Pylagrit: Error when running example "ideas_mesh"
Cocytus-kyon opened this issue · 3 comments
Cocytus-kyon commented
Deer all,
When I try to execute the example(/Lagrit/PyLaGriT/examples/ideas_mesh) with the following command
python ideas_mesh.py --dem dem0.5m.dat --exo ./
the error message is below:
...
1828 0 0.3350000E+02 0.5500000E+01 0.0000000E+00
975 0 0.7000000E+01 0.3000000E+01 0.0000000E+00
122 0 0.6050000E+02 0.0000000E+00 0.0000000E+00
ERROR: delaunay
> invalid number for element estimate: 0
> exiting with error num: 1
ERROR END: delaunay
Warning from: connect set info 0 elements
Dudding 5120 points that have no associated tetrahedra.
0.0000000E+00 0.0000000E+00 0.0000000E+00 1 0
0.5000000E+00 0.0000000E+00 0.0000000E+00 2 0
...
The mesh is complete but could not include all points.
Number of points that could not be connected: 5120
LaGriT FINISH: connect
Traceback (most recent call last):
File "ideas_mesh.py", line 106, in <module>
m2.createpts_xyz((nx,ny,1),[xx.min(),yy.min(),0.],[xx.max(),yy.max(),0],rz_switch=[1,1,1])
File "/usr/local/lib/python3.8/dist-packages/pylagrit-1.0.1-py3.8.egg/pylagrit/pylagrit.py", line 3597, in createpts_xyz
File "/usr/local/lib/python3.8/dist-packages/pylagrit-1.0.1-py3.8.egg/pylagrit/pylagrit.py", line 3585, in createpts
File "/usr/local/lib/python3.8/dist-packages/pylagrit-1.0.1-py3.8.egg/pylagrit/pylagrit.py", line 1540, in sendline
File "/usr/local/lib/python3.8/dist-packages/pylagrit-1.0.1-py3.8.egg/pylagrit/pylagrit.py", line 128, in sendline
Exception: ERROR: delaunay
It seems to be related to problem #75，What should I do with PyLagrit?
Could anyone help me to take a look at it?
thank you so much
millerta commented
Thank you for reaching out.
Unfortunately our pylagrit developers have all retired or left for other positions.
I am one of the lagrit developers and can help with lagrit issues, but not python errors.
I may need your lagrit.log (restart file) and the data to help you, but here is what I see.
The connect command is failing. Either your point distribution is not Delaunay or something
went wrong earlier in the work flow. You can check lagrit.out for a full screen report.
Note your point distribution must be convex to connect without errors.
A fully unstructured mesh can be built using volume surfaces that represent a geometry. It is necessary that these surfaces are coincident where they share a boundary. There cannot be any gaps or intersections where surfaces cross each other. The interface nodes may need refinement or buffering to ensure elements conform at the boundary.
For modeling applications that require the Delaunay criteria, this can be very difficult. The mesh elements will conform to the geometry, but the mesh quality will likely contain a poor topology and generate negative coupling coefficients. The solutions from simulations may be inaccurate. You can mitigate the impact by adjusting the mesh resolution. Generally high aspect ratio tet elements (long dimension along the external boundary) are more of a problem. This means that mesh refinement that brings the mesh closer to unit aspect ratio will help.
See some general discussion at
https://lanl.github.io/LaGriT/pages/docs/meshing.html
Here are some simple examples regarding non-convex mesh methods.
https://lanl.github.io/LaGriT/pages/docs/demos/main_connect.html
<https://lanl.github.io/LaGriT/pages/docs/meshing.html>
…________________________________
From: Cocytus-kyon ***@***.***>
Sent: Tuesday, June 14, 2022 3:24 AM
To: lanl/LaGriT
Cc: Subscribed
Subject: [EXTERNAL] [lanl/LaGriT] Pylagrit: Error when running example "ideas_mesh" (Issue #245)
Deer all,
When I try to execute the example(/Lagrit/PyLaGriT/examples/ideas_mesh) with the following command
python ideas_mesh.py<https://urldefense.com/v3/__http://ideas_mesh.py__;!!Bt8fGhp8LhKGRg!GmCsbR8oWE_nAK15A57rmTZD_Ng6sqaRbHWTjxqODRV3XhGPUgQIAMwvv45i7ynSGFUwuxjRom5eS0oGFEE48cQ8$> --dem dem0.5m.dat --exo ./
the error message is below:
...
1828 0 0.3350000E+02 0.5500000E+01 0.0000000E+00
975 0 0.7000000E+01 0.3000000E+01 0.0000000E+00
122 0 0.6050000E+02 0.0000000E+00 0.0000000E+00
ERROR: delaunay
invalid number for element estimate: 0
exiting with error num: 1
ERROR END: delaunay
Warning from: connect set info 0 elements
Dudding 5120 points that have no associated tetrahedra.
