Open lalzaben opened 3 years ago
adedner
commented
3 years ago Dear Linda.
Welcome to dune-vem! Sorry that it didn't work out directly for you.
There might be an issue with the versions of the different components of dune.
Could you run pip list and post the output?
Best
Andreas
lalzaben
commented
3 years ago Hi Adedner, Thank you for the email. This is what I get:
Package Version
cycler 0.10.0 dune-alugrid 2.8.0.dev20201218 dune-common 2.8.0.dev20201218 dune-fem 2.8.0.dev20201219 dune-geometry 2.8.0.dev20201218 dune-grid 2.8.0.dev20201218 dune-istl 2.8.0.dev20201218 dune-localfunctions 2.8.0.dev20201218 dune-vem 2.8.0.dev20201219 kiwisolver 1.3.1 matplotlib 3.3.4 mpi4py 3.0.3 numpy 1.20.0 Pillow 8.1.0 pip 20.0.2 pkg-resources 0.0.0 portalocker 2.2.1 pyparsing 2.4.7 python-dateutil 2.8.1 scipy 1.6.0 setuptools 44.0.0 six 1.15.0 sortedcontainers 2.3.0 triangle 20200424 UFL 2017.1.0 wheel 0.36.2
Best regards, Linda
On Sun, Feb 14, 2021 at 10:09 PM adedner notifications@github.com wrote:
Dear Linda. Welcome to dune-vem! Sorry that it didn't work out directly for you. There might be an issue with the versions of the different components of dune. Could you run pip list and post the output? Best Andreas
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://urldefense.com/v3/__https://github.com/adedner/dune-fempy/issues/1*issuecomment-778825721__;Iw!!Nmw4Hv0!niaLT0oOCTnEzNGOmsvNE3-A-GQBcnJx1ZFuAZWCMmRKmjLTeYQleR3pZVIxkLeLbCiyDtk$, or unsubscribe https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ANHEKYTFODDM7I7FNZNX2JDS7ANXLANCNFSM4XM4S6WA__;!!Nmw4Hv0!niaLT0oOCTnEzNGOmsvNE3-A-GQBcnJx1ZFuAZWCMmRKmjLTeYQleR3pZVIxkLeLt-vFTas$ .
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adedner
commented
3 years ago Another question: that looks like you did pip install dune-vem?
If that is the case then please run
python -m dune.fem
if the active virtual env (assuming you used one). That should give you the
scripts for tutorial which are up to date. The ones here are possibly a bit outdated compared to those
version of the dune modules.
Let me just mention that the whole dune-vem and the python bindings are quite new and we are just
finalizing a release version for them. So the versions you have to use are 'cutting edge' and one could say a bit 'rough around those edges'. But the scripts you get by calling the above command should work without issues.
Best
Andreas
From: Linda ALzaben notifications@github.com Sent: 15 February 2021 05:22 To: adedner/dune-fempy dune-fempy@noreply.github.com Cc: Dedner, Andreas A.S.Dedner@warwick.ac.uk; Comment comment@noreply.github.com Subject: Re: [adedner/dune-fempy] Error while running vemdemo (#1)
Hi Adedner, Thank you for the email. This is what I get:
Package Version
cycler 0.10.0 dune-alugrid 2.8.0.dev20201218 dune-common 2.8.0.dev20201218 dune-fem 2.8.0.dev20201219 dune-geometry 2.8.0.dev20201218 dune-grid 2.8.0.dev20201218 dune-istl 2.8.0.dev20201218 dune-localfunctions 2.8.0.dev20201218 dune-vem 2.8.0.dev20201219 kiwisolver 1.3.1 matplotlib 3.3.4 mpi4py 3.0.3 numpy 1.20.0 Pillow 8.1.0 pip 20.0.2 pkg-resources 0.0.0 portalocker 2.2.1 pyparsing 2.4.7 python-dateutil 2.8.1 scipy 1.6.0 setuptools 44.0.0 six 1.15.0 sortedcontainers 2.3.0 triangle 20200424 UFL 2017.1.0 wheel 0.36.2
Best regards, Linda
On Sun, Feb 14, 2021 at 10:09 PM adedner notifications@github.com wrote:
Dear Linda. Welcome to dune-vem! Sorry that it didn't work out directly for you. There might be an issue with the versions of the different components of dune. Could you run pip list and post the output? Best Andreas
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://urldefense.com/v3/__https://github.com/adedner/dune-fempy/issues/1*issuecomment-778825721__;Iw!!Nmw4Hv0!niaLT0oOCTnEzNGOmsvNE3-A-GQBcnJx1ZFuAZWCMmRKmjLTeYQleR3pZVIxkLeLbCiyDtk$, or unsubscribe https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ANHEKYTFODDM7I7FNZNX2JDS7ANXLANCNFSM4XM4S6WA__;!!Nmw4Hv0!niaLT0oOCTnEzNGOmsvNE3-A-GQBcnJx1ZFuAZWCMmRKmjLTeYQleR3pZVIxkLeLt-vFTas$ .
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adedner
commented
3 years ago Just to confirm, I tested
pip install dune-vem matplotlib scipy
python -m dune.fem
cd fem_tutorial
python vemdemo.pyin a fresh venv worked for me. So I hope that solves your issue.
Something that is perhaps not mentioned prominently (and is now the default in the newest version that isn't yet on pypi): run export DUNE_LOG_LEVEL=info to see a bit more output.
Hope this works now
Andreas
lalzaben
commented
3 years ago Dear Andreas,
Yes I have an active virtual environment, however, when I run the vemdemo.py file from the tutorials folder and I get the below error. I hope you can help me with that.
The error: program code[0]: Adding fem.verboserank = 0 generating new seeds for voronoi grid WARNING (ignored): Could not open file 'alugrid.cfg', using default values 0 < [balance] < 1.2, partitioning method 'ALUGRID_SpaceFillingCurve(9)'.
You are using DUNE-ALUGrid, please don't forget to cite the paper: Alkaemper, Dedner, Kloefkorn, Nolte. The DUNE-ALUGrid Module, 2016.
Created parallel ALUGrid<2,2,simplex,conforming> from input stream.
Adding default: fem.dofmanager.memoryfactor: 1.1
Adding default: fem.dofmanager.clearresizedarrays: true
Adding default: fem.solver.matrix.overflowfraction: 1
method:( lagrange galerkin ) Size: 832 L^2: 0.00014533036548239515 H^1:
0.006393416088471436 236
Traceback (most recent call last):
File "vemdemo.py", line 147, in
You are using DUNE-ALUGrid, please don't forget to cite the paper: Alkaemper, Dedner, Kloefkorn, Nolte. The DUNE-ALUGrid Module, 2016.
Thank you. Best regards, Linda
On Mon, Feb 15, 2021 at 8:56 PM adedner notifications@github.com wrote:
Another question: that looks like you did
pip install dune-vem? If that is the case then please run python -m dune.fem if the active virtual env (assuming you used one). That should give you the scripts for tutorial which are up to date. The ones here are possibly a bit outdated compared to those version of the dune modules. Let me just mention that the whole dune-vem and the python bindings are quite new and we are just finalizing a release version for them. So the versions you have to use are 'cutting edge' and one could say a bit 'rough around those edges'. But the scripts you get by calling the above command should work without issues. Best Andreas
From: Linda ALzaben notifications@github.com Sent: 15 February 2021 05:22 To: adedner/dune-fempy dune-fempy@noreply.github.com Cc: Dedner, Andreas A.S.Dedner@warwick.ac.uk; Comment < comment@noreply.github.com> Subject: Re: [adedner/dune-fempy] Error while running vemdemo (#1)
Hi Adedner, Thank you for the email. This is what I get:
Package Version
cycler 0.10.0 dune-alugrid 2.8.0.dev20201218 dune-common 2.8.0.dev20201218 dune-fem 2.8.0.dev20201219 dune-geometry 2.8.0.dev20201218 dune-grid 2.8.0.dev20201218 dune-istl 2.8.0.dev20201218 dune-localfunctions 2.8.0.dev20201218 dune-vem 2.8.0.dev20201219 kiwisolver 1.3.1 matplotlib 3.3.4 mpi4py 3.0.3 numpy 1.20.0 Pillow 8.1.0 pip 20.0.2 pkg-resources 0.0.0 portalocker 2.2.1 pyparsing 2.4.7 python-dateutil 2.8.1 scipy 1.6.0 setuptools 44.0.0 six 1.15.0 sortedcontainers 2.3.0 triangle 20200424 UFL 2017.1.0 wheel 0.36.2
Best regards, Linda
On Sun, Feb 14, 2021 at 10:09 PM adedner notifications@github.com wrote:
Dear Linda. Welcome to dune-vem! Sorry that it didn't work out directly for you. There might be an issue with the versions of the different components of dune. Could you run pip list and post the output? Best Andreas
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://urldefense.com/v3/__https://github.com/adedner/dune-fempy/issues/1*issuecomment-778825721__;Iw!!Nmw4Hv0!niaLT0oOCTnEzNGOmsvNE3-A-GQBcnJx1ZFuAZWCMmRKmjLTeYQleR3pZVIxkLeLbCiyDtk$ , or unsubscribe < https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ANHEKYTFODDM7I7FNZNX2JDS7ANXLANCNFSM4XM4S6WA__;!!Nmw4Hv0!niaLT0oOCTnEzNGOmsvNE3-A-GQBcnJx1ZFuAZWCMmRKmjLTeYQleR3pZVIxkLeLt-vFTas$
.
