how to set up nadamak - Githubissues

Dear Putanowr, Greetings to you. Please forgive my ignorance as I am quite new to gmesh with MATLAB. I find your gmesh nadamak, MATLAB program very extensive and I am trying to study how to set it up and run the test cases before proceeding. I have gmesh version 4.3. Please could you give me some guide on how to set it up ? I have also checked your site :https://putanowr.github.io/projects/nadamak/demos/html/demo_triangles_vs_quads.html#2, since I am interested in quadrilateral mesh but the error I get when testing a case is that "Running gmsh has failed". I believe I need to include the path to the gmesh into the program but do not know where to do it from after downloading your program. please help me as i need it to generate quadrilateral meshes for my research from gmesh and read them into MATLAB for further analysis. thank you in advance.

Hello,

Thank you for your interest in Nadamak. As you could see from the project history, this project was last active something like 5 years ago while I was still working at university. As many of such projects, it started with big ambitions, to quickly lose the steam (so to say).

You are the first person to ask me about Nadamak. I still have access to Matlab as I play with it as a hobby. At the moment I am on holidays so I cannot take a look at it right now, but what I can say is that within something like 2 weeks I will try to setup Nadamak again on my laptop and then be able to assist you more.

If you do not mind then you can tell me how urgent are your needs and in which field you are working. I cannot promise anything at the moment, but well if I can be of any help then why not - that was the idea of making Nadamak public.

Regards,

Roman

On Mon, Jul 29, 2024 at 8:51 PM austinerees @.***> wrote:

Dear Putanowr, Greetings to you. Please forgive my ignorance as I am quite new to gmesh with MATLAB. I find your gmesh nadamak, MATLAB program very extensive and I am trying to study how to set it up and run the test cases before proceeding. I have gmesh version 4.3. Please could you give me some guide on how to set it up ? I have also checked your site : https://putanowr.github.io/projects/nadamak/demos/html/demo_triangles_vs_quads.html#2, since I am interested in quadrilateral mesh but the error I get when testing a case is that "Running gmsh has failed". I believe I need to include the path to the gmesh into the program but do not know where to do it from after downloading your program. please help me as i need it to generate quadrilateral meshes for my research from gmesh and read them into MATLAB for further analysis. thank you in advance.

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Thank you so very much putanowr for your prompt response. I'm working in the field of structural mechanics for my thesis. I am trying to have a CAD model whose mesh would be generated with gmesh,parsed into Matlab and visualize the 3D shape. Although your code seem very elaborate and extensive,but I couldn't just set it up to start the test cases. I've searched for many solutions for over a month only to stumble on your work which seem to give me what I want. I am suppose to see my supervisor in few days time and need to show him what I've down. If I can understand the set up via this link :https://putanowr.github.io/projects/nadamak/demos/html/demo_triangles_vs_quads.html Was done, It would help me alot. I think issue is with how nadamak would find gmesh path included into the program. The program seem to do lot of the things I want from generating mesh to visualizing them via gmesh and through MATLAB interface. I really would love to have your assistance in directing me with the set up of that example in that link and I can sure handle things from there hopefully.

Thank you once again in anticipation.,

Well, looks I am addicted ;-).

1. I have cloned the nadamak repository:

git clone --recurse-submodules https://github.com/putanowr/nadamak.git

2. I have downloaded the binaries for GMSH, unpacked it to some folder.

ls C:\Users\Roman\Downloads\gmsh-4.13.1-Windows64\gmsh.exe

Directory: C:\Users\Roman\Downloads\gmsh-4.13.1-Windows64

Mode LastWriteTime Length Name

------ 5/24/2024 11:17 PM 87864832 gmsh.exe

3. I have configured Nadamak to find the gmsh executable by editing the file:

nadamak/src/core/setup/mp_setup_gmsh.m

I have edited the path to gmsh excutable:

If you use Linux then you have to play with lines 21 and 24 if on Windows then you have to fix line 30

I then started Matlab, changed to the nadama/src folder and run startup.m script.

