corrected small error for calculation of refinement functions; update…

…d documentation

docs/examples/bodyCenteredCubicCell2DCircle.rst

@@ -111,7 +111,7 @@ Code
                              "interInclusionRefinement": True,                     # flag to indicate active refinement of space between inclusions (inter-inclusion refinement)
                              "elementsPerCircumference": 18,                       # use 18 elements per inclusion circumference for inclusion refinement
                              "elementsBetweenInclusions": 3,                       # ensure 3 elements between close inclusions for inter-inclusion refinement
-                             "inclusionRefinementWidth": 3,                        # use a relative (to inclusion radius) refinement width of 1 for inclusion refinement
+                             "inclusionRefinementWidth": 3,                        # use a relative (to inclusion radius) refinement width of 3 for inclusion refinement
                              "transitionElements": "auto",                         # automatically calculate number of transitioning elements (elements in which tanh function jumps from h_min to h_max) for inter-inclusion refinement
                              "aspectRatio": 1.5                                    # aspect ratio for inter-inclusion refinement: ratio of refinement in inclusion distance and perpendicular directions
        }

docs/examples/faceCenteredCubicCell3DCylinder.rst

@@ -112,7 +112,7 @@ Code
                              "interInclusionRefinement": True,                     # flag to indicate active refinement of space between inclusions (inter-inclusion refinement)
                              "elementsPerCircumference": 18,                       # use 18 elements per inclusion circumference for inclusion refinement
                              "elementsBetweenInclusions": 3,                       # ensure 3 elements between close inclusions for inter-inclusion refinement
-                             "inclusionRefinementWidth": 3,                        # use a relative (to inclusion radius) refinement width of 1 for inclusion refinement
+                             "inclusionRefinementWidth": 3,                        # use a relative (to inclusion radius) refinement width of 3 for inclusion refinement
                              "transitionElements": "auto",                         # automatically calculate number of transitioning elements (elements in which tanh function jumps from h_min to h_max) for inter-inclusion refinement
                              "aspectRatio": 1.5                                    # aspect ratio for inter-inclusion refinement: ratio of refinement in inclusion distance and perpendicular directions
        }

docs/examples/helicalChain2DCircle.rst

@@ -118,7 +118,7 @@ Code
                              "interInclusionRefinement": True,                     # flag to indicate active refinement of space between inclusions (inter-inclusion refinement)
                              "elementsPerCircumference": 18,                       # use 18 elements per inclusion circumference for inclusion refinement
                              "elementsBetweenInclusions": 3,                       # ensure 3 elements between close inclusions for inter-inclusion refinement
-                             "inclusionRefinementWidth": 3,                        # use a relative (to inclusion radius) refinement width of 1 for inclusion refinement
+                             "inclusionRefinementWidth": 3,                        # use a relative (to inclusion radius) refinement width of 3 for inclusion refinement
                              "transitionElements": "auto",                         # automatically calculate number of transitioning elements (elements in which tanh function jumps from h_min to h_max) for inter-inclusion refinement
                              "aspectRatio": 1.5                                    # aspect ratio for inter-inclusion refinement: ratio of refinement in inclusion distance and perpendicular directions
        }

docs/examples/helicalChain3DSphere.rst

@@ -118,7 +118,7 @@ Code
                              "interInclusionRefinement": True,                     # flag to indicate active refinement of space between inclusions (inter-inclusion refinement)
                              "elementsPerCircumference": 18,                       # use 18 elements per inclusion circumference for inclusion refinement
                              "elementsBetweenInclusions": 3,                       # ensure 3 elements between close inclusions for inter-inclusion refinement
-                             "inclusionRefinementWidth": 3,                        # use a relative (to inclusion radius) refinement width of 1 for inclusion refinement
+                             "inclusionRefinementWidth": 3,                        # use a relative (to inclusion radius) refinement width of 3 for inclusion refinement
                              "transitionElements": "auto",                         # automatically calculate number of transitioning elements (elements in which tanh function jumps from h_min to h_max) for inter-inclusion refinement
                              "aspectRatio": 1.5                                    # aspect ratio for inter-inclusion refinement: ratio of refinement in inclusion distance and perpendicular directions
        }

