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_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_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_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)
class Test(unittest.TestCase):
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_density(self):
system = copy.copy(self.ref)
density_old = system.density
system.density = density_old * 1.1
self.assertAlmostEqual(system.density, density_old * 1.1)
def test_temperature(self):
system = copy.copy(self.ref)
system.set_temperature(1.0)
self.assertAlmostEqual(system.temperature, 1.0)
def test_cm(self):
system = copy.copy(self.ref)
system.set_temperature(1.0)
system.fix_momentum()
self.assertAlmostEqual(system.cm_velocity[0], 0.0)
self.assertAlmostEqual(system.cm_velocity[1], 0.0)
self.assertAlmostEqual(system.cm_velocity[2], 0.0)
pos_cm = system.cm_position
for p in system.particle:
p.position -= pos_cm
self.assertAlmostEqual(system.cm_position[0], 0.0)
self.assertAlmostEqual(system.cm_position[1], 0.0)
self.assertAlmostEqual(system.cm_position[2], 0.0)
def test_pbc_center(self):
system = copy.copy(self.ref)
# Move the center of the cell so that positions are within 0 and L
system.cell.center = system.cell.side / 2
for p in system.particle:
p.position += system.cell.side / 2
# Check that distances are the same
for i in range(len(system.particle)):
self.assertAlmostEqual(
sum(self.ref.particle[0].distance(self.ref.particle[i],
self.ref.cell)**2),
sum(system.particle[0].distance(system.particle[i],
system.cell)**2))
# Move one particle out of the box and fold it back
pos = copy.copy(system.particle[0].position)
system.particle[0].position += system.cell.side
system.particle[0].fold(system.cell)
self.assertAlmostEqual(pos[0], system.particle[0].position[0])
self.assertAlmostEqual(pos[1], system.particle[0].position[1])
self.assertAlmostEqual(pos[2], system.particle[0].position[2])
def test_fold(self):
system = copy.copy(self.ref)
pos = copy.copy(system.particle[0].position)
system.particle[0].position += system.cell.side
system.particle[0].fold(system.cell)
self.assertAlmostEqual(pos[0], system.particle[0].position[0])
self.assertAlmostEqual(pos[1], system.particle[0].position[1])
self.assertAlmostEqual(pos[2], system.particle[0].position[2])
def test_overlaps(self):
from atooms.system.particle import overlaps
system = copy.copy(self.ref)
for p in system.particle:
p.radius = 1e-10
pos = copy.copy(system.particle[1].position)
system.particle[0].position = pos
ov, ipart = overlaps(system.particle, system.cell)
self.assertTrue(ov)
self.assertEqual(ipart, [(0, 1)])
def test_dump(self):
self.assertEqual(
self.ref.dump('spe')[-1],
self.ref.dump('particle.species')[-1])
self.assertAlmostEqual(
self.ref.dump('pos')[-1][-1],
self.ref.dump('particle.position')[-1][-1])
self.assertAlmostEqual(
self.ref.dump('vel')[-1][-1],
self.ref.dump('particle.velocity')[-1][-1])
def test_species(self):
system = copy.copy(self.ref)
npart = len(system.particle)
for p in system.particle[0:10]:
p.species = 'B'
for p in system.particle[10:30]:
p.species = 'C'
from atooms.system.particle import composition, distinct_species
self.assertEqual(distinct_species(system.particle), ['A', 'B', 'C'])
self.assertEqual(system.distinct_species(), ['A', 'B', 'C'])
self.assertEqual(composition(system.particle)['A'], npart - 30)
self.assertEqual(composition(system.particle)['B'], 10)
self.assertEqual(composition(system.particle)['C'], 20)
def test_packing(self):
import math
system = copy.copy(self.ref)
self.assertAlmostEqual(system.packing_fraction * 6 / math.pi,
system.density)
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_interaction(self):
from atooms.interaction import Interaction
system = copy.copy(self.ref)
self.assertAlmostEqual(system.potential_energy(), 0.0)
system.interaction = Interaction([])
system.interaction.compute('energy', system.particle, system.cell)
system.interaction.compute('forces', system.particle, system.cell)
system.interaction.compute('stress', system.particle, system.cell)
self.assertAlmostEqual(system.potential_energy(), 0.0)
self.assertAlmostEqual(system.potential_energy(normed=True), 0.0)
self.assertAlmostEqual(system.total_energy(), system.kinetic_energy())
def test_overlap(self):
from atooms.system.particle import self_overlap, collective_overlap
sys1 = copy.deepcopy(self.ref)
sys2 = copy.deepcopy(self.ref)
sys1.particle = sys1.particle[:int(len(sys1.particle) / 2)]
sys2.particle = sys2.particle[int(len(sys2.particle) / 2):]
self.assertEqual(0, self_overlap(sys1.particle, sys2.particle, 0.001))
self.assertEqual(
0,
collective_overlap(sys1.particle, sys2.particle, 0.001,
sys1.cell.side))
sys1.particle = sys1.particle
sys2.particle = sys1.particle
self.assertEqual(1, self_overlap(sys1.particle, sys2.particle, 0.001))
self.assertEqual(
1,
collective_overlap(sys1.particle, sys2.particle, 0.001,
sys1.cell.side))
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 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_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_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_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 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 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')