def test_ovito(self):
try:
import ovito
except ImportError:
self.skipTest('missing ovito')
N = 3
L = 5.0
system = System()
system.cell = Cell([L, L, L])
system.particle = []
for _ in range(N):
pos = (numpy.random.random(len(system.cell.side)) -
0.5) * system.cell.side
p = Particle(position=pos)
system.particle.append(p)
image = system.show('ovito')
def test_write_initial_state(self):
p = [
PairPotential('lennard_jones', {
'epsilon': 1.0,
'sigma': 1.0
}, [1, 1], CutOff('CS', 2.5))
]
i = [Interaction(p, 'atomic')]
s = System()
s.cell = Cell([1.0, 1.0, 1.0])
t = TrajectoryHDF5('/tmp/test_potential.h5', 'w')
t.write_interaction(i)
t.close()
t = TrajectoryHDF5('/tmp/test_potential.h5', 'r')
i = t.read_interaction()
t.close()
def test_write_initial_state(self):
p = [
PairPotential("lennard_jones", {
"epsilon": 1.0,
"sigma": 1.0
}, [1, 1], CutOff("CS", 2.5))
]
i = [Interaction(p, "atomic")]
s = System()
s.particle = [
Particle(position=[1.0, 1.0, 1.0], velocity=[0.0, 0.0, 0.0])
]
s.cell = Cell([1.0, 1.0, 1.0])
with TrajectoryHDF5('/tmp/test_hdf5.h5', 'w') as t:
t.write_interaction(i)
t.write(s, 0)
with TrajectoryHDF5('/tmp/test_hdf5.h5', 'r') as t:
i = t.read_interaction()
s = t[0]
def read_sample(self, frame):
system = System()
s = self.trajectory["trajectory/realtime/sampleindex"].keys()[frame]
system.eigenvalues = self.trajectory["trajectory/normalmodes/eigenvalues/%s" % s][:]
system.eigenfreq = numpy.array([copysign(abs(x)**0.5, x) for x in system.eigenvalues])
mode_idx = self.trajectory["trajectory/normalmodes/eigenvectors/index/%s" % s][:]
eigv = {}
for idx in mode_idx:
# Modes are F-indexed
omega = system.eigenfreq[idx-1]
vect = self.trajectory["trajectory/normalmodes/eigenvectors/vector/%s_mode_%05d" % (s, idx)][:]
eigv[omega] = vect
system.eigenvectors = eigv
# Add positions
parent = os.path.splitext(self.trajectory.filename)[0]
step = self.steps[frame]
with TrajectoryHDF5(parent) as th:
# The step should be there
parent_frame = th.steps.index(step)
system.particle = th[parent_frame].particle
system.cell = th[parent_frame].cell
return system
def read_sample(self, frame):
# Read number of particles
idx, _ = self._index_db['NUMBER OF ATOMS'][frame]
self._fh.seek(idx)
self._fh.readline()
data = self._fh.readline()
npart = int(data)
# Build the system
system = System()
system.particle = []
for i in range(npart):
if self.first_particle > 0 and i < self.first_particle:
continue
if self.last_particle > 0 and i >= self.last_particle:
break
system.particle.append(Particle())
# Add cell
idx, data = self._index_db['BOX BOUNDS'][frame]
self._fh.seek(idx)
self._fh.readline()
ndim = len(data.split()) # line is ITEM: BOX BONDS pp pp pp
L, center = [], []
for i in range(ndim):
data = [float(x) for x in self._fh.readline().split()]
L.append(data[1] - data[0])
center.append((data[1] + data[0]) / 2)
system.cell = Cell(numpy.array(L), center=numpy.array(center))
# Read atoms data
idx, data = self._index_db['ATOMS'][frame]
fields = data.split() # fields on a line
_ = self._fh.readline()
# Add interaction if forces are present
# In atooms, forces belong to the interaction, not to particles
if 'fx' in fields or 'fy' in fields or 'fz' in fields:
# TODO: this won't work with first and last particles
system.interaction = Interaction([]) # empty list of potentials
system.interaction.forces = numpy.ndarray((npart, ndim))
else:
interaction = None
for i in range(npart):
# Limit reading the ATOMS section if requested
if self.first_particle > 0 and i < self.first_particle:
continue
if self.last_particle > 0 and i >= self.last_particle:
break
data = self._fh.readline().split()
# Accept unsorted particles by parsing their id
if 'id' in fields:
idx = int(data[0]) - 1
else:
idx = i
# Populate particle's attributes by reading fields
for j, field in enumerate(fields):
if field in self._cbk:
self._cbk[field](data[j], idx, system)
else:
# We should store these fields in particle anyway
pass
return system
