コード例 #1
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ファイル: test_binary_system.py プロジェクト: bjodah/chemreac
def test_serialization():
    rd = load(JSON_PATH)
    assert rd.n == 3
    assert rd.stoich_active == [[0, 1]]
    assert rd.stoich_prod == [[2]]
    assert list(rd.k) == [0.3]
    assert rd.D.tolist() == [0.1, 0.2, 0.3]
コード例 #2
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ファイル: test_binary_system.py プロジェクト: bjodah/chemreac
def test_chemistry():
    sbstncs = mk_sn_dict_from_names('ABC', D=[.1, .2, .3])
    r1 = Reaction({'A': 1, 'B': 1}, {'C': 1}, 0.3)
    rsys = ReactionSystem([r1], sbstncs)
    rd = ReactionDiffusion.from_ReactionSystem(rsys)
    serialized_rd = load(JSON_PATH)
    assert rd.stoich_active == serialized_rd.stoich_active
    assert rd.stoich_prod == serialized_rd.stoich_prod
    assert rd.stoich_inact == serialized_rd.stoich_inact
    assert np.allclose(rd.k, serialized_rd.k)
    assert np.allclose(rd.D, serialized_rd.D)
コード例 #3
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ファイル: test_binary_system.py プロジェクト: bjodah/chemreac
def test_f(log):
    logy, logt, use_log2 = log
    N = 1
    rd = load(JSON_PATH, N=N, logy=logy, logt=logt, use_log2=use_log2)
    y0 = np.array(C0)
    t0 = 42.0
    ref_f = _get_ref_f(rd, t0, y0, logy, logt, use_log2=use_log2)
    fout = rd.alloc_fout()

    y = rd.logb(y0) if logy else y0
    t = rd.logb(t0) if logt else t0
    rd.f(t, y, fout)
    assert np.allclose(fout, ref_f)
コード例 #4
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ファイル: test_serialization.py プロジェクト: bjodah/chemreac
def test_dump_load():
    rd1 = ReactionDiffusion(2, [[0]], [[1]], [1])
    f = tempfile.NamedTemporaryFile(delete=False)
    try:
        f.close()
        dump(rd1, f.name)
        rd2 = load(f.name)
        assert rd1.n == rd2.n
        assert rd1.k == rd2.k
        assert rd1.stoich_active == rd2.stoich_active
        assert rd1.stoich_prod == rd2.stoich_prod
    finally:
        os.unlink(f.name)
コード例 #5
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def main(tend=3.0, N=30, nt=30, plot=False, logy=False, logt=False,
         savefig='None', verbose=False):
    def mod1(x):
        return x/(x**2+1)

    # decay A->B is modulated with x
    rd = load(
        os.path.join(os.path.dirname(
            __file__), 'four_species.json'),
        N=N, modulation=[[mod1(x/3+0.1) for x in range(N)]],
        modulated_rxns=[1], logt=logt, logy=logy)

    y0 = np.array([1.3, 1e-4, 0.7, 1e-4])
    # y0 = np.concatenate([y0/(i+1)*(0.25*i**2+1) for i in range(N)])
    y0 = np.concatenate([y0 for i in range(N)])

    t0 = 1e-10
    tout = np.linspace(t0, tend, nt)
    integr = run(rd, y0, tout)
    if verbose:
        pprint(integr.info)

    cx = rd.x[:-1]+np.diff(rd.x)/2  # center x
    if plot:
        # Using matplotlib for 3D plots:
        from mpl_toolkits.mplot3d import Axes3D
        assert Axes3D  # silence pyflakes
        from matplotlib import cm
        from matplotlib import pyplot as plt

        from chemreac.util.plotting import save_and_or_show_plot

        fig = plt.figure()

        for i, l in enumerate('ABCD'):
            ax = fig.add_subplot(3, 2, i+1, projection='3d')
            T, X = np.meshgrid(cx, tout)
            ax.plot_surface(T, X, integr.Cout[:, :, i], rstride=1, cstride=1,
                            cmap=cm.YlGnBu_r)
            ax.set_xlabel('x / m')
            ax.set_ylabel('time / s')
            ax.set_zlabel(r'C / mol*m**-3')
            ax.set_title(l)
            ax.legend(loc='best')

        ax = fig.add_subplot(3, 2, 5)
        print(np.array(rd.modulation).shape)
        ax.plot(cx, np.array(rd.modulation)[0, :])

        save_and_or_show_plot(savefig=savefig)
コード例 #6
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ファイル: test_binary_system.py プロジェクト: bjodah/chemreac
def test_dense_jac_cmaj(log):
    logy, logt, use_log2 = log
    N = 1
    rd = load(JSON_PATH, N=N, logy=logy, logt=logt, use_log2=use_log2)
    y0 = np.array(C0)
    t0 = 42.0

    ref_J = _get_ref_J(rd, t0, y0, logy, logt, order='F', use_log2=use_log2)
    Jout = np.empty_like(ref_J)

    y = rd.logb(y0) if logy else y0
    t = rd.logb(t0) if logt else t0
    rd.dense_jac_cmaj(t, y, Jout)

    assert np.allclose(Jout, ref_J)
コード例 #7
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ファイル: test_binary_system.py プロジェクト: bjodah/chemreac
def _test_integrate(params):
    logy, logt, N, geom, use_log2 = params
    rd = load(JSON_PATH, N=N, logy=logy, logt=logt, geom=geom, use_log2=use_log2)
    assert rd.geom == geom
    y0 = np.array(C0*N)

    ref = np.genfromtxt(BLESSED_PATH)
    ref_t = ref[:, 0]
    ref_y = ref[:, 1:rd.n+1]

    t0 = 3.0
    tend = 5.0+t0
    nt = 137
    tout = np.linspace(t0, tend, nt+1)
    assert np.allclose(tout-t0, ref_t)

