Commit 870ede3b authored by Dion Haefner's avatar Dion Haefner

added referenced; fixed reference, muphi, ode evaluators

parent 5a415d14
......@@ -28,11 +28,15 @@ def evaluate(iniinfo,runtime):
raise ValueError("The muphi evaluator assumes the key _reference.path to be existent in the inifile")
if os.path.isfile(reference):
muphi_cells, muphi_head = muphi_reader.read(reference)
muphi_grid = grid.RegularGrid(np.dstack((muphi_cells[0,...],muphi_cells[1,...])))
muphi_grid = grid.RegularGrid(muphi_cells)
muphi_grid.add_data("head",muphi_head)
else:
raise RuntimeError("Reference file {} does not exist".format(reference))
if run_head.size != muphi_head.size:
print("Encountered different number of cells")
return False
run_head = run_head.reshape(muphi_head.shape)
diff = run_head - muphi_head
plt.figure()
......@@ -47,6 +51,7 @@ def evaluate(iniinfo,runtime):
im = plt.imshow(np.flipud(diff))
plt.colorbar(im)
plt.savefig("diff.png")
l2 = np.sqrt(np.mean(diff.flatten()**2))
l2 = np.sqrt(np.mean(np.square(diff))) # RMS error
print("L2: {:.2e}".format(l2))
return bool(l2 < 5E-3)
......@@ -10,6 +10,28 @@ from dorie.testtools.utilities.decorators import evaluation_script
from dorie.testtools.utilities import richards_equation
from dorie.parfield.parameter_file import read_parameter_file
def average_2d_mesh(xy, z, connectivity):
"""
Averages an array z defined on a triangular or rectangular mesh with vertices
xy and a certain connectivity.
"""
npt, dim = xy.shape
ncells, dim1 = connectivity.shape
assert ncells == len(z), "Shape mismatch (got: {}, {})".format(connectivity.shape, z.shape)
assert dim == 2, "Only two-dimensional geometry supported"
if dim1 == dim+1:
areafun = lambda t: .5 * abs(t[:,0,0] * t[:,1,1] - t[:,0,1] * t[:,1,0])
elif dim1 == dim+2:
areafun = lambda t: abs(t[:,0,0] * t[:,1,1])
else:
raise ValueError("Only triangular and rectangular geometry supported")
corners = xy[connectivity]
t = corners[:,1:,:] - corners[:,0,:][:,np.newaxis,:]
area = areafun(t)
zsum = np.sum(area * z)
areasum = np.sum(area)
return zsum / areasum
@evaluation_script
def evaluate(iniinfo,runtime):
pvd = iniinfo["output.fileName"] + ".pvd"
......@@ -41,7 +63,8 @@ def evaluate(iniinfo,runtime):
grid = vtk_file.read(["head"])
cells = grid.cellCenters()
y = cells[1].flatten()
y = cells[...,1].flatten()
tri, connectivity = grid.triangulation()
data = grid.data()
iy = np.argsort(y)
y = y[iy]
......@@ -52,29 +75,25 @@ def evaluate(iniinfo,runtime):
r.set_initial_value(initial_head, 0)
r.set_f_params(flux,par[0],par[1],edge)
r_t, r_y, y_y = [], [], []
for t, h in zip(y,head):
r_y = []
for t in y:
if t - r.t > 1E-6: # ODE solver can't handle step sizes of ~ 0
r.integrate(t)
r_t.append(r.t)
r_y.append(r_y)
y_y.append(h)
r_t = np.array(r_t)
r_y.append(r.y[0])
r_y = np.array(r_y)
y_y = np.array(y_h)
res = r_y - y_y
l2 = np.sqrt(integrate.simps(res**2, r_t) / (r_t.max()-r_t.min()))
res = r_y - head
l2 = np.sqrt(average_2d_mesh(tri.T,np.square(res),connectivity))
print("L2 error: {:.2e}\n".format(float(l2)))
plt.figure()
plt.plot(r_t,r_y,label="ODE solution")
plt.plot(r_t,y_y,label="DORiE solution")
plt.plot(y,r_y,label="ODE solution")
plt.plot(y,head,label="DORiE solution")
plt.legend(loc="best")
plt.savefig("{}/solutions.png".format(iniinfo["output.outputPath"]))
plt.figure()
plt.plot(r_t,res)
plt.plot(y,res)
plt.savefig("{}/residual.png".format(iniinfo["output.outputPath"]))
try:
......
