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_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 is_semigrandcanonical(trajectory, tests=1):
"""
Simple test to check if a trajectory is semigrandcanonical.
i.e. if the chemical concentrations fluctuate.
We compare the first frame to an integer number `tests` of other
frames starting from the end of `trajectory`.
"""
# This is adapted from is_cell_variable()
is_variable = False
if tests > 0:
skip = max(1, int(len(trajectory) / float(tests)))
else:
skip = 1
from atooms.system.particle import composition
x0 = composition(trajectory[0].particle)
for sample in range(len(trajectory) - 1, 0, -skip):
x1 = composition(trajectory[sample].particle)
is_variable = False
for sp in x0:
if x0[sp] != x1[sp]:
is_variable = True
break
return is_variable
def test_sk_field(self):
"""
Test that S(k) with a field that is 0 if id=A and 1 if id=B gives
the BB partial structure factor.
"""
# TODO: this test fails with python 3 because of a weird issue with xyz trajectory in atooms (_fallback)
f = os.path.join(self.reference_path, 'kalj-small.xyz')
ff = os.path.join(self.reference_path, 'kalj-small-field.xyz')
t = trajectory.TrajectoryXYZ(f)
p = postprocessing.StructureFactor(t, [4, 7.3, 10],
trajectory_field=ff)
p.compute()
# We multiply by x because the S(k) is normalized to 1/N
from atooms.system.particle import composition
x = composition(t[0].particle)['B'] / float(len(t[0].particle))
ref_value = x * numpy.array(
[0.86716496871363735, 0.86986885176760842, 0.98112175463699136])
self.assertLess(deviation(p.value, ref_value), 1e-2)
def test_sk_field(self):
"""
Test that S(k) with a field that is 0 if id=A and 1 if id=B gives
the BB partial structure factor.
"""
f = os.path.join(self.reference_path, 'kalj-small.xyz')
ff = os.path.join(self.reference_path, 'kalj-small-field.xyz')
th = trajectory.TrajectoryXYZ(f)
tt = trajectory.TrajectoryXYZ(ff)
p = postprocessing.StructureFactor(th, [4, 7.3, 10])
p.add_weight(trajectory=tt, field='field_B')
p.compute()
# We multiply by x because the S(k) is normalized to 1/N
from atooms.system.particle import composition
x = composition(th[0].particle)['B'] / float(len(th[0].particle))
ref_value = x * numpy.array(
[0.86716496871363735, 0.86986885176760842, 0.98112175463699136])
self.assertLess(deviation(p.value, ref_value), 1e-2)
th.close()
tt.close()
def info(trajectory, keys=None):
"""Return a string with information about a `trajectory` instance."""
from atooms.system.particle import distinct_species, composition
system = trajectory[0]
if keys is None:
# Default: full info
txt = ''
txt += 'path = %s\n' % trajectory.filename
txt += 'format = %s\n' % trajectory.__class__
txt += 'frames = %s\n' % len(trajectory)
txt += 'megabytes = %s\n' % (
os.path.getsize(trajectory.filename) / 1e6)
txt += 'particles = %s\n' % len(system.particle)
txt += 'species = %s\n' % ', '.join(
distinct_species(system.particle))
txt += 'composition = %s\n' % dict(
composition(system.particle))
txt += 'size dispersion = %s\n' % (
numpy.std([p.radius for p in system.particle]) /
numpy.mean([p.radius for p in system.particle]))
txt += 'density = %s\n' % round(system.density, 10)
if system.cell is not None:
txt += 'cell side = %s\n' % str(list(
system.cell.side))[1:-1]
txt += 'cell volume = %s\n' % system.cell.volume
if len(trajectory) > 1:
txt += 'steps = %s\n' % trajectory.steps[-1]
txt += 'duration = %s\n' % trajectory.times[-1]
txt += 'timestep = %s\n' % trajectory.timestep
txt += 'block size = %s\n' % trajectory.block_size
if trajectory.block_size == 1:
txt += 'steps between frames = %s\n' % (trajectory.steps[1] -
trajectory.steps[0])
txt += 'time between frames = %s\n' % (trajectory.times[1] -
trajectory.times[0])
else:
txt += 'block steps = %s\n' % trajectory.steps[
trajectory.block_size - 1]
txt += 'block = %s\n' % ([
trajectory.steps[i] for i in range(trajectory.block_size)
])
txt += 'grandcanonical = %s' % trajectory.grandcanonical
return txt
else:
# Selected infos.
# TODO: of course, it would be cleaner to have a little class for that
outs = []
for key in keys.split(','):
if key == 'path':
outs.append(trajectory.filename)
elif key == 'format':
outs.append(trajectory.__class__)
elif key == 'frames':
outs.append(len(trajectory))
elif key == 'megabytes':
outs.append(os.path.getsize(trajectory.filename) / 1e6)
elif key == 'particles':
outs.append(len(system.particle))
elif key == 'species':
outs.append(', '.join(distinct_species(system.particle)))
elif key == 'composition':
outs.append(dict(composition(system.particle)))
elif key == 'cell density':
outs.append(round(system.density, 10))
elif key == 'cell side':
outs.append(str(list(system.cell.side))[1:-1])
elif key == 'cell volume':
outs.append(system.cell.volume)
elif key == 'steps':
outs.append(trajectory.steps[-1])
elif key == 'duration':
outs.append(trajectory.times[-1])
elif key == 'timestep':
outs.append(trajectory.timestep)
elif key == 'block size':
outs.append(trajectory.block_size)
elif key == 'steps between frames':
outs.append(trajectory.steps[1] - trajectory.steps[0])
elif key == 'time between frames':
outs.append(trajectory.times[1] - trajectory.times[0])
elif key == 'block steps':
outs.append(trajectory.steps[trajectory.block_size - 1])
elif key == 'block':
outs.append([
trajectory.steps[i] for i in range(trajectory.block_size)
])
elif key == 'grandcanonical':
outs.append(trajectory.grandcanonical)
txt = ''
fmt = '%%-%ds : %%s\n' % (max([len(key) for key in keys.split(',')]))
for key, out in zip(keys.split(','), outs):
txt += fmt % (key, out)
return txt.strip('\n')
