[deal.II] Re: Publications based on deal.II
Dear Prof. Wolfgang Please add my PhD thesis which used DEAL.II on simulation of hydro mechanical coupling of fractured porous media by embedded fractured continuum approach (EFCA) Title: "A hydro-mechanical modeling of double porosity and double permeability fractured reservoirs", France, 2018 Link: ftp://ftp.univ-orleans.fr/theses/honglam-dang_3747.pdf By this email, I also thank to all DEAL.II users and DEAL.II developers especially Prof. Thomas WICK who helped me to finish my PhD work in France. On Tuesday, August 28, 2018 at 2:33:37 PM UTC+7, Alberto Salvadori wrote: > > Dear Wolfgang, > > we just published the paper: > > A. Salvadori Et Al, "Modeling and Simulation of VEGF Receptors Recruitment > in Angiogenesis," Mathematical Problems in Engineering, vol. 2018, Article > ID 4705472, 10 pages, 2018. https://doi.org/10.1155/2018/4705472/. > > using and quoting deal.ii . > > Best and thanks again for your efforts, deal.ii is a great tool for > numerical science indeed. > > Alberto > > Il giorno martedì 24 aprile 2018 19:41:14 UTC+2, Wolfgang Bangerth ha > scritto: >> >> >> All, >> >> as you may know, we try to list all publications based on deal.II at >> http://dealii.org/publications.html >> We use this list to justify the effort we spend on writing this >> software, both to our universities as well as the funding agencies that >> support its development. >> >> In anticipation of the next release, we would like to update this page. >> If you have (or know of) a publication that uses deal.II for numerical >> results and that isn't already listed, please let us know so we can put >> it on there. For this purpose, publications also include MSc, Diploma or >> PhD theses, or anything else that may seem appropriate. >> >> Thanks! >>Wolfgang >> >> -- >> >> Wolfgang Bangerth email: bang...@colostate.edu >> www: http://www.math.colostate.edu/~bangerth/ >> > -- 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 Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [deal.II] Repost Is the approach for the electrostatic Bi-linear form correct?
Hello Jean, I was going through the deail.ii documentation and I came
across this class:
https://dealii.org/9.0.0/doxygen/deal.II/classDataPostprocessorVector.html
Is this what you we referring to?
On Wednesday, September 5, 2018 at 3:17:14 AM UTC-4, Jean-Paul Pelteret
wrote:
>
> Dear Philip,
>
> It looks to me like you’re mixing things up a little bit. In all of the
> equations that you presented there is a mixture of governing equations,
> assumed relationships and the consequence of combining them. From what I
> can tell you’re actually trying to use the same equation more than once
> which is problematic. (I hope that I have clearly understood what you’re
> trying to do, otherwise what follows is a bit of a waste of space and time…)
>
> I think that if you work from the irrefutable, then there should be little
> confusion. So let me see if I can help by sketching out electrostatics from
> the basics, as I know it:
>
> The starting point is Maxwell’s equations. Let’s immediately simplify
> things by saying that we already assume a quasi-static state — this means
> that the electric and magnetic fields are now decoupled. We then get
> (1) div *d* = \rho^{f} [Gauss’ law]
> (2) curl *e* = *0* [Faraday’s law]
> on B. Here *d* is the electric displacement vector, *e* is the electric
> field vector, and \rho^{f} is the free charge density.
>
> There is a further fundamental constitutive law that links *d *and *e,*
> namely
> *(*3) *d* = \epsilon_{0} \epsilon_{r} *e*
> where \epsilon_{0} is the electric permittivity of free space and
> \epsilon_{r} is the relative permittivity of the material. Here I have
> assumed that this material is linearly polarisable, so that is that the
> polarisation is in the same direction as the electric field (that’s where
> the scaling factor \epsilon_{r} comes from).
>
> There are also the continuity conditions for Maxwells equations, which for
> this simplified scenario would be
> (4) *n* x [[*e*]] = *0*
> (5) *n* . [[*d*]] = 0(assuming no surface charges)
> on dB. Here *n* is a surface normal and [[ ]] denotes the jump of a
> quantity, “.” the dot product and “x” the cross product.
