Re: [Libmesh-users] Setting the linear solver

2020-12-09 Thread Roy Stogner
On Wed, 9 Dec 2020, Laura Scarabosio wrote: Thank you for your explanations. I built libmesh by disabling mpi, so is the default solver still PETSc? If you configured with PETSc (which can be configured with "mpiuni" rather than a real MPI), it is. If you didn't, it isn't. You can look for

Re: [Libmesh-users] Setting the linear solver

2020-12-08 Thread Roy Stogner
On Tue, 8 Dec 2020, Laura Scarabosio wrote: >> LinearSolver::set_solver_type(foo) and set_preconditioner_type(bar), But shouldn't I get the linear solver from the equation system or the system? If I declare a linear solver as you said, how does libmesh know that it has to be used to solve a p

Re: [Libmesh-users] Setting the linear solver

2020-12-08 Thread Roy Stogner
On Tue, 8 Dec 2020, Laura Scarabosio wrote: I would like to ask what are the default linear solver and preconditioner in Libmesh, GMRES and ILU, if you've configured with a linear algebra package supporting them. and how to specify in the code which ones to use (e.g. as flags or parameters

Re: [Libmesh-users] Neighbors of element

2020-10-23 Thread Roy Stogner
On Wed, 21 Oct 2020, John Peterson wrote: On Wed, Oct 21, 2020 at 12:39 PM Laura Scarabosio < laura.scarabo...@gmail.com> wrote: I would like to find the neighbors of a mesh element including those that share a vertex only with that element, not only those that share an edge with the element

Re: [Libmesh-users] PetscMatrix::print_matlab

2020-08-28 Thread Roy Stogner
On Fri, 28 Aug 2020, John Peterson wrote: On Fri, Aug 21, 2020 at 9:51 AM Nikhil Vaidya wrote: I need to print the sparse matrices (Petsc) and vectors involved in my calculations to file using print_matlab(). I have observed that the matrices and vectors that are written to the matlab scrip

Re: [Libmesh-users] Create an unstructured mesh of map of country/region

2020-06-08 Thread Roy Stogner
On Sat, 6 Jun 2020, Prashant K. Jha wrote: Thank you so much for your time in replying to my email. I have been able to create a Delaunay triangulation of the map of the Texas state. How I did it is as follows: 1. Get the shapefile for the map from  http://gis-txdot.opendata.arcgis.com/datase

Re: [Libmesh-users] A question for the ordering of unknowns

2020-05-26 Thread Roy Stogner
On Mon, 25 May 2020, Li Luo wrote: For a multicomponent system, such as Navier-Stokes equations, I found that the ordering of unknowns in the system depends on the order of polynomials used for the variables. Take a two-component system with variables u and p for example: -If using first ord

Re: [Libmesh-users] Best wishes

2020-03-26 Thread Roy Stogner
On Thu, 26 Mar 2020, John Peterson wrote: Thanks, I hope everyone is staying healthy as well. I spent last night working in my underwear and staying up too late, I haven't seen most of my coworkers in person in weeks, I sometimes don't shower until nearly dinner time, I'm tormenting my kids

Re: [Libmesh-users] Unusual memory error due to Eigen solver

2020-02-13 Thread Roy Stogner
On Thu, 13 Feb 2020, Bailey Curzadd wrote: /usr/local/lib/libmesh_opt.so.0 Well, this is the first thing you'll want to change. Often times a bug that exhibits as an incomprehensible segmentation fault in opt mode will instead trigger a sensible assertion failure in dbg mode. Valgrind con

Re: [Libmesh-users] Hisotry variables

2018-09-14 Thread Roy Stogner
On Fri, 14 Sep 2018, gmail wrote: I’ve recently added plasticity with implicit integration to my code. This requires keeping track of so called “history variables” (i.e. internal parameters of plasticity such as back stresses, equivalent plastic strain,..) on each quadrature point. I have come

Re: [Libmesh-users] Defining duplicate nodes on refinement

2018-09-11 Thread Roy Stogner
On Tue, 11 Sep 2018, Rossi, Simone wrote: If you start with the 10 node mesh on top and refine, then you will always have continuity of any C0 (or C1) solution variables at the two shared domain corner nodes. This is what I would like to have. The idea is to introduce some random “cuts” in th

Re: [Libmesh-users] Defining duplicate nodes on refinement

2018-09-11 Thread Roy Stogner
On Tue, 11 Sep 2018, John Peterson wrote: I’m trying to create a triangular mesh like the following 7 — — 8 —— 9 | /| / | | /| /| 3 —— 4/5—— 6 | /| / | | /| /| 0 —— 1 —— 2 Where the node 4 and 5 have the same

Re: [Libmesh-users] Periodic BCs for unstructured mesh

2018-08-07 Thread Roy Stogner
In that sense of "unstructured", strong enforcement of periodic boundaries would lead to "locking". Imagine piecewise linear or bilinear elements, with nodes like: AB--C--D--E-F on one side of the boundary and G-H---I-J---K---L on the other. Side AB forces GH and HI to have the

Re: [Libmesh-users] problem with ./configure

2018-08-01 Thread Roy Stogner
Would someone copy that broken config.log to my email? Looks like the attachment got stripped by the mailing list. --- Roy On Wed, 1 Aug 2018, Harry Pearce wrote: Paul, Here it is! There is another problem but I think I know what's causing it so I will ask if I can't figure it out. Thanks a

Re: [Libmesh-users] Problems with Reduced Basis Library

2018-07-24 Thread Roy Stogner
On Tue, 24 Jul 2018, Nikhil Vaidya wrote: Thanks for the answer. I tried removing the particular initialize call and ran it again. This time I get the following error message: Assertion `proc < _first_df.size()' failed. proc = 0 _first_df.size() = 0 That's an assertion failure from the DofM

Re: [Libmesh-users] Problems with Reduced Basis Library

2018-07-23 Thread Roy Stogner
On Mon, 23 Jul 2018, Nikhil Vaidya wrote: Starting InitializeRB::initialize() Assertion `!this->is_initialized()' failed. Detaching after fork from child process 17473. Stack frames: 13 0: libMesh::print_trace(std::ostream&) 1: libMesh::MacroFunctions::report_error(char const*, int, char cons

Re: [Libmesh-users] Questions regarding profiling examples using gprof

2018-07-10 Thread Roy Stogner
On Tue, 10 Jul 2018, Boris Boutkov wrote: Oh, that's unfortunate. I've uploaded the logs in question to a public google drive folder, they should be available for download at : https://drive.google.com/drive/u/1/folders/1-FqKx9FhtSgRAttGVW-4cYNUfzehbpTz The PerfLog in intro_ex3.log says 97

Re: [Libmesh-users] Questions regarding profiling examples using gprof

2018-07-10 Thread Roy Stogner
On Fri, 6 Jul 2018, Boris Boutkov wrote: I've been trying to do some profiling of some of the libMesh examples and am having some issues understanding the generated gprof output. It seems like much of the data that I am expecting is missing from the output (please see attached logs). Could y

Re: [Libmesh-users] Syncronize a vector among processes

2018-07-05 Thread Roy Stogner
On Thu, 5 Jul 2018, Renato Poli wrote: >> It sounds like you'd rather be doing a tuple? Well, that would be my second shot, which I consider dusty but healthy. *Ideally* I would do a MyClass { int p1; int p2; int p3; int p4; }. I'm afraid handling *that* automatically is not going to be poss

Re: [Libmesh-users] Syncronize a vector among processes

2018-07-04 Thread Roy Stogner
On Wed, 4 Jul 2018, Renato Poli wrote: Thanks. Will try that. It is constant size. In fact, I could make my way through in a dirty pair > > I'm debugging something else right now. I will have to come back later an ddo the specialization. It sounds like you'd rather be doing a tuple? I'll tr

Re: [Libmesh-users] Syncronize a vector among processes

2018-07-04 Thread Roy Stogner
On Wed, 4 Jul 2018, Renato Poli wrote: I am trying to implement this one: comm().allgather(vector). The compiler fails. It says MyClass is not a StandardType. I tried with a tuple<>, without success. There actually is a StandardType> specialization, but it's untested and it's only useable i

Re: [Libmesh-users] repartitioning

2018-06-29 Thread Roy Stogner
On Fri, 29 Jun 2018, Griffith, Boyce Eugene wrote: On Jun 20, 2018, at 9:48 AM, Griffith, Boyce Eugene wrote: On Jun 19, 2018, at 11:58 PM, Roy Stogner wrote: On Tue, 12 Jun 2018, Griffith, Boyce Eugene wrote: OK, so something like: partiontiner->repartition(); equation_syst

Re: [Libmesh-users] Adaptative Mesh Refinement

2018-06-29 Thread Roy Stogner
On Thu, 28 Jun 2018, Roy Stogner wrote: On Tue, 12 Jun 2018, Vinicius C. Reis wrote: Hi John, I pasted a somewhat smaller version of my code below. By playing with the refinement steps limit and the commented out init() and reinit() lines you should be able to reproduce the two

Re: [Libmesh-users] Syncronize a vector among processes

2018-06-28 Thread Roy Stogner
On Thu, 28 Jun 2018, Renato Poli wrote: How can I do this (I am not a MPI guy at all, so please be patient ...): > ... after each processor makes its own local vector, just > allgather those into a giant serial vector ... I'm not a big fan of MPI myself, which is why we've got it wrapped

Re: [Libmesh-users] Adaptative Mesh Refinement

2018-06-28 Thread Roy Stogner
On Tue, 12 Jun 2018, Vinicius C. Reis wrote: Hi John, I pasted a somewhat smaller version of my code below. By playing with the refinement steps limit and the commented out init() and reinit() lines you should be able to reproduce the two exceptions I got. Got it reproduced. The exceptions

