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merged the gmsh meshes (2/3D) into a single mesh, updated other files to support this

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This commit is contained in:
sm
2011-03-28 19:07:19 -06:00
parent f09a5b9da6
commit bf791deeb6
5 changed files with 70 additions and 116 deletions
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interp/grid/__init__.py
+7 -4
View File
@@ -77,6 +77,7 @@ class grid(object):
log.debug("simplex vert indicies: %s" % simplex.verts)
R = self.create_mesh(simplex.verts)
log.debug("R:\n%s", R)
log.debug('total attempts before finding simplex: %d' % attempts)
return R
@@ -92,7 +93,7 @@ class grid(object):
q = [self.q[i] for i in indicies]
return grid(p, q)
def get_simplex_and_nearest_points(self, X, extra_points = 3, simplex_size = 3):
def get_simplex_and_nearest_points(self, X, extra_points = 3):
"""
this returns two grid objects: R and S.
@@ -101,6 +102,7 @@ class grid(object):
S is S_j from baker's paper : some verts from all point that are not the
simplex
"""
simplex_size = self.dim + 1
log.debug("extra verts: %d" % extra_points)
log.debug("simplex size: %d" % simplex_size)
@@ -234,12 +236,13 @@ class cell(object):
return interp.grid.simplex.contains(X, [G.verts[i] for i in self.verts])
def __str__(self):
neighbors = [str(i.name) for i in self.neighbors]
return '<cell %s: verts: %s neighbors: [%s]>' %\
# neighbors = [str(i.name) for i in self.neighbors]
return '<cell %s: verts: %s neighbor count: %s>' %\
(
self.name,
self.verts,
", ".join(neighbors)
len(self.neighbors),
# ", ".join(neighbors)
)
__repr__ = __str__
interp/grid/delaunay.py
+1
View File
@@ -44,6 +44,7 @@ class dgrid(basegrid):
''', re.S|re.X)
def __init__(self, verts, q = None):
self.dim = len(verts[0])
basegrid.__init__(self, verts,q)
self.construct_connectivity()
interp/grid/gmsh.py
+17 -86
View File
@@ -22,27 +22,28 @@ EDGES_FOR_VOLUME_CONNECTIVITY = 3
class gmsh_grid(grid):
class ggrid(grid):
def __init__(self, filename):
def __init__(self, filename, dimension = 3):
"""
construct an interp.grid.grid-compliant grid
object out of a 2D gmsh file
object out of a {2,3}D gmsh file
"""
self.dim = dimension
log.debug("dimension: %d", self.dim)
gmsh_file = open(filename, 'r')
gmsh_file.readline() # $MeshFormat
format = gmsh_file.readline()
fmat = gmsh_file.readline()
gmsh_file.readline() # $EndMeshFormat
gmsh_file.readline() # $Nodes
node_count = int(gmsh_file.readline())
# for dim = 2, see note in next for loop
self.verts = np.empty((node_count, 2))
self.verts = np.empty((node_count, dimension))
self.q = np.empty(node_count)
for i in xrange(node_count):
@@ -53,13 +54,16 @@ class gmsh_grid(grid):
self.verts[i][0] = float(x)
self.verts[i][1] = float(y)
# for the general baker method to work, it must have 2
# components if it it a 2D mesh, so I removed:
# self.verts[i][2] = float(z)
if self.dim == 3:
self.verts[i][2] = float(z)
grid.__init__(self)
self.tree = KDTree(self.verts)
# initialize rest of structures about to be populated (cells,
# cells_for_vert)
grid.__init__(self)
gmsh_file.readline() # $EndNodes
gmsh_file.readline() # $Elements
@@ -74,7 +78,8 @@ class gmsh_grid(grid):
int(cur_line[1]),
[int(j) for j in cur_line[2:]])
if(node_type == THREE_NODE_TRIANGLE):
if (node_type == THREE_NODE_TRIANGLE and self.dim == 2) \
or (node_type == FOUR_NODE_TET and self.dim == 3):
points_for_cur_cell = [i-1 for i in rest[rest[0]+1:]]
cur_cell = cell(cur_cell_index)
@@ -85,81 +90,7 @@ class gmsh_grid(grid):
cur_cell.verts = points_for_cur_cell
self.cells[cur_cell_index] = cur_cell
edges = [tuple(sorted(i)) for i in combinations(points_for_cur_cell, EDGES_FOR_FACE_CONNECTIVITY)]
# edge is two verts
for edge in edges:
if edge in neighbors:
neighbors[edge].append(cur_cell_index)
else:
neighbors[edge] = [cur_cell_index]
for k,v in neighbors.iteritems():
if len(v) > 1:
self.cells[v[0]].add_neighbor(self.cells[v[1]])
self.cells[v[1]].add_neighbor(self.cells[v[0]])
class gmsh_grid3D(grid):
def __init__(self, filename):
"""
construct an interp.grid.grid-compliant grid
object out of a 3D gmsh file
"""
gmsh_file = open(filename, 'r')
gmsh_file.readline() # $MeshFormat
format = gmsh_file.readline()
gmsh_file.readline() # $EndMeshFormat
gmsh_file.readline() # $Nodes
node_count = int(gmsh_file.readline())
self.verts = np.empty((node_count, 3))
self.q = np.empty(node_count)
for i in xrange(node_count):
cur_line = gmsh_file.readline()
(index, x,y,z) = cur_line.split()
index = int(index) - 1
self.verts[i][0] = float(x)
self.verts[i][1] = float(y)
self.verts[i][2] = float(z)
grid.__init__(self)
self.tree = KDTree(self.verts)
gmsh_file.readline() # $EndNodes
gmsh_file.readline() # $Elements
# temporary dict used to compute cell connectivity
neighbors = {}
element_count = int(gmsh_file.readline())
for i in xrange(element_count):
cur_line = gmsh_file.readline()
cur_line = cur_line.split()
cur_cell_index, node_type, rest = (int(cur_line[0]),
int(cur_line[1]),
[int(j) for j in cur_line[2:]])
if(node_type == FOUR_NODE_TET):
points_for_cur_cell = [i-1 for i in rest[rest[0]+1:]]
cur_cell = cell(cur_cell_index)
for cur_point in points_for_cur_cell:
self.cells_for_vert[cur_point].append(cur_cell)
cur_cell.verts = points_for_cur_cell
self.cells[cur_cell_index] = cur_cell
edges = [tuple(sorted(i)) for i in combinations(points_for_cur_cell, EDGES_FOR_VOLUME_CONNECTIVITY)]
edges = [tuple(sorted(i)) for i in combinations(points_for_cur_cell, self.dim)]
for edge in edges:
if edge in neighbors: