Merge branch 'develop' into systemtests/add-nearest-projection-case-clean

Author: AdityaGupta716

changelog-entries/660.md

@@ -0,0 +1 @@
+- Added a new Partitioned Water Hammer tutorial including 1D–3D, 3D–1D, 1D–1D, and 3D–3D coupling configurations using OpenFOAM and Nutils [#660](https://github.com/precice/tutorials/pull/660) 

changelog-entries/677.md

@@ -0,0 +1 @@
+- Added a new Partitioned Pipe Multiscale tutorial including 1D–3D, 3D–1D, 1D–1D, and 3D–3D coupling configurations using OpenFOAM and Nutils [#677](https://github.com/precice/tutorials/pull/677)

changelog-entries/688.md

@@ -0,0 +1 @@
+- Added FEniCSx-based solver for the flow over heated plate tutorial following the [FEniCS solver](https://github.com/precice/tutorials/tree/develop/flow-over-heated-plate/solid-fenics)

flow-over-heated-plate/README.md

@@ -41,6 +41,8 @@ Solid participant:
 
 * FEniCS. For more information, have a look at the [FeniCS adapter documentation](https://precice.org/adapter-fenics.html).
 
+* FEniCSx. For more information, have a look at the [FeniCSx adapter documentation](https://precice.org/adapter-fenicsx.html).
+
 * Nutils. For more information, have a look at the [Nutils adapter documentation](https://precice.org/adapter-nutils.html).
 
 * Dune-Fem. For more information, have a look at the [official documentation of Dune-Fem](https://www.dune-project.org/sphinx/dune-fem/). The `run.sh` script installs the solver from [PyPI](https://pypi.org/project/dune-fem/) into a Python virtual environment. Please note that Dune-Fem uses just-in-time compilation: The first time you run the solver script, it will take some time.

flow-over-heated-plate/solid-fenicsx/clean.sh

@@ -0,0 +1,6 @@
+#!/bin/sh
+set -e -u
+
+. ../../tools/cleaning-tools.sh
+
+clean_fenicsx .

flow-over-heated-plate/solid-fenicsx/precice-adapter-config.json

@@ -0,0 +1,19 @@
+{
+  "participant_name": "Solid",
+  "precice_config_file_path": "../precice-config.xml",
+  "interfaces": [
+    {
+      "mesh_name": "Solid-Mesh",
+      "write_data": [
+        {
+          "name": "Heat-Flux"
+        }
+      ],
+      "read_data": [
+        {
+          "name": "Temperature"
+        }
+      ]
+    }
+  ]
+}

flow-over-heated-plate/solid-fenicsx/requirements.txt

@@ -0,0 +1,3 @@
+numpy
+fenicsxprecice
+mpi4py>=3

flow-over-heated-plate/solid-fenicsx/run.sh

@@ -0,0 +1,8 @@
+#!/bin/sh
+set -e -u
+
+python3 -m venv --system-site-packages .venv
+. .venv/bin/activate
+pip install -r requirements.txt
+
+python3 solid.py

