def test_dump_cbk(self):
"""
Make sure that applying callbacks or changing the particle array
size creates a new dump.
"""
import numpy
from atooms.system import Particle, System
for view in [False, True]:
p = [Particle(), Particle()]
s = System(p)
pos1 = s.dump("pos", view=view)
def cbk(system):
s = copy.copy(system)
s.particle = [system.particle[0]]
return s
s = cbk(s)
pos2 = s.dump('pos', view=view)
self.assertEqual(pos1.shape, (2, 3))
self.assertEqual(pos2.shape, (1, 3))
# Grandcanonical
s.particle.append(Particle())
self.assertEqual(s.dump('pos', view=view).shape, (2, 3))
# Reassign particle
# Expected failure with view = True
if not view:
s.particle[0] = Particle(position=[1.0, 1.0, 1.0])
self.assertEqual(s.dump('pos', view=view)[0][0], 1.0)
def test_gyration(self):
from atooms.system.particle import gyration_radius
system = copy.copy(self.ref)
# Ignore cell
rg1 = gyration_radius(system.particle, method='N1')
rg2 = gyration_radius(system.particle, method='N2')
self.assertAlmostEqual(rg1, rg2)
# With PBC all estimates are different but bounds must be ok
rg1 = gyration_radius(system.particle, system.cell, method='min')
rg2 = gyration_radius(system.particle, system.cell, method='N1')
rg3 = gyration_radius(system.particle, system.cell, method='N2')
self.assertLessEqual(rg1, rg2)
self.assertLessEqual(rg3, rg2)
# Equilateral triangle
system.particle = [Particle(), Particle(), Particle()]
system.particle[0].position = numpy.array([0.0, 0.0, 0.0])
system.particle[1].position = numpy.array([1.0, 0.0, 0.0])
system.particle[2].position = numpy.array([0.5, 0.5 * 3**0.5, 0])
# Put the triangle across the cell
system.particle[0].position -= 1.01 * system.cell.side / 2
system.particle[1].position -= 1.01 * system.cell.side / 2
system.particle[2].position -= 1.01 * system.cell.side / 2
system.particle[0].fold(system.cell)
system.particle[1].fold(system.cell)
system.particle[2].fold(system.cell)
rg1 = gyration_radius(system.particle, system.cell, method='min')
rg2 = gyration_radius(system.particle, system.cell, method='N1')
rg3 = gyration_radius(system.particle, system.cell, method='N2')
self.assertAlmostEqual(rg1, 0.57735026919)
self.assertAlmostEqual(rg2, 0.57735026919)
self.assertAlmostEqual(rg3, 0.57735026919)
def test_view(self):
import numpy
from atooms.system import Particle, System
p = [Particle(), Particle()]
s = System(p)
pos = s.dump("pos", order='F', view=True)
# Modify the dumped array in place preserves the view
pos[:, 0] += 1.0
self.assertTrue((p[0].position == pos[:, 0]).all())
self.assertTrue(numpy.may_share_memory(p[0].position, pos[:, 0]))
# Modify the position array in place preserves the view
p[0].position *= 2
self.assertTrue((p[0].position == pos[:, 0]).all())
self.assertTrue(numpy.may_share_memory(p[0].position, pos[:, 0]))
# Modify the position array in place preserves the view
p[0].position[:] = p[0].position[:] + 4
self.assertTrue((p[0].position == pos[:, 0]).all())
self.assertTrue(numpy.may_share_memory(p[0].position, pos[:, 0]))
pos[:, 0] = pos[:, 0] + 1.0
self.assertTrue((p[0].position == pos[:, 0]).all())
self.assertTrue(numpy.may_share_memory(p[0].position, pos[:, 0]))
# Reassining the position will of course destroy the view
p[0].position = p[0].position * 2
self.assertFalse((p[0].position == pos[:, 0]).all())
self.assertFalse(numpy.may_share_memory(p[0].position, pos[:, 0]))
def test_decimate(self):
from atooms.system import Particle, System
from atooms.system.particle import composition, decimate
p = [Particle(species='A')] * 20 + [Particle(species='B')] * 10
pnew = decimate(p, 12)
x = composition(pnew)
self.assertEqual(x['A'], 8)
self.assertEqual(x['B'], 4)
def read_sample(self, frame):
cfg, box, pos, typ, vel = self.__read_one(self.__f_frames[frame])
if vel is None:
particle = [Particle(species=t, position=numpy.array(p)) for p, t in zip(pos, typ)]
else:
particle = [Particle(species=t, position=numpy.array(p), velocity=numpy.array(v))
for p, t, v in zip(pos, typ, vel)]
cell = Cell(numpy.array(box))
return System(particle, cell)
def dump_config(filename,
pos=None,
diam=None,
ptypes=None,
box=None,
compress=None):
file_ext = os.path.splitext(filename)[1]
cell = Cell(side=box)
npart = pos.shape[0]
particles = []
for i in range(npart):
p = Particle(species=ptypes[i],
position=pos[i, :] - box / 2.,
radius=diam[i] / 2.)
