Hi Yuesu,
Essentially, yes. If you look at the code for partition_triangulation you
will find
// check for an easy return
if (n_partitions == 1)
{
for (const auto &cell : triangulation.active_cell_iterators())
cell->set_subdomain_id(0);
return;
}
Hence step-17 only tries to use
27;t understand the Mac OS or Linux environment too well, so please
> excuse me for asking - but when you say "compile yourself" - what do you
> mean? and is there a documented "procedure" for compiling that I can
> follow?
>
> Regards
> Deepak
>
>
>
Hi Deepak,
This is a known issue with the current version of the mac bundle - it
doesn't work with Catalina. We are in the process of fixing this. For now,
unfortunately, you will have to either use an older version of deal.II or
compile it yourself.
Sorry,
David
On Mon, Jun 22, 2020 at 7:05 PM
Dear everyone,
We are in the process of preparing the next (9.2) release of deal.II: it
should be done by the end of the month. Please let us know as soon as
possible if you have any unresolved issues with the master branch on GitHub
or if you have unmerged patches which you believe should be adde
Dear Sebastian,
This is a good question: I took a look at the history of the instantiation
file and I think this is just an oversight (we added explicit nonzero
codimension specializations for the non-hp case years ago and propagated
the lack of hp instantiations along the way).
Would you be will
Hi Shahab,
You are right that vertices themselves don't store any information - this
is an implementation detail of deal.II (points do not store any topological
information in a Triangulation, unlike lines, quadrilaterals, or hexahedra).
Just to check: when you write 'vertices', are you looking f
Dear Wilmar,
I suspect you have already tried this, but I think it is worth
mentioning just in case: are you running Debian or Ubuntu? If so, then
you can use apt-get to install the library without needing to compile
it yourself.
Additionally, if you need to decrease the amount of memory used in
Hi Victor,
> Is there a 9.1+eps coming up?
No, but we are planning on releasing 9.2.0 in May (tentatively
scheduled for May 15) - if you can wait then that might be the best
choice.
Thanks,
David
On Tue, Apr 28, 2020 at 10:25 AM Victor Eijkhout
wrote:
>
>
>
> On , 2020Apr24, at 18:03, Marc Feh
Hi David,
There are a lot of different ways to solve this problem, but I think the
relevant solution is to consider a more Lagrangian perspective - I
recommend that you do not modify the Triangulation directly (i.e., don't
move vertices) but instead represent the initial deformation as a finite
el
Hi Lex,
I think that this is more of a PDE question than a deal.II question
but I will try to answer.
At a fundamental level, if you impose nonzero boundary conditions or
have nonzero forcing on a component you force to equal zero you will
not be able to have a solution that makes sense: you will
Hi Krishna,
I'm not sure that I understand your question - those two functions
create a mass matrix and a laplace corresponding to the given
parameters (dof handler, mapping, quadrature, etc) - in the first case
only shape values are needed and in the second only shape gradients.
Hence the functio
Hi Chaitanya,
I apologize that no one has answered your question yet. Using
hp::DoFHandler with distributed triangulations is a new feature that
is not yet in a current release and there may still be some bugs in
the implementation. I suspect no one has responded to this simply
because no one know
Hi Toni,
I think that this is due to each individual program creating the same
number of threads as you have physical processors. Try adding
MultithreadInfo::set_thread_limit(1);
at the top of your code to prevent this from happening. Let us know if
this works!
Thanks,
David
On Tue, Feb 11, 20
Wolfgang pointed out to me that the pivot based answer is wrong -
fortunately I have another explanation :)
If we have the block matrix
A B^T
B 0
where A is SPD and B has linearly independent rows, this matrix has
equal eigenvalues to
I 0A B^T
difficulties as the issues with the spectra since one implies the
other.
Thanks
On Sat, Feb 1, 2020 at 2:45 PM Krishnakumar Gopalakrishnan
wrote:
>
> Dear Dr David Wells,
>
> Thank you for the explanation. However, this only satisfies me partially
> because the very next statement i
Hi Krishna,
This is a classic linear algebra result - a symmetric matrix is
positive definite if and only if it has positive pivots. Since this
matrix has a zero block it does not even have a full set of pivots so
it cannot be positive definite.
Thanks,
David Wells
On Sat, Feb 1, 2020 at 9:49
m it, send an
> email to dealii+unsubscr...@googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/dealii/32E00408-28C8-4FCD-AC68-ABDF158CDBEC%40gmail.com.
