def __init__(self,
filename,
path_to_table,
tablename='odesolution',
buffer_size=10):
"""
Constructor for HDF5 Result
Parameters
----------
filename : str
Path to file where the HDF5-File shall be stored
path_to_table : str
internal hdf5 path to the table where the results shall be stored inside the HDF5 structure
tablename : str
name of the table where the results shall be stored inside the HDF5 structure (default: odesolution)
buffer_size : int
number of slots in the RAM buffer until the writer is forced to write from disk to RAM (default: 10)
Attention: It is possible that the buffer is written to disk before this boundary is reached.
But it is never written later.
"""
super().__init__()
self._filename = filename
self._path_to_table = path_to_table
self._tablename = tablename
check_dir(filename)
self._fp = None
self._is_allocated = False
self._tabledict = {'t': Float64Col()}
self._wp = None
self._table = None
self._buffer_size = buffer_size
self._iteration = 0
def test_dummy_to_vtk_wrong_fileextension(self):
self.set_dummy_input()
filename = amfe_dir('results/.tests/vtk_dummy.abc')
check_dir(filename)
converter = VtkMeshConverter(filename=filename)
# Build nodes
self.run_build_commands(converter)
converter.return_mesh()
def test_dummy_to_vtk(self):
self.set_dummy_input()
filename = amfe_dir('results/.tests/vtk_dummy.vtk')
check_dir(filename)
converter = VtkMeshConverter(filename=filename)
# Run build commands
self.run_build_commands(converter)
converter.return_mesh()
def clean_test_outputs():
directory = amfe_dir('results/.tests/')
check_dir(directory + 'test.txt')
directory = amfe_dir('results/.tests/')
for f in os.listdir(directory):
if f == 'hdf5_dummy.hdf5' or f == 'hdf5postprocessing.hdf5':
return
filename = directory + f
if os.path.isfile(filename):
os.remove(filename)
return
def test_dummy_to_vtk_with_preallocation_too_late(self):
self.set_dummy_input()
filename = amfe_dir('results/.tests/vtk_dummy.vtk')
check_dir(filename)
converter = VtkMeshConverter(filename=filename)
# Build nodes
self.run_build_commands(converter)
converter.build_no_of_nodes(len(self.nodes_input))
converter.build_no_of_elements(len(self.elements_input))
converter.return_mesh()
def filename(self, filename):
"""
Parameters
----------
filename : str
Set a new filename
Returns
-------
None
"""
self._filename = filename
check_dir(filename)
def test_async_solve(self):
# Test Asnychronous solution
filename = amfe_dir('results/tests/amfe_solution_async_hdf5.h5')
check_dir(filename)
mysolver = DummySolver()
t0 = 0.0
tend = 1.0
dt = 0.1
# define task for asyncio
async def task(tfilename, tsolver, tt0, ttend, tdt):
no_of_buffer_slots = 3
print("Run Asynchronous HDF5 Version")
h5amfe = AmfeSolutionHdf5(tfilename, 'Sim1', 'asyncsolution')
with h5amfe as writer:
solverkwargs = {'t0': tt0, 'tend': ttend, 'dt': tdt}
await solve_async(no_of_buffer_slots, writer, tsolver, **solverkwargs)
return h5amfe
# Run asynchronous
_ = asyncio.run(task(filename, mysolver, t0, tend, dt))
# Test if results have been written into hdf5 correctly
with h5py.File(filename, mode='r') as fp:
# Get the desired results from solver
t, q, dq, ddq, strains, stresses = mysolver._initialize(t0, tend, dt, mysolver.ndof)
