def test_interacting_system(self):
p = PairPotential('lennard_jones', {
'epsilon': 1.0,
'sigma': 1.0
}, [1, 1], CutOff('CS', 2.5))
i = Interaction(p, 'atomic')
s = System()
s.interaction = i
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