particles.append(p)
system = System(particle=particles, cell=cell)
with Trajectory(filename, "w") as traj:
# Step is always 0 for now.
traj.write(system, 0)
if file_ext == ".xyz":
compress = True
else:
compress = False
if compress:
subprocess.run(["gzip", "-f", filename])
def particle(self):
# Warning n.1 : this is read only. If you change the particles, the
# modification won't be propoagated to the RUMD objects.
# One would have to create a new system.
#
# Warning n.2 : it ia assumed that particles are sorted by species.
# since RUMD does not have accessors to particle types (why??)
# and we can only access the number of particles of a given type.
npart = self.sample.GetNumberOfParticles()
pos = self.sample.GetPositions()
vel = self.sample.GetVelocities()
nsp = self.sample.GetNumberOfTypes()
ima = self.sample.GetImages()
mass = self.__get_mass()
spe = numpy.ndarray(npart, dtype=int)
ii = 0
for i in range(nsp):
ni = self.sample.GetNumberThisType(i)
spe[ii: ii + ni] = i
ii += ni
p = [Particle(species=spe_i, mass=mass_i, position=pos_i,
velocity=vel_i) for spe_i, mass_i, pos_i, vel_i
in zip(spe, mass, pos, vel)]
for pi, i in zip(p, ima):
pi.periodic_image = i
return p
def read_sample(self, frame):
""" returns System instance. """
snap = self.trajectory[frame]
ndim = snap.configuration.dimensions
# Convert typeid from [0, 0, 1, ...] to ['A', 'A', 'B', ...] when snap.particles.types = ['A', 'B']
distinct_species = snap.particles.types
distinct_typeids = list(range(len(distinct_species)))
typeid_to_species = {}
for i in distinct_typeids:
typeid_to_species[i] = distinct_species[i]
box = snap.configuration.box[:
ndim] # atooms does not handle sheared boxes.
cell = Cell(side=box)
N = snap.particles.position.shape[0]
particles = []
for i in range(N):
p = Particle(mass=snap.particles.mass[i],
species=typeid_to_species[snap.particles.typeid[i]],
position=snap.particles.position[i, :ndim],
velocity=snap.particles.velocity[i, :ndim],
radius=snap.particles.diameter[i] / 2)
particles.append(p)
return System(particle=particles, cell=cell)
def test_dump_species(self):
"""
Make sure that changing species in the dump is reflected in the
particle species and viceversa.
"""
import numpy
from atooms.system import Particle, System
view = True
p = [Particle(), Particle()]
s = System(p)
spe = s.dump("particle.species", view=True)
spe[0] = 'B'
self.assertEqual(spe[0], s.particle[0].species)
