Re: [deal.II] Reason for SolverGMRES being slower in parallel?

2018-04-06 Thread Weixiong Zheng
I would guess this would rather be the degeneration of ILUt in parallel than the implementation. If I am not wrong, ILU-T in parallel is not ILU-like preconditioner anymore, right? I remember the inter-core part is implemented in a block-Jacobi fashion. I've never used ILUT but used ILU a lot.

Re: [deal.II] Difference between dim and spacedim

2018-04-06 Thread Weixiong Zheng
Yep! I noticed that when doing my PR today. 在 2018年4月5日星期四 UTC-7下午5:45:28,Wolfgang Bangerth写道: > > On 04/05/2018 12:30 PM, Weixiong Zheng wrote: > > > > I always see spacedim and dim but couldn't tell what exactly they mean. > > Unfortunately, there seems not to be an

Re: [deal.II] extrude by providing z-coordinates

2018-04-05 Thread Weixiong Zheng
PR has been approved and will be merged sometime. Thanks for fill the project name into Applications entry. 在 2018年4月5日星期四 UTC-7下午3:48:05,Wolfgang Bangerth写道: > > > Weixiong, > > > By instruction, it's actually more for the testing. Maybe I will just > > follow how the other functions are

[deal.II] Re: Difference between dim and spacedim

2018-04-05 Thread Weixiong Zheng
I see. I normally do volumetric computations which was why I didn't understand why one differs from the other. Thanks. 在 2018年4月5日星期四 UTC-7上午11:46:49,Daniel Arndt写道: > > Weixiong, > > Have a look at step-38 ( > https://www.dealii.org/8.5.0/doxygen/deal.II/step_38.html) for an example. > We oftn

[deal.II] Difference between dim and spacedim

2018-04-05 Thread Weixiong Zheng
Hi I always see spacedim and dim but couldn't tell what exactly they mean. Unfortunately, there seems not to be an explanation in Glossary. Could anybody pls spare a min to enlighten me? Thanks, Weixiong -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum

Re: [deal.II] extrude by providing z-coordinates

2018-04-04 Thread Weixiong Zheng
Sir The Issue 6158 and 6159 have been opened for the proposed functionalities. Tell you if you have any thought. By instruction, it's actually more for the testing. Maybe I will just follow how the other functions are tested. By the way, I am at UC Berkeley leading an open source group

[deal.II] extrude by providing z-coordinates

2018-04-04 Thread Weixiong Zheng
Hi, I found out there is not a function for extruding triangulation by exact position of cell vertices along z-axis. So I wrote a piece of code by modifying GridGenerator::extrude_triangulation. The attachment is an example of what it does. Did for my own needs. Just wonder if I can

[deal.II] Re: manifold for multiple circles on 2D plane

2018-04-03 Thread Weixiong Zheng
Daniel, Thanks for confirming this. Yep, I read that after getting error. Also, I was wrong that 3D can be done in the way I thought before. Actually the same thing has to be done as 2D for repeated manifolds except we use cylinders along different axes with the same direction. Best,

[deal.II] Re: manifold for multiple circles on 2D plane

2018-04-03 Thread Weixiong Zheng
The initial description might be misleading. What I tried to do is repeatedly set manifolds for circles on X-Y plane. Now I use STL container to contain different pointers of SphericalManifold instance and correspondingly assign distinct manifold ids, it worked out. But it might be a non-smart

[deal.II] manifold for multiple circles on 2D plane

2018-04-03 Thread Weixiong Zheng
Hi I dealt with problem in both 2d and 3d that a domain with a lot of circles/cylinders along z-axis. In 3D, I use CylindricalManifold<3> with axis=2 for the fold type. Yet, I just realize being stuck in 2D that axis=2 is not available for CylindricalManifold<2> ( 0 or 1 cannot give me the

[deal.II] Re: cell shapes not the same on opposite side of a globally refined extruded triangulation