Re: [Libmesh-users] Syncronize a vector among processes

2018-06-28 Thread Roy Stogner
On Thu, 28 Jun 2018, Renato Poli wrote: I have a DG system (duplicated DOFs). By duplicated, you just mean the multiple DoFs "at" (in a Lagrangian evaluation sense) each node? I calculate the aperture at the DOFs sharing coordinates Aperture meaning the jump in values between the solutio

Re: [Libmesh-users] Syncronize a vector among processes

2018-06-28 Thread Roy Stogner
On Thu, 28 Jun 2018, Renato Poli wrote: Should I copy-paste code from NumericVector to build mine? Any suggestion? We're pretty far into XY Problem territory at this point. http://xyproblem.info/ What you've said about your vector is that you'll need to be able to do a maxloc() on it, that

Re: [Libmesh-users] Adaptative Mesh Refinement

2018-06-20 Thread Roy Stogner
On Tue, 12 Jun 2018, Vinicius C. Reis wrote: Hi John, I pasted a somewhat smaller version of my code below. By playing with the refinement steps limit and the commented out init() and reinit() lines you should be able to reproduce the two exceptions I got. Could you email me a copy of the m

Re: [Libmesh-users] repartitioning

2018-06-19 Thread Roy Stogner
On Tue, 12 Jun 2018, Griffith, Boyce Eugene wrote: OK, so something like: partiontiner->repartition(); equation_systems->reinit(); and then continue? Did this work for you? The code above is what I'd have written as v0.1 too, but I added a quick unit test to make sure and (at least with D

Re: [Libmesh-users] problems with mesh output

2018-06-13 Thread Roy Stogner
On Wed, 13 Jun 2018, John Peterson wrote: MPI is already initialized in LibMeshInit, so no need to do this manually unless your real code does MPI communication before LibMeshInit... MPI_Finalize(); MPI_Finalize is called in the LibMeshInit destructor, no need to call it manually. Just

Re: [Libmesh-users] Blood Vessel Adaptive Mesh

2018-06-06 Thread Roy Stogner
On Wed, 6 Jun 2018, Caleb M Phillips wrote: On Wed, Jun 6, 2018 at 1:45 PM, Roy Stogner wrote: How expensive depends on your time stepping, and on your topology, I believe.  My biggest question would be about the latter: do you really need to delete old nodes and add new

Re: [Libmesh-users] Blood Vessel Adaptive Mesh

2018-06-06 Thread Roy Stogner
On Wed, 6 Jun 2018, John Peterson wrote: On Wed, Jun 6, 2018 at 11:51 AM, Caleb M Phillips wrote: I'm a newer user to lib mesh and would like to attempt to incorporate it in my research. I am looking to take a list of objects (cells that make up a blood vessel) and add nodes and elements to

Re: [Libmesh-users] Adaptative Mesh Refinement

2018-06-05 Thread Roy Stogner
On Mon, 4 Jun 2018, Vinicius C. Reis wrote: The exception is thrown from within EquationSystems.init(). I'll do some cleanup and get back with a somewhat more concise reproduction. I've attached two text files with the exception and the stack trace. I'm afraid the attachments got stripped by

Re: [Libmesh-users] Variable groups to use blocked matrix (*BAIJ)

2018-05-31 Thread Roy Stogner
On Sat, 12 May 2018, Adriano Côrtes wrote: If we use a fixed grid with no AMR, then the code works pretty fine, but with AMR turned on we are having the same issue as reported by David in the mailing list thread pointed by Roy. That is, there is a MatSetValue in a position that is not preall

Re: [Libmesh-users] Connection between a 2D and 3D mesh

2018-05-18 Thread Roy Stogner
On Thu, 17 May 2018, Viviana Palacio Betancur wrote: Thank you for your response! I was able to find the parent element. Is there a way I could obtain the nodal information as well? Elem::node_ref, node_ptr, or node_id will get you a reference to, pointer to, or id() of a node indexed by loca

Re: [Libmesh-users] Variable groups to use blocked matrix (*BAIJ)

2018-05-10 Thread Roy Stogner
On Wed, 9 May 2018, John Peterson wrote: On Wed, May 9, 2018 at 11:56 AM, Linda G wrote: Dear Libmesh Users, We are trying to figure out how to set up a Stabilized NS FEM formulation to work in a blocked matrix fashion. After reading the documentation we realized that this boils down to def

Re: [Libmesh-users] Adding a variable group

2018-05-07 Thread Roy Stogner
On Mon, 7 May 2018, Harshad Sahasrabudhe wrote: I need to add a group of variables to my CondensedEigenSystem. My current code handles a single variable. What would be the shortest way to update my code to accommodate the variable group? I would like the PetscMatrix to be block sparse with a no

Re: [Libmesh-users] DG and boundary conditions

2018-05-03 Thread Roy Stogner
On Thu, 3 May 2018, Renato Poli wrote: you might as well add manual constraint equations between your solution triangles and the desired boundary values directly. Could you elaborate a little on that? Do you mean adding scalar variables with Lagrangian multipliers? Or "DofMap->add_constraint_