# With this syntax, the numpy scalar preserves the view!
# We should upgrade species to property and hide this inside
s.particle[0].species[()] = 'C'
self.assertEqual(spe[0], s.particle[0].species)
def setUp(self):
N = 100
L = 10.0
self.ref = System()
self.ref.cell = Cell([L, L, L])
self.ref.particle = []
self.ref.thermostat = Thermostat(1.0)
self.ref.barostat = Barostat(1.0)
self.ref.reservoir = Reservoir(1.0)
while len(self.ref.particle) <= N:
pos = [(random.random() - 0.5) * L, (random.random() - 0.5) * L,
(random.random() - 0.5) * L]
self.ref.particle.append(Particle(position=pos))
def test_view_clear(self):
import numpy
from atooms.system import Particle, System
p = [Particle(), Particle()]
s = System(p)
# We check that particle positions are views on dump array
pos = s.dump("pos", order='F', view=True)
self.assertTrue((p[0].position == pos[:, 0]).all())
self.assertTrue(numpy.may_share_memory(p[0].position, pos[:, 0]))
# We should get the same dump array
pos = s.dump("pos", order='F', view=True)
self.assertTrue((p[0].position == pos[:, 0]).all())
self.assertTrue(numpy.may_share_memory(p[0].position, pos[:, 0]))
# We clear the dump array
pos1 = s.dump("pos", order='F', view=True, clear=True)
pos1 += 1
self.assertFalse((p[0].position == pos[:, 0]).all())
self.assertFalse(numpy.may_share_memory(p[0].position, pos[:, 0]))
def test_overlap_random(self):
# This test may fail from time to time
from atooms.system.particle import collective_overlap
N = 1000
L = 5.0
sys = [System(), System()]
sys[0].cell = Cell([L, L, L])
sys[1].cell = Cell([L, L, L])
sys[0].particle = []
sys[1].particle = []
for _ in range(N):
pos = [(random.random() - 0.5) * L, (random.random() - 0.5) * L,
(random.random() - 0.5) * L]
sys[0].particle.append(Particle(position=pos))
for _ in range(N):
pos = [(random.random() - 0.5) * L, (random.random() - 0.5) * L,
(random.random() - 0.5) * L]
sys[1].particle.append(Particle(position=pos))
a = 0.3
q_rand = ((a**3 * 4. / 3 * 3.1415) * N / sys[0].cell.volume)
self.assertTrue(
abs(q_rand - collective_overlap(sys[0].particle, sys[1].particle,
a, sys[0].cell.side)) < 0.5)
def read_sample(self, frame):
# Read metadata of this frame
meta = self._read_comment(frame)
# Get number of particles
self.trajectory.seek(self._index_header[frame])
npart = int(self.trajectory.readline())
# Read frame now
self.trajectory.seek(self._index_frame[frame])
particle = []
for ipart in range(npart):
p = Particle()
data = self.trajectory.readline().split()
i = 0
for key, fmt, ndims in meta['Properties']:
ndims = int(ndims)
if key in self.alias:
key = self.alias[key]
if ndims == 1:
if fmt == 'R':
setattr(p, key, float(data[i]))
elif fmt == 'I':
setattr(p, key, int(data[i]))
elif fmt == 'S':
setattr(p, key, data[i])
else:
raise ValueError('unknown format key')
else:
if fmt == 'R':
setattr(
p, key,
numpy.array(data[i:i + ndims],
dtype=numpy.float64))
elif fmt == 'I':
setattr(
p, key,
numpy.array(data[i:i + ndims], dtype=numpy.int64))
elif fmt == 'S':
setattr(p, key, numpy.array(data[i:i + ndims]))
else:
raise ValueError('unknown format key')
i += ndims
particle.append(p)
side = meta["Lattice"]
# TODO: remove hard coded
cell = Cell([side[0], side[4], side[8]])
return System(particle, cell)
def read_sample(self, frame):
""" returns System instance. """
L = self.header[0]
if self.ndim == 3:
cell = Cell(side=[L, L, L])
elif self.ndim == 2:
cell = Cell(side=[L, L])
N = self.data.shape[0]
pos = self.data[:, :self.ndim]
# Lerner group format has positions from [0, 1).
pos = pos*L - L/2
if self.velocity_present:
# Next is the velocity, if it exists.
vel = self.data[:, self.ndim:2*self.ndim]
