[deal.II] open PhD position

Dear community a fully funded, three years long PhD position is available at the m4lab at the University of Brescia (https://m4lab.unibs.it), under the supervision of Prof. A. Salvadori. The candidate will collaborate in the development of deal.ii - based FEM codes for modeling thermo-chemo-mec

[deal.II] candi installation issue

Dear community while installing deal.ii on a new machine with candi I got this message. *candi tries now to download, configure, build and install:Project: deal.II-toolchainPlatform: deal.II-toolchain/platforms/supported/ubuntu.platformLoading dealii-prepareFetching opencascade

Re: [deal.II] Installing an older version with candi

Sorted out. Sorry to bother. Alberto *Alberto Salvadori* Dipartimento di Ingegneria Meccanica e Industriale (DIMI) Universita` di Brescia, via Branze 43, 25123 Brescia Italy tel 030 3715426 e-mail: alberto.salvad...@unibs.it web-page: http://m4lab.unibs.it/faculty.html On Tue, Feb 14

[deal.II] Installing an older version with candi

Dear community I would like to install the dealii version 9.2.0 via candi. I noticed the file VERSION and assumed that replacing "9.4.2-r2" with "9.2.0" would work. Apparently it is not effective, candi is still unpacking in the directory deal.ii-v9.4.2. Can anyone address me to solve the issue

Re: [deal.II] SEGMENTATION FAULT(CORE DUMPED)

the issue. Perhaps someone in the community has had similar problems and can address us. dealii-candi 9.4.0 was compiled with gcc 13.3.0 Alberto *Alberto Salvadori* Dipartimento di Ingegneria Meccanica e Industriale (DIMI) Universita` di Brescia, via Branze 43, 25123 Brescia Italy tel 030

[deal.II] Re: dealii-9.4.0 release candidate 1

Matthias, I wonder if this release is fully compatible with Apple M1 (and M2 as well) or not. Thank you, Alberto Il giorno giovedì 16 giugno 2022 alle 23:04:32 UTC+2 Matthias Maier ha scritto: > Dear all, > > We have tagged a first release candidate for the upcoming deal.II 9.4.0 > release

[deal.II] Re: Affine constraints distribute_local_to_global

ing those ideas, I found the .print method of AffineConstraints particularly useful. Alberto Il giorno martedì 10 agosto 2021 alle 06:52:40 UTC+2 Alberto Salvadori ha scritto: > Dear community > > I am asking your help today about imposing affine constraints. I > understood well example

[deal.II] Affine constraints distribute_local_to_global

Dear community I am asking your help today about imposing affine constraints. I understood well example 6, but when it comes to apply it to sparse MPI matrices I get lost. I am not sure if example 27 is of help for my case. What would I like to simulate? Take two separate domains, with conforma

Re: [deal.II] errors in running step-18 within Xcode

17 step-18 unix % which cmake /Applications/deal.II.app/Contents/Resources/Libraries/bin/cmake albertosalvadori@uu-guest-150-117 step-18 unix % *Alberto Salvadori* Dipartimento di Ingegneria Meccanica e Industriale (DIMI) Universita` di Brescia, via Branze 43, 25123 Brescia Italy tel 030

Re: [deal.II] errors in running step-18 within Xcode

release 5. make 6. ./step-18 Illegal instruction: 4 *Alberto Salvadori* Dipartimento di Ingegneria Meccanica e Industriale (DIMI) Universita` di Brescia, via Branze 43, 25123 Brescia Italy tel 030 3715426 e-mail: alberto.salvad...@unibs.it web-page: http://m4lab.unibs.it/faculty.html

Re: [deal.II] Re: issue in installing dealii 9.2 and .3 on centos

-476qnx2qlzhfboru3b6cn5sw4auxjtkp spec: gmsh@4.8.4%gcc@7.4.0~med+tetgen+oce spack install dealii%gcc@7.4.0 Thank you for your help. Alberto *Alberto Salvadori* Dipartimento di Ingegneria Meccanica e Industriale (DIMI) Universita` di Brescia, via Branze 43, 25123 Brescia Italy tel 030

Re: [deal.II] Re: issue in installing dealii 9.2 and .3 on centos

ant +tetgen, but spec asked for ~tetgen [asalvado@r000u07l02 uBS21_CivSal_0]$ *Alberto Salvadori* Dipartimento di Ingegneria Meccanica e Industriale (DIMI) Universita` di Brescia, via Branze 43, 25123 Brescia Italy tel 030 3715426 e-mail: alberto.salvad...@unibs.it web-page: h

