def trimesh2d(vertices,
segments=None,
holes=None,
maxArea=None,
quality=True,
dofs_per_node=1,
logFilename="tri.log",
triangleExecutablePath=None):
"""
Triangulates an area described by a number vertices (vertices) and a set
of segments that describes a closed polygon.
Parameters:
vertices array [nVertices x 2] with vertices describing the geometry.
[[v0_x, v0_y],
[ ... ],
[vn_x, vn_y]]
segments array [nSegments x 3] with segments describing the geometry.
[[s0_v0, s0_v1,marker],
[ ... ],
[sn_v0, sn_v1,marker]]
holes [Not currently used]
maxArea Maximum area for triangle. (None)
quality If true, triangles are prevented having angles < 30 degrees. (True)
dofs_per_node Number of degrees of freedom per node.
logFilename Filename for triangle output ("tri.log")
Returns:
coords Node coordinates
[[n0_x, n0_y],
[ ... ],
[nn_x, nn_y]]
edof Element topology
[[el0_dof1, ..., el0_dofn],
[ ... ],
[eln_dof1, ..., eln_dofn]]
dofs Node dofs
[[n0_dof1, ..., n0_dofn],
[ ... ],
[nn_dof1, ..., nn_dofn]]
bdofs Boundary dofs. Dictionary containing lists of dofs for
each boundary marker. Dictionary key = marker id.
"""
# Check for triangle executable
triangleExecutable = triangleExecutablePath
if triangleExecutable == None:
triangleExecutable = ""
if sys.platform == "win32":
triangleExecutable = which("triangle.exe")
else:
triangleExecutable = which("triangle")
else:
if not os.path.exists(triangleExecutable):
triangleExecutable = None
if triangleExecutable == None:
print(
"Error: Could not find triangle. Please make sure that the \ntriangle executable is available on the search path (PATH)."
)
return None, None, None, None
# Create triangle options
options = ""
if maxArea != None:
options += "-a%f " % maxArea + " "
if quality:
options += "-q"
# Set initial variables
nSegments = 0
nHoles = 0
nAttribs = 0
nBoundaryMarkers = 1
nVertices = len(vertices)
# All files are created as temporary files
if not os.path.exists("./trimesh.temp"):
os.mkdir("./trimesh.temp")
filename = "./trimesh.temp/polyfile.poly"
if not segments is None:
nSegments = len(segments)
if not holes is None:
nHoles = len(holes)
# Create a .poly file
polyFile = open(filename, "w")
polyFile.write("%d 2 %d \n" % (nVertices, nAttribs))
i = 0
for vertex in vertices:
polyFile.write("%d %g %g\n" % (i, vertex[0], vertex[1]))
i = i + 1
polyFile.write("%d %d \n" % (nSegments, nBoundaryMarkers))
i = 0
for segment in segments:
polyFile.write("%d %d %d %d\n" %
(i, segment[0], segment[1], segment[2]))
i = i + 1
polyFile.write("0\n")
polyFile.close()
# Execute triangle
os.system("%s %s %s > tri.log" % (triangleExecutable, options, filename))
# Read results from triangle
strippedName = os.path.splitext(filename)[0]
nodeFilename = "%s.1.node" % strippedName
elementFilename = "%s.1.ele" % strippedName
polyFilename = "%s.1.poly" % strippedName
# Read vertices
allVertices = None
boundaryVertices = {}
if os.path.exists(nodeFilename):
nodeFile = open(nodeFilename, "r")
nodeInfo = list(map(int, nodeFile.readline().split()))
nNodes = nodeInfo[0]
allVertices = np.zeros([nNodes, 2], 'd')
for i in range(nNodes):
vertexRow = list(map(float, nodeFile.readline().split()))