docs/examples/hexagonalCell3DSphere.rst

@@ -110,7 +110,7 @@ Code
                              "interInclusionRefinement": True,                     # flag to indicate active refinement of space between inclusions (inter-inclusion refinement)
                              "elementsPerCircumference": 18,                       # use 18 elements per inclusion circumference for inclusion refinement
                              "elementsBetweenInclusions": 3,                       # ensure 3 elements between close inclusions for inter-inclusion refinement
-                             "inclusionRefinementWidth": 3,                        # use a relative (to inclusion radius) refinement width of 1 for inclusion refinement
+                             "inclusionRefinementWidth": 3,                        # use a relative (to inclusion radius) refinement width of 3 for inclusion refinement
                              "transitionElements": "auto",                         # automatically calculate number of transitioning elements (elements in which tanh function jumps from h_min to h_max) for inter-inclusion refinement
                              "aspectRatio": 1.5                                    # aspect ratio for inter-inclusion refinement: ratio of refinement in inclusion distance and perpendicular directions
        }

docs/examples/randomInclusions2DCircle.rst

@@ -110,7 +110,7 @@ Code
                              "interInclusionRefinement": True,                     # flag to indicate active refinement of space between inclusions (inter-inclusion refinement)
                              "elementsPerCircumference": 18,                       # use 18 elements per inclusion circumference for inclusion refinement
                              "elementsBetweenInclusions": 3,                       # ensure 3 elements between close inclusions for inter-inclusion refinement
-                             "inclusionRefinementWidth": 3,                        # use a relative (to inclusion radius) refinement width of 1 for inclusion refinement
+                             "inclusionRefinementWidth": 3,                        # use a relative (to inclusion radius) refinement width of 3 for inclusion refinement
                              "transitionElements": "auto",                         # automatically calculate number of transitioning elements (elements in which tanh function jumps from h_min to h_max) for inter-inclusion refinement
                              "aspectRatio": 1.5                                    # aspect ratio for inter-inclusion refinement: ratio of refinement in inclusion distance and perpendicular directions
        }

docs/examples/randomInclusions3DCylinder.rst

@@ -116,7 +116,7 @@ Code
                              "interInclusionRefinement": True,                     # flag to indicate active refinement of space between inclusions (inter-inclusion refinement)
                              "elementsPerCircumference": 18,                       # use 18 elements per inclusion circumference for inclusion refinement
                              "elementsBetweenInclusions": 3,                       # ensure 3 elements between close inclusions for inter-inclusion refinement
-                             "inclusionRefinementWidth": 3,                        # use a relative (to inclusion radius) refinement width of 1 for inclusion refinement
+                             "inclusionRefinementWidth": 3,                        # use a relative (to inclusion radius) refinement width of 3 for inclusion refinement
                              "transitionElements": "auto",                         # automatically calculate number of transitioning elements (elements in which tanh function jumps from h_min to h_max) for inter-inclusion refinement
                              "aspectRatio": 1.5                                    # aspect ratio for inter-inclusion refinement: ratio of refinement in inclusion distance and perpendicular directions
        }

docs/examples/randomInclusions3DSphere.rst

@@ -109,7 +109,7 @@ Code
                              "interInclusionRefinement": True,                     # flag to indicate active refinement of space between inclusions (inter-inclusion refinement)
                              "elementsPerCircumference": 18,                       # use 18 elements per inclusion circumference for inclusion refinement
                              "elementsBetweenInclusions": 3,                       # ensure 3 elements between close inclusions for inter-inclusion refinement
-                             "inclusionRefinementWidth": 3,                        # use a relative (to inclusion radius) refinement width of 1 for inclusion refinement
+                             "inclusionRefinementWidth": 3,                        # use a relative (to inclusion radius) refinement width of 3 for inclusion refinement
                              "transitionElements": "auto",                         # automatically calculate number of transitioning elements (elements in which tanh function jumps from h_min to h_max) for inter-inclusion refinement
                              "aspectRatio": 1.5                                    # aspect ratio for inter-inclusion refinement: ratio of refinement in inclusion distance and perpendicular directions
        }

docs/examples/simpleCubicCell3DSphere.rst

@@ -110,7 +110,7 @@ Code
                              "interInclusionRefinement": True,                     # flag to indicate active refinement of space between inclusions (inter-inclusion refinement)
                              "elementsPerCircumference": 18,                       # use 18 elements per inclusion circumference for inclusion refinement
                              "elementsBetweenInclusions": 3,                       # ensure 3 elements between close inclusions for inter-inclusion refinement
-                             "inclusionRefinementWidth": 3,                        # use a relative (to inclusion radius) refinement width of 1 for inclusion refinement
+                             "inclusionRefinementWidth": 3,                        # use a relative (to inclusion radius) refinement width of 3 for inclusion refinement
                              "transitionElements": "auto",                         # automatically calculate number of transitioning elements (elements in which tanh function jumps from h_min to h_max) for inter-inclusion refinement
                              "aspectRatio": 1.5                                    # aspect ratio for inter-inclusion refinement: ratio of refinement in inclusion distance and perpendicular directions
        }