Re: [deal.II] Re: issue in installing dealii 9.2 and .3 on centos

Bruno, I do import gmsh triangulations in dealii simulations. Would this be possible without including gmsh ? Alberto *Alberto Salvadori* Dipartimento di Ingegneria Meccanica e Industriale (DIMI) Universita` di Brescia, via Branze 43, 25123 Brescia Italy tel 030 3715426 e-mail

Re: [deal.II] Re: issue in installing dealii 9.2 and .3 on centos

-centos7-broadwell I am using [asalvado@r000u07l02 uBS21_CivSal_0]$ spack --version 0.16.2-3715-a904418 Your help is appreciated. Alberto *Alberto Salvadori* Dipartimento di Ingegneria Meccanica e Industriale (DIMI) Universita` di Brescia, via Branze 43, 25123 Brescia Italy tel 030 3715426 e

[deal.II] issue in installing dealii 9.2 and .3 on centos

Dear community while installing deal.ii on a centos cluster, I am facing the following issue related to med : *==>* *Installing* *med-4.0.0-d65qwjrfigoxirhf5xy6lsumdwpcvluf* *==>* Warning: Spack will not check SSL certificates. You need to update your Python to enable certificate verification.

[deal.II] Fully funded PhD position at m4lab@UNIBS

Dear community, The Multiscale Mechanics and Multiphysics of Materials Lab ( http://m4lab.unibs.it) at the School of Engineering, University of Brescia, Italy announces a PhD fellowship on *Modeling and simulations for next generation lithium-ion cells via deal.ii*. The fellowship is fully funde

Re: [deal.II] AffineCostraints and MPI

Thank you, Wolfgang. I sorted it out, following the hanging node constraint sequence of instructions. It seems to work just fine. *Alberto Salvadori* Dipartimento di Ingegneria Meccanica e Industriale (DIMI) Universita` di Brescia, via Branze 43, 25123 Brescia Italy tel 030 3715426 e-mail

Re: [deal.II] dealii/spack on apple m1

limited, but with some further work (that I cannot recall now) I made it, even with Xcode projects. Hope it helps Alberto *Alberto Salvadori* Dipartimento di Ingegneria Meccanica e Industriale (DIMI) Universita` di Brescia, via Branze 43, 25123 Brescia Italy tel 030 3715426 e-mail: alberto.salvad

[deal.II] AffineCostraints and MPI

Dear community, I wonder if you could address me to study how to solve this problem, which I am sure is quite simple. Basically, I would like to rephrase The step-11 tutorial program for parallel::shared matrices, as in step 18. If I am not wrong the "condense" methods do not apply to MPI::Spars

Re: [deal.II] Re: issue in installing dealii@9.2 on ubuntu through spack

ll' ==> dealii: Successfully installed dealii-9.2.0-ixyu3bhuwzk3ydljzr64vspiwnqcqyoa Fetch: 0.14s. Build: 16m 12.77s. Total: 16m 12.91s. Alberto Il giorno venerdì 15 gennaio 2021 alle 17:44:44 UTC+1 Jean-Paul Pelteret ha scritto: > Hi Alberto, > > Thanks for pointin

Re: [deal.II] Re: issue in installing dealii@9.2 on ubuntu through spack

Thank you, very useful. I suggest adding this info to the wiki page , in place of git checkout master. *Alberto Salvadori* Dipartimento di Ingegneria Meccanica e Industriale (DIMI) Universita` di Brescia, via Branze 43, 25123 Brescia Italy tel 030 3715426 e-mail: alberto.salvad...@unibs.it

[deal.II] issue in installing dealii@9.2 on ubuntu through spack

Dear community I have been trying installing dealii@9.2 on ubuntu 18.04 gcc7.5.0, unsuccesfully. The version 9.1.1 is already installed and works just fine, at that installation time I did manage to install adol-c@2.7.3 and I put its path into the pacages.yaml as I did for dealii@9.1.1 URL in f

Re: [deal.II] FEInterfaceValues

ou suspected, I am computing terms for the interface matrix that are not part of the sparsity pattern of the Trilinos matrix. If this is correct, do you see a way to circumvent the TRILINOS problem I am facing? Thank you, Alberto *Alberto Salvadori* Dipartimento di Ingegneria Meccanica e

