def test_ram_copy(self):
particle = [Particle(position=[0.0, 0.0, 0.0])]
system = System(particle)
t = TrajectoryRam()
t[0] = system
t[0].particle[0].position = numpy.array([1.0, 1.0, 1.0])
# print system.particle[0].position, t[0].particle[0].position
# print id(t[0].particle[0])
# print id(t[0].particle[0])
particle = [Particle(position=[0.0, 0.0, 0.0])]
system = System(particle)
s = System(particle)
t = TrajectoryRamFull()
t[0] = system
s.update(t[0])
s.particle[0].position = numpy.array([1.0, 1.0, 1.0])
# print system.particle[0].position, t[0].particle[0].position, s.particle[0].position
# print id(t[0].particle[0])
# print id(t[0].particle[0])
particle = [Particle(position=[0.0, 0.0, 0.0])]
system = System(particle)
t = TrajectoryRamFull()
t[0] = system
system.particle[0].position = numpy.array([1.0, 1.0, 1.0])
def test_callback_copy(self):
import copy
from atooms.trajectory.decorators import filter_species
particle = [Particle(species='A'), Particle(species='B')]
system = System(particle)
t = TrajectoryRamFull()
t[0] = system
t.add_callback(copy.deepcopy)
t.add_callback(filter_species, 'A')
self.assertEqual(t[0].distinct_species(), ['A'])
t.callbacks.pop()
t.callbacks.pop()
self.assertEqual(t[0].distinct_species(), ['A', 'B'])
def setUp(self):
import copy
particle = [
Particle(position=[0.0, 0.0, 0.0], species='A', mass=1.0),
Particle(position=[1.0, 1.0, 1.0], species='B', mass=2.0),
]
cell = Cell([2.0, 2.0, 2.0])
self.system = []
self.system.append(System(copy.deepcopy(particle), cell))
self.system.append(System(copy.deepcopy(particle), cell))
self.inpfile = '/tmp/test_trajectory'
self.inpdir = '/tmp/test_trajectory.d'
from atooms.core.utils import mkdir
mkdir(self.inpdir)
def test_ram(self):
particle = [Particle(position=[0.0, 0.0, 0.0])]
system = System(particle)
t = TrajectoryRam()
t[0] = system
particle[0].position = numpy.array([1.0, 1.0, 1.0])
self.assertFalse(
(t[0].particle[0].position == particle[0].position).all())
def test_ram_inplace(self):
particle = [Particle(position=[0.0, 0.0, 0.0])]
system = System(particle)
t = TrajectoryRam()
t[0] = system
particle[0].position += 1.0
self.assertFalse(
(t[0].particle[0].position == particle[0].position).all())
def test_ram_full(self):
particle = [Particle(position=[0.0, 0.0, 0.0])]
system = System(particle)
t = TrajectoryRamFull()
t[0] = system
system.particle[0].position = numpy.array([2.0, 2.0, 2.0])
t[0] = system
particle[0].position += 1.0
self.assertFalse(
(t[0].particle[0].position == particle[0].position).all())
def test_change_species(self):
from copy import deepcopy
from atooms.system import System, Particle
system_A = System([Particle(species='A'), Particle(species='B')])
system_C = System([Particle(species='0'), Particle(species='1')])
system_F = System([Particle(species='1'), Particle(species='2')])
from atooms.trajectory.decorators import change_species
# DO nothing here
self.assertTrue(
_equal(system_A, change_species(deepcopy(system_A), 'A')))
self.assertTrue(
_equal(system_C, change_species(deepcopy(system_C), 'C')))
self.assertTrue(
_equal(system_F, change_species(deepcopy(system_F), 'F')))
# Change
self.assertTrue(
_equal(system_C, change_species(deepcopy(system_A), 'C')))
self.assertTrue(
_equal(system_F, change_species(deepcopy(system_A), 'F')))
self.assertTrue(
_equal(system_A, change_species(deepcopy(system_C), 'A')))
self.assertTrue(
_equal(system_F, change_species(deepcopy(system_C), 'F')))
self.assertTrue(
_equal(system_A, change_species(deepcopy(system_F), 'A')))
self.assertTrue(
_equal(system_C, change_species(deepcopy(system_F), 'C')))
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):
# 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
self.system = system
self.delta = delta
def run(self, steps):
for i in range(steps):
for nr, particle in enumerate(self.system.particle):
#TODO: dodaj zmianę pozycji w każdym kroku o wartość [nr+1] w każdym kierunku
pass
#callback function, called by atooms after specified amount of steps
def callback(sim, initial_position, db=None):
positions = numpy.array([x.position for x in sim.system.particle])
#TODO: narysuj pozycje punktów w każdym kroku
# hint: ax2d.scatter(?,?,label=sim.current_step), ax3d.scatter(?,?,?,label=sim.current_step)
ax2d = plt.subplot(121)
ax3d = plt.subplot(122, projection='3d')
system = System(
particle=[Particle(position=[10.0, 10.0, 10.0]) for _ in range(10)])
simulation = Simulation(RandomWalk(system))
simulation.add(callback,
5,
initial_position=[p.position.copy() for p in system.particle])
simulation.run(10)
simulation.run(10)
simulation.run(10)
plt.show()