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ENH: Enable querying FEM values from Python #4398

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merged 7 commits into from
Sep 13, 2023
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Merged

ENH: Enable querying FEM values from Python #4398

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d076a8a
Make it possible to query FEM mappings from Python
matthewturk Apr 6, 2023
8412144
Merge branch 'main' of github.com:yt-project/yt into python_fem_sampling
matthewturk May 15, 2023
804bbd1
Add check_contains and change position shape loop
matthewturk Sep 7, 2023
175cefa
Update yt/utilities/lib/element_mappings.pyx
matthewturk Sep 12, 2023
4c0f874
Update yt/utilities/lib/element_mappings.pyx
matthewturk Sep 12, 2023
72f9c34
Merge branch 'main' into python_fem_sampling
matthewturk Sep 12, 2023
59dc296
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 12, 2023
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28 changes: 28 additions & 0 deletions yt/utilities/lib/element_mappings.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -115,6 +115,34 @@ cdef class ElementSampler:
val = self.sample_at_unit_point(mapped_coord, field_values)
return val

@cython.boundscheck(False)
@cython.wraparound(False)
@cython.cdivision(True)
def map_reals_to_unit(self,
np.float64_t[:,::1] vertices,
np.float64_t[:,::1] positions):
cdef double mapped_x[3]
cdef int i, n
# We have N vertices, which each have three components.
cdef np.ndarray[np.float64_t, ndim=2] output_coords
output_coords = np.zeros((positions.shape[0], positions.shape[1]), dtype="float64")
# Now for each position, we map
for n in range(positions.shape[0]):
self.map_real_to_unit(mapped_x, &vertices[0,0], &positions[n, 0])
for i in range(3):
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output_coords[n, i] = mapped_x[i]
return output_coords

def sample_at_real_points(self,
np.float64_t[:,::1] vertices,
np.float64_t[::1] field_values,
np.float64_t[:,::1] positions):
cdef np.ndarray[np.float64_t, ndim=1] output_values
output_values = np.zeros(positions.shape[0], dtype="float64")
for n in range(positions.shape[0]):
output_values[n] = self.sample_at_real_point(
&vertices[0,0], &field_values[0], &positions[n,0])
return output_values

cdef class P1Sampler1D(ElementSampler):
'''
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6 changes: 3 additions & 3 deletions yt/utilities/mesh_code_generation.py
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Expand Up @@ -83,11 +83,11 @@ def _compute_jacobian(self):
assert self.num_vertices == len(self.N)
assert self.num_dim == self.num_mapped_coords

X = MatrixSymbol("vertices", self.num_vertices, self.num_dim)
self.X = MatrixSymbol("vertices", self.num_vertices, self.num_dim)
self.fx = MatrixSymbol("fx", self.num_dim, 1)
physical_position = MatrixSymbol("phys_x", self.num_dim, 1)
self.physical_position = MatrixSymbol("phys_x", self.num_dim, 1)

self.f = (self.N.T * Matrix(X)).T - physical_position
self.f = (self.N.T * Matrix(self.X)).T - self.physical_position

self.J = symarray("J", (self.num_dim, self.num_dim))
for i in range(self.num_dim):
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