def test_solve_serial(self):
solver = pac.FspSolverMultiSinks(mpi.COMM_SELF)
solver.SetModel(self.stoich_mat, tcoeff, propensity)
solver.SetFspShape(simple_constr, init_bounds)
X0 = np.array([[0, 0]])
p0 = np.array([1.0])
solver.SetInitialDist(X0, p0)
solution = solver.Solve(10.0, 1.0E-6)
prob = np.asarray(solution.GetProbViewer())
self.assertAlmostEqual(prob.sum(), 1.0, 4)
def test_solve_parallel_krylov(self):
solver = pac.FspSolverMultiSinks(mpi.COMM_WORLD)
solver.SetModel(self.stoich_mat, tcoeff, propensity)
solver.SetFspShape(simple_constr, init_bounds)
X0 = np.array([[0, 0]])
p0 = np.array([1.0])
solver.SetInitialDist(X0, p0)
solver.SetOdeSolver("Krylov")
solution = solver.Solve(10.0, 1.0e-6)
prob = np.asarray(solution.GetProbViewer())
psum1 = prob.sum()
psum = mpi.COMM_WORLD.allreduce(psum1)
self.assertAlmostEqual(psum, 1.0, 4)
if reaction is 12:
out[:] = gamma_cyt * X[:, 5]
return
def t_fun(time, out):
if time > t0:
out[1] = np.double(max(0.0, k10a - k10b * hog1pstar(time - t0)))
else:
out[1] = 0.0
init_bounds = np.array([1, 1, 1, 1, 50, 100])
# Create parallel solver object
solver = pacmensl.FspSolverMultiSinks(MPI.COMM_WORLD)
solver.SetModel(sm, t_fun, propensity, [1])
solver.SetFspShape(constr_fun=None, constr_bound=init_bounds)
solver.SetInitialDist(x0, p0)
solver.SetVerbosity(2)
solver.SetOdeSolver("petsc")
solver.SetUp()
tspan = np.linspace(0, 60 * 15, 5)
solution1 = solver.SolveTspan(tspan, 1.0e-4)
solver.ClearState()
# Create parallel solver object
solver = pacmensl.FspSolverMultiSinks(MPI.COMM_WORLD)
solver.SetModel(sm, t_fun, propensity, [1])
solver.SetFspShape(constr_fun=None, constr_bound=init_bounds)
def test_set_shape(self):
solver = pac.FspSolverMultiSinks(mpi.COMM_WORLD)
solver.SetModel(self.stoich_mat, tcoeff, propensity)
solver.SetFspShape(simple_constr, init_bounds)
def test_set_initial_distribution(self):
solver = pac.FspSolverMultiSinks(mpi.COMM_WORLD)
solver.SetModel(self.stoich_mat, tcoeff, propensity)
X0 = np.array([[0, 0]])
p0 = np.array([1.0])
solver.SetInitialDist(X0, p0)
def test_set_model(self):
solver = pac.FspSolverMultiSinks(mpi.COMM_WORLD)
solver.SetModel(self.stoich_mat, tcoeff, propensity)
def test_serial_constructor(self):
solver = pac.FspSolverMultiSinks(mpi.COMM_SELF)