boundaryMarker = int(vertexRow[3])
if not (boundaryMarker in boundaryVertices):
boundaryVertices[boundaryMarker] = []
allVertices[i, :] = [vertexRow[1], vertexRow[2]]
boundaryVertices[boundaryMarker].append(i + 1)
nodeFile.close()
# Read elements
elements = []
if os.path.exists(elementFilename):
elementFile = open(elementFilename, "r")
elementInfo = list(map(int, elementFile.readline().split()))
nElements = elementInfo[0]
elements = np.zeros([nElements, 3], 'i')
for i in range(nElements):
elementRow = list(map(int, elementFile.readline().split()))
elements[i, :] = [
elementRow[1] + 1, elementRow[2] + 1, elementRow[3] + 1
]
elementFile.close()
# Clean up
try:
pass
#os.remove(filename)
#os.remove(nodeFilename)
#os.remove(elementFilename)
#os.remove(polyFilename)
except:
pass
# Add dofs in edof and bcVerts
dofs = cfc.createdofs(np.size(allVertices, 0), dofs_per_node)
if dofs_per_node > 1:
expandedElements = np.zeros((np.size(elements, 0), 3 * dofs_per_node),
'i')
dofs = cfc.createdofs(np.size(allVertices, 0), dofs_per_node)
elIdx = 0
for elementTopo in elements:
for i in range(3):
expandedElements[elIdx, i * dofs_per_node:(
i * dofs_per_node + dofs_per_node)] = dofs[elementTopo[i] -
1, :]
elIdx += 1
for bVertIdx in boundaryVertices.keys():
bVert = boundaryVertices[bVertIdx]
bVertNew = []
for i in range(len(bVert)):
for j in range(dofs_per_node):
bVertNew.append(dofs[bVert[i] - 1][j])
boundaryVertices[bVertIdx] = bVertNew
return allVertices, np.asarray(
expandedElements), dofs, boundaryVertices
return allVertices, elements, dofs, boundaryVertices
def trimesh2d(
vertices,
segments=None,
holes=None,
maxArea=None,
quality=True,
dofsPerNode=1,
logFilename="tri.log",
triangleExecutablePath=None,
):
"""
Triangulates an area described by a number vertices (vertices) and a set
of segments that describes a closed polygon.
Parameters:
vertices array [nVertices x 2] with vertices describing the geometry.
[[v0_x, v0_y],
[ ... ],
[vn_x, vn_y]]
segments array [nSegments x 3] with segments describing the geometry.
[[s0_v0, s0_v1,marker],
[ ... ],
[sn_v0, sn_v1,marker]]
holes [Not currently used]
maxArea Maximum area for triangle. (None)
quality If true, triangles are prevented having angles < 30 degrees. (True)
dofsPerNode Number of degrees of freedom per node.
logFilename Filename for triangle output ("tri.log")
Returns:
coords Node coordinates
[[n0_x, n0_y],
[ ... ],
[nn_x, nn_y]]
edof Element topology
[[el0_dof1, ..., el0_dofn],
[ ... ],
[eln_dof1, ..., eln_dofn]]
dofs Node dofs
[[n0_dof1, ..., n0_dofn],
[ ... ],
[nn_dof1, ..., nn_dofn]]
bdofs Boundary dofs. Dictionary containing lists of dofs for
each boundary marker. Dictionary key = marker id.
"""
# Check for triangle executable
triangleExecutable = triangleExecutablePath
if triangleExecutable == None:
triangleExecutable = ""
if sys.platform == "win32":
triangleExecutable = which("triangle.exe")
else:
triangleExecutable = which("triangle")
else:
if not os.path.exists(triangleExecutable):
triangleExecutable = None
if triangleExecutable == None:
print(
"Error: Could not find triangle. Please make sure that the \ntriangle executable is available on the search path (PATH)."