Re: [Libmesh-users] new libmeshdm fails with newtonrsls

2018-05-03 Thread Roy Stogner
On Mon, 30 Apr 2018, gmail wrote: The new implementation of the libMeshDM unfortunately fails when using variational inequality solvers VINEWTONRSLS or VINEWTONSSLS (for example miscellaneous/ex7). This happens when PETSc tries to VecDuplicate the solution vector for lower bound in src/snes/imp

Re: [Libmesh-users] DG and boundary conditions

2018-05-03 Thread Roy Stogner
On Wed, 2 May 2018, Renato Poli wrote: Well, I am working with fracture creation in between mesh elements. In this case I believe it sort of makes sense to have 'strong' BCs and internal discontinuous DOFs being tied together by interior penalties... (not sure though) I think strong BCs will

Re: [Libmesh-users] DG and boundary conditions

2018-05-02 Thread Roy Stogner
On Tue, 1 May 2018, Renato Poli wrote: Are DirichletBoundary BCs expected to work in Discontinuous Galerkin (L2_LAGRANGE)? Nope. And you wouldn't want them to, would you? I'm not a DG person myself, but I was under the impression that you always want the solution to be allowed to be discont

Re: [Libmesh-users] Question regarding Subdivision Implementation in libMesh

2018-05-02 Thread Roy Stogner
On Tue, 1 May 2018, Lee, Jae Ho wrote: Actually, this issue is now resolved. The problem was that the default linear solver was not converging. This issue can be resolved by using a stronger linear solver. Thanks for the update! You had me worried at first - I don't think any of the most act

Re: [Libmesh-users] Qusetion about Implmentation of Gmsh

2018-04-24 Thread Roy Stogner
On Tue, 24 Apr 2018, 서승진 wrote:    ERROR: Finite element LAGRANGE on geometric element TRI3 only supports FEInterface::max_order =1, not fe_type.order = 2 TRI3 is a first-order geometric element, with only 3 nodes. It sounds like you're trying to set up a second-order finite element basis,

Re: [Libmesh-users] time varying Dirichlet Conditions

2018-04-23 Thread Roy Stogner
On Sat, 21 Apr 2018, Manav Bhatia wrote: I am trying to identify the best approach to handle time-varying Dirichlet conditions with libMesh. It appears that DirichletConstraints is used to create a set of DofConstraintRow that is used after the nonlinear solves through DofMap::enforce

Re: [Libmesh-users] About Libmesh guideline

2018-04-11 Thread Roy Stogner
On Wed, 11 Apr 2018, 서승진 wrote: 1) In visualization, I used paraview and open out_2.e (in introduction_ex4). The paraview displayed the white box. I think that this is mesh for the example. However, paraview didn't displayed the solution distribution (colored box). Is the problem is come fro

Re: [Libmesh-users] Install Libmesh with PETSc-3.2

2018-04-10 Thread Roy Stogner
On Mon, 9 Apr 2018, 서승진 wrote: I tried to reinstall the libmesh with PETSc 3.2 ver. (instead of PETSc 3.8.3 ver.) What was wrong with the PETSc 3.8.3 installation? I admit I'm on PETSc 3.7.6 right now myself, but I believe our other developers were keeping our support up to date with PETSc 3

Re: [Libmesh-users] About Libmesh guideline

2018-04-10 Thread Roy Stogner
On Sat, 7 Apr 2018, 서승진 wrote: I've tried to search informations in google and libmesh mailing list, but it is not sufficient yet. Well, let me Cc: the list with my replies, and hopefully the next person to search will have an easier time.   1) I will solve the non-linear 2D~3D Poisson pr

Re: [Libmesh-users] Starting out with libmesh

2018-03-28 Thread Roy Stogner
On Wed, 28 Mar 2018, Jorge Lopes wrote: \nabla V = Source(\phi) The source depends on the function \phi. The more complicated math probably makes the software questions easier: even in the implicit integration case you'll probably want to solve as a fully coupled system and then consider deco

Re: [Libmesh-users] Assertion `min_id == node->processor_id()' failed.;

2018-03-27 Thread Roy Stogner
On Tue, 27 Mar 2018, Salazar De Troya, Miguel wrote: Can I generate the cpa from the cpr without having to save the mesh again? No; if that's not reasonable just upload the CPR for me? >> It's 123 MB. > >I think my email system will bounce that, so if you could put it up >for HT

Re: [Libmesh-users] Assertion `min_id == node->processor_id()' failed.;

2018-03-26 Thread Roy Stogner
On Thu, 22 Mar 2018, Salazar De Troya, Miguel wrote: I've got the mesh in cpr right before calling make_node_proc_ids_parallel_consistent(), do you have a preferred way to share it to you? Could you put it up in cpa (compressed if need be) format? In the most heinous cases I find myself star

Re: [Libmesh-users] Quick questions about SCALAR variables

2018-03-26 Thread Roy Stogner
On Fri, 23 Mar 2018, Salazar De Troya, Miguel wrote: Are the SCALAR variables added to the local vectors for each processor? As ghosted dof coefficients? Yes. The only exception is that, if you have a processor which doesn't own any elements on which the SCALAR is defined (either because th

