Ksagiyam/restricted extrusion

firedrake/bcs.py

@@ -41,7 +41,7 @@ class BCBase(object):
     def __init__(self, V, sub_domain):
 
         self._function_space = V
-        self.sub_domain = sub_domain
+        self.sub_domain = (sub_domain, ) if isinstance(sub_domain, str) else as_tuple(sub_domain)
         # If this BC is defined on a subspace (IndexedFunctionSpace or
         # ComponentFunctionSpace, possibly recursively), pull out the appropriate
         # indices.
@@ -289,11 +289,9 @@ def __init__(self, V, g, sub_domain, method=None):
                 warnings.simplefilter('always', DeprecationWarning)
                 warnings.warn("Selecting a bcs method is deprecated. Only topological association is supported",
                               DeprecationWarning)
-        if len(V.boundary_set):
-            subs = [sub_domain] if type(sub_domain) in {int, str} else sub_domain
-            if any(sub not in V.boundary_set for sub in subs):
-                raise ValueError(f"Sub-domain {sub_domain} not in the boundary set of the restricted space.")
         super().__init__(V, sub_domain)
+        if len(V.boundary_set) and not set(self.sub_domain).issubset(V.boundary_set):
+            raise ValueError(f"Sub-domain {self.sub_domain} not in the boundary set of the restricted space {V.boundary_set}.")
         if len(V) > 1:
             raise ValueError("Cannot apply boundary conditions on mixed spaces directly.\n"
                              "Apply to the components by indexing the space with .sub(...)")

firedrake/cython/dmcommon.pyx

@@ -1205,14 +1205,18 @@ def create_section(mesh, nodes_per_entity, on_base=False, block_size=1, boundary
         PETSc.DM dm
         PETSc.Section section
         PETSc.IS renumbering
-        PetscInt i, p, layers, pStart, pEnd, dof, j
+        PetscInt i, p, layers, offset_top, pStart, pEnd, dof, j, k
         PetscInt dimension, ndof
         PetscInt *dof_array = NULL
         const PetscInt *entity_point_map
         np.ndarray nodes
         np.ndarray layer_extents
         np.ndarray points
         bint variable, extruded, on_base_
+        PETSc.SF point_sf
+        PetscInt nleaves
+        const PetscInt *ilocal = NULL
+        PetscInt factor
 
     dm = mesh.topology_dm
     if isinstance(dm, PETSc.DMSwarm) and on_base:
@@ -1221,32 +1225,31 @@ def create_section(mesh, nodes_per_entity, on_base=False, block_size=1, boundary
     extruded = mesh.cell_set._extruded
     extruded_periodic = mesh.cell_set._extruded_periodic
     on_base_ = on_base
+    dimension = get_topological_dimension(dm)
     nodes_per_entity = np.asarray(nodes_per_entity, dtype=IntType)
     if variable:
         layer_extents = mesh.layer_extents
+        nodes = nodes_per_entity.reshape(dimension + 1, -1)
     elif extruded:
         if on_base:
-            nodes_per_entity = sum(nodes_per_entity[:, i] for i in range(2))
+            nodes = sum(nodes_per_entity[:, i] for i in range(2)).reshape(dimension + 1, -1)
         else:
             if extruded_periodic:
-                nodes_per_entity = sum(nodes_per_entity[:, i]*(mesh.layers - 1) for i in range(2))
+                nodes = sum(nodes_per_entity[:, i]*(mesh.layers - 1) for i in range(2)).reshape(dimension + 1, -1)
             else:
-                nodes_per_entity = sum(nodes_per_entity[:, i]*(mesh.layers - i) for i in range(2))
+                nodes = sum(nodes_per_entity[:, i]*(mesh.layers - i) for i in range(2)).reshape(dimension + 1, -1)
+    else:
+        nodes = nodes_per_entity.reshape(dimension + 1, -1)
     section = PETSc.Section().create(comm=mesh._comm)
     get_chart(dm.dm, &pStart, &pEnd)
     section.setChart(pStart, pEnd)
 
-    if boundary_set:
-        renumbering, (constrainedStart, constrainedEnd) = plex_renumbering(dm,
-            mesh._entity_classes, reordering=mesh._default_reordering, boundary_set=boundary_set)
+    if boundary_set and not extruded:
+        renumbering = plex_renumbering(dm, mesh._entity_classes, reordering=mesh._default_reordering, boundary_set=boundary_set)
     else:
         renumbering = mesh._dm_renumbering
-        constrainedStart = -1
-        constrainedEnd = -1
 