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adedner
commented
3 years ago Hi Linda.
This one is now a bit more complicated - as you can see from the error message it is originating from numpy.
My virtual env is practically the same as yours and it is working on my machine, so we need to figure out what the differences are. One thing that I noticed is that the line number in the files bbox.py and qhul2d.py from your error message don't match the lines in my code (since they are from the same package I'm not quite sure what to mack of that). Could you please attach
/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/bbox.py and
/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py.
One thing of interest might also be your compiler and other settings. There should be a file
/home/alzabel/VirtualEnvs/Dune/.cache/dune-py/CMakeCache.txt which could give me some more information.
Best
Andreas
lalzaben
commented
3 years ago Dear Andreas,
Hope you are doing well. Did you have a chance to see why the vemdemo.py is not working and I'm getting the mentioned error?
Thank you. Appreciate your help. Best regards, Linda
On Tue, Feb 16, 2021 at 8:39 AM Linda Alzaben linda.alzaben@kaust.edu.sa wrote:
Dear Andreas,
Yes I have an active virtual environment, however, when I run the vemdemo.py file from the tutorials folder and I get the below error. I hope you can help me with that.
The error: program code[0]: Adding fem.verboserank = 0 generating new seeds for voronoi grid WARNING (ignored): Could not open file 'alugrid.cfg', using default values 0 < [balance] < 1.2, partitioning method 'ALUGRID_SpaceFillingCurve(9)'.
You are using DUNE-ALUGrid, please don't forget to cite the paper: Alkaemper, Dedner, Kloefkorn, Nolte. The DUNE-ALUGrid Module, 2016.
Created parallel ALUGrid<2,2,simplex,conforming> from input stream.
Adding default: fem.dofmanager.memoryfactor: 1.1 Adding default: fem.dofmanager.clearresizedarrays: true Adding default: fem.solver.matrix.overflowfraction: 1 method:( lagrange galerkin ) Size: 832 L^2: 0.00014533036548239515 H^1: 0.006393416088471436 236 Traceback (most recent call last): File "vemdemo.py", line 147, in
space = create.space(m[1], polyGrid, order=order, dimRange=1, storage="istl", *m[3]) File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/create.py", line 172, in creatorCall return create(args, *kwargs) File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/_vem.py", line 179, in vemSpace spc = module(field, includes, typeName, constructor, diameterMethod, File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/fem/space/init.py", line 307, in module spc = module.Space(ctorArgs) File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/bbox.py", line 12, in rotatedBBox hull_points = qhull2D(points) File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py", line 50, in qhull2D return link(dome(sample, base), dome(sample, base[::-1])) File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py", line 43, in dome return link(dome(outer, edge(h, pivot)), File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py", line 43, in dome return link(dome(outer, edge(h, pivot)), File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py", line 43, in dome return link(dome(outer, edge(h, pivot)), [Previous line repeated 981 more times] File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py", line 40, in dome outer = repeat(sample, dists>0, 0) File "<__array_function__ internals>", line 5, in repeat File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 480, in repeat return _wrapfunc(a, 'repeat', repeats, axis=axis) File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 53, in _wrapfunc bound = getattr(obj, method, None) RecursionError: maximum recursion depth exceeded while calling a Python object You are using DUNE-ALUGrid, please don't forget to cite the paper: Alkaemper, Dedner, Kloefkorn, Nolte. The DUNE-ALUGrid Module, 2016.
Thank you. Best regards, Linda
On Mon, Feb 15, 2021 at 8:56 PM adedner notifications@github.com wrote:
Another question: that looks like you did
pip install dune-vem? If that is the case then please run python -m dune.fem if the active virtual env (assuming you used one). That should give you the scripts for tutorial which are up to date. The ones here are possibly a bit outdated compared to those version of the dune modules. Let me just mention that the whole dune-vem and the python bindings are quite new and we are just finalizing a release version for them. So the versions you have to use are 'cutting edge' and one could say a bit 'rough around those edges'. But the scripts you get by calling the above command should work without issues. Best Andreas
From: Linda ALzaben notifications@github.com Sent: 15 February 2021 05:22 To: adedner/dune-fempy dune-fempy@noreply.github.com Cc: Dedner, Andreas A.S.Dedner@warwick.ac.uk; Comment < comment@noreply.github.com> Subject: Re: [adedner/dune-fempy] Error while running vemdemo (#1)
Hi Adedner, Thank you for the email. This is what I get:
Package Version
cycler 0.10.0 dune-alugrid 2.8.0.dev20201218 dune-common 2.8.0.dev20201218 dune-fem 2.8.0.dev20201219 dune-geometry 2.8.0.dev20201218 dune-grid 2.8.0.dev20201218 dune-istl 2.8.0.dev20201218 dune-localfunctions 2.8.0.dev20201218 dune-vem 2.8.0.dev20201219 kiwisolver 1.3.1 matplotlib 3.3.4 mpi4py 3.0.3 numpy 1.20.0 Pillow 8.1.0 pip 20.0.2 pkg-resources 0.0.0 portalocker 2.2.1 pyparsing 2.4.7 python-dateutil 2.8.1 scipy 1.6.0 setuptools 44.0.0 six 1.15.0 sortedcontainers 2.3.0 triangle 20200424 UFL 2017.1.0 wheel 0.36.2
Best regards, Linda
On Sun, Feb 14, 2021 at 10:09 PM adedner notifications@github.com wrote:
Dear Linda. Welcome to dune-vem! Sorry that it didn't work out directly for you. There might be an issue with the versions of the different components of dune. Could you run pip list and post the output? Best Andreas
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://urldefense.com/v3/__https://github.com/adedner/dune-fempy/issues/1*issuecomment-778825721__;Iw!!Nmw4Hv0!niaLT0oOCTnEzNGOmsvNE3-A-GQBcnJx1ZFuAZWCMmRKmjLTeYQleR3pZVIxkLeLbCiyDtk$ , or unsubscribe < https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ANHEKYTFODDM7I7FNZNX2JDS7ANXLANCNFSM4XM4S6WA__;!!Nmw4Hv0!niaLT0oOCTnEzNGOmsvNE3-A-GQBcnJx1ZFuAZWCMmRKmjLTeYQleR3pZVIxkLeLt-vFTas$
.
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This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.
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adedner
commented
3 years ago Hi Linda. Did you see my message above yours (from 7 days ago). I was waiting for a reply to that. Best Andreas
adedner
commented
3 years ago Hi. did you see my answers on the github issue? I added them directly into the issue instead of replying so I'm not sure if you saw them? Best Andreas
From: Linda ALzaben notifications@github.com Sent: 23 February 2021 15:22 To: adedner/dune-fempy dune-fempy@noreply.github.com Cc: Dedner, Andreas A.S.Dedner@warwick.ac.uk; Comment comment@noreply.github.com Subject: Re: [adedner/dune-fempy] Error while running vemdemo (#1)
Dear Andreas,
Hope you are doing well. Did you have a chance to see why the vemdemo.py is not working and I'm getting the mentioned error?
Thank you. Appreciate your help. Best regards, Linda
On Tue, Feb 16, 2021 at 8:39 AM Linda Alzaben linda.alzaben@kaust.edu.sa wrote:
Dear Andreas,
Yes I have an active virtual environment, however, when I run the vemdemo.py file from the tutorials folder and I get the below error. I hope you can help me with that.
The error: program code[0]: Adding fem.verboserank = 0 generating new seeds for voronoi grid WARNING (ignored): Could not open file 'alugrid.cfg', using default values 0 < [balance] < 1.2, partitioning method 'ALUGRID_SpaceFillingCurve(9)'.
You are using DUNE-ALUGrid, please don't forget to cite the paper: Alkaemper, Dedner, Kloefkorn, Nolte. The DUNE-ALUGrid Module, 2016.
Created parallel ALUGrid<2,2,simplex,conforming> from input stream.
Adding default: fem.dofmanager.memoryfactor: 1.1 Adding default: fem.dofmanager.clearresizedarrays: true Adding default: fem.solver.matrix.overflowfraction: 1 method:( lagrange galerkin ) Size: 832 L^2: 0.00014533036548239515 H^1: 0.006393416088471436 236 Traceback (most recent call last): File "vemdemo.py", line 147, in
space = create.space(m[1], polyGrid, order=order, dimRange=1, storage="istl", *m[3]) File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/create.py", line 172, in creatorCall return create(args, *kwargs) File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/_vem.py", line 179, in vemSpace spc = module(field, includes, typeName, constructor, diameterMethod, File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/fem/space/init.py", line 307, in module spc = module.Space(ctorArgs) File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/bbox.py", line 12, in rotatedBBox hull_points = qhull2D(points) File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py", line 50, in qhull2D return link(dome(sample, base), dome(sample, base[::-1])) File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py", line 43, in dome return link(dome(outer, edge(h, pivot)), File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py", line 43, in dome return link(dome(outer, edge(h, pivot)), File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py", line 43, in dome return link(dome(outer, edge(h, pivot)), [Previous line repeated 981 more times] File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py", line 40, in dome outer = repeat(sample, dists>0, 0) File "<__array_function__ internals>", line 5, in repeat File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 480, in repeat return _wrapfunc(a, 'repeat', repeats, axis=axis) File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 53, in _wrapfunc bound = getattr(obj, method, None) RecursionError: maximum recursion depth exceeded while calling a Python object You are using DUNE-ALUGrid, please don't forget to cite the paper: Alkaemper, Dedner, Kloefkorn, Nolte. The DUNE-ALUGrid Module, 2016.
Thank you. Best regards, Linda
On Mon, Feb 15, 2021 at 8:56 PM adedner notifications@github.com wrote:
Another question: that looks like you did
pip install dune-vem? If that is the case then please run python -m dune.fem if the active virtual env (assuming you used one). That should give you the scripts for tutorial which are up to date. The ones here are possibly a bit outdated compared to those version of the dune modules. Let me just mention that the whole dune-vem and the python bindings are quite new and we are just finalizing a release version for them. So the versions you have to use are 'cutting edge' and one could say a bit 'rough around those edges'. But the scripts you get by calling the above command should work without issues. Best Andreas
From: Linda ALzaben notifications@github.com Sent: 15 February 2021 05:22 To: adedner/dune-fempy dune-fempy@noreply.github.com Cc: Dedner, Andreas A.S.Dedner@warwick.ac.uk; Comment < comment@noreply.github.com> Subject: Re: [adedner/dune-fempy] Error while running vemdemo (#1)
Hi Adedner, Thank you for the email. This is what I get:
Package Version
cycler 0.10.0 dune-alugrid 2.8.0.dev20201218 dune-common 2.8.0.dev20201218 dune-fem 2.8.0.dev20201219 dune-geometry 2.8.0.dev20201218 dune-grid 2.8.0.dev20201218 dune-istl 2.8.0.dev20201218 dune-localfunctions 2.8.0.dev20201218 dune-vem 2.8.0.dev20201219 kiwisolver 1.3.1 matplotlib 3.3.4 mpi4py 3.0.3 numpy 1.20.0 Pillow 8.1.0 pip 20.0.2 pkg-resources 0.0.0 portalocker 2.2.1 pyparsing 2.4.7 python-dateutil 2.8.1 scipy 1.6.0 setuptools 44.0.0 six 1.15.0 sortedcontainers 2.3.0 triangle 20200424 UFL 2017.1.0 wheel 0.36.2
Best regards, Linda
On Sun, Feb 14, 2021 at 10:09 PM adedner notifications@github.com wrote:
Dear Linda. Welcome to dune-vem! Sorry that it didn't work out directly for you. There might be an issue with the versions of the different components of dune. Could you run pip list and post the output? Best Andreas
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lalzaben
commented
3 years ago Dear Adedner,
I have installed everything from scratch again, but I still get the below error, do you have any suggestions on that?
Thank you. (/ibex/scratch/omairyrm/linda/env) -bash-4.2$ vim vemdemo.py (/ibex/scratch/omairyrm/linda/env) -bash-4.2$ python vemdemo.py sys.version, sys.version_info, sys.prefix, sys.platform, sys.path, sys.exec_prefix, sys.base_prefix 3.7.10 | packaged by conda-forge | (default, Feb 19 2021, 16:07:37) [GCC 9.3.0] sys.version_info(major=3, minor=7, micro=10, releaselevel='final', serial=0) /ibex/scratch/omairyrm/linda/env linux ['/ibex/scratch/omairyrm/linda/fem_tutorial', '/ibex/scratch/omairyrm/linda/env/lib/python37.zip', '/ibex/scratch/omairyrm/linda/env/lib/python3.7', '/ibex/scratch/omairyrm/linda/env/lib/python3.7/lib-dynload', '/ibex/scratch/omairyrm/linda/env/lib/python3.7/site-packages'] /ibex/scratch/omairyrm/linda/env /ibex/scratch/omairyrm/linda/env program code[0]: Adding fem.verboserank = 0 WARNING (ignored): Could not open file 'alugrid.cfg', using default values 0 < [balance] < 1.2, partitioning method 'ALUGRID_SpaceFillingCurve(9)'.
You are using DUNE-ALUGrid, please don't forget to cite the paper: Alkaemper, Dedner, Kloefkorn, Nolte. The DUNE-ALUGrid Module, 2016.
Created parallel ALUGrid<2,2,simplex,conforming> from input stream.
setting up space
Adding default: fem.dofmanager.memoryfactor: 1.1
Adding default: fem.dofmanager.clearresizedarrays: true
Traceback (most recent call last):
File "vemdemo.py", line 104, in
You are using DUNE-ALUGrid, please don't forget to cite the paper: Alkaemper, Dedner, Kloefkorn, Nolte. The DUNE-ALUGrid Module, 2016. Best regards, Linda
On Wed, Feb 24, 2021 at 2:22 AM adedner @.***> wrote:
Hi. did you see my answers on the github issue? I added them directly into the issue instead of replying so I'm not sure if you saw them? Best Andreas
From: Linda ALzaben @.> Sent: 23 February 2021 15:22 To: adedner/dune-fempy @.> Cc: Dedner, Andreas @.>; Comment < @.> Subject: Re: [adedner/dune-fempy] Error while running vemdemo (#1)
Dear Andreas,
Hope you are doing well. Did you have a chance to see why the vemdemo.py is not working and I'm getting the mentioned error?
Thank you. Appreciate your help. Best regards, Linda
On Tue, Feb 16, 2021 at 8:39 AM Linda Alzaben @.***> wrote:
Dear Andreas,
Yes I have an active virtual environment, however, when I run the vemdemo.py file from the tutorials folder and I get the below error. I hope you can help me with that.
The error: program code[0]: Adding fem.verboserank = 0 generating new seeds for voronoi grid WARNING (ignored): Could not open file 'alugrid.cfg', using default values 0 < [balance] < 1.2, partitioning method 'ALUGRID_SpaceFillingCurve(9)'.
You are using DUNE-ALUGrid, please don't forget to cite the paper: Alkaemper, Dedner, Kloefkorn, Nolte. The DUNE-ALUGrid Module, 2016.
Created parallel ALUGrid<2,2,simplex,conforming> from input stream.
Adding default: fem.dofmanager.memoryfactor: 1.1 Adding default: fem.dofmanager.clearresizedarrays: true Adding default: fem.solver.matrix.overflowfraction: 1 method:( lagrange galerkin ) Size: 832 L^2: 0.00014533036548239515 H^1: 0.006393416088471436 236 Traceback (most recent call last): File "vemdemo.py", line 147, in
space = create.space(m[1], polyGrid, order=order, dimRange=1, storage="istl", **m[3]) File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/create.py", line 172, in creatorCall return create(*args, **kwargs) File
"/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/_vem.py", line 179, in vemSpace spc = module(field, includes, typeName, constructor, diameterMethod, File
"/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/fem/space/init.py", line 307, in module spc = module.Space(*ctorArgs) File
"/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/bbox.py", line 12, in rotatedBBox hull_points = qhull2D(points) File
"/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py", line 50, in qhull2D return link(dome(sample, base), dome(sample, base[::-1])) File
"/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py", line 43, in dome return link(dome(outer, edge(h, pivot)), File
"/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py", line 43, in dome return link(dome(outer, edge(h, pivot)), File
"/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py", line 43, in dome return link(dome(outer, edge(h, pivot)), [Previous line repeated 981 more times] File
"/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py", line 40, in dome outer = repeat(sample, dists>0, 0) File "<__array_function__ internals>", line 5, in repeat File
"/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 480, in repeat return _wrapfunc(a, 'repeat', repeats, axis=axis) File
"/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 53, in _wrapfunc bound = getattr(obj, method, None) RecursionError: maximum recursion depth exceeded while calling a Python object
You are using DUNE-ALUGrid, please don't forget to cite the paper: Alkaemper, Dedner, Kloefkorn, Nolte. The DUNE-ALUGrid Module, 2016.