Re: [deal.II] FEInterfaceValues

regard? Thank you so much, Alberto *Alberto Salvadori* Dipartimento di Ingegneria Meccanica e Industriale (DIMI) Universita` di Brescia, via Branze 43, 25123 Brescia Italy tel 030 3715426 e-mail: alberto.salvad...@unibs.it web-page: http://m4lab.unibs.it/faculty.html On Wed, Dec 23, 2020 a

Re: [deal.II] FEInterfaceValues

library. Thank you again Alberto *Alberto Salvadori* Dipartimento di Ingegneria Meccanica e Industriale (DIMI) Universita` di Brescia, via Branze 43, 25123 Brescia Italy tel 030 3715426 e-mail: alberto.salvad...@unibs.it web-page: http://m4lab.unibs.it/faculty.html On Sat, Dec 26, 2020

Re: [deal.II] FEInterfaceValues

07:11:47 UTC+1 Alberto Salvadori ha scritto: > Dear community > > After Timo's suggestions I attempted at assembling matrix and rhs for > problems with an interface, using continuum elements (not DG). > I mean at this: take two domains connected by springs and pull them apar

Re: [deal.II] FEInterfaceValues

e_constraints.close (); Can I ask from some hints? Thank you so much Alberto Il giorno martedì 22 dicembre 2020 alle 10:26:22 UTC+1 Alberto Salvadori ha scritto: > Timo, > thank you. These two files are extremely helpful and I guess I understood > a lot from them. Extremely well wr

Re: [deal.II] FEInterfaceValues

fe_face1_values.get_function_values ( accumulated_displacement, old_solution_values_at_face_0 ); I am concerned about the correspondence of quadrature points on the interface and on the cell faces. Is there a simple and effective way to find their association? Thanks, Alberto *Alberto Salvadori

Re: [deal.II] faces barycenter

You are right, of course, Wolfgang. I should offer to contribute in the development of this method. I will. Thank you Alberto *Alberto Salvadori* Dipartimento di Ingegneria Meccanica e Industriale (DIMI) Universita` di Brescia, via Branze 43, 25123 Brescia Italy tel 030 3715426 e-mail

[deal.II] faces barycenter

Dear community I observed that this instruction: Point centroid = cell->face(face_number)->barycenter() ; provides always centroid = {0,0,0}, whereas the following Point centroid = cell->face(face_number)->center() ; returns the correct amount. Am I misunderstanding something or may it be a b

[deal.II] FEInterfaceValues

Dear community I would like to have a few more details on the class FEInterfaceValues . since it is my feeling that FEInterfaceValues might b

Re: [deal.II] catching SolverControl::NoConvergence

itto: > On 7/29/20 5:37 AM, Alberto Salvadori wrote: > > > > try > > { > > iterate_on_tolerance = false ; > > this->pcout << " AMG - Bicgstab " << std::flush ; > > > > bicgstab.solve (this->system_matrix,

Re: [deal.II] Re: Memory loss in system solver

t; still help. > > Best, > Daniel > > Am Fr., 24. Juli 2020 um 12:07 Uhr schrieb Alberto Salvadori < > alberto@unibs.it>: > >> Dear community, >> >> if I am not mistaking my analysis, it turned out that the memory loss is >> caused by th

[deal.II] catching SolverControl::NoConvergence

Dear community in these days I am particularly bothering you, I apologize. Today, I wonder if I can receive some clarifications on catching the exception SolverControl::NoConvergence in using trilinos. I wrote the code below for a linear system solver: SolverControl bicgstab_solver_control (

Re: [deal.II] Memory loss in system solver

isposal, of course. Hope this helps. Alberto Il giorno sabato 25 luglio 2020 alle 05:46:08 UTC+2 Wolfgang Bangerth ha scritto: > On 7/24/20 3:32 AM, Alberto Salvadori wrote: > > > > It turns out that this code produces a memory loss, quite significant > since I > &g

Re: [deal.II] Memory loss in system solver

It happens to me the same, the memory loss increments at each call if the solver. It happens with BICG and with GMRES as well. Alberto Salvadori Associate Professor DIMI, University of Brescia, Italy > On 25 Jul 2020, at 10:24, Richard Schussnig > wrote: > > Hi Alberto,

[deal.II] Re: Memory loss in system solver

at all. Maybe this is of use. Thanks in advance. Alberto Il giorno venerdì 24 luglio 2020 alle 11:32:13 UTC+2 Alberto Salvadori ha scritto: > Dear community > > I have written the simple code below for solving a system using PETSc, > having defined > > Vector incrementa