It reported:

startup NADAMAK set from folder: C:\Users\Roman\work\Programming\Matlab\nadamak\src

5 I then run a single demo using the following call:

mp_run_single_demo 'LShapeGeom'

I am sorry for rush and sort of messy answer - howewer it looks the basic functionality of Nadama hasn't rotten :-) By the way I tested it with Matlab R2021b with some toolboxes - somewhere should be a list but definitely toolbox for symbolic calculations is necessary for dealing with shape functions.

This also works:

mp_run_single_demo 'triangles_vs_quads'

If you do not have access to symbolic toolbox or if you are just interested in running gmsh and then importing generated mesh to some data structure in Matlab it should be possible to "cannibalize" Nadamak. A lot of Nadamak complexity comes from the part where the shape functions are "automagically" generated. You would need just the part that calls gmsh and the part that parses generated gmsh file.

Such "cannibalization" approach is probably optimal if you do restricted scope project, just need some meshes and some computations on them, and then you can forget the whole thing. Very seldom, you will get credits for investing into code like Nadamak.

And just one more comment - Nadamak has two faces. It started and a series of ordinary matlab functions - the folder src/core. Then I started to experiment with Matlab packages and object oriented programming (I find it quite interesting in Matlab). For the start you could just stick to the low level interface presented by src/core - however, demos are written mostly with high level interface.

gmesh_triangle-quad Thank you so very much putanowr! I was able to follow your instruction and could generate the triangles_vs_quads demo and got those photo I uploaded. although the 'LShapeGeom' could not generate as it throws the "Unable to resolve the name 'mp.Mesher'.

Error in demo_LShapeGeom (line 12) mesher = mp.Mesher();

Error in run (line 91) evalin('caller', strcat(script, ';'));

Error in mp_run_single_demo (line 12) run(scriptName);" . I would like to ask, if I were to generate just quad mesh alone from my CAD model((in .stp and .stl file) via gmesh without opening mesh but through MATLAB, visualize it and store the elements ,i. e quad elements in this case for subsequent calculations, is there a simple way I could do that? I want to sincerely thank you because of this help you gave me. I really would love to use my model to generate the quad mesh as I have described. I am sorry I have disturbed your holidays. Also, if i chose to try other mesh type, is there a way to change it as well? Thank you so very much and I hope you could kindly assist me one more.

Let me write a more general comment.

First all, it is not clear to me if you need to generate surface mesh (in particular planar one) or volumetric mesh. You indicate quad elements, but then you talk about CAD model saved as STL file - which indicates triangulated surface of 3D model.

If we have 3D case and volumetric mesh then more appropriate would be to talk about hexahedra elements (hexahedron is3D equivalent of quad).

Then if we have the case of 3D volumetric mesh the next question is why do you need to use Matlab. There might be many reasons why you may need / want to use Matlab, but especially in 3D case you have to really know why.

In any case in my work I would touch Matlab at later stage. I do not know details so the step below might be not adequate but this is how I imagine the situation when I have 3D meshes to handle:

I would make sure I can generate proper 3D geometric model and save it in STL format. Very important is that in case of non-homogeneous material properties the model contains proper indication of material regions and other attributes. If in your research you just need geometry and its discretization then you can neglect things like materials and physical properties, boundary conditions, loads. If not, if you need a full set of information about your model, then this issue might be a pain in the neck.
1. I would then make sure I am able to load this STL model to GMSH and mesh it. First with tetrahedrons, then to try to generate all hex mes - which is much more difficult issue.
2. After the mesh is generated, I would make sure that all attributes attached to the geometric model can be properly transferred to the meshed model.
Only after making sure that I can handle the process of creating geometric models and meshing them with GMHS manually, I would turn to making it a batch process. Batch process in the sense that GMSH can be run from command line and feed via data files and command line parameters.

Then, if I am able to control mesh generation process, I would look how I can do it via Matlab scripts.

At this stage you may hit the wall, a hard one. Everything depends on what you need to do with your meshed models. But keep in mind that visualization of 3D meshes in Matlab with ordinary plot or plot3D, surf or mesh might not be the most convenient thing (also not most efficient if we talk about dense meshes).

At this stage there is too many unknowns about your project to give any advice, but again the most important question is why do you need to control the mesh generation process and visualization via MATLAB. There might be better alternatives.

I know, I am not helping, but ...