2018-04-01 Thread Weixiong Zheng
It turned out to be me mistakenly setting manifold using ID "2" which was one of the boundary ID. After I changed it to something else (specifically, 33), everything works as expected. 在 2018年4月1日星期日 UTC-7下午7:06:47,Weixiong Zheng写道: > > Hi > > Sorry for the messy title. W

[deal.II] cell shapes not the same on opposite side of a globally refined extruded triangulation

2018-04-01 Thread Weixiong Zheng
Hi Sorry for the messy title. What I did: 1. Create a 2D triangulation 2. extrude it 3. refine it globally Yet, I found that cells on opposite sides of the extruded triangulation do not have the same shape after uniform refinement. I was just wondering how this could happen. In my view, cells

[deal.II] functions to measure quality of mesh?

2018-03-29 Thread Weixiong Zheng
Hi Just a quick question: are there functions to measure mesh quality? I didn't see anything in FAQ and only saw one old post without an answer. Thanks in advance! Weixiong -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see

Re: [deal.II] set manifold for merged boundaries

2018-03-29 Thread Weixiong Zheng
he triangulation > object. In that case, the triangulation would have let lose of the manifold > object upon its destruction, and everything would have been fine. > > Best, > Jean-Paul > > > On 29 Mar 2018, at 08:14, Weixiong Zheng <zwxn...@gmail.com > > wrot

Re: [deal.II] set manifold for merged boundaries

2018-03-29 Thread Weixiong Zheng
before the triangulation > object. In that case, the triangulation would have let lose of the manifold > object upon its destruction, and everything would have been fine. > > Best, > Jean-Paul > > > On 29 Mar 2018, at 08:14, Weixiong Zheng <zwxn...@gmail.com >

Re: [deal.II] Any easy way to output cellwise average solution

2018-03-29 Thread Weixiong Zheng
n. > > Best, > Jean-Paul > > > On 28 Mar 2018, at 01:10, Weixiong Zheng <zwxn...@gmail.com > > wrote: > > I put my non-smart solution here in case if there's no easy way of doing > it in deal.II and someone else needs it. > > // The vector I want to out

Re: [deal.II] set manifold for merged boundaries

2018-03-29 Thread Weixiong Zheng
the issue for you. > > I hope this helps. > > Best, > Jean-Paul > > On 29 Mar 2018, at 07:13, Weixiong Zheng <zwxn...@gmail.com > > wrote: > > I changed the strategy that I don't assign manifold first. I merge two > triangulations. Then, I loop over ce

Re: [deal.II] set manifold for merged boundaries

2018-03-29 Thread Weixiong Zheng
rised, all of your > boundaries will have an indicator of 0. So try to use a manifold ID of, > say, 1. I think that this should fix the issue for you. > > I hope this helps. > > Best, > Jean-Paul > > On 29 Mar 2018, at 07:13, Weixiong Zheng <zwxn...@gmail.com > > wr

Re: [deal.II] set manifold for merged boundaries

2018-03-29 Thread Weixiong Zheng
fold ID of, > say, 1. I think that this should fix the issue for you. > > I hope this helps. > > Best, > Jean-Paul > > On 29 Mar 2018, at 07:13, Weixiong Zheng <zwxn...@gmail.com > > wrote: > > I changed the strategy that I don't assign manifold first. I merge t

Re: [deal.II] Re: Any easy way to output cellwise average solution

2018-03-29 Thread Weixiong Zheng
Nice catch! I forgot to mention it is bilinear. But thanks for all the explanation. 在 2018年3月28日星期三 UTC-7下午12:42:27,Wolfgang Bangerth写道: > > > > | > > // The vector I want to output is the solution for vector-valued > problem. > > // I want to output the cell-average value for the 0th

[deal.II] Re: set manifold for merged boundaries

2018-03-28 Thread Weixiong Zheng
(0.92<std::sqrt(x*x+y*y)<1.) { cell->set_all_manifold_ids(0); break; } } } tria.refine_global(2); The result is super strange that the boundary is also exterior boundary is also curved. 在 2018年3月28日星期三 UTC-7下午9:00:50,Weixiong Zheng写道: > > Hi, > >

[deal.II] Re: set manifold for merged boundaries

2018-03-28 Thread Weixiong Zheng
. refine global. Apperantly, the manifold setting is not working as what I initially thought. Any ideas how to fix it? 在 2018年3月28日星期三 UTC-7下午9:00:50,Weixiong Zheng写道: > > Hi, > > I just started to try manifold and tria merging functionalities. My > question comes from the prob

[deal.II] set manifold for merged boundaries

2018-03-28 Thread Weixiong Zheng
Hi, I just started to try manifold and tria merging functionalities. My question comes from the problem that I have to merge two curved triangulations. When refining, how do I make sure the merged boundaries are still curved? I currently set manifold before merging triangulation but it seems

[deal.II] Re: Any easy way to output cellwise average solution

2018-03-27 Thread Weixiong Zheng
= avg; } } } If anyone has any smarter idea, please let me know and thanks in advance. Weixiong 在 2018年3月27日星期二 UTC-7下午2:35:37,Weixiong Zheng写道: > > Hi > > I am trying to output an cell average solution for a code using DG > bilinear element in 2D. Is there a trivial way to

[deal.II] Any easy way to output cellwise average solution

2018-03-27 Thread Weixiong Zheng
Hi I am trying to output an cell average solution for a code using DG bilinear element in 2D. Is there a trivial way to project DG-1 to DG-0? Or is there any function I can call to output the solution at some specfic points, say the center point of the cell? Thanks -- The deal.II project is

Re: [deal.II] different results with different number of processors

2018-03-23 Thread Weixiong Zheng
-7下午2:47:46,Wolfgang Bangerth写道: > > On 07/06/2017 06:25 PM, Weixiong Zheng wrote: > > > > I suspect it would not be about the weak form directly. So, every time I > give > > an set of initial cells, I need to make sure total initial cell number >

Re: [deal.II] SOURCE_DIR for input data reading in user project unit testing

2018-02-06 Thread Weixiong Zheng
: > > On 02/06/2018 10:28 AM, Weixiong Zheng wrote: > > > > > #define SOURCE_DIR > /Users/GrillCheese/UCB/Research/xtrans/tests/mesh > > > > > > Thanks sir, > > > > I got confused a bit. So you meant even with quotes around it, the

Re: [deal.II] SOURCE_DIR for input data reading in user project unit testing

2018-02-06 Thread Weixiong Zheng
在 2018年2月6日星期二 UTC-8上午8:33:43,Wolfgang Bangerth写道: > > On 02/05/2018 11:37 PM, Weixiong Zheng wrote: > > > > What I've tried is to > > ADD_DEFINITION(-DSOURCE_DIR=${CMAKE_CURRENT_SOURCE_DIR}) in the > > CMakeLists.txt in the test directory. I tried tesing SOU

Re: [deal.II] SOURCE_DIR for input data reading in user project unit testing

2018-02-06 Thread Weixiong Zheng
Thanks, sir. I'd try that. Weixiong 在 2018年2月6日星期二 UTC-8上午8:33:43,Wolfgang Bangerth写道: > > On 02/05/2018 11:37 PM, Weixiong Zheng wrote: > > > > What I've tried is to > > ADD_DEFINITION(-DSOURCE_DIR=${CMAKE_CURRENT_SOURCE_DIR}) in the > > CMakeLists.txt in the

Re: [deal.II] SOURCE_DIR for input data reading in user project unit testing

2018-02-05 Thread Weixiong Zheng
guys have in mind. 在 2018年2月5日星期一 UTC-8下午10:37:38,Weixiong Zheng写道: > > Thanks Matthias, > > What I've tried is to > ADD_DEFINITION(-DSOURCE_DIR=${CMAKE_CURRENT_SOURCE_DIR}) in the > CMakeLists.txt in the test directory. I tried tesing SOURCE_DIR in *.cc > file like: std::cout