[deal.II] Memory loss in system solver

Dear community I have written the simple code below for solving a system using PETSc, having defined Vector incremental_displacement; Vector accumulated_displacement; in the class LargeStrainMechanicalProblem_OneField. It turns out that this code produces a memory loss, quite significant since

[deal.II] Re: 9.2 issue during compilation on macOSX

ease mode, providing the following output: bash-3.2$ ./step-17 dyld: malformed mach-o: load commands size (33840) > 32768 Abort trap: 6 Any help appreciated. Thanks Alberto Il giorno lunedì 15 giugno 2020 alle 19:15:09 UTC+2 Alberto Salvadori ha scritto: > Hi, > > I just installed r

[deal.II] 9.2 issue during compilation on macOSX

Hi, I just installed release 9.2, with great pleasure on my mac. Not working yet. Here is the error I receive, my OSX is 10.15.4 (19E287) and Xcode 11.5 (11E608c) *Developer Tools:* Version: 11.5 (11E608c) Location: /Applications/Xcode.app Applications: Xcode: 11.5 (16139)

Re: [deal.II] vertex and dofcells

Thank you, Jean Paul. Exhaustive, as usual. *Alberto Salvadori* Dipartimento di Ingegneria Meccanica e Industriale (DIMI) Universita` di Brescia, via Branze 43, 25123 Brescia Italy tel 030 3715426 e-mail: alberto.salvad...@unibs.it web-page: http://m4lab.unibs.it/faculty.html On Tue

[deal.II] vertex and dofcells

Dear community, this looks a simple question but I just cannot find a simple answer, I apologize. The code I aim at writing is similar to: *unsigned* vv = 0 ; *for* (*unsigned* *int* ii=0; ii this_node = cell->vertex(vv) ; [ ... omitted code

[deal.II] deal.ii 9.1.1 quit running after macOS Catalina update

Dear community, Luca in particular sorry for this bothering. It happened again, as on Dec. 2 , 2019 that after a macOS update deal.ii 9.1.1 quit running. There appears to be an issue with the PETScWrappers to MPI, for what I understand. I really appreciate your help. Alberto Here is a log:

Re: [deal.II] deal stopped working with latest macOS update (10.15)

It works very well. Thank you so much, Luca. Alberto *Alberto Salvadori* Dipartimento di Ingegneria Meccanica e Industriale (DIMI) Universita` di Brescia, via Branze 43, 25123 Brescia Italy tel 030 3711239 fax 030 3711312 e-mail: alberto.salvad...@unibs.it web-page: http://m4lab.unibs.it

Re: [deal.II] deal stopped working with latest macOS update (10.15)

*Alberto Salvadori* Dipartimento di Ingegneria Meccanica e Industriale (DIMI) Universita` di Brescia, via Branze 43, 25123 Brescia Italy tel 030 3711239 fax 030 3711312 e-mail: alberto.salvad...@unibs.it web-page: http://m4lab.unibs.it/faculty.html On Fri, Dec 6, 2019 at 11:18 AM luca.heltai

Re: [deal.II] deal stopped working with latest macOS update (10.15)

./step-20 Illegal instruction: 4 *Alberto Salvadori* Dipartimento di Ingegneria Meccanica e Industriale (DIMI) Universita` di Brescia, via Branze 43, 25123 Brescia Italy tel 030 3711239 fax 030 3711312 e-mail: alberto.salvad...@unibs.it web-page: http://m4lab.unibs.it/faculty.html

Re: [deal.II] Re: error during installation with spack on CentOS7

redefined in the spack system in order to configure the installation of deal.ii. Whom should I address this question to? Alberto *Alberto Salvadori* Dipartimento di Ingegneria Meccanica e Industriale (DIMI) Universita` di Brescia, via Branze 43, 25123 Brescia Italy tel 030 3711239 fax 030 3711312 e

[deal.II] Re: error during installation with spack on CentOS7

Sorry to invoke your help again, since though I am stuck in the very final step, I wonder if anyone can provide some suggestions to the issue below. I really appreciate Alberto Il giorno mercoledì 9 ottobre 2019 09:30:18 UTC+2, Alberto Salvadori ha scritto: > > Hi Denis > > thank y

[deal.II] Re: error during installation with spack on CentOS7

Spack Github. Thank you, Alberto Il giorno venerdì 4 ottobre 2019 12:50:24 UTC+2, Alberto Salvadori ha scritto: > > Dear community > > I apologize for this too long bothering on installing deal.ii on a linux > machine equipped with CentOS7. I am having quite a large amount of iss

