adtzlr · adtzlr · Feb 7, 2025 · Feb 7, 2025 · Feb 7, 2025 · Feb 7, 2025
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -26,6 +26,7 @@ All notable changes to this project will be documented in this file. The format
 ### Fixed
 - Fix `Boundary(..., mode="and")` by ignoring any undefined axis.
 - Fix `tools.hello_world(planestrain=True)` with the correct region `RegionQuad` for the plane-strain template.
+- Fix the cells-array in `RegionQuadraticQuadBoundary` for midpoints of edges.
 
 ### Removed
 - Remove the unused `shape`-argument in `element.Element(shape)`. Adopt the arbitrary-lagrange element to use its own `dim`-argument. This simplifies the creation of custom finite element formulations.

diff --git a/src/felupe/region/_boundary.py b/src/felupe/region/_boundary.py
@@ -71,9 +71,9 @@ def boundary_cells_quad8(mesh):
 
     # complementary midpoints of edges for the creation of "boundary" quadratic quads
     # (rotated quads with 1st edge as n-th edge of one original quad)
-    n = [5, 6, 7, 4]
-    p = [4, 5, 6, 7]
-    q = [6, 7, 4, 5]
+    n = [4, 6, 5, 7]
+    p = [5, 7, 6, 4]
+    q = [6, 4, 7, 5]
 
     cells = np.dstack(
         (

diff --git a/tests/test_constitution.py b/tests/test_constitution.py
@@ -302,7 +302,7 @@ def elasticity(x, mu, lmbda):
     dsde = linear_elastic.hessian([F, None])
 
 
-def test_umat_hyperelastic_statevars():
+def test_umat_hyperelastic_statevars(close_figs=True):
     r, x = pre(sym=False, add_identity=True)
     F = x[0]
 
@@ -329,8 +329,11 @@ def test_umat_hyperelastic_statevars():
         ux = fem.math.linsteps([1, 2, 1], num=10)
         ax = umat.plot(ux=ux, bx=None, ps=None, incompressible=True)
 
+        if close_figs:
+            plt.close(ax.get_figure())
+
 
-def test_umat_hyperelastic():
+def test_umat_hyperelastic(close_figs=True):
     r, x = pre(sym=False, add_identity=True)
     F = x[0]
 
@@ -433,18 +436,34 @@ def neo_hooke(C, mu=1):
 
     for incompressible in [False, True]:
         ax = umat.plot(incompressible=incompressible)
+
+        if close_figs:
+            plt.close(ax.get_figure())
+
         ax = umat.screenshot(incompressible=incompressible)
 
+        if close_figs:
+            plt.close(ax.get_figure())
+
     umat = fem.Hyperelastic(fem.neo_hooke, mu=np.nan)
 
     with pytest.raises(ValueError):
-        umat.plot(bx=None, ps=None)
+        ax = umat.plot(bx=None, ps=None)
+
+        if close_figs:
+            plt.close(ax.get_figure())
 
     with pytest.raises(ValueError):
-        umat.plot(ux=None, bx=None)
+        ax = umat.plot(ux=None, bx=None)
+
+        if close_figs:
+            plt.close(ax.get_figure())
 
     with pytest.raises(ValueError):
-        umat.plot(ux=None, ps=None)
+        ax = umat.plot(ux=None, ps=None)
+
+        if close_figs:
+            plt.close(ax.get_figure())
 
 
 def test_umat_hyperelastic2():
@@ -476,7 +495,7 @@ def neo_hooke(F, mu=1):
     assert np.allclose(dsde, dsde2)
 
 
-def test_umat_viscoelastic():
+def test_umat_viscoelastic(close_figs=True):
     r, x = pre(sym=False, add_identity=True, add_random=True)
     F = x[0]
 
@@ -503,13 +522,16 @@ def viscoelastic(C, Cin, mu, eta, dtime):
     umat = fem.Hyperelastic(
         fem.constitution.finite_strain_viscoelastic, nstatevars=6, **kwargs
     )
-    umat.plot(
+    ax = umat.plot(
         ux=fem.math.linsteps([1, 1.5, 1, 2, 1, 2.5, 1], num=15),
         ps=None,
         bx=None,
         incompressible=True,
     )
 
+    if close_figs:
+        plt.close(ax.get_figure())
+
     s2, statevars_new = umat.gradient([F, statevars])
     dsde2 = umat.hessian([F, statevars])
 
@@ -598,7 +620,7 @@ def test_elpliso():
     dsde = umat.hessian([F, statevars])
 
 
-def test_composite():
+def test_composite(close_figs=True):
     r, x = pre(sym=False, add_identity=True)
     F = x[0]
 
@@ -608,11 +630,14 @@ def test_composite():
 
     ax = umat.plot()
 
+    if close_figs:
+        plt.close(ax.get_figure())
+
     dWdF, statevars_new = umat.gradient([F, None])
     (d2WdFdF,) = umat.hessian([F, None])
 