>
>
> Best,
> Ihar Suvorau
>
>
>
> > On 30. Jan 2020, at 18:
OK, that also looks right. Could you also send me, from deal.II's
build directory,
cmake/config/deal.IIConfig.cmake
?
On Thu, Jan 30, 2020 at 11:05 AM Ihar Suvorau wrote:
>
> Hi, David,
>
> yes, here it is.
>
> On Thursday, January 30, 2020 at 6:02:56 PM UTC+2, David Wel
; Hi, David,
>
> okay, please, attaching these files also.
>
> On Tuesday, January 28, 2020 at 4:18:44 PM UTC+2, David Wells wrote:
>>
>> Hi Ihar,
>>
>> It looks like nothing went wrong with PETsc. Would you please also
>> send a copy of deal.II's detail
t;
> On Monday, January 27, 2020 at 5:42:39 PM UTC+2, David Wells wrote:
>>
>> Hi Ihar,
>>
>> This sounds like something has gone wrong inside either PETSc's or
>> deal.II's build process. Would you please show us a copy of PETSc's
>> configure.lo
Hi Simon,
It sounds like you want to use Patterns::Map or Patterns::List. As far
as I know both can accept an arbitrary number of input arguments.
Would either of those work for you?
Thanks,
David
On Sun, Jan 26, 2020 at 2:01 PM Simon Gauvin wrote:
>
> Greetings!
>
> I currently work on the Let
Hi Ihar,
This sounds like something has gone wrong inside either PETSc's or
deal.II's build process. Would you please show us a copy of PETSc's
configure.log?
Thanks,
David
On Sun, Jan 26, 2020 at 6:59 AM Ihar Suvorau wrote:
>
> Not yet, I have a running version via docker images though. I'll t
Hi Gerald,
I am not sure how to fix this, but a good workaround would be to just
download the offline documentation tarball from here
https://github.com/dealii/dealii/releases/tag/v8.4.2
(its under assets at the bottom of the page) and use that directly
instead of the Debian package. Our generic
Happy to help!
On Tue, Jan 7, 2020 at 1:42 PM Mohammed Hassan wrote:
>
> Hi David,
>
> Yes, I fixed the mesh file and it works fine for the stage of meshing, next I
> will to try to play with Boundary conditions. Many thanks for your support.
>
> Regards,
>
> On Tuesday, December 10, 2019 at 4:3
eason.
Thanks,
David Wells
On Tue, Jan 7, 2020 at 10:21 AM masod sadipour
wrote:
> Hello dear Dr. Wells,
> I am a graduate research assistant. I have recieved a project which I
> should solve the advection-diffusion equation using by deal.ii ASAP.
> Could you please let me know about t
3. I don't know how to couple the electromagnetic field to the thermal
problem.
Thanks,
David Wells
<https://dealii.org/publications.html>
On Tue, Jan 7, 2020 at 4:34 AM Andreas Gschwentner <
gschwentner.andr...@gmail.com> wrote:
> Dear deal.II community,
>
> i am working
Hi Hasan,
I loaded up your mesh in gmsh and it looks like something went wrong
with the extrusion: I only see quadrilaterals on two opposing faces
and no volume mesh at all. I think that if you fix the mesh you will
get past this error.
I attached a picture of what I see in gmsh to this message.
Hi Doug,
If I recall correctly, we added that comment since this is a part of
the library that is not very well tested. The code is probably fine.
Thanks,
David
On Tue, Dec 24, 2019 at 2:33 PM Doug Shi-Dong wrote:
>
> Hello everyone,
>
> I see that some functions within the constrained_linear_o
Dear Gerald,
This is great to hear! You are most welcome.
Thanks,
David
On Fri, Dec 20, 2019 at 11:50 AM Gerald Marewo wrote:
>
> Dear David and everyone,
>
> Here is an update and my way of saying that my problem has been completely
> solved.
>
> Upon watching Wolfgang's Lecturer video 8.01 n
Hi Gerald,
The best way to do this is to let CMake generate an eclipse project
for you by executing the command
cmake -G"Eclipse CDT4 - Unix Makefiles" -DDEAL_II_DIR=/path/to/deal.II .
in your project's base directory. See
https://github.com/dealii/dealii/wiki/Eclipse
for more information.
Dear Zhidong,
Thanks for finding and reporting this :)
When we compile the doxygen documentation we remove all occurrences of
dealii::
since, for a variety of reasons, it's easier to pretend in the manual
that all deal.II classes are in the global namespace. This is done
with, if I recall c
Dear Juan,
My best guess is that, at some point in the loop over all active
cells, you are also doing some computations involving the neighbor of
each cell. TriaAccessor::neighbor() returns the neighboring cell which
has, at most, the same level number as the current cell: i.e., if the
neighbor ce
Hi Zhidong,
I am happy to help!
