TypeErrors - Tutorial Examples

[MostafaMohamed2023]

Hi,

My name is Mostafa Mohamed and am a graduate student at Arizona State University.
I am reporting this bug as follows: the error appears:
"TypeError: FigureBase.gca() got an unexpected keyword argument 'projection'"

Thanks in advance for any help!

Regards,
Mostafa

[kip-hart]

Hi Mostafa,

Thanks for reaching out with this bug report. I believe matplotlib updated 3D graphics since I last wrote the code. It looks like this is the particular error: https://stackoverflow.com/questions/67095247/gca-and-latest-version-of-matplotlib.

I'll take a look in the next week at fixing this. If you need to use MicroStructPy in the meantime, you could use a virtual environment with a version of matplotlib from 2020 and it should work in there.

Best,
Kip

[MostafaMohamed2023]

Thanks for your help!
I followed up scripts to modify it, and it is working now.
Could you please help me to get the output format for Abaqus where I tried to change "format = 'abaqus' " at trimesh.py, but it didn't work?

Regards,

[kip-hart]

Hi Mostafa,

I'm glad the script is working now. Sorry there's an issue with using abaqus file format. What about it didn't work? Could you post a script that produces the error?

Best,
Kip

[MostafaMohamed2023]

Hi Kip,

Thanks for your prompt response.
No change happened when I changed the format to be in the output file for Abaqus. That's what "it didn't work" means.
So, is there any way to get geometry and mesh files to work with Abaqus?

Regards,
Mostafa

[kip-hart]

Hi Mostafa,

Could you clarify whether you changed the source code for trimesh.py or you changed the input keyword argument to an instance of the class?

Showing me some of the code would help.

Best,
Kip

https://github.com/kip-hart/MicroStructPy/blob/master/src/microstructpy/meshing/trimesh.py#L262

[MostafaMohamed2023]

Hi Kip,

The main objective is to execute this example: https://docs.microstructpy.org/en/latest/examples/cli/basalt.html
So, I did it as provided, then I have started getting the output file in Abaqus output format.

I have changed the input keyword argument at trimesh.py; the Abaqus input file option, format='abaqus' in [TriMesh.write()].
From being:
def write(self, filename, format='txt', seeds=None, polymesh=None):
to be:
def write(self, filename, format='abaqus', seeds=None, polymesh=None):

But, there is no change happened.
I used the following link:
(https://docs.microstructpy.org/en/latest/api/meshing/trimesh.html#microstructpy.meshing.TriMesh.write),

Regards,
Mostafa

[kip-hart]

Hi Mostafa,

Thanks for the explanation. Please change the write function back to format='txt' in the source code. Instead, you can create abaqus inp files by adding <tri> abaqus </tri> to the filetypes settings, since the default is txt. There's an explanation for the input settings on this page: https://docs.microstructpy.org/en/latest/cli/settings.html#filetypes

Try this input file and see if it writes the trimesh to an abaqus inp file:

<?xml version="1.0" encoding="UTF-8"?>
<input>
    <material>
        <name> Plagioclase </name>
        <fraction>
            <dist_type> norm </dist_type>
            <loc> 45.2 </loc>
            <scale> 0.2 </scale>
        </fraction>
        <size>
            <dist_type> cdf </dist_type>
            <filename> aphanitic_cdf.csv </filename>
        </size>
        <color> #BDBDBD </color>
    </material>

    <material>
        <name> Olivine </name>
        <shape> ellipse </shape>
        <fraction>
            <dist_type> norm </dist_type>
            <loc> 19.1 </loc>
            <scale> 0.2 </scale>
        </fraction>
        <size>
            <dist_type> cdf </dist_type>
            <filename> olivine_cdf.csv </filename>
        </size>
        <aspect_ratio>
            <dist_type> uniform </dist_type>
            <loc> 1.0 </loc>
            <scale> 2.0 </scale>
        </aspect_ratio>
        <angle_deg>
            <dist_type> uniform </dist_type>
            <loc> -90 </loc>
            <scale> 180 </scale>
        </angle_deg>
        <color> #99BA73 </color>
    </material>

