def _create_ions(self, constructor):
self.ions = []
for solution in constructor['solutions']:
self.ions.extend([ion.name for ion in solution.ions])
self.ions = list(set(self.ions))
# Replace strings with ion objects.
self.ions = ionize.Solution(self.ions, [0.1] * len(self.ions)).ions
def test_reference_frame(self):
solutions = [ionize.Solution(['acetic acid', 'b-alanine'],
[.02, .012]),
ionize.Solution(['acetic acid', 'pyridine', 'aniline'],
[.02, .009/2, .011/2]),
ionize.Solution(['acetic acid', 'sodium'],
[.02, .018]),
]
system = Frame(dict(lengths=[.01, .004, .01],
n_nodes=100,
interface_length=.0005,
solutions=solutions,
current_density=500,
domain_mode='left',
))
solver = Solver(system,
precondition=True,
flux_mode='slip')
db = ionize.Database()
solver.set_reference_frame(db['acetic acid'], 'right')
solver.solve('examples/test_reference_frame.hdf5', self.dt, self.tmax)
import emigrate
import ionize
import cProfile
solutions = [ionize.Solution(['hepes', 'tris'],
[.05, .105]),
ionize.Solution(['caproic acid', 'tris', 'fluorescein',
'alexa fluor 488', 'mops', 'acetic acid'],
[.01, .1, .01, .01, .01, .01]),
ionize.Solution(['hydrochloric acid', 'tris'],
[.04, .08]),
]
system = emigrate.Frame(dict(
n_nodes=137,
lengths=[.005, .001, .02],
interface_length=.0005,
solutions=solutions,
current=-500.,
))
solver = emigrate.Solver(system,
precondition=True,
flux_mode='slip')
tmax = 200
dt = 1
ode_solver = 'dopri5'
profile = True
cProfile.run("solver.solve('examples/benchmark.hdf5', dt, tmax)")