Unfortunately, this is a part of deal.II that has some older code that
has accumulated some inconsistencies over time. Both inconsistencies
stem from there, previously, being a third class PETScWrappers::Vector
which was a sequential PETSc vector: both PETScWrapper
Hi Zhidong,
In C++ constructors are not inherited, so this function call won't
work: it's not possible to create a PETScWrappers::MPI::Vector from a
Vec object directly.
I think that you can solve your problem by just using VectorBase: you
can create objects of this type directly that wrap around
Dear Muhammad,
I think Ross implemented vector_value_list() this way so that he could use
one function object to give correct values with multiple material IDs: see
https://github.com/rosskynch/MIT_Forward/blob/master/src/forwardsolver.cc#L724
to see where he uses an object inheriting from EddyC
Hi Konrad,
I don't think that it is possible to use MUMPS with a block matrix for
exactly this reason. I think that if you want to use MUMPS you will need to
copy the block matrix into a non-block matrix.
Thanks,
David
On Fri, Sep 6, 2019 at 12:25 PM Konrad wrote:
> Dear deal.ii community,
>
>
Hi Charlie,
The issue is that Trilinos really needs an actual Matrix object (not just a
linear operator) to compute the AMG preconditioner: i.e., it can only
construct the preconditioner if it has access to the actual matrix entries,
which are not available unless you explicitly calculate B (DA)^-
Hi Maxi,
The AffineConstraints class does not support using mixed precision and I am
not aware of any alternatives that can solve this problem directly.
There may be a better solution, but one way to solve this problem would be
to set up two different AffineConstraints objects (one for each float
Hi Gabriel,
In case you are interested, I have written a patch and a new test for this
issue: its available at
https://github.com/dealii/dealii/pull/7763
Thanks,
David Wells
On Tue, Feb 26, 2019 at 8:45 PM David Wells wrote:
> Hi Gabriel,
>
> step-32 does use a pressure element of
k due
to a bug in the library itself, but rewriting step-35 (or a similar code)
to use FESystem and blocks is a lot of work. Unfortunately, I think the
second approach is the most reasonable one since its what the other
parallel examples do.
Thanks,
David Wells
On Mon, Feb 25, 2019 at 12:32
uation) in a fully distributed setting. I believe they set up
the coupling of the matrix with velocity and pressure blocks in a different
way that should work for you.
Does this make sense?
Thanks,
David Wells
On Sunday, February 17, 2019 at 4:29:06 PM UTC-5, gabriel...@koeln.de wrote:
>
&g
cmake flag
-DDEAL_II_WITH_GSL=OFF.
Does this work for you? If not we can try to work out a way to get your GSL
installation working.
Thanks,
David Wells
On Thursday, January 24, 2019 at 4:43:14 PM UTC-5, ky...@math.uh.edu wrote:
>
> Hi all,
>
> I'm having trouble installing dea
think Jean-Paul wrote some code to do this at some point; I am not sure
what happened to it. Ultimately, since this just involves merging two
Triangulations, it should not be hard to get something working on your own.
Let me know if this works!
Best,
David Wells
On Tuesday, January 15, 2019 at
Hey there,
I would be happy to help you, but would you first please start another
thread (the OP is interested in SIMD configuration on windows, which is not
the same issue) and post in it your detailed.log file from configuring
deal.II? Thanks!
Best,
David Wells
On Thursday, December 27
).
Does this make sense? Let me know if you have more questions.
Thanks,
David Wells
On Fri, Dec 21, 2018 at 12:19 AM mani maran wrote:
> Dear David Wells,
>
> Thank you for your kind reply. I am a beginner of Ubuntu and deal_II.
> Could you say elaborately. I am not strong in the
if you have more questions.
Thanks,
David Wells
On Thursday, December 20, 2018 at 2:00:37 PM UTC-5, mani maran wrote:
>
> Dear all,
>
> I am new to deal_ii. I have installed deal_ii in my ubuntu 16.04 desktop.
> I don't know, how to link hdf5 with deal_ii.
>
> Do sugge
Dear Chucui,
I would like to extend Daniel's answer slightly.
The source code for channel_with_cylinder is is at about line 2180 of
https://www.dealii.org/developer/doxygen/deal.II/grid__generator_8cc_source.html
If you want to generate just the grid around the cylinder (i.e., without
the cha
.
Thanks,
David Wells
On Friday, December 14, 2018 at 8:41:10 AM UTC-5, Mustafa Aggul wrote:
>
> Hello,
> I have created my own block sparsity pattern by adding non-zero entries
> manually, and then compressed it. Upon some testings on this sparsity
> pattern, I have realized th
Hi Chucui,
StraightBoundary was removed in deal.II 9.0; it should not show up in any
object files so these errors don't make any sense. Did you use a clean
build directory?
Thanks,
David Wells
On Thursday, October 18, 2018 at 8:27:40 AM UTC-4, chucu...@gmail.com wrote:
>
> Dear
Dear Maxi,
This is a bug with the current implementation: it looks like one of the
recent commits broke something.
Thanks for reporting this!
Thanks,
David Wells
On Thursday, October 11, 2018 at 9:46:42 AM UTC-4, Maxi Miller wrote:
>
> When trying to run example 16 on a new installat
, at least, it is causing problems somewhere else).
Thanks,
David Wells
On Tuesday, October 9, 2018 at 6:29:25 AM UTC-4, Maxi Miller wrote:
>
> I tried to compile deal.II on a new computer, but I got multiple linking
> errors for some of the examples:
> /usr/lib64/gcc/x86_64-
idOut go;
std::ofstream out("grid.eps");
result_2.refine_global(1);
go.write_eps(result_2, out);
}
I attached a picture of the output. This script relies on a patch that I
need to add to deal.II that permits merging triangulations with a tolerance
(so it won't work yet on 9.0,
the grid from Cartesian pieces.
If you are using 8.5 instead of 9.0 you will need to make all Manifold
classes (including putting your own PolarManifold on the circle) before the
Triangulation.
I hope this helps!
Thanks,
David Wells
On Monday, May 21, 2018 at 7:06:19 PM UTC-4, Narendra N
dillo in a standard location? If so then you should
be able to just append
TARGET_LINK_LIBRARIES(${TARGET} armadillo)
to the end of CMakeLists.txt (after the call to PROJECT and
DEAL_II_INVOKE_AUTOPILOT)
and things should work correctly.
Thanks,
David Wells
P.S. the CMake module for setti
.
Thanks,
David Wells
On Wednesday, March 7, 2018 at 7:51:06 AM UTC-5, Maxi Miller wrote:
>
> Based on my question here:
> https://groups.google.com/d/msg/dealii/4YoJZ8d2-XM/0k3TjZrqAAAJ I would
> like to implement the suggested solution using project_matri
We merged the fix this morning into the development branch, including a
test based on your code.
A suggestion: on some versions of GCC, calling 'abs' results in calling the
C function 'int abs(int)': to be safe, use std::abs.
Let me know if things work :)
Thanks,
Davi
rrect? if there is a
> better/simpler way plz let me know.
> Is the solution merged with the latest master branch? I would like to have
> a working library for this particular example.
>
>
> El jueves, 18 de enero de 2018, 18:39:51 (UTC-5), David Wells escribió:
>>
>> I
assumption
created a bad initial value for a quasi-newton solver, which then failed to
converge.
I got rid of the cube assumption. see
https://github.com/dealii/dealii/pull/5761 for more information.
Do you mind if I use a modified version of your code for a new test in
deal.II?
Thanks,
David Wells
in addition to using it in a more general setting during mesh
refinement: put another way, our implementation has changed substantially,
so this problem is at least in an area of the library where we have
recently made huge changes.
Thanks,
David Wells
On Wednesday, January 17, 2018 at 3:05:48
your deal.II
application in debug mode? If not, I suspect that running the program again
in debug mode will show exactly where something was not initialized
(deal.II checks this in many places).
Thanks,
David Wells
On Thursday, September 21, 2017 at 2:16:26 PM UTC-4, Jaekwang Kim wrote
I think that this is a use case that we should support: for example,
PETScWrappers::VectorBase can act as a wrapper around a user-provided Vec
so we should definitely consider providing similar functionality for
PETScWrappers::MatrixBase.
On Wednesday, May 24, 2017 at 5:18:46 AM UTC-4, Juan Car
ymore (though a few people still
include the headers).
Thanks,
David Wells
On Thursday, April 20, 2017 at 10:32:52 AM UTC-4, Tobi Young wrote:
>
>
> I ocassionally scan GitHub to see if people are using features in deal.II
> outside of the library
>
>
> Please, clarify that stat
tures of deal.II people are using in their own
projects.
Thanks,
David Wells
--
The deal.II project is located at http://www.dealii.org/
For mailing list/forum options, see
https://groups.google.com/d/forum/dealii?hl=en
---
You received this message because you are subscribed to the Google G
deal.II with our own bundled subset of boost which is
known to work. Let me know if that does not fix things.