Re: [Libmesh-users] Starting out with libmesh

2018-03-26 Thread Roy Stogner
On Thu, 22 Mar 2018, Jorge Lopes wrote: 1) Understanding the structure of the documentation: It is highly non-trivial to browse through that. It is; it's a half-decent reference but not a tutorial. The closest thing we have to a tutorial is the examples, and even there you have to skim descr

Re: [Libmesh-users] Quick questions about SCALAR variables

2018-03-20 Thread Roy Stogner
On Tue, 20 Mar 2018, David Knezevic wrote: IIRC we stick them at the end, so typically the last (i.e. (rank-1)^th) processor will own all the SCALARs. This is correct, but please try to avoid writing codes depending on it; it's one of the upcoming items on our "Stuff I thought would be fine b

Re: [Libmesh-users] Assertion `min_id == node->processor_id()' failed.;

2018-03-20 Thread Roy Stogner
On Tue, 20 Mar 2018, Salazar De Troya, Miguel wrote: this->make_node_proc_ids_parallel_consistent(mesh) did not work. I get the exact same error. Is this strange? From the outside view, "Is it strange that extremely complicated parallel code isn't working perfectly" is sad but not strange

Re: [Libmesh-users] [RE]Re: [RB] How to obtain subdomain information from nodes

2018-03-20 Thread Roy Stogner
On Tue, 20 Mar 2018, David Knezevic wrote: No, you should not have to redefine anything. If you're using Trelis, then define the subdomains by defining "blocks" in an ExodusII mesh, and they will be read into libMesh and stored as subdomain_ids. You should not have to change node numbers. In ge

Re: [Libmesh-users] Assertion `min_id == node->processor_id()' failed.;

2018-03-19 Thread Roy Stogner
On Mon, 19 Mar 2018, Salazar De Troya, Miguel wrote: I found a slight difference between the trace files: The traceout_8_142118.txt contains libMesh::MeshTools::libmesh_assert_parallel_consistent_procids (mesh=...) at src/mesh/mesh_tools.C:1608 whereas traceout_57_85461.txt and traceout_11

Re: [Libmesh-users] enforce to partition mesh on each processor locally

2018-03-13 Thread Roy Stogner
On Tue, 13 Mar 2018, Vasileios Vavourakis wrote: oh, I thought that the default setting in the Parallel::Communicator (i.e. see default constructor:  http://libmesh.github.io/doxygen/classlibMesh_1_1Parallel_1_1Communicator.html#a697f8e599333609a45761828e14659c1) for the “communicator” is: MP

Re: [Libmesh-users] enforce to partition mesh on each processor locally

2018-03-13 Thread Roy Stogner
On Tue, 13 Mar 2018, Vasileios Vavourakis wrote: I would like to run (in parallel mode) a piece of libMesh code where on each processor, a libMesh::Mesh is initialised & stored locally and, hence, subsequently initialise the EquationSystems accordingly, and for each processor independently. Th

Re: [Libmesh-users] p-refinement for Lagrange variables?

2018-03-09 Thread Roy Stogner
On Fri, 9 Mar 2018, David Knezevic wrote: - If I were to look into adding a special case for non-uniform 1st to 2nd order refinement for LAGRANGE variables, do you think this would be of interest to include that in libMesh, or would it be too specific to include? (I'd like to know if it's poten

Re: [Libmesh-users] p-refinement for Lagrange variables?

2018-03-09 Thread Roy Stogner
p-refinement is supported, but adaptive p-refinement currently isn't. We require basis functions to be hierarchic (not necessarily HIERARCHIC) to generate constraint equations between neighboring elements of different p refinement levels. So you can do uniform refinement for error estimation, but

Re: [Libmesh-users] Compilation Libmesh with another code

2018-03-08 Thread Roy Stogner
On Thu, 8 Mar 2018, mohamed-aziz.na...@ensam.eu wrote: I have recently installed Libmesh and i try to use it. In fact, I have my C++ code working on a single Gauss point. Is it possible to use Libmesh with my code in order to obtain my finite element code (like Moose framework). Unfortunately

Re: [Libmesh-users] Periodic boundaries for circular segment domains

2018-03-01 Thread Roy Stogner
On Wed, 28 Feb 2018, David Knezevic wrote: I would like to implement a periodic boundary condition on a model with circular symmetry, e.g. solve on sector of a disk with periodicity. To implement this it seems like all I'd need to do is subclass PeriodicBoundary and override get_corresponding_p

Re: [Libmesh-users] Periodic boundaries for circular segment domains

2018-03-01 Thread Roy Stogner
On Thu, 1 Mar 2018, David Knezevic wrote: On Thu, Mar 1, 2018 at 10:50 AM, Roy Stogner wrote: If you have something vector or tensor valued, like e.g. a *velocity* variable, and your formulation doesn't already use polar coordinates for the components of that variable,