docs/gmshModel/MeshExport/MeshExport.rst

@@ -0,0 +1,11 @@
+MeshExport
+==========
+The MeshExport provides a simple mesh conversion for FEAP.
+
+
+Class Definition
+----------------
+
+.. autoclass:: gmshModel.MeshExport.MeshExport
+   :show-inheritance:
+   :members:

docs/gmshModel/MeshExport/index.rst

@@ -0,0 +1,13 @@
+.. _api_meshExport_ref:
+
+MeshExport
+==========
+
+This module provides additional methods for mesh export formats that cannot be
+handled using meshio. At the moment, only a special export method for FEAP is
+implemented - other export formats can be added here, if required.
+
+.. toctree::
+   :maxdepth: 1
+
+   MeshExport

docs/gmshModel/index.rst

@@ -3,28 +3,29 @@
 API Reference
 =============
 
-The core functionality of GmshModel is the mesh generation for complex models 
+The core functionality of GmshModel is the mesh generation for complex models
 using Gmsh and the Gmsh-Python-API. The creation of such complex models, often
-requires methods for the geometry generation. To this end, basic geometric objects 
-and helper methods for, e.g., distance calculations are provided within the 
-``Geometry`` module of GmshModel: using boolean operations for 
-groups of basic geometric objects, complex models can be defined step by step.  
+requires methods for the geometry generation. To this end, basic geometric objects
+and helper methods for, e.g., distance calculations are provided within the
+``Geometry`` module of GmshModel: using boolean operations for
+groups of basic geometric objects, complex models can be defined step by step.
 An extension of the modules will help to broaden the range of available models.
- 
-After the geometry is defined, it has to be transferred into a Gmsh model: all 
+
+After the geometry is defined, it has to be transferred into a Gmsh model: all
 geometric objects are translated to their Gmsh representations, boolean
 operations are performed and physical groups are added to the model. Within
 the Model module of ``Model``, predefined models can be found.
 Since, so far, the focus of GmshModel was on mesh models for representative
 volume elements with multiple, randomly placed inclusions, especially those models
-are already defined in GmshModel. However, since the GenericModel defines all required 
-methods for the model generation, the basic tasks for the development of a new 
-model are the definitions of required geometric objects and their arrangement within 
+are already defined in GmshModel. However, since the GenericModel defines all required
+methods for the model generation, the basic tasks for the development of a new
+model are the definitions of required geometric objects and their arrangement within
 the model, of boolean operations and physical groups to be performed/added in Gmsh
-and of refinement information for an auomated mesh size computation. 
+and of refinement information for an auomated mesh size computation.
 
 Finally, basic GUIs for the geometry and mesh visualization are defined within
-the ``Visualization`` module.
+the ``Visualization`` module while an extension of the mesh conversion capabilities
+of meshio for simulations using FEAP is defined within the ``MeshExport`` module.
 
 
 .. toctree::
@@ -33,3 +34,4 @@ the ``Visualization`` module.
    Model/index
    Geometry/index
    Visualization/index
+   MeshExport/index

docs/index.rst

@@ -36,7 +36,7 @@ and its features: ::
 
    $ python3 -m pip install gmshModel
 
-For ``conda`` users, the installation command is straightforward, too:
+For ``conda`` users, the installation command is straightforward, too: ::
 
    $ conda install -c conda-forge gmshModel
 
@@ -97,6 +97,7 @@ and how you can use them to generate your own model:
 * :ref:`api_geometry_ref` gives information on available geometric objects
 * :ref:`api_model_ref` explains all available models
 * :ref:`api_visualization_ref` gives information on the visualization capabilities of gmshModel
+* :ref:`api_meshExport_ref` comments on additional mesh output formats (extending meshio)
 
 .. toctree::
    :hidden:

gmshModel/MeshExport/MeshExport.py

@@ -1,41 +1,40 @@
 import numpy as np
-import math
 
 def FeapExport(model):
 