# Get dataset
dataset = fp['Sim1/asyncsolution']
# Test if the first two entries are correct
assert_array_equal(dataset[0]['q'], q[0, :])
assert_array_equal(dataset[1]['q'], q[1, :])
assert_array_equal(dataset[0]['dq'], dq[0, :])
assert_array_equal(dataset[1]['dq'], dq[1, :])
assert_array_equal(dataset[0]['ddq'], ddq[0, :])
assert_array_equal(dataset[1]['ddq'], ddq[1, :])
assert_array_equal(dataset[0]['strain'], strains[0, :, :])
assert_array_equal(dataset[1]['strain'], strains[1, :, :])
assert_array_equal(dataset[0]['stress'], stresses[0, :, :])
assert_array_equal(dataset[1]['stress'], stresses[1, :, :])
self.assertEqual(dataset[0]['t'], t[0])
self.assertEqual(dataset[1]['t'], t[1])
# test if all entries have been written
self.assertEqual(len(dataset), len(t))
def test_write_hdf5_timesteps(self):
filename = amfe_dir('results/tests/amfe_solution_hdf5.h5')
check_dir(filename)
q1 = np.arange(0, 60, dtype=float)
q2 = np.arange(10, 70, dtype=float)
dq1 = np.arange(20, 80, dtype=float)
dq2 = np.arange(30, 90, dtype=float)
ddq1 = np.arange(40, 100, dtype=float)
ddq2 = np.arange(50, 110, dtype=float)
strains1 = np.random.rand(60, 6)
strains2 = np.random.rand(60, 6)
stresses1 = np.random.rand(60, 6)
stresses2 = np.random.rand(60, 6)
t1 = 0.1
t2 = 0.5
# Only q
h5amfe = AmfeSolutionHdf5(filename, 'Sim1', tablename='testcase')
with h5amfe as writer:
# Only q
writer.write_timestep(t1, q1)
writer.write_timestep(t2, q2)
with h5py.File(filename, mode='r') as fp:
dataset = fp['Sim1/testcase']
assert_array_equal(dataset[0]['q'], q1)
assert_array_equal(dataset[1]['q'], q2)
self.assertEqual(dataset[0]['t'], t1)
self.assertEqual(dataset[1]['t'], t2)
self.assertEqual(len(dataset), 2)
# Only q and dq
h5amfe = AmfeSolutionHdf5(filename, 'Sim1', tablename='testcase')
with h5amfe as writer:
# Only q and dq
writer.write_timestep(t1, q1, dq1)
writer.write_timestep(t2, q2, dq2)
with h5py.File(filename, mode='r') as fp:
dataset = fp['Sim1/testcase']
assert_array_equal(dataset[0]['q'], q1)
assert_array_equal(dataset[1]['q'], q2)
assert_array_equal(dataset[0]['dq'], dq1)
assert_array_equal(dataset[1]['dq'], dq2)
self.assertEqual(dataset[0]['t'], t1)
self.assertEqual(dataset[1]['t'], t2)
self.assertEqual(len(dataset), 2)
# q, dq and ddq
h5amfe = AmfeSolutionHdf5(filename, 'Sim1', tablename='testcase')
with h5amfe as writer:
# q, dq and ddq
writer.write_timestep(t1, q1, dq1, ddq1)
writer.write_timestep(t2, q2, dq2, ddq2)
with h5py.File(filename, mode='r') as fp:
dataset = fp['Sim1/testcase']
assert_array_equal(dataset[0]['q'], q1)
assert_array_equal(dataset[1]['q'], q2)
assert_array_equal(dataset[0]['dq'], dq1)
assert_array_equal(dataset[1]['dq'], dq2)
assert_array_equal(dataset[0]['ddq'], ddq1)
assert_array_equal(dataset[1]['ddq'], ddq2)
self.assertEqual(dataset[0]['t'], t1)
self.assertEqual(dataset[1]['t'], t2)
self.assertEqual(len(dataset), 2)
# only q and ddq
h5amfe = AmfeSolutionHdf5(filename, 'Sim1', tablename='testcase')
with h5amfe as writer:
# only q and ddq
writer.write_timestep(t1, q1, ddq=ddq1)
writer.write_timestep(t2, q2, ddq=ddq2)
with h5py.File(filename, mode='r') as fp:
dataset = fp['Sim1/testcase']
assert_array_equal(dataset[0]['q'], q1)