     CHKERR(PetscSectionSetPermutation(section.sec, renumbering.iset))
-    dimension = get_topological_dimension(dm)
-    nodes = nodes_per_entity.reshape(dimension + 1, -1)
     for i in range(dimension + 1):
         get_depth_stratum(dm.dm, i, &pStart, &pEnd) # gets all points at dim i
         if not variable:
@@ -1260,9 +1263,27 @@ def create_section(mesh, nodes_per_entity, on_base=False, block_size=1, boundary
                     ndof = layers*nodes[i, 0] + (layers - 1)*nodes[i, 1]
             CHKERR(PetscSectionSetDof(section.sec, p, block_size * ndof))
 
+    if boundary_set and extruded and variable:
+        raise NotImplementedError("Not implemented for variable layer extrusion")
     if boundary_set:
+        # Handle "bottom" and "top" first.
+        if "bottom" in boundary_set and "top" in boundary_set:
+            factor = 2
+        elif "bottom" in boundary_set or "top" in boundary_set:
+            factor = 1
+        else:
+            factor = 0
+        if factor > 0:
+            for i in range(dimension + 1):
+                get_depth_stratum(dm.dm, i, &pStart, &pEnd)
+                dof = nodes_per_entity[i, 0]
+                for p in range(pStart, pEnd):
+                    CHKERR(PetscSectionSetConstraintDof(section.sec, p, factor * dof))
+        # Potentially overwrite ds_t and dS_t constrained DoFs set in the {"bottom", "top"} cases.
         for marker in boundary_set:
-            if marker == "on_boundary":
+            if marker in ["bottom", "top"]:
+                continue
+            elif marker == "on_boundary":
                 label = "exterior_facets"
                 marker = 1
             else:
@@ -1276,11 +1297,36 @@ def create_section(mesh, nodes_per_entity, on_base=False, block_size=1, boundary
                 CHKERR(PetscSectionGetDof(section.sec, p, &dof))
                 CHKERR(PetscSectionSetConstraintDof(section.sec, p, dof))
     section.setUp()
-
     if boundary_set:
         # have to loop again as we need to call section.setUp() first
+        CHKERR(PetscSectionGetMaxDof(section.sec, &dof))
+        CHKERR(PetscMalloc1(dof, &dof_array))
+        for i in range(dof):
+            dof_array[i] = -1
+        if "bottom" in boundary_set or "top" in boundary_set:
+            for i in range(dimension + 1):
+                get_depth_stratum(dm.dm, i, &pStart, &pEnd)
+                if pEnd == pStart:
+                    continue
+                dof = nodes_per_entity[i, 0]
+                j = 0
+                if "bottom" in boundary_set:
+                    for k in range(dof):
+                        dof_array[j] = k
+                        j += 1
+                if "top" in boundary_set:
+                    offset_top = (nodes_per_entity[i, 0] + nodes_per_entity[i, 1]) * (mesh.layers - 1)
+                    for k in range(dof):
+                        dof_array[j] = offset_top + k
+                        j += 1
+                for p in range(pStart, pEnd):
+                    # Potentially set wrong values for ds_t and dS_t constrained DoFs here,
+                    # but we will overwrite them in the below.
+                    CHKERR(PetscSectionSetConstraintIndices(section.sec, p, dof_array))
         for marker in boundary_set:
-            if marker == "on_boundary":
+            if marker in ["bottom", "top"]:
+                continue
+            elif marker == "on_boundary":
                 label = "exterior_facets"
                 marker = 1
             else:
@@ -1289,24 +1335,24 @@ def create_section(mesh, nodes_per_entity, on_base=False, block_size=1, boundary
             if n == 0:
                 continue
             points = dm.getStratumIS(label, marker).indices
-            CHKERR(PetscSectionGetMaxDof(section.sec, &dof))
-            CHKERR(PetscMalloc1(dof, &dof_array))
             for i in range(n):
                 p = points[i]
                 CHKERR(PetscSectionGetDof(section.sec, p, &dof))
                 for j in range(dof):
                     dof_array[j] = j
                 CHKERR(PetscSectionSetConstraintIndices(section.sec, p, dof_array))
-            CHKERR(PetscFree(dof_array))
-
+        CHKERR(PetscFree(dof_array))
     constrained_nodes = 0
-
-    CHKERR(ISGetIndices(renumbering.iset, &entity_point_map))
-    for entity in range(constrainedStart, constrainedEnd):
-        CHKERR(PetscSectionGetDof(section.sec, entity_point_map[entity], &dof))
+    get_chart(dm.dm, &pStart, &pEnd)
+    point_sf = dm.getPointSF()
+    CHKERR(PetscSFGetGraph(point_sf.sf, NULL, &nleaves, &ilocal, NULL))
+    for p in range(pStart, pEnd):
+        CHKERR(PetscSectionGetConstraintDof(section.sec, p, &dof))
         constrained_nodes += dof
-    CHKERR(ISRestoreIndices(renumbering.iset, &entity_point_map))
-
+    for i in range(nleaves):
+        p = ilocal[i] if ilocal else i
+        CHKERR(PetscSectionGetConstraintDof(section.sec, p, &dof))
+        constrained_nodes -= dof
     return section, constrained_nodes
 