Re: [deal.II] SOURCE_DIR for input data reading in user project unit testing

2018-02-05 Thread Weixiong Zheng
undeclared identifier 'xxx'" where xxx can be GrillCheese, UCB, Research etc. Anything obviously wrong to you? Thanks, Weixiong 在 2018年2月5日星期一 UTC-8下午9:25:22,Matthias Maier写道: > > > On Mon, Feb 5, 2018, at 22:15 CST, Weixiong Zheng <zwxn...@gmail.com > > wrote: > >

Re: [deal.II] SOURCE_DIR for input data reading in user project unit testing

2018-02-05 Thread Weixiong Zheng
在 2018年2月5日星期一 UTC-8下午8:55:19,Wolfgang Bangerth写道: > > On 02/05/2018 09:15 PM, Weixiong Zheng wrote: > > > > I am trying to get unit test work for my project. It works until > reaching the > > point of reading input data. I tried to specify the directory us

[deal.II] SOURCE_DIR for input data reading in user project unit testing

2018-02-05 Thread Weixiong Zheng
Hello All, I am trying to get unit test work for my project. It works until reaching the point of reading input data. I tried to specify the directory using getcwd() though it didn't work with ctest. I noticed there was another user having the same issue and the resolution was to use

Re: [deal.II] different results with different number of processors

2017-07-07 Thread Weixiong Zheng
Appreciated. I'll try this idea out. Sent from my iPhone > On Jul 7, 2017, at 16:47, Wolfgang Bangerth <bange...@colostate.edu> wrote: > >> On 07/06/2017 06:25 PM, Weixiong Zheng wrote: >> I suspect it would not be about the weak form directly. So, every time I >>

Re: [deal.II] different results with different number of processors

2017-07-06 Thread Weixiong Zheng
四 UTC-7上午8:26:06,Wolfgang Bangerth写道: > > On 07/06/2017 09:02 AM, Weixiong Zheng wrote: > > Both are generated with subdivided hyper rectangle with same reps and > diagonals. > > And no adaptive refinement? > > In that case, the solution *should* be the same, ass

Re: [deal.II] different results with different number of processors

2017-07-06 Thread Weixiong Zheng
Both are generated with subdivided hyper rectangle with same reps and diagonals. -- 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

Re: [deal.II] help with set_material_id and set_boundary_id

2017-07-03 Thread Weixiong Zheng
道: > > On 07/02/2017 02:40 PM, Weixiong Zheng wrote: > > > > The same thing happens to my function setting material ID, which takes > the > > same arguments in. Do you have any idea what's happening or what I can > provide > > to help diagnose the problem? >

[deal.II] help with set_material_id and set_boundary_id

2017-07-02 Thread Weixiong Zheng
Dear all, Couldn't find what I want in previous posts, so I post the problem here: I pass my triangulation to a function in my mesh generating class (by reference) and want to set the boundary ID and material IDs. My triangulation: parallel::distributed::Triangulation triangulation; How I

Re: [deal.II] Re: get_function_value error with hp class

2017-06-15 Thread Weixiong Zheng
在 2017年6月14日星期三 UTC-7下午5:44:37,Wolfgang Bangerth写道: > > On 06/13/2017 06:16 PM, Weixiong Zheng wrote: > > | > > > > | > > > > As the problem is a scalar problem, fv.shape_value and shape_grad work > as they > > are supposed to, but not the

[deal.II] Re: Compute jacobian at point (no quadrature point)

2017-06-13 Thread Weixiong Zheng
Felix, Would you take a look at if [1] is what you want to have? [1]: https://www.dealii.org/8.4.0/doxygen/deal.II/classFEValuesBase.html#a665ab681011424cb1b0ba11c4155a121 Best, Weixiong 在 2017年6月13日星期二 UTC-7上午9:35:09,Felix Lorenz写道: > > > Hi everyone, > > I want to compute the transformation

[deal.II] Re: get_function_value error with hp class

2017-06-13 Thread Weixiong Zheng
Thanks, Daniel, I used FESystem to wrap the scalar FiniteElement and the FE_Nothing together. Here are the hp-relevant variables: FESystem fe_continuous; FESystem fe_discontinuous; hp::FECollection fe_c; hp::QCollection q_c; hp::QCollection q_face_c; This is how I do initialization

[deal.II] Re: Any easy how-to: petsc and solver preconditioner selection from input?

2017-06-13 Thread Weixiong Zheng
:54:50 UTC+2 schrieb Weixiong Zheng: >> >> Hi all, >> >> I am developing something based on petsc solvers and preconditioners. We >> actually expect to invoke user-requested solvers and preconditioners from >> the input file. >> >> I saw se

[deal.II] Re: get_function_value error with hp class

2017-06-12 Thread Weixiong Zheng
下午3:25:13,Weixiong Zheng写道: > > Dear all, > > I am writing code using hp class. When accessing the solution as: > /*fe_c and q_c are fe and q collections*/ > hp::FEValue hp_fv(fe_c,q_c,update_values | update_quadrature_points); > for(cells) > { > const FEValues

[deal.II] get_function_value error with hp class

2017-06-12 Thread Weixiong Zheng
Dear all, I am writing code using hp class. When accessing the solution as: /*fe_c and q_c are fe and q collections*/ hp::FEValue hp_fv(fe_c,q_c,update_values | update_quadrature_points); for(cells) { const FEValues = hp_fv.get_present_fe_values(); std::vector

[deal.II] Any easy how-to: petsc and solver preconditioner selection from input?

2017-06-10 Thread Weixiong Zheng
Hi all, I am developing something based on petsc solvers and preconditioners. We actually expect to invoke user-requested solvers and preconditioners from the input file. I saw selector classes for deal.II based solvers and preconditioners but didn't find any for petsc wrappers. I am

Re: [deal.II] compress error for vector of PETScWrappers::MPI::SparseMatrix

2017-06-07 Thread Weixiong Zheng
Daniel and Dr Bangerth, Thanks for the help. I got it resolved with modifying the dsp. That does be my misunderstanding, hahaha. Best, Weixiong 在 2017年6月7日星期三 UTC-7上午10:33:57,Wolfgang Bangerth写道: > > On 06/07/2017 11:14 AM, Weixiong Zheng wrote: > > > > I see your point. I

Re: [deal.II] compress error for vector of PETScWrappers::MPI::SparseMatrix

2017-06-07 Thread Weixiong Zheng
Daniel, I see your point. I would double check later. The reason I didn't use locally relevant dofs is I didn't design the code to do h-refinement so I didn't see points using relevant dofs. Thanks, Weixiong 在 2017年6月7日星期三 UTC-7上午6:35:44,Daniel Arndt写道: > > Weixiong, > > [...] >>

Re: [deal.II] compress error for vector of PETScWrappers::MPI::SparseMatrix

2017-06-06 Thread Weixiong Zheng
d_dofs_per_processor (), mpi_communicator, locally_owned_dofs); 在 2017年6月6日星期二 UTC-7下午12:07:18,Wolfgang Bangerth写道: > > On 06/06/2017 12:10 PM, Weixiong Zheng wrote: > > It runs in serial. The error occurs when using multiple processors. > > And it

Re: [deal.II] compress error for vector of PETScWrappers::MPI::SparseMatrix

2017-06-06 Thread Weixiong Zheng
It runs in serial. The error occurs when using multiple processors. -- 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] Re: compress error for vector of PETScWrappers::MPI::SparseMatrix

2017-06-06 Thread Weixiong Zheng
在 2017年6月6日星期二 UTC-7上午2:13:28,Weixiong Zheng写道: > > Dear All, > > I am doing a radiation transport problem, which has multiple individual > equations (number determined by the number of directions we input). As the > number of directions is arbitrary, I put the sparsemat

[deal.II] compress error for vector of PETScWrappers::MPI::SparseMatrix

2017-06-06 Thread Weixiong Zheng
Dear All, I am doing a radiation transport problem, which has multiple individual equations (number determined by the number of directions we input). As the number of directions is arbitrary, I put the sparsematries are contained in std::vectors as raw pointers (using LA namespace to stand for