)
return None, None, None, None
# Create triangle options
options = ""
if maxArea != None:
options += "-a%f " % maxArea + " "
if quality:
options += "-q"
# Set initial variables
nSegments = 0
nHoles = 0
nAttribs = 0
nBoundaryMarkers = 1
nVertices = len(vertices)
# All files are created as temporary files
if not os.path.exists("./trimesh.temp"):
os.mkdir("./trimesh.temp")
filename = "./trimesh.temp/polyfile.poly"
if not segments is None:
nSegments = len(segments)
if not holes is None:
nHoles = len(holes)
# Create a .poly file
polyFile = open(filename, "w")
polyFile.write("%d 2 %d \n" % (nVertices, nAttribs))
i = 0
for vertex in vertices:
polyFile.write("%d %g %g\n" % (i, vertex[0], vertex[1]))
i = i + 1
polyFile.write("%d %d \n" % (nSegments, nBoundaryMarkers))
i = 0
for segment in segments:
polyFile.write("%d %d %d %d\n" % (i, segment[0], segment[1], segment[2]))
i = i + 1
polyFile.write("0\n")
polyFile.close()
# Execute triangle
os.system("%s %s %s > tri.log" % (triangleExecutable, options, filename))
# Read results from triangle
strippedName = os.path.splitext(filename)[0]
nodeFilename = "%s.1.node" % strippedName
elementFilename = "%s.1.ele" % strippedName
polyFilename = "%s.1.poly" % strippedName
# Read vertices
allVertices = None
boundaryVertices = {}
if os.path.exists(nodeFilename):
nodeFile = open(nodeFilename, "r")
nodeInfo = list(map(int, nodeFile.readline().split()))
nNodes = nodeInfo[0]
allVertices = np.zeros([nNodes, 2], "d")
for i in range(nNodes):
vertexRow = list(map(float, nodeFile.readline().split()))
boundaryMarker = int(vertexRow[3])
if not (boundaryMarker in boundaryVertices):
boundaryVertices[boundaryMarker] = []
allVertices[i, :] = [vertexRow[1], vertexRow[2]]
boundaryVertices[boundaryMarker].append(i + 1)
nodeFile.close()
# Read elements
elements = []
if os.path.exists(elementFilename):
elementFile = open(elementFilename, "r")
elementInfo = list(map(int, elementFile.readline().split()))
nElements = elementInfo[0]
elements = np.zeros([nElements, 3], "i")
for i in range(nElements):
elementRow = list(map(int, elementFile.readline().split()))
elements[i, :] = [elementRow[1] + 1, elementRow[2] + 1, elementRow[3] + 1]
elementFile.close()
# Clean up
try:
pass
# os.remove(filename)
# os.remove(nodeFilename)
# os.remove(elementFilename)
# os.remove(polyFilename)
except:
pass
# Add dofs in edof and bcVerts
dofs = cfc.createdofs(np.size(allVertices, 0), dofsPerNode)
if dofsPerNode > 1:
expandedElements = np.zeros((np.size(elements, 0), 3 * dofsPerNode), "i")
dofs = cfc.createdofs(np.size(allVertices, 0), dofsPerNode)
elIdx = 0
for elementTopo in elements:
for i in range(3):
expandedElements[elIdx, i * dofsPerNode : (i * dofsPerNode + dofsPerNode)] = dofs[elementTopo[i] - 1, :]
elIdx += 1
for bVertIdx in boundaryVertices.keys():
bVert = boundaryVertices[bVertIdx]
bVertNew = []
for i in range(len(bVert)):
for j in range(dofsPerNode):
bVertNew.append(dofs[bVert[i] - 1][j])
boundaryVertices[bVertIdx] = bVertNew
return allVertices, np.asarray(expandedElements), dofs, boundaryVertices
return allVertices, elements, dofs, boundaryVertices
def create(self, is3D=False):
'''
Meshes a surface or volume defined by the geometry in geoData.
Parameters:
is3D - Optional parameter that only needs to be set if geometry
is loaded from a geo-file, i.e. if geoData is a path string.
Default False.
