def myfcc(symbol, pbc):
"Make an fcc lattice with standard lattice constant"
if ismaster:
a = FaceCenteredCubic(symbol=symbol, size=(10,10,10), pbc=pbc)
dx = 0.01 * np.sin(0.1 * np.arange(len(a) * 3))
dx.shape = (len(a),3)
a.set_positions(a.get_positions() + dx)
a.set_momenta(np.zeros((len(a),3)))
#view(a)
else:
a = None
if isparallel:
a = MakeParallelAtoms(a, cpulayout)
return a
if ismaster:
atoms = FaceCenteredCubic(size=(2,10,10), symbol="Cu", pbc=False,
latticeconstant = 3.5)
else:
atoms = None
if isparallel:
atoms = MakeParallelAtoms(atoms, cpulayout)
atoms.set_calculator(asap3.EMT())
natoms = atoms.get_number_of_atoms()
ReportTest("Number of atoms", natoms, 800, 0)
# Make a small perturbation of the momenta
atoms.set_momenta(1e-6 * random.random([len(atoms), 3]))
print "Initializing ..."
predyn = VelocityVerlet(atoms, 0.5)
try:
predyn.run(2500)
except:
print atoms.arrays['positions']
print atoms.arrays['momenta']
print atoms.arrays['momenta'].shape
print atoms.get_masses()
print atoms.get_masses().shape
raise
initr = atoms.get_positions()
initp = atoms.get_momenta()
#AsapThreads()
cpulayout = (1, 1, 2)
element = 'Pt'
size = (20, 20, 100)
master = world.rank == 0
if master:
atoms = FaceCenteredCubic(symbol=element,
size=size,
pbc=(True, True, False))
atoms.center(vacuum=10.0, axis=2)
atoms.set_momenta(np.zeros((len(atoms), 3)))
# Select an atom to get a kick
r = atoms.get_positions()
uc = atoms.get_cell()
x = r[:, 0] - 0.5 * uc[0, 0]
y = r[:, 1] - 0.5 * uc[1, 1]
z = r[:, 2]
zprime = z - 0.01 * (x * x + y * y)
n = np.argmax(zprime)
#a = atoms[n]
#dp = np.sqrt(2 * a.mass * 1000.0)
#a.momentum = np.array([0, 0, dp])
t = np.zeros(len(atoms), int)
t[n] = 1
atoms.set_tags(t)
else:
tolerance = 0.01
timestep = 5 # fs
frict = 0.001
temp = 100 # K
repeats = 5
# Set up atoms in a regular simple-cubic lattice.
initial = FaceCenteredCubic(directions=[[1,0,0],[0,1,0],[0,0,1]],
size = (1,5,5), symbol="Cu", latticeconstant=3.5,
pbc=False, debug=0)
initial.set_calculator(EMT())
ReportTest("Number of atoms", len(initial), 100, 0)
# Make a small perturbation of the momenta
initial.set_momenta(1e-6 * np.random.normal(size=[len(initial), 3]))
print "Initializing (1) ..."
predyn = VelocityVerlet(initial, 0.5)
predyn.run(2500)
initial2 = FaceCenteredCubic(directions=[[1,0,0],[0,1,0],[0,0,1]],
size = (4,4,4), symbol="Cu", debug=0)
initial2.set_calculator(EMT())
# Make a small perturbation of the momenta
initial2.set_momenta(1e-6 * np.random.normal(size=[len(initial2), 3]))
print "Initializing (2) ..."
predyn = VelocityVerlet(initial2, 0.5)
predyn.run(2500)
class TemperatureMonitor:
else:
raise ValueError, ("Cannot run on %d CPUs." % (worldsize, ))
elements = [29]
epsilon = [0.15]
sigma = [2.7]
if ismaster:
initial = FaceCenteredCubic(directions=((1, 0, 0), (0, 1, 0), (0, 0, 1)),
size=(40, 40, 40),
symbol="Cu",
latticeconstant=1.09 * sigma[0] * 1.41,
pbc=(1, 1, 0))
momenta = sqrt(2 * 63.5 * units.kB * 400) * sin(arange(3 * len(initial)))
momenta.shape = (-1, 3)
initial.set_momenta(momenta)
stdout = sys.stdout
print "Number of atoms:", len(initial)
else:
initial = None
stdout = open("/dev/null", "w")
for cpulayout in layout:
if cpulayout:
print >> stdout, "Test with layout " + str(cpulayout)
atoms = MakeParallelAtoms(initial, cpulayout)
natoms = atoms.get_number_of_atoms()
else:
print >> stdout, "Serial test"
atoms = Atoms(initial)
natoms = len(atoms)
else:
raise ValueError, ("Cannot run on %d CPUs." % (worldsize,))
elements = [29]
epsilon = [0.15]
sigma = [2.7]
if ismaster:
initial = FaceCenteredCubic(directions=((1,0,0),(0,1,0),(0,0,1)),
size=(40,40,40), symbol="Cu",
latticeconstant=1.09*sigma[0]*1.41,
pbc=(1,1,0))
momenta = sqrt(2*63.5 * units.kB * 400) * sin(arange(3*len(initial)))
momenta.shape = (-1,3)
initial.set_momenta(momenta)
stdout = sys.stdout
print "Number of atoms:", len(initial)
else:
initial = None
stdout = open("/dev/null", "w")
for cpulayout in layout:
if cpulayout:
print >>stdout, "Test with layout "+str(cpulayout)
atoms = MakeParallelAtoms(initial, cpulayout)
natoms = atoms.get_number_of_atoms()
else:
print >>stdout, "Serial test"
atoms = Atoms(initial)
natoms = len(atoms)
fast = False
#AsapThreads()
cpulayout = (1,1,2)
element = 'Pt'
size = (20,20,100)
master = world.rank == 0
if master:
atoms = FaceCenteredCubic(symbol=element, size=size, pbc=(True, True, False))
atoms.center(vacuum=10.0, axis=2)
atoms.set_momenta(np.zeros((len(atoms),3)))
# Select an atom to get a kick
r = atoms.get_positions()
uc = atoms.get_cell()
x = r[:,0] - 0.5 * uc[0,0]
y = r[:,1] - 0.5 * uc[1,1]
z = r[:,2]
zprime = z - 0.01 * (x * x + y * y)
n = np.argmax(zprime)
#a = atoms[n]
#dp = np.sqrt(2 * a.mass * 1000.0)
#a.momentum = np.array([0, 0, dp])
t = np.zeros(len(atoms), int)
t[n] = 1
atoms.set_tags(t)
else:
