[Dune] Dune Digest, Vol 125, Issue 11
Jelena Grižić
jelena.grizic at gmail.com
Wed Nov 25 14:05:46 CET 2015
Hi all,
I've managed to solve the problem, the mesh contained quadrilaterals that
weren't convex and that caused degenerated hexagonal elements.
Thanks to Andreas who helped with detecting the source of the problem.
Best regards,
Jelena
2015-11-20 12:40 GMT+01:00 <dune-request at dune-project.org>:
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> Today's Topics:
>
> 1. Re: Dune Digest, Vol 125, Issue 9 (Jelena Gri?i?)
> 2. Re: Dune Digest, Vol 125, Issue 9 (Andreas Dedner)
>
>
> ---------- Proslijeđena poruka ----------
> From: "Jelena Grižić" <jelena.grizic at gmail.com>
> To: dune at dune-project.org
> Cc:
> Date: Fri, 20 Nov 2015 12:20:36 +0100
> Subject: Re: [Dune] Dune Digest, Vol 125, Issue 9
> Hi,
>
> I added variable p to the output. Again, I'm sending only the part where
> the error occurs (the whole output is too big).
>
> Thank you.
>
> Best regards,
>
> Jelena
>
> 2015-11-18 12:00 GMT+01:00 <dune-request at dune-project.org>:
>
>> Send Dune mailing list submissions to
>> dune at dune-project.org
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> http://lists.dune-project.org/mailman/listinfo/dune
>> or, via email, send a message with subject or body 'help' to
>> dune-request at dune-project.org
>>
>> You can reach the person managing the list at
>> dune-owner at dune-project.org
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of Dune digest..."
>>
>> Today's Topics:
>>
>> 1. Re: Dune Digest, Vol 125, Issue 7 (Andreas Dedner)
>>
>>
>> ---------- Proslijeđena poruka ----------
>> From: Andreas Dedner <a.s.dedner at warwick.ac.uk>
>> To: <dune at dune-project.org>
>> Cc:
>> Date: Tue, 17 Nov 2015 17:12:13 +0000
>> Subject: Re: [Dune] Dune Digest, Vol 125, Issue 7
>> I just realized that the TrilinearMap class does not only store the
>> a[.][.] (which describes the actual mapping) but
>> also the actual coordinates of the cube in p0,p1,p2,p3,p4,p5,p6,p7.
>> Having those of the offending cube would actually be even more
>> interesting. So if you could add those to your output
>> that would simplify figuring out what the problem is.
>> Andreas
>>
>> On 17/11/15 16:02, Andreas Dedner wrote:
>>
>> Hi.
>> To get that output of detDf and a[i][j] you must have added some lines to
>> the code - could you send me the corresponding
>> diff.
>> Andreas
>>
>> On 17/11/15 15:44, Jelena Grižić wrote:
>>
>> Dear all,
>>
>> my last mail was too big for some mailservers, so I'm sending attachment
>> only containing relevant information.
>>
>>
>> Thanks!
>>
>>
>> Best regards,
>>
>> Jelena Grižić
>>
>> 2015-11-13 13:09 GMT+01:00 Jelena Grižić <jelena.grizic at gmail.com>:
>>
>>> Hi Andreas,
>>>
>>> file with all requested information is in the attachment. I'm using
>>> module dune-alugrid.
>>> I can also share dgf file on Google Disc or Dropbox, if necessarily.
>>>
>>>
>>> Thank you!
>>>
>>> Best regards,
>>>
>>> Jelena
>>>
>>> 2015-11-13 12:00 GMT+01:00 <dune-request at dune-project.org>:
>>>
>>>> Send Dune mailing list submissions to
>>>> dune at dune-project.org
>>>>
>>>> To subscribe or unsubscribe via the World Wide Web, visit
>>>> http://lists.dune-project.org/mailman/listinfo/dune
>>>> or, via email, send a message with subject or body 'help' to
>>>> dune-request at dune-project.org
>>>>
>>>> You can reach the person managing the list at
>>>> dune-owner at dune-project.org
>>>>
>>>> When replying, please edit your Subject line so it is more specific
>>>> than "Re: Contents of Dune digest..."
>>>>
>>>> Today's Topics:
>>>>
>>>> 1. dune-alugrid: Assertion `DetDf > 0' failed (Jelena Gri?i?)
>>>> 2. Re: dune-alugrid: Assertion `DetDf > 0' failed (Andreas Dedner)
>>>>
>>>>
>>>> ---------- Proslijeđena poruka ----------
>>>> From: "Jelena Grižić" <jelena.grizic at gmail.com>
>>>> To: dune at dune-project.org
>>>> Cc:
>>>> Date: Thu, 12 Nov 2015 18:11:38 +0100
>>>> Subject: [Dune] dune-alugrid: Assertion `DetDf > 0' failed
>>>> Dear all,
>>>>
>>>>
>>>> while constructing mesh from dgf file, I receive message :
>>>>
>>>> dune-alugrid/dune/alugrid/3d/mappings_imp.cc:187: Dune::alu3d_ctype
>>>> Dune::TrilinearMapping::det(const coord_t&): Assertion `DetDf > 0' failed.
>>>>
>>>> Could you explain what that exactly means and what could be problem
>>>> with my mesh?
>>>>
>>>> Unfortunately, dgf file is to big (56,7 MB) to be included in mail.
>>>>
>>>>
>>>> Thank you.
>>>>
>>>> Best regards,
>>>>
>>>> Jelena Grižić
>>>>
>>>>
>>>> ---------- Proslijeđena poruka ----------
>>>> From: Andreas Dedner <a.s.dedner at warwick.ac.uk>
>>>> To: <dune at dune-project.org>
>>>> Cc:
>>>> Date: Thu, 12 Nov 2015 18:44:49 +0000
>>>> Subject: Re: [Dune] dune-alugrid: Assertion `DetDf > 0' failed
>>>> Hi.
>>>> The determinant in the alugrid TrilinearMapping class where the
>>>> assertion is triggered, is used to compute for example the integration
>>>> element or the volume of the cells in the grid. Alugrid assumes a
>>>> certain orientation of the grid elements (determinant > 0). I would have
>>>> thought that would be checked during the grid generation process and the
>>>> elements local vertex numbering changed if necessary but you might have
>>>> found a bad case here. I would need (at least):
>>>> 0) which alugrid type are you using, e.g., Cube<3> or Cube<2,3> or...
>>>> 1) the value of detDf (is it zero or negative)
>>>> 2) the call stack for the error
>>>> 3) The class also contains a variable 'a' which describes the mapping
>>>> and can be used to figure out which element in your dgf file is
>>>> causing the problem
>>>> 4) If that doesn't work then the dgf file...
>>>> Andreas
>>>>
>>>>
>>>> On 12/11/15 17:11, Jelena Grižić wrote:
>>>> > Dear all,
>>>> >
>>>> >
>>>> > while constructing mesh from dgf file, I receive message :
>>>> >
>>>> > dune-alugrid/dune/alugrid/3d/mappings_imp.cc:187: Dune::alu3d_ctype
>>>> > Dune::TrilinearMapping::det(const coord_t&): Assertion `DetDf > 0'
>>>> failed.
>>>> >
>>>> > Could you explain what that exactly means and what could be problem
>>>> with
>>>> > my mesh?
>>>> >
>>>> > Unfortunately, dgf file is to big (56,7 MB) to be included in mail.
>>>> >
>>>> >
>>>> > Thank you.
>>>> >
>>>> > Best regards,
>>>> >
>>>> > Jelena Grižić
>>>> >
>>>> >
>>>> > _______________________________________________
>>>> > Dune mailing list
>>>> > Dune at dune-project.org
>>>> > http://lists.dune-project.org/mailman/listinfo/dune
>>>> >
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Dune mailing list
>>>> Dune at dune-project.org
>>>> http://lists.dune-project.org/mailman/listinfo/dune
>>>>
>>>>
>>>
>>
>>
>> _______________________________________________
>> Dune mailing listDune at dune-project.orghttp://lists.dune-project.org/mailman/listinfo/dune
>>
>>
>>
>>
>> _______________________________________________
>> Dune mailing listDune at dune-project.orghttp://lists.dune-project.org/mailman/listinfo/dune
>>
>>
>>
>> _______________________________________________
>> Dune mailing list
>> Dune at dune-project.org
>> http://lists.dune-project.org/mailman/listinfo/dune
>>
>>
>
>
> ---------- Proslijeđena poruka ----------
> From: Andreas Dedner <a.s.dedner at warwick.ac.uk>
> To: <dune at dune-project.org>
> Cc:
> Date: Fri, 20 Nov 2015 11:40:23 +0000
> Subject: Re: [Dune] Dune Digest, Vol 125, Issue 9
> Is it possible that p0=p4, p1=p5 etc?