Re: [Libmesh-users] 1D/2D elements in 3D space

2018-02-13 Thread Roy Stogner
On Mon, 12 Feb 2018, Manav Bhatia wrote: So, would the shape function derivatives account the orientation of the element? For instance, a 1D element oriented along: x-axis vs y-axis vs x=y line. In all cases, there is only one shape function defined along the element coordinate. Bu

Re: [Libmesh-users] 1D/2D elements in 3D space

2018-02-12 Thread Roy Stogner
On Mon, 12 Feb 2018, Manav Bhatia wrote: I was looking through some code in FE and noticed some comments about 1D/2D elements in 3D space. What is the extent of support for this? IIRC: If you're using just one or just the other, then the support should be complete. If you're connectin

Re: [Libmesh-users] Initial mesh with hanging nodes

2018-02-03 Thread Roy Stogner
On Sat, 3 Feb 2018, Laura Scarabosio wrote: I apologize for the simple question but I could not find satisfactory answers on the web. I'm not surprised; I think the most relevant discussion was just a week ago: https://sourceforge.net/p/libmesh/mailman/message/36202144/ and even if we mana

Re: [Libmesh-users] ImplicitSystem::get_linear_solver()

2018-01-29 Thread Roy Stogner
On Mon, 29 Jan 2018, Manav Bhatia wrote: I ended up creating a function similar to the one in LInearImplicitSystem to get around this issue. Working out fine now. Good to hear. Is your get_linear_solver() anything general enough to move upstream to NonlinearImplicitSystem? The lack of a g

Re: [Libmesh-users] Requirements for adding dof_constraint_rows in parallel

2018-01-26 Thread Roy Stogner
On Thu, 25 Jan 2018, David Knezevic wrote: Thanks for that info. I'm only using ReplicatedMesh for now. Regarding this: IIRC: on ReplicatedMesh we try to avoid communication as much as  possible, so you have to add user constraints identically on every processor.  There might be wa

Re: [Libmesh-users] Requirements for adding dof_constraint_rows in parallel

2018-01-25 Thread Roy Stogner
On Thu, 25 Jan 2018, David Knezevic wrote: Hi all (though Roy I think you're the expert on this one ;) ), Well, I was the least-amateur when I refactored the code, but an *expert* would have also properly documented it, so apparently none of those were available. I know that in DofMap::proc

Re: [Libmesh-users] question on libMeshInit

2018-01-25 Thread Roy Stogner
On Thu, 25 Jan 2018, Michael Povolotskyi wrote: can libMeshInit accept NULL as constructor arguments? For argv? I sure wouldn't bet on it. We pass that to MPI, Slepc, PETSc, VTK, GetPot... I wouldn't even bet on all those codes supporting argc < 1 or an empty string in argv[0]; IIRC the C/

Re: [Libmesh-users] Defining hanging nodes in the XDA format

2018-01-25 Thread Roy Stogner
On Thu, 25 Jan 2018, Salazar De Troya, Miguel wrote: An easier question to make would be: Can I have a parent element with just two children? Ah! I'm not sure if this was an easier question to make, but it's a *much* easier question to answer: no. The last time I tried counting, we had lite

Re: [Libmesh-users] question about the numeric vector

2018-01-25 Thread Roy Stogner
12:17 PM, Roy Stogner wrote: On Thu, 25 Jan 2018, Michael Povolotskyi wrote: I will add another system and will not solve it. Make sure it's ExplicitSystem (no, wait, maybe just plain System? ExplicitSystem does still allocate an rhs, not just a solution). ImplicitSystem will t

Re: [Libmesh-users] question about the numeric vector

2018-01-25 Thread Roy Stogner
I don't know if anybody's ever tried it! So: give it a shot? Then if it works let us know, and if it doesn't then file a ticket and use ExplicitSystem instead? Thanks, --- Roy On 01/25/2018 12:17 PM, Roy Stogner wrote: On Thu, 25 Jan 2018, Michael Povolotskyi wrote: I will

Re: [Libmesh-users] question about the numeric vector

2018-01-25 Thread Roy Stogner
ether you plan to eventually assemble and solve with it or not, and that can get expensive. --- Roy On 01/25/2018 08:25 AM, Roy Stogner wrote: On Wed, 24 Jan 2018, Paul T. Bauman wrote: Sorry for slow response. I have nothing better to offer other than 3 vectors, but maybe others will.

Re: [Libmesh-users] Defining hanging nodes in the XDA format

2018-01-25 Thread Roy Stogner
Could you Cc: the picture to me? Our list server generally strips those, and I wasn't able to understand what you were trying to do based on the text alone. Thanks, --- Roy On Thu, 25 Jan 2018, Salazar De Troya, Miguel wrote: Attaching a picture. I drew the eight elements I removed. This way

Re: [Libmesh-users] question about the numeric vector

2018-01-25 Thread Roy Stogner
On Wed, 24 Jan 2018, Paul T. Bauman wrote: Sorry for slow response. I have nothing better to offer other than 3 vectors, but maybe others will. You can add another ExplicitSystem to the mesh, giving it a vector-valued variable corresponding to your solution system's scalar-valued variable. T

