Adaptive Multigrid

.github/workflows/ngsPETSc.yml

@@ -54,6 +54,7 @@ jobs:
           pytest -v tests/test_pc.py
           pytest -v tests/test_eps.py
           pytest -v tests/test_snes.py
+          pytest -v tests/test_adaptive_multigrid.py
 
       - name: Run test suite in parallel
         run: |

ngsPETSc/__init__.py

@@ -14,7 +14,10 @@
 if firedrake:
     from ngsPETSc.utils.firedrake.meshes import *
     from ngsPETSc.utils.firedrake.hierarchies import *
-    __all__ = __all__ + ["FiredrakeMesh", "NetgenHierarchy"]
+    from ngsPETSc.utils.firedrake.adaptive_hierarchy import *
+    from ngsPETSc.utils.firedrake.adaptive_transfer_manager import *
+    __all__ = __all__ + ["FiredrakeMesh", "NetgenHierarchy",
+                         "AdaptiveMeshHierarchy","AdaptiveTransferManager"]
 
 #FEniCSx
 try:

ngsPETSc/utils/firedrake/adaptive_hierarchy.py

@@ -0,0 +1,331 @@
+"""
+This module contains the class for the AdaptiveMeshHierarchy and related helper functions
+"""
+from fractions import Fraction
+from collections import defaultdict
+import numpy as np
+from firedrake import (Function, Cofunction, Mesh, Submesh, RelabeledMesh,
+                       HierarchyBase, FunctionSpace, conditional, gt
+)
+from firedrake.mg.utils import set_level, get_level
+
+__all__ = ["AdaptiveMeshHierarchy"]
+
+
+class AdaptiveMeshHierarchy(HierarchyBase):
+    """
+    HierarchyBase for hierarchies of adaptively refined meshes
+    """
+    def __init__(self, mesh, refinements_per_level=1, nested=True):
+        self.meshes = tuple(mesh)
+        self._meshes = tuple(mesh)
+        self.submesh_hierarchies = []
+        self.coarse_to_fine_cells = None
+        self.fine_to_coarse_cells = None
+        self.refinements_per_level = refinements_per_level
+        self.nested = nested
+        set_level(mesh[0], self, 0)
+        self.split_cache = {}
+
+    def add_mesh(self, mesh):
+        """
+        Adds newly refined mesh into hierarchy.
+        Then computes the coarse_to_fine and fine_to_coarse mappings.
+        Constructs intermediate submesh hierarchies with this.
+        """
+        if mesh.topological_dimension() <= 2:
+            max_children = 4
+        else:
+            max_children = 16
+        self._meshes += tuple(mesh)
+        self.meshes += tuple(mesh)
+        coarse_mesh = self.meshes[-2]
+        level = len(self.meshes)
+        set_level(self.meshes[-1], self, level - 1)
+        self._shared_data_cache = defaultdict(dict)
+
+        if len(self.meshes) <= 2:
+            self.coarse_to_fine_cells = {}
+            self.fine_to_coarse_cells = {}
+            self.fine_to_coarse_cells[Fraction(0, 1)] = None
+
+        # extract parent child relationships from netgen meshes
+        (c2f, f2c) = get_c2f_f2c_fd(mesh, coarse_mesh)
+
+        self.coarse_to_fine_cells[Fraction(len(self.meshes) - 2, 1)] = c2f
+        self.fine_to_coarse_cells[Fraction(len(self.meshes) - 1, 1)] = np.array(f2c)
+
+        # split both the fine and coarse meshes into the submeshes
+        (coarse_splits, fine_splits, num_children) = split_to_submesh(
+            mesh, coarse_mesh, c2f, f2c
+        )
+        for i in range(1, max_children + 1):
+            coarse_mesh.mark_entities(coarse_splits[i], i)
+            mesh.mark_entities(fine_splits[i], int(f"10{i}"))
+
+        coarse_mesh = RelabeledMesh(
+            coarse_mesh,
+            [coarse_splits[i] for i in range(1, max_children + 1)],
+            list(range(1, max_children + 1)),
+            name="Relabeled_coarse",
+        )
+        c_subm = {
+            j: Submesh(coarse_mesh, coarse_mesh.topology_dm.getDimension(), j)
+            for j in range(1, max_children + 1)
+            if any(num_children == j)
+        }
+        set_level(coarse_mesh, self, level - 2)
+
+        mesh = RelabeledMesh(
+            mesh,
+            [fine_splits[i] for i in range(1, max_children + 1)],
+            list(range(1, max_children + 1)),
+        )
+        f_subm = {
+            int(str(j)[-2:]): Submesh(mesh, mesh.topology_dm.getDimension(), j)
+            for j in [int("10" + str(i)) for i in range(1, max_children + 1)]
+            if any(num_children == int(str(j)[-2:]))
+        }
+        set_level(mesh, self, level - 1)
+