assert_array_equal(dataset[1]['q'], q2)
assert_array_equal(dataset[0]['ddq'], ddq1)
assert_array_equal(dataset[1]['ddq'], ddq2)
self.assertEqual(dataset[0]['t'], t1)
self.assertEqual(dataset[1]['t'], t2)
self.assertEqual(len(dataset), 2)
# only q and strain
h5amfe = AmfeSolutionHdf5(filename, 'Sim1', tablename='testcase')
with h5amfe as writer:
# Only q and strain
writer.write_timestep(t1, q1, strain=strains1)
writer.write_timestep(t2, q2, strain=strains2)
with h5py.File(filename, mode='r') as fp:
dataset = fp['Sim1/testcase']
assert_array_equal(dataset[0]['q'], q1)
assert_array_equal(dataset[1]['q'], q2)
assert_array_equal(dataset[0]['strain'], strains1)
assert_array_equal(dataset[1]['strain'], strains2)
self.assertEqual(dataset[0]['t'], t1)
self.assertEqual(dataset[1]['t'], t2)
self.assertEqual(len(dataset), 2)
# only q and stress
h5amfe = AmfeSolutionHdf5(filename, 'Sim1', tablename='testcase')
with h5amfe as writer:
# Only q and stress
writer.write_timestep(t1, q1, stress=stresses1)
writer.write_timestep(t2, q2, stress=stresses2)
with h5py.File(filename, mode='r') as fp:
dataset = fp['Sim1/testcase']
assert_array_equal(dataset[0]['q'], q1)
assert_array_equal(dataset[1]['q'], q2)
assert_array_equal(dataset[0]['stress'], stresses1)
assert_array_equal(dataset[1]['stress'], stresses2)
self.assertEqual(dataset[0]['t'], t1)
self.assertEqual(dataset[1]['t'], t2)
self.assertEqual(len(dataset), 2)
# only q, dq, strain and stress
h5amfe = AmfeSolutionHdf5(filename, 'Sim1', tablename='testcase')
with h5amfe as writer:
# Only q, dq, strain and stress
writer.write_timestep(t1, q1, dq1, strain=strains1, stress=stresses1)
writer.write_timestep(t2, q2, dq2, strain=strains2, stress=stresses2)
with h5py.File(filename, mode='r') as fp:
dataset = fp['Sim1/testcase']
assert_array_equal(dataset[0]['q'], q1)
assert_array_equal(dataset[1]['q'], q2)
assert_array_equal(dataset[0]['dq'], dq1)
assert_array_equal(dataset[1]['dq'], dq2)
assert_array_equal(dataset[0]['strain'], strains1)
assert_array_equal(dataset[1]['strain'], strains2)
assert_array_equal(dataset[0]['stress'], stresses1)
assert_array_equal(dataset[1]['stress'], stresses2)
self.assertEqual(dataset[0]['t'], t1)
self.assertEqual(dataset[1]['t'], t2)
self.assertEqual(len(dataset), 2)
# q, dq, ddq, strain and stress
h5amfe = AmfeSolutionHdf5(filename, 'Sim1', tablename='testcase')
with h5amfe as writer:
# q, dq, ddq, strain and stress
writer.write_timestep(t1, q1, dq1, ddq1, strains1, stresses1)
writer.write_timestep(t2, q2, dq2, ddq2, strains2, stresses2)
with h5py.File(filename, mode='r') as fp:
dataset = fp['Sim1/testcase']
assert_array_equal(dataset[0]['q'], q1)
assert_array_equal(dataset[1]['q'], q2)
assert_array_equal(dataset[0]['dq'], dq1)
assert_array_equal(dataset[1]['dq'], dq2)
assert_array_equal(dataset[0]['ddq'], ddq1)
assert_array_equal(dataset[1]['ddq'], ddq2)
assert_array_equal(dataset[0]['strain'], strains1)
assert_array_equal(dataset[1]['strain'], strains2)
assert_array_equal(dataset[0]['stress'], stresses1)
assert_array_equal(dataset[1]['stress'], stresses2)
self.assertEqual(dataset[0]['t'], t1)
self.assertEqual(dataset[1]['t'], t2)
self.assertEqual(len(dataset), 2)