> In that case you're looking at a zero volume hex and detDf should be zero.
> Alu can't handle the case.
> of degenerate elements.
> Andreas
>
> On 20/11/15 11:20, Jelena Grižić wrote:
>
> Hi,
>
> I added variable p to the output. Again, I'm sending only the part where
> the error occurs (the whole output is too big).
>
> Thank you.
>
> Best regards,
>
> Jelena
>
> 2015-11-18 12:00 GMT+01:00 <dune-request at dune-project.org>:
>
>> Send Dune mailing list submissions to
>> dune at dune-project.org
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> http://lists.dune-project.org/mailman/listinfo/dune
>> or, via email, send a message with subject or body 'help' to
>> dune-request at dune-project.org
>>
>> You can reach the person managing the list at
>> dune-owner at dune-project.org
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of Dune digest..."
>>
>> Today's Topics:
>>
>> 1. Re: Dune Digest, Vol 125, Issue 7 (Andreas Dedner)
>>
>>
>> ---------- Proslijeđena poruka ----------
>> From: Andreas Dedner <a.s.dedner at warwick.ac.uk>
>> To: <dune at dune-project.org>
>> Cc:
>> Date: Tue, 17 Nov 2015 17:12:13 +0000
>> Subject: Re: [Dune] Dune Digest, Vol 125, Issue 7
>> I just realized that the TrilinearMap class does not only store the
>> a[.][.] (which describes the actual mapping) but
>> also the actual coordinates of the cube in p0,p1,p2,p3,p4,p5,p6,p7.
>> Having those of the offending cube would actually be even more
>> interesting. So if you could add those to your output
>> that would simplify figuring out what the problem is.
>> Andreas
>>
>> On 17/11/15 16:02, Andreas Dedner wrote:
>>
>> Hi.
>> To get that output of detDf and a[i][j] you must have added some lines to
>> the code - could you send me the corresponding
>> diff.
>> Andreas
>>
>> On 17/11/15 15:44, Jelena Grižić wrote:
>>
>> Dear all,
>>
>> my last mail was too big for some mailservers, so I'm sending attachment
>> only containing relevant information.
>>
>>
>> Thanks!
>>
>>
>> Best regards,
>>
>> Jelena Grižić
>>
>> 2015-11-13 13:09 GMT+01:00 Jelena Grižić <jelena.grizic at gmail.com>:
>>
>>> Hi Andreas,
>>>
>>> file with all requested information is in the attachment. I'm using
>>> module dune-alugrid.
>>> I can also share dgf file on Google Disc or Dropbox, if necessarily.
>>>
>>>
>>> Thank you!
>>>
>>> Best regards,
>>>
>>> Jelena
>>>
>>> 2015-11-13 12:00 GMT+01:00 <dune-request at dune-project.org>:
>>>
>>>> Send Dune mailing list submissions to
>>>> dune at dune-project.org
>>>>
>>>> To subscribe or unsubscribe via the World Wide Web, visit
>>>> http://lists.dune-project.org/mailman/listinfo/dune
>>>> or, via email, send a message with subject or body 'help' to
>>>> dune-request at dune-project.org
>>>>
>>>> You can reach the person managing the list at
>>>> dune-owner at dune-project.org
>>>>
>>>> When replying, please edit your Subject line so it is more specific
>>>> than "Re: Contents of Dune digest..."
>>>>
>>>> Today's Topics:
>>>>
>>>> 1. dune-alugrid: Assertion `DetDf > 0' failed (Jelena Gri?i?)