 	# nodal transformation for connectivity needed for 2nd order tetrahedron
 	# -> swap last two entries
 	tet_2 = [0 , 1 , 2 , 3 , 4 , 5 , 6 , 7 , 9 , 8]
-	
+
 	# prerequisites - abbreviations for easier access
 	model = model.gmshAPI
 	mesh = model.mesh
 	meshfile = 'drve'
-	
+
 	# necessary information for writing feap mesh file
 	dim = model.getDimension()
 	print("Physical dimension:",dim)
 	meshfile = str(dim)+meshfile
-	
+
 	# get information on nodes
 	nodeTags, nodalCoord, paramCoord = mesh.getNodes(dim,-1,includeBoundary=True)
 	nodeTags,indices = np.unique(nodeTags, return_index=True)
 	nNodes = max(nodeTags)
 	print("Number of nodes:",nNodes)
-	
+
 	# sort nodes and coordinates before writing
 	nodalX = nodalCoord[0::3]
 	nodalY = nodalCoord[1::3]
 	nodalZ = nodalCoord[2::3]
 	nodalX = nodalX[indices]
 	nodalY = nodalY[indices]
 	nodalZ = nodalZ[indices]
-	
+
 	nodalCoord = np.zeros(int(nNodes*3))
 	nodalCoord[0::3] = nodalX
 	nodalCoord[1::3] = nodalY
 	nodalCoord[2::3] = nodalZ
-	
+
 	# get information on elements
 	elemTypes,elemTags,connectivity = mesh.getElements(dim,-1)
 	nElem = 0
@@ -48,11 +47,11 @@ def FeapExport(model):
 			maxNodesPerElem = int(currNodesPerElem)
 	print("Number of elements:", nElem)
 	print("Maximum number of nodes per element:",maxNodesPerElem)
-	
+
 	# get information on materials
 	phyGroup = model.getPhysicalGroups(dim)
 	numberOfMat = len(phyGroup)
-	
+
 	## build database where each element has a material
 	elem2mat = np.zeros((nElem,2),dtype=int)
 	startind = 0
@@ -65,19 +64,19 @@ def FeapExport(model):
 			elem2mat[startind:startind+len(currElemTags[0]),0] = currElemTags[0]
 			elem2mat[startind:startind+len(currElemTags[0]),1] = i+1
 			startind = startind+len(currElemTags[0])
-	
+
 	# write problem type file PROB_XXX with general definitions
 	with open('PROB_'+meshfile,'wt') as outfile:
 		outfile.writelines(str(nNodes)+' '+str(nElem)+' '+str(numberOfMat)+' '+str(dim)+' '+str(dim)+' '+str(maxNodesPerElem)+'\n')
 		outfile.writelines('! nodes, elements, material sets, mesh dimension, maximum nodal DOF (default = dim), max nodes/element')
-				
+
 	# write mesh file MESH_XXX with nodal coordinates and element connectivity for every element type
 	with open('MESH_'+meshfile,'wt') as outfile:
 		outfile.writelines('COORDinate\n')
 		for i in range(0,nNodes):
 			coordStr = np.array2string(nodalCoord[3*i:3*(i+1)],max_line_width=100000)
 			outfile.writelines(str(i+1)+' 0 '+coordStr[1:-1]+'\n')
-			
+
 		totalElemCount = 0
 		for i in range(0,len(elemTypes)):
 			currNodesPerElem = int(len(connectivity[i])/len(elemTags[i]))
@@ -87,7 +86,7 @@ def FeapExport(model):
 			print('Elements of current type:',elemsOfType)
 			outfile.writelines('\n')
 			outfile.writelines('ELEMent NODEs='+str(currNodesPerElem)+'\n')
-			
+
 			# due to limited input records in one line (=16), elements with more
     	# than 13 nodes have to be split into several rows
 			for j in range(0,elemsOfType):
@@ -103,7 +102,6 @@ def FeapExport(model):
 				outfile.writelines(connectStr13[1:-1]+'\n')
 				# writing entries 14 - x of connectivity in new lines
 				# automatic linebreak every 16th entry
-				for cLines in range(0,int(math.ceil(max(currNodesPerElem-13,0)/16))):
+				for cLines in range(0,int(np.ceil(max(currNodesPerElem-13,0)/16))):
 					connectStr14x = np.array2string(currConnectivity[13+cLines*16:min(13+(cLines+1)*16,currNodesPerElem)],max_line_width=100000)
 					outfile.writelines('    '+connectStr14x[1:-1]+'\n')
-

gmshModel/Model/GenericModel.py

@@ -287,7 +287,7 @@ def saveMesh(self,file=None):
         os.makedirs(fileDir,exist_ok=True)                                      # ensure that the file directory exists
         if fileExt == ".msh":                                                   # file extension is ".msh"
             gmsh.write(fileDir+"/"+fileName+fileExt)                            # -> save mesh using built-in gmsh.write method
-        elif fileExt == ".feap":																								# file extension is ".feap" -> write feap mesh files
+        elif fileExt == ".feap":                                                # file extension is ".feap" -> write feap mesh files
             FeapExport(self)
         else:                                                                   # file extension is different from ".msh"
             if fileExt in SUPPORTED_MESH_FORMATS:                               # -> check if file extension is supported by meshio