0.0000000E+00 0.0000000E+00 0.0000000E+00 1 0
0.5000000E+00 0.0000000E+00 0.0000000E+00 2 0
...
The mesh is complete but could not include all points.
Number of points that could not be connected: 5120
LaGriT FINISH: connect
Traceback (most recent call last):
File "ideas_mesh.py<https://urldefense.com/v3/__http://ideas_mesh.py__;!!Bt8fGhp8LhKGRg!GmCsbR8oWE_nAK15A57rmTZD_Ng6sqaRbHWTjxqODRV3XhGPUgQIAMwvv45i7ynSGFUwuxjRom5eS0oGFEE48cQ8$>", line 106, in <module>
m2.createpts_xyz((nx,ny,1),[xx.min(),yy.min(),0.],[xx.max(),yy.max(),0],rz_switch=[1,1,1])
File "/usr/local/lib/python3.8/dist-packages/pylagrit-1.0.1-py3.8.egg/pylagrit/pylagrit.py<https://urldefense.com/v3/__http://pylagrit.py__;!!Bt8fGhp8LhKGRg!GmCsbR8oWE_nAK15A57rmTZD_Ng6sqaRbHWTjxqODRV3XhGPUgQIAMwvv45i7ynSGFUwuxjRom5eS0oGFNLf0CP0$>", line 3597, in createpts_xyz
File "/usr/local/lib/python3.8/dist-packages/pylagrit-1.0.1-py3.8.egg/pylagrit/pylagrit.py<https://urldefense.com/v3/__http://pylagrit.py__;!!Bt8fGhp8LhKGRg!GmCsbR8oWE_nAK15A57rmTZD_Ng6sqaRbHWTjxqODRV3XhGPUgQIAMwvv45i7ynSGFUwuxjRom5eS0oGFNLf0CP0$>", line 3585, in createpts
File "/usr/local/lib/python3.8/dist-packages/pylagrit-1.0.1-py3.8.egg/pylagrit/pylagrit.py<https://urldefense.com/v3/__http://pylagrit.py__;!!Bt8fGhp8LhKGRg!GmCsbR8oWE_nAK15A57rmTZD_Ng6sqaRbHWTjxqODRV3XhGPUgQIAMwvv45i7ynSGFUwuxjRom5eS0oGFNLf0CP0$>", line 1540, in sendline
File "/usr/local/lib/python3.8/dist-packages/pylagrit-1.0.1-py3.8.egg/pylagrit/pylagrit.py<https://urldefense.com/v3/__http://pylagrit.py__;!!Bt8fGhp8LhKGRg!GmCsbR8oWE_nAK15A57rmTZD_Ng6sqaRbHWTjxqODRV3XhGPUgQIAMwvv45i7ynSGFUwuxjRom5eS0oGFNLf0CP0$>", line 128, in sendline
Exception: ERROR: delaunay
It seems to be related to problem #75<https://urldefense.com/v3/__https://github.com/lanl/LaGriT/issues/75__;!!Bt8fGhp8LhKGRg!GmCsbR8oWE_nAK15A57rmTZD_Ng6sqaRbHWTjxqODRV3XhGPUgQIAMwvv45i7ynSGFUwuxjRom5eS0oGFAooNlkR$>，What should I do with PyLagrit?
Could anyone help me to take a look at it?
thank you so much
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Cocytus-kyon commented
Thank you very much for your reply!
My 'lagrit.log' is empty and I don't know why. Input data is here.
I will try to solve the problem according to your comments.
If there is any progress, I will reply here.
Thank you again.
millerta commented
the log file might have a different name running under python.
Check files that are written, lagrit.out is the screen capture with errors.
lagrit.log is the command file that can run with lagrit < lagrit.log
It looks like you are getting points but many points are problematic.
You can run the workflow and add a lagrit "finish" command at each step,
just to make sure each of the previous commands are running as expected.
I can not look at this now, but maybe later in the week.
Remind me later if you can not locate the problem.
Good luck,
Terry
…________________________________
From: Cocytus-kyon ***@***.***>
Sent: Tuesday, June 14, 2022 8:46:02 AM
To: lanl/LaGriT
Cc: Miller, Terry Ann; Comment
Subject: [EXTERNAL] Re: [lanl/LaGriT] Pylagrit: Error when running example "ideas_mesh" (Issue #245)
Thank you very much for your reply!
My 'lagrit.log' is empty and I don't know why. Input data is here<https://urldefense.com/v3/__https://github.com/lanl/LaGriT/blob/master/PyLaGriT/examples/ideas_mesh/dem0.5m.dat__;!!Bt8fGhp8LhKGRg!Ggn4W1iYS7156Z6lBLQOtCDH9Lm2Q_Ka4krZmuJ0KRuOCbj20-SLSIS0ZmR9PFwxKzVY2I8B3fuI1iKFqtE9UwWL$>.
I will try to solve the problem according to your comments.
If there is any progress, I will reply here.
Thank you again.
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