>
> So, going back to Maxwell’s equations, you now need to choose which
> variable is going to be the primary variable, and which one follows from it
> (so use (3) in (1) or (2)). Since in general you wish to include source
> terms \rho^{f}, it is appropriate to choose the electric field to be the
> primary variable. what comes next is that you substitute (3) into (1)
> thereby eliminating the electric displacement from the equation:
> (6) div *[*\epsilon_{0} \epsilon_{r} *e*] = \rho^{f}
> —>
> (7) div *[**e*] = \rho^{f} / [\epsilon_{0} \epsilon_{r}]
>
> So now (7) represents an amended form of (1) that needs to be solved, but
> we still need to satisfy (2). So what we do is to exploit the identity
> (a) curl (grad (s)) = *0 *
> for all arbitrary scalars s. So we postulate the existence of an electric
> scalar potential field V that is linked to the electric field by
> (8) *e* = -grad V
> Using the identity (a), you can see that this satisfies (2):
> (b) curl *e* = curl (- grad V) == *0*
>
> Now we can put (8) into (7), knowing that if we solve
> (9) div *[*-grad V] = \rho^{f} / [\epsilon_{0} \epsilon_{r}]
> —>
> (10) - delta V = \rho^{f} / [\epsilon_{0} \epsilon_{r}]
> for V then we automatically satisfy (2). Remember that (10) is nothing
> other that (1) in disguise. So this actually satisfies both of Maxwell’s
> electrostatic governing equations at the same time (since we solve for the
> electric scalar potential).
>
> Now, about those continuity conditions… So when you discretise the field V
> using continuous finite elements, then (4) is automatically satisfied
> because the continuity of the solution ensures that there is no jump in the
> solution V, and therefore no tangential jump in grad V. You can see this
> from
> (11) *0 *= *n* x [[*e*]] =(8)= *n* x [[-grad V]] = *n* x grad [[V]]
> Finally, (5) is satisfied automatically through this same assumption
> (12) 0 = *n* . [[*d*]] =(3)= *n* . [[\epsilon_{0} \epsilon_{r} *e*]]
> =(8)= \epsilon_{0} \epsilon_{r} *n* . [[-grad V]] = -\epsilon_{0}
> \epsilon_{r} *n* . grad[[V]]
>
> So, in summary, the strong form of the governing equation to be
> implemented is (10), with the solution for V leading to the electric field
> by (8) and subsequently the electric displacement by (3). The continuity
> conditions (4,5) are satisfied if the solution for V is continuous.
>
> Does this make sense, and does it help clear up things?
>
> Best regards,
> Jean-Paul
>
> On 05 Sep 2018, at 04:59, phillip mobley > wrote:
>
> Hello Wolfgang,
> Thank you for your reply. What you described above is the first approach
> that I took. There are some differences but overall, it is the same thing.
> I am not familiar with the form:
>
> div E - Delta V = 0
>
> but, I was able to figure out how you came this.
Re: [deal.II] Re: Problems using MPI : program executed n times on n processors to execute the same thing
Bastien,
How can you uninstall MPI in a safe way? If I uninstall MPI, some related (
*important
*) packages will be broken.
Best,
Yaakov
On Monday, April 4, 2016 at 6:19:34 PM UTC+2, Bastien Lauras wrote:
>
> Bruno,
>
> The first time I ran mpirun --version, it said :
>
> mpirun (Open MPI) 1.6.5
>
> Report bugs to http://www.open-mpi.org/community/help/
>
>
> So I uninstalled openmpi and mpich, and then re-installed mpich. Now,
> mpirun --version gives me :
>
> HYDRA build details:
> Version: 3.0.4
> Release Date:Wed Apr 24 10:08:10 CDT 2013
> CC: cc -D_FORTIFY_SOURCE=2 -g -O2
> -fstack-protector --param=ssp-buffer-size=4 -Wformat
> -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro
> CXX: c++ -D_FORTIFY_SOURCE=2 -g -O2
> -fstack-protector --param=ssp-buffer-size=4 -Wformat
> -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro
> F77: gfortran -g -O2
> -Wl,-Bsymbolic-functions -Wl,-z,relro
> F90: gfortran -Wl,-Bsymbolic-functions
> -Wl,-z,relro
> Configure options: '--disable-option-checking'
> '--prefix=/usr' '--build=x86_64-linux-gnu' '--includedir=${prefix}/include'
> '--mandir=${prefix}/share/man' '--infodir=${prefix}/share/info'
> '--sysconfdir=/etc' '--localstatedir=/var'
> '--libdir=${prefix}/lib/x86_64-linux-gnu'
> '--libexecdir=${prefix}/lib/x86_64-linux-gnu' '--disable-maintainer-mode'
> '--disable-dependency-tracking' '--enable-shared' '--enable-fc'
> '--disable-rpath' '--disable-wrapper-rpath' '--sysconfdir=/etc/mpich'
> '--libdir=/usr/lib/x86_64-linux-gnu' '--includedir=/usr/include/mpich'
> '--docdir=/usr/share/doc/mpich' '--with-hwloc-prefix=system'
> '--enable-checkpointing' '--with-hydra-ckpointlib=blcr'
> 'build_alias=x86_64-linux-gnu' 'MPICHLIB_CFLAGS=-g -O2 -fstack-protector
> --param=ssp-buffer-size=4 -Wformat -Werror=format-security'
> 'MPICHLIB_CXXFLAGS=-g -O2 -fstack-protector --param=ssp-buffer-size=4
> -Wformat -Werror=format-security' 'MPICHLIB_FFLAGS=-g -O2'
> 'MPICHLIB_FCFLAGS=-g -O2' 'CFLAGS=-g -O2 -fstack-protector
> --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2
> -fstack-protector --param=ssp-buffer-size=4 -Wformat
> -Werror=format-security -O2' 'LDFLAGS=-Wl,-Bsymbolic-functions -Wl,-z,relro
> ' 'CPPFLAGS=-D_FORTIFY_SOURCE=2 -I/build/buildd/mpich-3.0.4/src/mpl/include
> -I/build/buildd/mpich-3.0.4/src/mpl/include
> -I/build/buildd/mpich-3.0.4/src/openpa/src
> -I/build/buildd/mpich-3.0.4/src/openpa/src
> -I/build/buildd/mpich-3.0.4/src/mpi/romio/include' 'CXXFLAGS=-g -O2
> -fstack-protector --param=ssp-buffer-size=4 -Wformat
> -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4
> -Wformat -Werror=format-security -O2' 'F77=gfortran' 'FFLAGS=-g -O2 -g -O2
> -O2' 'FC=gfortran' '--cache-file=/dev/null' '--srcdir=.' 'CC=cc' 'LIBS=-lrt
> -lcr -lpthread '
> Process Manager: pmi
> Launchers available: ssh rsh fork slurm ll lsf sge
> manual persist
> Topology libraries available:hwloc
> Resource management kernels available: user slurm ll lsf sge pbs
> cobalt
> Checkpointing libraries available: blcr
> Demux engines available: poll select
>
>
> I tried to run the step-17 tutorial, I had the same output than before
> (like : Number of degrees of freedom: 570 (by partition: 570) )
> Should I recompile Deal.II now?
>
> Thanks for your help.
>
> Bastien
>
>
> On Monday, April 4, 2016 at 10:31:16 AM UTC-5, Bruno Turcksin wrote:
>>
>> Bastien,
>>
>> Can you try mpirun --version it should say MPICH However, I strongly
>> advise you to have either openmpi or mpich installed but not both. Having
>> both installed will lead to hard to understand bug.
>>
>> Best,
>>
>> Bruno
>>
>> On Monday, April 4, 2016 at 11:23:12 AM UTC-4, Bastien Lauras wrote:
>>>
>>> And here is what I have in my *bin* folder :
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Monday, April 4, 2016 at 9:51:19 AM UTC-5, Bastien Lauras wrote:
Hi, Thanks for answering!
Here are the outputs :
bastien@PC-Bastien:~$ which mpirun
/usr/bin/mpirun
bastien@PC-Bastien:~$ which mpic++
/usr/bin/mpic++
bastien@PC-Bastien:~/build$ grep MPI detailed.log
#CMAKE_CXX_COMPILER: GNU 4.8.4 on platform Linux x86_64
#CMAKE_C_COMPILER: /usr/bin/cc
#CMAKE_Fortran_COMPILER: /usr/bin/gfortran
#DEAL_II_WITH_MPI set up with external dependencies
#MPI_VERSION = 3.0
#MPI_C_COMPILER = /usr/bin/mpicc
#MPI_CXX_COMPILER = /usr/bin/mpicxx
#
