There seem to be some problems with oommfodt 0.8.3. I have tested under Windows 10 Pro (native), docker, and a dual boot Ubuntu 18.10 using both python 3.7 and 3.6.
Running python -c "import oommfc; oommfc.test()" results in
============ 3 failed, 140 passed, 3 skipped, 5 deselected, 35 warnings in 249.23 seconds ============
For all combinations I tested, the errors were the same, and seem to arise from oommfodt. So today I downgraded to oommfodt 0.8.2 and everything is fine again.
============ 143 passed, 3 skipped, 5 deselected in 348.30 seconds ============
> dt = oommfodt.read(odt_file, replace_columns=False)
E TypeError: read() got an unexpected keyword argument 'replace_columns'
System object 'stdprob3':
hamiltonian: Exchange(A=1.5625e-10, name="exchange") + UniaxialAnisotropy(K1=100000.0, K2=0, u=(0, 0, 1), name="uniaxialanisotropy") + Demag(name="demag")
dynamics :
m : <Field(mesh=Mesh(p1=(0, 0, 0), p2=(1e-07, 1e-07, 1e-07), cell=(6.25e-09, 6.25e-09, 6.25e-09), pbc=set(), name="mesh"), dim=3, name="field")>
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
<ipython-input-19-de510c4400e2> in <module>
----> 1 system.total_energy()
~\Anaconda3\lib\site-packages\oommfc\system.py in total_energy(self)
24
25 def total_energy(self):
---> 26 return self.dt.tail(1)["E"][0]
~\Anaconda3\lib\site-packages\pandas\core\series.py in __getitem__(self, key)
765 key = com._apply_if_callable(key, self)
766 try:
--> 767 result = self.index.get_value(self, key)
768
769 if not is_scalar(result):
~\Anaconda3\lib\site-packages\pandas\core\indexes\base.py in get_value(self, series, key)
3116 try:
3117 return self._engine.get_value(s, k,
-> 3118 tz=getattr(series.dtype, 'tz', None))
3119 except KeyError as e1:
3120 if len(self) > 0 and self.inferred_type in ['integer', 'boolean']:
pandas\_libs\index.pyx in pandas._libs.index.IndexEngine.get_value()
pandas\_libs\index.pyx in pandas._libs.index.IndexEngine.get_value()
pandas\_libs\index.pyx in pandas._libs.index.IndexEngine.get_loc()
pandas\_libs\hashtable_class_helper.pxi in pandas._libs.hashtable.Int64HashTable.get_item()
pandas\_libs\hashtable_class_helper.pxi in pandas._libs.hashtable.Int64HashTable.get_item()
KeyError: 0
================================== FAILURES ===================================
___________________________ TestDerive.test_energy ____________________________
self = <oommfc.tests.test_derive.TestDerive object at 0x00000230F62B21D0>
def test_energy(self):
hamiltonian = self.system.hamiltonian
> assert isinstance(hamiltonian.exchange.energy, float)
Anaconda3\lib\site-packages\oommfc\tests\test_derive.py:26:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
Anaconda3\lib\site-packages\micromagneticmodel\hamiltonian\energyproperties.py:16: in energy
return self._data.energy
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <oommfc.data.Data object at 0x00000230F62B20F0>
@property
def energy(self):
_dict = {"Demag": "Demag::Energy",
"Exchange": "UniformExchange::Energy",
"UniaxialAnisotropy": "UniaxialAnisotropy::Energy",
"Zeeman": "FixedZeeman::Energy",
"Hamiltonian": "RungeKuttaEvolve:evolver:Totalenergy"}
td = oc.TimeDriver()
td.drive(self.system, derive="energy")
dirname = os.path.join(self.system.name, "")
odt_file = max(glob.iglob("{}*.odt".format(dirname)),
key=os.path.getctime)
> dt = oommfodt.read(odt_file, replace_columns=False)
E TypeError: read() got an unexpected keyword argument 'replace_columns'
Anaconda3\lib\site-packages\oommfc\data.py:41: TypeError
---------------------------- Captured stdout call -----------------------------
2019/01/14 11:54: Running OOMMF (derive_tests\derive_tests.mif) ... Start: "C:/Users/pdunn/derive_tests/derive_tests.mif"
Options: -exitondone 1 -threads 2
Boxsi version 2.0a0
Running on:
OS/machine: Windows NT/amd64
User: pdunn PID: 6096
Number of threads: 2
Mesh geometry: 4 x 4 x 2 = 32 cells
Checkpoint file: C:/Users/pdunn/derive_tests/derive_tests.restart
Boxsi run end.
