def test_potential(self):
import copy
si = Simulation(self.backend,
output_path='/tmp/test_rumd_single/trajectory',
steps=2000,
checkpoint_interval=100,
restart=False)
pos0 = si.system.particle[0].position[0]
s = copy.deepcopy(si.system)
si.run(100)
pos1 = si.system.particle[0].position[0]
si.system = s
si.run(100)
pos2 = si.system.particle[0].position[0]
self.assertTrue(abs(pos1 - pos0) > 1e-2)
self.assertTrue(abs(pos1 - pos2) < 1e-4)
def test_copy_and_run(self):
self.skipTest('skipped test')
import copy
import atooms.trajectory.ram
from atooms.backends.rumd import RUMD
import rumd
potential = rumd.Pot_LJ_12_6(cutoff_method=rumd.ShiftedPotential)
potential.SetVerbose(False)
potential.SetParams(i=0, j=0, Epsilon=1.0, Sigma=1.0, Rcut=2.5)
potential.SetParams(i=1, j=0, Epsilon=1.5, Sigma=0.8, Rcut=2.5)
potential.SetParams(i=0, j=1, Epsilon=1.5, Sigma=0.8, Rcut=2.5)
potential.SetParams(i=1, j=1, Epsilon=0.5, Sigma=0.88, Rcut=2.5)
input_file = os.path.join(os.path.dirname(__file__),
'../data/ka_N256_rho1.185_rumd.xyz.gz')
backend = RUMD(input_file,
integrator='nvt',
temperature=0.8,
dt=0.002,
forcefield=[potential])
sim = Simulation(backend,
output_path='/tmp/test_rumd_single/trajectory',
steps=100,
restart=False)
# First set if runs
# print sim.system.particle[0].position[0]
tr = atooms.trajectory.ram.TrajectoryRamFull()
th = atooms.trajectory.ram.TrajectoryRamFull()
tr[0] = sim.system
# print tr[0].particle[0].position[0]
sim.run(1000) # sometimes is nan, depending on steps
# Ram does not work with rumd because of change in System init
th[0] = sim.system
# print sim.system.particle[0].position, sim.system.potential_energy(per_particle=True)
sim.run(100)
# print sim.system.particle[0].position[0]
# this assignment leads to trouble, BUT ONLY IF WE STORE THE SAMPLES IN tr TRAJECTORY
# assigning tr[0] above also leads to a different trajectory...!!
sim.system = th[0]
def test_leakage(self):
#self.skipTest('skipped test')
from atooms.backends.rumd import System
from atooms.trajectory.ram import TrajectoryRamFull
from atooms.backends.rumd import unfold
si = Simulation(self.backend,
output_path='/tmp/test_rumd_single/trajectory',
steps=2000,
checkpoint_interval=100,
restart=False)
# self.backend.rumd_simulation.sample.__swig_destroy__(self.backend.rumd_simulation.sample)
#del self.backend.rumd_simulation.sample
# This does not leak memory
trj = TrajectoryRamFull()
trj[0] = si.system
for i in range(5):
si.system = trj[0]
si.run()
unfold(si.system).particle[0].position[0], unfold(
trj[0]).particle[0].position[0]
def test_simulation(self):
s = Simulation(self.backend, self.dout, steps=1)
system = System(self.sim.sample)
s.system = system
s.run()