# # In 2D, we add a zero z-coordinate to be consistent with other formats.
# if self.ndim == 3:
# # First ndim columns are always the position.
# elif self.ndim == 2:
# new_pos = np.zeros((N, 3)).astype(float)
# new_pos[:, :self.ndim] = pos
# pos = new_pos
# if self.velocity_present:
# vel = np.zeros((N, 3)).astype(float)
# vel[:, :self.ndim] = self.data[:, self.ndim:2*self.ndim]
particles = []
for i in range(N):
p = Particle()
p.position = pos[i, :]
if self.velocity_present:
p.velocity = vel[i, :]
if self.species_present and self.radius_present:
p.species = str( int(self.data[i, -1]) )
p.radius = self.data[i, -2]
elif self.radius_present:
p.radius = self.data[i, -1]
elif self.species_present:
p.species = str( int(self.data[i, -1]) )
particles.append(p)
return System(particle=particles, cell=cell)
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 read_sample(self, frame):
meta = self._read_comment(frame)
self.trajectory.seek(self._index_frame[frame])
# Read particles
particle = []
for _ in range(meta['npart']):
data = self.trajectory.readline().strip().split()
species = data[0]
r = numpy.array(data[1:4], dtype=float)
particle.append(Particle(species=species, position=r))
# Read cell
try:
side = meta['cell']
self._cell = Cell(side)
except KeyError:
pass
return System(particle, self._cell)
def unfold(system):
# s = system
# particle = system.particle
# for i, p in enumerate(particle):
# p.position += p.periodic_image * s.cell.side
# system.particle = particle
# return s
from atooms.system import System
npart = system.sample.GetNumberOfParticles()
pos = system.sample.GetPositions()
nsp = system.sample.GetNumberOfTypes()
ima = system.sample.GetImages()
spe = numpy.ndarray(npart, dtype=int)
ii = 0
for i in range(nsp):
ni = system.sample.GetNumberThisType(i)
spe[ii: ii + ni] = i
ii += ni
particle = [Particle(species=spe_i, position=pos_i) for spe_i, pos_i in
zip(spe, pos)]
for p, i in zip(particle, ima):
p.position += i * system.cell.side
return System(particle=particle, cell=system.cell)
def read_sample(self, frame):
# Setup fields again, in case they have changed
if self.__cache_fields != self.fields:
self._setup_fields()
# Read metadata of this frame
meta = self._read_comment(frame)
# Define read callbacks list before reading lines
callbacks_read = []
def _skip(p, data, meta):
return data[1:]
for key in self.fields:
# If the key is associated to a explicit callback, go
# for it. Otherwise we throw the field in an particle
# attribute named key. If the key is None it means we skip
# this column.
if key is None:
callbacks_read.append(_skip)
elif key in self.callback_read:
callbacks_read.append(self.callback_read[key])
else:
# Trick. We instantiate dynamically a fallback function
# to avoid adding `key` to the other callbacks' interface
namespace = {}
exec(
"""
from atooms.core.utils import tipify
def fallback(p, data, meta):
p.__dict__['%s'] = tipify(data[0])
return data[1:]
""" % key, namespace)
callbacks_read.append(namespace['fallback'])
# Read frame now
self.trajectory.seek(self._index_frame[frame])
particle = []
for i in range(meta['npart']):
p = Particle()
# Note: we cannot optimize by shifting an index instead of
# cropping lists all the time
data = self.trajectory.readline().split()
for cbk in callbacks_read:
data = cbk(p, data, meta)
particle.append(p)
