def test_setPositionsList_1DREnsemble(self):
exchange_dimensions = {"temperature": range(288, 310)}
replicas = len(exchange_dimensions["temperature"])
expected_pos = range(replicas)
self.group = ensemble.ReplicaExchange(
system=self.sys, exchange_dimensions=exchange_dimensions)
initial_positions = sorted([
self.group.replicas[replica]._currentPosition
for replica in self.group.replicas
])
self.group.set_replicas_positions(expected_pos)
setted_pos = sorted([
self.group.replicas[replica]._currentPosition
for replica in self.group.replicas
])
self.assertEqual(len(self.group.replicas),
22,
msg="not enough trajectories were retrieved!")
self.assertNotEqual(initial_positions,
setted_pos,
msg="Setted positions are the same as before!")
self.assertEqual(setted_pos,
list(expected_pos),
msg="The positions were not set correctly!")
def test_run_1DREnsemble(self):
from ensembler import ensemble
exchange_dimensions = {"temperature": range(288, 310)}
group = ensemble.ReplicaExchange(
system=self.sys, exchange_dimensions=exchange_dimensions)
group.run()
def test_init_2DREnsemble(self):
from ensembler import ensemble
exchange_dimensions = {
"temperature": range(288, 310),
"mass": range(1, 10)
}
ensemble.ReplicaExchange(system=self.sys,
exchange_dimensions=exchange_dimensions)
def test_getTotPot_1DREnsemble(self):
replicas = 22
nsteps = 100
from ensembler import ensemble
exchange_dimensions = {"temperature": range(288, 310)}
self.group = ensemble.ReplicaExchange(
system=self.sys, exchange_dimensions=exchange_dimensions)
self.group.nSteps_between_trials = nsteps
self.group.run()
totPots = self.group.get_total_energy()
##print(len(totPots))
##print(totPots)
self.assertEqual(len(totPots),
replicas,
msg="not enough trajectories were retrieved!")
def test_getTraj_1DREnsemble(self):
replicas = 22
nsteps = 100
group = None
from ensembler import ensemble
exchange_dimensions = {"temperature": range(288, 310)}
self.group = ensemble.ReplicaExchange(
system=self.sys, exchange_dimensions=exchange_dimensions)
self.group.nSteps_between_trials = nsteps
self.group.run()
trajectories = self.group.get_trajectories()
##print(len(trajectories))
##print([len(trajectories[t]) for t in trajectories])
self.assertEqual(len(trajectories),
22,
msg="not enough trajectories were retrieved!")
self.assertEquals([len(trajectories[t]) for t in trajectories],
second=[nsteps for x in range(replicas)],
msg="traj lengths are not correct!")