[deal.II] Re: error during installation with spack on CentOS7

xCompleteClone' collect2: error: ld returned 1 exit status gmake: *** [checklink] Error 1 ERROR: Unable to link with PETSc Could it be related to make? It is still the GNU Make 3.82 . Thank you so much Alberto Il giorno martedì 1 ottobre 2019 19:02:43 UTC+2, Alberto Salvadori ha

Re: [deal.II] Re: error during installation with spack on CentOS7

;> to the correct libstdc++ in my LD_LIBRARY_PATH when I load the module. >> So I guess you need to add that path somewhere in your compilers.yaml >> >> Best, >> >> Bruno >> >> Le mer. 2 oct. 2019 à 08:51, Alberto Salvadori >> a écrit

Re: [deal.II] Re: error during installation with spack on CentOS7

Bruno, I guess the point is that cmake invokes /lib64/libstdc++.so.6 rather than /usr/local/lib64/libstdc++.so.6 Is it correct? *Alberto Salvadori* Dipartimento di Ingegneria Meccanica e Industriale (DIMI) Universita` di Brescia, via Branze 43, 25123 Brescia Italy tel 030 3711239 fax 030

Re: [deal.II] Re: error during installation with spack on CentOS7

: {} extra_rpaths: [] flags: {} modules: [] operating_system: centos7 paths: cc: /usr/local/bin/gcc cxx: /usr/local/bin/g++ f77: /usr/local/bin/gfortran fc: /usr/local/bin/gfortran spec: gcc@9.2.0 target: x86_64 *Alberto* *Alberto Salvadori

Re: [deal.II] Re: error during installation with spack on CentOS7

2ih5ctlebz57xqk7kvgzv22tabfbq4/spack-build-out.txt Is it perhaps due to a conflict between cmake and the gcc compiler versions? Can you perhaps address me how to sort this out? I appreciate, Alberto *Alberto Salvadori* Dipartimento di Ingegneria Meccanica e Industriale (DIMI) Universita`

Re: [deal.II] Re: error during installation with spack on CentOS7

Thank you so much W and D, As you pointed out there seems to be a mistake in the most recent version of perl during installation. I will point this out in the proper communities. As Denis proposed *Alberto Salvadori* Dipartimento di Ingegneria Meccanica e Industriale (DIMI) Universita` di

[deal.II] error during installation with spack on CentOS7

Dear community I have been trying to install deal.ii on a linux machine equipped with CentOS7. As very clearly explained in " https://github.com/dealii/dealii/wiki/deal.II-in-Spack#check-before-build " I have installed the latest version of gcc, openmpi, cmake. [deal.ii@localhost spack]$ gcc -

Re: [deal.II] Extracting volume data to the boundary

Thank you very much, Luca. Alberto Salvadori Associate Professor DIMI, University of Brescia, Italy > On 11 Sep 2019, at 08:38, luca.heltai wrote: > > Alberto, > > be aware of the fact that, when you extract the boundary mesh, the > orientation of the cells may be diffe

Re: [deal.II] Re: Extracting volume data to the boundary

there a "simple way" to get the (volume) cell iterator and the face_number from the parallel::shared::Triangulation::face_iterator in the map returned by the extract_boundary_mesh() function? Or shall I use a different way to reinit FEFaceValues? Thank you Alberto *Alberto Salvadori* Di

[deal.II] Re: Extracting volume data to the boundary

lls_end; ++manifoldcells_to_volumecells_it) *this*->pcout << "[ " << manifoldcells_to_volumecells_it->first->*id*() << ", " << manifoldcells_to_volumecells_it->second->*id*() << " ], " << std ::flush;

[deal.II] Re: Extracting volume data to the boundary

Il giorno martedì 3 settembre 2019 18:36:59 UTC+2, Alberto Salvadori ha scritto: > > Dear community > > I am trying to find a good way to deal with the following problem. > > I am interested in a Laplace-Beltrami simulation (say with unknown scalar > field c) on a surface that adv

[deal.II] Extracting volume data to the boundary

Dear community I am trying to find a good way to deal with the following problem. I am interested in a Laplace-Beltrami simulation (say with unknown scalar field c) on a surface that advects (with displacement field u) enclosesing a volume of say elastic material. The two problems are per se un