Thank you. Best regards, Linda
On Mon, Feb 15, 2021 at 8:56 PM adedner @.***> wrote:
Another question: that looks like you did
pip install dune-vem? If that is the case then please run python -m dune.fem if the active virtual env (assuming you used one). That should give you the scripts for tutorial which are up to date. The ones here are possibly a bit outdated compared to those version of the dune modules. Let me just mention that the whole dune-vem and the python bindings are quite new and we are just finalizing a release version for them. So the versions you have to use are 'cutting edge' and one could say a bit 'rough around those edges'. But the scripts you get by calling the above command should work without issues. Best Andreas
From: Linda ALzaben @.> Sent: 15 February 2021 05:22 To: adedner/dune-fempy @.> Cc: Dedner, Andreas @.>; Comment < @.> Subject: Re: [adedner/dune-fempy] Error while running vemdemo (#1)
Hi Adedner, Thank you for the email. This is what I get:
Package Version
cycler 0.10.0 dune-alugrid 2.8.0.dev20201218 dune-common 2.8.0.dev20201218 dune-fem 2.8.0.dev20201219 dune-geometry 2.8.0.dev20201218 dune-grid 2.8.0.dev20201218 dune-istl 2.8.0.dev20201218 dune-localfunctions 2.8.0.dev20201218 dune-vem 2.8.0.dev20201219 kiwisolver 1.3.1 matplotlib 3.3.4 mpi4py 3.0.3 numpy 1.20.0 Pillow 8.1.0 pip 20.0.2 pkg-resources 0.0.0 portalocker 2.2.1 pyparsing 2.4.7 python-dateutil 2.8.1 scipy 1.6.0 setuptools 44.0.0 six 1.15.0 sortedcontainers 2.3.0 triangle 20200424 UFL 2017.1.0 wheel 0.36.2
Best regards, Linda
On Sun, Feb 14, 2021 at 10:09 PM adedner @.***> wrote:
Dear Linda. Welcome to dune-vem! Sorry that it didn't work out directly for you. There might be an issue with the versions of the different components of dune. Could you run pip list and post the output? Best Andreas
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <
, or unsubscribe <
.
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adedner
commented
3 years ago Hi Linda. This might be an issue with certain cases with some choices for seeds to build the voronoi grid. Since they are random it is difficult to reproduce and thus to be sure. Could you try editing the file (dune-env is the folder for your virtual env): dune-env/lib/python3.8/site-packages/dune/vem/qhull_2d.py line 38 is outer = repeat(sample, dists>0, 0) and perhaps changing that to outer = repeat(sample, dists>1e-16, 0) should fix the problem. I hope it is clear what you need to do if not I can upload a package with the change for you to download. Let me know if this helps Andreas
From: Linda ALzaben @.> Sent: 31 March 2021 07:48 To: adedner/dune-fempy @.> Cc: Dedner, Andreas @.>; Comment @.> Subject: Re: [adedner/dune-fempy] Error while running vemdemo (#1)
Dear Adedner,
I have installed everything from scratch again, but I still get the below error, do you have any suggestions on that?
Thank you. (/ibex/scratch/omairyrm/linda/env) -bash-4.2$ vim vemdemo.py (/ibex/scratch/omairyrm/linda/env) -bash-4.2$ python vemdemo.py sys.version, sys.version_info, sys.prefix, sys.platform, sys.path, sys.exec_prefix, sys.base_prefix 3.7.10 | packaged by conda-forge | (default, Feb 19 2021, 16:07:37) [GCC 9.3.0] sys.version_info(major=3, minor=7, micro=10, releaselevel='final', serial=0) /ibex/scratch/omairyrm/linda/env linux ['/ibex/scratch/omairyrm/linda/fem_tutorial', '/ibex/scratch/omairyrm/linda/env/lib/python37.zip', '/ibex/scratch/omairyrm/linda/env/lib/python3.7', '/ibex/scratch/omairyrm/linda/env/lib/python3.7/lib-dynload', '/ibex/scratch/omairyrm/linda/env/lib/python3.7/site-packages'] /ibex/scratch/omairyrm/linda/env /ibex/scratch/omairyrm/linda/env program code[0]: Adding fem.verboserank = 0 WARNING (ignored): Could not open file 'alugrid.cfg', using default values 0 < [balance] < 1.2, partitioning method 'ALUGRID_SpaceFillingCurve(9)'.
You are using DUNE-ALUGrid, please don't forget to cite the paper: Alkaemper, Dedner, Kloefkorn, Nolte. The DUNE-ALUGrid Module, 2016.
Created parallel ALUGrid<2,2,simplex,conforming> from input stream.
setting up space
Adding default: fem.dofmanager.memoryfactor: 1.1
Adding default: fem.dofmanager.clearresizedarrays: true
Traceback (most recent call last):
File "vemdemo.py", line 104, in
You are using DUNE-ALUGrid, please don't forget to cite the paper: Alkaemper, Dedner, Kloefkorn, Nolte. The DUNE-ALUGrid Module, 2016. Best regards, Linda
On Wed, Feb 24, 2021 at 2:22 AM adedner @.***> wrote:
Hi. did you see my answers on the github issue? I added them directly into the issue instead of replying so I'm not sure if you saw them? Best Andreas
From: Linda ALzaben @.> Sent: 23 February 2021 15:22 To: adedner/dune-fempy @.> Cc: Dedner, Andreas @.>; Comment < @.> Subject: Re: [adedner/dune-fempy] Error while running vemdemo (#1)
Dear Andreas,
Hope you are doing well. Did you have a chance to see why the vemdemo.py is not working and I'm getting the mentioned error?
Thank you. Appreciate your help. Best regards, Linda
On Tue, Feb 16, 2021 at 8:39 AM Linda Alzaben @.***> wrote:
Dear Andreas,
Yes I have an active virtual environment, however, when I run the vemdemo.py file from the tutorials folder and I get the below error. I hope you can help me with that.
The error: program code[0]: Adding fem.verboserank = 0 generating new seeds for voronoi grid WARNING (ignored): Could not open file 'alugrid.cfg', using default values 0 < [balance] < 1.2, partitioning method 'ALUGRID_SpaceFillingCurve(9)'.
You are using DUNE-ALUGrid, please don't forget to cite the paper: Alkaemper, Dedner, Kloefkorn, Nolte. The DUNE-ALUGrid Module, 2016.
Created parallel ALUGrid<2,2,simplex,conforming> from input stream.
Adding default: fem.dofmanager.memoryfactor: 1.1 Adding default: fem.dofmanager.clearresizedarrays: true Adding default: fem.solver.matrix.overflowfraction: 1 method:( lagrange galerkin ) Size: 832 L^2: 0.00014533036548239515 H^1: 0.006393416088471436 236 Traceback (most recent call last): File "vemdemo.py", line 147, in
space = create.space(m[1], polyGrid, order=order, dimRange=1, storage="istl", **m[3]) File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/create.py", line 172, in creatorCall return create(*args, **kwargs) File
"/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/_vem.py", line 179, in vemSpace spc = module(field, includes, typeName, constructor, diameterMethod, File
"/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/fem/space/init.py", line 307, in module spc = module.Space(*ctorArgs) File
"/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/bbox.py", line 12, in rotatedBBox hull_points = qhull2D(points) File
"/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py", line 50, in qhull2D return link(dome(sample, base), dome(sample, base[::-1])) File
"/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py", line 43, in dome return link(dome(outer, edge(h, pivot)), File
"/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py", line 43, in dome return link(dome(outer, edge(h, pivot)), File
"/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py", line 43, in dome return link(dome(outer, edge(h, pivot)), [Previous line repeated 981 more times] File
"/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py", line 40, in dome outer = repeat(sample, dists>0, 0) File "<__array_function__ internals>", line 5, in repeat File
"/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 480, in repeat return _wrapfunc(a, 'repeat', repeats, axis=axis) File
"/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 53, in _wrapfunc bound = getattr(obj, method, None) RecursionError: maximum recursion depth exceeded while calling a Python object
You are using DUNE-ALUGrid, please don't forget to cite the paper: Alkaemper, Dedner, Kloefkorn, Nolte. The DUNE-ALUGrid Module, 2016.