Returns:
coords Node coordinates
[[n0_x, n0_y, n0_z],
[ ... ],
[nn_x, nn_y, nn_z]]
edof Element topology
[[el0_dof1, ..., el0_dofn],
[ ... ],
[eln_dof1, ..., eln_dofn]]
dofs Node dofs
[[n0_dof1, ..., n0_dofn],
[ ... ],
[nn_dof1, ..., nn_dofn]]
bdofs Boundary dofs. Dictionary containing lists of dofs for
each boundary marker. Dictionary key = marker id.
elementmarkers List of integer markers. Row i contains the marker of
element i. Markers are similar to boundary markers and
can be used to identify in which region an element lies.
boundaryElements (optional) returned if self.return_boundary_elements is true.
Contains dictionary with boundary elements. The keys are markers
and the values are lists of elements for that marker.
Running this function also creates object variables:
nodesOnCurve Dictionary containing lists of node-indices. Key is a
curve-ID and the value is a list of indices of all nodes
on that curve, including its end points.
nodesOnSurface Dictionary containing lists of node-indices. Key is a
surface-ID and the value is a list of indices of the nodes
on that surface, including its boundary.
nodesOnVolume Dictionary containing lists of node-indices. Key is a
volume-ID and the value is a list of indices of the nodes
in that volume, including its surface.
'''
#Nodes per element for different element types:
#(taken from Chapter 9, page 89 of the gmsh manual)
nodesPerElmDict = {
1: 2,
2: 3,
3: 4,
4: 4,
5: 8,
6: 6,
7: 5,
8: 3,
9: 6,
10: 9,
11: 10,
12: 27,
13: 18,
14: 14,
15: 1,
16: 8,
17: 20,
18: 15,
19: 13,
20: 9,
21: 10,
22: 12,
23: 15,
24: 15,
25: 21,
26: 4,
27: 5,
28: 6,
29: 20,
30: 35,
31: 56,
92: 64,
93: 125
}
nodesPerElement = nodesPerElmDict[self.el_type]
# Check for GMSH executable [NOTE]Mostly copied from trimesh2d(). TODO: Test on different systems
gmshExe = self.gmsh_exec_path
if gmshExe == None:
gmshExe = ""
if sys.platform == "win32":
gmshExe = which("gmsh.exe")
else:
gmshExe = which("gmsh")
else:
if not os.path.exists(gmshExe):
gmshExe = os.path.join(os.getcwd(),
self.gmsh_exec_path) #Try relative path
if not os.path.exists(gmshExe):
gmshExe = None #Relative path didnt work either
if gmshExe == None:
raise IOError(
"Error: Could not find GMSH. Please make sure that the \GMSH executable is available on the search path (PATH)."
)
# Create a temporary directory for GMSH
oldStyleTempDir = False
if self.mesh_dir != "":
tempMeshDir = self.mesh_dir
os.mkdir(tempMeshDir)
else:
tempMeshDir = tempfile.mkdtemp()
if type(
self.geometry
) is str: #If geometry data is given as a .geo file we will just pass it on to gmsh later.
geoFilePath = self.geometry
dim = 3 if is3D else 2 #In this case geoData is a path string, so the dimension must be supplied by the user.
if not os.path.exists(geoFilePath):
geoFilePath = os.path.join(os.getcwd(),
geoFilePath) #Try relative path
if not os.path.exists(geoFilePath):
raise IOError("Error: Could not find geo-file " +
geoFilePath)
else:
dim = 3 if self.geometry.is3D else 2 #Get the dimension of the model from geoData.
if oldStyleTempDir:
if not os.path.exists("./gmshMeshTemp"):
os.mkdir("./gmshMeshTemp")
geoFilePath = os.path.normpath(
os.path.join(os.getcwd(), "gmshMeshTemp/tempGeometry.geo")
) #"gmshMeshTemp/tempGeometry.geo"
else:
geoFilePath = os.path.normpath(
os.path.join(tempMeshDir, 'tempGeometry.geo'))
self.geofile = open(geoFilePath, "w") #Create temp geometry file
self._writeGeoFile() #Write geoData to file
self.geofile.close()
if oldStyleTempDir:
mshFileName = os.path.normpath(
os.path.join(os.getcwd(), 'gmshMeshTemp/meshFile.msh')
) #Filepath to the msh-file that will be generated.
