Updating documentation to latest branch (expressions, free surface ex…

…amples)

.github/workflows/deploy_to_gh_pages.yml → .github/workflows/deploy_to_gh_pages.yml_disabled

@@ -23,7 +23,7 @@ jobs:
   deploy-book:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
 
     # Install dependencies
     # - name: Set up Python 3.7

Jupyterbook/Notebooks/Developers/Snippets/Contants.py

@@ -0,0 +1,154 @@
+# ---
+# jupyter:
+#   jupytext:
+#     formats: py:percent
+#     text_representation:
+#       extension: .py
+#       format_name: percent
+#       format_version: '1.3'
+#       jupytext_version: 1.16.1
+#   kernelspec:
+#     display_name: Python 3 (ipykernel)
+#     language: python
+#     name: python3
+# ---
+
+# %%
+import underworld3 as uw
+import sympy
+from underworld3.function import expression
+
+
+# %%
+import math
+rho = expression(r'\uprho', 10)
+three = expression(r'\textrm{[iii]}', 3)
+kappa = expression(r'\upkappa', 100)
+alpha = expression(r'\alpha', 3e-5)
+pi = expression(r'\pi', math.pi )
+
+
+# %%
+three
+
+# %% [markdown]
+# Now let's build a mesh and some mesh variables
+#
+#
+
+# %%
+mesh = uw.meshing.UnstructuredSimplexBox(
+        minCoords=(0, 0), 
+        maxCoords=(1, 1), 
+        cellSize=1/10, 
+        regular=False, 
+        qdegree=3 )
+
+x,y = mesh.X
+
+
+V = uw.discretisation.MeshVariable("U", mesh, 2, degree=2, continuous=True, varsymbol=r"\mathbf{u}")
+P = uw.discretisation.MeshVariable("P", mesh, 1, degree=1, continuous=True, varsymbol=r"P")
+T = uw.discretisation.MeshVariable("T", mesh, 1, degree=2, continuous=True, varsymbol=r"T")
+
+with mesh.access(V,T):
+    V.data[:,0] = uw.function.evaluate(x, V.coords)
+    V.data[:,1] = uw.function.evaluate(y, V.coords)
+    T.data[:,0] = uw.function.evaluate(sympy.sin(2 * sympy.pi * x), T.coords)
+
+# %%
+fn0 = V.sym[0] * 3 + x * T.sym[0]
+fn0_s = uw.function.expression.substitute(fn0)
+
+# %%
+fn1 = V.sym[0] * three + x * T.sym[0]
+fn1_s = uw.function.expression.substitute(fn1)
+
+# %%
+fn2 = alpha ** 2 * x + rho * sympy.sin(pi * y)
+fn2_s = uw.function.expression.substitute(fn2)
+
+# %%
+fn3 = V.sym * three
+print(uw.function.evaluate(fn3, mesh.data)[::10])
+
+# %%
+eta0 = expression(r"{\eta_0}", 1000, "ref viscosity")
+C0 = expression(r"{C_0}", 10, "viscosity C0")
+eta = eta0 * sympy.exp(-C0 * T.sym[0])
+
+# %%
+## Stokes problem / Navier-Stokes problem
+
+
+navier_stokes = uw.systems.NavierStokes(mesh, velocityField=V, 
+                                        pressureField=P, 
+                                        order=1,
+                                        solver_name="n-navier_stokes")
+navier_stokes.constitutive_model = uw.constitutive_models.ViscousFlowModel
+
+
+# %%
+navier_stokes.uf0
+
+# %%
+navier_stokes.uF1
+
+# %%
+navier_stokes.constitutive_model.viscosity
+
+# %%
+navier_stokes.constitutive_model.Parameters.shear_viscosity_0 = eta
+navier_stokes.constitutive_model.Parameters.yield_stress = 100
+
+
+# expression( r"\eta", 1, "Dynamic Viscosity")
+navier_stokes.penalty = 0
+navier_stokes.saddle_preconditioner = sympy.simplify(1 / (navier_stokes.constitutive_model.viscosity + navier_stokes.penalty))
+
+navier_stokes.petsc_options["fieldsplit_velocity_mg_coarse_pc_type"] = "svd"
+
+# Surface normals provided by DMPLEX
+
+navier_stokes.add_dirichlet_bc((sympy.oo, 0.0), "Top")
+navier_stokes.add_dirichlet_bc((sympy.oo,0.0), "Bottom")
+navier_stokes.add_dirichlet_bc((0.0,sympy.oo), "Left")
+navier_stokes.add_dirichlet_bc((0.0,sympy.oo), "Right")
+
+navier_stokes.bodyforce = sympy.Matrix((0, alpha * T.sym[0]))
+
+
+# %%
+navier_stokes.uf0
+
+# %%
+navier_stokes.uF1
+
+# %%
+navier_stokes.constitutive_model.viscosity
+
+# %%
+navier_stokes.Unknowns.E
+
+# %%
+navier_stokes.delta_t
+
+# %%
+navier_stokes.uF1.subs(navier_stokes.penalty, navier_stokes.penalty.value)
+
+# %%
+navier_stokes.uf0.simplify()
+
+# %%
+vfm = uw.constitutive_models.ViscousFlowModel(navier_stokes.Unknowns)
+vfm.flux
+
+# %%
+vpfm = uw.constitutive_models.ViscoPlasticFlowModel(navier_stokes.Unknowns)
+vpfm.flux
+
+# %%
+vepfm = uw.constitutive_models.ViscoElasticPlasticFlowModel(navier_stokes.Unknowns)
+vepfm.flux
+
+# %%