 
-def test_optimize():
+def test_optimize(close_figs=True):
     stretches, stresses = (
         np.array(
             [
@@ -646,11 +671,24 @@ def test_optimize():
         * np.array([1.0, 0.0980665])
     ).T
 
+    for model in [
+        fem.extended_tube,
+    ]:
+        umat = fem.Hyperelastic(model)
+        with pytest.warns():
+            umat_new, res = umat.optimize(ux=[stretches, stresses], incompressible=True)
+
+        ux = np.linspace(stretches.min(), stretches.max(), num=200)
+        ax = umat_new.plot(incompressible=True, ux=ux, bx=None, ps=None)
+        ax.plot(stretches, stresses, "C0x")
+
+        if close_figs:
+            plt.close(ax.get_figure())
+
     for model in [
         fem.neo_hooke,
         fem.ogden,
         fem.third_order_deformation,
-        fem.extended_tube,
         fem.alexander,
     ]:
         umat = fem.Hyperelastic(model)
@@ -660,6 +698,9 @@ def test_optimize():
         ax = umat_new.plot(incompressible=True, ux=ux, bx=None, ps=None)
         ax.plot(stretches, stresses, "C0x")
 
+        if close_figs:
+            plt.close(ax.get_figure())
+
     for model in [
         fem.neo_hooke,
         fem.miehe_goektepe_lulei,
@@ -673,6 +714,9 @@ def test_optimize():
         ax = umat_new.plot(incompressible=True, ux=ux, bx=None, ps=None)
         ax.plot(stretches, stresses, "C0x")
 
+        if close_figs:
+            plt.close(ax.get_figure())
+
 
 def test_lagrange():
     r, x = pre(sym=False, add_identity=True)
@@ -766,40 +810,52 @@ def test_laplace():
     assert A[0].shape == (3, 3, 3, 3, 1, 1)
 
 
-def test_plot_negative_stretches():
+def test_plot_negative_stretches(close_figs=True):
     stretches = np.linspace(-0.5, 1, 16)
     umat = fem.NeoHooke(mu=1.0, bulk=2.0)
 
     for incompressible in [False, True]:
         with pytest.raises(ValueError):
-            umat.plot(ux=stretches, incompressible=incompressible)
+            ax = umat.plot(ux=stretches, incompressible=incompressible)
+
+            if close_figs:
+                plt.close(ax.get_figure())
 
         with pytest.raises(ValueError):
-            umat.plot(bx=stretches, incompressible=incompressible)
+            ax = umat.plot(bx=stretches, incompressible=incompressible)
+
+            if close_figs:
+                plt.close(ax.get_figure())
 
         with pytest.raises(ValueError):
-            umat.plot(ps=stretches, incompressible=incompressible)
+            ax = umat.plot(ps=stretches, incompressible=incompressible)
+
+            if close_figs:
+                plt.close(ax.get_figure())
 
 
 if __name__ == "__main__":
+
+    close_figs = True
+
     test_nh()
     test_linear()
     test_linear_orthotropic()
     test_linear_planestress()
     test_linear_planestrain()
     test_kinematics()
     test_umat()
-    test_umat_hyperelastic()
+    test_umat_hyperelastic(close_figs=close_figs)
     test_umat_hyperelastic2()
-    test_umat_hyperelastic_statevars()
-    test_umat_viscoelastic()
+    test_umat_hyperelastic_statevars(close_figs=close_figs)
+    test_umat_viscoelastic(close_figs=close_figs)
     test_umat_viscoelastic2()
     test_umat_strain()
     test_umat_strain_plasticity()
     test_elpliso()
-    test_composite()
-    test_optimize()
+    test_composite(close_figs=close_figs)
+    test_optimize(close_figs=close_figs)
     test_lagrange()
     test_lagrange_statevars()
     test_laplace()
-    test_plot_negative_stretches()
+    test_plot_negative_stretches(close_figs=True)
diff --git a/tests/test_job.py b/tests/test_job.py
@@ -55,7 +55,9 @@ def test_job():
 
 
 def test_job_xdmf():
-    field, step = pre(SolidBodyForce=fem.SolidBodyGravity)
+    with pytest.warns():  # solidbodygravity is deprecated
+        field, step = pre(SolidBodyForce=fem.SolidBodyGravity)
+
     job = fem.Job(steps=[step])
     job.evaluate()
 

diff --git a/tests/test_region.py b/tests/test_region.py
@@ -166,5 +166,15 @@ def test_region():
     assert not np.any(r.dV <= 0)
 
 
+def test_region_negative_volumes_cells():
+
+    mesh = fem.Rectangle()
+    mesh.cells = mesh.cells[:, ::-1]
+
+    with pytest.warns():  # negative volumes of cells
+        region = fem.RegionQuad(mesh)
+
+
 if __name__ == "__main__":
     test_region()
+    test_region_negative_volumes_cells()