Re: [deal.II] Re: Application for the use in continuum mechanics

PRISMS at Michigan state? Looks similar to what you are looking for. Alberto Alberto Salvadori Associate Professor DIMI, University of Brescia, Italy > On 16 Aug 2019, at 10:57, Lukas Lamm wrote: > > Hey Lucas, > > thanks for your response. I was actually searching for s

Re: [deal.II] Re: deal.II User and Developer Workshop: August 6-9, 2019

> Dear Wolfgang and Timo, I believe this is a very good idea. Since I cannot attend the workshop I do support Steve's request. Cheers Alberto Alberto Salvadori Associate Professor DIMI, University of Brescia, Italy > On 20 Jun 2019, at 19:32, Stephen DeWitt wrote: > >

[deal.II] Post doc position at the University of Brescia

Dear community, There is an open call for a post-doc position at the University of Brescia, Italy, at the m4lab ( multiscale mechanics and multi physics of materials). The candidate will work with international colleagues on the deal.ii implementation of crystal plasticity models for high stren

Re: [deal.II] Re: Error in installing deal.ii with spack on CentOs7

The end solution would be the same: > (i) you need to choose suite-sparse@5.1.0 which can be built with GCC 4.8.5 > (ii) you need to choose older version of PETSc which support older versions > of suite-sparse. > > Regards, > Denis. > >> On Monday, October 22, 2018 at 7:5

Re: [deal.II] Error in installing deal.ii with spack on CentOs7

-lta 110 ls share/ You see that there are two calls "spack install dealii" since I had to edit the file ".spack/linux/packages.yam" in order to install petsc 3.10 Hope this helps Alberto *Alberto Salvadori* Dipartimento di Ingegneria Civile, Architettura, Territorio, Ambi

Re: [deal.II] Error in installing deal.ii with spack on CentOs7

J-P and Praveen, Thanks for your help. Spack installation for deal.ii worked out well. Petsc 3.10 or later is required, I used 3.10. Alberto Alberto Salvadori Associate Professor DIMI, University of Brescia, Italy > On 22 Oct 2018, at 09:28, Jean-Paul Pelteret wrote: > >>

Re: [deal.II] Error in installing deal.ii with spack on CentOs7

Thank you J-P. Can you please remind me how to do what you suggest? Shall I edit “.spack/linux/packages.yaml” file ? *Alberto Salvadori* Dipartimento di Ingegneria Civile, Architettura, Territorio, Ambiente e di Matematica (DICATAM) Universita` di Brescia, via Branze 43, 25123 Brescia Italy

Re: [deal.II] Error in installing deal.ii with spack on CentOs7

opensuse a couple of weeks ago without this issue. Shall I attach my “.spack/linux/packages.yaml” here? Alberto *Alberto Salvadori* Dipartimento di Ingegneria Civile, Architettura, Territorio, Ambiente e di Matematica (DICATAM) Universita` di Brescia, via Branze 43, 25123 Brescia Italy tel

[deal.II] Error in installing deal.ii with spack on CentOs7

Dear community I am installing deal.ii (latest release) on a CentOS7 equipped machine. After typing spack install --test=root dealii I see this error: ==> Error: An unsatisfiable version constraint has been detected for spec: suite-sparse@5.3.0%gcc@4.8.5~cuda~openmp+pic~tbb arch=linux-cen

Re: [deal.II] projecting values of the solution on the boundary

f any help in promoting the discussion on github I will definitely do. Thank you again, Alberto *Alberto Salvadori* Dipartimento di Ingegneria Civile, Architettura, Territorio, Ambiente e di Matematica (DICATAM) Universita` di Brescia, via Branze 43, 25123 Brescia Italy tel 030 3711239 fax 0

[deal.II] Re: Publications based on deal.II

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 . Be

Re: [deal.II] projecting values of the solution on the boundary

ect, how to pass the geometrical info to the deal.ii triangulation? Thank you very much for any suggestions, Alberto Il giorno venerdì 24 agosto 2018 14:39:41 UTC+2, Alberto Salvadori ha scritto: > > Thank you Wolgang and Jean Paul. > > In these days I made some implementation in the line y

Re: [deal.II] projecting values of the solution on the boundary

Thank you Wolgang and Jean Paul. In these days I made some implementation in the line you propose but I am not happy with it and thus I am asking advices on a different path of reasoning. In brief: I'd like to design an algorithm to solve a problem over two separate domains connected by an in

[deal.II] projecting values of the solution on the boundary

Dear community, I am asking some advices on the following issue. I am solving a simple problem, say a Poisson problem in the unknown field u, and a more involved problem separately. This second problem requires the values of u in the Neumann boundary conditions. Accordingly, I guess one could

Re: [deal.II] Re: Error in installing deal.ii with spack on linux openSuse

Thank you! Alberto Salvadori Associate Professor DICATAM, University of Brescia, Italy > On 19 Feb 2018, at 16:06, Bruno Turcksin wrote: > > Alberto, > >> On Monday, February 19, 2018 at 9:56:25 AM UTC-5, Alberto Salvadori wrote: >> dealii requires cmake version :3.