Thank you. Best regards, Linda
On Mon, Feb 15, 2021 at 8:56 PM adedner @.***> wrote:
Another question: that looks like you did
pip install dune-vem? If that is the case then please run python -m dune.fem if the active virtual env (assuming you used one). That should give you the scripts for tutorial which are up to date. The ones here are possibly a bit outdated compared to those version of the dune modules. Let me just mention that the whole dune-vem and the python bindings are quite new and we are just finalizing a release version for them. So the versions you have to use are 'cutting edge' and one could say a bit 'rough around those edges'. But the scripts you get by calling the above command should work without issues. Best Andreas
From: Linda ALzaben @.> Sent: 15 February 2021 05:22 To: adedner/dune-fempy @.> Cc: Dedner, Andreas @.>; Comment < @.> Subject: Re: [adedner/dune-fempy] Error while running vemdemo (#1)
Hi Adedner, Thank you for the email. This is what I get:
Package Version
cycler 0.10.0 dune-alugrid 2.8.0.dev20201218 dune-common 2.8.0.dev20201218 dune-fem 2.8.0.dev20201219 dune-geometry 2.8.0.dev20201218 dune-grid 2.8.0.dev20201218 dune-istl 2.8.0.dev20201218 dune-localfunctions 2.8.0.dev20201218 dune-vem 2.8.0.dev20201219 kiwisolver 1.3.1 matplotlib 3.3.4 mpi4py 3.0.3 numpy 1.20.0 Pillow 8.1.0 pip 20.0.2 pkg-resources 0.0.0 portalocker 2.2.1 pyparsing 2.4.7 python-dateutil 2.8.1 scipy 1.6.0 setuptools 44.0.0 six 1.15.0 sortedcontainers 2.3.0 triangle 20200424 UFL 2017.1.0 wheel 0.36.2
Best regards, Linda
On Sun, Feb 14, 2021 at 10:09 PM adedner @.***> wrote:
Dear Linda. Welcome to dune-vem! Sorry that it didn't work out directly for you. There might be an issue with the versions of the different components of dune. Could you run pip list and post the output? Best Andreas
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <
, or unsubscribe <
.
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This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.
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lalzaben
commented
3 years ago Dear Andreas, Would like to thank you for your help. I had to install Ubuntu 20 and now things are working fine.
Appreciate your help. Best regards, Linda
Sent from my iPhone
On 24 Feb 2021, at 02:22, adedner @.***> wrote:
Hi. did you see my answers on the github issue? I added them directly into the issue instead of replying so I'm not sure if you saw them? Best Andreas
From: Linda ALzaben @.> Sent: 23 February 2021 15:22 To: adedner/dune-fempy @.> Cc: Dedner, Andreas @.>; Comment @.> Subject: Re: [adedner/dune-fempy] Error while running vemdemo (#1)
Dear Andreas,
Hope you are doing well. Did you have a chance to see why the vemdemo.py is not working and I'm getting the mentioned error?
Thank you. Appreciate your help. Best regards, Linda
On Tue, Feb 16, 2021 at 8:39 AM Linda Alzaben @.***> wrote:
Dear Andreas,
Yes I have an active virtual environment, however, when I run the vemdemo.py file from the tutorials folder and I get the below error. I hope you can help me with that.
The error: program code[0]: Adding fem.verboserank = 0 generating new seeds for voronoi grid WARNING (ignored): Could not open file 'alugrid.cfg', using default values 0 < [balance] < 1.2, partitioning method 'ALUGRID_SpaceFillingCurve(9)'.
You are using DUNE-ALUGrid, please don't forget to cite the paper: Alkaemper, Dedner, Kloefkorn, Nolte. The DUNE-ALUGrid Module, 2016.
Created parallel ALUGrid<2,2,simplex,conforming> from input stream.
Adding default: fem.dofmanager.memoryfactor: 1.1 Adding default: fem.dofmanager.clearresizedarrays: true Adding default: fem.solver.matrix.overflowfraction: 1 method:( lagrange galerkin ) Size: 832 L^2: 0.00014533036548239515 H^1: 0.006393416088471436 236 Traceback (most recent call last): File "vemdemo.py", line 147, in
space = create.space(m[1], polyGrid, order=order, dimRange=1, storage="istl", *m[3]) File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/create.py", line 172, in creatorCall return create(args, *kwargs) File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/_vem.py", line 179, in vemSpace spc = module(field, includes, typeName, constructor, diameterMethod, File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/fem/space/init.py", line 307, in module spc = module.Space(ctorArgs) File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/bbox.py", line 12, in rotatedBBox hull_points = qhull2D(points) File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py", line 50, in qhull2D return link(dome(sample, base), dome(sample, base[::-1])) File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py", line 43, in dome return link(dome(outer, edge(h, pivot)), File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py", line 43, in dome return link(dome(outer, edge(h, pivot)), File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py", line 43, in dome return link(dome(outer, edge(h, pivot)), [Previous line repeated 981 more times] File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py", line 40, in dome outer = repeat(sample, dists>0, 0) File "<__array_function__ internals>", line 5, in repeat File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 480, in repeat return _wrapfunc(a, 'repeat', repeats, axis=axis) File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 53, in _wrapfunc bound = getattr(obj, method, None) RecursionError: maximum recursion depth exceeded while calling a Python object You are using DUNE-ALUGrid, please don't forget to cite the paper: Alkaemper, Dedner, Kloefkorn, Nolte. The DUNE-ALUGrid Module, 2016.
Thank you. Best regards, Linda
On Mon, Feb 15, 2021 at 8:56 PM adedner @.***> wrote:
Another question: that looks like you did
pip install dune-vem? If that is the case then please run python -m dune.fem if the active virtual env (assuming you used one). That should give you the scripts for tutorial which are up to date. The ones here are possibly a bit outdated compared to those version of the dune modules. Let me just mention that the whole dune-vem and the python bindings are quite new and we are just finalizing a release version for them. So the versions you have to use are 'cutting edge' and one could say a bit 'rough around those edges'. But the scripts you get by calling the above command should work without issues. Best Andreas
From: Linda ALzaben @.> Sent: 15 February 2021 05:22 To: adedner/dune-fempy @.> Cc: Dedner, Andreas @.>; Comment < @.> Subject: Re: [adedner/dune-fempy] Error while running vemdemo (#1)
Hi Adedner, Thank you for the email. This is what I get:
Package Version
cycler 0.10.0 dune-alugrid 2.8.0.dev20201218 dune-common 2.8.0.dev20201218 dune-fem 2.8.0.dev20201219 dune-geometry 2.8.0.dev20201218 dune-grid 2.8.0.dev20201218 dune-istl 2.8.0.dev20201218 dune-localfunctions 2.8.0.dev20201218 dune-vem 2.8.0.dev20201219 kiwisolver 1.3.1 matplotlib 3.3.4 mpi4py 3.0.3 numpy 1.20.0 Pillow 8.1.0 pip 20.0.2 pkg-resources 0.0.0 portalocker 2.2.1 pyparsing 2.4.7 python-dateutil 2.8.1 scipy 1.6.0 setuptools 44.0.0 six 1.15.0 sortedcontainers 2.3.0 triangle 20200424 UFL 2017.1.0 wheel 0.36.2
Best regards, Linda
On Sun, Feb 14, 2021 at 10:09 PM adedner @.***> wrote:
Dear Linda. Welcome to dune-vem! Sorry that it didn't work out directly for you. There might be an issue with the versions of the different components of dune. Could you run pip list and post the output? Best Andreas
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://urldefense.com/v3/__https://github.com/adedner/dune-fempy/issues/1*issuecomment-778825721__;Iw!!Nmw4Hv0!niaLT0oOCTnEzNGOmsvNE3-A-GQBcnJx1ZFuAZWCMmRKmjLTeYQleR3pZVIxkLeLbCiyDtk$ , or unsubscribe < https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ANHEKYTFODDM7I7FNZNX2JDS7ANXLANCNFSM4XM4S6WA__;!!Nmw4Hv0!niaLT0oOCTnEzNGOmsvNE3-A-GQBcnJx1ZFuAZWCMmRKmjLTeYQleR3pZVIxkLeLt-vFTas$
.
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adedner
commented
3 years ago Great - no idea why Ubuntu 18 doesn't work; I developed most of it on that distro.... But good that it is working now. Would be interested to hear what you plan to use the software for. Also if you is some feature you are unsure about then don't hesitate to ask. Best Andreas
From: Linda ALzaben @.> Sent: 05 April 2021 17:51 To: adedner/dune-fempy @.> Cc: Dedner, Andreas @.>; Comment @.> Subject: Re: [adedner/dune-fempy] Error while running vemdemo (#1)
Dear Andreas, Would like to thank you for your help. I had to install Ubuntu 20 and now things are working fine.