    <material>
        <name> Diopside </name>
        <fraction>
            <dist_type> norm </dist_type>
            <loc> 13.2 </loc>
            <scale> 0.2 </scale>
        </fraction>
        <size>
            <dist_type> cdf </dist_type>
            <filename> aphanitic_cdf.csv </filename>
        </size>
        <color> #709642 </color>
    </material>

    <material>
        <name> Hypersthene </name>
        <fraction>
            <dist_type> norm </dist_type>
            <loc> 16.6 </loc>
            <scale> 0.2 </scale>
        </fraction>
        <size>
            <dist_type> cdf </dist_type>
            <filename> aphanitic_cdf.csv </filename>
        </size>
        <color> #876E59 </color>
    </material>

    <material>
        <name> Magnetite </name>
        <fraction>
            <dist_type> norm </dist_type>
            <loc> 3.35 </loc>
            <scale> 0.2 </scale>
        </fraction>
        <size>
            <dist_type> cdf </dist_type>
            <filename> aphanitic_cdf.csv </filename>
        </size>
        <color> #6E6E6E </color>
    </material>

    <material>
        <name> Chromite </name>
        <fraction>
            <dist_type> norm </dist_type>
            <loc> 0.65 </loc>
            <scale> 0.2 </scale>
        </fraction>
        <size>
            <dist_type> cdf </dist_type>
            <filename> aphanitic_cdf.csv </filename>\
        </size>
        <color> #545454 </color>
    </material>

    <material>
        <name> Ilmenite </name>
        <fraction>
            <dist_type> norm </dist_type>
            <loc> 0.65 </loc>
            <scale> 0.2 </scale>
        </fraction>
        <size>
            <dist_type> cdf </dist_type>
            <filename> aphanitic_cdf.csv </filename>
        </size>
        <color> #6B6B6B </color>
    </material>

    <material>
        <name> Apatite </name>
        <fraction>
            <dist_type> norm </dist_type>
            <loc> 3.35 </loc>
            <scale> 0.2 </scale>
        </fraction>

        <size>
            <dist_type> cdf </dist_type>
            <filename> aphanitic_cdf.csv </filename>
        </size>
        <color> #ABA687 </color>
    </material>

    <domain>
        <shape> circle </shape>
        <diameter> 10 </diameter>
    </domain>

    <settings>
        <directory> basalt_circle </directory>
        <filetypes>
            <seeds_plot> png </seeds_plot>
            <poly_plot> png </poly_plot>
            <tri> abaqus </tri>   <!-- this is where trimesh output file type is specified --> 
            <tri_plot> png </tri_plot>
            <verify_plot> png </verify_plot>
        </filetypes>

        <plot_axes> False </plot_axes>
        <verbose> True </verbose>
        <verify> True </verify>

        <mesh_max_edge_length> 0.01 </mesh_max_edge_length>
        <mesh_min_angle> 20 </mesh_min_angle>
        <mesh_max_volume> 0.05 </mesh_max_volume>

        <seeds_kwargs>
            <linewidths> 0.2 </linewidths>
        </seeds_kwargs>
        <poly_kwargs>
            <linewidths> 0.2 </linewidths>
        </poly_kwargs>
        <tri_kwargs>
            <linewidths> 0.1 </linewidths>
        </tri_kwargs>
    </settings>
</input>

[MostafaMohamed2023]

Thank you for explaining everything so well.
I'm trying to run this script, but even when I run it at a small sample size, it takes a long time.
I'll let you know if I find anything new.

Regards,
Mostafa

[MostafaMohamed2023]

Hi Kip,

Sorry for confusion, but I got an Abaqus input file.

Thank you very much for your patience and consideration.

Regards,
Mostafa

[kip-hart]

Hi Mostafa,

The issue with TypeErrors has been resolved and I've updated microstructpy to v1.5.7. If you upgrade to the latest, that issue will be fixed. Feel free to reopen or submit another ticket if you have any other issues.

Best,
Kip

[MostafaMohamed2023]

Hi Kip,

We really appreciate the knowledge. Sure, I'll let you know if I have any questions.

Regards,
Mostafa