>>>> 2. Re: dune-alugrid: Assertion `DetDf > 0' failed (Andreas Dedner)
>>>>
>>>>
>>>> ---------- Proslijeđena poruka ----------
>>>> From: "Jelena Grižić" <jelena.grizic at gmail.com>
>>>> To: dune at dune-project.org
>>>> Cc:
>>>> Date: Thu, 12 Nov 2015 18:11:38 +0100
>>>> Subject: [Dune] dune-alugrid: Assertion `DetDf > 0' failed
>>>> Dear all,
>>>>
>>>>
>>>> while constructing mesh from dgf file, I receive message :
>>>>
>>>> dune-alugrid/dune/alugrid/3d/mappings_imp.cc:187: Dune::alu3d_ctype
>>>> Dune::TrilinearMapping::det(const coord_t&): Assertion `DetDf > 0' failed.
>>>>
>>>> Could you explain what that exactly means and what could be problem
>>>> with my mesh?
>>>>
>>>> Unfortunately, dgf file is to big (56,7 MB) to be included in mail.
>>>>
>>>>
>>>> Thank you.
>>>>
>>>> Best regards,
>>>>
>>>> Jelena Grižić
>>>>
>>>>
>>>> ---------- Proslijeđena poruka ----------
>>>> From: Andreas Dedner <a.s.dedner at warwick.ac.uk>
>>>> To: <dune at dune-project.org>
>>>> Cc:
>>>> Date: Thu, 12 Nov 2015 18:44:49 +0000
>>>> Subject: Re: [Dune] dune-alugrid: Assertion `DetDf > 0' failed
>>>> Hi.
>>>> The determinant in the alugrid TrilinearMapping class where the
>>>> assertion is triggered, is used to compute for example the integration
>>>> element or the volume of the cells in the grid. Alugrid assumes a
>>>> certain orientation of the grid elements (determinant > 0). I would have
>>>> thought that would be checked during the grid generation process and the
>>>> elements local vertex numbering changed if necessary but you might have
>>>> found a bad case here. I would need (at least):
>>>> 0) which alugrid type are you using, e.g., Cube<3> or Cube<2,3> or...
>>>> 1) the value of detDf (is it zero or negative)
>>>> 2) the call stack for the error
>>>> 3) The class also contains a variable 'a' which describes the mapping
>>>> and can be used to figure out which element in your dgf file is
>>>> causing the problem
>>>> 4) If that doesn't work then the dgf file...
>>>> Andreas
>>>>
>>>>
>>>> On 12/11/15 17:11, Jelena Grižić wrote:
>>>> > Dear all,
>>>> >
>>>> >
>>>> > while constructing mesh from dgf file, I receive message :
>>>> >
>>>> > dune-alugrid/dune/alugrid/3d/mappings_imp.cc:187: Dune::alu3d_ctype
>>>> > Dune::TrilinearMapping::det(const coord_t&): Assertion `DetDf > 0'
>>>> failed.
>>>> >
>>>> > Could you explain what that exactly means and what could be problem
>>>> with
>>>> > my mesh?
>>>> >
>>>> > Unfortunately, dgf file is to big (56,7 MB) to be included in mail.
>>>> >
>>>> >
>>>> > Thank you.
>>>> >
>>>> > Best regards,
>>>> >
>>>> > Jelena Grižić
>>>> >
>>>> >
>>>> > _______________________________________________
>>>> > Dune mailing list
>>>> > Dune at dune-project.org
>>>> > http://lists.dune-project.org/mailman/listinfo/dune
>>>> >
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Dune mailing list
>>>> Dune at dune-project.org
>>>> http://lists.dune-project.org/mailman/listinfo/dune
>>>>
>>>>
>>>
>>
>>
>> _______________________________________________
>> Dune mailing listDune at dune-project.orghttp://lists.dune-project.org/mailman/listinfo/dune
>>
>>
>>
>>
>> _______________________________________________
>> Dune mailing listDune at dune-project.orghttp://lists.dune-project.org/mailman/listinfo/dune
>>
>>
>>
>> _______________________________________________
>> Dune mailing list
>> Dune at dune-project.org
>> http://lists.dune-project.org/mailman/listinfo/dune
>>
>>
>
>
> _______________________________________________
> Dune mailing listDune at dune-project.orghttp://lists.dune-project.org/mailman/listinfo/dune
>
>
>
> _______________________________________________
> Dune mailing list
> Dune at dune-project.org
> http://lists.dune-project.org/mailman/listinfo/dune
>
>
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