Appreciate your help. Best regards, Linda
Sent from my iPhone
On 24 Feb 2021, at 02:22, adedner @.***> wrote:
Hi. did you see my answers on the github issue? I added them directly into the issue instead of replying so I'm not sure if you saw them? Best Andreas
From: Linda ALzaben @.> Sent: 23 February 2021 15:22 To: adedner/dune-fempy @.> Cc: Dedner, Andreas @.>; Comment @.> Subject: Re: [adedner/dune-fempy] Error while running vemdemo (#1)
Dear Andreas,
Hope you are doing well. Did you have a chance to see why the vemdemo.py is not working and I'm getting the mentioned error?
Thank you. Appreciate your help. Best regards, Linda
On Tue, Feb 16, 2021 at 8:39 AM Linda Alzaben @.***> wrote:
Dear Andreas,
Yes I have an active virtual environment, however, when I run the vemdemo.py file from the tutorials folder and I get the below error. I hope you can help me with that.
The error: program code[0]: Adding fem.verboserank = 0 generating new seeds for voronoi grid WARNING (ignored): Could not open file 'alugrid.cfg', using default values 0 < [balance] < 1.2, partitioning method 'ALUGRID_SpaceFillingCurve(9)'.
You are using DUNE-ALUGrid, please don't forget to cite the paper: Alkaemper, Dedner, Kloefkorn, Nolte. The DUNE-ALUGrid Module, 2016.
Created parallel ALUGrid<2,2,simplex,conforming> from input stream.
Adding default: fem.dofmanager.memoryfactor: 1.1 Adding default: fem.dofmanager.clearresizedarrays: true Adding default: fem.solver.matrix.overflowfraction: 1 method:( lagrange galerkin ) Size: 832 L^2: 0.00014533036548239515 H^1: 0.006393416088471436 236 Traceback (most recent call last): File "vemdemo.py", line 147, in
space = create.space(m[1], polyGrid, order=order, dimRange=1, storage="istl", *m[3]) File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/create.py", line 172, in creatorCall return create(args, *kwargs) File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/_vem.py", line 179, in vemSpace spc = module(field, includes, typeName, constructor, diameterMethod, File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/fem/space/init.py", line 307, in module spc = module.Space(ctorArgs) File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/bbox.py", line 12, in rotatedBBox hull_points = qhull2D(points) File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py", line 50, in qhull2D return link(dome(sample, base), dome(sample, base[::-1])) File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py", line 43, in dome return link(dome(outer, edge(h, pivot)), File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py", line 43, in dome return link(dome(outer, edge(h, pivot)), File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py", line 43, in dome return link(dome(outer, edge(h, pivot)), [Previous line repeated 981 more times] File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py", line 40, in dome outer = repeat(sample, dists>0, 0) File "<__array_function__ internals>", line 5, in repeat File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 480, in repeat return _wrapfunc(a, 'repeat', repeats, axis=axis) File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 53, in _wrapfunc bound = getattr(obj, method, None) RecursionError: maximum recursion depth exceeded while calling a Python object You are using DUNE-ALUGrid, please don't forget to cite the paper: Alkaemper, Dedner, Kloefkorn, Nolte. The DUNE-ALUGrid Module, 2016.
Thank you. Best regards, Linda
On Mon, Feb 15, 2021 at 8:56 PM adedner @.***> wrote:
Another question: that looks like you did
pip install dune-vem? If that is the case then please run python -m dune.fem if the active virtual env (assuming you used one). That should give you the scripts for tutorial which are up to date. The ones here are possibly a bit outdated compared to those version of the dune modules. Let me just mention that the whole dune-vem and the python bindings are quite new and we are just finalizing a release version for them. So the versions you have to use are 'cutting edge' and one could say a bit 'rough around those edges'. But the scripts you get by calling the above command should work without issues. Best Andreas
From: Linda ALzaben @.> Sent: 15 February 2021 05:22 To: adedner/dune-fempy @.> Cc: Dedner, Andreas @.>; Comment < @.> Subject: Re: [adedner/dune-fempy] Error while running vemdemo (#1)
Hi Adedner, Thank you for the email. This is what I get:
Package Version
cycler 0.10.0 dune-alugrid 2.8.0.dev20201218 dune-common 2.8.0.dev20201218 dune-fem 2.8.0.dev20201219 dune-geometry 2.8.0.dev20201218 dune-grid 2.8.0.dev20201218 dune-istl 2.8.0.dev20201218 dune-localfunctions 2.8.0.dev20201218 dune-vem 2.8.0.dev20201219 kiwisolver 1.3.1 matplotlib 3.3.4 mpi4py 3.0.3 numpy 1.20.0 Pillow 8.1.0 pip 20.0.2 pkg-resources 0.0.0 portalocker 2.2.1 pyparsing 2.4.7 python-dateutil 2.8.1 scipy 1.6.0 setuptools 44.0.0 six 1.15.0 sortedcontainers 2.3.0 triangle 20200424 UFL 2017.1.0 wheel 0.36.2
Best regards, Linda
On Sun, Feb 14, 2021 at 10:09 PM adedner @.***> wrote:
Dear Linda. Welcome to dune-vem! Sorry that it didn't work out directly for you. There might be an issue with the versions of the different components of dune. Could you run pip list and post the output? Best Andreas
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://urldefense.com/v3/__https://github.com/adedner/dune-fempy/issues/1*issuecomment-778825721__;Iw!!Nmw4Hv0!niaLT0oOCTnEzNGOmsvNE3-A-GQBcnJx1ZFuAZWCMmRKmjLTeYQleR3pZVIxkLeLbCiyDtk$ , or unsubscribe < https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ANHEKYTFODDM7I7FNZNX2JDS7ANXLANCNFSM4XM4S6WA__;!!Nmw4Hv0!niaLT0oOCTnEzNGOmsvNE3-A-GQBcnJx1ZFuAZWCMmRKmjLTeYQleR3pZVIxkLeLt-vFTas$
.
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lalzaben
commented
3 years ago Hi Andreas,
I need virtual elements to work on a project that my professor (Daniele Boffi) proposed. I didn't start it yet but as I need first to learn how Dune and specifically VEM works. Do you recommend any site or book to understand VEM?
Will be in contact for any help or even for future work together.
Thank you. Best regards, Linda
On Mon, Apr 5, 2021 at 10:03 PM adedner @.***> wrote:
Great - no idea why Ubuntu 18 doesn't work; I developed most of it on that distro.... But good that it is working now. Would be interested to hear what you plan to use the software for. Also if you is some feature you are unsure about then don't hesitate to ask. Best Andreas
From: Linda ALzaben @.> Sent: 05 April 2021 17:51 To: adedner/dune-fempy @.> Cc: Dedner, Andreas @.>; Comment @.> Subject: Re: [adedner/dune-fempy] Error while running vemdemo (#1)
Dear Andreas, Would like to thank you for your help. I had to install Ubuntu 20 and now things are working fine.
Appreciate your help. Best regards, Linda
Sent from my iPhone
On 24 Feb 2021, at 02:22, adedner @.***> wrote:
Hi. did you see my answers on the github issue? I added them directly into the issue instead of replying so I'm not sure if you saw them? Best Andreas
From: Linda ALzaben @.> Sent: 23 February 2021 15:22 To: adedner/dune-fempy @.> Cc: Dedner, Andreas @.>; Comment @.> Subject: Re: [adedner/dune-fempy] Error while running vemdemo (#1)
Dear Andreas,
Hope you are doing well. Did you have a chance to see why the vemdemo.py is not working and I'm getting the mentioned error?
Thank you. Appreciate your help. Best regards, Linda
On Tue, Feb 16, 2021 at 8:39 AM Linda Alzaben @.***> wrote:
Dear Andreas,
Yes I have an active virtual environment, however, when I run the vemdemo.py file from the tutorials folder and I get the below error. I hope you can help me with that.
The error: program code[0]: Adding fem.verboserank = 0 generating new seeds for voronoi grid WARNING (ignored): Could not open file 'alugrid.cfg', using default values 0 < [balance] < 1.2, partitioning method 'ALUGRID_SpaceFillingCurve(9)'.
You are using DUNE-ALUGrid, please don't forget to cite the paper: Alkaemper, Dedner, Kloefkorn, Nolte. The DUNE-ALUGrid Module, 2016.
Created parallel ALUGrid<2,2,simplex,conforming> from input stream.
