def main():
positions = np.zeros((N, 3))
positions[:,0] = d * np.arange(N)
if ismaster:
atoms = Atoms("Cu%i" % (N,), positions=positions, cell=(N*d, w, w),
pbc=False)
atoms.center()
else:
atoms = None
if isparallel:
atoms = MakeParallelAtoms(atoms, cpulayout)
id = atoms.get_ids()
else:
id = np.arange(N)
#view(atoms)
atoms.set_calculator(EMT())
f = atoms.get_forces()
x = atoms.get_positions()[:,0]
# time.sleep(world.rank)
for i in range(len(atoms)):
print world.rank, x[i], f[i]
# Now running actual tests - these are different on the two processors, but that should
# not be a problem
for i in range(len(f)):
if id[i] > 1 and id[i] < N - 2:
ftot = (f[i] * f[i]).sum()
ReportTest("Force on atom %i" % (id[i],), ftot, 0.0, 1e-13)
world.barrier()
ReportTest.Summary()
def main():
positions = np.zeros((N, 3))
positions[:, 0] = d * np.arange(N)
if ismaster:
atoms = Atoms("Cu%i" % (N, ),
positions=positions,
cell=(N * d, w, w),
pbc=False)
atoms.center()
else:
atoms = None
if isparallel:
atoms = MakeParallelAtoms(atoms, cpulayout)
id = atoms.get_ids()
else:
id = np.arange(N)
#view(atoms)
atoms.set_calculator(EMT())
f = atoms.get_forces()
x = atoms.get_positions()[:, 0]
# time.sleep(world.rank)
for i in range(len(atoms)):
print world.rank, x[i], f[i]
# Now running actual tests - these are different on the two processors, but that should
# not be a problem
for i in range(len(f)):
if id[i] > 1 and id[i] < N - 2:
ftot = (f[i] * f[i]).sum()
ReportTest("Force on atom %i" % (id[i], ), ftot, 0.0, 1e-13)
world.barrier()
ReportTest.Summary()
def report():
for i in range(world.size):
if i == world.rank:
print "Data on processor", i
for key in atoms.arrays.keys():
print " ", key, atoms.arrays[key].shape
r = atoms.get_positions()
if len(r):
print "Limits to the positions:"
print ("[%.4f, %.4f] [%.4f, %.4f] [%.4f, %.4f]" %
(min(r[:,0]), max(r[:,0]), min(r[:,1]), max(r[:,1]),
min(r[:,2]), max(r[:,2])))
if world.size > 1:
print "Ghost data on processor", i
for key in atoms.ghosts.keys():
print " ", key, atoms.ghosts[key].shape
r = atoms.ghosts['positions']
if len(r):
print "Limits to the ghost positions:"
print ("[%.4f, %.4f] [%.4f, %.4f] [%.4f, %.4f]" %
(min(r[:,0]), max(r[:,0]), min(r[:,1]), max(r[:,1]),
min(r[:,2]), max(r[:,2])))
world.barrier()
def _make_bundledir(self, filename):
"""Make the main bundle directory.
Since all MPI tasks might write to it, all tasks must wait for
the directory to appear.
For performance reasons, the first frame directory is created immediately.
"""
assert not os.path.isdir(filename)
world.barrier()
if self.master:
self.log("Making directory "+filename)
os.mkdir(filename)
framedir = os.path.join(filename, "F0")
self.log("Making directory "+ framedir)
os.mkdir(framedir)
else:
i = 0
while not os.path.isdir(filename):
time.sleep(1)
i += 1
if i > 10:
self.log("Waiting %d seconds for %s to appear!"
% (i, filename))
natoms = atoms.get_number_of_atoms()
else:
natoms = len(atoms)
report()
print
print
if world.size > 1:
atoms.distribute()
report()
print
print
print "Calculating total energy."
#if world.rank == 0:
# set_verbose(1)
atoms.set_calculator(EMT())
e = atoms.get_potential_energy()
report()
ReportTest("Potential energy", e, -2.40461833565e-3 * natoms / 4, 1e-5)
print "Exiting."
world.barrier()
#ReportTest.Summary()
import asap3
from asap3.mpi import world
from asap3.testtools import ReportTest
import numpy as np
if world.size == 1:
raise RuntimeError("Cannot test MPI communication on a single processor.")
if world.rank == 0:
asap3.print_version(1)
world.barrier()
outdata = np.array([world.rank * 2], int)
indata = np.zeros(1, int)
to = world.rank + 1
if to >= world.size:
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)
ReportTest("Data received by %s from %s" % (world.rank, fr), indata[0], 2*fr, 0)
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()