Re: [Libmesh-users] Best mesh format for writing and reading in parallel

2018-01-25 Thread Roy Stogner
On Wed, 24 Jan 2018, Paul T. Bauman wrote: Others can and should chime in, but I believe CheckpointIO will allow this. My only uncertainty is on whether is supports AMR meshes or not, but I think it does. It does. Beware we're not guaranteeing backward compatibility with it yet, so please

Re: [Libmesh-users] [Libmesh-devel] Example fem_system_ex2 failing to run

2018-01-22 Thread Roy Stogner
On Mon, 22 Jan 2018, Paul T. Bauman wrote: John: Should I go ahead and change that one to XFAIL? I'm not sure it will cause less confusion for users, but it would permit a blanket `make check`. Downside is it won't show up as a failure on CIVET testing. That's an extremely good idea. We can

Re: [Libmesh-users] Using gzstream from an app

2018-01-18 Thread Roy Stogner
On Thu, 18 Jan 2018, John Peterson wrote: On Thu, Jan 18, 2018 at 2:07 PM, David Knezevic wrote: I configured with gzstream support, and I'd like to use this from an app. To do that I've copied gzstream.h to the app directory, and then it works, but I was wondering if it's possible to use li

Re: [Libmesh-users] Non-symmetric constrained element matrices in case of recursive constraints

2018-01-16 Thread Roy Stogner
On Tue, 16 Jan 2018, David Knezevic wrote: I'm working with Jonas on this topic, and I just wanted to add a few - The original issue that Jonas ran into was indeed due to a "constraint cycle". Sorry my email crossed with yours! - Our preferred fix is to detect constraint cycles and fix them

Re: [Libmesh-users] Non-symmetric constrained element matrices in case of recursive constraints

2018-01-16 Thread Roy Stogner
On Sun, 14 Jan 2018, Jonas Ballani wrote: I have a question regarding constrained dofs that are themselves constrained by other dofs within the same element. Apparently, this leads to a non-symmetric constrained element matrix which I illustrate here by a small example: I consider an element

Re: [Libmesh-users] old_dof_object issue with xfem

2018-01-12 Thread Roy Stogner
akeStep(double) + 253 14: 14  libmoose-dbg.0.dylib                0x000101e449a3 Transient::execute() + 211 15: 15  libmoose-dbg.0.dylib                0x000101bac773 MooseApp::executeExecutioner() + 179 16: 16  libmoose-dbg.0.dylib                0x000101baeeda MooseApp::run() + 282

Re: [Libmesh-users] Question about unique_ids

2018-01-10 Thread Roy Stogner
On Wed, 10 Jan 2018, David Knezevic wrote: I'd like to use unique_ids to identify elements and nodes without worrying about renumbering, but before I do that I'd like to understand a bit more about how unique_ids are defined. In particular, what is the idea behind how we generate the unique_id

Re: [Libmesh-users] Constraint matrix

2018-01-08 Thread Roy Stogner
On Sat, 6 Jan 2018, Renato Poli wrote: Hi again, I am trying to close this issue here, but got into trouble again. Is there a common way to tie a dof against the derivative of other dofs. Not really. For one thing, there's no such thing as a spatial derivative of a dof. You can get the sp

Re: [Libmesh-users] Dirichlet boundary condition setting variable to zero?

2018-01-08 Thread Roy Stogner
On Sun, 7 Jan 2018, Renato Poli wrote: I am struggling with a Dirichlet boundary condition setting the boundary to zero, instead of the value I impose (3.e7). Previously, I was using the penalty method, and it was working fine. Is there any known corner condition where the DirichletBoundary wo

Re: [Libmesh-users] Constraint matrix

2018-01-05 Thread Roy Stogner
On Fri, 5 Jan 2018, Renato Poli wrote: I need to tie three dofs together. (u1 + C u2 + D u3=0). I read about the constraint matrix in the list, but I did not find an example to follow. The penalty method seems also a nice alternative. Is there any example of either to suggest? In systems_of_

Re: [Libmesh-users] Question about hybrid mesh

2017-12-14 Thread Roy Stogner
On Thu, 14 Dec 2017, Viviana Palacio Betancur wrote: Thank you! I was able to fix my problem. I was creating the quadrature rule before looping over the elements. Thus, "ERROR: Unsupported type: 4" appeared when the TRI6 elements appeared. I fixed this by creating the quadrature rule and build

Re: [Libmesh-users] Question about hybrid mesh

2017-12-14 Thread Roy Stogner
On Wed, 13 Dec 2017, Viviana Palacio Betancur wrote: I am trying to assemble the system's matrix for a mesh composed of TET10 (bulk) bounded by TRI6 (surface) elements but I get an error related to an unsupported type of elements. The problem solves for a single variable. This should be fine.