# Fix the masses.
# We assume masses read from the header are sorted by species name.
# The mass metadata must be adjusted to the given frame.
if 'mass' in meta:
if isinstance(meta['mass'], list) or isinstance(
meta['mass'], tuple):
species = distinct_species(particle)
# We must have as many mass entries as species
if len(species) != len(meta['mass']):
raise ValueError('mass metadata issue %s, %s' %
(species, meta['mass']))
db = {}
for key, value in zip(species, meta['mass']):
db[key] = value
for p in particle:
p.mass = float(db[p.species])
else:
for p in particle:
p.mass = float(meta['mass'])
# Add cell info
if 'cell' in meta:
cell = Cell(meta['cell'])
else:
cell = None
return System(particle, cell)
def read_init(self):
# read particles
group = self.trajectory['/initialstate/particle']
n = self.trajectory['/initialstate/particle/number_of_particles'][0]
rad = None
for entry in group:
# TODO: refactor this
if entry == 'element':
spe = group[entry][:]
if entry == 'mass':
mas = group[entry][:]
if entry == 'position':
pos = group[entry][:]
if entry == 'velocity':
vel = group[entry][:]
if entry == 'radius':
rad = group[entry][:]
if rad is not None:
particle = [
Particle(species=spe[i].decode().strip(),
mass=mas[i],
position=pos[i, :],
velocity=vel[i, :],
radius=rad[i]) for i in range(n)
]
else:
particle = [
Particle(species=spe[i].decode().strip(),
mass=mas[i],
position=pos[i, :],
velocity=vel[i, :]) for i in range(n)
]
# read cell
group = self.trajectory['/initialstate/cell']
for entry in group:
if entry == 'sidebox':
sidebox = group[entry][:]
cell = Cell(sidebox)
# read interaction
interaction = self.read_interaction()
# build system
self._system = System(particle, cell, interaction)
# read matrix
if 'matrix' in self.trajectory['/initialstate']:
group = self.trajectory['/initialstate/matrix']
for entry in group:
if entry == 'element':
spe = group[entry][:]
if entry == 'mass':
mas = group[entry][:]
if entry == 'position':
pos = group[entry][:]
matrix = [
Particle(species=spe[i].decode().strip(),
mass=mas[i],
position=pos[i, :]) for i in range(len(spe))
]
self._system.matrix = copy.deepcopy(matrix)
return self._system
def read_sample(self, frame, unfolded=False):
# TODO: due to unfolded argument this differs from the base class method Can we drop this?
# We must increase frame by 1 if we iterate over frames with len().
# This is some convention to be fixed once and for all
# TODO: read cell on the fly NPT
keys = list(self.trajectory['/trajectory/realtime/stepindex'].keys())
csample = '/' + keys[frame]
# read particles
group = self.trajectory['/trajectory/particle']
if unfolded:
if 'position_unfolded' not in group:
raise NotImplementedError(
'cannot unfold like this, use decorator instead')
else:
# fix for unfolded positions that were not written at the first step
# should be fixed once and for all in md.x
if frame == 0:
pos = self.trajectory['/initialstate/particle/position'][:]
else:
pos = group['position_unfolded' + csample][:]
else:
pos = group['position' + csample][:]
try:
vel = group['velocity' + csample][:]
except:
vel = numpy.zeros([len(pos), ndim])
# Dynamic properties
p = []
for r, v in zip(pos, vel):
p.append(Particle(position=r, velocity=v))
# Static properties
# TODO: optimize, this takes quite some additional time, almost x2
for pi, r in zip(p, self._system.particle):
pi.mass = r.mass
pi.species = r.species
pi.radius = r.radius
# Try update radii. This must be done after setting defaults.
try:
r = group['radius' + csample][:]
for i, pi in enumerate(p):
pi.radius = r[i]
if 'radius' not in self.fields:
self.fields.append('radius')
except KeyError:
if 'radius' in self.fields:
self.fields.remove('radius')
# Try update species. This must be done after setting defaults.
# TODO: refactor
try:
spe = group['species' + csample][:]
for i, pi in enumerate(p):
pi.species = spe[i].decode().strip()
if 'species' not in self.fields:
self.fields.append('species')
except KeyError:
if 'species' in self.fields:
self.fields.remove('species')
# Read cell
group = self.trajectory['/trajectory/cell']
side = group['sidebox' + csample][:]
# This fixes an issue with some hdf5 trajectories that stored
# cell as (1,3) array
if len(side.shape) == 2:
side = side[0]
self._system.cell.side = side
# Read also interaction.
has_int = True
try:
group = self.trajectory['/trajectory/interaction']
except:
has_int = False
if has_int:
self._system.interaction.total_energy = group['energy' +
csample][0]
self._system.interaction.total_virial = group['virial' +
csample][0]
self._system.interaction.total_stress = group['stress' +
csample][:]
return System(p, self._system.cell, self._system.interaction)