Adding default: fem.dofmanager.memoryfactor: 1.1 Adding default: fem.dofmanager.clearresizedarrays: true Adding default: fem.solver.matrix.overflowfraction: 1 method:( lagrange galerkin ) Size: 832 L^2: 0.00014533036548239515 H^1: 0.006393416088471436 236 Traceback (most recent call last): File "vemdemo.py", line 147, in
space = create.space(m[1], polyGrid, order=order, dimRange=1, storage="istl", **m[3]) File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/create.py",
line 172, in creatorCall return create(*args, **kwargs) File
"/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/_vem.py",
line 179, in vemSpace spc = module(field, includes, typeName, constructor, diameterMethod, File
"/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/fem/space/init.py",
line 307, in module spc = module.Space(*ctorArgs) File
"/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/bbox.py",
line 12, in rotatedBBox hull_points = qhull2D(points) File
"/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py",
line 50, in qhull2D return link(dome(sample, base), dome(sample, base[::-1])) File
"/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py",
line 43, in dome return link(dome(outer, edge(h, pivot)), File
"/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py",
line 43, in dome return link(dome(outer, edge(h, pivot)), File
"/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py",
line 43, in dome return link(dome(outer, edge(h, pivot)), [Previous line repeated 981 more times] File
"/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/vem/qhull_2d.py",
line 40, in dome outer = repeat(sample, dists>0, 0) File "<__array_function__ internals>", line 5, in repeat File
"/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/numpy/core/fromnumeric.py",
line 480, in repeat return _wrapfunc(a, 'repeat', repeats, axis=axis) File
"/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/numpy/core/fromnumeric.py",
line 53, in _wrapfunc bound = getattr(obj, method, None) RecursionError: maximum recursion depth exceeded while calling a Python object
You are using DUNE-ALUGrid, please don't forget to cite the paper: Alkaemper, Dedner, Kloefkorn, Nolte. The DUNE-ALUGrid Module, 2016.
Thank you. Best regards, Linda
On Mon, Feb 15, 2021 at 8:56 PM adedner @.***> wrote:
Another question: that looks like you did
pip install dune-vem? If that is the case then please run python -m dune.fem if the active virtual env (assuming you used one). That should give you the scripts for tutorial which are up to date. The ones here are possibly a bit outdated compared to those version of the dune modules. Let me just mention that the whole dune-vem and the python bindings are quite new and we are just finalizing a release version for them. So the versions you have to use are 'cutting edge' and one could say a bit 'rough around those edges'. But the scripts you get by calling the above command should work without issues. Best Andreas
From: Linda ALzaben @.> Sent: 15 February 2021 05:22 To: adedner/dune-fempy @.> Cc: Dedner, Andreas @.>; Comment < @.> Subject: Re: [adedner/dune-fempy] Error while running vemdemo (#1)
Hi Adedner, Thank you for the email. This is what I get:
Package Version
cycler 0.10.0 dune-alugrid 2.8.0.dev20201218 dune-common 2.8.0.dev20201218 dune-fem 2.8.0.dev20201219 dune-geometry 2.8.0.dev20201218 dune-grid 2.8.0.dev20201218 dune-istl 2.8.0.dev20201218 dune-localfunctions 2.8.0.dev20201218 dune-vem 2.8.0.dev20201219 kiwisolver 1.3.1 matplotlib 3.3.4 mpi4py 3.0.3 numpy 1.20.0 Pillow 8.1.0 pip 20.0.2 pkg-resources 0.0.0 portalocker 2.2.1 pyparsing 2.4.7 python-dateutil 2.8.1 scipy 1.6.0 setuptools 44.0.0 six 1.15.0 sortedcontainers 2.3.0 triangle 20200424 UFL 2017.1.0 wheel 0.36.2
Best regards, Linda
On Sun, Feb 14, 2021 at 10:09 PM adedner @.***> wrote:
Dear Linda. Welcome to dune-vem! Sorry that it didn't work out directly for you. There might be an issue with the versions of the different components of dune. Could you run pip list and post the output? Best Andreas
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adedner
commented
3 years ago Do you recommend any site or book to understand VEM? You probably already saw our paper on arxiv which might give you an idea on the approach we are taking and on which the code is based. It focuses on forth order PDEs but does have some remarks on second order as well. The ideas we use are an extension of a paper which we clearly cite so you can look at that as well. Both are perhaps not good papers to start learning about VEM.... There is a 'hitchhiker's guide" as well but you probably saw that one already.
lalzaben
commented
3 years ago Dear Andreas,
May this email find you well.
I Would like to ask you if I can apply an eigenvalue problem with vem? I have search for it but didn’t succeed. I tried to use the solver=eigen from fem but it doesn’t work. Please can you guid me on this?
Thank you in advance. Best regards, Linda --
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adedner
commented
3 years ago Hi. I'm not really an expert on Eigenvalueproblems so can't really help a lot. The 'storage' Eigen refers to the 'EIgen' linear algebra package and has nothing to do with Eigenvalueproblems. My suggestion would be to check what is available in Scipy and to extract the assembled system matrix as scipy sparse matrix and use something suitable from Scipy. Dune does not offer it's own Eigenvalue solvers that is something for the expert linear algebra packages. The tutorial shows how to extract the system matrix and use it with the scipy package. Andreas
From: Linda ALzaben @.> Sent: 13 July 2021 05:32 To: adedner/dune-fempy @.> Cc: Dedner, Andreas @.>; Comment @.> Subject: Re: [adedner/dune-fempy] Error while running vemdemo (#1)
Dear Andreas,
May this email find you well.
I Would like to ask you if I can apply an eigenvalue problem with vem? I have search for it but didn’t succeed. I tried to use the solver=eigen from fem but it doesn’t work. Please can you guid me on this?
This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.
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lalzaben
commented
3 years ago Hi Andreas,
Thank you for your reply and sorry to bother you again.
I have tried but couldn't figure out how to extract the matrices that I need with vem.
I would like to construct the model a = b with vemScheme and extract the left and write matrices. What I have is the following:
num_elements = 6
lower_point = [0,0] upper_point = [pi,pi]
division = [0,0] # [number_of_cells_on_x, numbre_of_cells_of_y]constructor = cartesianDomain(lower_point,upper_point,division)polyGrid = create.grid("agglomerate", voronoiCells(constructor, towers = num_elements, fileName="voronoiseeds", lloyd = 0) )
space = dune.vem.space http://dune.vem.space(view=polyGrid, order=1, dimRang=2, testSpaces=None, conforming=True, version='continuous', scalar=False, basisChoice=2, field='double', storage='fem')
x = SpatialCoordinate(space)
u = TrialFunction(space)v = TestFunction(space)
a = (inner(grad(u),grad(v)))dx # gradModelb = -dot(u,v) dx # massModel
dbc = [dune.ufl.DirichletBC(space, value , i+1) for i in range(4)] # DirichletBC
solver = 'cg'scheme = dune.vem.vemScheme( [a==b, dbc], space = space, solver=solver, gradStabilization=gradStabilization, massStabilization=massStabilization )*
A = linearOperator(scheme).as_numpy.tocsc() # Compressed Sparse Column matrixAd = A.todense()
I would like to extract the left and right matrices of the scheme to solve a generalized eigenvalue problem [Mx = lam Nx ] with eigs in python. How can I extract M and N from A?
Thank you for your time.
Best regards, Linda
On Tue, Jul 13, 2021 at 10:47 AM adedner @.***> wrote:
Hi. I'm not really an expert on Eigenvalueproblems so can't really help a lot. The 'storage' Eigen refers to the 'EIgen' linear algebra package and has nothing to do with Eigenvalueproblems. My suggestion would be to check what is available in Scipy and to extract the assembled system matrix as scipy sparse matrix and use something suitable from Scipy. Dune does not offer it's own Eigenvalue solvers that is something for the expert linear algebra packages. The tutorial shows how to extract the system matrix and use it with the scipy package. Andreas
From: Linda ALzaben @.> Sent: 13 July 2021 05:32 To: adedner/dune-fempy @.> Cc: Dedner, Andreas @.>; Comment @.> Subject: Re: [adedner/dune-fempy] Error while running vemdemo (#1)
Dear Andreas,
May this email find you well.
I Would like to ask you if I can apply an eigenvalue problem with vem? I have search for it but didn’t succeed. I tried to use the solver=eigen from fem but it doesn’t work. Please can you guid me on this?
Thank you in advance. Best regards, Linda
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adedner
commented
3 years ago The scheme doesn't know about lhs and rhs since the generated model solves L[u] =0 i.e. lhs-rhs=0
the easiest solution in your case is to setup two schemes one for lhs and one for rhs and extract the matrices for those two schemes. Would that work?