else:
mshFileName = os.path.normpath(
os.path.join(tempMeshDir, 'meshFile.msh'))
#construct options string:
options = ""
options += ' -' + str(dim)
options += ' -clscale ' + str(self.el_size_factor) #scale factor
options += ' -o \"%s\"' % mshFileName
options += ' -clcurv' if self.clcurv else ''
options += ' -clmin ' + str(
self.min_size) if self.min_size is not None else ''
options += ' -clmax ' + str(
self.max_size) if self.max_size is not None else ''
options += ' -algo ' + self.meshing_algorithm if self.meshing_algorithm is not None else ''
options += ' -order 2' if self.el_type in self._2ndOrderElms else ''
options += ' -format msh22'
options += ' ' + self.additional_options
#Execute gmsh
gmshExe = os.path.normpath(gmshExe)
print("GMSH binary: " + gmshExe)
#print('""%s" "%s" %s"' % (gmshExe, geoFilePath, options))
#os.system('""%s" "%s" %s"' % (gmshExe, geoFilePath, options))
#retval = os.system(r'"%s" "%s" %s' % (gmshExe, geoFilePath, options))
output = subprocess.Popen(r'"%s" "%s" %s' %
(gmshExe, geoFilePath, options),
shell=True,
stdout=subprocess.PIPE).stdout.read()
#Read generated msh file:
#print("Opening msh file " + mshFileName)#TEMP
mshFile = open(mshFileName, 'r')
print("Mesh file : " + mshFileName)
#print("Reading msh file...")#TEMP
ln = mshFile.readline()
while (ln != '$Nodes\n'): #Read until we find the nodes
ln = mshFile.readline()
nbrNodes = int(mshFile.readline())
allNodes = np.zeros([nbrNodes, dim], 'd')
for i in range(nbrNodes):
line = list(map(float, mshFile.readline().split()))
allNodes[i, :] = line[
1:dim + 1] #Grab the coordinates (1:3 if 2D, 1:4 if 3D)
while (mshFile.readline() !=
'$Elements\n'): #Read until we find the elements
pass
nbrElements = int(mshFile.readline()
) #The nbr of elements (including marker elements).
elements = []
elementmarkers = []
bdofs = {
} #temp dictionary of sets. Key:MarkerID. Value:Set. The sets will be converted to lists.
boundaryElements = {}
#nodeOnPoint = {} #dictionary pointID : nodeNumber
self.nodesOnCurve = {} #dictionary lineID : set of [nodeNumber]
self.nodesOnSurface = {} #dictionary surfID : set of [nodeNumber]
self.nodesOnVolume = {} #dictionary volID : set of [nodeNumber]
for i in range(
nbrElements): #Read all elements (points, surfaces, etc):
line = list(map(int, mshFile.readline().split()))
eType = line[1] #second int is the element type.
nbrTags = line[2] #Third int is the nbr of tags on this element.
marker = line[3] #Fourth int (first tag) is the marker.
entityID = line[
4] #Fifth int is the ID of the geometric entity (points, curves, etc) that the element belongs to
nodes = line[3 + nbrTags:len(
line)] #The rest after tags are node indices.
if (
eType == self.el_type
): #If the element type is the kind of element we are looking for:
elements.append(
nodes) #Add the nodes of the elements to the list.
elementmarkers.append(
marker
) #Add element marker. It is used for keeping track of elements (thickness, heat-production and such)
else: #If the element is not a "real" element we store its node at marker in bdof instead:
_insertInSetDict(bdofs, marker, nodes)
# We also store the full information as 'boundary elements'
_insertBoundaryElement(boundaryElements, eType, marker, nodes)
#if eType == 15: #If point. Commmented away because points only make elements if they have non-zero markers, so nodeOnPoint is not very useful.