<1> mmarchive killed
<2> mmarchive killed
<3> mmarchive killed
(6.0 s)
________________________________ test_stdprob3 ________________________________
@pytest.mark.oommf
def test_stdprob3():
name = "stdprob3"
# Remove any previous simulation directories.
if os.path.exists(name):
shutil.rmtree(name)
# Function for initiaising the flower state.
def m_init_flower(pos):
x, y, z = pos[0]/1e-9, pos[1]/1e-9, pos[2]/1e-9
mx = 0
my = 2*z - 1
mz = -2*y + 1
norm_squared = mx**2 + my**2 + mz**2
if norm_squared <= 0.05:
return (1, 0, 0)
else:
return (mx, my, mz)
# Function for initialising the vortex state.
def m_init_vortex(pos):
x, y, z = pos[0]/1e-9, pos[1]/1e-9, pos[2]/1e-9
mx = 0
my = np.sin(np.pi/2 * (x-0.5))
mz = np.cos(np.pi/2 * (x-0.5))
return (mx, my, mz)
def minimise_system_energy(L, m_init):
N = 16 # discretisation in one dimension
cubesize = 100e-9 # cube edge length (m)
cellsize = cubesize/N # discretisation in all three dimensions.
lex = cubesize/L # exchange length.
Km = 1e6 # magnetostatic energy density (J/m**3)
Ms = np.sqrt(2*Km/oc.mu0) # magnetisation saturation (A/m)
A = 0.5 * oc.mu0 * Ms**2 * lex**2 # exchange energy constant
K = 0.1*Km # Uniaxial anisotropy constant
u = (0, 0, 1) # Uniaxial anisotropy easy-axis
p1 = (0, 0, 0) # Minimum sample coordinate.
p2 = (cubesize, cubesize, cubesize) # Maximum sample coordinate.
cell = (cellsize, cellsize, cellsize) # Discretisation.
mesh = oc.Mesh(p1=(0, 0, 0), p2=(cubesize, cubesize, cubesize),
cell=(cellsize, cellsize, cellsize))
system = oc.System(name=name)
system.hamiltonian = oc.Exchange(A) + oc.UniaxialAnisotropy(K, u) + \
oc.Demag()
system.m = df.Field(mesh, value=m_init, norm=Ms)
md = oc.MinDriver()
md.drive(system)
return system
def energy_difference(L):
vortex = minimise_system_energy(L, m_init_vortex)
flower = minimise_system_energy(L, m_init_flower)
return vortex.total_energy() - flower.total_energy()
> cross_section = bisect(energy_difference, 8, 9, xtol=0.1)
..\test_stdprob3.py:74:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
..\..\..\scipy\optimize\zeros.py:287: in bisect
r = _zeros._bisect(f,a,b,xtol,rtol,maxiter,args,full_output,disp)
..\test_stdprob3.py:72: in energy_difference
return vortex.total_energy() - flower.total_energy()
..\..\system.py:26: in total_energy
return self.dt.tail(1)["E"][0]
..\..\..\pandas\core\series.py:767: in __getitem__
result = self.index.get_value(self, key)
..\..\..\pandas\core\indexes\base.py:3118: in get_value
tz=getattr(series.dtype, 'tz', None))
pandas\_libs\index.pyx:106: in pandas._libs.index.IndexEngine.get_value
???
pandas\_libs\index.pyx:114: in pandas._libs.index.IndexEngine.get_value
???
pandas\_libs\index.pyx:162: in pandas._libs.index.IndexEngine.get_loc
???
pandas\_libs\hashtable_class_helper.pxi:958: in pandas._libs.hashtable.Int64HashTable.get_item
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E KeyError: 0
pandas\_libs\hashtable_class_helper.pxi:964: KeyError
---------------------------- Captured stdout call -----------------------------
2019/01/14 11:57: Running OOMMF (stdprob3\stdprob3.mif) ... Start: "C:/Users/pdunn/Anaconda3/Lib/site-packages/oommfc/tests/test_files/stdprob3/stdprob3.mif"
Options: -exitondone 1 -threads 2
Boxsi version 2.0a0
Running on:
OS/machine: Windows NT/amd64
User: pdunn PID: 16168
Number of threads: 2
Mesh geometry: 16 x 16 x 16 = 4 096 cells
Checkpoint file: C:/Users/pdunn/Anaconda3/Lib/site-packages/oommfc/tests/test_files/stdprob3/stdprob3.restart
Boxsi run end.