[deal.II] Error in installing deal.ii with spack on linux openSuse

Dear community, I am trying to install deal.ii on a linux machine, equipped with openSuse ( openSUSE 12.3 (x86_64) VERSION = 12.3 CODENAME = Dartmouth) via spack. I am having the following error: spack install dealii *==>* Error: An unsatisfiable version constraint has been detected for spe

Re: AW: [deal.II] step-42 clarification

->user_pointer(), data of the loads and mesh. How can one store information on the latter, - as for the partition and the hanging nodes - correctly? I understand that saving the mesh in a "ucd" or alternative form may not be the right strategy. Thank you very much. Alberto *Albe

Re: AW: [deal.II] step-42 clarification

ated_displacement = distributed_solution; // We then merge the constraints from hanging nodes into the ConstraintMatrix object that already contains the active set. this->contact_constraints.close();// it was this->all_constraints.close(); this->all_constraints.merge(thi

[deal.II] step-42 clarification

Dear community, I am studying with pleasure step-42 and I got a bit confused in the method PlasticityContactProblem::solve_newton. At the very end of it, we find these instructions: old_active_set = active_set; previous_residual_norm = residual_norm; if (Utilities::MPI::sum

[deal.II] mesh refinement on a multilayerd hyperball (for Mie scattering problem)

Dear community, this might be a little "off topic" but perhaps of interest anyway. I am using the multilayerd hyperball proposed by Konstantin Ladutenko in the post https://groups.google.com/forum/#!searchin/dealii/sphere$20mesh%7Csort:date/dealii/pvqNQUM3eyM/o0USYKbGBQAJ. I find it a neat way

Re: [deal.II] deal.II on Mac OS Sierra

Hi Pawan, This issue has been dealt with in https://groups.google.com/forum/m/#!topic/dealii/KypFL9X0bVo Best, Alberto > On Oct 25, 2017, at 3:22 AM, Pawan Takhar wrote: > > I am a new user of deal.II. I installed 8.5.0 on Mac OS Sierra a few months > ago. I used .dmg and cmake .dmg file

Re: [deal.II] Re: Deal for Mac OS 10.13

Sure, I will. Am I understanding properly that deal.ii is trying to use the accelerate framework (I guess because of some lapack calls) when compiled for MacOS? *Alberto Salvadori* Dipartimento di Ingegneria Civile, Architettura, Territorio, Ambiente e di Matematica (DICATAM) Universita` di

[deal.II] Re: Deal for Mac OS 10.13

Hi Daniel. After installation of High Sierra, Xcode9, upgrading cmake and using deal.ii/8.5.1 provided by Timo, I run usual regression tests that worked well under Xcode8.x. It turned out that they could not be linked anymore with this error (sorry for the code name): make[2]: *** No rule to m

Re: [deal.II] Deal for Mac OS 10.13

Hi, I had a similar problem. It looks like that deal.ii is currently not compatible with Xcode 9. You can however install both Xcode9 (just rename it) and an older version of Xcode8.x This sorted out all issues to me. Hope it helps. Alberto *Alberto Salvadori* Dipartimento di Ingegneria Civile

Re: [deal.II] Re: Post-processing: how can the method compute_derived_quantities_vector be informed about cell->user_pointer() ?

Great, thank you all.I'll think about it and see what I can come up with. Alberto *Alberto Salvadori* Dipartimento di Ingegneria Civile, Architettura, Territorio, Ambiente e di Matematica (DICATAM) Universita` di Brescia, via Branze 43, 25123 Brescia Italy tel 030 3711239 fax 030 37113

Re: [deal.II] Re: Post-processing: how can the method compute_derived_quantities_vector be informed about cell->user_pointer() ?