Re: [deal.II] some parameters determine whether or not I declare entries for other parameters

2017-05-09 Thread Weixiong Zheng
All right, those work for me. Thanks! Best, Weixiong 在 2017年5月9日星期二 UTC-7下午6:48:05,Wolfgang Bangerth写道: > > On 05/09/2017 05:59 PM, Weixiong Zheng wrote: > > > > I got bothered a bit about the problem: the existence of some parameters > > depends on the other paramet

[deal.II] some parameters determine whether or not I declare entries for other parameters

2017-05-09 Thread Weixiong Zheng
Hi, Don't know if this is relevant but I cannot find an answer from the previous posts. I got bothered a bit about the problem: the existence of some parameters depends on the other parameters defining the problem. what I am doing now is that I have two methods called: declare_parameter(prm)

Re: [deal.II] estimate globally integrated quantity with mpi

2017-05-04 Thread Weixiong Zheng
s::MPI::sum(), > max(), ... > - you can always use MPI directly > - If you have parallel vectors you can use things functions like norms > that will do the reduction > > On Thu, May 4, 2017 at 4:29 PM, Weixiong Zheng <zwxn...@gmail.com > > wrote: > > Hi > >

Re: [deal.II] write_vtk fail when using hp functionality

2017-03-02 Thread Weixiong Zheng
I will try after CSE17. Best, Weixiong 在 2017年2月27日星期一 UTC-5下午9:12:44,Wolfgang Bangerth写道: > > On 02/27/2017 12:24 PM, Weixiong Zheng wrote: > > Dear all, > > > > Might be a trivial questions to you guys. I get a scalar problem using > hp > > class. When I

[deal.II] write_vtk fail when using hp functionality

2017-02-27 Thread Weixiong Zheng
Dear all, Might be a trivial questions to you guys. I get a scalar problem using hp class. When I tried to output the results using std::vector solution_names; solution_names.push_back ("phi"); std::vector data_component_interpretation(1,

Re: [deal.II] std::vector error

2017-01-10 Thread Weixiong Zheng
Sir, Just recalled I asked this before. So I put what I have tried here. 在 2015年10月1日星期四 UTC-5下午10:58:40,Wolfgang Bangerth写道: > > On 10/01/2015 10:52 PM, Weixiong Zheng wrote: > > I tried to understand what you said and looked at step-9. So what you > suggest is: >

Re: [deal.II] Can one FE be used over discontiguous domain

2017-01-05 Thread Weixiong Zheng
All right, I will try and come back if something's wrong. Thanks, sir. 在 2017年1月5日星期四 UTC-6下午9:08:56,Wolfgang Bangerth写道: > > On 01/05/2017 08:07 PM, Weixiong Zheng wrote: > > > > I am coding up a code such that DG is used in one subdomain, while CG is > used > &

[deal.II] Can one FE be used over discontiguous domain

2017-01-05 Thread Weixiong Zheng
Dear all, I am coding up a code such that DG is used in one subdomain, while CG is used in all other subdomains. The implementation is with hp::FECollection class. As the CG-subdomains are discontiguous, i.e. they are spatially disconnected, can I still use only one FE_Q for all disconnected

[deal.II] Re: 1D version of step3

2016-09-16 Thread Weixiong Zheng
Bruno, Yeah, I noticed an old discussion with the same problem and solved it. Thanks, Weixiong 在 2016年9月16日星期五 UTC-5上午10:42:30,Bruno Turcksin写道: > > Weixong, > > On Friday, September 16, 2016 at 11:35:09 AM UTC-4, Weixiong Zheng wrote: >> >> When running the progr

[deal.II] 1D version of step3

2016-09-16 Thread Weixiong Zheng
Dear all, I just tried to modify step-3 to 1D. The changes are minor. The equation is changed to be with a small reaction. The mesh is generated with subdivided_hyper_cube (triangulation, 50, 0, 10); I changed all the <2>, the dimension, to <1>. When running the program, the solution is zero