# nodeOnPoint[entityID-1] = nodes[0] #insert node into nodeOnPoint. (ID-1 because we want 0-based indices)
if eType in [1, 8, 26, 27, 28]: #If line
_insertInSetDict(self.nodesOnCurve, entityID - 1,
_offsetIndices(
nodes,
-1)) #insert nodes into nodesOnCurve
elif eType in [2, 3, 9, 10, 16, 20, 21, 22, 23, 24,
25]: #If surfaceelement
_insertInSetDict(self.nodesOnSurface, entityID - 1,
_offsetIndices(
nodes,
-1)) #insert nodes into nodesOnSurface
else: #if volume element.
_insertInSetDict(self.nodesOnVolume, entityID - 1,
_offsetIndices(nodes, -1))
elements = np.array(elements)
for key in bdofs.keys(): #Convert the sets of boundary nodes to lists.
bdofs[key] = list(bdofs[key])
for key in self.nodesOnCurve.keys(): #Convert set to list
self.nodesOnCurve[key] = list(self.nodesOnCurve[key])
for key in self.nodesOnSurface.keys(): #Convert set to list
self.nodesOnSurface[key] = list(self.nodesOnSurface[key])
for key in self.nodesOnVolume.keys(): #Convert set to list
self.nodesOnVolume[key] = list(self.nodesOnVolume[key])
mshFile.close()
# Remove temporary mesh directory if not explicetly specified.
if self.mesh_dir == "":
shutil.rmtree(tempMeshDir)
dofs = createdofs(np.size(allNodes, 0), self.dofs_per_node)
if self.dofs_per_node > 1: #This if-chunk copied from pycalfem_utils.py
self.topo = elements
expandedElements = np.zeros(
(np.size(elements, 0), nodesPerElement * self.dofs_per_node),
'i')
elIdx = 0
for elementTopo in elements:
for i in range(nodesPerElement):
expandedElements[elIdx, i * self.dofs_per_node:(
i * self.dofs_per_node +
self.dofs_per_node)] = dofs[elementTopo[i] - 1, :]
elIdx += 1
for keyID in bdofs.keys():
bVerts = bdofs[keyID]
bVertsNew = []
for i in range(len(bVerts)):
for j in range(self.dofs_per_node):
bVertsNew.append(dofs[bVerts[i] - 1][j])
bdofs[keyID] = bVertsNew
if self.return_boundary_elements:
return allNodes, np.asarray(
expandedElements
), dofs, bdofs, elementmarkers, boundaryElements
return allNodes, np.asarray(
expandedElements), dofs, bdofs, elementmarkers
if self.return_boundary_elements:
return allNodes, elements, dofs, bdofs, elementmarkers, boundaryElements
return allNodes, elements, dofs, bdofs, elementmarkers
def create(self, is3D=False):
"""
Meshes a surface or volume defined by the geometry in geoData.
Parameters:
is3D - Optional parameter that only needs to be set if geometry
is loaded from a geo-file, i.e. if geoData is a path string.
Default False.
Returns:
coords Node coordinates
[[n0_x, n0_y, n0_z],
[ ... ],
[nn_x, nn_y, nn_z]]
edof Element topology
[[el0_dof1, ..., el0_dofn],
[ ... ],
[eln_dof1, ..., eln_dofn]]
dofs Node dofs
[[n0_dof1, ..., n0_dofn],
[ ... ],
[nn_dof1, ..., nn_dofn]]
bdofs Boundary dofs. Dictionary containing lists of dofs for
each boundary marker. Dictionary key = marker id.
elementmarkers List of integer markers. Row i contains the marker of
element i. Markers are similar to boundary markers and
can be used to identify in which region an element lies.
Running this function also creates object variables:
nodesOnCurve Dictionary containing lists of node-indices. Key is a
curve-ID and the value is a list of indices of all nodes
on that curve, including its end points.
nodesOnSurface Dictionary containing lists of node-indices. Key is a
surface-ID and the value is a list of indices of the nodes
on that surface, including its boundary.
nodesOnVolume Dictionary containing lists of node-indices. Key is a
volume-ID and the value is a list of indices of the nodes
in that volume, including its surface.