 
@@ -2460,7 +2506,7 @@ def plex_renumbering(PETSc.DM plex,
     perm_is.setType("general")
     CHKERR(ISGeneralSetIndices(perm_is.iset, pEnd - pStart,
                                perm, PETSC_OWN_POINTER))
-    return perm_is, (lidx[1], lidx[3])
+    return perm_is
 
 @cython.boundscheck(False)
 @cython.wraparound(False)
@@ -3310,23 +3356,31 @@ def make_global_numbering(PETSc.Section lsec, PETSc.Section gsec):
     :arg lsec: Section describing local dof layout and numbers.
     :arg gsec: Section describing global dof layout and numbers."""
     cdef:
-        PetscInt c, p, pStart, pEnd, dof, cdof, loff, goff
+        PetscInt c, cc, p, pStart, pEnd, dof, cdof, loff, goff
         np.ndarray val
+        PetscInt *dof_array = NULL
 
     val = np.empty(lsec.getStorageSize(), dtype=IntType)
     pStart, pEnd = lsec.getChart()
-
     for p in range(pStart, pEnd):
         CHKERR(PetscSectionGetDof(lsec.sec, p, &dof))
         CHKERR(PetscSectionGetConstraintDof(lsec.sec, p, &cdof))
         if dof > 0:
             CHKERR(PetscSectionGetOffset(lsec.sec, p, &loff))
             CHKERR(PetscSectionGetOffset(gsec.sec, p, &goff))
+            goff = cabs(goff)
             if cdof > 0:
+                CHKERR(PetscSectionGetConstraintIndices(lsec.sec, p, &dof_array))
+                for c in range(dof):
+                    val[loff + c] = -2
+                for c in range(cdof):
+                    val[loff + dof_array[c]] = -1
+                cc = 0
                 for c in range(dof):
-                    val[loff + c] = -1
+                    if val[loff + c] < -1:
+                        val[loff + c] = goff + cc
+                        cc += 1
             else:
-                goff = cabs(goff)
                 for c in range(dof):
                     val[loff + c] = goff + c
     return val

firedrake/cython/petschdr.pxi

@@ -97,6 +97,7 @@ cdef extern from "petscis.h" nogil:
     int PetscSectionGetConstraintDof(PETSc.PetscSection,PetscInt,PetscInt*)
     int PetscSectionSetConstraintDof(PETSc.PetscSection,PetscInt,PetscInt)
     int PetscSectionSetConstraintIndices(PETSc.PetscSection,PetscInt, PetscInt[])
+    int PetscSectionGetConstraintIndices(PETSc.PetscSection,PetscInt, const PetscInt**)
     int PetscSectionGetMaxDof(PETSc.PetscSection,PetscInt*)
     int PetscSectionSetPermutation(PETSc.PetscSection,PETSc.PetscIS)
     int ISGetIndices(PETSc.PetscIS,PetscInt*[])

