def test_dc(): n = 7 k = [1]*(n-1) rd = ReactionDiffusion(n, [[i] for i in range(n-1)], [[i] for i in range(1, n)], k=k) fout = rd.alloc_fout() y0 = [0]*n y0[0] = 1 y_ = [0] + y0 y0 = np.asarray(y0, dtype=np.float64) rd.f(0, y0, fout) pos, neg = [0]+k, k+[0] _test_f(rd, 0, y0) fref = [pos[i]*y_[i] - neg[i]*y_[i+1] for i in range(n)] assert np.allclose(fref, fout) jout = rd.alloc_jout(order='C') rd.dense_jac_rmaj(0, y0, jout) jref = np.zeros_like(jout) for i in range(n): if i < n - 1: jref[i, i] = -k[i] if i > 0: jref[i, i-1] = k[i-1] assert np.allclose(jref, jout) _test_dense_jac_rmaj(rd, 0, y0)
def test_per_bin_diffusion(): rd = ReactionDiffusion(1, [], [], [], N=5, D=[0, 0, 1, 0, 0]) fout = rd.alloc_fout() y = [0, 1, 2, 1, 0] rd.f(0.0, np.asarray(y, dtype=np.float64), fout) assert np.all(fout[:2] == 0) and np.all(fout[-2:] == 0) and fout[2] < 0