"""
# Nodes per element for different element types:
# (taken from Chapter 9, page 89 of the gmsh manual)
nodesPerElmDict = {
1: 2,
2: 3,
3: 4,
4: 4,
5: 8,
6: 6,
7: 5,
8: 3,
9: 6,
10: 9,
11: 10,
12: 27,
13: 18,
14: 14,
15: 1,
16: 8,
17: 20,
18: 15,
19: 13,
20: 9,
21: 10,
22: 12,
23: 15,
24: 15,
25: 21,
26: 4,
27: 5,
28: 6,
29: 20,
30: 35,
31: 56,
92: 64,
93: 125,
}
nodesPerElement = nodesPerElmDict[self.elType]
# Check for GMSH executable [NOTE]Mostly copied from trimesh2d(). TODO: Test on different systems
gmshExe = self.gmshExecPath
if gmshExe == None:
gmshExe = ""
if sys.platform == "win32":
gmshExe = which("gmsh.exe")
else:
gmshExe = which("gmsh")
else:
if not os.path.exists(gmshExe):
gmshExe = os.path.join(os.getcwd(), self.gmshExecPath) # Try relative path
if not os.path.exists(gmshExe):
gmshExe = None # Relative path didnt work either
if gmshExe == None:
raise IOError(
"Error: Could not find GMSH. Please make sure that the \GMSH executable is available on the search path (PATH)."
)
if (
type(self.geometry) is str
): # If geometry data is given as a .geo file we will just pass it on to gmsh later.
geoFilePath = self.geometry
dim = (
3 if is3D else 2
) # In this case geoData is a path string, so the dimension must be supplied by the user.
if not os.path.exists(geoFilePath):
geoFilePath = os.path.join(os.getcwd(), geoFilePath) # Try relative path
if not os.path.exists(geoFilePath):
raise IOError("Error: Could not find geo-file " + geoFilePath)
else:
dim = 3 if self.geometry.is3D else 2 # Get the dimension of the model from geoData.
if not os.path.exists("./gmshMeshTemp"):
os.mkdir("./gmshMeshTemp")
geoFilePath = os.path.normpath(
os.path.join(os.getcwd(), "gmshMeshTemp/tempGeometry.geo")
) # "gmshMeshTemp/tempGeometry.geo"
self.geofile = open(geoFilePath, "w") # Create temp geometry file
self._writeGeoFile() # Write geoData to file
self.geofile.close()
mshFileName = os.path.normpath(
os.path.join(os.getcwd(), "gmshMeshTemp/meshFile.msh")
) # Filepath to the msh-file that will be generated.
# construct options string:
options = ""
options += " -" + str(dim)
options += " -clscale " + str(self.elSizeFactor) # scale factor
options += ' -o "%s"' % mshFileName
options += " -clcurv" if self.clcurv else ""
options += " -clmin " + str(self.minSize) if self.minSize is not None else ""
options += " -clmax " + str(self.maxSize) if self.maxSize is not None else ""
options += " -algo " + self.meshingAlgorithm if self.meshingAlgorithm is not None else ""
options += " -order 2" if self.elType in self._2ndOrderElms else ""
options += " " + self.additionalOptions
# Execute gmsh
gmshExe = os.path.normpath(gmshExe)
os.system('%s "%s" %s' % (gmshExe, geoFilePath, options))
# Read generated msh file:
# print("Opening msh file " + mshFileName)#TEMP
mshFile = open(mshFileName, "r")
# print("Reading msh file...")#TEMP
ln = mshFile.readline()
while ln != "$Nodes\n": # Read until we find the nodes
ln = mshFile.readline()
nbrNodes = int(mshFile.readline())
allNodes = np.zeros([nbrNodes, dim], "d")
for i in range(nbrNodes):
line = list(map(float, mshFile.readline().split()))
allNodes[i, :] = line[1 : dim + 1] # Grab the coordinates (1:3 if 2D, 1:4 if 3D)
while mshFile.readline() != "$Elements\n": # Read until we find the elements
pass
nbrElements = int(mshFile.readline()) # The nbr of elements (including marker elements).
elements = []
elementmarkers = []
bdofs = {} # temp dictionary of sets. Key:MarkerID. Value:Set. The sets will be converted to lists.
