[2016.2] Examples fixes and updates

[rpep]

With no CI currently, the examples aren't getting built. I've ran through them one by one - ticked means working, others need some work.

• finmag/examples/boost_python/

  Cannot build these examples.

• finmag/examples/demag
  Nmag examples not tested, Makefile doesn't make sense as files are now missing, so can
  probably be safely removed. Removed some code in 471e7dd to make this work.

• finmag/examples/edge_damping

• finmag/examples/exchange_demag
  Relies on nmag so not tested

• /finmag/examples/macrospin

• finmag/examples/meshes
  Not executable, but really out of date - these have completely changed in recent versions of FEniCs.

• /finmag/examples/precession

• /finmag/examples/spatially_varying_anisotropy

• /finmag/examples/std_prob_4

+--------------------+------------------------------+--------+------------+--------------+
| class/module       | name                         |  calls |  total (s) | per call (s) |
+--------------------+------------------------------+--------+------------+--------------+
| FKDemag            | compute_field                |  39356 |   3.77e+03 |       0.0958 |
| LLG                | sundials_jtimes              |  75653 |         96 |      0.00127 |
| Tablewriter        | save                         |    201 |       84.1 |        0.418 |
| Exchange           | compute_field                | 114607 |       80.2 |       0.0007 |
| FKDemag            | compute_energy               |    402 |       40.3 |          0.1 |
| LLG                | solve                        |  38551 |       10.8 |     0.000281 |
| FKDemag            | setup                        |      1 |       2.19 |         2.19 |
| Exchange           | compute_energy               |    402 |       1.99 |      0.00495 |
| Simulation         | __init__                     |      1 |      0.201 |        0.201 |
| LLG                | __init__                     |      1 |       0.15 |         0.15 |
+--------------------+------------------------------+--------+------------+--------------+

Timings grouped by class or module.

+--------------------+----------+------+
| class/module       | time (s) |    % |
+--------------------+----------+------+
| FKDemag            | 3.81e+03 | 96.3 |
| redundant          |      129 | -3.25 |
| LLG                |      107 |  2.7 |
| Tablewriter        |     84.1 | 2.13 |
| Exchange           |     82.4 | 2.08 |
| Simulation         |    0.201 | 0.00509 |
+--------------------+----------+------+

Total wall time 1:05:56.
Traceback (most recent call last):
  File "test_std_prob_4.py", line 144, in <module>
    test_std_prob_4_field_1(stop_when_mx_eq_zero=False)
  File "test_std_prob_4.py", line 140, in test_std_prob_4_field_1
    assert abs(t_0 - t_ref_martinez) < PRECISION
AssertionError

• /finmag/examples/magnetic_grain

• finmag/examples/varying_alpha
  Makefile doesn't work (remove?), but example runs.

• finmag/examples/cubic_anisotropy
  hysteresis.py does not work:

016-12-08 23:23:07] DEBUG: Creating LLG object.
/home/ryan/finmag/src/finmag/util/helpers.py:1822: VisibleDeprecationWarning: using a non-integer number instead of an integer will result in an error in the future
  v2d_xxx = ((v2d_xyz.reshape(n1/dim, dim)).transpose()).reshape(-1,)
[2016-12-08 23:23:07] DEBUG: Creating Exchange object with method box-matrix-petsc, in Jacobian.
[2016-12-08 23:23:07] DEBUG: Adding interaction Exchange to simulation.
Traceback (most recent call last):
  File "hysteresis.py", line 31, in <module>
    sim.add(CubicAnisotropy(K1, u1, K2, u2, K3, u3))
  File "/home/ryan/finmag/src/finmag/energies/cubic_anisotropy.py", line 43, in __init__
    self.u3_value = np.cross(u1, u2)  # u3 perpendicular to u1 and u2
  File "/usr/lib/python2.7/dist-packages/numpy/core/numeric.py", line 1673, in cross
    raise ValueError(axis_msg.format('a'))
ValueError: 'axisa' out of bounds

• /home/ryan/finmag/examples/dispersion_curves/

Traceback (most recent call last):
  File "dispersion.py", line 99, in <module>
    excite_system()
  File "dispersion.py", line 65, in excite_system
    my = np.array([sim._m(x, 0, 0)[1] for x in xs])
AttributeError: 'Simulation' object has no attribute '_m'
[1]    23900 abort (core dumped)  python dispersion.py

• finmag/examples/exchange_1D
  None of these examples work.

• finmag/examples/llb

Traceback (most recent call last):
  File "macrospin.py", line 147, in <module>
    print StochasticSpinTest(mesh,640)
  File "macrospin.py", line 103, in StochasticSpinTest
    llb.set_up_stochastic_solver(dt=dt,use_evans2012_noise=True)
TypeError: set_up_stochastic_solver() got an unexpected keyword argument 'use_evans2012_noise'
[1]    27558 abort (core dumped)  python macrospin.py

• finmag/examples/scheduling
  sim_with_notification.py

• finmag/examples/std_prob3

• finmag/examples/time-dependent-applied-field