Exodus sizing function from python netcdf4

[js34654]

Hello,

I am new to Cubit (and Exodus) and I would like to be able to add a mesh sizing function to a Cubit generated exodus file. I was previously using the background mesh strategy in Gmsh, but have decided to move on.

Using the netCDF4 Python module, I am able to convert the file to a format I can use in my simulator. I would now like to add a sizing function back into the original exodus file.

According to this documentation, this needs to be a time-based (element or nodal) variable:
https://coreform.com/cubit_help/mesh_generation/adaptivity_and_sizing_functions/exodus2_field_function.htm

Are there any available examples for doing this? If I do a nodal array, does it just need to be the same dimension as the coordinates of the whole structure? If I do an element array, does it need to be the size of the block, or the total size of all the elements?

Regards,

Juan

[js34654]

This is what I have been able to come up with so far, but I have no insight if this format will be close to correct.
timedata.py (488 Bytes)

[gvernon]

Welcome @js34654!

You can find comprehensive Exodus documentation on Sandia’s open-source repository for their SEACAS project, which owns the Exodus format. (SEACAS stands for: "Sandia Engineering Analysis Code Access System)

If you have access to Linux or Mac, you can build the SEACAS project, which will give you access to a few useful utilities utilities to convert Exodus to & from ASCII text (exotxt / txtexo), and to/from Matlab *.mat files ( exo2mat / mat2exo ). There are also extensive APIs for C, Fortran, and Python ( exodus.py ). You may find these tools useful for understanding & creating your Exodus file.

Of course, you could also use the meshio Python module to convert into Exodus from a format that’s more familiar to you.

I’ve attached two files to this email to help get you started with Exodus:

• Geometry
  ASTM_E8-Round-1.step (10.2 KB)
• Simulation Results
  params_out.e (1.7 MB)

And here’s a script that will operate on those files to do sizing. Note that Cubit computes mesh size range by scaling the variable range to the min_size - max_size in the sizing command - small values result in smaller elements. This may seem counter-intuitive if you’ve used a stress variable as your sizing function as high positive values result in larger elements, while small numbers (large negative values if they exist) will correspond to the smallest elements. So I would recommend creating a custom scalar variable where you compute the sizing function.

reset
import step "/path/to/ASTM_E8-Round-1.step" heal
webcut volume all  with loop curve 1  
webcut volume all with loop curve 1  
webcut volume all with loop curve 4  
webcut volume all with loop curve 7  
webcut volume all  with loop curve 3  

imprint all
merge all

## Use Element Variable (Von Mises Stress) as sizing Function
#import sizing function "/path/to/params_out.e" block 1 variable "von_mises" time 1

## Use Nodal Variable (Z-Displacement) as sizing Function
import sizing function "/path/to/params_out.e" block 1 variable "disp_z" time 1

volume all sizing function type exodus min_size 1 max_size 10
mesh volume all

Sizing by Von Mises Stress

Sizing by Z-Displacement

[js34654]

Thanks for the files and links to the site. I am hoping the ncdump of params_out.e has all of the info I need. It looks like I just need to follow this format:

double vals_nod_var1(time_step, num_nodes) ;
double vals_nod_var2(time_step, num_nodes) ;
double vals_nod_var3(time_step, num_nodes) ;
char name_nod_var(num_nod_var, len_name) ;

and put the names in the name_node_var array and the values into the vals_nod_var*. And expand:

time_whole = 0, 1 ;

[js34654]

I was able to write a script to update a sizing variable, mytestvar, to the values of coordx.
test.py (558 Bytes)

@gvernon Thanks again for your help reverse engineering the format.

[js34654]

I am memorializing the numbering of the element sides here:
https://gsjaardema.github.io/seacas-docs/html/element_types.html#tet

if I need to do any sideset conversions for new elements.

[js34654]

@gvernon are the sizing function values the distance between nodes (edge length), or some other calculation?

[gvernon]

Yes, it should be approximately the edge length. Recall, however, that the values are mapped to the range of (min_size, max_size) in the command.

[js34654]

Thanks for your response. So the appropriate strategy would be for me to put the desired node sizes in the time dependent variable, and not specify min_size and max_size on the sizing function statement? Is setting a growth factor in conjunction with the sizing function available?

[gvernon]

Essentially, the time-dependent variable will store the relative sizes of the elements. Let’s say you have a 4-element 1-D mesh with the values of the sizing variable:

s = [42, 50, 88, 130]

and using the command

volume all sizing function type exodus min_size 1 max_size 10

Then the resulting element sizes would be:

element_size = [1, 1.8, 5.7, 10]

However, this may not be attainable if the geometry doesn’t permit this sizing (e.g. if the entire length of the curve is only 3 units). But this is my understanding of what the sizing function is trying to do.

[js34654]

So when I reload my .cub5 with my initial mesh, and try to remesh from the command line, it doesn’t seem to work. When I try it from the gui, it asks me about deleting the existing mesh and proceeding. Do I need to somehow delete the initial mesh before trying the sizing function?