+        # update c2f and f2c for submeshes by mapping numberings
+        # on full mesh to numberings on coarse mesh
+        n = [
+            len([el for el in c2f if len(el) == j]) for j in range(1, max_children + 1)
+        ]
+        c2f_adjusted = {
+            j: np.zeros((n, j))
+            for n, j in zip(n, list(range(1, max_children + 1)))
+            if n != 0
+        }
+        f2c_adjusted = {
+            j: np.zeros((n * j, 1))
+            for n, j in zip(n, list(range(1, max_children + 1)))
+            if n != 0
+        }
+
+        coarse_full_to_sub_map = {
+            i: full_to_sub(coarse_mesh, c_subm[i], i) for i in c_subm
+        }
+        fine_full_to_sub_map = {
+            j: full_to_sub(mesh, f_subm[j], int("10" + str(j))) for j in f_subm
+        }
+
+        for i, children in enumerate(c2f):
+            n = len(children)
+            if 1 <= n <= max_children:
+                c2f_adjusted[n][coarse_full_to_sub_map[n](i)] = fine_full_to_sub_map[n](
+                    np.array(children)
+                )
+
+        for j, parent in enumerate(f2c):
+            n = int(num_children[parent].item())
+            if 1 <= n <= max_children:
+                f2c_adjusted[n][fine_full_to_sub_map[n](j), 0] = coarse_full_to_sub_map[
+                    n
+                ](parent.item())
+
+        c2f_subm = {
+            i: {Fraction(0, 1): c2f_adjusted[i].astype(int)} for i in c2f_adjusted
+        }
+        f2c_subm = {i: {Fraction(1, 1): f2c_adjusted[i]} for i in f2c_adjusted}
+
+        hierarchy_dict = {
+            i: HierarchyBase(
+                [c_subm[i], f_subm[i]], c2f_subm[i], f2c_subm[i], nested=True
+            )
+            for i in c_subm
+        }
+        self.submesh_hierarchies.append(hierarchy_dict)
+
+    def refine(self, refinements):
+        """
+        Refines and adds mesh if input a boolean vector corresponding to cells
+        """
+        ngmesh = self.meshes[-1].netgen_mesh
+        for l, el in enumerate(ngmesh.Elements2D()):
+            el.refine = 0
+            if refinements[l] == 1:
+                el.refine = 1
+
+        ngmesh.Refine(adaptive=True)
+        mesh = Mesh(ngmesh)
+        self.add_mesh(mesh)
+
+    def adapt(self, eta, theta):
+        """
+        Implement Dorfler marking, refines mesh from error estimator
+        """
+        mesh = self.meshes[-1]
+        W = FunctionSpace(mesh, "DG", 0)
+        markers = Function(W)
+
+        with eta.dat.vec_ro as eta_:
+            eta_max = eta_.max()[1]
+
+        should_refine = conditional(gt(eta, theta * eta_max), 1, 0)
+        markers.interpolate(should_refine)
+
+        refined_mesh = mesh.refine_marked_elements(markers)
+        self.add_mesh(refined_mesh)
+        return refined_mesh
+
+    def split_function(self, u, child=True):
+        """
+        Split input function across submeshes
+        """
+        V = u.function_space()
+        full_mesh = V.mesh()
+        _, level = get_level(full_mesh)
+
+        ind = 1 if child else 0
+        hierarchy_dict = self.submesh_hierarchies[int(level) - ind]
+        parent_mesh = hierarchy_dict[[*hierarchy_dict][0]].meshes[ind].submesh_parent
+        parent_space = V.reconstruct(parent_mesh)
+        u_corr_space = Function(parent_space, val=u.dat)
+        key = (u, child)
+        try:
+            split_functions = self.split_cache[key]
+        except KeyError:
+            split_functions = self.split_cache.setdefault(key, {})
+
+        for i in hierarchy_dict:
+            try:
+                f = split_functions[i].zero()
+            except KeyError:
+                V_split = V.reconstruct(mesh=hierarchy_dict[i].meshes[ind])
+                assert (
+                    V_split.mesh().submesh_parent
+                    == u_corr_space.function_space().mesh()
+                )
+                f = split_functions.setdefault(i, Function(V_split, name=str(i)))
+
+            f.assign(u_corr_space)
+        return split_functions
+
+    def use_weight(self, V, child):
+        """
+        Counts DoFs across submeshes, computes partition of unity
+        """
+        w = Function(V).assign(1)
+        splits = self.split_function(w, child)
+
+        self.recombine(splits, w, child)
