From 8fd2ac02a5cff7d01ee3b42eb72289e4a1863082 Mon Sep 17 00:00:00 2001
From: benSepanski <ben_sepanski@alumni.baylor.edu>
Date: Sun, 5 Jul 2020 09:51:46 -0500
Subject: [PATCH] Some bug fixes to allow for FromBdyConnection, be more
careful with flipping local facet nrs
---
meshmode/interop/firedrake/__init__.py | 7 ++-
meshmode/interop/firedrake/connection.py | 2 +-
meshmode/interop/firedrake/mesh.py | 55 ++++++++++++++----------
3 files changed, 39 insertions(+), 25 deletions(-)
diff --git a/meshmode/interop/firedrake/__init__.py b/meshmode/interop/firedrake/__init__.py
index 890dbaf7..6ebacd91 100644
--- a/meshmode/interop/firedrake/__init__.py
+++ b/meshmode/interop/firedrake/__init__.py
@@ -22,10 +22,13 @@ THE SOFTWARE.
import numpy as np
-from meshmode.interop.firedrake.connection import FromFiredrakeConnection
+from meshmode.interop.firedrake.connection import (
+ FromBdyFiredrakeConnection, FromFiredrakeConnection)
from meshmode.interop.firedrake.mesh import import_firedrake_mesh
-__all__ = ["FromFiredrakeConnection", "import_firedrake_mesh"]
+__all__ = ["FromBdyFiredrakeConnection", "FromFiredrakeConnection",
+ "import_firedrake_mesh",
+ ]
def _compute_cells_near_bdy(mesh, bdy_id):
diff --git a/meshmode/interop/firedrake/connection.py b/meshmode/interop/firedrake/connection.py
index b63dfc9a..0501bc65 100644
--- a/meshmode/interop/firedrake/connection.py
+++ b/meshmode/interop/firedrake/connection.py
@@ -529,7 +529,7 @@ def _compute_cells_near_bdy(mesh, bdy_id):
# Reduce along each cell: Is a vertex of the cell in boundary nodes?
cell_is_near_bdy = np.any(np.isin(cell_node_list, boundary_nodes), axis=1)
- return np.arange(cell_node_list.shape[0], dtype=np.int32)[cell_is_near_bdy]
+ return np.nonzero(cell_is_near_bdy)[0].astype(np.int32)
class FromBdyFiredrakeConnection(FiredrakeConnection):
diff --git a/meshmode/interop/firedrake/mesh.py b/meshmode/interop/firedrake/mesh.py
index 569a3b9f..59a72ac4 100644
--- a/meshmode/interop/firedrake/mesh.py
+++ b/meshmode/interop/firedrake/mesh.py
@@ -142,7 +142,11 @@ def _get_firedrake_nodal_info(fdrake_mesh_topology, cells_to_use=None):
# Next go ahead and compute nodal adjacency by creating
# neighbors and neighbor_starts as specified by :class:`NodalAdjacency`
neighbors = []
- neighbors_starts = np.zeros(top.num_cells() + 1, dtype=np.int32)
+ if cells_to_use is None:
+ num_cells = top.num_cells()
+ else:
+ num_cells = np.size(cells_to_use)
+ neighbors_starts = np.zeros(num_cells + 1, dtype=np.int32)
for iel in range(len(cell_to_nodal_neighbors)):
neighbors += cell_to_nodal_neighbors[iel]
neighbors_starts[iel+1] = len(neighbors)
@@ -270,11 +274,11 @@ def _get_firedrake_facial_adjacency_groups(fdrake_mesh_topology,
np.arange(np.size(cells_to_use))))
# Only keep cells that using, and change to new cell index
- int_elements = [cells_to_use_inv[icell]
- for icell in int_elements[to_keep]]
+ int_elements = np.vectorize(cells_to_use_inv.__getitem__)(
+ int_elements[to_keep])
int_element_faces = int_element_faces[to_keep]
- int_neighbors = int_elements[to_keep]
- int_neighbor_faces = int_element_faces[to_keep]
+ int_neighbors = int_neighbors[to_keep]
+ int_neighbor_faces = int_neighbor_faces[to_keep]
# For neighbor cells, change to new cell index or mark
# as a new boundary (if the neighbor cell is not being used)
for ndx, icell in enumerate(int_neighbors):
