
def get_center_of_mass_momentum(self):
"Get the center of mass momentum."
cm = self.atoms.get_momenta().sum(0)
world.sum(cm)
return cm
to = 0
fr = world.rank - 1
if fr < 0:
fr += world.size
print "%d: to=%d from=%d" % (world.rank, to, fr)
rq = world.send(outdata, to, block=False)
world.receive(indata, fr)
#world.wait(rq)
print "Request completed:", rq.test()
rq.wait()
assert (indata == fr * np.arange(10000000)).all()
s = world.sum(2.5 * world.rank)
ReportTest("Float sum", s, 2.5 * 0.5 * world.size * (world.size - 1), 1e-9)
s = world.sum(world.rank)
ReportTest("Integer sum", s, world.size * (world.size - 1) / 2, 0)
s = world.max(1.0 * world.rank)
ReportTest("Float max", s, world.size - 1, 0)
s = world.max(world.rank)
ReportTest("Int max", s, world.size - 1, 0)
print "Checking reduces on arrays..."
d0 = np.arange(10) + world.rank
f0 = d0 + 0.0
atoms = FaceCenteredCubic(size=size * layout, symbol='Cu')
atoms.set_calculator(EMT())
natoms = atoms.get_number_of_atoms()
print "Number of atoms:", natoms
assert natoms == ncpu * 500000
print "Potential energy:", atoms.get_potential_energy()
start = time.time()
d = 0.1
for i in range(nsteps):
atoms.arrays['positions'][50][0] += d
d = -d
f = atoms.get_forces()
wall = time.time() - start
if cmd in "SM":
master = world.rank == 0
wall = world.sum(wall)
wall /= world.size
else:
master = True
if master:
report_timing()
print "Wall time elapsed:", wall
f = open(sys.argv[2], "a")
pickle.dump((cmd, ncpu, wall), f)
f.close()
def get_center_of_mass_momentum(self):
"Get the center of mass momentum."
cm = self.atoms.get_momenta().sum(0)
world.sum(cm)
return cm
def main(element, T_up, T_low, T_expect, bulkmodulus, makepot):
def set_temp_fric(dyn, atoms):
z = atoms.get_positions()[:,2]
zmax = atoms.get_cell()[2,2]
zmin = 0
T = T_low + (T_up - T_low) * (z - zmin) / (zmax - zmin)
dyn.set_temperature(T * units.kB)
rnd = world.sum(random.randint(0,2**32)) # Insures the same number on all nodes.
prefix = "melt-%s-%s" % (element, hex(rnd)[2:])
if master:
print "Using output directory", prefix
os.mkdir(prefix)
else:
while not os.path.exists(prefix):
time.sleep(1)
if master:
atoms = FaceCenteredCubic(symbol=element, size=size, pbc=(True, True, False))
atoms.center(vacuum=10.0, axis=2)
else:
atoms = None
atoms = MakeParallelAtoms(atoms, cpulayout1)
print world.rank, '-', len(atoms), atoms.get_number_of_atoms()
atoms.set_calculator(makepot())
#view(atoms)
dyn = Langevin(atoms, 5*units.fs, 0.0, friction)
logger = MDLogger(dyn, atoms, prefix+'/Melt-phase1.log', stress=True, peratom=True)
dyn.attach(logger, interval=100)
set_temp_fric(dyn, atoms)
unstress = Inhomogeneous_NPTBerendsen(atoms, 50*units.fs, 0, taup=500*units.fs,
compressibility=1/bulkmodulus)
dyn.attach(unstress.scale_positions_and_cell, interval=10)
#traj = PickleTrajectory("melting-phase1.traj", "w", atoms)
fn1 = prefix + "/Melt-phase1.bundle"
if master:
print "Opening file", fn1
traj = BundleTrajectory(fn1, "w", atoms, split=True)
dyn.attach(traj, interval=500)
therm = Thermometer(atoms, prefix+"/TempProfile-phase1.dat")
dyn.attach(therm.update, interval=500)
for i in range(steps1 / 100):
dyn.run(100)
set_temp_fric(dyn, atoms)
if master:
print "Closing file", fn1
traj.close()
del traj, atoms
# Reread the bundle
atoms = BundleTrajectory(fn1).get_atoms(-1, cpulayout2)
atoms.set_calculator(makepot())
dyn = VelocityVerlet(atoms, 5*units.fs)
logger = MDLogger(dyn, atoms, prefix+'/PtMelt-phase2.log', stress=True, peratom=True)
dyn.attach(logger, interval=1000)
unstress = Inhomogeneous_NPTBerendsen(atoms, 50*units.fs, 0,
taup=5000*units.fs,
compressibility=1/bulkmodulus)
dyn.attach(unstress.scale_positions_and_cell, interval=10)
fn2 = prefix + "/Melt-phase2.bundle"
if master:
print "Opening file", fn2
traj = BundleTrajectory(fn2, "w", atoms)
dyn.attach(traj, interval=steps2/100)
therm = Thermometer(atoms, prefix+"/TempProfile-phase2.dat")
dyn.attach(therm.update, interval=steps2/10)
dyn.run(steps2 - takedata)
therm2 = AveragingThermometer(atoms)
dyn.attach(therm2.update, interval=100)
dyn.run(takedata) # Run the last part
T = therm2.get_temp()
if master:
print "Melting temperature:", T
ReportTest("Melting temperature", T, T_expect, 3)
if cleanup:
world.barrier()
# Cleanup may fail due to the directory not being updated from
# writes on the other nodes. Wait for NFS file system.
time.sleep(60)
if master:
shutil.rmtree(prefix)
world.barrier()
ReportTest.Summary()