<1> mmarchive killed
<2> mmarchive killed
(8.6 s)
2019/01/14 11:57: Running OOMMF (stdprob3\stdprob3.mif) ... Start: "C:/Users/pdunn/Anaconda3/Lib/site-packages/oommfc/tests/test_files/stdprob3/stdprob3.mif"
Options: -exitondone 1 -threads 2
Boxsi version 2.0a0
Running on:
OS/machine: Windows NT/amd64
User: pdunn PID: 13308
Number of threads: 2
Mesh geometry: 16 x 16 x 16 = 4 096 cells
Checkpoint file: C:/Users/pdunn/Anaconda3/Lib/site-packages/oommfc/tests/test_files/stdprob3/stdprob3.restart
Boxsi run end.
<1> mmarchive killed
<2> mmarchive killed
(6.3 s)
________________________________ test_stdprob5 ________________________________
@pytest.mark.oommf
def test_stdprob5():
name = "stdprob5"
# Remove any previous simulation directories.
if os.path.exists(name):
shutil.rmtree(name)
# Geometry
lx = 100e-9 # x dimension of the sample(m)
ly = 100e-9 # y dimension of the sample (m)
lz = 10e-9 # sample thickness (m)
# Material (permalloy) parameters
Ms = 8e5 # saturation magnetisation (A/m)
A = 1.3e-11 # exchange energy constant (J/m)
# Dynamics (LLG + STT equation) parameters
gamma = 2.211e5 # gyromagnetic ratio (m/As)
alpha = 0.1 # Gilbert damping
ux = -72.35 # velocity in x direction
beta = 0.05 # non-adiabatic STT parameter
system = oc.System(name=name)
mesh = oc.Mesh(p1=(0, 0, 0), p2=(100e-9, 100e-9, 10e-9),
cell=(5e-9, 5e-9, 5e-9))
system.hamiltonian = oc.Exchange(A) + oc.Demag()
def m_vortex(pos):
x, y, z = pos[0]/1e-9-50, pos[1]/1e-9-50, pos[2]/1e-9
return (-y, x, 10)
system.m = df.Field(mesh, value=m_vortex, norm=Ms)
md = oc.MinDriver()
md.drive(system)
system.dynamics += oc.Precession(gamma) + oc.Damping(alpha) + \
oc.STT(u=(ux, 0, 0), beta=beta)
td = oc.TimeDriver()
td.drive(system, t=8e-9, n=100)
mx = system.dt["mx"].values
> assert -0.03 < mx.max() < 0
E assert 1.397303195124719e-12 < 0
E + where 1.397303195124719e-12 = <built-in method max of numpy.ndarray object at 0x00000230FA44E990>()
E + where <built-in method max of numpy.ndarray object at 0x00000230FA44E990> = array([3.60159902e-17, 4.56456993e-13, 1.06732815e-12, 1.28478808e-12,\n 1.39730320e-12, 5.30105142e-13, 5.275923...631e-13, 4.60973702e-13,\n 4.63244432e-13, 4.58266329e-13, 4.50678307e-13, 4.49944833e-13,\n 4.53052926e-13]).max
..\test_stdprob5.py:56: AssertionError
---------------------------- Captured stdout call -----------------------------
2019/01/14 11:58: Running OOMMF (stdprob5\stdprob5.mif) ... Start: "C:/Users/pdunn/Anaconda3/Lib/site-packages/oommfc/tests/test_files/stdprob5/stdprob5.mif"
Options: -exitondone 1 -threads 2
Boxsi version 2.0a0
Running on:
OS/machine: Windows NT/amd64
User: pdunn PID: 12524
Number of threads: 2
Mesh geometry: 20 x 20 x 2 = 800 cells
Checkpoint file: C:/Users/pdunn/Anaconda3/Lib/site-packages/oommfc/tests/test_files/stdprob5/stdprob5.restart
Boxsi run end.
<1> mmarchive killed
<2> mmarchive killed
(6.1 s)
2019/01/14 11:58: Running OOMMF (stdprob5\stdprob5.mif) ... Start: "C:/Users/pdunn/Anaconda3/Lib/site-packages/oommfc/tests/test_files/stdprob5/stdprob5.mif"
Options: -exitondone 1 -threads 2
Boxsi version 2.0a0
Running on:
OS/machine: Windows NT/amd64
User: pdunn PID: 7160
Number of threads: 2
Mesh geometry: 20 x 20 x 2 = 800 cells
Checkpoint file: C:/Users/pdunn/Anaconda3/Lib/site-packages/oommfc/tests/test_files/stdprob5/stdprob5.restart
Boxsi run end.
<1> mmarchive killed
<2> mmarchive killed
<3> mmarchive killed
(22.1 s)
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