    _test_f_and_dense_jac_rmaj(rd, t0, rd.logb(y0) if logy else y0)
    integr = run(rd, y0, tout, with_jacobian=True)
    for i in range(N):
        assert np.allclose(integr.Cout[:, i, :], ref_y, atol=1e-4)
コード例 #8
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def integrate_rd(t0=1e-7,
                 tend=.1,
                 doserate=15,
                 N=1000,
                 nt=512,
                 nstencil=3,
                 logy=False,
                 logt=False,
                 num_jacobian=False,
                 savefig='None',
                 verbose=False,
                 plot=False,
                 plot_jacobians=False):
    null_conc = 1e-24

    mu = 1.0  # linear attenuation
    rho = 1.0  # kg/dm3
    rd = load(os.path.join(os.path.dirname(__file__),
                           'aqueous_radiolysis.json'),
              ReactionDiffusion,
              N=N,
              logy=logy,
              logt=logt,
              bin_k_factor=[[doserate * rho * exp(-mu * i / N)]
                            for i in range(N)],
              nstencil=nstencil)
    y0_by_name = json.load(
        open(
            os.path.join(os.path.dirname(__file__),
                         'aqueous_radiolysis.y0.json'), 'rt'))

    # y0 with a H2 gradient
    y0 = np.array([[
        y0_by_name.get(k, null_conc) if k != 'H2' else 1e-3 / (i + 2)
        for k in rd.substance_names
    ] for i in range(rd.N)])

    tout = np.logspace(log(t0), log(tend), nt + 1, base=e)
    integr = run(rd, y0, tout, with_jacobian=(not num_jacobian))
コード例 #9
0
ファイル: four_species.py プロジェクト: bjodah/chemreac
def integrate_rd(tend=10.0, N=1, nt=500, jac_spy=False,
                 linear_solver='default', logy=False, logt=False,
                 plot=False, savefig='None', verbose=False, graph=False,
                 **kwargs):
    """
    Integrates the reaction system defined by
    :download:`four_species.json <examples/four_species.json>`
    """
    rd = load(os.path.join(os.path.dirname(
        __file__), 'four_species.json'), N=N, x=N, logy=logy, logt=logt)

    y0 = np.array([1.3, 1e-4, 0.7, 1e-4])
    y0 = np.concatenate([y0/(i+1)*(0.25*i**2+1) for i in range(N)])
    t0 = 1e-10

    if linear_solver == 'default':
        if rd.N == 1:
            linear_solver = 'dense'
        elif rd.N > 1:
            linear_solver = 'banded'
    if linear_solver not in ('dense', 'banded'):
        raise NotImplementedError("dense or banded linear_solver")

    import matplotlib.pyplot as plt
    if jac_spy:
        fout = np.empty(rd.n*rd.N)
        rd.f(t0, y0, fout)
        print(fout)
        if linear_solver == 'dense':
            jout = np.zeros((rd.n*rd.N, rd.n*rd.N), order='F')
            rd.dense_jac_cmaj(t0, y0, jout)
            coloured_spy(np.log(np.abs(jout)))
        elif linear_solver == 'banded':
            # note rd.n*3 needed in call from scipy.integrate.ode
            jout = np.zeros((rd.n*2+1, rd.n*rd.N), order='F')
            rd.banded_packed_jac_cmaj(t0, y0, jout)
            coloured_spy(np.log(np.abs(jout)))
        print(jout)
        plt.show()
    else:
        tout = np.linspace(t0, tend, nt)
        integr = run(rd, y0, tout, **kwargs)
        if verbose:
            print(integr.info)
        if plot:
            plt.figure(figsize=(6, 4))
            for i, l in enumerate('ABCD'):
                plt.plot(integr.tout, integr.Cout[:, 0, i], label=l)
            plt.title("Time evolution of concentrations")
            plt.legend()
            save_and_or_show_plot(savefig=savefig)

            plt.figure(figsize=(6, 10))
            plot_jacobian(
                rd,
                np.log(integr.tout) if rd.logt else integr.tout,
                np.log(integr.Cout) if rd.logy else integr.Cout,
                'ABCD',
                lintreshy=1e-10
            )
            plt.tight_layout()
            if savefig != 'None':
                base, ext = os.path.splitext(savefig)
                savefig = base + '_jacobian' + ext
            save_and_or_show_plot(savefig=savefig)

            plt.figure(figsize=(6, 10))
            plot_per_reaction_contribution(
                integr,
                'ABCD'
            )
            plt.tight_layout()
            if savefig != 'None':
                savefig = base + '_per_reaction' + ext
            save_and_or_show_plot(savefig=savefig)
    if graph:
        print(rsys2graph(ReactionSystem.from_ReactionDiffusion(rd, 'ABCD'),
                         'four_species_graph.png', save='.'))
    return integr