surf2mesh tetgen error

[Taahirah Mangera]

Good Day,

I have obtained microCT scan data of 3 mice femora in the form of .stl files. I require a volumetric mesh of these in order to perform a FEA using ANSYS/Abaqus. From what I have understood, .stl files are surface meshes which can be converted to volumetric meshes using Iso2Mesh. I have written the following code to perform this (getMesh):

[F,V] = stlread('CD10.stl'); 

[V, F] = MeshRepair(V, F);

[node2,elem2,face2] = s2m(V,F,1,0.3);

%scale the nodes by the pixel size in the relevant directions

node2 = node2*diag(pixelScale);

%create the abaqus mesh, expect a warning for only having a single element

%set, a 4th col of 1's will be added to elem2

%mesh2abaqus(node2,elem2,[inpName,'.inp']);

however when I attempt to run the file I receive the following error:

>> getMesh

98873 duplicated nodes were removed

generating tetrahedral mesh from closed surfaces ...

creating volumetric mesh from a surface mesh ...

WARNING: the license for "tetgen" is non-free and does not permit commercial use.

Please use the "cgalmesh" or "cgalpoly" options where free-software is desired.

is fix volume=1 maxvol=0.300000  

Opening C:\Users\455841\AppData\Local\Temp\iso2mesh-455841\post_vmesh.poly. 

Constructing Delaunay tetrahedralization. 

  Creating initial tetrahedralization. 

  Incrementally inserting points. 

  366198 Flips (T23 217617, T32 148580, T22 0, T44 1) 

Delaunay seconds:  0.894 

Creating surface mesh. 

  Constructing mapping from indices to points. 

  Constructing mapping from points to tetrahedra. 

  Unifying segments. 

  Constructing mapping from points to subfaces. 

  Merging coplanar facets. 

  Marking acute vertices. 

  Constructing mapping from points to segments. 

  19035 acute vertices. 

Perturbing vertices. 

  0 break points. 

Delaunizing segments. 

  Constructing mapping from points to tetrahedra. 

  Queuing missing segments. 

Error:  Out of memory. 

Error using fscanf

Invalid file identifier.  Use fopen to generate a valid file identifier.

Error in readtetgen (line 27)

[dim,count] = fscanf(fp,'%d',4);

Error in surf2mesh (line 101)

[node,elem,face]=readtetgen(mwpath('post_vmesh.1'));

Error in s2m (line 25)

[node,elem,face]=surf2mesh(v,f,p0,p1,keepratio,maxvol,[],[]);

Error in getMesh (line 27)

[node2,elem2,face2] = s2m(V,F,1,0.3);

I understand the error is from tetgen. I am however using a system with 16GB RAM and do not understand the memory error. The code does not seem to generate the post_vmesh.1.node, .face and .elem files necessary for surf2mesh.

Any assistance would be greatly appreciated. 

[Qianqian Fang]

On 07/14/2014 02:21 AM, Taahirah Mangera wrote:

Good Day,

I have obtained microCT scan data of 3 mice femora in the form of .stl files. I require a volumetric mesh of these in order to perform a FEA using ANSYS/Abaqus. From what I have understood, .stl files are surface meshes which can be converted to volumetric meshes using Iso2Mesh. I have written the following code to perform this (getMesh):

...

Delaunizing segments. 

  Constructing mapping from points to tetrahedra. 

  Queuing missing segments. 

Error:  Out of memory. 

Error using fscanf

Invalid file identifier.  Use fopen to generate a valid file identifier.

...

I understand the error is from tetgen. I am however using a system with 16GB RAM and do not understand the memory error. The code does not seem to generate the post_vmesh.1.node, .face and .elem files necessary for surf2mesh.

depends on the target mesh density, you can easily fill up
16GB memory when you set the density too high. To lower
the density, increase opt (or opt.radbound) and maxvol.

Qianqian

Any assistance would be greatly appreciated. 

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