@@ -299,17 +303,16 @@ def _get_firedrake_facial_adjacency_groups(fdrake_mesh_topology,
ext_element_faces = np.array([fd_loc_fac_nr_to_mm[fac_nr] for fac_nr in
top.exterior_facets.local_facet_dat.data])
ext_element_faces = ext_element_faces.astype(Mesh.face_id_dtype)
- ext_neighbor_faces = np.zeros(ext_element_faces.shape, dtype=np.int32)
- ext_neighbor_faces = ext_neighbor_faces.astype(Mesh.face_id_dtype)
+ ext_neighbor_faces = np.zeros(ext_element_faces.shape,
+ dtype=Mesh.face_id_dtype)
# If only using some of the cells, throw away unused cells and
# move to new cell index
if cells_to_use is not None:
to_keep = np.isin(ext_elements, cells_to_use)
- ext_elements = [cells_to_use_inv[icell]
- for icell in ext_elements[to_keep]]
+ ext_elements = np.vectorize(cells_to_use_inv.__getitem__)(
+ ext_elements[to_keep])
ext_element_faces = ext_element_faces[to_keep]
- ext_neighbors = ext_elements[to_keep]
- ext_neighbor_faces = ext_element_faces[to_keep]
+ ext_neighbor_faces = ext_neighbor_faces[to_keep]
# tag the boundary
ext_neighbors = np.zeros(ext_elements.shape, dtype=np.int32)
@@ -510,6 +513,15 @@ def import_firedrake_mesh(fdrake_mesh, cells_to_use=None,
bdy_tags = _get_firedrake_boundary_tags(fdrake_mesh, no_boundary=no_boundary)
vertex_indices, nodal_adjacency = \
_get_firedrake_nodal_info(fdrake_mesh, cells_to_use=cells_to_use)
+ # If only using some cells, vertices may need new indices as many
+ # will be removed
+ if cells_to_use is not None:
+ vert_ndx_new2old = np.unique(vertex_indices.flatten())
+ vert_ndx_old2new = dict(zip(vert_ndx_new2old,
+ np.arange(np.size(vert_ndx_new2old),
+ dtype=vertex_indices.dtype)))
+ vertex_indices = \
+ np.vectorize(vert_ndx_old2new.__getitem__)(vertex_indices)
# Grab the mesh reference element and cell dimension
coord_finat_elt = fdrake_mesh.coordinates.function_space().finat_element
@@ -602,11 +614,14 @@ def import_firedrake_mesh(fdrake_mesh, cells_to_use=None,
# be flipped.
def flip_local_face_indices(faces, elements):
faces = np.copy(faces)
- to_no_one = np.logical_and(orient[elements] < 0,
- faces == no_zero_face_ndx)
- to_no_zero = np.logical_and(orient[elements] < 0,
- faces == no_one_face_ndx)
- faces[to_no_one], faces[to_no_zero] = no_one_face_ndx, no_zero_face_ndx
+ neg_elements = np.full(elements.shape, False)
+ # To handle neighbor case, we only need to flip at elements
+ # who have a neighbor, i.e. where neighbors is not a negative
+ # bitmask of bdy tags
+ neg_elements[elements >= 0] = (orient[elements[elements >= 0]] < 0)
+ no_zero = np.logical_and(neg_elements, faces == no_zero_face_ndx)
+ no_one = np.logical_and(neg_elements, faces == no_one_face_ndx)
+ faces[no_zero], faces[no_one] = no_one_face_ndx, no_zero_face_ndx
return faces
# Create new facial adjacency groups that have been flipped
@@ -616,12 +631,8 @@ def import_firedrake_mesh(fdrake_mesh, cells_to_use=None,
for ineighbor_group, fagrp in six.iteritems(fagrps):
new_element_faces = flip_local_face_indices(fagrp.element_faces,
fagrp.elements)
- if ineighbor_group is None:
- new_neighbor_faces = fagrp.neighbor_faces
- else:
- new_neighbor_faces = \
- flip_local_face_indices(fagrp.neighbor_faces,
- fagrp.neighbors)
+ new_neighbor_faces = flip_local_face_indices(fagrp.neighbor_faces,
+ fagrp.neighbors)
new_fagrp = FacialAdjacencyGroup(igroup=igroup,
ineighbor_group=ineighbor_group,
elements=fagrp.elements,
--
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