flow-over-heated-plate/solid-fenicsx/solid.py

@@ -0,0 +1,195 @@
+import numpy as np
+from mpi4py import MPI
+import basix.ufl
+from petsc4py import PETSc
+import ufl
+from dolfinx import fem, io, mesh as msh, default_scalar_type
+from dolfinx.fem.petsc import assemble_matrix, assemble_vector, apply_lifting, create_vector, set_bc, LinearProblem
+from dolfinx.mesh import create_rectangle
+import basix
+from fenicsxprecice import Adapter, CouplingMesh
+
+
+# geometry
+nx = 100
+ny = 25
+nz = 1
+
+y_top = 0
+y_bottom = y_top - .25
+x_left = 0
+x_right = x_left + 1
+
+fenics_dt = 0.01  # time step size
+
+
+def top_boundary(x):
+    tol = 1E-14
+    return np.isclose(x[1], y_top, tol)
+
+
+def bottom_boundary(x):
+    tol = 1E-14
+    return np.isclose(x[1], y_bottom, tol)
+
+
+class initial_value():
+    def __init__(self, constant):
+        self.constant = constant
+
+    def __call__(self, x):
+        return np.full(x[0].shape, self.constant)
+
+
+class GradientSolver:
+    """
+    compute flux following http://hplgit.github.io/INF5620/doc/pub/fenics_tutorial1.1/tu2.html#tut-poisson-gradu
+    The solver has been changed since the original version from the link above introduces larger errors
+
+    :param V_g: Vector function space
+    :param u: solution where gradient is to be determined
+    """
+
+    def __init__(self, domain, V_g):
+        self.domain = domain,
+        self.V_g = V_g
+
+        w = ufl.TrialFunction(V_g)
+        self.v = ufl.TestFunction(V_g)
+        a = fem.form(ufl.inner(w, self.v) * ufl.dx)
+        self.A = assemble_matrix(a)
+        self.A.assemble()
+
+        self.solver = PETSc.KSP().create(domain.comm)
+        self.solver.setOperators(self.A)
+        self.solver.setType(PETSc.KSP.Type.PREONLY)
+        self.solver.getPC().setType(PETSc.PC.Type.LU)
+
+        self.returnValue = fem.Function(V_g)
+
+    def compute(self, u, k):
+        L = fem.form(ufl.inner(-k * ufl.grad(u), self.v) * ufl.dx)
+        b = create_vector(fem.extract_function_spaces(L))
+        assemble_vector(b, L)
+        b.ghostUpdate(addv=PETSc.InsertMode.ADD_VALUES, mode=PETSc.ScatterMode.REVERSE)
+        self.solver.solve(b, self.returnValue.x.petsc_vec)
+        return self.returnValue
+
+
+p0 = (x_left, y_bottom)
+p1 = (x_right, y_top)
+
+mesh = create_rectangle(MPI.COMM_WORLD, [np.asarray(p0), np.asarray(p1)], [nx, ny], msh.CellType.triangle)
+V = fem.functionspace(mesh, ('P', 2))
+# for the vector function space
+element = basix.ufl.element("Lagrange", mesh.topology.cell_name(), 1, shape=(mesh.geometry.dim,))
+V_g = fem.functionspace(mesh, element)
+W, map_to_W = V_g.sub(1).collapse()
+
+gradient_solver = GradientSolver(mesh, V_g)
+
+alpha = 1  # m^2/s, https://en.wikipedia.org/wiki/Thermal_diffusivity
+k = 100  # kg * m / s^3 / K, https://en.wikipedia.org/wiki/Thermal_conductivity
+
+# We will only exchange flux in y direction on coupling interface. No initialization necessary.
+flux_y = fem.Function(W)
+
+# Define initial value
+u_n = fem.Function(V)
+u_n.name = "T"
+u_n.interpolate(initial_value(310))
+
+tdim = mesh.topology.dim
+fdim = tdim - 1
+mesh.topology.create_connectivity(fdim, tdim)
+dofs_coupling = fem.locate_dofs_geometrical(V, top_boundary)
+dofs_bottom = fem.locate_dofs_geometrical(V, bottom_boundary)
+
+# Adapter definition and initialization
+precice = Adapter(adapter_config_filename="precice-adapter-config.json", mpi_comm=MPI.COMM_WORLD)
+
+# top_boundary is coupling boundary
+coupling_mesh = CouplingMesh("Solid-Mesh", top_boundary, {"Temperature": V}, {"Heat-Flux": flux_y})
+precice.initialize([coupling_mesh])
+
+# boundary function for the coupling interface
+coupling_function = fem.Function(V)
+
+# Assigning appropriate dt
+precice_dt = precice.get_max_time_step_size()
+dt = np.min([fenics_dt, precice_dt])
+
+# Define variational problem
+u = ufl.TrialFunction(V)
+v = ufl.TestFunction(V)
+F = u * v / dt * ufl.dx + alpha * ufl.dot(ufl.grad(u), ufl.grad(v)) * ufl.dx - u_n * v / dt * ufl.dx
+
+# apply constant Dirichlet boundary condition at bottom edge
+# apply Dirichlet boundary condition on coupling interface
+bcs = [fem.dirichletbc(coupling_function, dofs_coupling), fem.dirichletbc(default_scalar_type(310), dofs_bottom, V)]
+
+a = fem.form(ufl.lhs(F))
+L = fem.form(ufl.rhs(F))
+
+A = assemble_matrix(a, bcs=bcs)
+A.assemble()
+b = create_vector(fem.extract_function_spaces(L))
+uh = fem.Function(V)
+solver = PETSc.KSP().create(mesh.comm)
+solver.setOperators(A)
+solver.setType(PETSc.KSP.Type.PREONLY)
+solver.getPC().setType(PETSc.PC.Type.LU)
+
+
+# Time-stepping
+t = 0
+
+vtxwriter = io.VTXWriter(MPI.COMM_WORLD, f"output_solid.bp", [u_n])
+vtxwriter.write(t)
+
+n = 0
+
+flux = fem.Function(V_g)
+
+while precice.is_coupling_ongoing():
+
+    if precice.requires_writing_checkpoint():
+        precice.store_checkpoint(u_n, t, 0)
+
+    precice_dt = precice.get_max_time_step_size()
+    dt = np.min([fenics_dt, precice_dt])
+    precice.read_data(coupling_mesh.get_name(), "Temperature", dt, coupling_function)
+
+    # Update the right hand side reusing the initial vector
+    with b.localForm() as loc_b:
+        loc_b.set(0)
+    assemble_vector(b, L)
+
+    apply_lifting(b, [a], [bcs])
+    set_bc(b, bcs)
+
+    # Solve linear problem
+    solver.solve(b, uh.x.petsc_vec)
+
+    # Dirichlet problem obtains flux from solution and sends flux on boundary to Neumann problem
+    flux = gradient_solver.compute(u_n, k)
+    flux_y.interpolate(flux.sub(1))
+    precice.write_data(coupling_mesh.get_name(), "Heat-Flux", flux_y)
+
+    precice.advance(dt)
+
+    if precice.requires_reading_checkpoint():
+        u_cp, t_cp, _ = precice.retrieve_checkpoint()
+        u_n.x.array[:] = u_cp.x.array
+        t = t_cp
+    else:  # update solution
+        # Update solution at previous time step (u_n)
+        u_n.x.array[:] = uh.x.array
+        t += float(dt)
+        n += 1
+        if n % 20 == 0:
+            vtxwriter.write(t)
+
+
+precice.finalize()
+vtxwriter.close()