# nodeOnPoint = {} #dictionary pointID : nodeNumber
self.nodesOnCurve = {} # dictionary lineID : set of [nodeNumber]
self.nodesOnSurface = {} # dictionary surfID : set of [nodeNumber]
self.nodesOnVolume = {} # dictionary volID : set of [nodeNumber]
for i in range(nbrElements): # Read all elements (points, surfaces, etc):
line = list(map(int, mshFile.readline().split()))
eType = line[1] # second int is the element type.
nbrTags = line[2] # Third int is the nbr of tags on this element.
marker = line[3] # Fourth int (first tag) is the marker.
entityID = line[
4
] # Fifth int is the ID of the geometric entity (points, curves, etc) that the element belongs to
nodes = line[3 + nbrTags : len(line)] # The rest after tags are node indices.
if eType == self.elType: # If the element type is the kind of element we are looking for:
elements.append(nodes) # Add the nodes of the elements to the list.
elementmarkers.append(
marker
) # Add element marker. It is used for keeping track of elements (thickness, heat-production and such)
else: # If the element is not a "real" element we store its node at marker in bdof instead:
_insertInSetDict(bdofs, marker, nodes)
# if eType == 15: #If point. Commmented away because points only make elements if they have non-zero markers, so nodeOnPoint is not very useful.
# nodeOnPoint[entityID-1] = nodes[0] #insert node into nodeOnPoint. (ID-1 because we want 0-based indices)
if eType in [1, 8, 26, 27, 28]: # If line
_insertInSetDict(
self.nodesOnCurve, entityID - 1, _offsetIndices(nodes, -1)
) # insert nodes into nodesOnCurve
elif eType in [2, 3, 9, 10, 16, 20, 21, 22, 23, 24, 25]: # If surfaceelement
_insertInSetDict(
self.nodesOnSurface, entityID - 1, _offsetIndices(nodes, -1)
) # insert nodes into nodesOnSurface
else: # if volume element.
_insertInSetDict(self.nodesOnVolume, entityID - 1, _offsetIndices(nodes, -1))
elements = np.array(elements)
for key in bdofs.keys(): # Convert the sets of boundary nodes to lists.
bdofs[key] = list(bdofs[key])
for key in self.nodesOnCurve.keys(): # Convert set to list
self.nodesOnCurve[key] = list(self.nodesOnCurve[key])
for key in self.nodesOnSurface.keys(): # Convert set to list
self.nodesOnSurface[key] = list(self.nodesOnSurface[key])
for key in self.nodesOnVolume.keys(): # Convert set to list
self.nodesOnVolume[key] = list(self.nodesOnVolume[key])
# print("Closing msh file...")#TEMP
mshFile.close()
dofs = createdofs(np.size(allNodes, 0), self.dofsPerNode)
if self.dofsPerNode > 1: # This if-chunk copied from pycalfem_utils.py
self.topo = elements
expandedElements = np.zeros((np.size(elements, 0), nodesPerElement * self.dofsPerNode), "i")
elIdx = 0
for elementTopo in elements:
for i in range(nodesPerElement):
expandedElements[elIdx, i * self.dofsPerNode : (i * self.dofsPerNode + self.dofsPerNode)] = dofs[
elementTopo[i] - 1, :
]
elIdx += 1
for keyID in bdofs.keys():
bVerts = bdofs[keyID]
bVertsNew = []
for i in range(len(bVerts)):
for j in range(self.dofsPerNode):
bVertsNew.append(dofs[bVerts[i] - 1][j])
bdofs[keyID] = bVertsNew
return allNodes, np.asarray(expandedElements), dofs, bdofs, elementmarkers
return allNodes, elements, dofs, bdofs, elementmarkers