......@@ -9,15 +9,15 @@ def read(filename):
- three 32-bit integers encoding number of grid cells per dimension
- three single precision floats encoding grid extensions in each dimension
- three single-precision floats encoding grid extensions in each dimension
- array data as double precision floats, in zyx order (z running fastest)
- array data as double precision floats
Returns the array data and a meshgrid (assumes that the grid is regularly spaced).
:param str filename: path to the muPhi binary (.bin) file
:raises RuntimeError: if the input file is not readable
:returns: result of :func:`np.meshgrid <numpy.meshgrid>`, data array
:returns: grid cells, data array
:rtype: (list of numpy arrays, numpy array)
"""
......@@ -31,14 +31,14 @@ def read(filename):
skip_header = struct.calcsize(header_spec)
header_raw = f.read(skip_header)
header = struct.unpack(header_spec,header_raw)
cells = [c for c in header[:3] if c > 1] # number of cells in xyz order
extensions = [h for h in header[3:] if h != 0] # grid extensions in xyz order
cells = [c for c in header[:3] if c > 1]
extensions = [h for h in header[3:] if h != 0]
# read array data with numpy (double-precision floats)
data = np.fromfile(f, dtype=np.double).reshape(cells,order='F')
data = np.fromfile(f, dtype=np.double).reshape(cells).T
f.close()
# assemble grid
x = [np.arange(.5*e/float(c),e,e/float(c)) for e,c in zip(extensions,cells)]
grid = np.array(np.meshgrid(*x))
grid = np.dstack(np.meshgrid(*x))
return grid, data
......@@ -18,9 +18,7 @@ def test_dorie(iniinfo,inifile,executable):
# Run DORiE and measure total execution time
start = time.clock()
print("Running DORiE")
return_code = subprocess.call(command)
print("DORiE done")
end = time.clock()
runtime = end - start
......
......@@ -20,7 +20,7 @@ class BaseGrid(object):
"""
if self._cellCenters is None:
self._calcCellCenters()
return np.moveaxis(self._cellCenters, -1, 0)
return self._cellCenters #np.array((self._cellCenters[...,0],self._cellCenters[...,1]))
def add_data(self,name,data):
"""
......@@ -30,12 +30,10 @@ class BaseGrid(object):
:param array_like data: Variable data. First dimensions must match the cell dimensions.
"""
if self._cellCenters is None:
self._calcCellCenters()
if name in self._cellVariables:
raise ValueError("Cell variable {} already added".format(name))
data = np.squeeze(np.array(data))
if any([a != b for a,b in zip(data.shape, self._cellCenters.shape[:-1])]):
if any([a != b for a,b in zip(data.shape, self.cellCenters().shape[:-1])]):
raise TypeError("First dimensions of data array must match cell dimensions")
self._cellVariables = self._cellVariables + (name,)
self._cellValues = self._cellValues + (data,)
......@@ -132,8 +130,7 @@ class UnstructuredVTKGrid(BaseGrid):
:rtype: tuple
"""
tri = self.points.T, self.connectivity.reshape(self._numCells,self.ppc)
return tri
return self.points.T, self.connectivity.reshape(self._numCells,self.ppc)
def _calcCellCenters(self):
"""
......