Thank you so very much Patanwr. Your response is very helpful. The steps you outline are actually what I am trying to follow. mesh3D The mesh I intend to create in gmesh through MATLAB or within gmesh and visualize via MATLAB would look like what I uploaded in the photo, just a surface quad mesh. with regards to step 1, I do not need any local mesh formation or special material about it. just an unstructured quad mesh from the surface from an already modeled CAD file. The CAD file will be in .stp or .stl format which I already did with rhinoceros, a 3D CAD modelling tool .The reason why I am doing everything from MATLAB is because I feel it would be easier and since I'm new to scripting in gmesh (.geo ) to create the file. Also, my supervisor asked that I use one environment for everything possibly so I chose MATLAB .I would just want to do the following:1. import or read my CAD model(in .stl or preferable .stp file format) 2. generate the unstructured quad surface mesh from the imported CAD model (with options to control the size) via gmesh through MATLAB 3. visualize the mesh of the CAD model and store each quad coordinates to a variable or possibly to a struct for further processing in MATLAB.I know its a lot but basically this is what need. If you could guide me and if Nadamak could do this I would truly be grateful. Thank you in advance

Your object looks to me as 2.5D geometry - a planar thin walled shape extruded in a normal direction.

If it is just this geometry - it may be parametric with parameters like total width or height, filet radii and wall thickness then I wouldn't bother with rhinoceros nor anything else and I would do everything in GMSH. In GMSH you can easily describe such shape via parametric script - that gives you the control over geometry. Then you can mesh it and also visualize.

Only then I would read the mesh points coordinates and topology for further processing in Matlab - though you are still very vague what do you need to do with that mesh in MATLAB.

In Nadamak it is possible to generate such geometry and mesh but IMO it is waste of time - In order to handle more complex geometries in Nadamak you have to write GMSH geometry model anyway. Please take a look at nadamak/src/core/geom/geomodels

You will find in this folder files with extension .tpl - There are nothing else as GMSH script templates. In Nadamak such template file is read, then some values and placeholders are filled from the values defined in matlab script - this way one gets correct GMSH geometry script - this script is then send to GMSH.exe for meshing and results are read back into Matlab.

So as you can see, you will not escape GMSH programming. Thus instead of starting from Nadama and its complications, I suggest starting with GMSH script. Depending on your needs and the variability of the geometry you may even not need to parameterize the script or the whole parameterization can be confined to GMSH script.

For start, define in GMSH script a simple trapezium and mesh it. Then define a trapezium with rounded corners and mesh it.

Then start to modify your script toward the geometry you have shown to me.

If you do not want to model geometry in GMSH then for the start make sure that you can read in STEP files into GMSH.

Thank you patwanwr. here is the original .stp CAD model: and I am also attaching it too. boatModel.zip I do not want any thickness or fillet, any parametric modification or any other modification. I just want it meshed into quadrilateral meshes as this : The mesh would be unstructured quad meshes. I am not familiar with scripting in gmesh but i have seen some .geo file which claims to produce meshes but they apply them to simple shapes on youtube and other places. I just would want the following :1. import this model into gmesh without opening mesh 2. mesh into quadrilateral meshes . If I can have mesh control with respect to size it would be desirable as it would help me with sensitivity analysis 3. visualize the meshed model as seen in my photo and save the coordinates. I want to use the coordinates to compute normal, areas of the meshes for further structural analysis in my research. If I can produce this for this model, then I would try for other models. Also if you could point me to resources on scripting with gmesh ,I would also be grateful. Any assistance to solving these 3 key areas holding my research would be highly appreciated. thank you in anticipation

Dear Patwanowr, thank you so very much for the assistance so far. If you could guide me with regards to the last message on how to achieve those goals, I will truly appreciate. Thank you for taking out time from your holidays to help me.

Could you offer me some assistance or give me some directions?

I have looked at GMSH Python interface. If you look at the examples in GMSH documentation and if you consult the available functions (like filleting two edges) then you will see that with Python GMSH interface you have much more robust and comprehensive solution than the one you have with Nadamak. So you can write a python script in which you can program the geometric model, then mesh, save it etc. You just switch Matlab to Python. This is definitely the way I would go (first of all because of the fillet 2D function that can free us from painfully calculating the stitching point between circular arc and segments.