+        with w.dat.vec as wvec:
+            wvec.reciprocal()
+        return w
+
+    def recombine(self, split_funcs, f, child=True):
+        """
+        Recombines functions on submeshes back full mesh
+        """
+        V = f.function_space()
+        f.zero()
+        parent_mesh = (
+            split_funcs[[*split_funcs][0]].function_space().mesh().submesh_parent
+        )
+        V_label = V.reconstruct(mesh=parent_mesh)
+        if isinstance(f, Function):
+            f_label = Function(V_label, val=f.dat)
+        elif isinstance(f, Cofunction):
+            f_label = Cofunction(V_label, val=f.dat)
+
+        for split_label, val in split_funcs.items():
+            assert val.function_space().mesh().submesh_parent == parent_mesh
+            if child:
+                split_label = int("10" + str(split_label))
+            if isinstance(f_label, Function):
+                f_label.assign(val, allow_missing_dofs=True)
+            else:
+                curr = Function(f_label.function_space()).assign(
+                    val, allow_missing_dofs=True
+                )
+                f_label.assign(f_label + curr)  # partition of unity for restriction
+        return f
+
+
+def get_c2f_f2c_fd(mesh, coarse_mesh):
+    """
+    Construct coarse->fine and fine->coarse relations by mapping netgen elements to firedrake ones
+    """
+    _ = FunctionSpace(mesh, "DG", 0)
+    _ = FunctionSpace(coarse_mesh, "DG", 0)
+    ngmesh = mesh.netgen_mesh
+    num_parents = coarse_mesh.num_cells()
+
+    if mesh.topology_dm.getDimension() == 2:
+        parents = ngmesh.parentsurfaceelements.NumPy()
+        elements = ngmesh.Elements2D()
+    else:
+        parents = ngmesh.parentelements.NumPy()
+        elements = ngmesh.Elements3D()
+
+    c2f = [[] for _ in range(num_parents)]
+    f2c = [[] for _ in range(mesh.num_cells())]
+
+    if parents.shape[0] == 0:
+        raise RuntimeError("Added mesh has not refined any cells from previous mesh")
+    for l, _ in enumerate(elements):
+        if parents[l][0] == -1 or l < num_parents:
+            f2c[mesh._cell_numbering.getOffset(l)].append(coarse_mesh._cell_numbering.getOffset(l))
+            c2f[coarse_mesh._cell_numbering.getOffset(l)].append(mesh._cell_numbering.getOffset(l))
+
+        elif parents[l][0] < num_parents:
+            fine_ind = mesh._cell_numbering.getOffset(l)
+            coarse_ind = coarse_mesh._cell_numbering.getOffset(parents[l][0])
+            f2c[fine_ind].append(coarse_ind)
+            c2f[coarse_ind].append(fine_ind)
+
+        else:
+            a = parents[parents[l][0]][0]
+            while a >= num_parents:
+                a = parents[a][0]
+
+            f2c[mesh._cell_numbering.getOffset(l)].append(coarse_mesh._cell_numbering.getOffset(a))
+            c2f[coarse_mesh._cell_numbering.getOffset(a)].append(mesh._cell_numbering.getOffset(l))
+
+    return c2f, np.array(f2c).astype(int)
+
+
+def split_to_submesh(mesh, coarse_mesh, c2f, f2c):
+    """
+    Computes submesh split from full mesh
+    """
+    if mesh.topological_dimension() <= 2:
+        max_children = 4
+    else:
+        max_children = 16
+    V = FunctionSpace(mesh, "DG", 0)
+    V2 = FunctionSpace(coarse_mesh, "DG", 0)
+    coarse_splits = {
+        i: Function(V2, name=f"{i}_elements") for i in range(1, max_children + 1)
+    }
+    fine_splits = {
+        i: Function(V, name=f"{i}_elements") for i in range(1, max_children + 1)
+    }
+    num_children = np.zeros((len(c2f)))
+
+    for i, children in enumerate(c2f):
+        n = len(children)
+        if 1 <= n <= max_children:
+            coarse_splits[n].dat.data[i] = 1
+            num_children[i] = n
+
+    for i in range(1, max_children + 1):
+        fine_splits[i].dat.data[num_children[f2c.squeeze()] == i] = 1
+
+    return coarse_splits, fine_splits, num_children
+
+
+def full_to_sub(mesh, submesh, label):
+    """
+    Returns the submesh element id associated with the full mesh element id
+    """
+    V1 = FunctionSpace(mesh, "DG", 0)
+    V2 = FunctionSpace(submesh, "DG", 0)
+    u1 = Function(V1)
+    u2 = Function(V2)
+    u2.dat.data[:] = np.arange(len(u2.dat.data))
+    u1.interpolate(u2, subset=mesh.cell_subset(label))
+
+    return lambda x: u1.dat.data[x].astype(int)