message(STATUS "Handling system tests")
configure_file(convergence.mini.in ${CMAKE_CURRENT_LIST_DIR}/convergence.mini)
#dune_add_system_test(TARGET dorie INIFILE convergence.mini SCRIPT test_dorie.py)
dune_add_system_test(TARGET dorie INIFILE convergence.mini SCRIPT test_dorie.py)
configure_file(ode.mini.in ${CMAKE_CURRENT_LIST_DIR}/ode.mini)
dune_add_system_test(TARGET dorie INIFILE ode.mini SCRIPT test_dorie.py)
configure_file(ode_higherorder.mini.in ${CMAKE_CURRENT_LIST_DIR}/ode_higherorder.mini)
dune_add_system_test(TARGET dorie INIFILE ode_higherorder.mini SCRIPT test_dorie.py)
configure_file(parfield_muphi.mini.in ${CMAKE_CURRENT_LIST_DIR}/parfield_muphi.mini)
dune_add_system_test(TARGET dorie-pfg INIFILE parfield_muphi.mini SCRIPT test_dorie_pfg.py)
......@@ -20,4 +23,4 @@ configure_file(reference_3d.mini.in ${CMAKE_CURRENT_LIST_DIR}/reference_3d.mini)
dune_add_system_test(TARGET dorie INIFILE reference_3d.mini SCRIPT test_dorie.py)
configure_file(correlation.mini.in ${CMAKE_CURRENT_LIST_DIR}/correlation.mini)
dune_add_system_test(TARGET dorie-pfg INIFILE correlation.mini SCRIPT test_dorie_pfg.py)
#dune_add_system_test(TARGET dorie-pfg INIFILE correlation.mini SCRIPT test_dorie_pfg.py)
......@@ -18,7 +18,7 @@ adaptivity.useAdaptivity = false, true | expand distribution
grid.gridType = rectangular, gmsh | expand gridtype
grid.cells = 1 100
grid.initialLevel = 3, 0 | expand distribution
grid.gridFile = "{_asset_path}/meshes/mesh.msh"
grid.gridFile = "{_asset_path}/meshes/square.msh"
boundary.file = "{_asset_path}/bcs/infiltration_2d.dat"
......
include ${CMAKE_BINARY_DIR}/doc/default_files/config.ini
__name = ode_higherorder
__inifile_optionkey = run
_asset_path = "${CMAKE_CURRENT_LIST_DIR}"
_evaluation = ode
output.fileName = ode_higherorder | unique
output.outputPath = ode_higherorder | unique
output.verbose = 0
time.end = 1E7
time.maxTimestep = 1E7
time.startTimestep = 1E4
adaptivity.threshold = 1E-8
adaptivity.useAdaptivity = false, true | expand distribution
grid.FEorder = 2, 3 | expand feorder
grid.gridType = gmsh, rectangular | expand distribution
# higher FEorders seem to have a problem with asymmetric grids
grid.cells = 5 20
grid.initialLevel = 2, 0 | expand distribution
grid.gridFile = "{_asset_path}/meshes/square.msh"
boundary.file = "{_asset_path}/bcs/infiltration_2d.dat"
parameters.arrayFile = "{_asset_path}/parfields/sand.h5", "{_asset_path}/parfields/layered.h5" | expand distribution
[_ode]
flux = -3e-6
l2_abstol = 1E-5
[NewtonParameters]
AbsoluteLimit = 1E-8
Reduction = 1E-8
......@@ -8,7 +8,7 @@ _reference.path = {_asset_path}/references/2d/
output.fileName = reference_2d | unique name
output.outputPath = reference_2d | unique name
output.verbose = 2
output.verbose = 0
time.end = 1E5
time.maxTimestep = 1E5
......
......@@ -14,15 +14,18 @@ time.end = 1E5
time.maxTimestep = 1E5
time.startTimestep = 1E4
adaptivity.useAdaptivity = false, true | expand adaptivity
adaptivity.threshold = 1E-8
adaptivity.useAdaptivity = false
adaptivity.threshold = 1E-6
grid.dimensions = 3
grid.initialLevel = 2, 0 | expand adaptivity
grid.gridType = gmsh, rectangular | expand
grid.cells = 20 20 20
grid.initialLevel = 1
grid.gridType = gmsh
grid.extensions = 1 1 1
grid.gridFile = "{_asset_path}/meshes/3dcube.msh"
boundary.file = "{_asset_path}/bcs/infiltration_3d.dat"
parameters.arrayFile = "{_asset_path}/parfields/fft_3d.h5", "{_asset_path}/parfields/fft_3d_miller.h5" | expand
parameters.scale = 1 1 1
parameters.offset = 0 0 0
parameters.interpolation = linear
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<?xml version="1.0"?>
<VTKFile type="UnstructuredGrid" version="0.1" byte_order="LittleEndian">
<UnstructuredGrid>
<Piece NumberOfCells="184" NumberOfPoints="109">
<CellData Scalars="head" Vectors="flux">
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