Re: [Libmesh-users] how to read a distributed mesh

2017-12-12 Thread Roy Stogner
On Tue, 12 Dec 2017, Jahrul Alam wrote: First, I wrote the mesh as     [CheckpointIO(mymesh).write("test.cp");] Next, I re-compiled the code (only to change 'read' to 'write'), and read the mesh as      [CheckpointIO(mymesh).read("test.cp");] mymesh.print_info() shows n_nodes=33153, n_local_n

Re: [Libmesh-users] how to read a distributed mesh

2017-12-11 Thread Roy Stogner
On Sat, 9 Dec 2017, Jahrul Alam wrote: Nemesis IO reads the mesh in parallel (not the solution); however, the reader destroys the multi-level structure of the mesh. Is there a work around to handle this problem? I'm afraid not; not even ExodusII ("serial Nemesis") lets us store AMR structure.

Re: [Libmesh-users] how to read a distributed mesh

2017-12-04 Thread Roy Stogner
On Mon, 4 Dec 2017, John Peterson wrote: On Mon, Dec 4, 2017 at 10:59 AM, Alam, Jahrul wrote: Thanks for the clarification. Can you suggest a work around? If I do, mesh0.read(lshaped_0.vtu) and mesh1.read(lshaped_1.vtu), and so on, is it possible to end up with a DistributedMesh by combining

Re: [Libmesh-users] (no subject)

2017-11-28 Thread Roy Stogner
On Tue, 28 Nov 2017, Zack Vitoh wrote: *Question 2* For the cases above, I noticed that I am no longer running libmesh in parallel when I read in the mesh. I found, and tried to use libMesh::Partitioner part(); // Partitioner()::partition_unpartitioned_elements(mesh); // Partitioner.partition_

Re: [Libmesh-users] question about NumericVector

2017-11-27 Thread Roy Stogner
So sorry nobody got back to you on this already! On Tue, 14 Nov 2017, Michael Povolotskyi wrote: I would like to output a nodal data stored in NumericVector, using void libMesh::MeshOutput< MT >::write_nodal_data ( const std::string & fname, const NumericVector< Number > & parall

Re: [Libmesh-users] Using Ubuntu, Configuring with Petsc, Specified PETSC_DIR and PETSC_ARCH, but petsc, triangle, tetgen not found?

2017-11-26 Thread Roy Stogner
On Sun, 26 Nov 2017, Zack Vitoh wrote: Sorry about that, I figured it out, I'll post the solution in a bit. I'm waiting anxiously! I added the configuration tests myself to auto-detect Debian/Ubuntu/etc PETSC installation, years ago, but I stopped using it regularly shortly afterward, and I

Re: [Libmesh-users] Reading Mesh produced from Gmsh to use as as Unstructured Mesh--Higher Order Elements?

2017-11-22 Thread Roy Stogner
On Wed, 22 Nov 2017, Zack Vitoh wrote: GmshIO gmsh_io(mesh); gmsh_io.read("disk.vtu"); but--and I am not sure if this is possible--imposing additional nodes on each element generated in the triangularization generated by gmsh with nodes such that I have, say, Tri6 elements. You have Tri3 e

Re: [Libmesh-users] Miscellaneous Example 6 Does not produce anything?

2017-11-21 Thread Roy Stogner
On Mon, 20 Nov 2017, Zack Vitoh wrote: This does not work for me, as it does not produce anything there is a flag #ifdef LIBMESH_HAVE_TRIANGLE which is apparently false Right - if you don't have Triangle enabled, we can't run programs which require Triangle. I looked at 'configure' and i

Re: [Libmesh-users] GMSH read - bad EDGE2 elemtype for second order approximation

2017-11-17 Thread Roy Stogner
On Thu, 16 Nov 2017, John Peterson wrote: I think you need to run gmsh with a special option (maybe "-2") to make sure that you get EDGE3 elements. Those are required for using SECOND, LAGRANGE finite elements. Alternatively, if you have a mesh object with lower-order elements, you can conver

Re: [Libmesh-users] Given a physical (or reference, outside of domain) point, which element does it belong to?

2017-11-16 Thread Roy Stogner
Oh, and now that I've noticed: please keep Cc:ing the mailing list; the more helpful discussion that gets archived where future users' search engines can find it, the better. Thanks, --- Roy On Thu, 16 Nov 2017, Roy Stogner wrote: On Wed, 15 Nov 2017, Zack Vitoh wrote: Pu

Re: [Libmesh-users] Given a physical (or reference, outside of domain) point, which element does it belong to?

2017-11-15 Thread Roy Stogner
On Wed, 15 Nov 2017, Zack Vitoh wrote: I think http://libmesh.github.io/doxygen/classlibMesh_1_1SubdomainPartitioner.html#details May help, but still not sure if this is the best approach No, that's unrelated to what you want to do. The class you should look up is https://libmesh.github.io/

Re: [Libmesh-users] Defining Quadrature Rule (like QGauss) to be used with FEBase

2017-11-08 Thread Roy Stogner
On Tue, 7 Nov 2017, Zack Vitoh wrote: I want to develop a nonstandard quadrature rule and use it as in introduction_ex3. Is there a way to do this simply, Yes: after you add your new files (and the corresponding entry in quadrature_build.C), run a few scripts (as detailed in https://github.c

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