firedrake/functionspaceimpl.py

@@ -14,6 +14,7 @@
 import finat.ufl
 
 from pyop2 import op2, mpi
+from pyop2.utils import as_tuple
 
 from firedrake import dmhooks, utils
 from firedrake.functionspacedata import get_shared_data, create_element
@@ -876,6 +877,16 @@ class RestrictedFunctionSpace(FunctionSpace):
     """
     def __init__(self, function_space, boundary_set=frozenset(), name=None):
         label = ""
+        boundary_set_ = []
+        for boundary_domain in boundary_set:
+            if isinstance(boundary_domain, str):
+                boundary_set_.append(boundary_domain)
+            else:
+                # Currently, can not handle intersection of boundaries;
+                # e.g., boundary_set = [(1, 2)], which is different from [1, 2].
+                bd, = as_tuple(boundary_domain)
+                boundary_set_.append(bd)
+        boundary_set = boundary_set_
         for boundary_domain in boundary_set:
             label += str(boundary_domain)
             label += "_"
@@ -896,7 +907,8 @@ def set_shared_data(self):
         self.node_set = sdata.node_set
         r"""A :class:`pyop2.types.set.Set` representing the function space nodes."""
         self.dof_dset = op2.DataSet(self.node_set, self.shape or 1,
-                                    name="%s_nodes_dset" % self.name)
+                                    name="%s_nodes_dset" % self.name,
+                                    apply_local_global_filter=sdata.extruded)
         r"""A :class:`pyop2.types.dataset.DataSet` representing the function space
         degrees of freedom."""
 

firedrake/mesh.py

@@ -1245,7 +1245,7 @@ def _renumber_entities(self, reorder):
         else:
             # No reordering
             reordering = None
-        return dmcommon.plex_renumbering(self.topology_dm, self._entity_classes, reordering)[0]
+        return dmcommon.plex_renumbering(self.topology_dm, self._entity_classes, reordering)
 
     @utils.cached_property
     def cell_closure(self):
@@ -1979,7 +1979,7 @@ def _renumber_entities(self, reorder):
             perm_is.setIndices(perm)
             return perm_is
         else:
-            return dmcommon.plex_renumbering(self.topology_dm, self._entity_classes, None)[0]
+            return dmcommon.plex_renumbering(self.topology_dm, self._entity_classes, None)
 
     @utils.cached_property  # TODO: Recalculate if mesh moves
     def cell_closure(self):

firedrake/slate/static_condensation/hybridization.py

@@ -1,5 +1,4 @@
 import functools
-import numbers
 
 import numpy as np
 import ufl
@@ -11,7 +10,6 @@
 from firedrake.petsc import PETSc
 from firedrake.parloops import par_loop, READ, INC
 from firedrake.slate.slate import Tensor, AssembledVector
-from pyop2.utils import as_tuple
 from firedrake.slate.static_condensation.la_utils import SchurComplementBuilder
 from firedrake.ufl_expr import adjoint
 
@@ -153,11 +151,7 @@ def initialize(self, pc):
                 if bc.function_space().index != self.vidx:
                     raise NotImplementedError("Dirichlet bc set on unsupported space.")
                 # append the set of sub domains
-                subdom = bc.sub_domain
-                if isinstance(subdom, str):
-                    neumann_subdomains |= set([subdom])
-                else:
-                    neumann_subdomains |= set(as_tuple(subdom, numbers.Integral))
+                neumann_subdomains |= set(bc.sub_domain)
 
             # separate out the top and bottom bcs
             extruded_neumann_subdomains = neumann_subdomains & {"top", "bottom"}

pyop2/types/dat.py

@@ -807,15 +807,37 @@ def _vec(self):
         # But use getSizes to save an Allreduce in computing the
         # global size.
         size = self.dataset.layout_vec.getSizes()
-        data = self._data[:size[0]]
+        if self.dataset._apply_local_global_filter:
+            data = self._data_filtered
+        else:
+            data = self._data[:size[0]]
         return PETSc.Vec().createWithArray(data, size=size, bsize=self.cdim, comm=self.comm)
 
+    @utils.cached_property
+    def _data_filtered(self):
+        size, _ = self.dataset.layout_vec.getSizes()
+        size //= self.dataset.layout_vec.block_size
+        data = self._data[:size]
+        return np.empty_like(data)
+
+    @utils.cached_property
+    def _data_filter(self):
+        lgmap = self.dataset.lgmap
+        n = self.dataset.size
+        lgmap_owned = lgmap.block_indices[:n]
+        return lgmap_owned >= 0
+
     @contextlib.contextmanager
     def vec_context(self, access):
         r"""A context manager for a :class:`PETSc.Vec` from a :class:`Dat`.
 
         :param access: Access descriptor: READ, WRITE, or RW."""
+        size = self.dataset.size
+        if self.dataset._apply_local_global_filter and access is not Access.WRITE:
+            self._data_filtered[:] = self._data[:size][self._data_filter]
         yield self._vec
+        if self.dataset._apply_local_global_filter and access is not Access.READ:
+            self._data[:size][self._data_filter] = self._data_filtered[:]
         if access is not Access.READ:
             self.halo_valid = False