Sent from my Huawei phone
-------- Original message -------- From: Linda ALzaben @.> Date: Sun, 8 Aug 2021, 10:02 To: adedner/dune-fempy @.> Cc: "Dedner, Andreas" @.>, Comment @.> Subject: Re: [adedner/dune-fempy] Error while running vemdemo (#1)
Hi Andreas,
Thank you for your reply and sorry to bother you again.
I have tried but couldn't figure out how to extract the matrices that I need with vem.
I would like to construct the model a = b with vemScheme and extract the left and write matrices. What I have is the following:
num_elements = 6
lower_point = [0,0] upper_point = [pi,pi]
division = [0,0] # [number_of_cells_on_x, numbre_of_cells_of_y]constructor = cartesianDomain(lower_point,upper_point,division)polyGrid = create.grid("agglomerate", voronoiCells(constructor, towers = num_elements, fileName="voronoiseeds", lloyd = 0) )
space = dune.vem.space http://dune.vem.space(view=polyGrid, order=1, dimRang=2, testSpaces=None, conforming=True, version='continuous', scalar=False, basisChoice=2, field='double', storage='fem')
x = SpatialCoordinate(space)
u = TrialFunction(space)v = TestFunction(space)
a = (inner(grad(u),grad(v)))dx # gradModelb = -dot(u,v) dx # massModel
dbc = [dune.ufl.DirichletBC(space, value , i+1) for i in range(4)] # DirichletBC
solver = 'cg'scheme = dune.vem.vemScheme( [a==b, dbc], space = space, solver=solver, gradStabilization=gradStabilization, massStabilization=massStabilization )*
A = linearOperator(scheme).as_numpy.tocsc() # Compressed Sparse Column matrixAd = A.todense()
I would like to extract the left and right matrices of the scheme to solve a generalized eigenvalue problem [Mx = lam Nx ] with eigs in python. How can I extract M and N from A?
Thank you for your time.
Best regards, Linda
On Tue, Jul 13, 2021 at 10:47 AM adedner @.***> wrote:
Hi. I'm not really an expert on Eigenvalueproblems so can't really help a lot. The 'storage' Eigen refers to the 'EIgen' linear algebra package and has nothing to do with Eigenvalueproblems. My suggestion would be to check what is available in Scipy and to extract the assembled system matrix as scipy sparse matrix and use something suitable from Scipy. Dune does not offer it's own Eigenvalue solvers that is something for the expert linear algebra packages. The tutorial shows how to extract the system matrix and use it with the scipy package. Andreas
From: Linda ALzaben @.> Sent: 13 July 2021 05:32 To: adedner/dune-fempy @.> Cc: Dedner, Andreas @.>; Comment @.> Subject: Re: [adedner/dune-fempy] Error while running vemdemo (#1)
Dear Andreas,
May this email find you well.
I Would like to ask you if I can apply an eigenvalue problem with vem? I have search for it but didn’t succeed. I tried to use the solver=eigen from fem but it doesn’t work. Please can you guid me on this?
Thank you in advance. Best regards, Linda
This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.
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lalzaben
commented
3 years ago Dear Andreas,
Thank you, this approach got me what I needed.
I had two questions:
1- The stabilization parameters in the scheme (gradStabilization and mass Stabilization) can be different from the diffCoeff, massCoeff in the examples. It was a choice they took, right? 2- Also, can we set a mixed scheme with vem, like applying vem space and the Raviart-Thomas (vector field) space as a mixed space and setting the bilinear forms then extracting the matrices?
Thank you.
Best regards, Linda
On Sun, Aug 8, 2021 at 10:07 PM adedner @.***> wrote:
The scheme doesn't know about lhs and rhs since the generated model solves L[u] =0 i.e. lhs-rhs=0
the easiest solution in your case is to setup two schemes one for lhs and one for rhs and extract the matrices for those two schemes. Would that work?
Sent from my Huawei phone
-------- Original message -------- From: Linda ALzaben @.> Date: Sun, 8 Aug 2021, 10:02 To: adedner/dune-fempy @.> Cc: "Dedner, Andreas" @.>, Comment @.> Subject: Re: [adedner/dune-fempy] Error while running vemdemo (#1)
Hi Andreas,
Thank you for your reply and sorry to bother you again.
I have tried but couldn't figure out how to extract the matrices that I need with vem.
I would like to construct the model a = b with vemScheme and extract the left and write matrices. What I have is the following:
num_elements = 6
lower_point = [0,0] upper_point = [pi,pi]
division = [0,0] # [number_of_cells_on_x, numbre_of_cells_of_y]constructor = cartesianDomain(lower_point,upper_point,division)polyGrid = create.grid("agglomerate", voronoiCells(constructor, towers = num_elements, fileName="voronoiseeds", lloyd = 0) )
space = dune.vem.space http://dune.vem.space(view=polyGrid <https://urldefense.com/v3/__http://dune.vem.space3E(view=polyGrid__;JQ!!Nmw4Hv0!lDf5W_4CugIi8jlQhoa7lJAXc3v4wAwlq8K_TYgDJMPs3nJlw5X8xIubIxXPJ90kBZA7O3Y$> , order=1, dimRang=2, testSpaces=None, conforming=True, version='continuous', scalar=False, basisChoice=2, field='double', storage='fem')*
x = SpatialCoordinate(space)
u = TrialFunction(space)v = TestFunction(space)
a = (inner(grad(u),grad(v)))dx # gradModelb = -dot(u,v) dx # massModel
dbc = [dune.ufl.DirichletBC(space, value , i+1) for i in range(4)] # DirichletBC
solver = 'cg'scheme = dune.vem.vemScheme( [a==b, dbc], space = space, solver=solver, gradStabilization=gradStabilization, massStabilization=massStabilization )*
A = linearOperator(scheme).as_numpy.tocsc() # Compressed Sparse Column matrixAd = A.todense()
I would like to extract the left and right matrices of the scheme to solve a generalized eigenvalue problem [Mx = lam Nx ] with eigs in python. How can I extract M and N from A?
Thank you for your time.
Best regards, Linda
On Tue, Jul 13, 2021 at 10:47 AM adedner @.***> wrote:
Hi. I'm not really an expert on Eigenvalueproblems so can't really help a lot. The 'storage' Eigen refers to the 'EIgen' linear algebra package and has nothing to do with Eigenvalueproblems. My suggestion would be to check what is available in Scipy and to extract the assembled system matrix as scipy sparse matrix and use something suitable from Scipy. Dune does not offer it's own Eigenvalue solvers that is something for the expert linear algebra packages. The tutorial shows how to extract the system matrix and use it with the scipy package. Andreas
From: Linda ALzaben @.> Sent: 13 July 2021 05:32 To: adedner/dune-fempy @.> Cc: Dedner, Andreas @.>; Comment @.> Subject: Re: [adedner/dune-fempy] Error while running vemdemo (#1)
Dear Andreas,
May this email find you well.
I Would like to ask you if I can apply an eigenvalue problem with vem? I have search for it but didn’t succeed. I tried to use the solver=eigen from fem but it doesn’t work. Please can you guid me on this?
Thank you in advance. Best regards, Linda
This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.
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adedner
commented
3 years ago The stabilization parameters passed to the scheme can be chosen anyway you like. The only thing added in the scheme is the right grid spacing for the different terms. Mixed spaces is not really easily done at the moment. The only situation were I needed that so far was for a Stokes problem but there I ended up wanting to solve the Shur complement problem anyway so needed the four block matrices and separate dof vectors. You can have a look at the Stokes problem in the tutorial https://dune-project.org/sphinx/content/sphinx/dune-fem/uzawa-scipy_nb.html
Dear sir, I'm new to vem and would like to use it for my research. However, i tried to run the vemdemo.py but I encountered a problem in the Laplace demo the error is :
------------------------------------------------------------------------------------
program code[0]: Adding fem.verboserank = 0 loading seeds for voronoi grid Traceback (most recent call last): File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/create.py", line 164, in creatorCall create = self.registry[key][0] KeyError: 'polygrid'
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "vemdemo_new.py", line 86, in
polyGrid = create.grid("polygrid", voronoiCells(constructor,50,"voronoiseeds",True,lloyd=100) )
File "/home/alzabel/VirtualEnvs/Dune/lib/python3.8/site-packages/dune/create.py", line 166, in creatorCall
raise RuntimeError('No ' + self.obj + ' implementation: ' + key +\
RuntimeError: No grid implementation: polygrid. Available: alu aluconform alucube alusimplex oned yasp agglomerate.
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I hope you can help me in identifying the problem.
Thank you Linda