Thanks,
David Wells
On Sunday, February 5, 2017 at 6:31:56 AM UTC-5, H. Vukman wrote:
>
> I have a problem with the installation. This is the error I get:
>
> In file includ
Dear Vinayak,
Jean-Paul is right: we got rid of this function in the fall in favor of
parse_input so that we can mark errors by raising exceptions (instead of
returning a boolean, which is what read_input does).
Thanks,
David Wells
On Sunday, January 29, 2017 at 1:14:58 PM UTC-5, Jean-Paul
Hi Giulia,
I used deal.II in my thesis to do model reduction (Wolfgang was kind enough
to include a link), but I used POD and not RB. Let me know if you have
questions about the thesis :)
Thanks,
David Wells
On Thursday, December 1, 2016 at 8:18:56 AM UTC-5, Giulia Deolmi wrote:
>
> Dea
A useful flag that I use in release mode is -funsafe-loop-optimizations,
which assumes that loop counters cannot overflow and other such things. I
don't remember the exact numbers but I do remember that using this flag
made a small, but measurable, performance improvement.
On Thursday, Septembe
Hi Jiaqi,
I have to admit that it has been about a year since I last really looked at
step-35 and I do not know the answer off the top of my head for this. I saw
that Daniel responded to this question elsewhere; was that enough to figure
things out?
Thanks,
David Wells
On Friday, July 29
Thanks,
David Wells
#!/usr/bin/env python
import collections
import datetime
import matplotlib.pyplot as plt
# data generated with
#
# git log --date=iso | grep '^Date:' | awk '{print $2}' >
commit-dates.txt
#
dates = list()
with open('commit-dates.txt', 'r&#
our machine. But I
> have installed necessary packages for Deal.II, i.e. CMake 2.8.10.2, GNU
> make 3.81, as well as gcc 4.7.2 and the other ones.
>
> Thank you very much!
>
> Yours sincerely,
> Nguyen Thien Binh
>
> 2016-07-12 9:17 GMT+09:00 David Wells :
>
>> T
installing
just that through apt-get should suffice. What exactly was the error
message when you tried just that?
Regardless, the library should just work with the latest Ubuntu release so
this is an issue on our end. Thank you for reporting this.
Thanks,
David Wells
On Monday, July 11, 2016 at 11:58
Thank you JP :)
Did you try compiling the library without threads?
I believe you said earlier that you were using centOS. What is the exact
version information of your operating system?
Thanks,
David Wells
On Mon, Jul 11, 2016 at 2:29 PM, Jean-Paul Pelteret
wrote:
> Thanks for point
Someone with administrative priviledges: the last message also has a
picture in it with an IP address. Could you delete that too?
--
The deal.II project is located at http://www.dealii.org/
For mailing list/forum options, see
https://groups.google.com/d/forum/dealii?hl=en
---
You received this
thing).
I am running out of explanations for this error. Would you humor me and
check that you do have /usr/lib/libpthread.so or /usr/lib64/libpthread.so
on your system? Perhaps the libraries are in some strange place that CMake
cannot find.
Thanks,
David Wells
On Tuesday, July 5, 2016 at 12:
your build directory)? Mine specifies the
variable THREAD_LINKER_FLAGS; I suspect that variable is not correct in
your copy.
Thanks,
David Wells
On Sun, Jul 3, 2016 at 9:30 PM, Thien Binh Nguyen
wrote:
> Dear Mr. Wells,
>
> Thank you very much for your prompt response, and I am als
particular library.
Since it looks like the library is in '/root/': did you compile this as
root? If so weird things can happen; you should build it as an unprivileged
user.
Thanks,
David Wells
On Thursday, June 30, 2016 at 2:00:22 AM UTC-4, deal.II newbie wrote:
>
> Hi! I am a n
r possible
work around would be to project that point onto the face and then see if
the vector from the point to the projected point faces in or out of the
cell.
I hope that one of these helps.
Thanks,
David Wells
On Thursday, May 19, 2016 at 9:47:36 AM UTC-4, Andreas Krämer wrote:
>
> Hi,
implemented an example of this in the cdr code gallery entry:
https://github.com/dealii/code-gallery/tree/master/cdr
Let me know if this helps.
Thanks,
David Wells
On Monday, May 30, 2016 at 10:35:14 AM UTC-4, Juan Carlos Araujo Cabarcas
wrote:
>
> Dear all,
>
> I have several independent
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