I can manage by projecting tensors on three orthogonal directions and visualize as vectors, but I find this inelegant. Thanks Alberto *Alberto Salvadori* Dipartimento di Ingegneria Civile, Architettura, Territorio, Ambiente e di Matematica (DICATAM) Universita` di Brescia, via Branze 43, 25

Re: [deal.II] Re: Post-processing: how can the method compute_derived_quantities_vector be informed about cell->user_pointer() ?

en/deal.II/classDataPostprocessor.html#aadecdd040447b395164397ea1196f721> () const; private: const unsigned int partition; const double minimal_pressure; }; Can you perhaps provide some further information, to fill the gap? Thank you, Alberto *Alberto Salvadori* Dipartimento di Ingegneria Civile,

[deal.II] Post-processing: how can the method compute_derived_quantities_vector be informed about cell->user_pointer() ?

Dear all, I have been studying step-32 and I have found the class Postprocessor nice and effective. It is my understanding that the method compute_derived_quantities_vector within the class operates at a call level, i.e. that beyond the hood the class Postprocessor implements loops over the tr

[deal.II] transitioning from parallel::shared::Triangulation to parallel::distributed::Triangulation

Hi deal.ii community, I am bothering today about a code I have been writing in the shared triangulation framework and its transition to the parallel::distributed:: Triangulation framework. The shared version works just fine, and so does the parallel if run with 1 single process. I understand

[deal.II] GridGenerator::extract_boundary_mesh for parallel::shared::Triangulation

Hi all, I am trying to reproduce the code in Step 38 that extracts the boundary mesh, but I'd love to use a parallel::shared::Triangulation rather than a Triangulation class. In a nutshell, I did this: template class Sm

Re: [deal.II] Re: component mask and Dirichlet bc application

Thank you Jean Paul, very clear. Perhaps your notes could be added on the deal.II documentation system, I believe this comprehensive description is not simple to been acquired directly from the tutorials examples and class description. Alberto *Alberto Salvadori* Dipartimento di Ingegneria

[deal.II] Re: component mask and Dirichlet bc application

dim + 2; return_value( c_component ) = ... ; } Does it make sense? Thanks Alberto Il giorno mercoledì 31 maggio 2017 17:48:13 UTC-4, Alberto Salvadori ha scritto: > > Dear all, > > your help is appreciated about how component mask and Dirichlet bc > application work.

[deal.II] component mask and Dirichlet bc application

Dear all, your help is appreciated about how component mask and Dirichlet bc application work. I am implementing a SmallStrainDiffusionMechanicalProblem class, with 4 fields: displacements, pressure, dilatation, and concentration. template class SmallStrainDiffusionMechanicalProblem { ..

Re: [deal.II] Re: imposing boundary conditions for a three-fields formulation

not converge I can try GMRes rather than aborting? Is the usual try-catch instruction working? 2 - I see that the class PETScWrappers implements both BiCGStab and GMRes. Can you pinpoint to an example? Thanks Alberto *Alberto Salvadori* Dipartimento di Ingegneria Civile, Architettura, Territor

Re: [deal.II] Re: imposing boundary conditions for a three-fields formulation

that this is not happening, in all cases, is it correct? Then my question is about the solver, can we still use CG as a solver if the system matrix looses symmetry? Does deal.II make some further elaboration? Thank you again Alberto *Alberto Salvadori* Dipartimento di Ingegneria Civile

[deal.II] imposing boundary conditions for a three-fields formulation

Hi, sorry for asking your help again, that I really appreciated. Today's issue is about imposing boundary conditions for a three-fields formulation. In brief, I defined a 4 nodes square element, of type: fe(FE_Q(poly_degree), dim, // displacement FE_DGPMonomial(poly_degree - 1), 1, // pre

Re: [deal.II] Separate components from the solution vector

Thanks Wolfgang, step-22 is exactly what I was looking for. It works just fine, now. Alberto Il giorno lunedì 17 aprile 2017 10:43:56 UTC-4, Wolfgang Bangerth ha scritto: > > On 04/17/2017 08:37 AM, Alberto Salvadori wrote: > > Thanks Wolfgang. > > What you surmised is

Re: [deal.II] Separate components from the solution vector

ts is 4.* Il giorno lunedì 17 aprile 2017 10:24:23 UTC-4, Wolfgang Bangerth ha scritto: > > On 04/17/2017 08:09 AM, Alberto Salvadori wrote: > > DataOut data_out; > > > > data_out.attach_dof_handler(dof_handler); > > > > > > > > /

[deal.II] Separate components from the solution vector

Hi, thanks in advance for your suggestions. I have been working on a small strain version of the three-fields formulation proposed in step 44. To this aim, I have been extended step 18, including some non linear material models. It is my understanding that there are two ways of assembling and

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