I have Python on my laptop, i was able to install gmsh package and then I run one of the sample python scripts. https://gitlab.onelab.info/gmsh/gmsh/-/tree/master/tutorials/python

I know that the above is a departure from Matlab, but in my opinion this is the most flexible option. And in fact one can mix Python and Matlab by calling python code or scripts from Matlab.

Today I am not able but tomorrow I will prepare a part of your geometry to give you a proof of concep.

On Tue, Jul 30, 2024 at 10:00 PM austinerees @.***> wrote:

Could you offer me some assistance or give me some directions?

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Wow!

Wow! Thank you so very much. ! Thank you so very much.if python have flexible libraries and I could call them from MATLAB Then it would help greatly. I would be relying on the proof of concept you'd provide for me tomorrow with my geometry. Thank you once more

Hello Patwnorwr, greetings to you. any luck with the quad mesh been generated by my model?

Dear Patwnorwr, thank you so very much for your assistance so far. I am still struggling with this simple task of generating and visualizing this quad mesh for my model. I have understood Nadamak such that the starting point is from the template files which are the .tpl files. I do believe if I can generate a .tpl for my model, it should be straightforward as that is exactly what I need subsequently for similar model. Is there a way you could help me with that? here is my mesh from gmesh window and this is the .msh file :$MeshFormat 4.1 0 8 $EndMeshFormat $Entities 5 8 3 0 1 0 0 1219.432 0 2 0 -3544.005 2698.779 0 3 0 3544.005 2698.779 0 4 39057.4 0 2984.981 0 5 36226.95 0 120.0104 0 1 0 0 0 0 0 0 0 2 1 -1 2 -2.911754639002567 -3544.005 1219.432 4.225286054963624 0 2698.779 0 2 1 -2 3 0 -3544.005 2698.779 0 3544.005 2698.779 0 2 2 -3 4 -2.911754639002571 0 1219.432 4.225286054963627 3544.005 2698.779 0 2 3 -1 5 0 0 2698.779 39057.4 4241.400638555574 2984.981 0 2 3 -4 6 36226.95 0 120.0103999999999 39057.4 0 2984.981 0 2 4 -5 7 0 0 29.6543628289528 36226.95 0 1219.432 0 2 5 -1 8 0 -4241.400638555574 2698.779 39057.4 0 2984.981 0 2 2 -4 1 -2.911754639002571 -3544.005 1219.432 4.225286054963627 3544.005 2698.779 0 4 1 2 3 4 2 -2.911754639004357 0 29.6543628289528 39057.4 4241.400638555574 2984.981 0 4 5 6 7 -4 3 -2.911754639004357 -4241.400638555574 29.6543628289528 39057.4 0 2984.981 0 4 -2 -7 -6 -8 $EndEntities $Nodes 16 227 1 227 0 1 0 1 1 0 0 1219.432 0 2 0 1 2 0 -3544.005 2698.779 0 3 0 1 3 0 3544.005 2698.779 0 4 0 1 4 39057.4 0 2984.981 0 5 0 1 5 36226.95 0 120.0104 1 1 0 0 1 2 0 3 6 7 8 4.225286054963624 -1031.569112783053 1286.023256154083 2.379816724784349 -2053.625843727305 1434.861236562361 -2.911754639002568 -2992.006837284101 1849.226381184197 1 3 0 3 9 10 11 0 -1772.002500000001 2698.779 0 -4.092726157978177e-12 2698.779 0 1772.002499999998 2698.779 1 4 0 3 12 13 14 -2.911754639002571 2992.006837284101 1849.226381184197 2.379816724784342 2053.625843727306 1434.861236562362 4.225286054963627 1031.569112783053 1286.023256154083 1 5 0 19 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 1987.809942880016 3704.360745129456 2699.774891674847 3977.20593090254 3843.733544693317 2700.772609548489 5967.631765361903 3967.466855821891 2701.771174612476 7959.755906575783 4059.436327489588 2702.76486254949 9953.004093581427 4123.309918469389 2703.495635703197 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If you could help me with the generate of the .tpl file, I do believe following the numerous example that nadamak provides, I should be able to generate different quad mesh qualities for my model and similar models using the .tpl file. thank you so very much. I honestly await your response.

putanowr / nadamak

how to set up nadamak #19